Lessons learned from IDeAl - 33 recommendations from the IDeAl-net about design and analysis of small population clinical trials.

PubMed

Hilgers, Ralf-Dieter; Bogdan, Malgorzata; Burman, Carl-Fredrik; Dette, Holger; Karlsson, Mats; König, Franz; Male, Christoph; Mentré, France; Molenberghs, Geert; Senn, Stephen

2018-05-11

IDeAl (Integrated designs and analysis of small population clinical trials) is an EU funded project developing new statistical design and analysis methodologies for clinical trials in small population groups. Here we provide an overview of IDeAl findings and give recommendations to applied researchers. The description of the findings is broken down by the nine scientific IDeAl work packages and summarizes results from the project's more than 60 publications to date in peer reviewed journals. In addition, we applied text mining to evaluate the publications and the IDeAl work packages' output in relation to the design and analysis terms derived from in the IRDiRC task force report on small population clinical trials. The results are summarized, describing the developments from an applied viewpoint. The main result presented here are 33 practical recommendations drawn from the work, giving researchers a comprehensive guidance to the improved methodology. In particular, the findings will help design and analyse efficient clinical trials in rare diseases with limited number of patients available. We developed a network representation relating the hot topics developed by the IRDiRC task force on small population clinical trials to IDeAl's work as well as relating important methodologies by IDeAl's definition necessary to consider in design and analysis of small-population clinical trials. These network representation establish a new perspective on design and analysis of small-population clinical trials. IDeAl has provided a huge number of options to refine the statistical methodology for small-population clinical trials from various perspectives. A total of 33 recommendations developed and related to the work packages help the researcher to design small population clinical trial. The route to improvements is displayed in IDeAl-network representing important statistical methodological skills necessary to design and analysis of small-population clinical trials. The methods

Coarse-grained sequences for protein folding and design

PubMed Central

Brown, Scott; Fawzi, Nicolas J.; Head-Gordon, Teresa

2003-01-01

We present the results of sequence design on our off-lattice minimalist model in which no specification of native-state tertiary contacts is needed. We start with a sequence that adopts a target topology and build on it through sequence mutation to produce new sequences that comprise distinct members within a target fold class. In this work, we use the α/β ubiquitin fold class and design two new sequences that, when characterized through folding simulations, reproduce the differences in folding mechanism seen experimentally for proteins L and G. The primary implication of this work is that patterning of hydrophobic and hydrophilic residues is the physical origin for the success of relative contact-order descriptions of folding, and that these physics-based potentials provide a predictive connection between free energy landscapes and amino acid sequence (the original protein folding problem). We present results of the sequence mapping from a 20- to the three-letter code for determining a sequence that folds into the WW domain topology to illustrate future extensions to protein design. PMID:12963815

Coarse-grained sequences for protein folding and design.

PubMed

Brown, Scott; Fawzi, Nicolas J; Head-Gordon, Teresa

2003-09-16

We present the results of sequence design on our off-lattice minimalist model in which no specification of native-state tertiary contacts is needed. We start with a sequence that adopts a target topology and build on it through sequence mutation to produce new sequences that comprise distinct members within a target fold class. In this work, we use the alpha/beta ubiquitin fold class and design two new sequences that, when characterized through folding simulations, reproduce the differences in folding mechanism seen experimentally for proteins L and G. The primary implication of this work is that patterning of hydrophobic and hydrophilic residues is the physical origin for the success of relative contact-order descriptions of folding, and that these physics-based potentials provide a predictive connection between free energy landscapes and amino acid sequence (the original protein folding problem). We present results of the sequence mapping from a 20- to the three-letter code for determining a sequence that folds into the WW domain topology to illustrate future extensions to protein design.

Design of Concept of Sustainable Marketing Communication Strategy for a Ideal Industrial Enterprise and Practical Applications of this Concept

NASA Astrophysics Data System (ADS)

Šujaková, Monika; Golejová, Simona; Sakál, Peter

2017-09-01

In the contribution the authors deal with the design and use of a sustainable marketing communication strategy of an ideal industrial enterprise in the Slovak Republic. The concept of an ideal enterprise is designed to increase the enterprise's sustainable competitiveness through the formation of a corporate image. In the framework of the research, the practical application of the draft concept was realized through a semi-structured interview in the form of propositional logic.

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences

PubMed Central

Sevy, Alexander M.; Jacobs, Tim M.; Crowe, James E.; Meiler, Jens

2015-01-01

Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a ‘single state’ design (SSD) paradigm. Multi-specificity design (MSD), on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON). The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain) an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design “promiscuous”, polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes. PMID:26147100

SP-Designer: a user-friendly program for designing species-specific primer pairs from DNA sequence alignments.

PubMed

Villard, Pierre; Malausa, Thibaut

2013-07-01

SP-Designer is an open-source program providing a user-friendly tool for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. SP-Designer selects PCR primer pairs for the amplification of DNA from a target species on the basis of several criteria: (i) primer specificity, as assessed by interspecific sequence polymorphism in the annealing regions, (ii) the biochemical characteristics of the primers and (iii) the intended PCR conditions. SP-Designer generates tables, detailing the primer pair and PCR characteristics, and a FASTA file locating the primer sequences in the original sequence alignment. SP-Designer is Windows-compatible and freely available from http://www2.sophia.inra.fr/urih/sophia_mart/sp_designer/info_sp_designer.php. © 2013 John Wiley & Sons Ltd.

Design of Mariner 9 Science Sequences using Interactive Graphics Software

NASA Technical Reports Server (NTRS)

Freeman, J. E.; Sturms, F. M, Jr.; Webb, W. A.

1973-01-01

This paper discusses the analyst/computer system used to design the daily science sequences required to carry out the desired Mariner 9 science plan. The Mariner 9 computer environment, the development and capabilities of the science sequence design software, and the techniques followed in the daily mission operations are discussed. Included is a discussion of the overall mission operations organization and the individual components which played an essential role in the sequence design process. A summary of actual sequences processed, a discussion of problems encountered, and recommendations for future applications are given.

antaRNA: ant colony-based RNA sequence design.

PubMed

Kleinkauf, Robert; Mann, Martin; Backofen, Rolf

2015-10-01

RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step to generate novel biochemical components. In this article ,: the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution ,: specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Medical ethics and more: ideal theories, non-ideal theories and conscientious objection.

PubMed

Luna, Florencia

2015-01-01

Doing 'good medical ethics' requires acknowledgment that it is often practised in non-ideal circumstances! In this article I present the distinction between ideal theory (IT) and non-ideal theory (NIT). I show how IT may not be the best solution to tackle problems in non-ideal contexts. I sketch a NIT framework as a useful tool for bioethics and medical ethics and explain how NITs can contribute to policy design in non-ideal circumstances. Different NITs can coexist and be evaluated vis-à-vis the IT. Additionally, I address what an individual doctor ought to do in this non-ideal context with the view that knowledge of NITs can facilitate the decision-making process. NITs help conceptualise problems faced in the context of non-compliance and scarcity in a better and more realistic way. Deciding which policy is optimal in such contexts may influence physicians' decisions regarding their patients. Thus, this analysis-usually identified only with policy making-may also be relevant to medical ethics. Finally, I recognise that this is merely a first step in an unexplored but fundamental theoretical area and that more work needs to be done. 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.

Ideal flow theory for the double - shearing model as a basis for metal forming design

NASA Astrophysics Data System (ADS)

Alexandrov, S.; Trung, N. T.

2018-02-01

In the case of Tresca’ solids (i.e. solids obeying the Tresca yield criterion and its associated flow rule) ideal flows have been defined elsewhere as solenoidal smooth deformations in which an eigenvector field associated everywhere with the greatest principal stress (and strain rate) is fixed in the material. Under such conditions all material elements undergo paths of minimum plastic work, a condition which is often advantageous for metal forming processes. Therefore, the ideal flow theory is used as the basis of a procedure for the preliminary design of such processes. The present paper extends the theory of stationary planar ideal flow to pressure dependent materials obeying the double shearing model and the double slip and rotation model. It is shown that the original problem of plasticity reduces to a purely geometric problem. The corresponding system of equations is hyperbolic. The characteristic relations are integrated in elementary functions. In regions where one family of characteristics is straight, mapping between the principal lines and Cartesian coordinates is determined by linear ordinary differential equations. An illustrative example is provided.

The IDEAL (Integrated Design and Engineering Analysis Languages) modeling methodology: Capabilities and Applications

NASA Technical Reports Server (NTRS)

Evers, Ken H.; Bachert, Robert F.

1987-01-01

The IDEAL (Integrated Design and Engineering Analysis Languages) modeling methodology has been formulated and applied over a five-year period. It has proven to be a unique, integrated approach utilizing a top-down, structured technique to define and document the system of interest; a knowledge engineering technique to collect and organize system descriptive information; a rapid prototyping technique to perform preliminary system performance analysis; and a sophisticated simulation technique to perform in-depth system performance analysis.

Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance.

PubMed

Bashir, Ali; Bansal, Vikas; Bafna, Vineet

2010-06-18

Massively parallel DNA sequencing technologies have enabled the sequencing of several individual human genomes. These technologies are also being used in novel ways for mRNA expression profiling, genome-wide discovery of transcription-factor binding sites, small RNA discovery, etc. The multitude of sequencing platforms, each with their unique characteristics, pose a number of design challenges, regarding the technology to be used and the depth of sequencing required for a particular sequencing application. Here we describe a number of analytical and empirical results to address design questions for two applications: detection of structural variations from paired-end sequencing and estimating mRNA transcript abundance. For structural variation, our results provide explicit trade-offs between the detection and resolution of rearrangement breakpoints, and the optimal mix of paired-read insert lengths. Specifically, we prove that optimal detection and resolution of breakpoints is achieved using a mix of exactly two insert library lengths. Furthermore, we derive explicit formulae to determine these insert length combinations, enabling a 15% improvement in breakpoint detection at the same experimental cost. On empirical short read data, these predictions show good concordance with Illumina 200 bp and 2 Kbp insert length libraries. For transcriptome sequencing, we determine the sequencing depth needed to detect rare transcripts from a small pilot study. With only 1 Million reads, we derive corrections that enable almost perfect prediction of the underlying expression probability distribution, and use this to predict the sequencing depth required to detect low expressed genes with greater than 95% probability. Together, our results form a generic framework for many design considerations related to high-throughput sequencing. We provide software tools http://bix.ucsd.edu/projects/NGS-DesignTools to derive platform independent guidelines for designing sequencing experiments

Coupling Ideality of Integrated Planar High-Q Microresonators

NASA Astrophysics Data System (ADS)

Pfeiffer, Martin H. P.; Liu, Junqiu; Geiselmann, Michael; Kippenberg, Tobias J.

2017-02-01

Chip-scale optical microresonators with integrated planar optical waveguides are useful building blocks for linear, nonlinear, and quantum-optical photonic devices alike. Loss reduction through improving fabrication processes results in several integrated microresonator platforms attaining quality (Q ) factors of several millions. Beyond the improvement of the quality factor, the ability to operate the microresonator with high coupling ideality in the overcoupled regime is of central importance. In this regime, the dominant source of loss constitutes the coupling to a single desired output channel, which is particularly important not only for quantum-optical applications such as the generation of squeezed light and correlated photon pairs but also for linear and nonlinear photonics. However, to date, the coupling ideality in integrated photonic microresonators is not well understood, in particular, design-dependent losses and their impact on the regime of high ideality. Here we investigate design-dependent parasitic losses described by the coupling ideality of the commonly employed microresonator design consisting of a microring-resonator waveguide side coupled to a straight bus waveguide, a system which is not properly described by the conventional input-output theory of open systems due to the presence of higher-order modes. By systematic characterization of multimode high-Q silicon nitride microresonator devices, we show that this design can suffer from low coupling ideality. By performing 3D simulations, we identify the coupling to higher-order bus waveguide modes as the dominant origin of parasitic losses which lead to the low coupling ideality. Using suitably designed bus waveguides, parasitic losses are mitigated with a nearly unity ideality and strong overcoupling (i.e., a ratio of external coupling to internal resonator loss rate >9 ) are demonstrated. Moreover, we find that different resonator modes can exchange power through the coupler, which, therefore

Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

PubMed

Deroost, Natacha; Coomans, Daphné

2018-02-01

We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

Design and Analysis of Single-Cell Sequencing Experiments.

PubMed

Grün, Dominic; van Oudenaarden, Alexander

2015-11-05

Recent advances in single-cell sequencing hold great potential for exploring biological systems with unprecedented resolution. Sequencing the genome of individual cells can reveal somatic mutations and allows the investigation of clonal dynamics. Single-cell transcriptome sequencing can elucidate the cell type composition of a sample. However, single-cell sequencing comes with major technical challenges and yields complex data output. In this Primer, we provide an overview of available methods and discuss experimental design and single-cell data analysis. We hope that these guidelines will enable a growing number of researchers to leverage the power of single-cell sequencing. Copyright © 2015 Elsevier Inc. All rights reserved.

The optimal design of stepped wedge trials with equal allocation to sequences and a comparison to other trial designs.

PubMed

Thompson, Jennifer A; Fielding, Katherine; Hargreaves, James; Copas, Andrew

2017-12-01

Background/Aims We sought to optimise the design of stepped wedge trials with an equal allocation of clusters to sequences and explored sample size comparisons with alternative trial designs. Methods We developed a new expression for the design effect for a stepped wedge trial, assuming that observations are equally correlated within clusters and an equal number of observations in each period between sequences switching to the intervention. We minimised the design effect with respect to (1) the fraction of observations before the first and after the final sequence switches (the periods with all clusters in the control or intervention condition, respectively) and (2) the number of sequences. We compared the design effect of this optimised stepped wedge trial to the design effects of a parallel cluster-randomised trial, a cluster-randomised trial with baseline observations, and a hybrid trial design (a mixture of cluster-randomised trial and stepped wedge trial) with the same total cluster size for all designs. Results We found that a stepped wedge trial with an equal allocation to sequences is optimised by obtaining all observations after the first sequence switches and before the final sequence switches to the intervention; this means that the first sequence remains in the control condition and the last sequence remains in the intervention condition for the duration of the trial. With this design, the optimal number of sequences is [Formula: see text], where [Formula: see text] is the cluster-mean correlation, [Formula: see text] is the intracluster correlation coefficient, and m is the total cluster size. The optimal number of sequences is small when the intracluster correlation coefficient and cluster size are small and large when the intracluster correlation coefficient or cluster size is large. A cluster-randomised trial remains more efficient than the optimised stepped wedge trial when the intracluster correlation coefficient or cluster size is small. A

SNAD: Sequence Name Annotation-based Designer.

PubMed

Sidorov, Igor A; Reshetov, Denis A; Gorbalenya, Alexander E

2009-08-14

A growing diversity of biological data is tagged with unique identifiers (UIDs) associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Here we introduce SNAD (Sequence Name Annotation-based Designer) that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list) into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

Molecular Design of Performance Proteins With Repetitive Sequences

NASA Astrophysics Data System (ADS)

Vendrely, Charlotte; Ackerschott, Christian; Römer, Lin; Scheibel, Thomas

Most performance proteins responsible for the mechanical stability of cells and organisms reveal highly repetitive sequences. Mimicking such performance proteins is of high interest for the design of nanostructured biomaterials. In this article, flagelliform silk is exemplary introduced to describe a general principle for designing genes of repetitive performance proteins for recombinant expression in Escherichia coli . In the first step, repeating amino acid sequence motifs are reversely transcripted into DNA cassettes, which can in a second step be seamlessly ligated, yielding a designed gene. Recombinant expression thereof leads to proteins mimicking the natural ones. The recombinant proteins can be assembled into nanostructured materials in a controlled manner, allowing their use in several applications.

Use of designed sequences in protein structure recognition.

PubMed

Kumar, Gayatri; Mudgal, Richa; Srinivasan, Narayanaswamy; Sandhya, Sankaran

2018-05-09

Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold. These strategically designed sequences enable detection of distant relationships and here, we have employed them for the purpose of structure recognition of protein families of yet unknown structure. We first measured the success rate of our approach using a dataset of protein families of known fold and achieved a success rate of 88%. Next, for 1392 families of yet unknown structure, we made structural assignments for part/full length of the proteins. Fold association for 423 domains of unknown function (DUFs) are provided as a step towards functional annotation. The results indicate that knowledge-based filling of gaps in protein sequence space is a lucrative approach for structure recognition. Such sequences assist in traversal through protein sequence space and effectively function as 'linkers', where natural linkers between distant proteins are unavailable. This article was reviewed by Oliviero Carugo, Christine Orengo and Srikrishna Subramanian.

A Multiple-Sequence Variant of the Multiple-Baseline Design: A Strategy for Analysis of Sequence Effects and Treatment Comparison.

ERIC Educational Resources Information Center

Noell, George H.; Gresham, Frank M.

2001-01-01

Describes design logic and potential uses of a variant of the multiple-baseline design. The multiple-baseline multiple-sequence (MBL-MS) consists of multiple-baseline designs that are interlaced with one another and include all possible sequences of treatments. The MBL-MS design appears to be primarily useful for comparison of treatments taking…

Designing robust watermark barcodes for multiplex long-read sequencing.

PubMed

Ezpeleta, Joaquín; Krsticevic, Flavia J; Bulacio, Pilar; Tapia, Elizabeth

2017-03-15

To attain acceptable sample misassignment rates, current approaches to multiplex single-molecule real-time sequencing require upstream quality improvement, which is obtained from multiple passes over the sequenced insert and significantly reduces the effective read length. In order to fully exploit the raw read length on multiplex applications, robust barcodes capable of dealing with the full single-pass error rates are needed. We present a method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing. The manuscript focuses on the design of barcodes for full-length single-pass reads, impaired by challenging error rates in the order of 11%. The proposed barcodes can multiplex hundreds or thousands of samples while achieving sample misassignment probabilities as low as 10-7 under the above conditions, and are designed to be compatible with chemical constraints imposed by the sequencing process. Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads, are freely available at www.cifasis-conicet.gov.ar/ezpeleta/NS-watermark . ezpeleta@cifasis-conicet.gov.ar. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Ideal AFROC and FROC observers.

PubMed

Khurd, Parmeshwar; Liu, Bin; Gindi, Gene

2010-02-01

Detection of multiple lesions in images is a medically important task and free-response receiver operating characteristic (FROC) analyses and its variants, such as alternative FROC (AFROC) analyses, are commonly used to quantify performance in such tasks. However, ideal observers that optimize FROC or AFROC performance metrics have not yet been formulated in the general case. If available, such ideal observers may turn out to be valuable for imaging system optimization and in the design of computer aided diagnosis techniques for lesion detection in medical images. In this paper, we derive ideal AFROC and FROC observers. They are ideal in that they maximize, amongst all decision strategies, the area, or any partial area, under the associated AFROC or FROC curve. Calculation of observer performance for these ideal observers is computationally quite complex. We can reduce this complexity by considering forms of these observers that use false positive reports derived from signal-absent images only. We also consider a Bayes risk analysis for the multiple-signal detection task with an appropriate definition of costs. A general decision strategy that minimizes Bayes risk is derived. With particular cost constraints, this general decision strategy reduces to the decision strategy associated with the ideal AFROC or FROC observer.

The advantages of SMRT sequencing.

PubMed

Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

2013-07-03

Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

Study design requirements for RNA sequencing-based breast cancer diagnostics.

PubMed

Mer, Arvind Singh; Klevebring, Daniel; Grönberg, Henrik; Rantalainen, Mattias

2016-02-01

Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic.

Genetic and environmental influences on thin-ideal internalization.

PubMed

Suisman, Jessica L; O'Connor, Shannon M; Sperry, Steffanie; Thompson, J Kevin; Keel, Pamela K; Burt, S Alexandra; Neale, Michael; Boker, Steven; Sisk, Cheryl; Klump, Kelly L

2012-12-01

Current research on the etiology of thin-ideal internalization focuses on psychosocial influences (e.g., media exposure). The possibility that genetic influences also account for variance in thin-ideal internalization has never been directly examined. This study used a twin design to estimate genetic effects on thin-ideal internalization and examine if environmental influences are primarily shared or nonshared in origin. Participants were 343 postpubertal female twins (ages: 12-22 years; M = 17.61) from the Michigan State University Twin Registry. Thin-ideal internalization was assessed using the Sociocultural Attitudes toward Appearance Questionnaire-3. Twin modeling suggested significant additive genetic and nonshared environmental influences on thin-ideal internalization. Shared environmental influences were small and non-significant. Although prior research focused on psychosocial factors, genetic influences on thin-ideal internalization were significant and moderate in magnitude. Research is needed to investigate possible interplay between genetic and nonshared environmental factors in the development of thin-ideal internalization. Copyright © 2012 Wiley Periodicals, Inc.

Not All Ideals are Equal: Intrinsic and Extrinsic Ideals in Relationships.

PubMed

Rodriguez, Lindsey M; Hadden, Benjamin W; Knee, C Raymond

2015-03-01

The ideal standards model suggests that greater consistency between ideal standards and actual perceptions of one's relationship predicts positive relationship evaluations; however, no research has evaluated whether this differs across types of ideals. A self-determination theory perspective was derived to test whether satisfaction of intrinsic ideals buffers the importance of extrinsic ideals. Participants (N=195) in committed relationships directly and indirectly reported the extent to which their partner met their ideal on two dimensions: intrinsic (e.g., warm, intimate) and extrinsic (e.g., attractive, successful). Relationship need fulfillment and relationship quality were also assessed. Hypotheses were largely supported, such that satisfaction of intrinsic ideals more strongly predicted relationship functioning, and satisfaction of intrinsic ideals buffered the relevance of extrinsic ideals for outcomes.

Not All Ideals are Equal: Intrinsic and Extrinsic Ideals in Relationships

PubMed Central

Rodriguez, Lindsey M.; Hadden, Benjamin W.; Knee, C. Raymond

2015-01-01

The ideal standards model suggests that greater consistency between ideal standards and actual perceptions of one’s relationship predicts positive relationship evaluations; however, no research has evaluated whether this differs across types of ideals. A self-determination theory perspective was derived to test whether satisfaction of intrinsic ideals buffers the importance of extrinsic ideals. Participants (N=195) in committed relationships directly and indirectly reported the extent to which their partner met their ideal on two dimensions: intrinsic (e.g., warm, intimate) and extrinsic (e.g., attractive, successful). Relationship need fulfillment and relationship quality were also assessed. Hypotheses were largely supported, such that satisfaction of intrinsic ideals more strongly predicted relationship functioning, and satisfaction of intrinsic ideals buffered the relevance of extrinsic ideals for outcomes. PMID:25821396

Design of the hairpin ribozyme for targeting specific RNA sequences.

PubMed

Hampel, A; DeYoung, M B; Galasinski, S; Siwkowski, A

1997-01-01

The following steps should be taken when designing the hairpin ribozyme to cleave a specific target sequence: 1. Select a target sequence containing BN*GUC where B is C, G, or U. 2. Select the target sequence in areas least likely to have extensive interfering structure. 3. Design the conventional hairpin ribozyme as shown in Fig. 1, such that it can form a 4 bp helix 2 and helix 1 lengths up to 10 bp. 4. Synthesize this ribozyme from single-stranded DNA templates with a double-stranded T7 promoter. 5. Prepare a series of short substrates capable of forming a range of helix 1 lengths of 5-10 bp. 6. Identify these by direct RNA sequencing. 7. Assay the extent of cleavage of each substrate to identify the optimal length of helix 1. 8. Prepare the hairpin tetraloop ribozyme to determine if catalytic efficiency can be improved.

Molecular design of sequence specific DNA alkylating agents.

PubMed

Minoshima, Masafumi; Bando, Toshikazu; Shinohara, Ken-ichi; Sugiyama, Hiroshi

2009-01-01

Sequence-specific DNA alkylating agents have great interest for novel approach to cancer chemotherapy. We designed the conjugates between pyrrole (Py)-imidazole (Im) polyamides and DNA alkylating chlorambucil moiety possessing at different positions. The sequence-specific DNA alkylation by conjugates was investigated by using high-resolution denaturing polyacrylamide gel electrophoresis (PAGE). The results showed that polyamide chlorambucil conjugates alkylate DNA at flanking adenines in recognition sequences of Py-Im polyamides, however, the reactivities and alkylation sites were influenced by the positions of conjugation. In addition, we synthesized conjugate between Py-Im polyamide and another alkylating agent, 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI). DNA alkylation reactivies by both alkylating polyamides were almost comparable. In contrast, cytotoxicities against cell lines differed greatly. These comparative studies would promote development of appropriate sequence-specific DNA alkylating polyamides against specific cancer cells.

Sequence signatures of allosteric proteins towards rational design.

PubMed

Namboodiri, Saritha; Verma, Chandra; Dhar, Pawan K; Giuliani, Alessandro; Nair, Achuthsankar S

2010-12-01

Allostery is the phenomenon of changes in the structure and activity of proteins that appear as a consequence of ligand binding at sites other than the active site. Studying mechanistic basis of allostery leading to protein design with predetermined functional endpoints is an important unmet need of synthetic biology. Here, we screened the amino acid sequence landscape in search of sequence-signatures of allostery using Recurrence Quantitative Analysis (RQA) method. A characteristic vector, comprised of 10 features extracted from RQA was defined for amino acid sequences. Using Principal Component Analysis, four factors were found to be important determinants of allosteric behavior. Our sequence-based predictor method shows 82.6% accuracy, 85.7% sensitivity and 77.9% specificity with the current dataset. Further, we show that Laminarity-Mean-hydrophobicity representing repeated hydrophobic patches is the most crucial indicator of allostery. To our best knowledge this is the first report that describes sequence determinants of allostery based on hydrophobicity. As an outcome of these findings, we plan to explore possibility of inducing allostery in proteins.

An experimental investigation of a psychoeducational strategy designed to reduce men's endorsement of societal ideals of women's attractiveness.

PubMed

Yamamiya, Yuko; Thompson, J Kevin

2009-01-01

The current study evaluated whether a psychoeducational manipulation, focused on reducing an unrealistic view of women's attractiveness, might affect men's ratings of the attractiveness of females. The participants were 159 male undergraduate students who were randomly assigned to four conditions: psychoeducational message (beauty ideals; marketing strategies) and photo exposure (attractive females; household products). The results indicated that males pre-exposed to attractive female images subsequently evaluated average females as less attractive than those exposed to household products. However, a psychoeducational information condition designed to challenge "beauty ideals" did not reduce the adverse exposure effect and was comparable in effectiveness to the "marketing strategies" manipulation. The limitations of the findings are discussed and avenues for future research in this area offered.

Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs.

PubMed

Pancoska, Petr; Moravek, Zdenek; Moll, Ute M

2004-01-01

Nucleic acids are molecules of choice for both established and emerging nanoscale technologies. These technologies benefit from large functional densities of 'DNA processing elements' that can be readily manufactured. To achieve the desired functionality, polynucleotide sequences are currently designed by a process that involves tedious and laborious filtering of potential candidates against a series of requirements and parameters. Here, we present a complete novel methodology for the rapid rational design of large sets of DNA sequences. This method allows for the direct implementation of very complex and detailed requirements for the generated sequences, thus avoiding 'brute force' filtering. At the same time, these sequences have narrow distributions of melting temperatures. The molecular part of the design process can be done without computer assistance, using an efficient 'human engineering' approach by drawing a single blueprint graph that represents all generated sequences. Moreover, the method eliminates the necessity for extensive thermodynamic calculations. Melting temperature can be calculated only once (or not at all). In addition, the isostability of the sequences is independent of the selection of a particular set of thermodynamic parameters. Applications are presented for DNA sequence designs for microarrays, universal microarray zip sequences and electron transfer experiments.

Optimal control design of turbo spin‐echo sequences with applications to parallel‐transmit systems

PubMed Central

Hoogduin, Hans; Hajnal, Joseph V.; van den Berg, Cornelis A. T.; Luijten, Peter R.; Malik, Shaihan J.

2016-01-01

Purpose The design of turbo spin‐echo sequences is modeled as a dynamic optimization problem which includes the case of inhomogeneous transmit radiofrequency fields. This problem is efficiently solved by optimal control techniques making it possible to design patient‐specific sequences online. Theory and Methods The extended phase graph formalism is employed to model the signal evolution. The design problem is cast as an optimal control problem and an efficient numerical procedure for its solution is given. The numerical and experimental tests address standard multiecho sequences and pTx configurations. Results Standard, analytically derived flip angle trains are recovered by the numerical optimal control approach. New sequences are designed where constraints on radiofrequency total and peak power are included. In the case of parallel transmit application, the method is able to calculate the optimal echo train for two‐dimensional and three‐dimensional turbo spin echo sequences in the order of 10 s with a single central processing unit (CPU) implementation. The image contrast is maintained through the whole field of view despite inhomogeneities of the radiofrequency fields. Conclusion The optimal control design sheds new light on the sequence design process and makes it possible to design sequences in an online, patient‐specific fashion. Magn Reson Med 77:361–373, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine PMID:26800383

Turboprop IDEAL: a motion-resistant fat-water separation technique.

PubMed

Huo, Donglai; Li, Zhiqiang; Aboussouan, Eric; Karis, John P; Pipe, James G

2009-01-01

Suppression of the fat signal in MRI is very important for many clinical applications. Multi-point water-fat separation methods, such as IDEAL (Iterative Decomposition of water and fat with Echo Asymmetry and Least-squares estimation), can robustly separate water and fat signal, but inevitably increase scan time, making separated images more easily affected by patient motions. PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) and Turboprop techniques offer an effective approach to correct for motion artifacts. By combining these techniques together, we demonstrate that the new TP-IDEAL method can provide reliable water-fat separation with robust motion correction. The Turboprop sequence was modified to acquire source images, and motion correction algorithms were adjusted to assure the registration between different echo images. Theoretical calculations were performed to predict the optimal shift and spacing of the gradient echoes. Phantom images were acquired, and results were compared with regular FSE-IDEAL. Both T1- and T2-weighted images of the human brain were used to demonstrate the effectiveness of motion correction. TP-IDEAL images were also acquired for pelvis, knee, and foot, showing great potential of this technique for general clinical applications.

Sex Education and Ideals

ERIC Educational Resources Information Center

de Ruyter, Doret J.; Spiecker, Ben

2008-01-01

This article argues that sex education should include sexual ideals. Sexual ideals are divided into sexual ideals in the strict sense and sexual ideals in the broad sense. It is argued that ideals that refer to the context that is deemed to be most ideal for the gratification of sexual ideals in the strict sense are rightfully called sexual…

RNAblueprint: flexible multiple target nucleic acid sequence design.

PubMed

Hammer, Stefan; Tschiatschek, Birgit; Flamm, Christoph; Hofacker, Ivo L; Findeiß, Sven

2017-09-15

Realizing the value of synthetic biology in biotechnology and medicine requires the design of molecules with specialized functions. Due to its close structure to function relationship, and the availability of good structure prediction methods and energy models, RNA is perfectly suited to be synthetically engineered with predefined properties. However, currently available RNA design tools cannot be easily adapted to accommodate new design specifications. Furthermore, complicated sampling and optimization methods are often developed to suit a specific RNA design goal, adding to their inflexibility. We developed a C ++  library implementing a graph coloring approach to stochastically sample sequences compatible with structural and sequence constraints from the typically very large solution space. The approach allows to specify and explore the solution space in a well defined way. Our library also guarantees uniform sampling, which makes optimization runs performant by not only avoiding re-evaluation of already found solutions, but also by raising the probability of finding better solutions for long optimization runs. We show that our software can be combined with any other software package to allow diverse RNA design applications. Scripting interfaces allow the easy adaption of existing code to accommodate new scenarios, making the whole design process very flexible. We implemented example design approaches written in Python to demonstrate these advantages. RNAblueprint , Python implementations and benchmark datasets are available at github: https://github.com/ViennaRNA . s.hammer@univie.ac.at, ivo@tbi.univie.ac.at or sven@tbi.univie.ac.at. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Sequence determinants of improved CRISPR sgRNA design.

PubMed

Xu, Han; Xiao, Tengfei; Chen, Chen-Hao; Li, Wei; Meyer, Clifford A; Wu, Qiu; Wu, Di; Cong, Le; Zhang, Feng; Liu, Jun S; Brown, Myles; Liu, X Shirley

2015-08-01

The CRISPR/Cas9 system has revolutionized mammalian somatic cell genetics. Genome-wide functional screens using CRISPR/Cas9-mediated knockout or dCas9 fusion-mediated inhibition/activation (CRISPRi/a) are powerful techniques for discovering phenotype-associated gene function. We systematically assessed the DNA sequence features that contribute to single guide RNA (sgRNA) efficiency in CRISPR-based screens. Leveraging the information from multiple designs, we derived a new sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments. Our model confirmed known features and suggested new features including a preference for cytosine at the cleavage site. The model was experimentally validated for sgRNA-mediated mutation rate and protein knockout efficiency. Tested on independent data sets, the model achieved significant results in both positive and negative selection conditions and outperformed existing models. We also found that the sequence preference for CRISPRi/a is substantially different from that for CRISPR/Cas9 knockout and propose a new model for predicting sgRNA efficiency in CRISPRi/a experiments. These results facilitate the genome-wide design of improved sgRNA for both knockout and CRISPRi/a studies. © 2015 Xu et al.; Published by Cold Spring Harbor Laboratory Press.

PRISE2: software for designing sequence-selective PCR primers and probes.

PubMed

Huang, Yu-Ting; Yang, Jiue-in; Chrobak, Marek; Borneman, James

2014-09-25

PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.

An Ideal Remedial Reading Program.

ERIC Educational Resources Information Center

Boettcher, Judith A.

An ideal secondary level remedial reading program would be based on the philosophy that both freedom and structure are required, that learning demands involvement and feedback, and that success breeds success. Such programs should be structured (i.e., based on clearly defined content and a clearly designated mode of presentation). There are many…

Soft sensor based composition estimation and controller design for an ideal reactive distillation column.

PubMed

Vijaya Raghavan, S R; Radhakrishnan, T K; Srinivasan, K

2011-01-01

In this research work, the authors have presented the design and implementation of a recurrent neural network (RNN) based inferential state estimation scheme for an ideal reactive distillation column. Decentralized PI controllers are designed and implemented. The reactive distillation process is controlled by controlling the composition which has been estimated from the available temperature measurements using a type of RNN called Time Delayed Neural Network (TDNN). The performance of the RNN based state estimation scheme under both open loop and closed loop have been compared with a standard Extended Kalman filter (EKF) and a Feed forward Neural Network (FNN). The online training/correction has been done for both RNN and FNN schemes for every ten minutes whenever new un-trained measurements are available from a conventional composition analyzer. The performance of RNN shows better state estimation capability as compared to other state estimation schemes in terms of qualitative and quantitative performance indices. Copyright © 2010 ISA. Published by Elsevier Ltd. All rights reserved.

Unimodular sequence design under frequency hopping communication compatibility requirements

NASA Astrophysics Data System (ADS)

Ge, Peng; Cui, Guolong; Kong, Lingjiang; Yang, Jianyu

2016-12-01

The integrated design for both radar and anonymous communication has drawn more attention recently since wireless communication system appeals to enhance security and reliability. Given the frequency hopping (FH) communication system, an effective way to realize integrated design is to meet the spectrum compatibility between these two systems. The paper deals with a unimodular sequence design technique which considers optimizing both the spectrum compatibility and peak sidelobes levels (PSL) of auto-correlation function (ACF). The spectrum compatibility requirement realizes anonymous communication for the FH system and provides this system lower probability of intercept (LPI) since the spectrum of the FH system is hidden in that of the radar system. The proposed algorithm, named generalized fitting template (GFT) technique, converts the sequence optimization design problem to a iterative fitting process. In this process, the power spectrum density (PSD) and PSL behaviors of the generated sequences fit both PSD and PSL templates progressively. Two templates are established based on the spectrum compatibility requirement and the expected PSL. As noted, in order to ensure the communication security and reliability, spectrum compatibility requirement is given a higher priority to achieve in the GFT algorithm. This algorithm realizes this point by adjusting the weight adaptively between these two terms during the iteration process. The simulation results are analyzed in terms of bit error rate (BER), PSD, PSL, and signal-interference rate (SIR) for both the radar and FH systems. The performance of GFT is compared with SCAN, CAN, FRE, CYC, and MAT algorithms in the above aspects, which shows its good effectiveness.

Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

PubMed

Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

2017-11-13

A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

Estimation of liver T₂ in transfusion-related iron overload in patients with weighted least squares T₂ IDEAL.

PubMed

Vasanawala, Shreyas S; Yu, Huanzhou; Shimakawa, Ann; Jeng, Michael; Brittain, Jean H

2012-01-01

MRI imaging of hepatic iron overload can be achieved by estimating T(2) values using multiple-echo sequences. The purpose of this work is to develop and clinically evaluate a weighted least squares algorithm based on T(2) Iterative Decomposition of water and fat with Echo Asymmetry and Least-squares estimation (IDEAL) technique for volumetric estimation of hepatic T(2) in the setting of iron overload. The weighted least squares T(2) IDEAL technique improves T(2) estimation by automatically decreasing the impact of later, noise-dominated echoes. The technique was evaluated in 37 patients with iron overload. Each patient underwent (i) a standard 2D multiple-echo gradient echo sequence for T(2) assessment with nonlinear exponential fitting, and (ii) a 3D T(2) IDEAL technique, with and without a weighted least squares fit. Regression and Bland-Altman analysis demonstrated strong correlation between conventional 2D and T(2) IDEAL estimation. In cases of severe iron overload, T(2) IDEAL without weighted least squares reconstruction resulted in a relative overestimation of T(2) compared with weighted least squares. Copyright © 2011 Wiley-Liss, Inc.

Design of optimal and ideal 2-D concentrators with the collector immersed in a dielectric tube

NASA Astrophysics Data System (ADS)

Minano, J. C.; Ruiz, J. M.; Luque, A.

1983-12-01

A method is presented for designing ideal and optimal 2-D concentrators when the collector is placed inside a dielectric tube, for the particular case of a bifacial solar collector. The prototype 2-D (cylindrical geometry) concentrator is the compound parabolic concentrator or CPC, and from the beginning of development, it was found by Winston (1978) that filling up the concentrator with a transparent dielectric medium results in a big improvement of the optical properties. The method reported here is based on the extreme ray principle of design and avoids the use of differential equations by means of a proper appliction of Fermat's principle. One advantage of these concentrators is that they allow the size to be small compared with classical CPCs.

Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

PubMed

Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

2011-01-01

The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

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

Zhou, Xiaofan; Peris, David; Kominek, Jacek

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimentalmore » design and analysis, we developed iWGS (in silico Whole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design of de novo genome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.« less

in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies

DOE PAGES

Zhou, Xiaofan; Peris, David; Kominek, Jacek; ...

2016-09-16

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding its potential for understanding the biology and evolution of the full spectrum of biodiversity. The increasing diversity of sequencing technologies, assays, and de novo assembly algorithms have augmented the complexity of de novo genome sequencing projects in nonmodel organisms. To reduce the costs and challenges in de novo genome sequencing projects and streamline their experimentalmore » design and analysis, we developed iWGS (in silico Whole Genome Sequencer and Analyzer), an automated pipeline for guiding the choice of appropriate sequencing strategy and assembly protocols. iWGS seamlessly integrates the four key steps of a de novo genome sequencing project: data generation (through simulation), data quality control, de novo assembly, and assembly evaluation and validation. The last three steps can also be applied to the analysis of real data. iWGS is designed to enable the user to have great flexibility in testing the range of experimental designs available for genome sequencing projects, and supports all major sequencing technologies and popular assembly tools. Three case studies illustrate how iWGS can guide the design of de novo genome sequencing projects, and evaluate the performance of a wide variety of user-specified sequencing strategies and assembly protocols on genomes of differing architectures. iWGS, along with a detailed documentation, is freely available at https://github.com/zhouxiaofan1983/iWGS.« less

Ideal Gas Laws: Experiments for General Chemistry

ERIC Educational Resources Information Center

Deal, Walter J.

1975-01-01

Describes a series of experiments designed to verify the various relationships implicit in the ideal gas equation and shows that the success of the Graham's law effusion experiments can be explained by elementary hydrodynamics. (GS)

Designing and Evaluating Research-Based Instructional Sequences for Introducing Magnetic Fields

ERIC Educational Resources Information Center

Guisasola, Jenaro; Almudi, Jose Manuel; Ceberio, Mikel; Zubimendi, Jose Luis

2009-01-01

This study examines the didactic suitability of introducing a teaching sequence when teaching the concept of magnetic fields within introductory physics courses at the university level. This instructional sequence was designed taking into account students' common conceptions, an analysis of the course content, and the history of the development of…

Usefulness of IDEAL T2 imaging for homogeneous fat suppression and reducing susceptibility artefacts in brachial plexus MRI at 3.0 T.

PubMed

Tagliafico, Alberto; Bignotti, Bianca; Tagliafico, Giulio; Martinoli, Carlo

2016-01-01

To quantitatively and qualitatively compare fat-suppressed MR imaging quality using iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL) with that using frequency-selective fat-suppressed (FSFS) T2 images of the brachial plexus at 3.0 T. Prospective MR image analysis was performed in 40 volunteers and 40 patients at a single centre. Oblique-sagittal and coronal IDEAL fat-suppressed T2 images and FSFS T2 images were compared. Visual assessment was performed by two independent musculoskeletal radiologists with respect to: (1) susceptibility artefacts around the neck, (2) homogeneity of fat suppression, (3) image sharpness and (4) tissue resolution contrast of pathologies. The signal-to-noise ratios (SNR) for each image sequence were assessed. Compared to FSFS sequences, IDEAL fat-suppressed T2 images significantly reduced artefacts around the brachial plexus and significantly improved homogeneous fat suppression (p < 0.05). IDEAL significantly improved sharpness and lesion-to-tissue contrast (p < 0.05). The mean SNRs were significantly improved on T2-weighted IDEAL images (p < 0.05). IDEAL technique improved image quality by reducing artefacts around the brachial plexus while maintaining a high SNR and provided superior homogeneous fat suppression than FSFS sequences.

Application of ideal pressure distribution in development process of automobile seats.

PubMed

Kilincsoy, U; Wagner, A; Vink, P; Bubb, H

2016-07-19

In designing a car seat the ideal pressure distribution is important as it is the largest contact surface between the human and the car. Because of obstacles hindering a more general application of the ideal pressure distribution in seating design, multidimensional measuring techniques are necessary with extensive user tests. The objective of this study is to apply and integrate the knowledge about the ideal pressure distribution in the seat design process for a car manufacturer in an efficient way. Ideal pressure distribution was combined with pressure measurement, in this case pressure mats. In order to integrate this theoretical knowledge of seating comfort in the seat development process for a car manufacturer a special user interface was defined and developed. The mapping of the measured pressure distribution in real-time and accurately scaled to actual seats during test setups directly lead to design implications for seat design even during the test situation. Detailed analysis of the subject's feedback was correlated with objective measurements of the subject's pressure distribution in real time. Therefore existing seating characteristics were taken into account as well. A user interface can incorporate theoretical and validated 'state of the art' models of comfort. Consequently, this information can reduce extensive testing and lead to more detailed results in a shorter time period.

incaRNAfbinv: a web server for the fragment-based design of RNA sequences

PubMed Central

Drory Retwitzer, Matan; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny

2016-01-01

Abstract In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv. PMID:27185893

Developing Ideal Student and Residency Programs.

ERIC Educational Resources Information Center

Selvin, Gerald J.

1993-01-01

The Veterans Administration (VA) is a primary educator of optometry students, with each college of optometry being affiliated with at least one VA hospital. Ideally, fourth-year optometry students rotate through a specific VA facility for about 12 weeks. Guidelines are designed to provide optimum care in a rich learning environment. (MSE)

Ideals versus reality: Are weight ideals associated with weight change in the population?

PubMed

Kärkkäinen, Ulla; Mustelin, Linda; Raevuori, Anu; Kaprio, Jaakko; Keski-Rahkonen, Anna

2016-04-01

To quantify weight ideals of young adults and to examine whether the discrepancy between actual and ideal weight is associated with 10-year body mass index (BMI) change in the population. This study comprised 4,964 adults from the prospective population-based FinnTwin16 study. They reported their actual and ideal body weight at age 24 (range 22-27) and 10 years later (attrition 24.6%). The correlates of discrepancy between actual and ideal body weight and the impact on subsequent BMI change were examined. The discrepancy between actual and ideal weight at 24 years was on average 3.9 kg (1.4 kg/m(2) ) among women and 1.2 kg (0.4 kg/m(2) ) among men. On average, participants gained weight during follow-up irrespective of baseline ideal weight: women ¯x = +4.8 kg (1.7 kg/m(2) , 95% CI 1.6-1.9 kg/m(2) ), men ¯x = +6.3 kg (2.0 kg/m(2) , 95% CI 1.8-2.1 kg/m(2) ). Weight ideals at 24 years were not correlated with 10-year weight change. At 34 years, just 13.2% of women and 18.9% of men were at or below the weight they had specified as their ideal weight at 24 years. Women and men adjusted their ideal weight upward over time. Irrespective of ideal weight at baseline, weight gain was nearly universal. Weight ideals were shifted upward over time. © 2016 The Obesity Society.

Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software.

PubMed

Nakano, Shogo; Asano, Yasuhisa

2015-02-03

Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs.

Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software

NASA Astrophysics Data System (ADS)

Nakano, Shogo; Asano, Yasuhisa

2015-02-01

Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs.

(Fuzzy) Ideals of BN-Algebras

PubMed Central

Walendziak, Andrzej

2015-01-01

The notions of an ideal and a fuzzy ideal in BN-algebras are introduced. The properties and characterizations of them are investigated. The concepts of normal ideals and normal congruences of a BN-algebra are also studied, the properties of them are displayed, and a one-to-one correspondence between them is presented. Conditions for a fuzzy set to be a fuzzy ideal are given. The relationships between ideals and fuzzy ideals of a BN-algebra are established. The homomorphic properties of fuzzy ideals of a BN-algebra are provided. Finally, characterizations of Noetherian BN-algebras and Artinian BN-algebras via fuzzy ideals are obtained. PMID:26125050

Qualifications of an Ideal Teacher According to Social Studies Preservice Teachers

ERIC Educational Resources Information Center

Gencturk, Ebru; Akbas, Yavuz; Kaymakci, Selahattin

2012-01-01

In this study, the question of what kind of qualifications an ideal social studies teacher has tried to be investigated. For this purpose, freshman social studies preservice teachers' perceptions about the concept of "ideal teacher" were explored. This study was designed with document analysis, one of the methods of qualitative approach.…

Media-portrayed idealized images, body shame, and appearance anxiety.

PubMed

Monro, Fiona; Huon, Gail

2005-07-01

This study was designed to determine the effects of media-portrayed idealized images on young women's body shame and appearance anxiety, and to establish whether the effects depend on advertisement type and on participant self-objectification. Participants were 39 female university students. Twenty-four magazine advertisements comprised 12 body-related and 12 non-body-related products, one half of each with, and the other one half without, idealized images. Preexposure and post exposure body shame and appearance anxiety measures were recorded. Appearance anxiety increased after viewing advertisements featuring idealized images. There was also a significant interaction between self-objectification level and idealized body (presence vs. absence). No differences emerged for body-related compared with non-body-related product advertisements. The only result for body shame was a main effect for time. Participants' body shame increased after exposure to idealized images, irrespective of advertisement type. Although our findings reveal that media-portrayed idealized images detrimentally affect the body image of young women, they highlight the individual differences in vulnerability and the different effects for different components of body image. These results are discussed in terms of their implications for the prevention and early intervention of body image and dieting-related disorders. ( Copyright 2005 by Wiley Periodicals, Inc

Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

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

Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.

2015-10-15

Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helixmore » bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).« less

Complementary construction of ideal nonimaging concentrators and its applications.

PubMed

Gordon, J M

1996-10-01

A construction principle for ideal nonimaging concentrators based on the complementary edge rays outside the nominal field of view is presented, with illustrations for the trumpet, compound parabolic concentrator, and compound hyperbolic concentrator. A simple string construction for the trumpet concentrator is shown to follow from this observation-the trumpet having been the one ideal concentrator for which no string-construction method had previously been noted. An application of these observations for solar concentrator design when nonisothermal receivers are advantageous is also presented.

Content, Structure, and Sequence of the Detailing Discipline at Kendall College of Art and Design.

ERIC Educational Resources Information Center

Mulder, Bruce E.

A study identified the appropriate general content, structure, and sequence for a detailing discipline that promoted student achievement to professional levels. Its focus was the detailing discipline, a sequence of studio courses within the furniture design program at Kendall College of Art and Design, Grand Rapids, Michigan. (Detailing, an…

RiboMaker: computational design of conformation-based riboregulation.

PubMed

Rodrigo, Guillermo; Jaramillo, Alfonso

2014-09-01

The ability to engineer control systems of gene expression is instrumental for synthetic biology. Thus, bioinformatic methods that assist such engineering are appealing because they can guide the sequence design and prevent costly experimental screening. In particular, RNA is an ideal substrate to de novo design regulators of protein expression by following sequence-to-function models. We have implemented a novel algorithm, RiboMaker, aimed at the computational, automated design of bacterial riboregulation. RiboMaker reads the sequence and structure specifications, which codify for a gene regulatory behaviour, and optimizes the sequences of a small regulatory RNA and a 5'-untranslated region for an efficient intermolecular interaction. To this end, it implements an evolutionary design strategy, where random mutations are selected according to a physicochemical model based on free energies. The resulting sequences can then be tested experimentally, providing a new tool for synthetic biology, and also for investigating the riboregulation principles in natural systems. Web server is available at http://ribomaker.jaramillolab.org/. Source code, instructions and examples are freely available for download at http://sourceforge.net/projects/ribomaker/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Designing of deployment sequence for braking and drift systems in atmosphere of Mars and Venus

NASA Astrophysics Data System (ADS)

Vorontsov, Victor

2006-07-01

Analysis of project development and space research using contact method, namely, by means of automatic descent modules and balloons shows that designing formation of entry, descent and landing (EDL) sequence and operation in the atmosphere are of great importance. This process starts at the very beginning of designing, has undergone a lot of iterations and influences processing of normal operation results. Along with designing of descent module systems, including systems of braking in the atmosphere, designing of flight operation sequence and trajectories of motion in the atmosphere is performed. As the entire operation sequence and transfer from one phase to another was correctly chosen, the probability of experiment success on the whole and efficiency of application of various systems vary. By now the most extensive experience of Russian specialists in research of terrestrial planets has been gained with the help of automatic interplanetary stations “Mars”, “Venera”, “Vega” which had descent modules and drifting in the atmosphere balloons. Particular interest and complicity of formation of EDL and drift sequence in the atmosphere of these planets arise from radically different operation conditions, in particular, strongly rarefied atmosphere of the one planet and extremely dense atmosphere of another. Consequently, this determines the choice of braking systems and their parameters and method of EDL consequence formation. At the same time there are general fundamental methods and designed research techniques that allowed taking general technical approach to designing of EDL and drift sequence in the atmosphere.

Universal sequence map (USM) of arbitrary discrete sequences

PubMed Central

2002-01-01

Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM), is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR). The latter enables the representation of 4 unit type sequences (like DNA) as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules. PMID:11895567

Pulseq: A rapid and hardware-independent pulse sequence prototyping framework.

PubMed

Layton, Kelvin J; Kroboth, Stefan; Jia, Feng; Littin, Sebastian; Yu, Huijun; Leupold, Jochen; Nielsen, Jon-Fredrik; Stöcker, Tony; Zaitsev, Maxim

2017-04-01

Implementing new magnetic resonance experiments, or sequences, often involves extensive programming on vendor-specific platforms, which can be time consuming and costly. This situation is exacerbated when research sequences need to be implemented on several platforms simultaneously, for example, at different field strengths. This work presents an alternative programming environment that is hardware-independent, open-source, and promotes rapid sequence prototyping. A novel file format is described to efficiently store the hardware events and timing information required for an MR pulse sequence. Platform-dependent interpreter modules convert the file to appropriate instructions to run the sequence on MR hardware. Sequences can be designed in high-level languages, such as MATLAB, or with a graphical interface. Spin physics simulation tools are incorporated into the framework, allowing for comparison between real and virtual experiments. Minimal effort is required to implement relatively advanced sequences using the tools provided. Sequences are executed on three different MR platforms, demonstrating the flexibility of the approach. A high-level, flexible and hardware-independent approach to sequence programming is ideal for the rapid development of new sequences. The framework is currently not suitable for large patient studies or routine scanning although this would be possible with deeper integration into existing workflows. Magn Reson Med 77:1544-1552, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

The Place of Ideals in Teaching.

ERIC Educational Resources Information Center

Hansen, David T.

This paper examines whether ideals and idealism have a role to play in teaching, identifying some ambiguities and problems associated with ideals and arguing that ideals figure importantly in teaching, but they are ideals of character or personhood as much as they are ideals of educational purpose. The first section focuses on the promise and…

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

PubMed Central

2012-01-01

Background RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. Results Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. Conclusions This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates. PMID:22985019

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing.

PubMed

Robles, José A; Qureshi, Sumaira E; Stephen, Stuart J; Wilson, Susan R; Burden, Conrad J; Taylor, Jennifer M

2012-09-17

RNA sequencing (RNA-Seq) has emerged as a powerful approach for the detection of differential gene expression with both high-throughput and high resolution capabilities possible depending upon the experimental design chosen. Multiplex experimental designs are now readily available, these can be utilised to increase the numbers of samples or replicates profiled at the cost of decreased sequencing depth generated per sample. These strategies impact on the power of the approach to accurately identify differential expression. This study presents a detailed analysis of the power to detect differential expression in a range of scenarios including simulated null and differential expression distributions with varying numbers of biological or technical replicates, sequencing depths and analysis methods. Differential and non-differential expression datasets were simulated using a combination of negative binomial and exponential distributions derived from real RNA-Seq data. These datasets were used to evaluate the performance of three commonly used differential expression analysis algorithms and to quantify the changes in power with respect to true and false positive rates when simulating variations in sequencing depth, biological replication and multiplex experimental design choices. This work quantitatively explores comparisons between contemporary analysis tools and experimental design choices for the detection of differential expression using RNA-Seq. We found that the DESeq algorithm performs more conservatively than edgeR and NBPSeq. With regard to testing of various experimental designs, this work strongly suggests that greater power is gained through the use of biological replicates relative to library (technical) replicates and sequencing depth. Strikingly, sequencing depth could be reduced as low as 15% without substantial impacts on false positive or true positive rates.

Neural-network-designed pulse sequences for robust control of singlet-triplet qubits

NASA Astrophysics Data System (ADS)

Yang, Xu-Chen; Yung, Man-Hong; Wang, Xin

2018-04-01

Composite pulses are essential for universal manipulation of singlet-triplet spin qubits. In the absence of noise, they are required to perform arbitrary single-qubit operations due to the special control constraint of a singlet-triplet qubit, while in a noisy environment, more complicated sequences have been developed to dynamically correct the error. Tailoring these sequences typically requires numerically solving a set of nonlinear equations. Here we demonstrate that these pulse sequences can be generated by a well-trained, double-layer neural network. For sequences designed for the noise-free case, the trained neural network is capable of producing almost exactly the same pulses known in the literature. For more complicated noise-correcting sequences, the neural network produces pulses with slightly different line shapes, but the robustness against noises remains comparable. These results indicate that the neural network can be a judicious and powerful alternative to existing techniques in developing pulse sequences for universal fault-tolerant quantum computation.

Designing the optimal shutter sequences for the flutter shutter imaging method

NASA Astrophysics Data System (ADS)

Jelinek, Jan

2010-04-01

Acquiring iris or face images of moving subjects at larger distances using a flash to prevent the motion blur quickly runs into eye safety concerns as the acquisition distance is increased. For that reason the flutter shutter method recently proposed by Raskar et al.has generated considerable interest in the biometrics community. The paper concerns the design of shutter sequences that produce the best images. The number of possible sequences grows exponentially in both the subject' s motion velocity and desired exposure value, with their majority being useless. Because the exact solution leads to an intractable mixed integer programming problem, we propose an approximate solution based on pre - screening the sequences according to the distribution of roots in their Fourier transform. A very fast algorithm utilizing the Jury' s criterion allows the testing to be done without explicitly computing the roots, making the approach practical for moderately long sequences.

The voice of the customer--Part 2: Benchmarking battery chargers against the Consumer's Ideal Product.

PubMed

Bauer, S M; Lane, J P; Stone, V I; Unnikrishnan, N

1998-01-01

The Rehabilitation Engineering Research Center on Technology Evaluation and Transfer is exploring how the end users of assistive technology devices define the ideal device. This work is called the Consumer Ideal Product program. In this work, end users identify and establish the importance of a broad range of product design features, along with the related product support and service provided by manufacturers and vendors. This paper describes a method for systematically transforming end-user defined requirements into a form that is useful and accessible to product designers, manufacturers, and vendors. In particular, product requirements, importance weightings, and metrics are developed from the Consumer Ideal Product battery charger outcomes. Six battery charges are benchmarked against these product requirements using the metrics developed. The results suggest improvements for each product's design, service, and support. Overall, the six chargers meet roughly 45-75% of the ideal product's requirements. Many of the suggested improvements are low-cost changes that, if adopted, could provide companies a competitive advantage in the marketplace.

Using Genome Sequence to Enable the Design of Medicines and Chemical Probes.

PubMed

Angelbello, Alicia J; Chen, Jonathan L; Childs-Disney, Jessica L; Zhang, Peiyuan; Wang, Zi-Fu; Disney, Matthew D

2018-02-28

Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.

Chomskyan Cognitivism and Linguistic: Irreproachable Ideals for Educational Psychology and Designing Learning

ERIC Educational Resources Information Center

Paleeri, Sankaranarayanan

2011-01-01

This paper makes an attempt to highlight the significance of Chomskyan concepts of linguistic and cognitivism in restructuring educational ideals and directions regarding learning in Educational Psychology. His specific views on educational aspects are the need of the hour in education scenario especially in the context of globalization. This…

Systematic optimization model and algorithm for binding sequence selection in computational enzyme design

PubMed Central

Huang, Xiaoqiang; Han, Kehang; Zhu, Yushan

2013-01-01

A systematic optimization model for binding sequence selection in computational enzyme design was developed based on the transition state theory of enzyme catalysis and graph-theoretical modeling. The saddle point on the free energy surface of the reaction system was represented by catalytic geometrical constraints, and the binding energy between the active site and transition state was minimized to reduce the activation energy barrier. The resulting hyperscale combinatorial optimization problem was tackled using a novel heuristic global optimization algorithm, which was inspired and tested by the protein core sequence selection problem. The sequence recapitulation tests on native active sites for two enzyme catalyzed hydrolytic reactions were applied to evaluate the predictive power of the design methodology. The results of the calculation show that most of the native binding sites can be successfully identified if the catalytic geometrical constraints and the structural motifs of the substrate are taken into account. Reliably predicting active site sequences may have significant implications for the creation of novel enzymes that are capable of catalyzing targeted chemical reactions. PMID:23649589

Multilocus sequence typing of total-genome-sequenced bacteria.

PubMed

Larsen, Mette V; Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W; Aarestrup, Frank M; Lund, Ole

2012-04-01

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

Quantification of non-ideal explosion violence with a shock tube

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

Jackson, Scott I; Hill, Larry G

There is significant interest in quantifying the blast violence associated with various nonideal explosions. Such data is essential to evaluate the damage potential of both explosive cookoff and terrorist explosive scenarios. We present a technique designed to measure the source energy associated with a non-ideal, asymmetrical, and three-dimensional explosion. A tube is used to confine and focus energy from a blast event into a one-dimensional, quasi-planar shock front. During propagation along the length of the tube, the wave is allowed to shocksteepen into a more ideal form. Pressure transducers then measure the shock overpressure as a function of the distancemore » from the source. One-dimensional blast scaling theory allows calculation of the source energy from this data. This small-scale test method addresses cost and noise concerns as well as boosting and symmetry issues associated with large-scale, three-dimensional, blast arena tests. Results from both ideal explosives and non-ideal explosives are discussed.« less

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

PubMed

Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

2017-07-01

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Developmental Idealism in China

PubMed Central

Thornton, Arland; Xie, Yu

2016-01-01

This paper examines the intersection of developmental idealism with China. It discusses how developmental idealism has been widely disseminated within China and has had enormous effects on public policy and programs, on social institutions, and on the lives of individuals and their families. This dissemination of developmental idealism to China began in the 19th century, when China met with several military defeats that led many in the country to question the place of China in the world. By the beginning of the 20th century, substantial numbers of Chinese had reacted to the country’s defeats by exploring developmental idealism as a route to independence, international respect, and prosperity. Then, with important but brief aberrations, the country began to implement many of the elements of developmental idealism, a movement that became especially important following the assumption of power by the Communist Party of China in 1949. This movement has played a substantial role in politics, in the economy, and in family life. The beliefs and values of developmental idealism have also been directly disseminated to the grassroots in China, where substantial majorities of Chinese citizens have assimilated them. These ideas are both known and endorsed by very large numbers in China today. PMID:28316833

Developmental Idealism in China.

PubMed

Thornton, Arland; Xie, Yu

2016-10-01

This paper examines the intersection of developmental idealism with China. It discusses how developmental idealism has been widely disseminated within China and has had enormous effects on public policy and programs, on social institutions, and on the lives of individuals and their families. This dissemination of developmental idealism to China began in the 19 th century, when China met with several military defeats that led many in the country to question the place of China in the world. By the beginning of the 20 th century, substantial numbers of Chinese had reacted to the country's defeats by exploring developmental idealism as a route to independence, international respect, and prosperity. Then, with important but brief aberrations, the country began to implement many of the elements of developmental idealism, a movement that became especially important following the assumption of power by the Communist Party of China in 1949. This movement has played a substantial role in politics, in the economy, and in family life. The beliefs and values of developmental idealism have also been directly disseminated to the grassroots in China, where substantial majorities of Chinese citizens have assimilated them. These ideas are both known and endorsed by very large numbers in China today.

Sequencing of Dust Filter Production Process Using Design Structure Matrix (DSM)

NASA Astrophysics Data System (ADS)

Sari, R. M.; Matondang, A. R.; Syahputri, K.; Anizar; Siregar, I.; Rizkya, I.; Ursula, C.

2018-01-01

Metal casting company produces machinery spare part for manufactures. One of the product produced is dust filter. Most of palm oil mill used this product. Since it is used in most of palm oil mill, company often have problems to address this product. One of problem is the disordered of production process. It carried out by the job sequencing. The important job that should be solved first, least implement, while less important job and could be completed later, implemented first. Design Structure Matrix (DSM) used to analyse and determine priorities in the production process. DSM analysis is sort of production process through dependency sequencing. The result of dependency sequences shows the sequence process according to the inter-process linkage considering before and after activities. Finally, it demonstrates their activities to the coupled activities for metal smelting, refining, grinding, cutting container castings, metal expenditure of molds, metal casting, coating processes, and manufacture of molds of sand.

No Surgical Innovation Without Evaluation: Evolution and Further Development of the IDEAL Framework and Recommendations.

PubMed

Hirst, Allison; Philippou, Yiannis; Blazeby, Jane; Campbell, Bruce; Campbell, Marion; Feinberg, Joshua; Rovers, Maroeska; Blencowe, Natalie; Pennell, Christopher; Quinn, Tom; Rogers, Wendy; Cook, Jonathan; Kolias, Angelos G; Agha, Riaz; Dahm, Philipp; Sedrakyan, Art; McCulloch, Peter

2018-04-24

To update, clarify, and extend IDEAL concepts and recommendations. New surgical procedures, devices, and other complex interventions need robust evaluation for safety, efficacy, and effectiveness. Unlike new medicines, there is no internationally agreed evaluation pathway for generating and analyzing data throughout the life cycle of surgical innovations. The IDEAL Framework and Recommendations were designed to provide this pathway and they have been used increasingly since their introduction in 2009. Based on a Delphi survey, expert workshop and major discussions during IDEAL conferences held in Oxford (2016) and New York (2017), this article updates and extends the IDEAL Recommendations, identifies areas for future research, and discusses the ethical problems faced by investigators at each IDEAL stage. The IDEAL Framework describes 5 stages of evolution for new surgical therapeutic interventions-Idea, Development, Exploration, Assessment, and Long-term Study. This comprehensive update proposes several modifications. First, a "Pre-IDEAL" stage describing preclinical studies has been added. Second we discuss potential adaptations to expand the scope of IDEAL (originally designed for surgical procedures) to accommodate therapeutic devices, through an IDEAL-D variant. Third, we explicitly recognise the value of comprehensive data collection through registries at all stages in the Framework and fourth, we examine the ethical issues that arise at each stage of IDEAL and underpin the recommendations. The Recommendations for each stage are reviewed, clarified and additional detail added. The intention of this article is to widen the practical use of IDEAL by clarifying the rationale for and practical details of the Recommendations. Additional research based on the experience of implementing these Recommendations is needed to further improve them.

Innovation in neurosurgery: less than IDEAL? A systematic review.

PubMed

Muskens, I S; Diederen, S J H; Senders, J T; Zamanipoor Najafabadi, A H; van Furth, W R; May, A M; Smith, T R; Bredenoord, A L; Broekman, M L D

2017-10-01

Surgical innovation is different from the introduction of novel pharmaceuticals. To help address this, in 2009 the IDEAL Collaboration (Idea, Development, Exploration, Assessment, Long-term follow-up) introduced the five-stage framework for surgical innovation. To evaluate the framework feasibility for novel neurosurgical procedure introduction, two innovative surgical procedures were examined: the endoscopic endonasal approach for skull base meningiomas (EEMS) and the WovenEndobridge (WEB device) for endovascular treatment of intracranial aneurysms. The published literature on EEMS and WEB devices was systematically reviewed. Identified studies were classified according to the IDEAL framework stage. Next, studies were evaluated for possible categorization according to the IDEAL framework. Five hundred seventy-six papers describing EEMS were identified of which 26 papers were included. No prospective studies were identified, and no studies reported on ethical approval or patient informed consent for the innovative procedure. Therefore, no clinical studies could be categorized according to the IDEAL Framework. For WEB devices, 6229 articles were screened of which 21 were included. In contrast to EEMS, two studies were categorized as 2a and two as 2b. The results of this systematic review demonstrate that both EEMS and WEB devices were not introduced according to the (later developed in the case of EEMS) IDEAL framework. Elements of the framework such as informed consent, ethical approval, and rigorous outcomes reporting are important and could serve to improve the quality of neurosurgical research. Alternative study designs and the use of big data could be useful modifications of the IDEAL framework for innovation in neurosurgery.

Primer3_masker: integrating masking of template sequence with primer design software.

PubMed

Kõressaar, Triinu; Lepamets, Maarja; Kaplinski, Lauris; Raime, Kairi; Andreson, Reidar; Remm, Maido

2018-06-01

Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical model to detect and mask failure-prone regions on the DNA template prior to primer design. We implemented the software as a standalone software primer3_masker and integrated it into the primer design program Primer3. The standalone version of primer3_masker is implemented in C. The source code is freely available at https://github.com/bioinfo-ut/primer3_masker/ (standalone version for Linux and macOS) and at https://github.com/primer3-org/primer3/ (integrated version). Primer3 web application that allows masking sequences of 196 animal and plant genomes is available at http://primer3.ut.ee/. maido.remm@ut.ee. Supplementary data are available at Bioinformatics online.

Sequence-based design of bioactive small molecules that target precursor microRNAs.

PubMed

Velagapudi, Sai Pradeep; Gallo, Steven M; Disney, Matthew D

2014-04-01

Oligonucleotides are designed to target RNA using base pairing rules, but they can be hampered by poor cellular delivery and nonspecific stimulation of the immune system. Small molecules are preferred as lead drugs or probes but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA hairpin precursors, and it identified bioactive small molecules that inhibit biogenesis by binding nuclease-processing sites (44% hit rate). Among 27 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Markedly, microRNA profiling shows that 1 only affects microRNA-96 biogenesis and is at least as selective as an oligonucleotide.

Sequence-based design of bioactive small molecules that target precursor microRNAs

PubMed Central

Velagapudi, Sai Pradeep; Gallo, Steven M.; Disney, Matthew D.

2014-01-01

Oligonucleotides are designed to target RNA using base pairing rules, however, they are hampered by poor cellular delivery and non-specific stimulation of the immune system. Small molecules are preferred as lead drugs or probes, but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA precursors and identified bioactive small molecules that inhibit biogenesis by binding to nuclease processing sites (41% hit rate). Amongst 29 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Importantly, microRNA profiling shows that 1 only significantly effects microRNA-96 biogenesis and is more selective than an oligonucleotide. PMID:24509821

High-resolution proton density weighted three-dimensional fast spin echo (3D-FSE) of the knee with IDEAL at 1.5 Tesla: comparison with 3D-FSE and 2D-FSE--initial experience.

PubMed

McMahon, Colm J; Madhuranthakam, Ananth J; Wu, Jim S; Yablon, Corrie M; Wei, Jesse L; Rofsky, Neil M; Hochman, Mary G

2012-02-01

To assess the feasibility of combining three-dimensional fast spin echo (3D-FSE) and Iterative-decomposition-of water-and-fat-with-echo asymmetry-and-least-squares-estimation (IDEAL) at 1.5 Tesla (T), generating a high-resolution 3D isotropic proton density-weighted image set with and without "fat-suppression" (FS) in a single acquisition, and to compare with 2D-FSE and 3D-FSE (without IDEAL). Ten asymptomatic volunteers prospectively underwent sagittal 3D-FSE-IDEAL, 3D-FSE, and 2D-FSE sequences at 1.5T (slice thickness [ST]: 0.8 mm, 0.8 mm, and 3.5 mm, respectively). 3D-FSE and 2D-FSE were repeated with frequency-selective FS. Fluid, cartilage, and muscle signal-to-noise ratio (SNR) and fluid-cartilage contrast-to-noise ratio (CNR) were compared among sequences. Three blinded reviewers independently scored quality of menisci/cartilage depiction for all sequences. "Fat-suppression" was qualitatively scored and compared among sequences. 3D-FSE-IDEAL fluid-cartilage CNR was higher than in 2D-FSE (P < 0.05), not different from 3D-FSE (P = 0.31). There was no significant difference in fluid SNR among sequences. 2D-FSE cartilage SNR was higher than in 3D FSE-IDEAL (P < 0.05), not different to 3D-FSE (P = 0.059). 2D-FSE muscle SNR was higher than in 3D-FSE-IDEAL (P < 0.05) and 3D-FSE (P < 0.05). Good or excellent depiction of menisci/cartilage was achieved using 3D-FSE-IDEAL in the acquired sagittal and reformatted planes. Excellent, homogeneous "fat-suppression" was achieved using 3D-FSE-IDEAL, superior to FS-3D-FSE and FS-2D-FSE (P < 0.05). 3D FSE-IDEAL is a feasible approach to acquire multiplanar images of diagnostic quality, both with and without homogeneous "fat-suppression" from a single acquisition. Copyright © 2011 Wiley Periodicals, Inc.

"The part of me that you bring out": ideal similarity and the Michelangelo phenomenon.

PubMed

Rusbult, Caryl E; Kumashiro, Madoka; Kubacka, Kaska E; Finkel, Eli J

2009-01-01

This work examines the Michelangelo phenomenon, an interpersonal model of the means by which people move closer to (vs. further from) their ideal selves. The authors propose that partner similarity--similarity to the ideal self, in particular--plays an important role in this process. Across 4 studies employing diverse designs and measurement techniques, they observed consistent evidence that when partners possess key elements of one another's ideal selves, each person affirms the other by eliciting important aspects of the other's ideals, each person moves closer to his or her ideal self, and couple well-being is enhanced. Partner similarity to the actual self also accounts for unique variance in key elements of this model. The associations of ideal similarity and actual similarity with couple well-being are fully attributable to the Michelangelo process, to partner affirmation and target movement toward the ideal self. The authors also performed auxiliary analyses to rule out several alternative interpretations of these findings.

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

PubMed

Smith, Colin A; Kortemme, Tanja

2011-01-01

Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

Improving Students' Conceptual Understanding of a Specific Content Learning: A Designed Teaching Sequence

ERIC Educational Resources Information Center

Ahmad, N. J.; Lah, Y. Che

2012-01-01

The efficacy of a teaching sequence designed for a specific content of learning of electrochemistry is described in this paper. The design of the teaching draws upon theoretical insights into perspectives on learning and empirical studies to improve the teaching of this topic. A case study involving two classes, the experimental and baseline…

The ideal imaging AR waveguide

NASA Astrophysics Data System (ADS)

Grey, David J.

2017-06-01

Imaging waveguides are a key development that are helping to create the Augmented Reality revolution. They have the ability to use a small projector as an input and produce a wide field of view, large eyebox, full colour, see-through image with good contrast and resolution. WaveOptics is at the forefront of this AR technology and has developed and demonstrated an approach which is readily scalable. This paper presents our view of the ideal near-to-eye imaging AR waveguide. This will be a single-layer waveguide which can be manufactured in high volume and low cost, and is suitable for small form factor applications and all-day wear. We discuss the requirements of the waveguide for an excellent user experience. When enhanced (AR) viewing is not required, the waveguide should have at least 90% transmission, no distracting artifacts and should accommodate the user's ophthalmic prescription. When enhanced viewing is required, additionally, the waveguide requires excellent imaging performance, this includes resolution to the limit of human acuity, wide field of view, full colour, high luminance uniformity and contrast. Imaging waveguides are afocal designs and hence cannot provide ophthalmic correction. If the user requires this correction then they must wear either contact lenses, prescription spectacles or inserts. The ideal imaging waveguide would need to cope with all of these situations so we believe it must be capable of providing an eyebox at an eye relief suitable for spectacle wear which covers a significant range of population inter-pupillary distances. We describe the current status of our technology and review existing imaging waveguide technologies against the ideal component.

How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives.

PubMed

Dal Molin, Alessandra; Di Camillo, Barbara

2018-01-31

The sequencing of the transcriptome of single cells, or single-cell RNA-sequencing, has now become the dominant technology for the identification of novel cell types in heterogeneous cell populations or for the study of stochastic gene expression. In recent years, various experimental methods and computational tools for analysing single-cell RNA-sequencing data have been proposed. However, most of them are tailored to different experimental designs or biological questions, and in many cases, their performance has not been benchmarked yet, thus increasing the difficulty for a researcher to choose the optimal single-cell transcriptome sequencing (scRNA-seq) experiment and analysis workflow. In this review, we aim to provide an overview of the current available experimental and computational methods developed to handle single-cell RNA-sequencing data and, based on their peculiarities, we suggest possible analysis frameworks depending on specific experimental designs. Together, we propose an evaluation of challenges and open questions and future perspectives in the field. In particular, we go through the different steps of scRNA-seq experimental protocols such as cell isolation, messenger RNA capture, reverse transcription, amplification and use of quantitative standards such as spike-ins and Unique Molecular Identifiers (UMIs). We then analyse the current methodological challenges related to preprocessing, alignment, quantification, normalization, batch effect correction and methods to control for confounding effects. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.

PubMed

Weinbrand, Lina; Avihoo, Assaf; Barash, Danny

2013-11-15

In RNA design problems, it is plausible to assume that the user would be interested in preserving a particular RNA secondary structure motif, or fragment, for biological reasons. The preservation could be in structure or sequence, or both. Thus, the inverse RNA folding problem could benefit from considering fragment constraints. We have developed a new interactive Java application called RNA fragment-based inverse that allows users to insert an RNA secondary structure in dot-bracket notation. It then performs sequence design that conforms to the shape of the input secondary structure, the specified thermodynamic stability, the specified mutational robustness and the user-selected fragment after shape decomposition. In this shape-based design approach, specific RNA structural motifs with known biological functions are strictly enforced, while others can possess more flexibility in their structure in favor of preserving physical attributes and additional constraints. RNAfbinv is freely available for download on the web at http://www.cs.bgu.ac.il/~RNAexinv/RNAfbinv. The site contains a help file with an explanation regarding the exact use.

The Real/Ideal Research Project: Fostering Students' Emotional Literacy

ERIC Educational Resources Information Center

Martorana, Christine

2016-01-01

The Real/Ideal Research Project is comprised of three components, ordered in purposeful succession, designed to emphasize the interconnectedness of emotion, reason, and action. In the first component, students compose a personal narrative focused on a specific inequity they (have) experience(d) or witnessed. Here, students are encouraged to…

The Design and Analysis of Transposon-Insertion Sequencing Experiments

PubMed Central

Chao, Michael C.; Abel, Sören; Davis, Brigid M.; Waldor, Matthew K.

2016-01-01

Preface Transposon-insertion sequencing (TIS) is a powerful approach that can be widely applied to genome-wide definition of loci that are required for growth in diverse conditions. However, experimental design choices and stochastic biological processes can heavily influence the results of TIS experiments and affect downstream statistical analysis. Here, we discuss TIS experimental parameters and how these factors relate to the benefits and limitations of the various statistical frameworks that can be applied to computational analysis of TIS data. PMID:26775926

From the ideal market to the ideal clinic: constructing a normative standard of fairness for human subjects research.

PubMed

Phillips, Trisha

2011-02-01

Preventing exploitation in human subjects research requires a benchmark of fairness against which to judge the distribution of the benefits and burdens of a trial. This paper proposes the ideal market and its fair market price as a criterion of fairness. The ideal market approach is not new to discussions about exploitation, so this paper reviews Wertheimer's inchoate presentation of the ideal market as a principle of fairness, attempt of Emanuel and colleagues to apply the ideal market to human subjects research, and Ballantyne's criticisms of both the ideal market and the resulting benchmark of fairness. It argues that the criticism of this particular benchmark is on point, but the rejection of the ideal market is mistaken. After presenting a complete account of the ideal market, this paper proposes a new method for applying the ideal market to human subjects research and illustrates the proposal by considering a sample case.

Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

PubMed Central

Cai, Yizhi; Lux, Matthew W.; Adam, Laura; Peccoud, Jean

2009-01-01

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology. PMID:19816554

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

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

Whitehead, Timothy A.; Chevalier, Aaron; Song, Yifan

2012-06-19

We show that comprehensive sequence-function maps obtained by deep sequencing can be used to reprogram interaction specificity and to leapfrog over bottlenecks in affinity maturation by combining many individually small contributions not detectable in conventional approaches. We use this approach to optimize two computationally designed inhibitors against H1N1 influenza hemagglutinin and, in both cases, obtain variants with subnanomolar binding affinity. The most potent of these, a 51-residue protein, is broadly cross-reactive against all influenza group 1 hemagglutinins, including human H2, and neutralizes H1N1 viruses with a potency that rivals that of several human monoclonal antibodies, demonstrating that computational design followedmore » by comprehensive energy landscape mapping can generate proteins with potential therapeutic utility.« less

Ideals and Category Typicality

ERIC Educational Resources Information Center

Kim, ShinWoo; Murphy, Gregory L.

2011-01-01

Barsalou (1985) argued that exemplars that serve category goals become more typical category members. Although this claim has received support, we investigated (a) whether categories have a single ideal, as negatively valenced categories (e.g., cigarette) often have conflicting goals, and (b) whether ideal items are in fact typical, as they often…

Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm.

PubMed

Tian, Ye; Huang, Xiaoqiang; Zhu, Yushan

2015-08-01

Enzyme amino-acid sequences at ligand-binding interfaces are evolutionarily optimized for reactions, and the natural conformation of an enzyme-ligand complex must have a low free energy relative to alternative conformations in native-like or non-native sequences. Based on this assumption, a combined energy function was developed for enzyme design and then evaluated by recapitulating native enzyme sequences at ligand-binding interfaces for 10 enzyme-ligand complexes. In this energy function, the electrostatic interaction between polar or charged atoms at buried interfaces is described by an explicitly orientation-dependent hydrogen-bonding potential and a pairwise-decomposable generalized Born model based on the general side chain in the protein design framework. The energy function is augmented with a pairwise surface-area based hydrophobic contribution for nonpolar atom burial. Using this function, on average, 78% of the amino acids at ligand-binding sites were predicted correctly in the minimum-energy sequences, whereas 84% were predicted correctly in the most-similar sequences, which were selected from the top 20 sequences for each enzyme-ligand complex. Hydrogen bonds at the enzyme-ligand binding interfaces in the 10 complexes were usually recovered with the correct geometries. The binding energies calculated using the combined energy function helped to discriminate the active sequences from a pool of alternative sequences that were generated by repeatedly solving a series of mixed-integer linear programming problems for sequence selection with increasing integer cuts.

Review of sequencing platforms and their applications in phaeochromocytoma and paragangliomas.

PubMed

Pillai, Suja; Gopalan, Vinod; Lam, Alfred King-Yin

2017-08-01

Genetic testing is recommended for patients with phaeochromocytoma (PCC) and paraganglioma (PGL) because of their genetic heterogeneity and heritability. Due to the large number of susceptibility genes associated with PCC/PGL, next-generation sequencing (NGS) technology is ideally suited for carrying out genetic screening of these individuals. New generations of DNA sequencing technologies facilitate the development of comprehensive genetic testing in PCC/PGL at a lower cost. Whole-exome sequencing and targeted NGS are the preferred methods for screening of PCC/PGL, both having precise mutation detection methods and low costs. RNA sequencing and DNA methylation studies using NGS technology in PCC/PGL can be adopted to act as diagnostic or prognostic biomarkers as well as in planning targeted epigenetic treatment of patients with PCC/PGL. The designs of NGS having a high depth of coverage and robust analytical pipelines can lead to the successful detection of a wide range of genomic defects in PCC/PGL. Nevertheless, the major challenges of this technology must be addressed before it has practical applications in the clinical diagnostics to fulfill the goal of personalized medicine in PCC/PGL. In future, novel approaches of sequencing, such as third and fourth generation sequencing can alter the workflow, cost, analysis, and interpretation of genomics associated with PCC/PGL. Copyright © 2017 Elsevier B.V. All rights reserved.

Simple equations to simulate closed-loop recycling liquid-liquid chromatography: Ideal and non-ideal recycling models.

PubMed

Kostanyan, Artak E

2015-12-04

The ideal (the column outlet is directly connected to the column inlet) and non-ideal (includes the effects of extra-column dispersion) recycling equilibrium-cell models are used to simulate closed-loop recycling counter-current chromatography (CLR CCC). Simple chromatogram equations for the individual cycles and equations describing the transport and broadening of single peaks and complex chromatograms inside the recycling closed-loop column for ideal and non-ideal recycling models are presented. The extra-column dispersion is included in the theoretical analysis, by replacing the recycling system (connecting lines, pump and valving) by a cascade of Nec perfectly mixed cells. To evaluate extra-column contribution to band broadening, two limiting regimes of recycling are analyzed: plug-flow, Nec→∞, and maximum extra-column dispersion, Nec=1. Comparative analysis of ideal and non-ideal models has shown that when the volume of the recycling system is less than one percent of the column volume, the influence of the extra-column processes on the CLR CCC separation may be neglected. Copyright © 2015 Elsevier B.V. All rights reserved.

Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

PubMed Central

Tanaka, Fumiaki; Kameda, Atsushi; Yamamoto, Masahito; Ohuchi, Azuma

2005-01-01

We have developed an algorithm for designing multiple sequences of nucleic acids that have a uniform melting temperature between the sequence and its complement and that do not hybridize non-specifically with each other based on the minimum free energy (ΔGmin). Sequences that satisfy these constraints can be utilized in computations, various engineering applications such as microarrays, and nano-fabrications. Our algorithm is a random generate-and-test algorithm: it generates a candidate sequence randomly and tests whether the sequence satisfies the constraints. The novelty of our algorithm is that the filtering method uses a greedy search to calculate ΔGmin. This effectively excludes inappropriate sequences before ΔGmin is calculated, thereby reducing computation time drastically when compared with an algorithm without the filtering. Experimental results in silico showed the superiority of the greedy search over the traditional approach based on the hamming distance. In addition, experimental results in vitro demonstrated that the experimental free energy (ΔGexp) of 126 sequences correlated well with ΔGmin (|R| = 0.90) than with the hamming distance (|R| = 0.80). These results validate the rationality of a thermodynamic approach. We implemented our algorithm in a graphic user interface-based program written in Java. PMID:15701762

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

PubMed Central

2012-01-01

Background Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs) and other related compounds. To improve PAs production in Crataegus tissues, the sequences of genes encoding PAs biosynthetic enzymes are required. Findings Different bioinformatics tools, including BLAST, multiple sequence alignment and alignment PCR analysis were used to design primers suitable for the amplification of DNA fragments from 10 candidate genes encoding enzymes involved in PAs biosynthesis in C. aronia. DNA sequencing results proved the utility of the designed primers. The primers were used successfully to amplify DNA fragments of different PAs biosynthesis genes in different Rosaceae plants. Conclusion To the best of our knowledge, this is the first use of the alignment PCR approach to isolate DNA sequences encoding PAs biosynthetic enzymes in Rosaceae plants. PMID:22883984

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

PubMed

Zuiter, Afnan Saeid; Sawwan, Jammal; Al Abdallat, Ayed

2012-08-10

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

CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing.

PubMed

Boyer, François; Boutouil, Hend; Dalloul, Iman; Dalloul, Zeinab; Cook-Moreau, Jeanne; Aldigier, Jean-Claude; Carrion, Claire; Herve, Bastien; Scaon, Erwan; Cogné, Michel; Péron, Sophie

2017-05-15

B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study. Copyright © 2017 by The American Association of Immunologists, Inc.

Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA.

PubMed

Sproul, John S; Maddison, David R

2017-11-01

Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3-6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58-159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1-10 ng). We also explored low-cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low-input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers and library amplification. We present these guidelines to facilitate more economical use of valuable DNA and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens. © 2017 John Wiley & Sons Ltd.

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

PubMed

Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

2013-07-01

The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity. In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure. IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/. Supplementary data are available at Bioinformatics online.

EPSE Project 2: Designing and Evaluating Short Teaching Sequences, Informed by Research Evidence.

ERIC Educational Resources Information Center

Leach, John; Hind, Andy; Lewis, Jenny; Scott, Phil

2002-01-01

Reports on Project 2 from the Evidence-based Practice in Science Education (EPSE) Research Network. In this project, teachers and researchers worked collaboratively on the design of three short teaching sequences on electric circuits. (DDR)

A ribonucleotide Origin for Life - Fluctuation and Near-ideal Reactions

NASA Astrophysics Data System (ADS)

Yarus, Michael

2013-02-01

Oligoribonucleotides are potentially capable of Darwinian evolution - they may replicate and can express an independent chemical phenotype, as embodied in modern enzymatic cofactors. Using quantitative chemical kinetics on a sporadically fed ribonucleotide pool, unreliable supplies of unstable activated ribonucleotides A and B at low concentrations recurrently yield a replicating AB polymer with a potential chemical phenotype. Self-complementary replication in the pool occurs during a minority (here ≈ 35 %) of synthetic episodes that exploit coincidental overlaps between 4, 5 or 6 spikes of arbitrarily arriving substrates. Such uniquely productive synthetic episodes, in which near-ideal reaction sequences recur at random, account for most AB oligonucleotide synthesis, and therefore underlie the emergence of net replication under realistic primordial conditions. Because overlapping substrate spikes are unexpectedly frequent, and in addition, complex spike sequences appear disproportionately, a sporadically fed pool can host unexpectedly complex syntheses. Thus, primordial substrate fluctuations are not necessarily a barrier to Darwinism, but instead can facilitate early evolution.

A ribonucleotide Origin for Life--fluctuation and near-ideal reactions.

PubMed

Yarus, Michael

2013-02-01

Oligoribonucleotides are potentially capable of Darwinian evolution - they may replicate and can express an independent chemical phenotype, as embodied in modern enzymatic cofactors. Using quantitative chemical kinetics on a sporadically fed ribonucleotide pool, unreliable supplies of unstable activated ribonucleotides A and B at low concentrations recurrently yield a replicating AB polymer with a potential chemical phenotype. Self-complementary replication in the pool occurs during a minority (here ≈ 35 %) of synthetic episodes that exploit coincidental overlaps between 4, 5 or 6 spikes of arbitrarily arriving substrates. Such uniquely productive synthetic episodes, in which near-ideal reaction sequences recur at random, account for most AB oligonucleotide synthesis, and therefore underlie the emergence of net replication under realistic primordial conditions. Because overlapping substrate spikes are unexpectedly frequent, and in addition, complex spike sequences appear disproportionately, a sporadically fed pool can host unexpectedly complex syntheses. Thus, primordial substrate fluctuations are not necessarily a barrier to Darwinism, but instead can facilitate early evolution.

Task analysis in curriculum design: a hierarchically sequenced introductory mathematics curriculum1

PubMed Central

Resnick, Lauren B.; Wang, Margaret C.; Kaplan, Jerome

1973-01-01

A method of systematic task analysis is applied to the problem of designing a sequence of learning objectives that will provide an optimal match for the child's natural sequence of acquisition of mathematical skills and concepts. The authors begin by proposing an operational definition of the number concept in the form of a set of behaviors which, taken together, permit the inference that the child has an abstract concept of “number”. These are the “objectives” of the curriculum. Each behavior in the defining set is then subjected to an analysis that identifies hypothesized components of skilled performance and prerequisites for learning these components. On the basis of these analyses, specific sequences of learning objectives are proposed. The proposed sequences are hypothesized to be those that will best facilitate learning, by maximizing transfer from earlier to later objectives. Relevant literature on early learning and cognitive development is considered in conjunction with the analyses and the resulting sequences. The paper concludes with a discussion of the ways in which the curriculum can be implemented and studied in schools. Examples of data on individual children are presented, and the use of such data for improving the curriculum itself, as well as for examining the effects of other treatment variables, is considered. PMID:16795452

Ideal Knowing: Logics of Knowledge in Primary School Curricula

ERIC Educational Resources Information Center

Macknight, Vicki

2011-01-01

This paper is written to draw attention to the ideal knower and the logic of knowledge embedded in curricula. New logics and new knowers, I argue, are conjured with the hope they will be capable of succeeding in curriculum designers' imagined future. I frame this discussion in terms of debates about the place of knowledge in the sociology of…

Effects of real fluid properties on axial turbine meanline design and off-design analysis

NASA Astrophysics Data System (ADS)

MacLean, Cameron

The effects of real fluid properties on axial turbine meanline analysis have been investigated employing two meanline analysis codes, namely Turbine Meanline Design (TMLD) and Turbine Meanline Off-Design (TMLO). The previously developed TMLD code assumed the working fluid was an ideal gas. Therefore it was modified to use real fluid properties. TMLO was then developed from TMLD Both codes can be run using either the ideal gas assumption or real fluid properties. TMLD was employed for the meanline design of several axial turbines for a range of inlet conditions, using both the ideal gas assumption and real fluid properties. The resulting designs were compared to see the effects of real fluid properties. Meanline designs, generated using the ideal gas assumption, were then analysed with TMLO using real fluid properties. This was done over a range of inlet conditions that correspond to varying degrees of departure from ideal gas conditions. The goal was to show how machines designed with the ideal gas assumption would perform with the real working fluid. The working fluid used in both investigations was supercritical carbon dioxide. Results from the investigation show that real fluid properties had a strong effect on the gas path areas of the turbine designs as well as the performance of turbines designed using the ideal gas assumption. Specifically, power output and the velocities of the working fluid were affected. It was found that accounting for losses tended to lessen the effects of the real fluid properties.

Studies of a biochemical factory: tomato trichome deep expressed sequence tag sequencing and proteomics.

PubMed

Schilmiller, Anthony L; Miner, Dennis P; Larson, Matthew; McDowell, Eric; Gang, David R; Wilkerson, Curtis; Last, Robert L

2010-07-01

Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces beta-caryophyllene and alpha-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells.

Using Sequence Diagrams to Detect Communication Problems Between Systems

NASA Technical Reports Server (NTRS)

Lindvall, Mikael; Ackermann, Chris; Stratton, William C.; Sibol, Deane E.; Ray, Arnab; Yonkwa, Lyly; Kresser, Jan; Godfrey, Sally H.; Knodel, Jens

2008-01-01

Many software systems are evolving complex system of systems (SoS) for which inter-system communication is both mission-critical and error-prone. Such communication problems ideally would be detected before deployment. In a NASA-supported Software Assurance Research Program (SARP) project, we are researching a new approach addressing such problems. In this paper, we show that problems in the communication between two systems can be detected by using sequence diagrams to model the planned communication and by comparing the planned sequence to the actual sequence. We identify different kinds of problems that can be addressed by modeling the planned sequence using different level of abstractions.

An Automated Pipeline for Engineering Many-Enzyme Pathways: Computational Sequence Design, Pathway Expression-Flux Mapping, and Scalable Pathway Optimization.

PubMed

Halper, Sean M; Cetnar, Daniel P; Salis, Howard M

2018-01-01

Engineering many-enzyme metabolic pathways suffers from the design curse of dimensionality. There are an astronomical number of synonymous DNA sequence choices, though relatively few will express an evolutionary robust, maximally productive pathway without metabolic bottlenecks. To solve this challenge, we have developed an integrated, automated computational-experimental pipeline that identifies a pathway's optimal DNA sequence without high-throughput screening or many cycles of design-build-test. The first step applies our Operon Calculator algorithm to design a host-specific evolutionary robust bacterial operon sequence with maximally tunable enzyme expression levels. The second step applies our RBS Library Calculator algorithm to systematically vary enzyme expression levels with the smallest-sized library. After characterizing a small number of constructed pathway variants, measurements are supplied to our Pathway Map Calculator algorithm, which then parameterizes a kinetic metabolic model that ultimately predicts the pathway's optimal enzyme expression levels and DNA sequences. Altogether, our algorithms provide the ability to efficiently map the pathway's sequence-expression-activity space and predict DNA sequences with desired metabolic fluxes. Here, we provide a step-by-step guide to applying the Pathway Optimization Pipeline on a desired multi-enzyme pathway in a bacterial host.

Kirkwood–Buff integrals for ideal solutions

PubMed Central

Ploetz, Elizabeth A.; Bentenitis, Nikolaos; Smith, Paul E.

2010-01-01

The Kirkwood–Buff (KB) theory of solutions is a rigorous theory of solution mixtures which relates the molecular distributions between the solution components to the thermodynamic properties of the mixture. Ideal solutions represent a useful reference for understanding the properties of real solutions. Here, we derive expressions for the KB integrals, the central components of KB theory, in ideal solutions of any number of components corresponding to the three main concentration scales. The results are illustrated by use of molecular dynamics simulations for two binary solutions mixtures, benzene with toluene, and methanethiol with dimethylsulfide, which closely approach ideal behavior, and a binary mixture of benzene and methanol which is nonideal. Simulations of a quaternary mixture containing benzene, toluene, methanethiol, and dimethylsulfide suggest this system displays ideal behavior and that ideal behavior is not limited to mixtures containing a small number of components. PMID:20441282

An investigation of application of the golden ratio and Fibonacci sequence in fashion design and pattern making

NASA Astrophysics Data System (ADS)

Kazlacheva, Z. I.

2017-10-01

The Golden ratio and Fibonacci sequence are used as proportions in design as symbols of beauty and harmony. That symbolism is a result of the strong connections in their mathematical nature. The Golden section is a number, introduced with Greek letter φ, which is found by dividing a line into two parts as the longer part divided by the smaller part is equal as the whole length of longer and smaller parts divided by the longer part. Fibonacci sequence is a series of numbers where every number is equal to the two numbers before it. An investigation of application of proportions based on the Golden ratio and Fibonacci sequence in the fashion design and pattern making of ladies’ clothing is the main aim of the paper. Based on the study it may be concluded that in fashion design and pattern making the Golden ratio and Fibonacci sequence can be used in creation of beautiful and harmonic forms directly or with the help of geometrical figures as: In directly use the Golden and Fibonacci numbers proportions can be in one and the same or different directions. In the application with the help of geometrical shapes the Golden and Fibonacci figures combine proportioning and form creation. The Golden and Fibonacci shapes can be used directly as forms or as frames of forms creation of elements and pieces. Its application can be in different directions and location according the bodice. The Golden section and Fibonacci sequence can combine proportions with other principles of design as symmetry, rhythm, etc.

Value-based HR practices, i-deals and clinical error control with CSR as a moderator.

PubMed

Luu, Tuan; Rowley, Chris; Siengthai, Sununta; Thanh Thao, Vo

2017-05-08

Purpose Notwithstanding the rising magnitude of system factors in patient safety improvement, "human factors" such as idiosyncratic deals (i-deals) which also contribute to the adjustment of system deficiencies should not be neglected. The purpose of this paper is to investigate the role of value-based HR practices in catalyzing i-deals, which then influence clinical error control. The research further examines the moderating role of corporate social responsibility (CSR) on the effect of value-based HR practices on i-deals. Design/methodology/approach The data were collected from middle-level clinicians from hospitals in the Vietnam context. Findings The research results confirmed the effect chain from value-based HR practices through i-deals to clinical error control with CSR as a moderator. Originality/value The HRM literature is expanded through enlisting i-deals and clinical error control as the outcomes of HR practices.

Joint electrical engineering/physics course sequence for optics fundamentals and design

NASA Astrophysics Data System (ADS)

Magnusson, Robert; Maldonado, Theresa A.; Black, Truman D.

2000-06-01

Optics is a key technology in a broad range of engineering and science applications of high national priority. Engineers and scientists with a sound background in this field are needed to preserve technical leadership and to establish new directions of research and development. To meet this educational need, a joint Electrical Engineering/Physics optics course sequence was created as PHYS 3445 Fundamentals of Optics and EE 4444 Optical Systems Design, both with a laboratory component. The objectives are to educate EE and Physics undergraduate students in the fundamentals of optics; in interdisciplinary problem solving; in design and analysis; in handling optical components; and in skills such as communications and team cooperation. Written technical reports in professional format are required, formal presentations are given, and participation in paper design contests is encouraged.

Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results.

PubMed

Just, Rebecca S; Irwin, Jodi A

2018-05-01

Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for enhanced genotyping and mixture deconvolution, the sequence variation among same-length products must be utilized in some form. Here, we propose use of the longest uninterrupted stretch (LUS) in allele designations as a simple method to represent sequence variation within the STR repeat regions and facilitate - in the nearterm - probabilistic interpretation of NGS-based typing results. An examination of published population data indicated that a reference LUS region is straightforward to define for most autosomal STR loci, and that using repeat unit plus LUS length as the allele designator can represent greater than 80% of the alleles detected by sequencing. A proof of concept study performed using a freely available probabilistic software demonstrated that the LUS length can be used in allele designations when a program does not require alleles to be integers, and that utilizing sequence information improves interpretation of both single-source and mixed contributor STR typing results as compared to using repeat unit information alone. The LUS concept for allele designation maintains the repeat-based allele nomenclature that will permit backward compatibility to extant STR databases, and the LUS lengths themselves will be concordant regardless of the NGS assay or analysis tools

Ideal regularization for learning kernels from labels.

PubMed

Pan, Binbin; Lai, Jianhuang; Shen, Lixin

2014-08-01

In this paper, we propose a new form of regularization that is able to utilize the label information of a data set for learning kernels. The proposed regularization, referred to as ideal regularization, is a linear function of the kernel matrix to be learned. The ideal regularization allows us to develop efficient algorithms to exploit labels. Three applications of the ideal regularization are considered. Firstly, we use the ideal regularization to incorporate the labels into a standard kernel, making the resulting kernel more appropriate for learning tasks. Next, we employ the ideal regularization to learn a data-dependent kernel matrix from an initial kernel matrix (which contains prior similarity information, geometric structures, and labels of the data). Finally, we incorporate the ideal regularization to some state-of-the-art kernel learning problems. With this regularization, these learning problems can be formulated as simpler ones which permit more efficient solvers. Empirical results show that the ideal regularization exploits the labels effectively and efficiently. Copyright © 2014 Elsevier Ltd. All rights reserved.

Intuitionistic fuzzy n-fold KU-ideal of KU-algebra

NASA Astrophysics Data System (ADS)

Mostafa, Samy M.; Kareem, Fatema F.

2018-05-01

In this paper, we apply the notion of intuitionistic fuzzy n-fold KU-ideal of KU-algebra. Some types of ideals such as intuitionistic fuzzy KU-ideal, intuitionistic fuzzy closed ideal and intuitionistic fuzzy n-fold KU-ideal are studied. Also, the relations between intuitionistic fuzzy n-fold KU-ideal and intuitionistic fuzzy KU-ideal are discussed. Furthermore, a few results of intuitionistic fuzzy n-fold KU-ideals of a KU-algebra under homomorphism are discussed.

Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions.

PubMed

Du, Q S; Ma, Y; Xie, N Z; Huang, R B

2014-01-01

In the design of peptide inhibitors the huge possible variety of the peptide sequences is of high concern. In collaboration with the fast accumulation of the peptide experimental data and database, a statistical method is suggested for peptide inhibitor design. In the two-level peptide prediction network (2L-QSAR) one level is the physicochemical properties of amino acids and the other level is the peptide sequence position. The activity contributions of amino acids are the functions of physicochemical properties and the sequence positions. In the prediction equation two weight coefficient sets {ak} and {bl} are assigned to the physicochemical properties and to the sequence positions, respectively. After the two coefficient sets are optimized based on the experimental data of known peptide inhibitors using the iterative double least square (IDLS) procedure, the coefficients are used to evaluate the bioactivities of new designed peptide inhibitors. The two-level prediction network can be applied to the peptide inhibitor design that may aim for different target proteins, or different positions of a protein. A notable advantage of the two-level statistical algorithm is that there is no need for host protein structural information. It may also provide useful insight into the amino acid properties and the roles of sequence positions.

Examples for Non-Ideal Solution Thermodynamics Study

ERIC Educational Resources Information Center

David, Carl W.

2004-01-01

A mathematical model of a non-ideal solution is presented, where it is shown how and where the non-ideality manifests itself in the standard thermodynamics tableau. Examples related to the non-ideal solution thermodynamics study are also included.

Ideal Magnetic Dipole Scattering

NASA Astrophysics Data System (ADS)

Feng, Tianhua; Xu, Yi; Zhang, Wei; Miroshnichenko, Andrey E.

2017-04-01

We introduce the concept of tunable ideal magnetic dipole scattering, where a nonmagnetic nanoparticle scatters light as a pure magnetic dipole. High refractive index subwavelength nanoparticles usually support both electric and magnetic dipole responses. Thus, to achieve ideal magnetic dipole scattering one has to suppress the electric dipole response. Such a possibility was recently demonstrated for the so-called anapole mode, which is associated with zero electric dipole scattering. By spectrally overlapping the magnetic dipole resonance with the anapole mode, we achieve ideal magnetic dipole scattering in the far field with tunable strong scattering resonances in the near infrared spectrum. We demonstrate that such a condition can be realized at least for two subwavelength geometries. One of them is a core-shell nanosphere consisting of a Au core and silicon shell. It can be also achieved in other geometries, including nanodisks, which are compatible with current nanofabrication technology.

Improved Classification of Mammograms Following Idealized Training

PubMed Central

Hornsby, Adam N.; Love, Bradley C.

2014-01-01

People often make decisions by stochastically retrieving a small set of relevant memories. This limited retrieval implies that human performance can be improved by training on idealized category distributions (Giguère & Love, 2013). Here, we evaluate whether the benefits of idealized training extend to categorization of real-world stimuli, namely classifying mammograms as normal or tumorous. Participants in the idealized condition were trained exclusively on items that, according to a norming study, were relatively unambiguous. Participants in the actual condition were trained on a representative range of items. Despite being exclusively trained on easy items, idealized-condition participants were more accurate than those in the actual condition when tested on a range of item types. However, idealized participants experienced difficulties when test items were very dissimilar from training cases. The benefits of idealization, attributable to reducing noise arising from cognitive limitations in memory retrieval, suggest ways to improve real-world decision making. PMID:24955325

Improved Classification of Mammograms Following Idealized Training.

PubMed

Hornsby, Adam N; Love, Bradley C

2014-06-01

People often make decisions by stochastically retrieving a small set of relevant memories. This limited retrieval implies that human performance can be improved by training on idealized category distributions (Giguère & Love, 2013). Here, we evaluate whether the benefits of idealized training extend to categorization of real-world stimuli, namely classifying mammograms as normal or tumorous. Participants in the idealized condition were trained exclusively on items that, according to a norming study, were relatively unambiguous. Participants in the actual condition were trained on a representative range of items. Despite being exclusively trained on easy items, idealized-condition participants were more accurate than those in the actual condition when tested on a range of item types. However, idealized participants experienced difficulties when test items were very dissimilar from training cases. The benefits of idealization, attributable to reducing noise arising from cognitive limitations in memory retrieval, suggest ways to improve real-world decision making.

Design of association studies with pooled or un-pooled next-generation sequencing data.

PubMed

Kim, Su Yeon; Li, Yingrui; Guo, Yiran; Li, Ruiqiang; Holmkvist, Johan; Hansen, Torben; Pedersen, Oluf; Wang, Jun; Nielsen, Rasmus

2010-07-01

Most common hereditary diseases in humans are complex and multifactorial. Large-scale genome-wide association studies based on SNP genotyping have only identified a small fraction of the heritable variation of these diseases. One explanation may be that many rare variants (a minor allele frequency, MAF <5%), which are not included in the common genotyping platforms, may contribute substantially to the genetic variation of these diseases. Next-generation sequencing, which would allow the analysis of rare variants, is now becoming so cheap that it provides a viable alternative to SNP genotyping. In this paper, we present cost-effective protocols for using next-generation sequencing in association mapping studies based on pooled and un-pooled samples, and identify optimal designs with respect to total number of individuals, number of individuals per pool, and the sequencing coverage. We perform a small empirical study to evaluate the pooling variance in a realistic setting where pooling is combined with exon-capturing. To test for associations, we develop a likelihood ratio statistic that accounts for the high error rate of next-generation sequencing data. We also perform extensive simulations to determine the power and accuracy of this method. Overall, our findings suggest that with a fixed cost, sequencing many individuals at a more shallow depth with larger pool size achieves higher power than sequencing a small number of individuals in higher depth with smaller pool size, even in the presence of high error rates. Our results provide guidelines for researchers who are developing association mapping studies based on next-generation sequencing. (c) 2010 Wiley-Liss, Inc.

Artificial neural network implementation of a near-ideal error prediction controller

NASA Technical Reports Server (NTRS)

Mcvey, Eugene S.; Taylor, Lynore Denise

1992-01-01

A theory has been developed at the University of Virginia which explains the effects of including an ideal predictor in the forward loop of a linear error-sampled system. It has been shown that the presence of this ideal predictor tends to stabilize the class of systems considered. A prediction controller is merely a system which anticipates a signal or part of a signal before it actually occurs. It is understood that an exact prediction controller is physically unrealizable. However, in systems where the input tends to be repetitive or limited, (i.e., not random) near ideal prediction is possible. In order for the controller to act as a stability compensator, the predictor must be designed in a way that allows it to learn the expected error response of the system. In this way, an unstable system will become stable by including the predicted error in the system transfer function. Previous and current prediction controller include pattern recognition developments and fast-time simulation which are applicable to the analysis of linear sampled data type systems. The use of pattern recognition techniques, along with a template matching scheme, has been proposed as one realizable type of near-ideal prediction. Since many, if not most, systems are repeatedly subjected to similar inputs, it was proposed that an adaptive mechanism be used to 'learn' the correct predicted error response. Once the system has learned the response of all the expected inputs, it is necessary only to recognize the type of input with a template matching mechanism and then to use the correct predicted error to drive the system. Suggested here is an alternate approach to the realization of a near-ideal error prediction controller, one designed using Neural Networks. Neural Networks are good at recognizing patterns such as system responses, and the back-propagation architecture makes use of a template matching scheme. In using this type of error prediction, it is assumed that the system error

An ideal free-kick

NASA Astrophysics Data System (ADS)

De Luca, R.; Faella, O.

2017-01-01

The kinematics of a free-kick is studied. As in projectile motion, the free-kick is ideal since we assume that a point-like ball moves in the absence of air resistance. We have experienced the fortunate conjuncture of a classical mechanics lecture taught right before an important football game. These types of sports events might trigger a great deal of attention from the classroom. The idealized problem is devised in such a way that students are eager to come to the end of the whole story.

On controlling nonlinear dissipation in high order filter methods for ideal and non-ideal MHD

NASA Technical Reports Server (NTRS)

Yee, H. C.; Sjogreen, B.

2004-01-01

The newly developed adaptive numerical dissipation control in spatially high order filter schemes for the compressible Euler and Navier-Stokes equations has been recently extended to the ideal and non-ideal magnetohydrodynamics (MHD) equations. These filter schemes are applicable to complex unsteady MHD high-speed shock/shear/turbulence problems. They also provide a natural and efficient way for the minimization of Div(B) numerical error. The adaptive numerical dissipation mechanism consists of automatic detection of different flow features as distinct sensors to signal the appropriate type and amount of numerical dissipation/filter where needed and leave the rest of the region free from numerical dissipation contamination. The numerical dissipation considered consists of high order linear dissipation for the suppression of high frequency oscillation and the nonlinear dissipative portion of high-resolution shock-capturing methods for discontinuity capturing. The applicable nonlinear dissipative portion of high-resolution shock-capturing methods is very general. The objective of this paper is to investigate the performance of three commonly used types of nonlinear numerical dissipation for both the ideal and non-ideal MHD.

Mariner Mars 1971 television picture catalog. Volume 2: Sequence design and picture coverage

NASA Technical Reports Server (NTRS)

Koskela, P. E.; Helton, M. R.; Seeley, L. N.; Zawacki, S. J.

1972-01-01

A collection of data relating to the Mariner 9 TV picture is presented. The data are arranged to offer speedy identification of what took place during entire science cycles, on individual revolutions, and during individual science links or sequences. Summary tables present the nominal design for each of the major picture-taking cycles, along with the sequences actually taken on each revolution. These tables permit identification at a glance, all TV sequences and the corresponding individual pictures for the first 262 revolutions (primary mission). A list of TV pictures, categorized according to their latitude and longitude, is also provided. Orthographic and/or mercator plots for all pictures, along with pertinent numerical data for their center points are presented. Other tables and plots of interest are also included. This document is based upon data contained in the Supplementary Experiment Data Record (SEDR) files as of 21 August 1972.

Recharging Our Sense of Idealism: Concluding Thoughts

ERIC Educational Resources Information Center

D'Andrea, Michael; Dollarhide, Colette T.

2011-01-01

In this article, the authors aim to recharge one's sense of idealism. They argue that idealism is the Vitamin C that sustains one's commitment to implementing humanistic principles and social justice practices in the work of counselors and educators. The idealism that characterizes counselors and educators who are humanistic and social justice…

The potential role of IDEAL MRI for identification of lipids and hemorrhage in carotid artery plaques.

PubMed

Khosa, Faisal; Clough, Rachel E; Wang, Xiaoen; Madhuranthakam, Ananth J; Greenman, Robert L

2018-06-01

Hemorrhage and lipid deposits contribute to instability in atherosclerotic plaques. Unstable carotid artery plaques can lead to cerebral ischemic events. While MRI studies have shown the ability to identify plaque components, the identification of hemorrhage and lipids has proven to be problematic. The purpose of this study was to quantitatively evaluate the potential of the MRI fat/water separation method known as iterative decomposition of water and fat with echo asymmetry and least squares estimation (IDEAL) to complement and improve existing methods for the identification of hemorrhage and lipids in carotid artery plaques. Fifteen asymptomatic subjects with 50-79% stenosis of at least one carotid artery were enrolled. Hemorrhage and lipid components within carotid plaques were identified using previously published criteria based on the multiple contrast-weighted (MCW) method (3D Time-of-Flight (3D-TOF), T1-Weighted (T1W) and T2-Weighted (T2W)). The hemorrhage:muscle, lipid:muscle and intra-plaque lipid:hemorrhage signal intensity ratios (SIR) and contrast to noise ratios (CNR) were measured on MCW and compared to IDEAL black-blood images. No differences were found between any of the MCW methods for any of the SIRs measured. The IDEAL Fat images had higher lipid:muscle and lipid/hemorrhage SIRs (p<0.001) compared to IDEAL Water and all MCW image sequence types. The mean values of IDEAL Fat hemorrhage:muscle SIR and CNR were nearly unity (1.1±0.6) and nearly zero (0.1±1.1), respectively. The IDEAL Water imaging was not significantly different than any of the MCW methods for any of the SIRs or for the hemorrhage:muscle CNR of 3D-TOF, while its CNRs were significantly higher than IDEAL Fat lipid:muscle (p<0.05) and lipid:hemorrhage (p<0.001) and all MCW methods (p<0.001). The addition of IDEAL Water and Fat imaging to the MCW method shows potential to improve the identification of hemorrhage and lipid structures in carotid artery plaques. Copyright © 2017

Sequence Complexity of Amyloidogenic Regions in Intrinsically Disordered Human Proteins

PubMed Central

Das, Swagata; Pal, Uttam; Das, Supriya; Bagga, Khyati; Roy, Anupam; Mrigwani, Arpita; Maiti, Nakul C.

2014-01-01

An amyloidogenic region (AR) in a protein sequence plays a significant role in protein aggregation and amyloid formation. We have investigated the sequence complexity of AR that is present in intrinsically disordered human proteins. More than 80% human proteins in the disordered protein databases (DisProt+IDEAL) contained one or more ARs. With decrease of protein disorder, AR content in the protein sequence was decreased. A probability density distribution analysis and discrete analysis of AR sequences showed that ∼8% residue in a protein sequence was in AR and the region was in average 8 residues long. The residues in the AR were high in sequence complexity and it seldom overlapped with low complexity regions (LCR), which was largely abundant in disorder proteins. The sequences in the AR showed mixed conformational adaptability towards α-helix, β-sheet/strand and coil conformations. PMID:24594841

Designing the future of healthcare.

PubMed

Fidsa, Gianfranco Zaccai

2009-01-01

This paper describes the application of a holistic design process to a variety of problems plaguing current healthcare systems. A design process for addressing complex, multifaceted problems is contrasted with the piecemeal application of technological solutions to specific medical or administrative problems. The goal of this design process is the ideal customer experience, specifically the ideal experience for patients, healthcare providers, and caregivers within a healthcare system. Holistic design is shown to be less expensive and wasteful in the long run because it avoids solving one problem within a complex system at the cost of creating other problems within that system. The article applies this approach to the maintenance of good health throughout life; to the creation of an ideal experience when a person does need medical care; to the maintenance of personal independence as one ages; and to the enjoyment of a comfortable and dignified death. Virginia Mason Medical Center is discussed as an example of a healthcare institution attempting to create ideal patient and caregiver experiences, in this case by applying the principles of the Toyota Production System ("lean manufacturing") to healthcare. The article concludes that healthcare is inherently dedicated to an ideal, that science and technology have brought it closer to that ideal, and that design can bring it closer still.

Family Life and Developmental Idealism in Yazd, Iran

PubMed Central

Abbasi-Shavazi, Mohammad Jalal; Askari-Nodoushan, Abbas

2012-01-01

BACKGROUND This paper is motivated by the theory that developmental idealism has been disseminated globally and has become an international force for family and demographic change. Developmental idealism is a set of cultural beliefs and values about development and how development relates to family and demographic behavior. It holds that modern societies are causal forces producing modern families, that modern families help to produce modern societies, and that modern family change is to be expected. OBJECTIVE We examine the extent to which developmental idealism has been disseminated in Iran. We also investigate predictors of the dissemination of developmental idealism. METHODS We use survey data collected in 2007 from a sample of women in Yazd, a city in Iran. We examine the distribution of developmental idealism in the sample and the multivariate predictors of developmental idealism. RESULTS We find considerable support for the expectation that many elements of developmental idealism have been widely disseminated. Statistically significant majorities associate development with particular family attributes, believe that development causes change in families, believe that fertility reductions and age-at-marriage increases help foster development, and perceive family trends in Iran headed toward modernity. As predicted, parental education, respondent education, and income affect adherence to developmental idealism. CONCLUSIONS Developmental idealism has been widely disseminated in Yazd, Iran and is related to social and demographic factors in predicted ways. COMMENTS Although our data come from only one city, we expect that developmental idealism has been widely distributed in Iran, with important implications for family and demographic behavior. PMID:22942772

The mechanical design of spider silks: from fibroin sequence to mechanical function.

PubMed

Gosline, J M; Guerette, P A; Ortlepp, C S; Savage, K N

1999-12-01

Spiders produce a variety of silks, and the cloning of genes for silk fibroins reveals a clear link between protein sequence and structure-property relationships. The fibroins produced in the spider's major ampullate (MA) gland, which forms the dragline and web frame, contain multiple repeats of motifs that include an 8-10 residue long poly-alanine block and a 24-35 residue long glycine-rich block. When fibroins are spun into fibres, the poly-alanine blocks form (&bgr;)-sheet crystals that crosslink the fibroins into a polymer network with great stiffness, strength and toughness. As illustrated by a comparison of MA silks from Araneus diadematus and Nephila clavipes, variation in fibroin sequence and properties between spider species provides the opportunity to investigate the design of these remarkable biomaterials.

Ideal form of optical plasma lenses

NASA Astrophysics Data System (ADS)

Gordon, D. F.; Stamm, A. B.; Hafizi, B.; Johnson, L. A.; Kaganovich, D.; Hubbard, R. F.; Richardson, A. S.; Zhigunov, D.

2018-06-01

The canonical form of an optical plasma lens is a parabolic density channel. This form suffers from spherical aberrations, among others. Spherical aberration is partially corrected by adding a quartic term to the radial density profile. Ideal forms which lead to perfect focusing or imaging are obtained. The fields at the focus of a strong lens are computed with high accuracy and efficiency using a combination of eikonal and full Maxwell descriptions of the radiation propagation. The calculations are performed using a new computer propagation code, SeaRay, which is designed to transition between various solution methods as the beam propagates through different spatial regions. The calculations produce the full Maxwell vector fields in the focal region.

From synthetic coiled coils to functional proteins: automated design of a receptor for the calmodulin-binding domain of calcineurin.

PubMed

Ghirlanda, G; Lear, J D; Lombardi, A; DeGrado, W F

1998-08-14

A series of synthetic receptors capable of binding to the calmodulin-binding domain of calcineurin (CN393-414) was designed, synthesized and characterized. The design was accomplished by docking CN393-414 against a two-helix receptor, using an idealized three-stranded coiled coil as a starting geometry. The sequence of the receptor was chosen using a side-chain re-packing program, which employed a genetic algorithm to select potential binders from a total of 7.5x10(6) possible sequences. A total of 25 receptors were prepared, representing 13 sequences predicted by the algorithm as well as 12 related sequences that were not predicted. The receptors were characterized by CD spectroscopy, analytical ultracentrifugation, and binding assays. The receptors predicted by the algorithm bound CN393-414 with apparent dissociation constants ranging from 0.2 microM to >50 microM. Many of the receptors that were not predicted by the algorithm also bound to CN393-414. Methods to circumvent this problem and to improve the automated design of functional proteins are discussed. Copyright 1998 Academic Press

Ideal Cardiovascular Health and Incident Cardiovascular Events

PubMed Central

Ommerborn, Mark J.; Blackshear, Chad T.; Hickson, DeMarc A.; Griswold, Michael E.; Kwatra, Japneet; Djousse, Luc; Clark, Cheryl R.

2016-01-01

Introduction The epidemiology of American Heart Association ideal cardiovascular health (CVH) metrics has not been fully examined in African Americans. This study examines associations of CVH metrics with incident cardiovascular disease (CVD) in the Jackson Heart Study, a longitudinal cohort study of CVD in African Americans. Methods Jackson Heart Study participants without CVD (N=4,702) were followed prospectively between 2000 and 2011. Incidence rates and Cox proportional hazard ratios estimated risks for incident CVD (myocardial infarction, stroke, cardiac procedures, and CVD mortality) associated with seven CVH metrics by sex. Analyses were performed in 2015. Results Participants were followed for a median 8.3 years; none had ideal health on all seven CVH metrics. The prevalence of ideal health was low for nutrition, physical activity, BMI, and blood pressure metrics. The age-adjusted CVD incidence rate (IR) per 1,000 person years was highest for individuals with the least ideal health metrics: zero to one (IR=12.5, 95% CI=9.7, 16.1), two (IR=8.2, 95% CI=6.5, 10.4), three (IR=5.7, 95% CI=4.2, 7.6), and four or more (IR=3.4, 95% CI=2.0, 5.9). Adjusting for covariates, individuals with four or more ideal CVH metrics had lower risks of incident CVD compared with those with zero or one ideal CVH metric (hazard ratio, 0.29; 95% CI=0.17, 0.52; p<0.001). Conclusions African Americans with more ideal CVH metrics have lower risks of incident CVD. Comprehensive preventive behavioral and clinical supports should be intensified to improve CVD risk for African Americans with few ideal CVH metrics. PMID:27539974

Studies of a Biochemical Factory: Tomato Trichome Deep Expressed Sequence Tag Sequencing and Proteomics1[W][OA

PubMed Central

Schilmiller, Anthony L.; Miner, Dennis P.; Larson, Matthew; McDowell, Eric; Gang, David R.; Wilkerson, Curtis; Last, Robert L.

2010-01-01

Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces β-caryophyllene and α-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells. PMID:20431087

Putative and unique gene sequence utilization for the design of species specific probes as modeled by Lactobacillus plantarum

USDA-ARS?s Scientific Manuscript database

The concept of utilizing putative and unique gene sequences for the design of species specific probes was tested. The abundance profile of assigned functions within the Lactobacillus plantarum genome was used for the identification of the putative and unique gene sequence, csh. The targeted gene (cs...

Just-About-Right and ideal scaling provide similar insights into the influence of sensory attributes on liking.

PubMed

Li, Bangde; Hayes, John E; Ziegler, Gregory R

2014-10-01

Just-about-right (JAR) scaling is criticized for measuring attribute intensity and acceptability simultaneously. Using JAR scaling, an attribute is evaluated for its appropriateness relative to one's hypothetical ideal level that is pre-defined at the middle of a continuum. Alternatively, ideal scaling measures these two constructs separately. Ideal scaling allows participants to rate their ideal freely on the scale (i.e., without assuming the "Too Little" and "Too Much" regions are equal in size). We hypothesized that constraining participants' ideal to the center point, as is done in the JAR scale, may cause a scaling bias and, thereby, influence the magnitude of "Too Little" and "Too Much". Furthermore, we hypothesized that the magnitude of "Too Little" and "Too Much" would influence liking to different extents. Coffee-flavored dairy beverages (n=20) were formulated using a fractional, constrained-mixture design that varied the ratio of water, milk, coffee extract, and sucrose. Participants tasted 4 of 20 prototypes that were served in a monadic sequential order using a balanced incomplete block design. Data reported here are for participants randomly assigned to one of two research conditions: ideal scaling (n=129) or JAR scaling (n=132). For both conditions, participants rated overall liking using a 9-point hedonic scale. Four attributes ( sweetness, milk flavor, coffee flavor and thickness ) were evaluated. The reliability of an individual participant's ideal rating for an attribute was evaluated using the standard deviation of their ideal ratings (n=4). All data from a participant were eliminated from further analyses when his/her standard deviation of the ideal ratings for any of the four rated attributes was identified as a statistical outlier. This resulted in the elimination of 15 of 129 (12 %) of participants in the ideal scaling group. Multiple linear regression was employed to model liking as a function of "Too Little" or "Too Much" attribute

Random-effects linear modeling and sample size tables for two special crossover designs of average bioequivalence studies: the four-period, two-sequence, two-formulation and six-period, three-sequence, three-formulation designs.

PubMed

Diaz, Francisco J; Berg, Michel J; Krebill, Ron; Welty, Timothy; Gidal, Barry E; Alloway, Rita; Privitera, Michael

2013-12-01

Due to concern and debate in the epilepsy medical community and to the current interest of the US Food and Drug Administration (FDA) in revising approaches to the approval of generic drugs, the FDA is currently supporting ongoing bioequivalence studies of antiepileptic drugs, the EQUIGEN studies. During the design of these crossover studies, the researchers could not find commercial or non-commercial statistical software that quickly allowed computation of sample sizes for their designs, particularly software implementing the FDA requirement of using random-effects linear models for the analyses of bioequivalence studies. This article presents tables for sample-size evaluations of average bioequivalence studies based on the two crossover designs used in the EQUIGEN studies: the four-period, two-sequence, two-formulation design, and the six-period, three-sequence, three-formulation design. Sample-size computations assume that random-effects linear models are used in bioequivalence analyses with crossover designs. Random-effects linear models have been traditionally viewed by many pharmacologists and clinical researchers as just mathematical devices to analyze repeated-measures data. In contrast, a modern view of these models attributes an important mathematical role in theoretical formulations in personalized medicine to them, because these models not only have parameters that represent average patients, but also have parameters that represent individual patients. Moreover, the notation and language of random-effects linear models have evolved over the years. Thus, another goal of this article is to provide a presentation of the statistical modeling of data from bioequivalence studies that highlights the modern view of these models, with special emphasis on power analyses and sample-size computations.

Thought-shape fusion in young healthy females appears after vivid imagination of thin ideals.

PubMed

Wyssen, Andrea; Coelho, Jennifer S; Wilhelm, Peter; Zimmermann, Grégoire; Munsch, Simone

2016-09-01

It has been shown that exposure to female thin ideals in media has minimal to moderate direct effects on body image satisfaction (BIS), mood and dysfunctional eating in healthy young women. Evidence has been found for several intervening variables such as social comparison processes. Accordingly it is assumed, that cognitive processing (rather than mere media exposure) is crucial. Consequently, vivid imagination of thin ideals after exposure to a fashion magazine was induced in order to trigger cognitive processes. Changes in mood, BIS and resulting bodyrelated cognitive distortions (Thought-Shape Fusion Body, TSF-B) were assessed. A total of 91 healthy women (mean age 21.9 years, SD = 2.0) were exposed to either a fashion magazine (thin-ideal group) or a nature magazine (control group) in a waiting room design. Afterwards they were instructed to vividly imagine either the thin ideals or landscapes. When exposed to thin ideals, a significant decrease in mood and BIS emerged after vivid imagination, but not after mere magazine exposure. Imagining thin ideals triggered body-related cognitive distortions (TSF-B). A higher degree of eating disorder (ED) symptomatology amplified this effect. These findings apply to young healthy females and cannot be generalized to samples with obesity, EDs or males. Internal validity is limited since the intensity of the exposure has not been systematically controlled. Vivid imagination of thin ideals promoted by magazines results in impaired mood and BIS and moreover in body-related cognitive distortions (TSF-B) in healthy women, especially, for those with stronger ED symptomatology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers.

PubMed

Pan, Jin; Wang, Baosheng; Pei, Zhi-Yong; Zhao, Wei; Gao, Jie; Mao, Jian-Feng; Wang, Xiao-Ru

2015-07-01

Flexibility and low cost make genotyping-by-sequencing (GBS) an ideal tool for population genomic studies of nonmodel species. However, to utilize the potential of the method fully, many parameters affecting library quality and single nucleotide polymorphism (SNP) discovery require optimization, especially for conifer genomes with a high repetitive DNA content. In this study, we explored strategies for effective GBS analysis in pine species. We constructed GBS libraries using HpaII, PstI and EcoRI-MseI digestions with different multiplexing levels and examined the effect of restriction enzymes on library complexity and the impact of sequencing depth and size selection of restriction fragments on sequence coverage bias. We tested and compared UNEAK, Stacks and GATK pipelines for the GBS data, and then developed a reference-free SNP calling strategy for haploid pine genomes. Our GBS procedure proved to be effective in SNP discovery, producing 7000-11 000 and 14 751 SNPs within and among three pine species, respectively, from a PstI library. This investigation provides guidance for the design and analysis of GBS experiments, particularly for organisms for which genomic information is lacking. © 2014 John Wiley & Sons Ltd.

The Statistical Mechanics of Ideal MHD Turbulence

NASA Technical Reports Server (NTRS)

Shebalin, John V.

2003-01-01

Turbulence is a universal, nonlinear phenomenon found in all energetic fluid and plasma motion. In particular. understanding magneto hydrodynamic (MHD) turbulence and incorporating its effects in the computation and prediction of the flow of ionized gases in space, for example, are great challenges that must be met if such computations and predictions are to be meaningful. Although a general solution to the "problem of turbulence" does not exist in closed form, numerical integrations allow us to explore the phase space of solutions for both ideal and dissipative flows. For homogeneous, incompressible turbulence, Fourier methods are appropriate, and phase space is defined by the Fourier coefficients of the physical fields. In the case of ideal MHD flows, a fairly robust statistical mechanics has been developed, in which the symmetry and ergodic properties of phase space is understood. A discussion of these properties will illuminate our principal discovery: Coherent structure and randomness co-exist in ideal MHD turbulence. For dissipative flows, as opposed to ideal flows, progress beyond the dimensional analysis of Kolmogorov has been difficult. Here, some possible future directions that draw on the ideal results will also be discussed. Our conclusion will be that while ideal turbulence is now well understood, real turbulence still presents great challenges.

Lifestyle constraints, not inadequate nutrition education, cause gap between breakfast ideals and realities among Japanese in Tokyo.

PubMed

Melby, Melissa K; Takeda, Wakako

2014-01-01

Japanese public health nutrition often promotes 'traditional' cuisine. In-depth interviews with 107 Japanese adults were conducted in Tokyo from 2009 to 2011, using free-listing methods to examine dietary ideals and realities to assess the extent to which realities reflect inadequate nutrition education or lifestyle constraints. Ideal-reality gaps were widest for breakfast. Most people reported Japanese ideals: rice and miso soup were prototypical foods. However, breakfast realities were predominantly western (bread-based). While those aged 40-59 were more likely to hold Japanese ideals (P=0.063), they were less likely to achieve them (P=0.007). All those reporting western ideals achieved them on weekdays, while only 64% of those with Japanese ideals achieved them (P<0.001). Partial correlations controlling for age and gender showed achievement of Japanese ideals were positively correlated with proportion of cooking-related housework, and negatively correlated with living standard and income. Ideal menu content was in line with current Japanese nutrition advice, suggesting that more nutrition education may not change dietary ideals or behavior. Participant-reported reasons for ideal-reality discordance demonstrate that work-life balance issues, especially lack of time and family structure/life rhythm, are the largest obstacles to the attainment of dietary ideals. People reporting 'no time' as a primary reason for ideal-reality gaps were less likely to achieve their Japanese ideals (odds ratio=0.212). Time realities of people's lives may undermine educational efforts promoting Japanese breakfasts. When dietary reality/behavior departs from guidelines, it is often assumed that people lack knowledge. If ideals are in line with dietary guidelines, then lack of knowledge is not the likely cause and nutrition education is not the optimal solution. By asking people about the reasons for gaps between their ideals and realities, we can identify barriers and design more

Predicting Film Genres with Implicit Ideals

PubMed Central

Olney, Andrew McGregor

2013-01-01

We present a new approach to defining film genre based on implicit ideals. When viewers rate the likability of a film, they indirectly express their ideal of what a film should be. Across six studies we investigate the category structure that emerges from likability ratings and the category structure that emerges from the features of film. We further compare these data-driven category structures with human annotated film genres. We conclude that film genres are structured more around ideals than around features of film. This finding lends experimental support to the notion that film genres are set of shifting, fuzzy, and highly contextualized psychological categories. PMID:23423823

Predicting film genres with implicit ideals.

PubMed

Olney, Andrew McGregor

2012-01-01

We present a new approach to defining film genre based on implicit ideals. When viewers rate the likability of a film, they indirectly express their ideal of what a film should be. Across six studies we investigate the category structure that emerges from likability ratings and the category structure that emerges from the features of film. We further compare these data-driven category structures with human annotated film genres. We conclude that film genres are structured more around ideals than around features of film. This finding lends experimental support to the notion that film genres are set of shifting, fuzzy, and highly contextualized psychological categories.

Ideal Theory in Semigroups Based on Intersectional Soft Sets

PubMed Central

Song, Seok Zun; Jun, Young Bae

2014-01-01

The notions of int-soft semigroups and int-soft left (resp., right) ideals are introduced, and several properties are investigated. Using these notions and the notion of inclusive set, characterizations of subsemigroups and left (resp., right) ideals are considered. Using the notion of int-soft products, characterizations of int-soft semigroups and int-soft left (resp., right) ideals are discussed. We prove that the soft intersection of int-soft left (resp., right) ideals (resp., int-soft semigroups) is also int-soft left (resp., right) ideals (resp., int-soft semigroups). The concept of int-soft quasi-ideals is also introduced, and characterization of a regular semigroup is discussed. PMID:25101310

Maneuver sequence design for the post-Jupiter leg of Pioneer Saturn

NASA Technical Reports Server (NTRS)

Frauenholz, R. B.; Brady, W. F.

1976-01-01

After passing the planet Jupiter in December 1974, Pioneer 11 is on a flight path on which it will encounter Saturn in late 1979. Following an uncorrected trajectory, the spacecraft would pass 2 million km behind Saturn. A sequence of midcourse maneuvers for modifying the Pioneer trajectory is discussed. The corrected flight path is to bring the spacecraft within 500,000 km of Saturn's satellite Titan. Attention is given to maneuver capabilities and constraints, the maneuver design concept, questions related to the selection of an interim aimpoint, and aspects of maneuver implementation.

The ideal ear position in Caucasian females.

PubMed

Broer, P Niclas; Thiha, Aung; Ehrl, Denis; Sinno, Sammy; Juran, Sabrina; Szpalski, Caroline; Ng, Reuben; Ninkovic, Milomir; Prantl, Lukas; Heidekrueger, Paul I

2018-03-01

Ear position contributes significantly to facial appearance. However, while objective measurements remain the foundation for esthetic evaluations, little is known about how an ear should ideally be positioned regarding its rotational axis. This study aimed to further evaluate whether there exists a universally applicable ideal ear axis, and how sociodemographic factors impact such preferences. An interactive online survey was designed, enabling participants to change the axis of a female model's ear in terms of its forward and backward rotation. The questionnaire was sent out internationally to plastic surgeons and the general public. Demographic data were collected and analysis of variance was used to investigate respective preferences. A total of 1016 responses from 35 different countries (response rate: 18.5%) were gathered. Overall, 60% of survey takers chose the minus 10 or 5° angles to be most attractive. Significant differences were found regarding sex, ethnicity, country of residence, profession and respective ear axis preferences. Across multiple countries and ethnicities, an ear position in slight reclination of minus 5-10° is considered most pleasing in Caucasian females. However, sociodemographic factors significantly impact individual ear axis preferences and should be taken into consideration when performing reconstructive ear surgery. Copyright © 2018 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

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

Song, Qijian; Jia, Gaofeng; Hyten, David L.

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of largemore » scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.« less

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean.

PubMed

Song, Qijian; Jia, Gaofeng; Hyten, David L; Jenkins, Jerry; Hwang, Eun-Young; Schroeder, Steven G; Osorno, Juan M; Schmutz, Jeremy; Jackson, Scott A; McClean, Phillip E; Cregan, Perry B

2015-08-28

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad. Copyright © 2015 Song et al.

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

DOE PAGES

Song, Qijian; Jia, Gaofeng; Hyten, David L.; ...

2015-08-28

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of largemore » scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.« less

[Complete genome sequencing and sequence analysis of BCG Tice].

PubMed

Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

2012-10-04

The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

Maintaining ideal body weight counseling sessions

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

Brammer, S.H.

The purpose of this program is to provide employees with the motivation, knowledge and skills necessary to maintain ideal body weight throughout life. The target audience for this program, which is conducted in an industrial setting, is the employee 40 years of age or younger who is at or near his/her ideal body weight.

Recommended design and fabrication sequence of AMTEC test assembly

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

Schock, A.; Kumar, V.; Noravian, H.

1998-01-01

A series of previous OSC papers described: 1) a novel methodology for the coupled thermal, fluid flow, and electrical analysis of multitube AMTEC (Alkali Metal Thermal-to-Electric Conversion) cells; 2) the application of that methodology to determine the effect of numerous design variations on the cell{close_quote}s performance, leading to selection and performance characterization of an OSC-recommended cell design; and 3) the design, analysis, and characterization of an OSC-generated power system design combining sixteen of the above AMTEC cells with two or three GPHS (General Purpose Heat Source) radioisotope heat source modules, and the applicability of those power systems to future spacemore » missions ({ital e.g.} Pluto Express and Europa Orbiter) under consideration by NASA. The OSC system design studies demonstrated the critical importance of the thermal insulation subsystem, and culminated in a design in which the eight AMTEC cells on each end of the heat source stack are embedded in Min-K fibrous insulation, and the Min-K and the GPHS modules are surrounded by graded-length Mo multifoil insulation. The present paper depicts the OSC-recommended AMTEC cell and generator designs, and identifies the need for an electrically heated (scaled-down but otherwise prototypic) test assembly for the experimental validation of the generator{close_quote}s system performance predictions. It then describes the design of an OSC-recommended test assembly consisting of an electrical heater enclosed in a graphite box to simulate the radioisotope heat source, four series-connected prototypic AMTEC cells of the OSC-recommended configuration, and a prototypic hybrid insulation package consisting of Min-K and graded-length Mo multifoils. Finally, the paper describes and illustrates an OSC-recommended detailed fabrication sequence and procedure for the above cell and test assembly. That fabrication procedure is being implemented by AMPS, Inc. with the support of DOE

The Ideal Man and Woman According to University Students

ERIC Educational Resources Information Center

Weinstein, Lawrence; Laverghetta, Antonio V.; Peterson, Scott A.

2009-01-01

The present study determined if the ideal man has changed over the years and who and what the ideal woman is. We asked students at Cameron University to rate the importance of character traits that define the ideal man and woman. Subjects also provided examples of famous people exemplifying the ideal, good, average, and inferior man and woman. We…

Genetic and environmental influences on thin-ideal internalization across puberty and preadolescent, adolescent, and young adult development.

PubMed

Suisman, Jessica L; Thompson, J Kevin; Keel, Pamela K; Burt, S Alexandra; Neale, Michael; Boker, Steven; Sisk, Cheryl; Klump, Kelly L

2014-11-01

Mean-levels of thin-ideal internalization increase during adolescence and pubertal development, but it is unknown whether these phenotypic changes correspond to developmental changes in etiological (i.e., genetic and environmental) risk. Given the limited knowledge on risk for thin-ideal internalization, research is needed to guide the identification of specific types of risk factors during critical developmental periods. The present twin study examined genetic and environmental influences on thin-ideal internalization across adolescent and pubertal development. Participants were 1,064 female twins (ages 8-25 years) from the Michigan State University Twin Registry. Thin-ideal internalization and pubertal development were assessed using self-report questionnaires. Twin moderation models were used to examine if age and/or pubertal development moderate genetic and environmental influences on thin-ideal internalization. Phenotypic analyses indicated significant increases in thin-ideal internalization across age and pubertal development. Twin models suggested no significant differences in etiologic effects across development. Nonshared environmental influences were most important in the etiology of thin-ideal internalization, with genetic, shared environmental, and nonshared environmental accounting for approximately 8%, 15%, and 72%, respectively, of the total variance. Despite mean-level increases in thin-ideal internalization across development, the relative influence of genetic versus environmental risk did not differ significantly across age or pubertal groups. The majority of variance in thin-ideal internalization was accounted for by environmental factors, suggesting that mean-level increases in thin-ideal internalization may reflect increases in the magnitude/strength of environmental risk across this period. Replication is needed, particularly with longitudinal designs that assess thin-ideal internalization across key developmental phases. © 2014 Wiley

Chemical and radiation mutagenesis: Induction and detection by whole genome sequencing

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon has emerged as an effective model system to address fundamental questions in grass biology. With its small sequenced genome, short generation time and rapidly expanding array of genetic tools B. distachyon is an ideal system to elucidate the molecular basis of important trai...

Just-About-Right and ideal scaling provide similar insights into the influence of sensory attributes on liking

PubMed Central

Li, Bangde; Hayes, John E.; Ziegler, Gregory R.

2014-01-01

Just-about-right (JAR) scaling is criticized for measuring attribute intensity and acceptability simultaneously. Using JAR scaling, an attribute is evaluated for its appropriateness relative to one’s hypothetical ideal level that is pre-defined at the middle of a continuum. Alternatively, ideal scaling measures these two constructs separately. Ideal scaling allows participants to rate their ideal freely on the scale (i.e., without assuming the “Too Little” and “Too Much” regions are equal in size). We hypothesized that constraining participants’ ideal to the center point, as is done in the JAR scale, may cause a scaling bias and, thereby, influence the magnitude of “Too Little” and “Too Much”. Furthermore, we hypothesized that the magnitude of “Too Little” and “Too Much” would influence liking to different extents. Coffee-flavored dairy beverages (n=20) were formulated using a fractional, constrained-mixture design that varied the ratio of water, milk, coffee extract, and sucrose. Participants tasted 4 of 20 prototypes that were served in a monadic sequential order using a balanced incomplete block design. Data reported here are for participants randomly assigned to one of two research conditions: ideal scaling (n=129) or JAR scaling (n=132). For both conditions, participants rated overall liking using a 9-point hedonic scale. Four attributes (sweetness, milk flavor, coffee flavor and thickness) were evaluated. The reliability of an individual participant’s ideal rating for an attribute was evaluated using the standard deviation of their ideal ratings (n=4). All data from a participant were eliminated from further analyses when his/her standard deviation of the ideal ratings for any of the four rated attributes was identified as a statistical outlier. This resulted in the elimination of 15 of 129 (12 %) of participants in the ideal scaling group. Multiple linear regression was employed to model liking as a function of “Too Little�

The de Bono LAMS Sequence Series: Template Designs as Knowledge-Mobilising Strategy for 21st Century Higher Education

ERIC Educational Resources Information Center

Dobozy, Eva

2012-01-01

In this paper, the five interlocking de Bono LAMS sequences are introduced as a new form of generic template designs. This transdisciplinary knowledge-mobilising strategy is based on Edward de Bono's attention-directing ideas and thinking skills, commonly known as the CoRT tools. The development of the de Bono LAMS sequence series is an important…

Mutual optical intensity propagation through non-ideal mirrors

DOE PAGES

Meng, Xiangyu; Shi, Xianbo; Wang, Yong; ...

2017-08-18

The mutual optical intensity (MOI) model is extended to include the propagation of partially coherent radiation through non-ideal mirrors. The propagation of the MOI from the incident to the exit plane of the mirror is realised by local ray tracing. The effects of figure errors can be expressed as phase shifts obtained by either the phase projection approach or the direct path length method. Using the MOI model, the effects of figure errors are studied for diffraction-limited cases using elliptical cylinder mirrors. Figure errors with low spatial frequencies can vary the intensity distribution, redistribute the local coherence function and distortmore » the wavefront, but have no effect on the global degree of coherence. The MOI model is benchmarked againstHYBRIDand the multi-electronSynchrotron Radiation Workshop(SRW) code. The results show that the MOI model gives accurate results under different coherence conditions of the beam. Other than intensity profiles, the MOI model can also provide the wavefront and the local coherence function at any location along the beamline. The capability of tuning the trade-off between accuracy and efficiency makes the MOI model an ideal tool for beamline design and optimization.« less

Designing a Bioengine for Detection and Analysis of Base String on an Affected Sequence in High-Concentration Regions

PubMed Central

Mandal, Bijoy Kumar; Kim, Tai-hoon

2013-01-01

We design an Algorithm for bioengine. As a program are enable optimal alignments searching between two sequences, the host sequence (normal plant) as well as query sequence (virus). Searching for homologues has become a routine operation of biological sequences in 4 × 4 combination with different subsequence (word size). This program takes the advantage of the high degree of homology between such sequences to construct an alignment of the matching regions. There is a main aim which is to detect the overlapping reading frames. This program also enables to find out the highly infected colones selection highest matching region with minimum gap or mismatch zones and unique virus colones matches. This is a small, portable, interactive, front-end program intended to be used to find out the regions of matching between host sequence and query subsequences. All the operations are carried out in fraction of seconds, depending on the required task and on the sequence length. PMID:24000321

Three-dimensional ideal theta(1)/theta(2) angular transformer and its uses in fiber optics.

PubMed

Ning, X

1988-10-01

A 3-D ideal theta(1)/theta(2) angular transformer in nonimaging optics is introduced. The axially symmetric transformer, combining a portion of a hyperbolic concentrator with two lenses, transforms an input limited Lambertian over an angle theta(1) to an output limited Lambertian over an angle theta(2) without losing throughput. This is the first known transformer with such ideal properties. Results of computer simulations of a transformer with planospherical lenses are presented. Because of its ideal angular transforming property, the transformer offers an excellent solution for power launching and fiber-fiber coupling in optical fiber systems. In principle, the theoretical maximum coupling efficiency based on radiance conservation can be achieved with this transformer. Several conceptual designs of source-fiber and fiber-fiber couplers using the transformer are given.

Idealism and materialism in perception.

PubMed

Rose, David; Brown, Dora

2015-01-01

Koenderink (2014, Perception, 43, 1-6) has said most Perception readers are deluded, because they believe an 'All Seeing Eye' observes an objective reality. We trace the source of Koenderink's assertion to his metaphysical idealism, and point to two major weaknesses in his position-namely, its dualism and foundationalism. We counter with arguments from modern philosophy of science for the existence of an objective material reality, contrast Koenderink's enactivism to his idealism, and point to ways in which phenomenology and cognitive science are complementary and not mutually exclusive.

Analysis of Ideal Towers for Tall Wind Applications

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

Dykes, Katherine L; Damiani, Rick R; Roberts, Joseph O

Innovation in wind turbine tower design is of significant interest for future development of wind power plants. First, wind turbine towers account for a large portion of overall capital expenditures for wind power projects. Second, for low wind-resource regions of the world, the use of low-cost tall-tower technology has the potential to open new markets for development. This study investigates the relative potential of various tower configurations in terms of mass and cost. For different market applications and hub heights, idealized tall towers are designed and compared. The results show that innovation in wind turbine controls makes reaching higher hubmore » heights with current technology economically viable. At the same time, new technologies hold promise for reducing tower costs as these technologies mature and hub heights reach twice the current average.« less

Progress in ion torrent semiconductor chip based sequencing.

PubMed

Merriman, Barry; Rothberg, Jonathan M

2012-12-01

In order for next-generation sequencing to become widely used as a diagnostic in the healthcare industry, sequencing instrumentation will need to be mass produced with a high degree of quality and economy. One way to achieve this is to recast DNA sequencing in a format that fully leverages the manufacturing base created for computer chips, complementary metal-oxide semiconductor chip fabrication, which is the current pinnacle of large scale, high quality, low-cost manufacturing of high technology. To achieve this, ideally the entire sensory apparatus of the sequencer would be embodied in a standard semiconductor chip, manufactured in the same fab facilities used for logic and memory chips. Recently, such a sequencing chip, and the associated sequencing platform, has been developed and commercialized by Ion Torrent, a division of Life Technologies, Inc. Here we provide an overview of this semiconductor chip based sequencing technology, and summarize the progress made since its commercial introduction. We described in detail the progress in chip scaling, sequencing throughput, read length, and accuracy. We also summarize the enhancements in the associated platform, including sample preparation, data processing, and engagement of the broader development community through open source and crowdsourcing initiatives. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Negotiated media effects. Peer feedback modifies effects of media's thin-body ideal on adolescent girls.

PubMed

Veldhuis, Jolanda; Konijn, Elly A; Seidell, Jacob C

2014-02-01

The present study introduces a theoretical framework on negotiated media effects. Specifically, we argue that feedback of peers on thin-body ideal media images and individual dispositions guide effects on adolescent girls' psychosocial responses to media exposure. Therefore, we examined the thin-body ideal as portrayed in media and peers' feedback on such thin-ideal images in their combined effects on adolescent girls' body dissatisfaction, objectified body consciousness, and social comparison with media models. Hence, media models and peer comments were systematically combined as incorporated entities in YouTube-formats. Hypotheses were tested in a 3 (media models: extremely thin vs. thin vs. normal weight)×3 (peer comments: 6kg-underweight vs. 3kg-underweight vs. normal-weight)×2 (appearance schematicity: lower vs. higher) between-subjects design (N=216). Results showed that peer comments indicating that a media model was 'only 3kg-underweight' exerted most negative responses, particularly in girls who strongly process appearance relevant information. Peer feedback interacts with media models in guiding perceptions of what is considered an 'ideal' body shape. Results highlight the important role of peers as well as individual predispositions in view of understanding how thin-ideal media images may impact adolescent girls' body image concerns. Copyright © 2013 Elsevier Ltd. All rights reserved.

Medical learning curves and the Kantian ideal.

PubMed

Le Morvan, P; Stock, B

2005-09-01

A hitherto unexamined problem for the "Kantian ideal" that one should always treat patients as ends in themselves, and never only as a means to other ends, is explored in this paper. The problem consists of a prima facie conflict between this Kantian ideal and the reality of medical practice. This conflict arises because, at least presently, medical practitioners can only acquire certain skills and abilities by practising on live, human patients, and given the inevitability and ubiquity of learning curves, this learning requires some patients to be treated only as a means to this end. A number of ways of attempting to establish the compatibility of the Kantian Ideal with the reality of medical practice are considered. Each attempt is found to be unsuccessful. Accordingly, until a way is found to reconcile them, we conclude that the Kantian ideal is inconsistent with the reality of medical practice.

Medical learning curves and the Kantian ideal

PubMed Central

Le Morvan, P; Stock, B

2005-01-01

A hitherto unexamined problem for the "Kantian ideal" that one should always treat patients as ends in themselves, and never only as a means to other ends, is explored in this paper. The problem consists of a prima facie conflict between this Kantian ideal and the reality of medical practice. This conflict arises because, at least presently, medical practitioners can only acquire certain skills and abilities by practising on live, human patients, and given the inevitability and ubiquity of learning curves, this learning requires some patients to be treated only as a means to this end. A number of ways of attempting to establish the compatibility of the Kantian Ideal with the reality of medical practice are considered. Each attempt is found to be unsuccessful. Accordingly, until a way is found to reconcile them, we conclude that the Kantian ideal is inconsistent with the reality of medical practice. PMID:16131552

Computational Design of Self-Assembling Cyclic Protein Homo-oligomers

PubMed Central

Fallas, Jorge A.; Ueda, George; Sheffler, William; Nguyen, Vanessa; McNamara, Dan E.; Sankaran, Banumathi; Pereira, Jose Henrique; Parmeggiani, Fabio; Brunette, TJ; Cascio, Duilio; Yeates, Todd R.; Zwart, Peter; Baker, David

2016-01-01

Self-assembling cyclic protein homo-oligomers play important roles in biology and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue pair transform method for assessing the design ability of a protein-protein interface. This method is sufficiently rapid to enable systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces. We use this method to design interfaces onto idealized repeat proteins that direct their assembly into complexes that possess cyclic symmetry. Of 96 designs that were experimentally characterized, 21 were found to form stable monodisperse homo-oligomers in solution, and 15 (4 homodimers, 6 homotrimers, 6 homotetramers and 1 homopentamer) had solution small angle X-ray scattering data consistent with the design models. X-ray crystal structures were obtained for five of the designs and each of these were shown to be very close to their design model. PMID:28338692

Genetic and Environmental Influences on Thin-Ideal Internalization across Puberty and Pre-Adolescent, Adolescent, and Young Adult Development

PubMed Central

Suisman, Jessica L.; Thompson, J. Kevin; Keel, Pamela K.; Burt, S. Alexandra; Neale, Michael; Boker, Steven; Sisk, Cheryl; Klump, Kelly L.

2014-01-01

Objective Mean-levels of thin-ideal internalization increase during adolescence and pubertal development, but it is unknown whether these phenotypic changes correspond to developmental changes in etiological (i.e., genetic and environmental) risk. Given the limited knowledge on risk for thin-ideal internalization, research is needed to guide the identification of specific types of risk factors during critical developmental periods. The present twin study examined genetic and environmental influences on thin-ideal internalization across adolescent and pubertal development. Method Participants were 1,064 female twins (ages 8–25 years) from the Michigan State University Twin Registry. Thin-ideal internalization and pubertal development were assessed using self-report questionnaires. Twin moderation models were used to examine if age and/or pubertal development moderate genetic and environmental influences on thin-ideal internalization. Results Phenotypic analyses indicated significant increases in thin-ideal internalization across age and pubertal development. Twin models suggested no significant differences in etiologic effects across development. Nonshared environmental influences were most important in the etiology of thin-ideal internalization, with genetic, shared environmental, and nonshared environmental accounting for approximately 8%, 15%, and 72%, respectively, of the total variance. Discussion Despite mean-level increases in thin-ideal internalization across development, the relative influence of genetic versus environmental risk did not differ significantly across age or pubertal groups. The majority of variance in thin-ideal internalization was accounted for by environmental factors, suggesting that mean-level increases in thin-ideal internalization may reflect increases in the magnitude/strength of environmental risk across this period. Replication is needed, particularly with longitudinal designs that assess thin-ideal internalization across key

[The style of leadership idealized by nurses].

PubMed

Higa, Elza de Fátima Ribeiro; Trevizan, Maria Auxiliadora

2005-01-01

This study focuses on nursing leadership on the basis of Grid theories. According to the authors, these theories are an alternative that allows for leadership development in nursing. The research aimed to identify and analyze the style of leadership idealized by nurses, according to their own view, and to compare the styles of leadership idealized by nurses between the two research institutions. Study subjects were 13 nurses. The results show that nurses at both institutions equally mention they idealize style 9.9, followed by 5.5 and 1.9, with a tendency to reject styles 9.1 and 1.1.

Design Pattern Mining Using Distributed Learning Automata and DNA Sequence Alignment

PubMed Central

Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

2014-01-01

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

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

PubMed

Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

2014-01-01

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

Concepts of Ideal and Nonideal Explosives.

DTIC Science & Technology

1981-12-01

Akst and J. Hershkowitz, "Explosive Performance Modification by Cosolidifaction of Ammonium Nitrate with Fuels ," Technical Report 4987, Picatinny...explosives Equations of state Diameter effect Ammonium nitrate 20. ASSrRACr (ca’mes r w re t N netwezy ad identity by block number) The purpose of...this report is to stimulate discussion on the nonideality of ammonium nitrate and its composite explosives. The concept of ideal and non- ideal

Optimization of an idealized Y-Shaped Extracardiac Fontan Baffle

NASA Astrophysics Data System (ADS)

Yang, Weiguang; Feinstein, Jeffrey; Mohan Reddy, V.; Marsden, Alison

2008-11-01

Research has showed that vascular geometries can significantly impact hemodynamic performance, particularly in pediatric cardiology, where anatomy varies from one patient to another. In this study we optimize a newly proposed design for the Fontan procedure, a surgery used to treat single ventricle heart patients. The current Fontan procedure connects the inferior vena cava (IVC) to the pulmonary arteries (PA's) via a straight Gore-Tex tube, forming a T-shaped junction. In the Y-graft design, the IVC is connected to the left and right PAs by two branches. Initial studies on the Y-graft design showed an increase in efficiency and improvement in flow distribution compared to traditional designs in a single patient-specific model. We now optimize an idealized Y-graft model to refine the design prior to patient testing. A derivate-free optimization algorithm using Kriging surrogate functions and mesh adaptive direct search is coupled to a 3-D finite element Navier-Stokes solver. We will present optimization results for rest and exercise conditions and examine the influence of energy efficiency, wall shear stress, pulsatile flow, and flow distribution on the optimal design.

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs

PubMed Central

2014-01-01

Background We introduce Sequence Bundles--a novel data visualisation method for representing multiple sequence alignments (MSAs). We identify and address key limitations of the existing bioinformatics data visualisation methods (i.e. the Sequence Logo) by enabling Sequence Bundles to give salient visual expression to sequence motifs and other data features, which would otherwise remain hidden. Methods For the development of Sequence Bundles we employed research-led information design methodologies. Sequences are encoded as uninterrupted, semi-opaque lines plotted on a 2-dimensional reconfigurable grid. Each line represents a single sequence. The thickness and opacity of the stack at each residue in each position indicates the level of conservation and the lines' curved paths expose patterns in correlation and functionality. Several MSAs can be visualised in a composite image. The Sequence Bundles method is designed to favour a tangible, continuous and intuitive display of information. Results We have developed a software demonstration application for generating a Sequence Bundles visualisation of MSAs provided for the BioVis 2013 redesign contest. A subsequent exploration of the visualised line patterns allowed for the discovery of a number of interesting features in the dataset. Reported features include the extreme conservation of sequences displaying a specific residue and bifurcations of the consensus sequence. Conclusions Sequence Bundles is a novel method for visualisation of MSAs and the discovery of sequence motifs. It can aid in generating new insight and hypothesis making. Sequence Bundles is well disposed for future implementation as an interactive visual analytics software, which can complement existing visualisation tools. PMID:25237395

Ideal strength of bcc molybdenum and niobium

NASA Astrophysics Data System (ADS)

Luo, Weidong; Roundy, D.; Cohen, Marvin L.; Morris, J. W.

2002-09-01

The behavior of bcc Mo and Nb under large strain was investigated using the ab initio pseudopotential density-functional method. We calculated the ideal shear strength for the {211}<111> and {011}<111> slip systems and the ideal tensile strength in the <100> direction, which are believed to provide the minimum shear and tensile strengths. As either material is sheared in either of the two systems, it evolves toward a stress-free tetragonal structure that defines a saddle point in the strain-energy surface. The inflection point on the path to this tetragonal ``saddle-point'' structure sets the ideal shear strength. When either material is strained in tension along <100>, it initially follows the tetragonal, ``Bain,'' path toward a stress-free fcc structure. However, before the strained crystal reaches fcc, its symmetry changes from tetragonal to orthorhombic; on continued strain it evolves toward the same tetragonal saddle point that is reached in shear. In Mo, the symmetry break occurs after the point of maximum tensile stress has been passed, so the ideal strength is associated with the fcc extremum as in W. However, a Nb crystal strained in <100> becomes orthorhombic at tensile stress below the ideal strength. The ideal tensile strength of Nb is associated with the tetragonal saddle point and is caused by failure in shear rather than tension. In dimensionless form, the ideal shear and tensile strengths of Mo (τ*=τm/G111=0.12, σ*=σm/E100=0.078) are essentially identical to those previously calculated for W. Nb is anomalous. Its dimensionless shear strength is unusually high, τ*=0.15, even though the saddle-point structure that causes it is similar to that in Mo and W, while its dimensionless tensile strength, σ*=0.079, is almost the same as that of Mo and W, even though the saddle-point structure is quite different.

Design of pseudorandom binary sequence generator using lithium-niobate-based Mach-Zehnder interferometers

NASA Astrophysics Data System (ADS)

Choudhary, Kuldeep; Kumar, Santosh

2017-05-01

The application of electro-optic effect in lithium-niobate-based Mach-Zehnder interferometer to design a 3-bit optical pseudorandom binary sequence (PRBS) generator has been proposed, which is characterized by its simplicity of generation and stability. The proposed device is optoelectronic in nature. The PBRS generator is immensely applicable for pattern generation, encryption, and coding applications in optical networks. The study is carried out by simulating the proposed device with beam propagation method.

Prospective Teachers' Cognitive Constructs Concerning Ideal Teacher Qualifications: A Phenomenological Analysis Based on Repertory Grid Technique

ERIC Educational Resources Information Center

Kozikoglu, Ishak

2017-01-01

The aim of this study is to identify cognitive constructs of prospective teachers about ideal teacher qualifications. This study was designed as phenomenological pattern which is one of the qualitative research designs. The study was conducted with 36 prospective teachers selected from Yüzüncü Yil University, Faculty of Education. The study group…

DNA Shape Dominates Sequence Affinity in Nucleosome Formation

NASA Astrophysics Data System (ADS)

Freeman, Gordon S.; Lequieu, Joshua P.; Hinckley, Daniel M.; Whitmer, Jonathan K.; de Pablo, Juan J.

2014-10-01

Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and the mechanisms that dictate their position at specific locations along a DNA sequence are of central importance to genetics. In this Letter, we employ molecular models of DNA and proteins to elucidate various aspects of nucleosome positioning. In particular, we show how DNA's histone affinity is encoded in its sequence-dependent shape, including subtle deviations from the ideal straight B-DNA form and local variations of minor groove width. By relying on high-precision simulations of the free energy of nucleosome complexes, we also demonstrate that, depending on DNA's intrinsic curvature, histone binding can be dominated by bending interactions or electrostatic interactions. More generally, the results presented here explain how sequence, manifested as the shape of the DNA molecule, dominates molecular recognition in the problem of nucleosome positioning.

Ideal and Nonideal Reasoning in Educational Theory

ERIC Educational Resources Information Center

Jaggar, Alison M.

2015-01-01

The terms "ideal theory" and "nonideal theory" are used in contemporary Anglophone political philosophy to identify alternative methodological approaches for justifying normative claims. Each term is used in multiple ways. In this article Alison M. Jaggar disentangles several versions of ideal and nonideal theory with a view to…

Idealized cultural beliefs about gender: implications for mental health.

PubMed

Mahalingam, Ramaswami; Jackson, Benita

2007-12-01

In this paper, we examined the relationship between culture-specific ideals (chastity, masculinity, caste beliefs) and self-esteem, shame and depression using an idealized cultural model proposed by Mahalingam (2006, In: Mahalingam R (ed) Cultural psychology of immigrants. Lawrence Erlbaum, Mahwah, NJ, pp 1-14). Participants were from communities with a history of extreme male-biased sex ratios in Tamilnadu, India (N = 785). We hypothesized a dual-process model of self-appraisals suggesting that achieving idealized cultural identities would increase both self-esteem and shame, with the latter leading to depression, even after controlling for key covariates. We tested this using structural equation modeling. The proposed idealized cultural identities model had an excellent fit (CFI = 0.99); the effect of idealized identities on self-esteem, shame and depression differed by gender. Idealized beliefs about gender relate to psychological well-being in gender specific ways in extreme son preference communities. We discuss implications of these findings for future research and community-based interventions.

A “SMART” Design for Building Individualized Treatment Sequences

PubMed Central

Lei, H.; Nahum-Shani, I.; Lynch, K.; Oslin, D.; Murphy, S.A.

2013-01-01

Interventions often involve a sequence of decisions. For example, clinicians frequently adapt the intervention to an individual’s outcomes. Altering the intensity and type of intervention over time is crucial for many reasons, such as to obtain improvement if the individual is not responding or to reduce costs and burden when intensive treatment is no longer necessary. Adaptive interventions utilize individual variables (severity, preferences) to adapt the intervention and then dynamically utilize individual outcomes (response to treatment, adherence) to readapt the intervention. The Sequential Multiple Assignment Randomized Trial (SMART)provides high-quality data that can be used to construct adaptive interventions. We review the SMART and highlight its advantages in constructing and revising adaptive interventions as compared to alternative experimental designs. Selected examples of SMART studies are described and compared. A data analysis method is provided and illustrated using data from the Extending Treatment Effectiveness of Naltrexone SMART study. PMID:22224838

Susceptibility for thin ideal media and eating styles.

PubMed

Anschutz, Doeschka J; Engels, Rutger C M E; Van Strien, Tatjana

2008-03-01

This study examined the relations between susceptibility for thin ideal media and restrained, emotional and external eating, directly and indirectly through body dissatisfaction. Thin ideal media susceptibility, body dissatisfaction and eating styles were measured in a sample of 163 female students. Structural equation modelling was used for analyses, controlling for BMI. Higher susceptibility for thin ideal media was directly related to higher scores on all eating styles, and indirectly related to higher restrained and emotional eating through elevated levels of body dissatisfaction. So, thin ideal media susceptibility was not only related to restraint through body dissatisfaction, but also directly. Emotional eaters might be more vulnerable for negative affect, whereas external eaters might be more sensitive to external cues in general.

Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

PubMed Central

Nakazato, Takeru; Ohta, Tazro; Bono, Hidemasa

2013-01-01

High-throughput sequencing technology, also called next-generation sequencing (NGS), has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA). As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs) from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH) extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called “Gendoo”. We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called “DBCLS SRA” (http://sra.dbcls.jp/). This service will improve accessibility to high-quality data from SRA. PMID:24167589

Advanced scatter search approach and its application in a sequencing problem of mixed-model assembly lines in a case company

NASA Astrophysics Data System (ADS)

Liu, Qiong; Wang, Wen-xi; Zhu, Ke-ren; Zhang, Chao-yong; Rao, Yun-qing

2014-11-01

Mixed-model assembly line sequencing is significant in reducing the production time and overall cost of production. To improve production efficiency, a mathematical model aiming simultaneously to minimize overtime, idle time and total set-up costs is developed. To obtain high-quality and stable solutions, an advanced scatter search approach is proposed. In the proposed algorithm, a new diversification generation method based on a genetic algorithm is presented to generate a set of potentially diverse and high-quality initial solutions. Many methods, including reference set update, subset generation, solution combination and improvement methods, are designed to maintain the diversification of populations and to obtain high-quality ideal solutions. The proposed model and algorithm are applied and validated in a case company. The results indicate that the proposed advanced scatter search approach is significant for mixed-model assembly line sequencing in this company.

Designing Better Scaffolding in Teaching Complex Systems with Graphical Simulations

NASA Astrophysics Data System (ADS)

Li, Na

Complex systems are an important topic in science education today, but they are usually difficult for secondary-level students to learn. Although graphic simulations have many advantages in teaching complex systems, scaffolding is a critical factor for effective learning. This dissertation study was conducted around two complementary research questions on scaffolding: (1) How can we chunk and sequence learning activities in teaching complex systems? (2) How can we help students make connections among system levels across learning activities (level bridging)? With a sample of 123 seventh-graders, this study employed a 3x2 experimental design that factored sequencing methods (independent variable 1; three levels) with level-bridging scaffolding (independent variable 2; two levels) and compared the effectiveness of each combination. The study measured two dependent variables: (1) knowledge integration (i.e., integrating and connecting content-specific normative concepts and providing coherent scientific explanations); (2) understanding of the deep causal structure (i.e., being able to grasp and transfer the causal knowledge of a complex system). The study used a computer-based simulation environment as the research platform to teach the ideal gas law as a system. The ideal gas law is an emergent chemical system that has three levels: (1) experiential macro level (EM) (e.g., an aerosol can explodes when it is thrown into the fire); (2) abstract macro level (AM) (i.e., the relationships among temperature, pressure and volume); (3) micro level (Mi) (i.e., molecular activity). The sequencing methods of these levels were manipulated by changing the order in which they were delivered with three possibilities: (1) EM-AM-Mi; (2) Mi-AM-EM; (3) AM-Mi-EM. The level-bridging scaffolding variable was manipulated on two aspects: (1) inserting inter-level questions among learning activities; (2) two simulations dynamically linked in the final learning activity. Addressing the first

Childhood Lifestyle and Clinical Determinants of Adult Ideal

PubMed Central

Laitinen, Tomi T.; Pahkala, Katja; Venn, Alison; Woo, Jessica G; Oikonen, Mervi; Dwyer, Terence; Mikkilä, Vera; Hutri-Kähönen, Nina; Smith, Kylie J.; Gall, Seana L.; Morrison, John A.; Viikari, Jorma S.A.; Raitakari, Olli T.; Magnussen, Costan G.; Juonala, Markus

2013-01-01

Background The American Heart Association recently defined ideal cardiovascular health by simultaneous presence of seven health behaviors and factors. The concept is associated with cardiovascular disease incidence, and cardiovascular disease and all-cause mortality. To effectively promote ideal cardiovascular health already early in life, childhood factors predicting future ideal cardiovascular health should be investigated. Our aim was thus to comprehensively explore childhood determinants of adult ideal cardiovascular health in population based cohorts from three continents. Methods The sample comprised a total of 4409 participants aged 3–19 years at baseline from the Cardiovascular Risk in Young Finns Study (YFS; N=1883) from Finland, Childhood Determinants of Adult Health Study (CDAH; N=1803) from Australia and Princeton Follow-up Study (PFS; N=723) from the United States. Participants were re-examined 19–31 years later when aged 30–48 years. Results In multivariable analyses, independent childhood predictors of adult ideal cardiovascular health were family socioeconomic status (P<0.01; direct association) and BMI (P<0.001; inverse association) in all cohorts. In addition, blood pressure (P=0.007), LDL-cholesterol (P<0.001) and parental smoking (P=0.006) in the YFS, and own smoking (P=0.001) in CDAH were inversely associated with future ideal cardiovascular health. Conclusions Among several lifestyle and clinical indicators studied, higher family socioeconomic status and non-smoking (parental/own) in childhood independently predict ideal cardiovascular health in adulthood. As atherosclerotic cardiovascular diseases are rooted in childhood, our findings suggest that special attention could be paid to children who are from low socioeconomic status families, and who smoke or whose parents smoke, to prevent cardiovascular disease morbidity and mortality. PMID:24075574

On the union of graded prime ideals

NASA Astrophysics Data System (ADS)

Uregen, Rabia Nagehan; Tekir, Unsal; Hakan Oral, Kursat

2016-01-01

In this paper we investigate graded compactly packed rings, which is defined as; if any graded ideal I of R is contained in the union of a family of graded prime ideals of R, then I is actually contained in one of the graded prime ideals of the family. We give some characterizations of graded compactly packed rings. Further, we examine this property on h - Spec(R). We also define a generalization of graded compactly packed rings, the graded coprimely packed rings. We show that R is a graded compactly packed ring if and only if R is a graded coprimely packed ring whenever R be a graded integral domain and h - dim R = 1.

Improved PCR-Based Detection of Soil Transmitted Helminth Infections Using a Next-Generation Sequencing Approach to Assay Design.

PubMed

Pilotte, Nils; Papaiakovou, Marina; Grant, Jessica R; Bierwert, Lou Ann; Llewellyn, Stacey; McCarthy, James S; Williams, Steven A

2016-03-01

The soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world's most economically depressed locations. With growing emphasis on disease mapping and eradication, the availability of accurate and cost-effective diagnostic measures is of paramount importance to global control and elimination efforts. While real-time PCR-based molecular detection assays have shown great promise, to date, these assays have utilized sub-optimal targets. By performing next-generation sequencing-based repeat analyses, we have identified high copy-number, non-coding DNA sequences from a series of soil transmitted pathogens. We have used these repetitive DNA elements as targets in the development of novel, multi-parallel, PCR-based diagnostic assays. Utilizing next-generation sequencing and the Galaxy-based RepeatExplorer web server, we performed repeat DNA analysis on five species of soil transmitted helminths (Necator americanus, Ancylostoma duodenale, Trichuris trichiura, Ascaris lumbricoides, and Strongyloides stercoralis). Employing high copy-number, non-coding repeat DNA sequences as targets, novel real-time PCR assays were designed, and assays were tested against established molecular detection methods. Each assay provided consistent detection of genomic DNA at quantities of 2 fg or less, demonstrated species-specificity, and showed an improved limit of detection over the existing, proven PCR-based assay. The utilization of next-generation sequencing-based repeat DNA analysis methodologies for the identification of molecular diagnostic targets has the ability to improve assay species-specificity and limits of detection. By exploiting such high copy-number repeat sequences, the assays described here will facilitate soil transmitted helminth diagnostic efforts. We recommend similar analyses when designing PCR-based diagnostic tests for the detection of other eukaryotic pathogens.

Why Education in Public Schools Should Include Religious Ideals

ERIC Educational Resources Information Center

de Ruyter, Doret J.; Merry, Michael S.

2009-01-01

This article aims to open a new line of debate about religion in public schools by focusing on religious ideals. The article begins with an elucidation of the concept "religious ideals" and an explanation of the notion of reasonable pluralism, in order to be able to explore the dangers and positive contributions of religious ideals and their…

Is athletic really ideal? An examination of the mediating role of body dissatisfaction in predicting disordered eating and compulsive exercise.

PubMed

Bell, Hayley S; Donovan, Caroline L; Ramme, Robin

2016-04-01

Investigations into female body image have suggested that rather than thinness, preference is now being given to a female "athletic ideal" characterised by a toned abdomen, firmer lower body and muscular upper body. This study sought to investigate a) whether greater internalization of the athletic-ideal is associated with higher body dissatisfaction, dieting, bulimic symptoms and compulsive exercise, and b) whether body dissatisfaction mediates the relationship between athletic-ideal internalization and the disordered eating and exercise behaviours of dieting, bulimic symptoms and compulsive exercise. Participants were 388 females aged between 17 and 35years. Participants completed a battery of questionnaires measuring athletic-ideal internalization, body dissatisfaction, dieting, compulsive exercise and bulimic symptoms. Athletic-ideal internalization was not found to be associated with body dissatisfaction, but was found to predict dieting, bulimic symptoms and compulsive exercise directly. Body dissatisfaction did not mediate the relationship between athletic-ideal internalization and any of the disordered eating and exercise behaviours. The study was limited by its cross sectional design which precluded conclusions being drawn about the direction of causality and temporal associations. Athletic-ideal internalization, while not associated with body dissatisfaction, was associated with a range of disordered eating and exercise behaviours. Results from the study suggest that the female athletic-ideal is an equally unrealistic and problematic ideal for women to strive towards. Copyright © 2015 Elsevier Ltd. All rights reserved.

Idealization of the analyst by the young adult.

PubMed

Chused, J F

1987-01-01

Idealization is an intrapsychic process that serves many functions. In addition to its use defensively and for gratification of libidinal and aggressive drive derivatives, it can contribute to developmental progression, particularly during late adolescence and young adulthood. During an analysis, it is important to recognize all the determinants of idealization, including those related to the reworking of developmental conflicts. If an analyst understands idealization solely as a manifestation of pathology, he may interfere with his patient's use of it for the development of autonomous functioning.

A stationary bulk planar ideal flow solution for the double shearing model

NASA Astrophysics Data System (ADS)

Lyamina, E. A.; Kalenova, N. V.; Date, P. P.

2018-04-01

This paper provides a general ideal flow solution for the double shearing model of pressure-dependent plasticity. This new solution is restricted to a special class of stationary planar flows. A distinguished feature of this class of solutions is that one family of characteristic lines is straight. The solution is analytic. The mapping between Cartesian and principal lines based coordinate systems is given in parametric form with characteristic coordinates being the parameters. A simple relation that connects the scale factor for one family of coordinate curves of the principal lines based coordinate system and the magnitude of velocity is derived. The original ideal flow theory is widely used as the basis for inverse methods for the preliminary design of metal forming processes driven by minimum plastic work. The new theory extends this area of application to granular materials.

BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

PubMed Central

Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Pareja, Eduardo; Tobes, Raquel

2012-01-01

BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version – which is developed in Java, takes advantage of Amazon Web Services (AWS) cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future. PMID:23185310

Ideal MHD stability and characteristics of edge localized modes on CFETR

NASA Astrophysics Data System (ADS)

Li, Ze-Yu; Chan, V. S.; Zhu, Yi-Ren; Jian, Xiang; Chen, Jia-Le; Cheng, Shi-Kui; Zhu, Ping; Xu, Xue-Qiao; Xia, Tian-Yang; Li, Guo-Qiang; Lao, L. L.; Snyder, P. B.; Wang, Xiao-Gang; the CFETR Physics Team

2018-01-01

Investigation on the equilibrium operation regime, its ideal magnetohydrodynamics (MHD) stability and edge localized modes (ELM) characteristics is performed for the China Fusion Engineering Test Reactor (CFETR). The CFETR operation regime study starts with a baseline scenario (R  =  5.7 m, B T  =  5 T) derived from multi-code integrated modeling, with key parameters {{β }N},{{β }T},{{β }p} varied to build a systematic database. These parameters, under profile and pedestal constraints, provide the foundation for the engineering design. The long wavelength low-n global ideal MHD stability of the CFETR baseline scenario, including the wall stabilization effect, is evaluated by GATO. It is found that the low-n core modes are stable with a wall at r/a  =  1.2. An investigation of intermediate wavelength ideal MHD modes (peeling ballooning modes) is also carried out by multi-code benchmarking, including GATO, ELITE, BOUT++ and NIMROD. A good agreement is achieved in predicting edge-localized instabilities. Nonlinear behavior of ELMs for the baseline scenario is simulated using BOUT++. A mix of grassy and type I ELMs is identified. When the size and magnetic field of CFETR are increased (R  =  6.6 m, B T  =  6 T), collisionality correspondingly increases and the instability is expected to shift to grassy ELMs.

The multilocus sequence typing network: mlst.net.

PubMed

Aanensen, David M; Spratt, Brian G

2005-07-01

The unambiguous characterization of strains of a pathogen is crucial for addressing questions relating to its epidemiology, population and evolutionary biology. Multilocus sequence typing (MLST), which defines strains from the sequences at seven house-keeping loci, has become the method of choice for molecular typing of many bacterial and fungal pathogens (and non-pathogens), and MLST schemes and strain databases are available for a growing number of prokaryotic and eukaryotic organisms. Sequence data are ideal for strain characterization as they are unambiguous, meaning strains can readily be compared between laboratories via the Internet. Laboratories undertaking MLST can quickly progress from sequencing the seven gene fragments to characterizing their strains and relating them to those submitted by others and to the population as a whole. We provide the gateway to a number of MLST schemes, each of which contain a set of tools for the initial characterization of strains, and methods for relating query strains to other strains of the species, including clustering based on differences in allelic profiles, phylogenetic trees based on concatenated sequences, and a recently developed method (eBURST) for identifying clonal complexes within a species and displaying the overall structure of the population. This network of MLST websites is available at http://www.mlst.net.

Program Synthesizes UML Sequence Diagrams

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

Moral identity as moral ideal self: links to adolescent outcomes.

PubMed

Hardy, Sam A; Walker, Lawrence J; Olsen, Joseph A; Woodbury, Ryan D; Hickman, Jacob R

2014-01-01

The purposes of this study were to conceptualize moral identity as moral ideal self, to develop a measure of this construct, to test for age and gender differences, to examine links between moral ideal self and adolescent outcomes, and to assess purpose and social responsibility as mediators of the relations between moral ideal self and outcomes. Data came from a local school sample (Data Set 1: N = 510 adolescents; 10-18 years of age) and a national online sample (Data Set 2: N = 383 adolescents; 15-18 years of age) of adolescents and their parents. All outcome measures were parent-report (Data Set 1: altruism, moral personality, aggression, and cheating; Data Set 2: environmentalism, school engagement, internalizing, and externalizing), whereas other variables were adolescent-report. The 20-item Moral Ideal Self Scale showed good reliability, factor structure, and validity. Structural equation models demonstrated that, even after accounting for moral identity internalization, in Data Set 1 moral ideal self positively predicted altruism and moral personality and negatively predicted aggression, whereas in Data Set 2 moral ideal self positively predicted environmentalism and negatively predicted internalizing and externalizing symptoms. Further, purpose and social responsibility mediated most relations between moral ideal self and the outcomes in Data Set 2. Moral ideal self was unrelated to age but differentially predicted some outcomes across age. Girls had higher levels of moral ideal self than boys, although moral identity did not differentially predict outcomes between genders. Thus, moral ideal self is a salient element of moral identity and may play a role in morally relevant adolescent outcomes. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Mapping algorithm for freeform construction using non-ideal light sources

NASA Astrophysics Data System (ADS)

Li, Chen; Michaelis, D.; Schreiber, P.; Dick, L.; Bräuer, A.

2015-09-01

Using conventional mapping algorithms for the construction of illumination freeform optics' arbitrary target pattern can be obtained for idealized sources, e.g. collimated light or point sources. Each freeform surface element generates an image point at the target and the light intensity of an image point is corresponding to the area of the freeform surface element who generates the image point. For sources with a pronounced extension and ray divergence, e.g. an LED with a small source-freeform-distance, the image points are blurred and the blurred patterns might be different between different points. Besides, due to Fresnel losses and vignetting, the relationship between light intensity of image points and area of freeform surface elements becomes complicated. These individual light distributions of each freeform element are taken into account in a mapping algorithm. To this end the method of steepest decent procedures are used to adapt the mapping goal. A structured target pattern for a optics system with an ideal source is computed applying corresponding linear optimization matrices. Special weighting factor and smoothing factor are included in the procedures to achieve certain edge conditions and to ensure the manufacturability of the freefrom surface. The corresponding linear optimization matrices, which are the lighting distribution patterns of each of the freeform surface elements, are gained by conventional raytracing with a realistic source. Nontrivial source geometries, like LED-irregularities due to bonding or source fine structures, and a complex ray divergence behavior can be easily considered. Additionally, Fresnel losses, vignetting and even stray light are taken into account. After optimization iterations, with a realistic source, the initial mapping goal can be achieved by the optics system providing a structured target pattern with an ideal source. The algorithm is applied to several design examples. A few simple tasks are presented to discussed

Analysis of Ideal Towers for Tall Wind Applications: Preprint

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

Dykes, Katherine L; Damiani, Rick R; Roberts, Joseph O

Innovation in wind turbine tower design is of significant interest for future development of wind power plants. First, wind turbine towers account for a large portion of overall capital expenditures for wind power projects. Second, for low wind-resource regions of the world, the use of low-cost tall-tower technology has the potential to open new markets for development. This study investigates the relative potential of various tower configurations in terms of mass and cost. For different market applications and hub heights, idealized tall towers are designed and compared. The results show that innovation in wind turbine controls makes reaching higher hubmore » heights with current technology economically viable. At the same time, new technologies hold promise for reducing tower costs as these technologies mature and hub heights reach twice the current average.« less

Use of the melting curve assay as a means for high-throughput quantification of Illumina sequencing libraries.

PubMed

Shinozuka, Hiroshi; Forster, John W

2016-01-01

Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches have been established, none are ideal for highly multiplexed sequencing due to issues of cost and/or processing time. Methods. An inexpensive and high-throughput library quantification method has been developed, based on an adaptation of the melting curve assay. Sequencing libraries were subjected to the assay using the Bio-Rad Laboratories CFX Connect(TM) Real-Time PCR Detection System. The library quantity was calculated through summation of reduction of relative fluorescence units between 86 and 95 °C. Results.PCR-enriched sequencing libraries are suitable for this quantification without pre-purification of DNA. Short DNA molecules, which ideally should be eliminated from the library for subsequent processing, were differentiated from the target DNA in a mixture on the basis of differences in melting temperature. Quantification results for long sequences targeted using the melting curve assay were correlated with those from existing methods (R (2) > 0.77), and that observed from MiSeq sequencing (R (2) = 0.82). Discussion.The results of multiplexed sequencing suggested that the normalisation performance of the described method is equivalent to that of another recently reported high-throughput bead-based method, BeNUS. However, costs for the melting curve assay are considerably lower and processing times shorter than those of other existing methods, suggesting greater suitability for highly multiplexed sequencing applications.

SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

PubMed

Ramu, Chenna

2003-07-01

SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

Beyond the bucket: testing the effect of experimental design on rate and sequence of decay

NASA Astrophysics Data System (ADS)

Gabbott, Sarah; Murdock, Duncan; Purnell, Mark

2016-04-01

Experimental decay has revealed the potential for profound biases in our interpretations of exceptionally preserved fossils, with non-random sequences of character loss distorting the position of fossil taxa in phylogenetic trees. By characterising these sequences we can rewind this distortion and make better-informed interpretations of the affinity of enigmatic fossil taxa. Equally, rate of character loss is crucial for estimating the preservation potential of phylogentically informative characters, and revealing the mechanisms of preservation themselves. However, experimental decay has been criticised for poorly modeling 'real' conditions, and dismissed as unsophisticated 'bucket science'. Here we test the effect of a differing experimental parameters on the rate and sequence of decay. By doing so, we can test the assumption that the results of decay experiments are applicable to informing interpretations of exceptionally preserved fossils from diverse preservational settings. The results of our experiments demonstrate the validity of using the sequence of character loss as a phylogenetic tool, and sheds light on the extent to which environment must be considered before making decay-informed interpretations, or reconstructing taphonomic pathways. With careful consideration of experimental design, driven by testable hypotheses, decay experiments are robust and informative - experimental taphonomy needn't kick the bucket just yet.

[Challenges and risks in the development of the ego ideal in adolescence].

PubMed

Helbing-Tietze, Brigitte

2003-11-01

The author proposes to speak of representations concerning the ideal self, the ideal relationship, the ideal society instead of ego ideal. An active self develops ideals and uses them as standards for orientation, to regulate the affects, and to fulfill needs. The different ideals often do not fit together and are therefore difficult to realize. Adolescents normally refuse their parents' ideals and create new ones with the help of their peers. This developmental step is full of challenges and risks as will be explained in this article.

Career Academy Course Sequences.

ERIC Educational Resources Information Center

Markham, Thom; Lenz, Robert

This career academy course sequence guide is designed to give teachers a quick overview of the course sequences of well-known career academy and career pathway programs from across the country. The guide presents a variety of sample course sequences for the following academy themes: (1) arts and communication; (2) business and finance; (3)…

The ideal subject distance for passport pictures.

PubMed

Verhoff, Marcel A; Witzel, Carsten; Kreutz, Kerstin; Ramsthaler, Frank

2008-07-04

In an age of global combat against terrorism, the recognition and identification of people on document images is of increasing significance. Experiments and calculations have shown that the camera-to-subject distance - not the focal length of the lens - can have a significant effect on facial proportions. Modern passport pictures should be able to function as a reference image for automatic and manual picture comparisons. This requires a defined subject distance. It is completely unclear which subject distance, in the taking of passport photographs, is ideal for the recognition of the actual person. We show here that the camera-to-subject distance that is perceived as ideal is dependent on the face being photographed, even if the distance of 2m was most frequently preferred. So far the problem of the ideal camera-to-subject distance for faces has only been approached through technical calculations. We have, for the first time, answered this question experimentally with a double-blind experiment. Even if there is apparently no ideal camera-to-subject distance valid for every face, 2m can be proposed as ideal for the taking of passport pictures. The first step would actually be the determination of a camera-to-subject distance for the taking of passport pictures within the standards. From an anthropological point of view it would be interesting to find out which facial features allow the preference of a shorter camera-to-subject distance and which allow the preference of a longer camera-to-subject distance.

Learning Hypotheses and an Associated Tool to Design and to Analyse Teaching-Learning Sequences. Special Issue

ERIC Educational Resources Information Center

Buty, Christian; Tiberghien, Andree; Le Marechal, Jean-Francois

2004-01-01

This contribution presents a tool elaborated from a theoretical framework linking epistemological, learning and didactical hypotheses. This framework lead to design teaching sequences from a socio-constructivist perspective, and is based on the role of models in physics or chemistry, and on the role of students' initial knowledge in learning…

Designed Electroresponsive Biomaterials: Sequence-Controlled Behavior

DTIC Science & Technology

2010-06-29

protein of the M13 . Traditional phage and yeast display methodologies indicate that peptide sequences with high affinities for electrode materials...drug delivery. The original vision for this work was to employ combinatorial tools such as phage and yeast display under electrical selection pressure...and drug delivery. The original vision for this work was to employ combinatorial tools such as phage and yeast display under electrical selection

Effect of solution non-ideality on erythrocyte volume regulation.

PubMed

Levin, R L; Cravalho, E G; Huggins, C E

1977-03-01

A non-ideal, hydrated, non-dilute pseudo-binary salt-protein-water solution model of the erythrocyte intracellular solution is presented to describe the osmotic behavior of human erythrocytes. Existing experimental activity data for salts and proteins in aqueous solutions are used to formulate van Laar type expressions for the solvent and solute activity coefficients. Reasonable estimates can therefore be made of the non-ideality of the erythrocyte intracellular solution over a wide range of osmolalities. Solution non-ideality is shown to affect significantly the degree of solute polarization within the erythrocyte intracellular solution during freezing. However, the non-ideality has very little effect upon the amount of water retained within erythrocytes cooled at sub-zero temperatures.

Molecular Design of Antifouling Polymer Brushes Using Sequence-Specific Peptoids.

PubMed

Lau, King Hang Aaron; Sileika, Tadas S; Park, Sung Hyun; Sousa, Ana Maria Leal; Burch, Patrick; Szleifer, Igal; Messersmith, Phillip B

2015-01-07

Material systems that can be used to flexibly and precisely define the chemical nature and molecular arrangement of a surface would be invaluable for the control of complex biointerfacial interactions. For example, progress in antifouling polymer biointerfaces that prevent non-specific protein adsorption and cell attachment, which can significantly improve the performance of an array of biomedical and industrial applications, is hampered by a lack of chemical models to identify the molecular features conferring their properties. Poly(N-substituted glycine) "peptoids" are peptidomimetic polymers that can be conveniently synthesized with specific monomer sequences and chain lengths, and are presented as a versatile platform for investigating the molecular design of antifouling polymer brushes. Zwitterionic antifouling polymer brushes have captured significant recent attention, and a targeted library of zwitterionic peptoid brushes with a different charge densities, hydration, separations between charged groups, chain lengths, and grafted chain densities, is quantitatively evaluated for their antifouling properties through a range of protein adsorption and cell attachment assays. Specific zwitterionic brush designs were found to give rise to distinct but subtle differences in properties. The results also point to the dominant roles of the grafted chain density and chain length in determining the performance of antifouling polymer brushes.

Molecular Design of Antifouling Polymer Brushes Using Sequence-Specific Peptoids

DOE PAGES

Lau, King Hang Aaron; Sileika, Tadas S.; Park, Sung Hyun; ...

2014-11-26

Material systems that can be used to flexibly and precisely define the chemical nature and molecular arrangement of a surface would be invaluable for the control of complex biointerfacial interactions. For example, progress in antifouling polymer biointerfaces that prevents nonspecific protein adsorption and cell attachment, which can significantly improve the performance of an array of biomedical and industrial applications, is hampered by a lack of chemical models to identify the molecular features conferring their properties. Poly(N-substituted glycine) “peptoids” are peptidomimetic polymers that can be conveniently synthesized with specific monomer sequences and chain lengths, and are presented as a versatile platformmore » for investigating the molecular design of antifouling polymer brushes. Zwitterionic antifouling polymer brushes have captured significant recent attention, and a targeted library of zwitterionic peptoid brushes with different charge densities, hydration, separations between charged groups, chain lengths, and grafted chain densities, is quantitatively evaluated for their antifouling properties through a range of protein adsorption and cell attachment assays. Specific zwitterionic brush designs are found to give rise to distinct but subtle differences in properties. In conclusion, the results also point to the dominant roles of the grafted chain density and chain length in determining the performance of antifouling polymer brushes.« less

Integrating design and communication in engineering education: a collaboration between Northwestern University and the Rehabilitation Institute of Chicago.

PubMed

Hirsch, Penny L; Yarnoff, Charles

2011-01-01

The required course for freshmen in Northwestern University's engineering school - a 2-quarter sequence called Engineering Design and Communication (EDC) - is noteworthy not only for its project-based focus on user-centered design, but also for its innovative integrated approach to teaching communication, teamwork, and ethics. Thanks to the collaboration between EDC faculty and staff at the Rehabilitation Institute of Chicago, EDC students, at the beginning of their education, experience the excitement of solving problems for real clients and users. At the same time, these authentic design projects offer an ideal setting for teaching students how to communicate effectively to different audiences and perform productively as team members and future leaders in engineering.

Benchmark analysis of native and artificial NAD+-dependent enzymes generated by a sequence based design method with or without phylogenetic data.

PubMed

Nakano, Shogo; Motoyama, Tomoharu; Miyashita, Yurina; Ishizuka, Yuki; Matsuo, Naoya; Tokiwa, Hiroaki; Shinoda, Suguru; Asano, Yasuhisa; Ito, Sohei

2018-05-22

The expansion of protein sequence databases has enabled us to design artificial proteins by sequence-based design methods, such as full consensus design (FCD) and ancestral sequence reconstruction (ASR). Artificial proteins with enhanced activity levels compared with native ones can potentially be generated by such methods, but successful design is rare because preparing a sequence library by curating the database and selecting a method is difficult. Utilizing a curated library prepared by reducing conservation energies, we successfully designed two artificial L-threonine 3-dehydrogenase (SDR-TDH) with higher activity levels than native SDR-TDH, FcTDH-N1 and AncTDH, using FCD and ASR, respectively. The artificial SDR-TDHs had excellent thermal stability and NAD+ recognition compared to native SDR-TDH from Cupriavidus necator (CnTDH): the melting temperatures of FcTDH-N1 and AncTDH were about 10 and 5°C higher than CnTDH, respectively, and the dissociation constants toward NAD+ of FcTDH-N1 and AncTDH were two- and seven-fold lower than that of CnTDH, respectively. Enzymatic efficiency of the artificial SDR-TDHs were comparable to that of CnTDH. Crystal structures of FcTDH-N1 and AncTDH were determined at 2.8 and 2.1 Å resolution, respectively. Structural and MD simulation analysis of the SDR-TDHs indicated that only the flexibility at specific regions was changed, suggesting that multiple mutations introduced in the artificial SDR-TDHs altered their flexibility and thereby affected their enzymatic properties. Benchmark analysis of the SDR-TDHs indicated that both FCD and ASR can generate highly functional proteins if a curated library is prepared appropriately.

Designable and dynamic single-walled stiff nanotubes assembled from sequence-defined peptoids

DOE PAGES

Jin, Haibao; Ding, Yan-Huai; Wang, Mingming; ...

2018-01-18

Despite recent advances in assembly of organic nanotubes, conferral of sequence-defined engineering and dynamic response characteristics to the tubules remains a challenge. Here we report a new family of highly-designable and dynamic single-walled nanotubes assembled from sequence-defined peptoids through a unique “rolling-up and closure of nanosheet” mechanism. During the assembly process, amorphous spherical particles of amphiphilic peptoid oligomers (APOs) crystallized to form well-defined nanosheets which were then folded to form single-walled peptoid nanotubes (SW-PNTs). These SW-PNTs undergo a pH-triggered, reversible contraction-expansion motion. By varying the number of hydrophobic residues of APOs, we demonstrate the tuning of PNT wall thickness andmore » diameter, and mechanical properties. AFM-based mechanical measurements indicate that PNTs are highly stiff (Young’s Modulus ~13-17 GPa), comparable to the stiffest known biological materials. We further demonstrate that the precise incorporation of functional groups within PNTs and the application of functional PNTs in water decontamination. We believe these SW-PNTs can provide a robust platform for development of biomimetic materials tailored to specific applications.« less

Designable and dynamic single-walled stiff nanotubes assembled from sequence-defined peptoids

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

Jin, Haibao; Ding, Yan-Huai; Wang, Mingming

Despite recent advances in assembly of organic nanotubes, conferral of sequence-defined engineering and dynamic response characteristics to the tubules remains a challenge. Here we report a new family of highly-designable and dynamic single-walled nanotubes assembled from sequence-defined peptoids through a unique “rolling-up and closure of nanosheet” mechanism. During the assembly process, amorphous spherical particles of amphiphilic peptoid oligomers (APOs) crystallized to form well-defined nanosheets which were then folded to form single-walled peptoid nanotubes (SW-PNTs). These SW-PNTs undergo a pH-triggered, reversible contraction-expansion motion. By varying the number of hydrophobic residues of APOs, we demonstrate the tuning of PNT wall thickness andmore » diameter, and mechanical properties. AFM-based mechanical measurements indicate that PNTs are highly stiff (Young’s Modulus ~13-17 GPa), comparable to the stiffest known biological materials. We further demonstrate that the precise incorporation of functional groups within PNTs and the application of functional PNTs in water decontamination. We believe these SW-PNTs can provide a robust platform for development of biomimetic materials tailored to specific applications.« less

Inter-level Scaffolding and Sequences of Representational Activities in Teaching a Chemical System with Graphical Simulations

NASA Astrophysics Data System (ADS)

Li, Na; Black, John B.

2016-10-01

Chemistry knowledge can be represented at macro-, micro- and symbolic levels, and learning a chemistry topic requires students to engage in multiple representational activities. This study focused on scaffolding for inter-level connection-making in learning chemistry knowledge with graphical simulations. We also tested whether different sequences of representational activities produced different student learning outcomes in learning a chemistry topic. A sample of 129 seventh graders participated in this study. In a simulation-based environment, participants completed three representational activities to learn several ideal gas law concepts. We conducted a 2 × 3 factorial design experiment. We compared two scaffolding conditions: (1) the inter- level scaffolding condition in which participants received inter-level questions and experienced the dynamic link function in the simulation-based environment and (2) the intra- level scaffolding condition in which participants received intra-level questions and did not experience the dynamic link function. We also compared three different sequences of representational activities: macro-symbolic-micro, micro-symbolic-macro and symbolic-micro-macro. For the scaffolding variable, we found that the inter- level scaffolding condition produced significantly better performance in both knowledge comprehension and application, compared to the intra- level scaffolding condition. For the sequence variable, we found that the macro-symbolic-micro sequence produced significantly better knowledge comprehension performance than the other two sequences; however, it did not benefit knowledge application performance. There was a trend that the treatment group who experienced inter- level scaffolding and the micro-symbolic-macro sequence achieved the best knowledge application performance.

Non-ideal magnetohydrodynamics on a moving mesh

NASA Astrophysics Data System (ADS)

Marinacci, Federico; Vogelsberger, Mark; Kannan, Rahul; Mocz, Philip; Pakmor, Rüdiger; Springel, Volker

2018-05-01

In certain astrophysical systems, the commonly employed ideal magnetohydrodynamics (MHD) approximation breaks down. Here, we introduce novel explicit and implicit numerical schemes of ohmic resistivity terms in the moving-mesh code AREPO. We include these non-ideal terms for two MHD techniques: the Powell 8-wave formalism and a constrained transport scheme, which evolves the cell-centred magnetic vector potential. We test our implementation against problems of increasing complexity, such as one- and two-dimensional diffusion problems, and the evolution of progressive and stationary Alfvén waves. On these test problems, our implementation recovers the analytic solutions to second-order accuracy. As first applications, we investigate the tearing instability in magnetized plasmas and the gravitational collapse of a rotating magnetized gas cloud. In both systems, resistivity plays a key role. In the former case, it allows for the development of the tearing instability through reconnection of the magnetic field lines. In the latter, the adopted (constant) value of ohmic resistivity has an impact on both the gas distribution around the emerging protostar and the mass loading of magnetically driven outflows. Our new non-ideal MHD implementation opens up the possibility to study magneto-hydrodynamical systems on a moving mesh beyond the ideal MHD approximation.

Comparison of biomechanical function at ideal and varied surgical placement for two lumbar artificial disc implant designs: mobile-core versus fixed-core.

PubMed

Moumene, Missoum; Geisler, Fred H

2007-08-01

Finite element model. To estimate the effect of lumbar mobile-core and fixed-core artificial disc design and placement on the loading of the facet joints, and stresses on the polyethylene core. Although both mobile-core and fixed-core lumbar artificial disc designs have been used clinically, the effect of their design and the effect of placement within the disc space on the structural element loading, and in particular the facets and the implant itself, have not been investigated. A 3D nonlinear finite element model of an intact ligamentous L4-L5 motion segment was developed and validated in all 6 df based on previous experiments conducted on human cadavers. Facet loading of a mobile-core TDR and a fixed-core TDR were estimated with 4 different prosthesis placements for 3 different ranges of motion. Placing the mobile-core TDR anywhere within the disc space reduced facet loading by more than 50%, while the fixed-core TDR increased facet loading by more than 10% when compared with the intact disc in axial rotation. For central (ideal) placement, the mobile- and fixed-core implants were subjected to compressive stresses on the order of 3 MPa and 24 MPa, respectively. The mobile-core stresses were not affected by implant placement, while the fixed-core stresses increased by up to 40%. A mobile-core artificial disc design is less sensitive to placement, and unloads the facet joints, compared with a fixed-core design. The decreased core stress may result in a reduced potential for wear in a mobile-core prosthesis compared with a fixed-core prosthesis, which may increase the functional longevity of the device.

Automated design of genomic Southern blot probes

PubMed Central

2010-01-01

Background Sothern blotting is a DNA analysis technique that has found widespread application in molecular biology. It has been used for gene discovery and mapping and has diagnostic and forensic applications, including mutation detection in patient samples and DNA fingerprinting in criminal investigations. Southern blotting has been employed as the definitive method for detecting transgene integration, and successful homologous recombination in gene targeting experiments. The technique employs a labeled DNA probe to detect a specific DNA sequence in a complex DNA sample that has been separated by restriction-digest and gel electrophoresis. Critically for the technique to succeed the probe must be unique to the target locus so as not to cross-hybridize to other endogenous DNA within the sample. Investigators routinely employ a manual approach to probe design. A genome browser is used to extract DNA sequence from the locus of interest, which is searched against the target genome using a BLAST-like tool. Ideally a single perfect match is obtained to the target, with little cross-reactivity caused by homologous DNA sequence present in the genome and/or repetitive and low-complexity elements in the candidate probe. This is a labor intensive process often requiring several attempts to find a suitable probe for laboratory testing. Results We have written an informatic pipeline to automatically design genomic Sothern blot probes that specifically attempts to optimize the resultant probe, employing a brute-force strategy of generating many candidate probes of acceptable length in the user-specified design window, searching all against the target genome, then scoring and ranking the candidates by uniqueness and repetitive DNA element content. Using these in silico measures we can automatically design probes that we predict to perform as well, or better, than our previous manual designs, while considerably reducing design time. We went on to experimentally validate a number

The IDEAL study : towards personalized drug treatment of hypertension.

PubMed

Bejan-Angoulvant, Theodora; Baguet, Jean-Philippe; Erpeldinger, Sylvie; Boivin, Jean-Marc; Mercier, Alain; Leftheriotis, Georges; Gagnol, Jean-Pierre; Fauvel, Jean-Pierre; Giraud, Céline; Bricca, Giampiero; Gueyffier, François

2012-01-01

To identify markers (phenotypic, genetic, or environmental) of blood pressure (BP) response profiles to angiotensin converting enzyme inhibitors (ACEIs) and diuretics. IDEAL was a crossover (two active and two wash out phases), double-blind, placebo-controlled trial. Eligible patients were untreated hypertensive, aged 25 to 70. After two visits, patients were randomized to one of four sequences. The main outcome was BP differences between the active treatment and placebo. One hundred and twenty-four patients were randomised: mean age 53, men 65%, family history of hypertension 60%. Average BP fall at each visit before randomisation was about 2% of the initial level reflecting both a regression to the mean and a placebo effect. The results are expected to improve knowledge in drug's mechanisms of action and pathophysiology of hypertension, and to help in personalizing treatment. The estimation of BP responses to each drug in standardized conditions provided a benefit to each participant. © 2012 Société Française de Pharmacologie et de Thérapeutique.

The effects of female "Thin Ideal" media on men's appearance schema, cognitive performance, and self-evaluations: A self-determination theory approach.

PubMed

Baker, Amanda; Blanchard, Céline

2017-09-01

Research has primarily focused on the consequences of the female thin ideal on women and has largely ignored the effects on men. Two studies were designed to investigate the effects of a female thin ideal video on cognitive (Study 1: appearance schema, Study 2: visual-spatial processing) and self-evaluative measures in male viewers. Results revealed that the female thin ideal predicted men's increased appearance schema activation and poorer cognitive performance on a visual-spatial task. Constructs from self-determination theory (i.e., global autonomous and controlled motivation) were included to help explain for whom the video effects might be strongest or weakest. Findings demonstrated that a global autonomous motivation orientation played a protective role against the effects of the female thin ideal. Given that autonomous motivation was a significant moderator, SDT is an area worth exploring further to determine whether motivational strategies can benefit men who are susceptible to media body ideals. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sharp Truncation of an Electric Field: An Idealized Model that Warrants Caution

NASA Astrophysics Data System (ADS)

Tu, Hong; Zhu, Jiongming

2016-03-01

In physics, idealized models are often used to simplify complex situations. The motivation of the idealization is to make the real complex system tractable by adopting certain simplifications. In this treatment some unnecessary, negligible aspects are stripped away (so-called Aristotelian idealization), or some deliberate distortions are involved (so-called Galilean idealization). The most important principle in using an idealized model is to make sure that all the neglected aspects do not affect our analysis or result. Point charges, rigid bodies, simple pendulums, frictionless planes, and isolated systems are all frequently used idealized models. However, when they are applied to certain uncommon models, extra precautions should be taken. The possibilities and necessities of adopting the idealizations have to be considered carefully. Sometimes some factors neglected or ignored in the idealization could completely change the result, even make the treatment unphysical and conclusions unscientific.

Sequence invariant state machines

NASA Technical Reports Server (NTRS)

Whitaker, S.; Manjunath, S.

1990-01-01

A synthesis method and new VLSI architecture are introduced to realize sequential circuits that have the ability to implement any state machine having N states and m inputs, regardless of the actual sequence specified in the flow table. A design method is proposed that utilizes BTS logic to implement regular and dense circuits. A given state sequence can be programmed with power supply connections or dynamically reallocated if stored in a register. Arbitrary flow table sequences can be modified or programmed to dynamically alter the function of the machine. This allows VLSI controllers to be designed with the programmability of a general purpose processor but with the compact size and performance of dedicated logic.

Sequence-invariant state machines

NASA Technical Reports Server (NTRS)

Whitaker, Sterling R.; Manjunath, Shamanna K.; Maki, Gary K.

1991-01-01

A synthesis method and an MOS VLSI architecture are presented to realize sequential circuits that have the ability to implement any state machine having N states and m inputs, regardless of the actual sequence specified in the flow table. The design method utilizes binary tree structured (BTS) logic to implement regular and dense circuits. The desired state sequence can be hardwired with power supply connections or can be dynamically reallocated if stored in a register. This allows programmable VLSI controllers to be designed with a compact size and performance approaching that of dedicated logic. Results of ICV implementations are reported and an example sequence-invariant state machine is contrasted with implementations based on traditional methods.

Ideal thermodynamic processes of oscillatory-flow regenerative engines will go to ideal stirling cycle?

NASA Astrophysics Data System (ADS)

Luo, Ercang

2012-06-01

This paper analyzes the thermodynamic cycle of oscillating-flow regenerative machines. Unlike the classical analysis of thermodynamic textbooks, the assumptions for pistons' movement limitations are not needed and only ideal flowing and heat transfer should be maintained in our present analysis. Under such simple assumptions, the meso-scale thermodynamic cycles of each gas parcel in typical locations of a regenerator are analyzed. It is observed that the gas parcels in the regenerator undergo Lorentz cycle in different temperature levels, whereas the locus of all gas parcels inside the regenerator is the Ericson-like thermodynamic cycle. Based on this new finding, the author argued that ideal oscillating-flow machines without heat transfer and flowing losses is not the Stirling cycle. However, this new thermodynamic cycle can still achieve the same efficiency of the Carnot heat engine and can be considered a new reversible thermodynamic cycle under two constant-temperature heat sinks.

Moral Identity as Moral Ideal Self: Links to Adolescent Outcomes

ERIC Educational Resources Information Center

Hardy, Sam A.; Walker, Lawrence J.; Olsen, Joseph A.; Woodbury, Ryan D.; Hickman, Jacob R.

2014-01-01

The purposes of this study were to conceptualize moral identity as moral ideal self, to develop a measure of this construct, to test for age and gender differences, to examine links between moral ideal self and adolescent outcomes, and to assess purpose and social responsibility as mediators of the relations between moral ideal self and outcomes.…

A Competence-Based Approach to the Design of a Teaching Sequence about Oral and Dental Health and Hygiene: A Case Study

ERIC Educational Resources Information Center

Blanco-López, Ángel; Franco-Mariscal, Antonio Joaquín; España-Ramos, Enrique

2016-01-01

We present a case study to illustrate the design and implementation of a teaching sequence about oral and dental health and hygiene. This teaching sequence was aimed at year 10 students (age 15-16) and sought to develop their scientific competences. In line with the PISA assessment framework for science and the tenets of a context-based approach…

User-centered design of multi-gene sequencing panel reports for clinicians.

PubMed

Cutting, Elizabeth; Banchero, Meghan; Beitelshees, Amber L; Cimino, James J; Fiol, Guilherme Del; Gurses, Ayse P; Hoffman, Mark A; Jeng, Linda Jo Bone; Kawamoto, Kensaku; Kelemen, Mark; Pincus, Harold Alan; Shuldiner, Alan R; Williams, Marc S; Pollin, Toni I; Overby, Casey Lynnette

2016-10-01

The objective of this study was to develop a high-fidelity prototype for delivering multi-gene sequencing panel (GS) reports to clinicians that simulates the user experience of a final application. The delivery and use of GS reports can occur within complex and high-paced healthcare environments. We employ a user-centered software design approach in a focus group setting in order to facilitate gathering rich contextual information from a diverse group of stakeholders potentially impacted by the delivery of GS reports relevant to two precision medicine programs at the University of Maryland Medical Center. Responses from focus group sessions were transcribed, coded and analyzed by two team members. Notification mechanisms and information resources preferred by participants from our first phase of focus groups were incorporated into scenarios and the design of a software prototype for delivering GS reports. The goal of our second phase of focus group, to gain input on the prototype software design, was accomplished through conducting task walkthroughs with GS reporting scenarios. Preferences for notification, content and consultation from genetics specialists appeared to depend upon familiarity with scenarios for ordering and delivering GS reports. Despite familiarity with some aspects of the scenarios we proposed, many of our participants agreed that they would likely seek consultation from a genetics specialist after viewing the test reports. In addition, participants offered design and content recommendations. Findings illustrated a need to support customized notification approaches, user-specific information, and access to genetics specialists with GS reports. These design principles can be incorporated into software applications that deliver GS reports. Our user-centered approach to conduct this assessment and the specific input we received from clinicians may also be relevant to others working on similar projects. Copyright © 2016 Elsevier Inc. All rights

Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture[W

PubMed Central

Lu, Zefu; Yu, Hong; Xiong, Guosheng; Wang, Jing; Jiao, Yongqing; Liu, Guifu; Jing, Yanhui; Meng, Xiangbing; Hu, Xingming; Qian, Qian; Fu, Xiangdong; Wang, Yonghong; Li, Jiayang

2013-01-01

IDEAL PLANT ARCHITECTURE1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The SQUAMOSA PROMOTER BINDING PROTEIN-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen PROMOTER BINDING FACTOR1 or PROMOTER BINDING FACTOR2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice TEOSINTE BRANCHED1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate DENSE AND ERECT PANICLE1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture. PMID:24170127

AK Sco: a tidally induced atmospheric dynamo in a pre-main sequence binary?

NASA Astrophysics Data System (ADS)

Gómez de Castro, A. I.

2009-02-01

AK Sco is a unique source: a 10-30 Myrs old pre-main sequence spectroscopic binary composed by two nearly equal F5 stars that at periastron are separated by barely eleven stellar radii so, the stellar magnetospheres fill the Roche lobe at periastron. The orbit is not yet circularized (e = 0.47) and very strong tides are expected. This makes of AK Sco, the ideal laboratory to study the effect of gravitational tides in the stellar magnetic field building up during pre-main sequence evolution. Evidence of this effect is reported in this contribution.

Sequence-specific bias correction for RNA-seq data using recurrent neural networks.

PubMed

Zhang, Yao-Zhong; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru

2017-01-25

The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning to bare on a host of bioinformatical problems. Deep learning is ideally suited for biological problems that require automatic or hierarchical feature representation for biological data when prior knowledge is limited. In this work, we address the sequence-specific bias correction problem for RNA-seq data redusing Recurrent Neural Networks (RNNs) to model nucleotide sequences without pre-determining sequence structures. The sequence-specific bias of a read is then calculated based on the sequence probabilities estimated by RNNs, and used in the estimation of gene abundance. We explore the application of two popular RNN recurrent units for this task and demonstrate that RNN-based approaches provide a flexible way to model nucleotide sequences without knowledge of predetermined sequence structures. Our experiments show that training a RNN-based nucleotide sequence model is efficient and RNN-based bias correction methods compare well with the-state-of-the-art sequence-specific bias correction method on the commonly used MAQC-III data set. RNNs provides an alternative and flexible way to calculate sequence-specific bias without explicitly pre-determining sequence structures.

Jung's Red Book and its relation to aspects of German idealism.

PubMed

Bishop, Paul

2012-06-01

The late nineteenth century saw a renaissance of interest in the thought of the German Romantic philosopher, F.W.J. Schelling. This paper takes Jung's engagement with Schelling and his awareness of Schellingian ideas and interests (notably, the mysterious Kabeiroi worshipped at Samothrace) as its starting-point. It goes on to argue that a key set of problematics in German Idealism - the relation between freedom and necessity, between science and art, and ultimately between realism and idealism - offers a useful conceptual framework within which to approach Jung's Red Book. For the problem of the ideal is central to this work, which can be read as a journey from eternal ideals to the ideal of eternity. (Although the term 'idealism' has at least four distinct meanings, their distinct senses can be related in different ways to Jung's thinking.) The eloquent embrace of idealism by F.T. Vischer in a novel, Auch Einer, for which Jung had the highest praise, reminds us of the persistence of this tradition, which is still contested and debated in the present day. © 2012, The Society of Analytical Psychology.

A Generalized Deduction of the Ideal-Solution Model

ERIC Educational Resources Information Center

Leo, Teresa J.; Perez-del-Notario, Pedro; Raso, Miguel A.

2006-01-01

A new general procedure for deriving the Gibbs energy of mixing is developed through general thermodynamic considerations, and the ideal-solution model is obtained as a special particular case of the general one. The deduction of the Gibbs energy of mixing for the ideal-solution model is a rational one and viewed suitable for advanced students who…

Experimental characterization of powered Fontan hemodynamics in an idealized total cavopulmonary connection model

NASA Astrophysics Data System (ADS)

Kerlo, Anna-Elodie M.; Delorme, Yann T.; Xu, Duo; Frankel, Steven H.; Giridharan, Guruprasad A.; Rodefeld, Mark D.; Chen, Jun

2013-08-01

A viscous impeller pump (VIP) based on the Von Karman viscous pump is specifically designed to provide cavopulmonary assist in a univentricular Fontan circulation. The technology will make it possible to biventricularize the univentricular Fontan circulation. Ideally, it will reduce the number of surgeries required for Fontan conversion from three to one early in life, while simultaneously improving physiological conditions. Later in life, it will provide a currently unavailable means of chronic support for adolescent and adult patients with failing Fontan circulations. Computational fluid dynamics simulations demonstrate that the VIP can satisfactorily augment cavopulmonary blood flow in an idealized total cavopulmonary connection (TCPC). When the VIP is deployed at the TCPC intersection as a static device, it stabilizes the four-way flow pattern and is not obstructive to the flow. Experimental studies are carried out to assess performance, hemodynamic characteristics, and flow structures of the VIP in an idealized TCPC model. Stereoscopic particle image velocimetry is applied using index-matched blood analog. Results show excellent performance of the VIP without cavitation and with reduction of the energy losses. The non-rotating VIP smoothes and accelerates flow, and decreases stresses and turbulence in the TCPC. The rotating VIP generates the desired low-pressure Fontan flow augmentation (0-10 mmHg) while maintaining acceptable stress thresholds.

Media-portrayed idealized images, self-objectification, and eating behavior.

PubMed

Monro, Fiona J; Huon, Gail F

2006-11-01

This study examined the effects of media-portrayed idealized images on young women's eating behavior. The study compared the effects for high and low self-objectifiers. 72 female university students participated in this experiment. Six magazine advertisements featuring idealized female models were used as the experimental stimuli, and the same six advertisements with the idealized body digitally removed became the control stimuli. Eating behavior was examined using a classic taste test that involved both sweet and savory food. Participants' restraint status was assessed. We found that total food intake after exposure was the same in the body present and absent conditions. There were also no differences between high and low self-objectifiers' total food intake. However, for the total amount of food consumed and for sweet food there were significant group by condition interaction effects. High self-objectifiers ate more food in the body present than the body absent condition. In contrast, low self-objectifiers ate more food in the body absent than in the body present condition. Restraint status was not found to moderate the relationship between exposure to idealized images the amount of food consumed. Our results indicate that exposure to media-portrayed idealized images can lead to changes in eating behavior and highlight the complexity of the association between idealized image exposure and eating behavior. These results are discussed in terms of their implications for the prevention of dieting-related disorders.

Sequence Diversity Diagram for comparative analysis of multiple sequence alignments.

PubMed

Sakai, Ryo; Aerts, Jan

2014-01-01

The sequence logo is a graphical representation of a set of aligned sequences, commonly used to depict conservation of amino acid or nucleotide sequences. Although it effectively communicates the amount of information present at every position, this visual representation falls short when the domain task is to compare between two or more sets of aligned sequences. We present a new visual presentation called a Sequence Diversity Diagram and validate our design choices with a case study. Our software was developed using the open-source program called Processing. It loads multiple sequence alignment FASTA files and a configuration file, which can be modified as needed to change the visualization. The redesigned figure improves on the visual comparison of two or more sets, and it additionally encodes information on sequential position conservation. In our case study of the adenylate kinase lid domain, the Sequence Diversity Diagram reveals unexpected patterns and new insights, for example the identification of subgroups within the protein subfamily. Our future work will integrate this visual encoding into interactive visualization tools to support higher level data exploration tasks.

Relationship Between Ideal Cardiovascular Health and Disability in Older Adults: The Chilean National Health Survey (2009-10).

PubMed

García-Hermoso, Antonio; Ramírez-Vélez, Robinson; Ramirez-Campillo, Rodrigo; Izquierdo, Mikel

2017-12-01

This study aimed to examine the relationship between disability and the American Heart Association metric of ideal cardiovascular health (CVH) in older adults from the 2009-10 Chilean National Health Survey. Data from 460 older adults were analyzed. All subjects were interviewed using the standardized World Health Survey, which includes 16 health-related questions and assesses the domains of mobility, self-care, pain and discomfort, cognition, interpersonal activities, vision, sleep and energy, and affect. A person who responds with a difficulty rating of severe, extreme, or unable to do in at least one of these eight functioning domains is considered to have a disability. Ideal CVH was defined as meeting the ideal levels of four behaviors (smoking, body mass index, physical activity, diet adherence) and three factors (total cholesterol, fasting glucose, blood pressure). Logistic regression analysis suggested that ideal physical activity reduces the odds of disability (odds ratio (OR) = 0.55, 95% confidence interval (CI) = 0.36-0.85). Moreover, participants with intermediate (3-4 metrics) (OR = 0.63, 95% CI = 0.41-0.97) and ideal (5-7 metrics) (OR = 0.51, 95% CI = 0.24-0.97) CVH profiles had lower odds of disability independent of history of vascular events and arthritis disease than those with a poor profile (0-2 metrics). In conclusion, despite the cross-sectional design, this study suggests the importance of promoting ideal CVH because of their relationship with disability. © 2017, Copyright the Authors Journal compilation © 2017, The American Geriatrics Society.

Two‐phase designs for joint quantitative‐trait‐dependent and genotype‐dependent sampling in post‐GWAS regional sequencing

PubMed Central

Espin‐Garcia, Osvaldo; Craiu, Radu V.

2017-01-01

ABSTRACT We evaluate two‐phase designs to follow‐up findings from genome‐wide association study (GWAS) when the cost of regional sequencing in the entire cohort is prohibitive. We develop novel expectation‐maximization‐based inference under a semiparametric maximum likelihood formulation tailored for post‐GWAS inference. A GWAS‐SNP (where SNP is single nucleotide polymorphism) serves as a surrogate covariate in inferring association between a sequence variant and a normally distributed quantitative trait (QT). We assess test validity and quantify efficiency and power of joint QT‐SNP‐dependent sampling and analysis under alternative sample allocations by simulations. Joint allocation balanced on SNP genotype and extreme‐QT strata yields significant power improvements compared to marginal QT‐ or SNP‐based allocations. We illustrate the proposed method and evaluate the sensitivity of sample allocation to sampling variation using data from a sequencing study of systolic blood pressure. PMID:29239496

Ideal Cardiovascular Health and Arterial Stiffness in Spanish Adults-The EVIDENT Study.

PubMed

García-Hermoso, Antonio; Martínez-Vizcaíno, Vicente; Gomez-Marcos, Manuel Ángel; Cavero-Redondo, Iván; Recio-Rodriguez, José Ignacio; García-Ortiz, Luis

2018-05-01

Studies concerning ideal cardiovascular (CV) health and its relationship with arterial stiffness are lacking. This study examined the association between arterial stiffness with ideal CV health as defined by the American Heart Association, across age groups and gender. The cross-sectional study included 1365 adults. Ideal CV health was defined as meeting ideal levels of the following components: 4 behaviors (smoking, body mass index, physical activity, and Mediterranean diet adherence) and 3 factors (total cholesterol, blood pressure, and glycated hemoglobin). Patients were grouped into 3 categories according to their number of ideal CV health metrics: ideal (5-7 metrics), intermediate (3-4 metrics), and poor (0-2 metrics). We analyzed the pulse wave velocity (PWV), the central and radial augmentation indexes, and the ambulatory arterial stiffness index (AASI). The ideal CV health profile was inversely associated with lower arterial radial augmentation index and AASI in both genders, particularly in middle-aged (45-65 years) and in elderly subjects (>65 years). Also in elderly subjects, adjusted models showed that adults with at least 3 health metrics at ideal levels had significantly lower PWV than those with 2 or fewer ideal health metrics. An association was found between a favorable level of ideal CV health metrics and lower arterial stiffness across age groups. Copyright © 2018 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Ideal-Magnetohydrodynamic-Stable Tilting in Field-Reversed Configurations

NASA Astrophysics Data System (ADS)

Kanno, Ryutaro; Ishida, Akio; Steinhauer, Loren

1995-02-01

The tilting mode in field-reversed configurations (FRC) is examined using ideal-magnetohydrodynamic stability theory. Tilting, a global mode, is the greatest threat for disruption of FRC confinement. Previous studies uniformly found tilting to be unstable in ideal theory: the objective here is to ascertain if stable equilibria were overlooked in past work. Solving the variational problem with the Rayleigh-Ritz technique, tilting-stable equilibria are found for sufficiently hollow current profile and sufficient racetrackness of the separatrix shape. Although these equilibria were not examined previously, the present conclusion is quite surprising. Consequently checks of the method are offered. Even so it cannot yet be claimed with complete certainty that stability has been proved: absolute confirmation of ideal-stable tilting awaits the application of more complete methods.

The equivalence of a human observer and an ideal observer in binary diagnostic tasks

NASA Astrophysics Data System (ADS)

He, Xin; Samuelson, Frank; Gallas, Brandon D.; Sahiner, Berkman; Myers, Kyle

2013-03-01

The Ideal Observer (IO) is "ideal" for given data populations. In the image perception process, as the raw images are degraded by factors such as display and eye optics, there is an equivalent IO (EIO). The EIO uses the statistical information that exits the perception/cognitive degradations as the data. We assume a human observer who received sufficient training, e.g., radiologists, and hypothesize that such a human observer can be modeled as if he is an EIO. To measure the likelihood ratio (LR) distributions of an EIO, we formalize experimental design principles that encourage rationality based on von Neumann and Morgenstern's (vNM) axioms. We present examples to show that many observer study design refinements, although motivated by empirical principles explicitly, implicitly encourage rationality. Our hypothesis is supported by a recent review paper on ROC curve convexity by Pesce, Metz, and Berbaum. We also provide additional evidence based on a collection of observer studies in medical imaging. EIO theory shows that the "sub-optimal" performance of a human observer can be mathematically formalized in the form of an IO, and measured through rationality encouragement.

The genome sequence of the colonial chordate, Botryllus schlosseri

PubMed Central

Voskoboynik, Ayelet; Neff, Norma F; Sahoo, Debashis; Newman, Aaron M; Pushkarev, Dmitry; Koh, Winston; Passarelli, Benedetto; Fan, H Christina; Mantalas, Gary L; Palmeri, Karla J; Ishizuka, Katherine J; Gissi, Carmela; Griggio, Francesca; Ben-Shlomo, Rachel; Corey, Daniel M; Penland, Lolita; White, Richard A; Weissman, Irving L; Quake, Stephen R

2013-01-01

Botryllus schlosseri is a colonial urochordate that follows the chordate plan of development following sexual reproduction, but invokes a stem cell-mediated budding program during subsequent rounds of asexual reproduction. As urochordates are considered to be the closest living invertebrate relatives of vertebrates, they are ideal subjects for whole genome sequence analyses. Using a novel method for high-throughput sequencing of eukaryotic genomes, we sequenced and assembled 580 Mbp of the B. schlosseri genome. The genome assembly is comprised of nearly 14,000 intron-containing predicted genes, and 13,500 intron-less predicted genes, 40% of which could be confidently parceled into 13 (of 16 haploid) chromosomes. A comparison of homologous genes between B. schlosseri and other diverse taxonomic groups revealed genomic events underlying the evolution of vertebrates and lymphoid-mediated immunity. The B. schlosseri genome is a community resource for studying alternative modes of reproduction, natural transplantation reactions, and stem cell-mediated regeneration. DOI: http://dx.doi.org/10.7554/eLife.00569.001 PMID:23840927

Primitive ideals of C q [ SL(3)

NASA Astrophysics Data System (ADS)

Hodges, Timothy J.; Levasseur, Thierry

1993-10-01

The primitive ideals of the Hopf algebra C q [ SL(3)] are classified. In particular it is shown that the orbits in Prim C q [ SL(3)] under the action of the representation group H ≅ C *× C * are parameterized naturally by W×W, where W is the associated Weyl group. It is shown that there is a natural one-to-one correspondence between primitive ideals of C q [ SL(3)] and symplectic leaves of the associated Poisson algebraic group SL(3, C).

Temperature and the Ideal Gas

ERIC Educational Resources Information Center

Daisley, R. E.

1973-01-01

Presents some organized ideas in thermodynamics which are suitable for use with high school (GCE A level or ONC) students. Emphases are placed upon macroscopic observations and intimate connection of the modern definition of temperature with the concept of ideal gas. (CC)

Evaluation Designs for Practitioners. TM Report No. 35.

ERIC Educational Resources Information Center

Eash, Maurice J.; And Others

Practitioners are not afforded the luxury of ideal laboratory conditions. The natural settings of the classroom, the school, or the school system place constraints on the type of data obtainable; hence, educators must work with less than an ideal experimental design. Four evaluation designs used in natural settings are described. Each involves an…

Ideal photon number amplifier and duplicator

NASA Technical Reports Server (NTRS)

Dariano, G. M.

1992-01-01

The photon number-amplification and number-duplication mechanism are analyzed in the ideal case. The search for unitary evolutions leads to consider also a number-deamplification mechanism, the symmetry between amplification and deamplification being broken by the integer-value nature of the number operator. Both transformations, amplification and duplication, need an auxiliary field which, in the case of amplification, turns out to be amplified in the inverse way. Input-output energy conservation is accounted for using a classical pump or through frequency-conversion of the fields. Ignoring one of the fields is equivalent to considering the amplifier as an open system involving entropy production. The Hamiltonians of the ideal devices are given and compared with those of realistic systems.

Elastin: a representative ideal protein elastomer.

PubMed Central

Urry, D W; Hugel, T; Seitz, M; Gaub, H E; Sheiba, L; Dea, J; Xu, J; Parker, T

2002-01-01

During the last half century, identification of an ideal (predominantly entropic) protein elastomer was generally thought to require that the ideal protein elastomer be a random chain network. Here, we report two new sets of data and review previous data. The first set of new data utilizes atomic force microscopy to report single-chain force-extension curves for (GVGVP)(251) and (GVGIP)(260), and provides evidence for single-chain ideal elasticity. The second class of new data provides a direct contrast between low-frequency sound absorption (0.1-10 kHz) exhibited by random-chain network elastomers and by elastin protein-based polymers. Earlier composition, dielectric relaxation (1-1000 MHz), thermoelasticity, molecular mechanics and dynamics calculations and thermodynamic and statistical mechanical analyses are presented, that combine with the new data to contrast with random-chain network rubbers and to detail the presence of regular non-random structural elements of the elastin-based systems that lose entropic elastomeric force upon thermal denaturation. The data and analyses affirm an earlier contrary argument that components of elastin, the elastic protein of the mammalian elastic fibre, and purified elastin fibre itself contain dynamic, non-random, regularly repeating structures that exhibit dominantly entropic elasticity by means of a damping of internal chain dynamics on extension. PMID:11911774

Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design

PubMed Central

Ramsey, John S; Wilson, Alex CC; de Vos, Martin; Sun, Qi; Tamborindeguy, Cecilia; Winfield, Agnese; Malloch, Gaynor; Smith, Dawn M; Fenton, Brian; Gray, Stewart M; Jander, Georg

2007-01-01

Background The green peach aphid, Myzus persicae (Sulzer), is a world-wide insect pest capable of infesting more than 40 plant families, including many crop species. However, despite the significant damage inflicted by M. persicae in agricultural systems through direct feeding damage and by its ability to transmit plant viruses, limited genomic information is available for this species. Results Sequencing of 16 M. persicae cDNA libraries generated 26,669 expressed sequence tags (ESTs). Aphids for library construction were raised on Arabidopsis thaliana, Nicotiana benthamiana, Brassica oleracea, B. napus, and Physalis floridana (with and without Potato leafroll virus infection). The M. persicae cDNA libraries include ones made from sexual and asexual whole aphids, guts, heads, and salivary glands. In silico comparison of cDNA libraries identified aphid genes with tissue-specific expression patterns, and gene expression that is induced by feeding on Nicotiana benthamiana. Furthermore, 2423 genes that are novel to science and potentially aphid-specific were identified. Comparison of cDNA data from three aphid lineages identified single nucleotide polymorphisms that can be used as genetic markers and, in some cases, may represent functional differences in the protein products. In particular, non-conservative amino acid substitutions in a highly expressed gut protease may be of adaptive significance for M. persicae feeding on different host plants. The Agilent eArray platform was used to design an M. persicae oligonucleotide microarray representing over 10,000 unique genes. Conclusion New genomic resources have been developed for M. persicae, an agriculturally important insect pest. These include previously unknown sequence data, a collection of expressed genes, molecular markers, and a DNA microarray that can be used to study aphid gene expression. These resources will help elucidate the adaptations that allow M. persicae to develop compatible interactions with its

Deep sequencing methods for protein engineering and design.

PubMed

Wrenbeck, Emily E; Faber, Matthew S; Whitehead, Timothy A

2017-08-01

The advent of next-generation sequencing (NGS) has revolutionized protein science, and the development of complementary methods enabling NGS-driven protein engineering have followed. In general, these experiments address the functional consequences of thousands of protein variants in a massively parallel manner using genotype-phenotype linked high-throughput functional screens followed by DNA counting via deep sequencing. We highlight the use of information rich datasets to engineer protein molecular recognition. Examples include the creation of multiple dual-affinity Fabs targeting structurally dissimilar epitopes and engineering of a broad germline-targeted anti-HIV-1 immunogen. Additionally, we highlight the generation of enzyme fitness landscapes for conducting fundamental studies of protein behavior and evolution. We conclude with discussion of technological advances. Copyright © 2016 Elsevier Ltd. All rights reserved.

Two-phase designs for joint quantitative-trait-dependent and genotype-dependent sampling in post-GWAS regional sequencing.

PubMed

Espin-Garcia, Osvaldo; Craiu, Radu V; Bull, Shelley B

2018-02-01

We evaluate two-phase designs to follow-up findings from genome-wide association study (GWAS) when the cost of regional sequencing in the entire cohort is prohibitive. We develop novel expectation-maximization-based inference under a semiparametric maximum likelihood formulation tailored for post-GWAS inference. A GWAS-SNP (where SNP is single nucleotide polymorphism) serves as a surrogate covariate in inferring association between a sequence variant and a normally distributed quantitative trait (QT). We assess test validity and quantify efficiency and power of joint QT-SNP-dependent sampling and analysis under alternative sample allocations by simulations. Joint allocation balanced on SNP genotype and extreme-QT strata yields significant power improvements compared to marginal QT- or SNP-based allocations. We illustrate the proposed method and evaluate the sensitivity of sample allocation to sampling variation using data from a sequencing study of systolic blood pressure. © 2017 The Authors. Genetic Epidemiology Published by Wiley Periodicals, Inc.

Predictive Validity and Adjustment of Ideal Partner Preferences Across the Transition Into Romantic Relationships.

PubMed

Gerlach, Tanja M; Arslan, Ruben C; Schultze, Thomas; Reinhard, Selina K; Penke, Lars

2017-09-18

Although empirical research has investigated what we ideally seek in a romantic partner for decades, the crucial question of whether ideal partner preferences actually guide our mating decisions in real life has remained largely unanswered. One reason for this is the lack of designs that assess individuals' ideal partner preferences before entering a relationship and then follow up on them over an extended period. In the Göttingen Mate Choice Study (GMCS), a preregistered, large-scale online study, we used such a naturalistic prospective design. We investigated partner preferences across 4 preference domains in a large sample of predominantly heterosexual singles (N = 763, aged 18-40 years) and tracked these individuals across a period of 5 months upon a possible transition into romantic relationships. Attesting to their predictive validity, partner preferences prospectively predicted the characteristics of later partners. This was equally true for both sexes, except for vitality-attractiveness where men's preferences were more predictive of their later partners' standing on this dimension than women's. Self-perceived mate value did not moderate the preference-partner characteristics relations. Preferences proved to be relatively stable across the 5 months interval, yet were less stable for those who entered a relationship. Subgroup analyses using a newly developed indicator of preference adjustment toward (vs. away from) partner characteristics revealed that participants adjusted their preferences downward when partners fell short of initial preferences, but showed no consistent adjustment when partners exceeded them. Results and implications are discussed against the background of ongoing controversies in mate choice and romantic relationship research. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Topological photonic crystal with ideal Weyl points

NASA Astrophysics Data System (ADS)

Wang, Luyang; Jian, Shao-Kai; Yao, Hong

Weyl points in three-dimensional photonic crystals behave as monopoles of Berry flux in momentum space. Here, based on symmetry analysis, we show that a minimal number of symmetry-related Weyl points can be realized in time-reversal invariant photonic crystals. We propose to realize these ``ideal'' Weyl points in modified double-gyroid photonic crystals, which is confirmed by our first-principle photonic band-structure calculations. Photonic crystals with ideal Weyl points are qualitatively advantageous in applications such as angular and frequency selectivity, broadband invisibility cloaking, and broadband 3D-imaging.

Analytic solution of field distribution and demagnetization function of ideal hollow cylindrical field source

NASA Astrophysics Data System (ADS)

Xu, Xiaonong; Lu, Dingwei; Xu, Xibin; Yu, Yang; Gu, Min

2017-09-01

The Halbach type hollow cylindrical permanent magnet array (HCPMA) is a volume compact and energy conserved field source, which have attracted intense interests in many practical applications. Here, using the complex variable integration method based on the Biot-Savart Law (including current distributions inside the body and on the surfaces of magnet), we derive analytical field solutions to an ideal multipole HCPMA in entire space including the interior of magnet. The analytic field expression inside the array material is used to construct an analytic demagnetization function, with which we can explain the origin of demagnetization phenomena in HCPMA by taking into account an ideal magnetic hysteresis loop with finite coercivity. These analytical field expressions and demagnetization functions provide deeper insight into the nature of such permanent magnet array systems and offer guidance in designing optimized array system.

Determination of performance of non-ideal aluminized explosives.

PubMed

Keshavarz, Mohammad Hossein; Mofrad, Reza Teimuri; Poor, Karim Esmail; Shokrollahi, Arash; Zali, Abbas; Yousefi, Mohammad Hassan

2006-09-01

Non-ideal explosives can have Chapman-Jouguet (C-J) detonation pressure significantly different from those expected from existing thermodynamic computer codes, which usually allows finding the parameters of ideal detonation of individual high explosives with good accuracy. A simple method is introduced by which detonation pressure of non-ideal aluminized explosives with general formula C(a)H(b)N(c)O(d)Al(e) can be predicted only from a, b, c, d and e at any loading density without using any assumed detonation products and experimental data. Calculated detonation pressures show good agreement with experimental values with respect to computed results obtained by complicated computer code. It is shown here how loading density and atomic composition can be integrated into an empirical formula for predicting detonation pressure of proposed aluminized explosives.

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)

PubMed Central

Martin, Andrew C. R.

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

PubMed

Martin, Andrew C R

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

Prevalence of ideal cardiovascular health in European adolescents: The HELENA study.

PubMed

Henriksson, Pontus; Henriksson, Hanna; Gracia-Marco, Luis; Labayen, Idoia; Ortega, Francisco B; Huybrechts, Inge; España-Romero, Vanesa; Manios, Yannis; Widhalm, Kurt; Dallongeville, Jean; González-Gross, Marcela; Marcos, Ascensión; Moreno, Luis A; Castillo, Manuel J; Ruiz, Jonatan R

2017-08-01

The ideal cardiovascular health (iCVH) construct consists of 4 health behaviours and 3 health factors and is strongly related to later cardiovascular disease. However, the prevalence of iCVH in European adolescents is currently unknown. The Healthy Lifestyle in Europe by Nutrition in Adolescence (HELENA) study is a cross-sectional, multicentre study conducted in 9 European countries during 2006-2007 and included 3528 adolescents (1683 boys and 1845 girls) between 12.5 and 17.5years of age. Status (ideal vs. non-ideal) for the health behaviours (smoking status, body mass index, physical activity and diet) and health factors (total cholesterol, blood pressure and fasting glucose) were determined. Overall, the prevalence of ideal health behaviours was low; non-smoking (60.9% ideal), body mass index (76.8%), physical activity (62.1%), and diet (1.7%). The prevalence of ideal health factors was; total cholesterol (65.8%), blood pressure (62.0%) and plasma glucose (88.8%). The low prevalence of iCVH behaviours, especially diet and physical activity, identified in European adolescents is likely to influence later cardiovascular health which strongly motivates efforts to increase ideal health behaviours in this population. Copyright © 2017 Elsevier B.V. All rights reserved.

Ideal affect in daily life: implications for affective experience, health, and social behavior.

PubMed

Tsai, Jeanne L

2017-10-01

Over the last decade, researchers have increasingly demonstrated that ideal affect-the affective states that people value and ideally want to feel-shapes different aspects of daily life. Here I briefly review Affect Valuation Theory (AVT), which integrates ideal affect into existing models of affect and emotion by identifying the causes and consequences of variation in ideal affect. I then describe recent research that applies AVT to the valuation of negative states as well as more complex states, examines how ideal affect shapes momentary affective experience, suggests that ideal affect has both direct and indirect effects on health, and illustrates that people's ideal affect shapes how they judge and respond to others. Finally, I discuss the implications of cultural and individual differences in ideal affect for clinical, educational, work, and leisure settings. Copyright © 2017 Elsevier Ltd. All rights reserved.

Next-generation sequencing in clinical virology: Discovery of new viruses.

PubMed

Datta, Sibnarayan; Budhauliya, Raghvendra; Das, Bidisha; Chatterjee, Soumya; Vanlalhmuaka; Veer, Vijay

2015-08-12

Viruses are a cause of significant health problem worldwide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of next-generation sequencers (NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequence-independent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.

Optimum stacking sequence design of laminated composite circular plates with curvilinear fibres by a layer-wise optimization method

NASA Astrophysics Data System (ADS)

Guenanou, A.; Houmat, A.

2018-05-01

The optimum stacking sequence design for the maximum fundamental frequency of symmetrically laminated composite circular plates with curvilinear fibres is investigated for the first time using a layer-wise optimization method. The design variables are two fibre orientation angles per layer. The fibre paths are constructed using the method of shifted paths. The first-order shear deformation plate theory and a curved square p-element are used to calculate the objective function. The blending function method is used to model accurately the geometry of the circular plate. The equations of motion are derived using Lagrange's method. The numerical results are validated by means of a convergence test and comparison with published values for symmetrically laminated composite circular plates with rectilinear fibres. The material parameters, boundary conditions, number of layers and thickness are shown to influence the optimum solutions to different extents. The results should serve as a benchmark for optimum stacking sequences of symmetrically laminated composite circular plates with curvilinear fibres.

Spreadsheet macros for coloring sequence alignments.

PubMed

Haygood, M G

1993-12-01

This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

Sequence repeats and protein structure

NASA Astrophysics Data System (ADS)

Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

2012-11-01

Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications

PubMed Central

Hilson, Pierre; Allemeersch, Joke; Altmann, Thomas; Aubourg, Sébastien; Avon, Alexandra; Beynon, Jim; Bhalerao, Rishikesh P.; Bitton, Frédérique; Caboche, Michel; Cannoot, Bernard; Chardakov, Vasil; Cognet-Holliger, Cécile; Colot, Vincent; Crowe, Mark; Darimont, Caroline; Durinck, Steffen; Eickhoff, Holger; de Longevialle, Andéol Falcon; Farmer, Edward E.; Grant, Murray; Kuiper, Martin T.R.; Lehrach, Hans; Léon, Céline; Leyva, Antonio; Lundeberg, Joakim; Lurin, Claire; Moreau, Yves; Nietfeld, Wilfried; Paz-Ares, Javier; Reymond, Philippe; Rouzé, Pierre; Sandberg, Goran; Segura, Maria Dolores; Serizet, Carine; Tabrett, Alexandra; Taconnat, Ludivine; Thareau, Vincent; Van Hummelen, Paul; Vercruysse, Steven; Vuylsteke, Marnik; Weingartner, Magdalena; Weisbeek, Peter J.; Wirta, Valtteri; Wittink, Floyd R.A.; Zabeau, Marc; Small, Ian

2004-01-01

Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics. PMID:15489341

Simulation-Based Evaluation of Learning Sequences for Instructional Technologies

ERIC Educational Resources Information Center

McEneaney, John E.

2016-01-01

Instructional technologies critically depend on systematic design, and learning hierarchies are a commonly advocated tool for designing instructional sequences. But hierarchies routinely allow numerous sequences and choosing an optimal sequence remains an unsolved problem. This study explores a simulation-based approach to modeling learning…

Cardiorespiratory fitness and ideal cardiovascular health in European adolescents.

PubMed

Ruiz, Jonatan R; Huybrechts, Inge; Cuenca-García, Magdalena; Artero, Enrique G; Labayen, Idoia; Meirhaeghe, Aline; Vicente-Rodriguez, German; Polito, Angela; Manios, Yannis; González-Gross, Marcela; Marcos, Ascensión; Widhalm, Kurt; Molnar, Denes; Kafatos, Anthony; Sjöström, Michael; Moreno, Luis A; Castillo, Manuel J; Ortega, Francisco B

2015-05-15

We studied in European adolescents (i) the association between cardiorespiratory fitness and ideal cardiovascular health as defined by the American Heart Association and (ii) whether there is a cardiorespiratory fitness threshold associated with a more favourable cardiovascular health profile. Participants included 510 (n=259 girls) adolescents from 9 European countries. The 20 m shuttle run test was used to estimate cardiorespiratory fitness. Ideal cardiovascular health was defined as meeting ideal levels of the following components: four behaviours (smoking, body mass index, physical activity and diet) and three factors (total cholesterol, blood pressure and glucose). Higher levels of cardiorespiratory fitness were associated with a higher number of ideal cardiovascular health components in both boys and girls (both p for trend ≤0.001). Levels of cardiorespiratory fitness were significantly higher in adolescents meeting at least four ideal components (13% higher in boys, p<0.001; 6% higher in girls, p=0.008). Receiver operating characteristic curve analyses showed a significant discriminating accuracy of cardiorespiratory fitness in identifying the presence of at least four ideal cardiovascular health components (43.8 mL/kg/min in boys and 34.6 mL/kg/min in girls, both p<0.001). The results suggest a hypothetical cardiorespiratory fitness level associated with a healthier cardiovascular profile in adolescents. The fitness standards could be used in schools as part of surveillance and/or screening systems to identify youth with poor health behaviours who might benefit from intervention programmes. 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.

Non-ideal Solution Thermodynamics of Cytoplasm

PubMed Central

Ross-Rodriguez, Lisa U.; McGann, Locksley E.

2012-01-01

Quantitative description of the non-ideal solution thermodynamics of the cytoplasm of a living mammalian cell is critically necessary in mathematical modeling of cryobiology and desiccation and other fields where the passive osmotic response of a cell plays a role. In the solution thermodynamics osmotic virial equation, the quadratic correction to the linear ideal, dilute solution theory is described by the second osmotic virial coefficient. Herein we report, for the first time, intracellular solution second osmotic virial coefficients for four cell types [TF-1 hematopoietic stem cells, human umbilical vein endothelial cells (HUVEC), porcine hepatocytes, and porcine chondrocytes] and further report second osmotic virial coefficients indistinguishable from zero (for the concentration range studied) for human hepatocytes and mouse oocytes. PMID:23840923

Ideal Standards, Acceptance, and Relationship Satisfaction: Latitudes of Differential Effects

PubMed Central

Buyukcan-Tetik, Asuman; Campbell, Lorne; Finkenauer, Catrin; Karremans, Johan C.; Kappen, Gesa

2017-01-01

We examined whether the relations of consistency between ideal standards and perceptions of a current romantic partner with partner acceptance and relationship satisfaction level off, or decelerate, above a threshold. We tested our hypothesis using a 3-year longitudinal data set collected from heterosexual newlywed couples. We used two indicators of consistency: pattern correspondence (within-person correlation between ideal standards and perceived partner ratings) and mean-level match (difference between ideal standards score and perceived partner score). Our results revealed that pattern correspondence had no relation with partner acceptance, but a positive linear/exponential association with relationship satisfaction. Mean-level match had a significant positive association with actor’s acceptance and relationship satisfaction up to the point where perceived partner score equaled ideal standards score. Partner effects did not show a consistent pattern. The results suggest that the consistency between ideal standards and perceived partner attributes has a non-linear association with acceptance and relationship satisfaction, although the results were more conclusive for mean-level match. PMID:29033876

Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.

PubMed

Altmüller, Janine; Budde, Birgit S; Nürnberg, Peter

2014-02-01

Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

Sequence investigation of 34 forensic autosomal STRs with massively parallel sequencing.

PubMed

Zhang, Suhua; Niu, Yong; Bian, Yingnan; Dong, Rixia; Liu, Xiling; Bao, Yun; Jin, Chao; Zheng, Hancheng; Li, Chengtao

2018-05-01

STRs vary not only in the length of the repeat units and the number of repeats but also in the region with which they conform to an incremental repeat pattern. Massively parallel sequencing (MPS) offers new possibilities in the analysis of STRs since they can simultaneously sequence multiple targets in a single reaction and capture potential internal sequence variations. Here, we sequenced 34 STRs applied in the forensic community of China with a custom-designed panel. MPS performance were evaluated from sequencing reads analysis, concordance study and sensitivity testing. High coverage sequencing data were obtained to determine the constitute ratios and heterozygous balance. No actual inconsistent genotypes were observed between capillary electrophoresis (CE) and MPS, demonstrating the reliability of the panel and the MPS technology. With the sequencing data from the 200 investigated individuals, 346 and 418 alleles were obtained via CE and MPS technologies at the 34 STRs, indicating MPS technology provides higher discrimination than CE detection. The whole study demonstrated that STR genotyping with the custom panel and MPS technology has the potential not only to reveal length and sequence variations but also to satisfy the demands of high throughput and high multiplexing with acceptable sensitivity.

HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment1

PubMed Central

Johnson, Matthew G.; Gardner, Elliot M.; Liu, Yang; Medina, Rafael; Goffinet, Bernard; Shaw, A. Jonathan; Zerega, Nyree J. C.; Wickett, Norman J.

2016-01-01

Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper. PMID:27437175

Handgrip Strength and Ideal Cardiovascular Health among Colombian Children and Adolescents.

PubMed

Ramírez-Vélez, Robinson; Tordecilla-Sanders, Alejandra; Correa-Bautista, Jorge Enrique; Peterson, Mark D; Garcia-Hermoso, Antonio

2016-12-01

To evaluate the association between handgrip strength and ideal cardiovascular health (CVH) in Colombian children and adolescents. During the 2014-2015 school years, we examined a cross-sectional component of the FUPRECOL (Association for Muscular Strength with Early Manifestation of Cardiovascular Disease Risk Factors among Colombian Children and Adolescents) study. Participants included 1199 (n = 627 boys) youths from Bogota (Colombia). Handgrip strength was measured with a standard adjustable hand held dynamometer and expressed relative to body mass (handgrip/body mass) and as absolute values in kilograms. Ideal CVH, as defined by the American Heart Association, was determined as meeting ideal levels of the following components: 4 behaviors (smoking status, body mass index, cardiorespiratory fitness, and diet) and 3 factors (total cholesterol, blood pressure, and glucose). Higher levels of handgrip strength (both absolute and relative values) were associated with a higher frequency of ideal CVH metrics in both sexes (P for trend ≤ .001). Also, higher levels of handgrip strength were associated with a greater number of ideal health behaviors (P for trend < .001 in both boys and girls), and with a higher number of ideal health factors in boys (P for trend < .001). Finally, levels of handgrip strength were similar between ideal versus nonideal glucose or total cholesterol groups in girls. Handgrip strength was strongly associated with ideal CVH in Colombian children and adolescents, and thus supports the relevance of early targeted interventions to promote strength adaptation and preservation as part of primordial prevention. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantification of bone marrow fat content using iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL): reproducibility, site variation and correlation with age and menopause.

PubMed

Aoki, Takatoshi; Yamaguchi, Shinpei; Kinoshita, Shunsuke; Hayashida, Yoshiko; Korogi, Yukunori

2016-09-01

To determine the reproducibility of the quantitative chemical shift-based water-fat separation method with a multiecho gradient echo sequence [iteraterative decomposition of water and fat with echo asymmetry and least-squares estimation quantitation sequence (IDEAL-IQ)] for assessing bone marrow fat fraction (FF); to evaluate variation of FF at different bone sites; and to investigate its association with age and menopause. 31 consecutive females who underwent pelvic iterative decomposition of water and fat with echo asymmetry and least-squares estimation at 3-T MRI were included in this study. Quantitative FF using IDEAL-IQ of four bone sites were analyzed. The coefficients of variance (CV) on each site were evaluated repeatedly 10 times to assess the reproducibility. Correlations between FF and age were evaluated on each site, and the FFs between pre- and post-menopausal groups were compared. The CV in the quantification of marrow FF ranged from 0.69% to 1.70%. A statistically significant correlation was established between the FF and the age in lumbar vertebral body, ilium and intertrochanteric region of the femur (p < 0.001). The average FF of post-menopausal females was significantly higher than that of pre-menopausal females in these sites (p < 0.05). In the greater trochanter of the femur, there was no significant correlation between FF and age. In vivo IDEAL-IQ would provide reliable quantification of bone marrow fat. IDEAL-IQ is simple to perform in a short time and may be practical for providing information on bone quality in clinical settings.

The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

PubMed

Khoe, Clairine V; Chung, Long H; Murray, Vincent

2018-06-01

The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

Chemical Laws, Idealization and Approximation

NASA Astrophysics Data System (ADS)

Tobin, Emma

2013-07-01

This paper examines the notion of laws in chemistry. Vihalemm ( Found Chem 5(1):7-22, 2003) argues that the laws of chemistry are fundamentally the same as the laws of physics they are all ceteris paribus laws which are true "in ideal conditions". In contrast, Scerri (2000) contends that the laws of chemistry are fundamentally different to the laws of physics, because they involve approximations. Christie ( Stud Hist Philos Sci 25:613-629, 1994) and Christie and Christie ( Of minds and molecules. Oxford University Press, New York, pp. 34-50, 2000) agree that the laws of chemistry are operationally different to the laws of physics, but claim that the distinction between exact and approximate laws is too simplistic to taxonomise them. Approximations in chemistry involve diverse kinds of activity and often what counts as a scientific law in chemistry is dictated by the context of its use in scientific practice. This paper addresses the question of what makes chemical laws distinctive independently of the separate question as to how they are related to the laws of physics. From an analysis of some candidate ceteris paribus laws in chemistry, this paper argues that there are two distinct kinds of ceteris paribus laws in chemistry; idealized and approximate chemical laws. Thus, while Christie ( Stud Hist Philos Sci 25:613-629, 1994) and Christie and Christie ( Of minds and molecules. Oxford University Press, New York, pp. 34--50, 2000) are correct to point out that the candidate generalisations in chemistry are diverse and heterogeneous, a distinction between idealizations and approximations can nevertheless be used to successfully taxonomise them.

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability.

PubMed

Goldenzweig, Adi; Goldsmith, Moshe; Hill, Shannon E; Gertman, Or; Laurino, Paola; Ashani, Yacov; Dym, Orly; Unger, Tamar; Albeck, Shira; Prilusky, Jaime; Lieberman, Raquel L; Aharoni, Amir; Silman, Israel; Sussman, Joel L; Tawfik, Dan S; Fleishman, Sarel J

2016-07-21

Upon heterologous overexpression, many proteins misfold or aggregate, thus resulting in low functional yields. Human acetylcholinesterase (hAChE), an enzyme mediating synaptic transmission, is a typical case of a human protein that necessitates mammalian systems to obtain functional expression. We developed a computational strategy and designed an AChE variant bearing 51 mutations that improved core packing, surface polarity, and backbone rigidity. This variant expressed at ∼2,000-fold higher levels in E. coli compared to wild-type hAChE and exhibited 20°C higher thermostability with no change in enzymatic properties or in the active-site configuration as determined by crystallography. To demonstrate broad utility, we similarly designed four other human and bacterial proteins. Testing at most three designs per protein, we obtained enhanced stability and/or higher yields of soluble and active protein in E. coli. Our algorithm requires only a 3D structure and several dozen sequences of naturally occurring homologs, and is available at http://pross.weizmann.ac.il. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Charge-Trapping-Induced Non-Ideal Behaviors in Organic Field-Effect Transistors.

PubMed

Un, Hio-Ieng; Cheng, Peng; Lei, Ting; Yang, Chi-Yuan; Wang, Jie-Yu; Pei, Jian

2018-05-01

Organic field-effect transistors (OFETs) with impressively high hole mobilities over 10 cm 2 V -1 s -1 and electron mobilities over 1 cm 2 V -1 s -1 have been reported in the past few years. However, significant non-ideal electrical characteristics, e.g., voltage-dependent mobilities, have been widely observed in both small-molecule and polymer systems. This issue makes the accurate evaluation of the electrical performance impossible and also limits the practical applications of OFETs. Here, a semiconductor-unrelated, charge-trapping-induced non-ideality in OFETs is reported, and a revised model for the non-ideal transfer characteristics is provided. The trapping process can be directly observed using scanning Kelvin probe microscopy. It is found that such trapping-induced non-ideality exists in OFETs with different types of charge carriers (p-type or n-type), different types of dielectric materials (inorganic and organic) that contain different functional groups (OH, NH 2 , COOH, etc.). As fas as it is known, this is the first report for the non-ideal transport behaviors in OFETs caused by semiconductor-independent charge trapping. This work reveals the significant role of dielectric charge trapping in the non-ideal transistor characteristics and also provides guidelines for device engineering toward ideal OFETs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

PubMed Central

2012-01-01

Background Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. Results We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line ‘CUDH2150’ and the genetically distant Indian landrace ‘Nasik Red’, using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of ‘Nasik Red’ reads onto ‘CUDH2150’ assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F2 progeny from a very large F2 family developed from the ‘Nasik Red’ x ‘CUDH2150’ inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on

A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.).

PubMed

Baldwin, Samantha; Revanna, Roopashree; Thomson, Susan; Pither-Joyce, Meeghan; Wright, Kathryn; Crowhurst, Ross; Fiers, Mark; Chen, Leshi; Macknight, Richard; McCallum, John A

2012-11-19

Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line 'CUDH2150' and the genetically distant Indian landrace 'Nasik Red', using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of 'Nasik Red' reads onto 'CUDH2150' assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F(2) progeny from a very large F(2) family developed from the 'Nasik Red' x 'CUDH2150' inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis. The generic

Development and Validation of a Hypersonic Vehicle Design Tool Based On Waverider Design Technique

NASA Astrophysics Data System (ADS)

Dasque, Nastassja

Methodologies for a tool capable of assisting design initiatives for practical waverider based hypersonic vehicles were developed and validated. The design space for vehicle surfaces was formed using an algorithm that coupled directional derivatives with the conservation laws to determine a flow field defined by a set of post-shock streamlines. The design space is used to construct an ideal waverider with a sharp leading edge. A blunting method was developed to modify the ideal shapes to a more practical geometry for real-world application. Empirical and analytical relations were then systematically applied to the resulting geometries to determine local pressure, skin-friction and heat flux. For the ideal portion of the geometry, flat plate relations for compressible flow were applied. For the blunted portion of the geometry modified Newtonian theory, Fay-Riddell theory and Modified Reynolds analogy were applied. The design and analysis methods were validated using analytical solutions as well as empirical and numerical data. The streamline solution for the flow field generation technique was compared with a Taylor-Maccoll solution and showed very good agreement. The relationship between the local Stanton number and skin friction coefficient with local Reynolds number along the ideal portion of the body showed good agreement with experimental data. In addition, an automated grid generation routine was formulated to construct a structured mesh around resulting geometries in preparation for Computational Fluid Dynamics analysis. The overall analysis of the waverider body using the tool was then compared to CFD studies. The CFD flow field showed very good agreement with the design space. However, the distribution of the surface properties was near CFD results but did not have great agreement.

The place of the ideal observer in medical ethics.

PubMed

Churchill, L R

1983-01-01

The idea of an ideal observer is frequently employed in ethical reasoning and has recently been introduced into medical ethics. The contemporary use of this idea, however, is deeply flawed. It ignores important social and personal dimensions of ethics. By espousing a perspective of observation removed from history and community, the ideal observer notion encourages a pretense of objectivity and overlooks the distortions of distance. If taken seriously as a model for choice, the ideal observer is incoherent, as it dispenses with the concrete moral agent and the locus of choice. Adam Smith's 'impartial spectator' is examined as a more adequate statement of the need for appreciating diverse perspectives in ethical choices.

Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array

PubMed Central

Stranges, P. Benjamin; Palla, Mirkó; Kalachikov, Sergey; Nivala, Jeff; Dorwart, Michael; Trans, Andrew; Kumar, Shiv; Porel, Mintu; Chien, Minchen; Tao, Chuanjuan; Morozova, Irina; Li, Zengmin; Shi, Shundi; Aberra, Aman; Arnold, Cleoma; Yang, Alexander; Aguirre, Anne; Harada, Eric T.; Korenblum, Daniel; Pollard, James; Bhat, Ashwini; Gremyachinskiy, Dmitriy; Bibillo, Arek; Chen, Roger; Davis, Randy; Russo, James J.; Fuller, Carl W.; Roever, Stefan; Ju, Jingyue; Church, George M.

2016-01-01

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an α-hemolysin (αHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin–polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform. PMID:27729524

Quantifying ataxia: ideal trajectory analysis--a technical note

NASA Technical Reports Server (NTRS)

McPartland, M. D.; Krebs, D. E.; Wall, C. 3rd

2000-01-01

We describe a quantitative method to assess repeated stair stepping stability. In both the mediolateral (ML) and anterioposterior (AP) directions, the trajectory of the subject's center of mass (COM) was compared to an ideal sinusoid. The two identified sinusoids were unique in each direction but coupled. Two dimensionless numbers-the mediolateral instability index (IML) and AP instability index (IAP)-were calculated using the COM trajectory and ideal sinusoids for each subject with larger index values resulting from less stable performance. The COM trajectories of nine nonimpaired controls and six patients diagnosed with unilateral or bilateral vestibular labyrinth hypofunction were analyzed. The average IML and IAP values of labyrinth disorder patients were respectively 127% and 119% greater than those of controls (p<0.014 and 0.006, respectively), indicating that the ideal trajectory analysis distinguishes persons with labyrinth disorder from those without. The COM trajectories also identify movement inefficiencies attributable to vestibulopathy.

The mechanism and design of sequencing batch reactor systems for nutrient removal--the state of the art.

PubMed

Artan, N; Wilderer, P; Orhon, D; Morgenroth, E; Ozgür, N

2001-01-01

The Sequencing Batch Reactor (SBR) process for carbon and nutrient removal is subject to extensive research, and it is finding a wider application in full-scale installations. Despite the growing popularity, however, a widely accepted approach to process analysis and modeling, a unified design basis, and even a common terminology are still lacking; this situation is now regarded as the major obstacle hindering broader practical application of the SBR. In this paper a rational dimensioning approach is proposed for nutrient removal SBRs based on scientific information on process stoichiometry and modelling, also emphasizing practical constraints in design and operation.

A Unified Theory of Non-Ideal Gas Lattice Boltzmann Models

NASA Technical Reports Server (NTRS)

Luo, Li-Shi

1998-01-01

A non-ideal gas lattice Boltzmann model is directly derived, in an a priori fashion, from the Enskog equation for dense gases. The model is rigorously obtained by a systematic procedure to discretize the Enskog equation (in the presence of an external force) in both phase space and time. The lattice Boltzmann model derived here is thermodynamically consistent and is free of the defects which exist in previous lattice Boltzmann models for non-ideal gases. The existing lattice Boltzmann models for non-ideal gases are analyzed and compared with the model derived here.

Chemical Laws, Idealization and Approximation

ERIC Educational Resources Information Center

Tobin, Emma

2013-01-01

This paper examines the notion of laws in chemistry. Vihalemm ("Found Chem" 5(1):7-22, 2003) argues that the laws of chemistry are fundamentally the same as the laws of physics they are all "ceteris paribus" laws which are true "in ideal conditions". In contrast, Scerri (2000) contends that the laws of chemistry are…

Perception of a Communication Source: An Examination of the Ideal Supervisor and Subordinate within a Military Organization.

ERIC Educational Resources Information Center

Hellweg, Susan A.

A study was designed to examine an underlying assumption regarding the use of the semantic differential in measuring the credibility and homophily of a communicator, namely, that responses to an ideal source position themselves at one extreme end of the scale, reflecting the monotonic function of the instrument such that the highest response…

Delivering ideal employee experiences.

PubMed

Weiss, Marjorie D; Tyink, Steve; Kubiak, Curt

2009-05-01

Employee-centric strategies have moved from employee satisfaction and brand awareness to employee "affinity" or "attachment." In today's marketplace, occupational health nurses understand that differentiation (i.e., the perception of uniqueness) is the direct result of superior employee interactions, which lead to better employee care, enduring employee relationships, loyal employees, and satisfied employers. What drives employees to occupational health nurse attachment? The answer is a passion for rising above the competition to create ideal employee experiences.

Robotic kidney transplantation with regional hypothermia: evolution of a novel procedure utilizing the IDEAL guidelines (IDEAL phase 0 and 1).

PubMed

Menon, Mani; Abaza, Ronney; Sood, Akshay; Ahlawat, Rajesh; Ghani, Khurshid R; Jeong, Wooju; Kher, Vijay; Kumar, Ramesh K; Bhandari, Mahendra

2014-05-01

Surgical innovation is essential for progress of surgical science, but its implementation comes with potential harms during the learning phase. The Balliol Collaboration has recommended a set of guidelines (Innovation, Development, Exploration, Assessment, Long-term study [IDEAL]) that permit innovation while minimizing complications. To utilize the IDEAL model of surgical innovation in the development of a novel surgical technique, robotic kidney transplantation (RKT) with regional hypothermia, and describe the process of discovery and development. Phase 0 (simulation) studies included the establishment of techniques for pelvic cooling, graft placement in a robotic prostatectomy model, and simulation of the RKT procedure in a cadaveric model. Phase 1 (innovation) studies began in January 2013 and involved treatment of a highly selective small group of patients (n=7), using the principles utilized in the phase 0 studies, at a tertiary referral center. IDEAL model implementation in the development of RKT with regional hypothermia. For phase 0 studies, the outcomes evaluated included pelvic and body temperature measurements, and technical feasibility assessment. The primary outcome during phase 1 was post-transplant graft function. Other outcomes measured were operative and ischemic times, perioperative complications, and intracorporeal graft surface temperature. Phase 0 (simulation phase): Pelvic cooling to 15-20(o)C was achieved reproducibly. Using the surgical approach developed for robotic radical prostatectomy, vascular and ureterovesical anastomoses could be done without redocking the robot. Phase 1 (innovation phase): All patients underwent live-donor RKT in the lithotomy position. All grafts functioned immediately. Mean console, anastomotic, and warm ischemia times were 154 min, 29 min, and 2 min, respectively. One patient was re-explored on postoperative day 1. Adherence to the IDEAL guidelines put forth by the Balliol Collaboration provided a practical

Sharp Truncation of an Electric Field: An Idealized Model That Warrants Caution

ERIC Educational Resources Information Center

Tu, Hong; Zhu, Jiongming

2016-01-01

In physics, idealized models are often used to simplify complex situations. The motivation of the idealization is to make the real complex system tractable by adopting certain simplifications. In this treatment some unnecessary, negligible aspects are stripped away (so-called Aristotelian idealization), or some deliberate distortions are involved…

Caste and Choice: The Influence of Developmental Idealism on Marriage Behavior

PubMed Central

Allendorf, Keera; Thornton, Arland

2015-01-01

Is young people’s marriage behavior determined by their socioeconomic characteristics or their endorsement of developmental idealism? This article addresses this question using a unique, longitudinal data set from Nepal and provides the first individual-level test of developmental idealism theory. We find that unmarried individuals with greater endorsement of developmental idealism in 2008 were more likely by 2012 to choose their own spouse, including a spouse of a different caste, rather than have an arranged marriage. Those with salaried work experience were also less likely to have arranged marriages, but urban proximity and education were not significant. We conclude that both developmental idealism and socioeconomic characteristics influence marriage and their influences are largely independent. PMID:26430712

Neurocultural evidence that ideal affect match promotes giving

PubMed Central

Park, BoKyung; Blevins, Elizabeth; Knutson, Brian

2017-01-01

Abstract Why do people give to strangers? We propose that people trust and give more to those whose emotional expressions match how they ideally want to feel (“ideal affect match”). European Americans and Koreans played multiple trials of the Dictator Game with recipients who varied in emotional expression (excited, calm), race (White, Asian) and sex (male, female). Consistent with their culture’s valued affect, European Americans trusted and gave more to excited than calm recipients, whereas Koreans trusted and gave more to calm than excited recipients. These findings held regardless of recipient race and sex. We then used fMRI to probe potential affective and mentalizing mechanisms. Increased activity in the nucleus accumbens (associated with reward anticipation) predicted giving, as did decreased activity in the right temporo-parietal junction (rTPJ; associated with reduced belief prediction error). Ideal affect match decreased rTPJ activity, suggesting that people may trust and give more to strangers whom they perceive to share their affective values. PMID:28379542

Reported Effects of Masculine Ideals on Gay Men.

PubMed

Sánchez, Francisco J; Greenberg, Stefanie T; Liu, William Ming; Vilain, Eric

2009-01-01

This exploratory study used consensual qualitative research methodology (Hill et al., 2005) to analyze what gay men associate with masculinity and femininity, how they feel masculine ideals affect their self-image, and how masculine ideals affect their same-sex relationships. Written responses were collected from 547 self-identified gay men in the U.S. via an Internet-based survey. Findings supported previous reports that perceptions of gender roles among gay men appear based on masculine and feminine stereotypes. Additionally, more adverse versus positive effects on self-image and same-sex romantic relationships were reported including difficulty being emotional and affectionate, pressure to be physically attractive, and pressure to appear masculine in order to be accepted by society and to be seen as desirable by other gay men. While research on gay men's experience with masculinity continues, psychologists should consider the possible influence of traditional masculine ideals when conceptualizing their gay male clients.

Reported Effects of Masculine Ideals on Gay Men

PubMed Central

Sánchez, Francisco J.; Greenberg, Stefanie T.; Liu, William Ming; Vilain, Eric

2010-01-01

This exploratory study used consensual qualitative research methodology (Hill et al., 2005) to analyze what gay men associate with masculinity and femininity, how they feel masculine ideals affect their self-image, and how masculine ideals affect their same-sex relationships. Written responses were collected from 547 self-identified gay men in the U.S. via an Internet-based survey. Findings supported previous reports that perceptions of gender roles among gay men appear based on masculine and feminine stereotypes. Additionally, more adverse versus positive effects on self-image and same-sex romantic relationships were reported including difficulty being emotional and affectionate, pressure to be physically attractive, and pressure to appear masculine in order to be accepted by society and to be seen as desirable by other gay men. While research on gay men’s experience with masculinity continues, psychologists should consider the possible influence of traditional masculine ideals when conceptualizing their gay male clients. PMID:20628534

Structural arrest in an ideal gas.

PubMed

van Ketel, Willem; Das, Chinmay; Frenkel, Daan

2005-04-08

We report a molecular dynamics study of a simple model system that has the static properties of an ideal gas, yet exhibits nontrivial "glassy" dynamics behavior at high densities. The constituent molecules of this system are constructs of three infinitely thin hard rods of length L, rigidly joined at their midpoints. The crosses have random but fixed orientation. The static properties of this system are those of an ideal gas, and its collision frequency can be computed analytically. For number densities NL(3)/V>1, the single-particle diffusivity goes to zero. As the system is completely structureless, standard mode-coupling theory cannot describe the observed structural arrest. Nevertheless, the system exhibits many dynamical features that appear to be mode-coupling-like. All high-density incoherent intermediate scattering functions collapse onto master curves that depend only on the wave vector.

Tempting Fate or Inviting Happiness? Unrealistic idealization prevents the decline of marital satisfaction

PubMed Central

Murray, Sandra L.; Griffin, Dale W.; Derrick, Jaye L.; Harris, Brianna; Aloni, Maya; Leder, Sadie

2014-01-01

The authors examine whether unrealistically viewing a romantic partner as the image of one’s ideal partner accelerates or slows declines in marital satisfaction among newlyweds. A longitudinal study linked unrealistic idealization at the point of marriage to changes in satisfaction over the first three years of marriage. Overall, satisfaction declined markedly, consistent with past research. However, seeing a less-than-ideal partner as a reflection of one’s ideals predicted a certain level of immunity to the corrosive effects of time: People who initially idealized their partner highly experienced no declines in satisfaction. The obtained benefits of idealization remained in analyses that separately controlled for the positivity of partner perceptions and the possibility that better adjusted people might be in better relationships. PMID:21467549

Critical Thinking and Educational Ideal

ERIC Educational Resources Information Center

Liu, Qian

2007-01-01

Critical thinking, as an educational trend, has been much discussed and proposed nowadays. In this paper, an analysis is made on the gap between our present educational practice and educational ideal from three different aspects, that is, the content, the manner and the one-sidedness of our teaching. It's observed that there is still a long way to…

Network Analysis of Sequence-Function Relationships and Exploration of Sequence Space of TEM β-Lactamases.

PubMed

Zeil, Catharina; Widmann, Michael; Fademrecht, Silvia; Vogel, Constantin; Pleiss, Jürgen

2016-05-01

The Lactamase Engineering Database (www.LacED.uni-stuttgart.de) was developed to facilitate the classification and analysis of TEM β-lactamases. The current version contains 474 TEM variants. Two hundred fifty-nine variants form a large scale-free network of highly connected point mutants. The network was divided into three subnetworks which were enriched by single phenotypes: one network with predominantly 2be and two networks with 2br phenotypes. Fifteen positions were found to be highly variable, contributing to the majority of the observed variants. Since it is expected that a considerable fraction of the theoretical sequence space is functional, the currently sequenced 474 variants represent only the tip of the iceberg of functional TEM β-lactamase variants which form a huge natural reservoir of highly interconnected variants. Almost 50% of the variants are part of a quartet. Thus, two single mutations that result in functional enzymes can be combined into a functional protein. Most of these quartets consist of the same phenotype, or the mutations are additive with respect to the phenotype. By predicting quartets from triplets, 3,916 unknown variants were constructed. Eighty-seven variants complement multiple quartets and therefore have a high probability of being functional. The construction of a TEM β-lactamase network and subsequent analyses by clustering and quartet prediction are valuable tools to gain new insights into the viable sequence space of TEM β-lactamases and to predict their phenotype. The highly connected sequence space of TEM β-lactamases is ideally suited to network analysis and demonstrates the strengths of network analysis over tree reconstruction methods. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Shotgun Protein Sequencing with Meta-contig Assembly*

PubMed Central

Guthals, Adrian; Clauser, Karl R.; Bandeira, Nuno

2012-01-01

Full-length de novo sequencing from tandem mass (MS/MS) spectra of unknown proteins such as antibodies or proteins from organisms with unsequenced genomes remains a challenging open problem. Conventional algorithms designed to individually sequence each MS/MS spectrum are limited by incomplete peptide fragmentation or low signal to noise ratios and tend to result in short de novo sequences at low sequencing accuracy. Our shotgun protein sequencing (SPS) approach was developed to ameliorate these limitations by first finding groups of unidentified spectra from the same peptides (contigs) and then deriving a consensus de novo sequence for each assembled set of spectra (contig sequences). But whereas SPS enables much more accurate reconstruction of de novo sequences longer than can be recovered from individual MS/MS spectra, it still requires error-tolerant matching to homologous proteins to group smaller contig sequences into full-length protein sequences, thus limiting its effectiveness on sequences from poorly annotated proteins. Using low and high resolution CID and high resolution HCD MS/MS spectra, we address this limitation with a Meta-SPS algorithm designed to overlap and further assemble SPS contigs into Meta-SPS de novo contig sequences extending as long as 100 amino acids at over 97% accuracy without requiring any knowledge of homologous protein sequences. We demonstrate Meta-SPS using distinct MS/MS data sets obtained with separate enzymatic digestions and discuss how the remaining de novo sequencing limitations relate to MS/MS acquisition settings. PMID:22798278

Shotgun protein sequencing with meta-contig assembly.

PubMed

Guthals, Adrian; Clauser, Karl R; Bandeira, Nuno

2012-10-01

Full-length de novo sequencing from tandem mass (MS/MS) spectra of unknown proteins such as antibodies or proteins from organisms with unsequenced genomes remains a challenging open problem. Conventional algorithms designed to individually sequence each MS/MS spectrum are limited by incomplete peptide fragmentation or low signal to noise ratios and tend to result in short de novo sequences at low sequencing accuracy. Our shotgun protein sequencing (SPS) approach was developed to ameliorate these limitations by first finding groups of unidentified spectra from the same peptides (contigs) and then deriving a consensus de novo sequence for each assembled set of spectra (contig sequences). But whereas SPS enables much more accurate reconstruction of de novo sequences longer than can be recovered from individual MS/MS spectra, it still requires error-tolerant matching to homologous proteins to group smaller contig sequences into full-length protein sequences, thus limiting its effectiveness on sequences from poorly annotated proteins. Using low and high resolution CID and high resolution HCD MS/MS spectra, we address this limitation with a Meta-SPS algorithm designed to overlap and further assemble SPS contigs into Meta-SPS de novo contig sequences extending as long as 100 amino acids at over 97% accuracy without requiring any knowledge of homologous protein sequences. We demonstrate Meta-SPS using distinct MS/MS data sets obtained with separate enzymatic digestions and discuss how the remaining de novo sequencing limitations relate to MS/MS acquisition settings.

Hybrid normed ideal perturbations of n-tuples of operators I

NASA Astrophysics Data System (ADS)

Voiculescu, Dan-Virgil

2018-06-01

In hybrid normed ideal perturbations of n-tuples of operators, the normed ideal is allowed to vary with the component operators. We begin extending to this setting the machinery we developed for normed ideal perturbations based on the modulus of quasicentral approximation and an adaptation of our non-commutative generalization of the Weyl-von Neumann theorem. For commuting n-tuples of hermitian operators, the modulus of quasicentral approximation remains essentially the same when Cn- is replaced by a hybrid n-tuple Cp1,…- , … , Cpn- , p1-1 + ⋯ + pn-1 = 1. The proof involves singular integrals of mixed homogeneity.

Health care market deviations from the ideal market.

PubMed

Mwachofi, Ari; Al-Assaf, Assaf F

2011-08-01

A common argument in the health policy debate is that market forces allocate resources efficiently in health care, and that government intervention distorts such allocation. Rarely do those making such claims state explicitly that the market they refer to is an ideal in economic theory which can only exist under very strict conditions. This paper explores the strict conditions necessary for that ideal market in the context of health care as a means of examining the claim that market forces do allocate resources efficiently in health care.

Idealness and similarity in goal-derived categories: a computational examination.

PubMed

Voorspoels, Wouter; Storms, Gert; Vanpaemel, Wolf

2013-02-01

The finding that the typicality gradient in goal-derived categories is mainly driven by ideals rather than by exemplar similarity has stood uncontested for nearly three decades. Due to the rather rigid earlier implementations of similarity, a key question has remained--that is, whether a more flexible approach to similarity would alter the conclusions. In the present study, we evaluated whether a similarity-based approach that allows for dimensional weighting could account for findings in goal-derived categories. To this end, we compared a computational model of exemplar similarity (the generalized context model; Nosofsky, Journal of Experimental Psychology. General 115:39-57, 1986) and a computational model of ideal representation (the ideal-dimension model; Voorspoels, Vanpaemel, & Storms, Psychonomic Bulletin & Review 18:1006-114, 2011) in their accounts of exemplar typicality in ten goal-derived categories. In terms of both goodness-of-fit and generalizability, we found strong evidence for an ideal approach in nearly all categories. We conclude that focusing on a limited set of features is necessary but not sufficient to account for the observed typicality gradient. A second aspect of ideal representations--that is, that extreme rather than common, central-tendency values drive typicality--seems to be crucial.

Umbilical hernia repair with mesh: identifying effectors of ideal outcomes.

PubMed

Colavita, Paul D; Belyansky, Igor; Walters, Amanda L; Zemlyak, Alla Y; Lincourt, Amy E; Heniford, B Todd; Augenstein, Vedra A

2014-09-01

Quality of life has become an important focus for improvement in hernia repair. The International Hernia Mesh Registry was queried. The Carolinas Comfort Scale quantitated quality of life at 1-month, 6-month, and annual follow-up. Scores of 0 (completely asymptomatic) in all categories without recurrence defined an ideal outcome. The analysis consisted of 363 umbilical hernia repairs; 18.7% were laparoscopic. Demographics included age of 51.5 ± 13.8 years, 24.5% were female, and the average body mass index was 30.63 ± 5.9 kg/m(2). Mean defect size was 4.3 ± 3.1 cm(2). Mean follow-up was 18.2 months. Absent/minimal preoperative symptoms were predictive of ideal outcome at all time points and increasing age was predictive at 6 months and 1 year. At 6 months, the use of fixation sutures alone versus tacks (odds ratio 14.1) predicted ideal outcome. Ideal outcomes are dependent on both patient-specific and operative factors. The durable, ideal outcome in umbilical hernia repair is most likely in an older, asymptomatic patient who undergoes mesh fixation with permanent suture. Copyright © 2014 Elsevier Inc. All rights reserved.

Personality traits and appearance-ideal internalization: Differential associations with body dissatisfaction and compulsive exercise.

PubMed

Martin, Shelby J; Racine, Sarah E

2017-12-01

Thin-ideal internalization is a robust risk factor for body dissatisfaction and eating pathology. Conversely, athletic-ideal internalization is often unrelated to body dissatisfaction, but predicts compulsive exercise (i.e., rigid, rule-driven exercise that is continued despite adverse consequences). Distinct personality traits could relate to internalization of different appearance ideals, which may be associated with divergent eating disorder outcomes. Past research has shown that neuroticism is related to body dissatisfaction, whereas extraversion and conscientiousness have been associated with regular and problematic exercise. The current study examined associations among personality traits (i.e., neuroticism, extraversion, conscientiousness), appearance-ideal internalization (i.e., thin- and athletic-ideal), and eating disorder cognitions/behaviors (i.e., body dissatisfaction, compulsive exercise) among 531 college men and women. Moreover, we tested whether appearance-ideal internalization mediated the relationships between personality traits with body dissatisfaction and compulsive exercise. As expected, body dissatisfaction was positively related to neuroticism, and compulsive exercise was positively associated with extraversion. Thin-ideal internalization positively correlated with neuroticism, athletic-ideal internalization positively correlated with conscientiousness, and both thin- and athletic-ideal internalization were positively related to extraversion. After controlling for gender, body mass index, the other appearance-ideal internalization, and the remaining personality traits, the indirect effects of both neuroticism and extraversion on body dissatisfaction through thin-ideal internalization were significant. Extraversion and conscientiousness were indirectly related to compulsive exercise through athletic-ideal internalization, whereas the indirect effect of neuroticism was dependent on covariates. As such, personality traits may be related to

Optimal platform design using non-dominated sorting genetic algorithm II and technique for order of preference by similarity to ideal solution; application to automotive suspension system

NASA Astrophysics Data System (ADS)

Shojaeefard, Mohammad Hassan; Khalkhali, Abolfazl; Faghihian, Hamed; Dahmardeh, Masoud

2018-03-01

Unlike conventional approaches where optimization is performed on a unique component of a specific product, optimum design of a set of components for employing in a product family can cause significant reduction in costs. Increasing commonality and performance of the product platform simultaneously is a multi-objective optimization problem (MOP). Several optimization methods are reported to solve these MOPs. However, what is less discussed is how to find the trade-off points among the obtained non-dominated optimum points. This article investigates the optimal design of a product family using non-dominated sorting genetic algorithm II (NSGA-II) and proposes the employment of technique for order of preference by similarity to ideal solution (TOPSIS) method to find the trade-off points among the obtained non-dominated results while compromising all objective functions together. A case study for a family of suspension systems is presented, considering performance and commonality. The results indicate the effectiveness of the proposed method to obtain the trade-off points with the best possible performance while maximizing the common parts.

Young men's endorsement and pursuit of appearance ideals: The prospective role of appearance investment.

PubMed

Kling, Johanna; Rodgers, Rachel F; Frisén, Ann

2016-03-01

Appearance investment has been proposed as a risk factor for the development of body dissatisfaction. Despite this, few studies have explored men's investment in their appearance. The aim of the present study was therefore to examine appearance investment as a prospective predictor of young men's endorsement and pursuit of appearance ideals. A community sample of 187 young men participated in a study at ages 21 and 24. Hierarchical multiple regressions revealed that appearance investment, as hypothesized, was a prospective predictor of increases in leanness orientation, media-ideal internalization, and muscularity behaviors. However, appearance investment did not predict increases in muscularity dissatisfaction. The present findings highlight the importance of including appearance investment in sociocultural models of the development of men's body image, and suggest that appearance investment may be an important target variable to consider when designing body dissatisfaction prevention and intervention programs tailored to young men. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ideal GLM-MHD: About the entropy consistent nine-wave magnetic field divergence diminishing ideal magnetohydrodynamics equations

NASA Astrophysics Data System (ADS)

Derigs, Dominik; Winters, Andrew R.; Gassner, Gregor J.; Walch, Stefanie; Bohm, Marvin

2018-07-01

The paper presents two contributions in the context of the numerical simulation of magnetized fluid dynamics. First, we show how to extend the ideal magnetohydrodynamics (MHD) equations with an inbuilt magnetic field divergence cleaning mechanism in such a way that the resulting model is consistent with the second law of thermodynamics. As a byproduct of these derivations, we show that not all of the commonly used divergence cleaning extensions of the ideal MHD equations are thermodynamically consistent. Secondly, we present a numerical scheme obtained by constructing a specific finite volume discretization that is consistent with the discrete thermodynamic entropy. It includes a mechanism to control the discrete divergence error of the magnetic field by construction and is Galilean invariant. We implement the new high-order MHD solver in the adaptive mesh refinement code FLASH where we compare the divergence cleaning efficiency to the constrained transport solver available in FLASH (unsplit staggered mesh scheme).

Teachers' Ethnotheories of the "Ideal Student" in Five Western Cultures

ERIC Educational Resources Information Center

Harkness, Sara; Blom, Marjolijn; Oliva, Alfredo; Moscardino, Ughetta; Zylicz, Piotr Olaf; Bermudez, Moises Rios; Feng, Xin; Carrasco-Zylicz, Agnieszka; Axia, Giovanna; Super, Charles M.

2007-01-01

This paper explores teachers' ethnotheories of the "ideal student" in five western societies: Italy, The Netherlands, Poland, Spain, and the US. Quantitative and qualitative methods are used to derive culture-specific profiles of the "ideal student" as described by kindergarten and primary school teachers in semi-structured…

Thermodynamics of an ideal generalized gas: I. Thermodynamic laws.

PubMed

Lavenda, B H

2005-11-01

The equations of state for an ideal relativistic, or generalized, gas, like an ideal quantum gas, are expressed in terms of power laws of the temperature. In contrast to an ideal classical gas, the internal energy is a function of volume at constant temperature, implying that the ideal generalized gas will show either attractive or repulsive interactions. This is a necessary condition in order that the third law be obeyed and for matter to have an electromagnetic origin. The transition from an ideal generalized to a classical gas occurs when the two independent solutions of the subsidiary equation to Lagrange's equation coalesce. The equation of state relating the pressure to the internal energy encompasses the full range of cosmological scenarios, from the radiation to the matter dominated universes and finally to the vacuum energy, enabling the coefficient of proportionality, analogous to the Grüeisen ratio, to be interpreted in terms of the degrees of freedom related to the temperature exponents of the internal energy and the absolute temperature expressed in terms of a power of the empirical temperature. The limit where these exponents merge is shown to be the ideal classical gas limit. A corollary to Carnot's theorem is proved, asserting that the ratio of the work done over a cycle to the heat absorbed to increase the temperature at constant volume is the same for all bodies at the same volume. As power means, the energy and entropy are incomparable, and a new adiabatic potential is introduced by showing that the volume raised to a characteristic exponent is also the integrating factor for the quantity of heat so that the second law can be based on the property that power means are monotonically increasing functions of their order. The vanishing of the chemical potential in extensive systems implies that energy cannot be transported without matter and is equivalent to the condition that Clapeyron's equation be satisfied.

SCPRED: accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences.

PubMed

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-05-01

Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of the features, which are

SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences

PubMed Central

Kurgan, Lukasz; Cios, Krzysztof; Chen, Ke

2008-01-01

Background Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus determining structural similarity without the sequence similarity would be desirable for the structure prediction. The folding type of a protein or its domain is defined as the structural class. Current structural class prediction methods that predict the four structural classes defined in SCOP provide up to 63% accuracy for the datasets in which sequence identity of any pair of sequences belongs to the twilight-zone. We propose SCPRED method that improves prediction accuracy for sequences that share twilight-zone pairwise similarity with sequences used for the prediction. Results SCPRED uses a support vector machine classifier that takes several custom-designed features as its input to predict the structural classes. Based on extensive design that considers over 2300 index-, composition- and physicochemical properties-based features along with features based on the predicted secondary structure and content, the classifier's input includes 8 features based on information extracted from the secondary structure predicted with PSI-PRED and one feature computed from the sequence. Tests performed with datasets of 1673 protein chains, in which any pair of sequences shares twilight-zone similarity, show that SCPRED obtains 80.3% accuracy when predicting the four SCOP-defined structural classes, which is superior when compared with over a dozen recent competing methods that are based on support vector machine, logistic regression, and ensemble of classifiers predictors. Conclusion The SCPRED can accurately find similar structures for sequences that share low identity with sequence used for the prediction. The high predictive accuracy achieved by SCPRED is attributed to the design of

Developmental Idealism and Cultural Models of the Family in Malawi

PubMed Central

Pierotti, Rachael S.; Young-DeMarco, Linda; Watkins, Susan

2014-01-01

This paper examines the extent to which developmental idealism has been disseminated in Malawi. Developmental idealism is a set of beliefs and values about development and the relationships between development and family structures and behavior. Developmental idealism states that attributes of societies and families defined as modern are better than attributes defined as traditional, that modern societies help produce modern families, that modern families facilitate the achievement of modern societies, and that the future will bring family change in the direction of modernity. Previous research has demonstrated that knowledge of developmental idealism is widespread in many places around the world, but provides little systematic data about it in sub-Saharan Africa or how knowledge of it is associated with certain demographic characteristics in that region. In this paper, we address this issue by examining whether ordinary people in two settings in Malawi, a sub-Saharan African country, have received and understood messages that are intended to associate development with certain types of family forms and family behaviors. We then examine associations between demographic characteristics and developmental idealism to investigate possible mechanisms linking global discourse about development to the grassroots. We analyze data collected in face-to-face surveys from two samples of Malawian men in 2009 and 2010, one rural, the other in a low-to-medium income neighborhood of a city. Our analysis of these survey data shows considerable evidence that many developmental idealism beliefs have been spread in that country and that education has positive effects on beliefs in the association between development and family attributes. We also find higher levels of developmental idealism awareness in the urban sample than we do in the rural sample, but once dissimilarities in education and wealth between the two samples are controlled, awareness levels no longer differed between

Evaluating and Redesigning Teaching Learning Sequences at the Introductory Physics Level

ERIC Educational Resources Information Center

Guisasola, Jenaro; Zuza, Kristina; Ametller, Jaume; Gutierrez-Berraondo, José

2017-01-01

In this paper we put forward a proposal for the design and evaluation of teaching and learning sequences in upper secondary school and university. We will connect our proposal with relevant contributions on the design of teaching sequences, ground it on the design-based research methodology, and discuss how teaching and learning sequences designed…

Tailored edge-ray concentrators as ideal second stages for Fresnel reflectors.

PubMed

Gordon, J M; Ries, H

1993-05-01

For both linear and point-focus Fresnel reflectors, we present a new type of ideal nonimaging secondary concentrator, the tailored edge-ray concentrator, that can closely approach the thermodynamic limit of concentration. For large rim-angle heliostat fields, practical-sized secondaries with shapes that should be relatively easy to fabricate can achieve concentrations substantially above those of compound parabolic concentrators. This superiority stems from designing so as to accommodate the particular flux from the heliostat field. The edge-ray principle used for generating the new secondary dictates a heliostat tracking strategy that is different from the conventional one but is equally easy to implement.

Pooled-DNA Sequencing for Elucidating New Genomic Risk Factors, Rare Variants Underlying Alzheimer's Disease.

PubMed

Jin, Sheng Chih; Benitez, Bruno A; Deming, Yuetiva; Cruchaga, Carlos

2016-01-01

Analyses of genome-wide association studies (GWAS) for complex disorders usually identify common variants with a relatively small effect size that only explain a small proportion of phenotypic heritability. Several studies have suggested that a significant fraction of heritability may be explained by low-frequency (minor allele frequency (MAF) of 1-5 %) and rare-variants that are not contained in the commercial GWAS genotyping arrays (Schork et al., Curr Opin Genet Dev 19:212, 2009). Rare variants can also have relatively large effects on risk for developing human diseases or disease phenotype (Cruchaga et al., PLoS One 7:e31039, 2012). However, it is necessary to perform next-generation sequencing (NGS) studies in a large population (>4,000 samples) to detect a significant rare-variant association. Several NGS methods, such as custom capture sequencing and amplicon-based sequencing, are designed to screen a small proportion of the genome, but most of these methods are limited in the number of samples that can be multiplexed (i.e. most sequencing kits only provide 96 distinct index). Additionally, the sequencing library preparation for 4,000 samples remains expensive and thus conducting NGS studies with the aforementioned methods are not feasible for most research laboratories.The need for low-cost large scale rare-variant detection makes pooled-DNA sequencing an ideally efficient and cost-effective technique to identify rare variants in target regions by sequencing hundreds to thousands of samples. Our recent work has demonstrated that pooled-DNA sequencing can accurately detect rare variants in targeted regions in multiple DNA samples with high sensitivity and specificity (Jin et al., Alzheimers Res Ther 4:34, 2012). In these studies we used a well-established pooled-DNA sequencing approach and a computational package, SPLINTER (short indel prediction by large deviation inference and nonlinear true frequency estimation by recursion) (Vallania et al., Genome Res

A simplified Sanger sequencing method for full genome sequencing of multiple subtypes of human influenza A viruses.

PubMed

Deng, Yi-Mo; Spirason, Natalie; Iannello, Pina; Jelley, Lauren; Lau, Hilda; Barr, Ian G

2015-07-01

Full genome sequencing of influenza A viruses (IAV), including those that arise from annual influenza epidemics, is undertaken to determine if reassorting has occurred or if other pathogenic traits are present. Traditionally IAV sequencing has been biased toward the major surface glycoproteins haemagglutinin and neuraminidase, while the internal genes are often ignored. Despite the development of next generation sequencing (NGS), many laboratories are still reliant on conventional Sanger sequencing to sequence IAV. To develop a minimal and robust set of primers for Sanger sequencing of the full genome of IAV currently circulating in humans. A set of 13 primer pairs was designed that enabled amplification of the six internal genes of multiple human IAV subtypes including the recent avian influenza A(H7N9) virus from China. Specific primers were designed to amplify the HA and NA genes of each IAV subtype of interest. Each of the primers also incorporated a binding site at its 5'-end for either a forward or reverse M13 primer, such that only two M13 primers were required for all subsequent sequencing reactions. This minimal set of primers was suitable for sequencing the six internal genes of all currently circulating human seasonal influenza A subtypes as well as the avian A(H7N9) viruses that have infected humans in China. This streamlined Sanger sequencing protocol could be used to generate full genome sequence data more rapidly and easily than existing influenza genome sequencing protocols. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Health Care Market Deviations from the Ideal Market

PubMed Central

Mwachofi, Ari; Al-Assaf, Assaf F.

2011-01-01

A common argument in the health policy debate is that market forces allocate resources efficiently in health care, and that government intervention distorts such allocation. Rarely do those making such claims state explicitly that the market they refer to is an ideal in economic theory which can only exist under very strict conditions. This paper explores the strict conditions necessary for that ideal market in the context of health care as a means of examining the claim that market forces do allocate resources efficiently in health care. PMID:22087373

Flavitrack: an annotated database of flavivirus sequences

PubMed Central

Misra, Milind

2009-01-01

Motivation Properly annotated sequence data for flaviviruses, which cause diseases, such as tick-borne encephalitis (TBE), dengue fever (DF), West Nile (WN) and yellow fever (YF), can aid in the design of antiviral drugs and vaccines to prevent their spread. Flavitrack was designed to help identify conserved sequence motifs, interpret mutational and structural data and track evolution of phenotypic properties. Summary Flavitrack contains over 590 complete flavivirus genome/protein sequences and information on known mutations and literature references. Each sequence has been manually annotated according to its date and place of isolation, phenotype and lethality. Internal tools are provided to rapidly determine relationships between viruses in Flavitrack and sequences provided by the user. Availability http://carnot.utmb.edu/flavitrack Contact chschein@utmb.edu Supplementary information http://carnot.utmb.edu/flavitrack/B1S1.html PMID:17660525

Nine Suggestions for Improving Sequences. Technology.

ERIC Educational Resources Information Center

Muro, Don

1995-01-01

Maintains that many educators are using sequences to create accompaniments and practice tapes geared to student abilities. Describes musical instruction using Musical Instrument Digital Interface (MIDI). Discusses eight suggestions designed to make the process of sequencing more efficient. (CFR)

Coherent control of acoustic vibrations in metal nanoparticles and thin films with sequences of femtosecond pulses: Harmonic-oscillator model

NASA Astrophysics Data System (ADS)

Zheltikov, A. M.

2002-08-01

A harmonic oscillator model is used to demonstrate the possibility of coherent control of acoustic vibrations of metal nanoparticles and thin films with sequences of femtosecond laser pulses. When the interval between the pulses in such a sequence is chosen equal to the oscillation period of the expansion mode of a nanoscale system, the relevant acoustic vibrations can be excited in a resonant and selective way. Sequences of femtosecond pulses with picosecond time intervals between the pulses are shown to be ideally suited for a resonant excitation and coherent control of acoustic modes of silver nanoparticles.

Thin-ideal internalization: How much is too much?

PubMed

Schaefer, Lauren M; Burke, Natasha L; Thompson, J Kevin

2018-03-16

Internalization of the thin-ideal is a risk factor for eating disorders that frequently persists into recovery and increases patient risk for relapse. Addressing thin-ideal internalization as a core element of eating disorder prevention and treatment produces significant reductions in eating pathology. However, research has not yet quantified levels of thin-ideal internalization that may signal increased versus decreased risk for disordered eating. To address this gap in the literature, receiver operating characteristic (ROC) curve analysis was used to identify a thin-ideal internalization cutoff score that signified clinically-meaningful eating disorder pathology. 787 college women (age M = 20.17, SD = 2.41; BMI M = 23.58, SD = 5.29) were classified as "healthy" (N = 717) or those with significant disordered eating (N = 70) using established clinical cutoffs for the Eating Disorder Examination-Questionnaire. ROC curve analysis was used to test the performance of the Sociocultural Attitudes Towards Appearance Questionnaire-4 (SATAQ-4) Internalization: Thin/Low Body Fat subscale in predicting disordered eating status, and to identify a cutoff score that maximized sensitivity and specificity to discriminate between healthy and disordered eating samples. Mean SATAQ-4 internalization scores were 3.29 (SD = 0.92) and 4.27 (SD = 0.62) for healthy and disordered eating participants, respectively. The SATAQ-4 internalization scores were good predictors of disordered eating status (area under the curve = 0.81, 95% CI: 0.76-0.86). The optimal cutoff of 3.78 (measured on a 1-5 Likert scale) yielded a sensitivity of 0.81 and specificity of 0.64. Overall, results provide preliminary support for the discriminant validity of SATAQ-4 thin internalization scores and suggest that even moderate levels of thin-ideal internalization may be predictive of clinically-significant eating pathology. It may be important for prevention and intervention work to actively seek to reduce

Ideal Teaching: Exploring the Attributes of an "Ideal Teacher" in the Church Educational System for the Church of Jesus Christ of Latter-Day Saints

ERIC Educational Resources Information Center

Strader, Matthew W.

2009-01-01

The purpose of this study was to identify the profile of an ideal teacher for the Church Educational System (CES) for the Church of Jesus Christ of Latter-day Saints. This study surveyed 159 students, teachers, and administrators in order to find the characteristics perceived to be ideal in a CES teacher. The survey included 16 characteristics of…

Newly designed 11-gene panel reveals first case of hereditary amyloidosis captured by massive parallel sequencing.

PubMed

Chyra Kufova, Zuzana; Sevcikova, Tereza; Januska, Jaroslav; Vojta, Petr; Boday, Arpad; Vanickova, Pavla; Filipova, Jana; Growkova, Katerina; Jelinek, Tomas; Hajduch, Marian; Hajek, Roman

2018-02-17

Amyloidosis is caused by deposition of abnormal protein fibrils, leading to damage of organ function. Hereditary amyloidosis represents a monogenic disease caused by germline mutations in 11 amyloidogenic precursor protein genes. One of the important but non-specific symptoms of amyloidosis is hypertrophic cardiomyopathy. Diagnostics of hereditary amyloidosis is complicated and the real cause can remain overlooked. We aimed to design hereditary amyloidosis gene panel and to introduce new next-generation sequencing (NGS) approach to investigate hereditary amyloidosis in a cohort of patients with hypertrophic cardiomyopathy of unknown significance. Design of target enrichment DNA library preparation using Haloplex Custom Kit containing 11 amyloidogenic genes was followed by MiSeq Illumina sequencing and bioinformatics identification of germline variants using tool VarScan in a cohort of 40 patients. We present design of NGS panel for 11 genes ( TTR , FGA , APOA1 , APOA2 , LYZ , GSN , CST3 , PRNP , APP , B2M , ITM2B ) connected to various forms of amyloidosis. We detected one mutation, which is responsible for hereditary amyloidosis. Some other single nucleotide variants are so far undescribed or rare variants or represent common polymorphisms in European population. We report one positive case of hereditary amyloidosis in a cohort of patients with hypertrophic cardiomyopathy of unknown significance and set up first panel for NGS in hereditary amyloidosis. This work may facilitate successful implementation of the NGS method by other researchers or clinicians and may improve the diagnostic process after validation. © 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.

Your Ideal Silhouette. Courseware Evaluation for Vocational and Technical Education.

ERIC Educational Resources Information Center

Tierney, Margaret S.; And Others

This courseware evaluation rates the "Your Ideal Silhouette" program developed by Your Image, Inc. This program (not contained in this document) uses the computer to identify figure faults and illustrate personalized corrective style lines to achieve the ideal silhouette. Part A describes the program in terms of subject area (textiles…

The "Ideal Professor" and Gender Effects in Christian Higher Education

ERIC Educational Resources Information Center

Woods, Robert H., Jr.; Badzinski, Diane M.; Fritz, Janie M. Harden; Yeates, Sarah E.

2012-01-01

A survey was administered to 451 undergraduate students at a private liberal arts Christian university to identify students' perceptions of the ideal professor. The survey revealed that the ideal professor places great emphasis on the integration of faith and learning, is flexible (and even easy), maintains high academic standards, encourages…

Why the Kantian ideal survives medical learning curves, and why it matters.

PubMed

Brecher, B

2006-09-01

The "Kantian ideal" is often misunderstood as invoking individual autonomy rather than rational self legislation. Le Morvan and Stock's otherwise insightful discussion of "Medical learning curves and the Kantian ideal"--for example--draws the mistaken inference that that ideal is inconsistent with the realities of medical practice. But it is not. Rationally to be a patient entails accepting its necessary conditions.

A control system design approach for flexible spacecraft

NASA Technical Reports Server (NTRS)

Silverberg, L. M.

1985-01-01

A control system design approach for flexible spacecraft is presented. The control system design is carried out in two steps. The first step consists of determining the ideal control system in terms of a desirable dynamic performance. The second step consists of designing a control system using a limited number of actuators that possess a dynamic performance that is close to the ideal dynamic performance. The effects of using a limited number of actuators is that the actual closed-loop eigenvalues differ from the ideal closed-loop eigenvalues. A method is presented to approximate the actual closed-loop eigenvalues so that the calculation of the actual closed-loop eigenvalues can be avoided. Depending on the application, it also may be desirable to apply the control forces as impulses. The effect of digitizing the control to produce the appropriate impulses is also examined.

An efficient study design to test parent-of-origin effects in family trios.

PubMed

Yu, Xiaobo; Chen, Gao; Feng, Rui

2017-11-01

Increasing evidence has shown that genes may cause prenatal, neonatal, and pediatric diseases depending on their parental origins. Statistical models that incorporate parent-of-origin effects (POEs) can improve the power of detecting disease-associated genes and help explain the missing heritability of diseases. In many studies, children have been sequenced for genome-wide association testing. But it may become unaffordable to sequence their parents and evaluate POEs. Motivated by the reality, we proposed a budget-friendly study design of sequencing children and only genotyping their parents through single nucleotide polymorphism array. We developed a powerful likelihood-based method, which takes into account both sequence reads and linkage disequilibrium to infer the parental origins of children's alleles and estimate their POEs on the outcome. We evaluated the performance of our proposed method and compared it with an existing method using only genotypes, through extensive simulations. Our method showed higher power than the genotype-based method. When either the mean read depth or the pair-end length was reasonably large, our method achieved ideal power. When single parents' genotypes were unavailable or parental genotypes at the testing locus were not typed, both methods lost power compared with when complete data were available; but the power loss from our method was smaller than the genotype-based method. We also extended our method to accommodate mixed genotype, low-, and high-coverage sequence data from children and their parents. At presence of sequence errors, low-coverage parental sequence data may lead to lower power than parental genotype data. © 2017 WILEY PERIODICALS, INC.

Developmental Idealism: The Cultural Foundations of World Development Programs

PubMed Central

Thornton, Arland; Dorius, Shawn F.; Swindle, Jeffrey

2015-01-01

This paper extends theory and research concerning cultural models of development beyond family and demographic matters to a broad range of additional factors, including government, education, human rights, daily social conventions, and religion. Developmental idealism is a cultural model—a set of beliefs and values—that identifies the appropriate goals of development and the ends for achieving these goals. It includes beliefs about positive cause and effect relationships among such factors as economic growth, educational achievement, health, and political governance, as well as strong values regarding many attributes, including economic growth, education, small families, gender equality, and democratic governance. This cultural model has spread from its origins among the elites of northwest Europe to elites and ordinary people throughout the world. Developmental idealism has become so entrenched in local, national, and global social institutions that it has now achieved a taken-for-granted status among many national elites, academics, development practitioners, and ordinary people around the world. We argue that developmental idealism culture has been a fundamental force behind many cultural clashes within and between societies, and continues to be an important cause of much global social change. We suggest that developmental idealism should be included as a causal factor in theories of human behavior and social change. PMID:26457325

Neurocultural evidence that ideal affect match promotes giving.

PubMed

Park, BoKyung; Blevins, Elizabeth; Knutson, Brian; Tsai, Jeanne L

2017-07-01

Why do people give to strangers? We propose that people trust and give more to those whose emotional expressions match how they ideally want to feel ("ideal affect match"). European Americans and Koreans played multiple trials of the Dictator Game with recipients who varied in emotional expression (excited, calm), race (White, Asian) and sex (male, female). Consistent with their culture's valued affect, European Americans trusted and gave more to excited than calm recipients, whereas Koreans trusted and gave more to calm than excited recipients. These findings held regardless of recipient race and sex. We then used fMRI to probe potential affective and mentalizing mechanisms. Increased activity in the nucleus accumbens (associated with reward anticipation) predicted giving, as did decreased activity in the right temporo-parietal junction (rTPJ; associated with reduced belief prediction error). Ideal affect match decreased rTPJ activity, suggesting that people may trust and give more to strangers whom they perceive to share their affective values. © The Author (2017). Published by Oxford University Press.

Perceptual thresholds for non-ideal diffuse field reverberation.

PubMed

Romblom, David; Guastavino, Catherine; Depalle, Philippe

2016-11-01

The objective of this study is to understand listeners' sensitivity to directional variations in non-ideal diffuse field reverberation. An ABX discrimination test was conducted using a semi-spherical 28-loudspeaker array; perceptual thresholds were estimated by systematically varying the level of a segment of loudspeakers for lateral, height, and frontal conditions. The overall energy was held constant using a gain compensation scheme. When compared to an ideal diffuse field, the perceptual threshold for detection is -2.5 dB for the lateral condition, -6.8 dB for the height condition, and -3.2 dB for the frontal condition. Measurements of the experimental stimuli were analyzed using a Head and Torso Simulator as well as with opposing cardioid microphones aligned on the three Cartesian axes. Additionally, opposing cardioid measurements made in an acoustic space demonstrate that level differences corresponding to the perceptual thresholds can be found in practice. These results suggest that non-ideal diffuse field reverberation may be a previously unrecognized component of spatial impression.

Measuring explosive non-ideality

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

Souers, P C

1999-02-17

The sonic reaction zone length may be measured by four methods: (1) size effect, (2) detonation front curvature, (3) crystal interface velocity and (4) in-situ gauges. The amount of data decreases exponentially from (1) to (4) with there being almost no gauge data for prompt detonation at steady state. The ease and clarity of obtaining the reaction zone length increases from (1) to (4). The method of getting the reaction zone length, , is described for the four methods. A measure of non-ideality is proposed: the reaction zone length divided by the cylinder radius. N = /R{sub o}.more » N = 0 for true ideality. It also decreases with increasing radius as it should. For N < 0.10, an equilibrium EOS like the JWL may be used. For N > 0.10, a time-dependent description is essential. The crystal experiment, which measures the particle velocity of an explosive-transparent material interface, is presently rising in importance. We examine the data from three experiments and apply: (1) an impedance correction that transfers the explosive C-J particle velocity to the corresponding value for the interface, and (2) multiplies the interface time by 3/4 to simulate the explosive speed of sound. The result is a reaction zone length comparable to those obtained by other means. A few explosives have reaction zones so small that the change of slope in the particle velocity is easily seen.« less

The effect of priming materialism on women's responses to thin-ideal media.

PubMed

Ashikali, Eleni-Marina; Dittmar, Helga

2012-12-01

Consumer culture is characterized by two prominent ideals: the 'body perfect' and the material 'good life'. Although the impact of these ideals has been investigated in separate research literatures, no previous research has examined whether materialism is linked to women's responses to thin-ideal media. Data from several studies confirm that the internalization of materialistic and body-ideal values is positively linked in women. After developing a prime for materialism (N = 50), we present an experimental examination (N = 155) of the effects of priming materialism on women's responses to thin-ideal media, using multiple outcome measures of state body dissatisfaction. Priming materialism affects women's body dissatisfaction after exposure to thin media models, but differently depending on the dimension of body image measured. The two main novel findings are that (1) priming materialism heightens the centrality of appearance to women's self-concept and (2) priming materialism influences the activation of body-related self-discrepancies (BRSDs), particularly for highly materialistic women. Exposure to materialistic media has a clear influence on women's body image, with trait materialism a further vulnerability factor for negative exposure effects in response to idealized, thin media models. ©2011 The British Psychological Society.

Quantum cryptography with an ideal local relay

NASA Astrophysics Data System (ADS)

Spedalieri, Gaetana; Ottaviani, Carlo; Braunstein, Samuel L.; Gehring, Tobias; Jacobsen, Christian S.; Andersen, Ulrik L.; Pirandola, Stefano

2015-10-01

We consider two remote parties connected to a relay by two quantum channels. To generate a secret key, they transmit coherent states to the relay, where the states are subject to a continuous-variable (CV) Bell detection. We study the ideal case where Alice's channel is lossless, i.e., the relay is locally in her lab and the Bell detection is perfomed with unit efficiency. This configuration allows us to explore the optimal performances achievable by CV measurement-device-independent quantum key distribution. This corresponds to the limit of a trusted local relay, where the detection loss can be re-scaled. Our theoretical analysis is confirmed by an experimental simulation where 10-4 secret bits per use can potentially be distributed at 170km assuming ideal reconciliation.

Self-guide framing and persuasion: responsibly increasing message processing to ideal levels.

PubMed

Evans, Lisa M; Petty, Richard E

2003-03-01

The current research examines the effect that framing persuasive messages in terms of self-guides (ideal vs. ought) has on the attitudes and cognitive responses of individuals with chronic ideal versus ought self-guides. The strength of participants' ideal and ought self-guides and the magnitude of participants' ideal and ought self-discrepancies were measured using a computerized reaction time program. One week later, participants read a persuasive message about a fictional breakfast product, framed in terms of either ideals or oughts. Matching framing to stronger self-guide led to enhanced message processing activity, especially among individuals who were low in need for cognition. Individuals who read messages framed to match their stronger self-guides paid more attention to argument quality, as reflected in their attitudes and cognitive responses. Messages with self-guide framing that matched individuals' stronger self-discrepancies did not have this effect on processing.

A Darker Shade of Love: Machiavellianism and Positive Assortative Mating Based on Romantic Ideals

PubMed Central

Ináncsi, Tamás; Láng, András; Bereczkei, Tamás

2016-01-01

Machiavellianism is a personality trait that is characterized by manipulative and exploitative attitude toward others, lack of empathy, and a cynical view of human nature. In itself or as part of the Dark Triad it has been the target of several studies investigating romantic relations. Nevertheless, the relationship between Machiavellianism and romantic ideals has not been revealed yet. An undergraduate sample of 143 (92 females) with an average age of 19.83 years (SD = 1.51 years) filled out self-report measures of Machiavellianism (Mach-IV Scale) and romantic ideals (Ideal Standards Scale and NEO-FFI-IDEAL). According to our results, Machiavellianism correlated negatively with the importance of partner’s warmth-trustworthiness, extraversion, openness, agreeableness, and with the importance of intimacy and loyalty in their ideal relationships. Machiavellianism correlated positively with the ideal partner’s possession over status and resources. Explorative factor analysis revealed three components of ideal partner’s characteristics. Machiavellianism loaded significantly on two out of three components. Results are discussed with regard to Ideal Standards Model and the Big Five model of personality. PMID:27247697

Ambivalent Sexism in Close Relationships: (Hostile) Power and (Benevolent) Romance Shape Relationship Ideals

PubMed Central

Lee, Tiane L.; Fiske, Susan T.; Glick, Peter; Chen, Zhixia

2013-01-01

Gender-based structural power and heterosexual dependency produce ambivalent gender ideologies, with hostility and benevolence separately shaping close-relationship ideals. The relative importance of romanticized benevolent versus more overtly power-based hostile sexism, however, may be culturally dependent. Testing this, northeast US (N=311) and central Chinese (N=290) undergraduates rated prescriptions and proscriptions (ideals) for partners and completed Ambivalent Sexism and Ambivalence toward Men Inventories (ideologies). Multiple regressions analyses conducted on group-specific relationship ideals revealed that benevolent ideologies predicted partner ideals, in both countries, especially for US culture’s romance-oriented relationships. Hostile attitudes predicted men’s ideals, both American and Chinese, suggesting both societies’ dominant-partner advantage. PMID:23914004

Axisymmetric ideal MHD stellar wind flow

NASA Technical Reports Server (NTRS)

Heinemann, M.; Olbert, S.

1978-01-01

The ideal MHD equations are reduced to a single equation under the assumption of axisymmetric flow. A variational principle from which the equation is derivable is given. The characteristics of the equation are briefly discussed. The equation is used to rederive the theorem of Gussenhoven and Carovillano.

Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients.

PubMed

Lim, Eileen C P; Brett, Maggie; Lai, Angeline H M; Lee, Siew-Peng; Tan, Ee-Shien; Jamuar, Saumya S; Ng, Ivy S L; Tan, Ene-Choo

2015-12-14

Next-generation sequencing (NGS) has revolutionized genetic research and offers enormous potential for clinical application. Sequencing the exome has the advantage of casting the net wide for all known coding regions while targeted gene panel sequencing provides enhanced sequencing depths and can be designed to avoid incidental findings in adult-onset conditions. A HaloPlex panel consisting of 180 genes within commonly altered chromosomal regions is available for use on both the Ion Personal Genome Machine (PGM) and MiSeq platforms to screen for causative mutations in these genes. We used this Haloplex ICCG panel for targeted sequencing of 15 patients with clinical presentations indicative of an abnormality in one of the 180 genes. Sequencing runs were done using the Ion 318 Chips on the Ion Torrent PGM. Variants were filtered for known polymorphisms and analysis was done to identify possible disease-causing variants before validation by Sanger sequencing. When possible, segregation of variants with phenotype in family members was performed to ascertain the pathogenicity of the variant. More than 97% of the target bases were covered at >20×. There was an average of 9.6 novel variants per patient. Pathogenic mutations were identified in five genes for six patients, with two novel variants. There were another five likely pathogenic variants, some of which were unreported novel variants. In a cohort of 15 patients, we were able to identify a likely genetic etiology in six patients (40%). Another five patients had candidate variants for which further evaluation and segregation analysis are ongoing. Our results indicate that the HaloPlex ICCG panel is useful as a rapid, high-throughput and cost-effective screening tool for 170 of the 180 genes. There is low coverage for some regions in several genes which might have to be supplemented by Sanger sequencing. However, comparing the cost, ease of analysis, and shorter turnaround time, it is a good alternative to exome

Sustainable Design of EPA's Campus in Research Triangle Park, NC—Environmental Performance Specifications in Construction Contracts—Section 01450 Sequence of Finishes Installation

EPA Pesticide Factsheets

Learn more about the special construction scheduling/sequencing requirements and procedures necessary to assure achievement of designed Indoor Air Quality (IAQ) levels for the completed project required by the EPA IAQ Program.

Kinetic modeling of non-ideal explosives with CHEETAH

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

Fried, L E; Howard, W M; Souers, P C

1998-08-06

We report an implementation of the Wood-Kirkwood kinetic detonation model based on multi-species equations of state and multiple reaction rate laws. Finite rate laws are used for the slowest chemical reactions. Other reactions are given infinite rates and are kept in constant thermodynamic equilibrium. We model a wide range of ideal and non-ideal composite energetic materials. We find that we can replicate experimental detonation velocities to within a few per cent, while obtaining good agreement with estimated reaction zone lengths. The detonation velocity as a function of charge radius is also correctly reproduced.

Complexity of culture: the role of identity and context in bicultural individuals' body ideals.

PubMed

Guan, Mei; Lee, Fiona; Cole, Elizabeth R

2012-07-01

Culture plays an important role in shaping body image, and people from different cultures have different beliefs about what constitutes the "ideal" body type. This study examines the relationship between culture and body ideals in Asian-American and Black-American women. Results from two studies show that subjective cultural identity and situational cultural cues had different relationships with body ideals. Among Asian-American women, identification with Asian culture was related to a thinner body ideal, but exposure to Asian cultural cues (relative to American cultural cues) was related to a thicker body ideal. Among Black-American women, identification with Black culture was related to a thicker body ideal, but exposure to Black cultural cues (relative to American cultural cues) was related to a thinner body ideal. These results have theoretical and practical implications for understanding how internal and external manifestations of culture can differentially influence body image.

A Comparison of Learning Management Systems in a School District: Searching for the Ideal Personalized Integrated Educational System (PIES)

ERIC Educational Resources Information Center

Yildirim, Zahide; Reigeluth, Charles M.; Kwon, Seolim; Kageto, Yuichi; Shao, Zihang

2014-01-01

This study explored the use of several learning management systems (LMS), their benefits, and their limitations in relation to the desired characteristics of an ideal Personalized Integrated Educational System (PIES) for the information age. A qualitative research design was used. The participants of the study were teachers, administrators, and…

Analysis of first and second order binary quantized digital phase-locked loops for ideal and white Gaussian noise inputs

NASA Technical Reports Server (NTRS)

Blasche, P. R.

1980-01-01

Specific configurations of first and second order all digital phase locked loops are analyzed for both ideal and additive white gaussian noise inputs. In addition, a design for a hardware digital phase locked loop capable of either first or second order operation is presented along with appropriate experimental data obtained from testing of the hardware loop. All parameters chosen for the analysis and the design of the digital phase locked loop are consistent with an application to an Omega navigation receiver although neither the analysis nor the design are limited to this application.

Current and ideal skin tone: Associations with tanning behavior among sexual minority men.

PubMed

Klimek, Patrycja; Lamb, Kalina M; Nogg, Kelsey A; Rooney, Benjamin M; Blashill, Aaron J

2018-06-01

Sexual minority men have high rates of skin cancer, yet little is known about skin cancer risk behaviors in this population. It was hypothesized that current skin tone would moderate the association between darker ideals and tanning behaviors. Data were collected online from 231 sexual minority men in San Diego, United States of America, with a mean age of 24.66 (SD = 5.44). Ideal and current skin tone ratings and indoor and outdoor tanning behaviors were assessed. Darker ideals were significantly associated with increased indoor and outdoor tanning. The effect of darker ideals on tanning was strongest among individuals with lighter current skin tone, indicating a significant interaction. Sexual minority men whose perceived skin tone did not match their ideal were more likely to engage in skin cancer risk behaviors. Future skin cancer prevention programs aimed at sexual minority men may consider techniques that modify ideal skin tone internalization. Copyright © 2018 Elsevier Ltd. All rights reserved.

Water: The Ideal Early Learning Environment

ERIC Educational Resources Information Center

Grosse, Susan J.

2008-01-01

Bathtubs and swimming pools provide the ideal learning environment for people with special needs. For young preschool children, the activities that take place through water can help them develop physical fitness, facilitate motor development, reinforce perceptual-motor ability, encourage social development, and enhance self-esteem and confidence.…

Evaluation of Frameworks for HSCT Design Optimization

NASA Technical Reports Server (NTRS)

Krishnan, Ramki

1998-01-01

This report is an evaluation of engineering frameworks that could be used to augment, supplement, or replace the existing FIDO 3.5 (Framework for Interdisciplinary Design and Optimization Version 3.5) framework. The report begins with the motivation for this effort, followed by a description of an "ideal" multidisciplinary design and optimization (MDO) framework. The discussion then turns to how each candidate framework stacks up against this ideal. This report ends with recommendations as to the "best" frameworks that should be down-selected for detailed review.

What Do We Make of Design? Design as a Concept in Educational Technology

ERIC Educational Resources Information Center

Smith, Kennon M.; Boling, Elizabeth

2009-01-01

The purpose of the research reported in this article is to identify, where possible, fundamental qualities which tend to be associated with idealized representations of the concept of "design" in educational technology. Accordingly, the authors ask, "What are essential characteristics of design in educational technology, as represented in and…

Ideal light concentrators with reflector gaps

DOEpatents

Winston, Roland

1980-01-01

A cylindrical or trough-like radiant energy concentration and collection device is provided. The device includes an energy absorber, a glazing enveloping the absorber and a reflective wall. The ideal contour of the reflective wall is determined with reference to a virtual absorber and not the actual absorber cross section.

Ideal MHD Stability Prediction and Required Power for EAST Advanced Scenario

NASA Astrophysics Data System (ADS)

Chen, Junjie; Li, Guoqiang; Qian, Jinping; Liu, Zixi

2012-11-01

The Experimental Advanced Superconducting Tokamak (EAST) is the first fully superconducting tokamak with a D-shaped cross-sectional plasma presently in operation. The ideal magnetohydrodynamic (MHD) stability and required power for the EAST advanced tokamak (AT) scenario with negative central shear and double transport barrier (DTB) are investigated. With the equilibrium code TOQ and stability code GATO, the ideal MHD stability is analyzed. It is shown that a moderate ratio of edge transport barriers' (ETB) height to internal transport barriers' (ITBs) height is beneficial to ideal MHD stability. The normalized beta βN limit is about 2.20 (without wall) and 3.70 (with ideal wall). With the scaling law of energy confinement time, the required heating power for EAST AT scenario is calculated. The total heating power Pt increases as the toroidal magnetic field BT or the normalized beta βN is increased.

Good feelings in christianity and buddhism: religious differences in ideal affect.

PubMed

Tsai, Jeanne L; Miao, Felicity F; Seppala, Emma

2007-03-01

Affect valuation theory (AVT) predicts cultural variation in the affective states that people ideally want to feel (i.e., "ideal affect"). National and ethnic comparisons support this prediction: For instance, European Americans (EA) value high arousal positive (HAP) states (e.g., excitement) more and low arousal positive (LAP) states (e.g., calm) less than Hong Kong Chinese. In this article, the authors examine whether religions differ in the ideal affective states they endorse. The authors predicted that Christianity values HAP more and LAP less than Buddhism. In Study 1, they compared Christian and Buddhist practitioners' ideal affect. In Studies 2 and 3, they compared the endorsement of HAP and LAP in Christian and Buddhist classical texts (e.g., Gospels, Lotus Sutra) and contemporary self-help books (e.g., Your Best Life Now, Art of Happiness). Findings supported predictions, suggesting that AVT applies to religious and to national and ethnic cultures.

Avatars mirroring the actual self versus projecting the ideal self: the effects of self-priming on interactivity and immersion in an exergame, Wii Fit.

PubMed

Jin, Seung-A Annie

2009-12-01

As exergames are increasingly being used as an interventional tool to fight the obesity epidemic in clinical studies, society is absorbing their impact to a more intense degree. Interactivity and immersion are key factors that attract exergame consumers. This research asks, What are the effects of priming the actual self versus the ideal self on users' perceived interactivity and immersion in avatar-based exergame playing? and What are important moderators that play a role in exergame users' self-concept perception? To answer these research questions, this study leveraged the Wii's avatar-creating function (Mii Channel) and exergame feature (Wii Fit) in a controlled, randomized experimental design (N = 126). The results of a 2 x 2 factorial design experiment demonstrated the significant main effect of self-priming on interactivity and the moderating role of the actual-ideal self-concept discrepancy in influencing immersion during exergame playing. Game players who created an avatar reflecting the ideal self reported greater perceived interactivity than those who created a replica avatar mirroring the actual self. A two-way ANOVA demonstrated the moderating role of the actual-ideal self-concept discrepancy in determining the effects of the primed regulatory focus on immersion in the exergame play. The underlying theoretical mechanism is derived from and explained by Higgins's self-concept discrepancy perspective. Practical implications for game developers and managerial implications for the exergame industry are discussed.

Insights into the role of protein molecule size and structure on interfacial properties using designed sequences

PubMed Central

Dwyer, Mirjana Dimitrijev; He, Lizhong; James, Michael; Nelson, Andrew; Middelberg, Anton P. J.

2013-01-01

Mixtures of a large, structured protein with a smaller, unstructured component are inherently complex and hard to characterize at interfaces, leading to difficulties in understanding their interfacial behaviours and, therefore, formulation optimization. Here, we investigated interfacial properties of such a mixed system. Simplicity was achieved using designed sequences in which chemical differences had been eliminated to isolate the effect of molecular size and structure, namely a short unstructured peptide (DAMP1) and its longer structured protein concatamer (DAMP4). Interfacial tension measurements suggested that the size and bulk structuring of the larger molecule led to much slower adsorption kinetics. Neutron reflectometry at equilibrium revealed that both molecules adsorbed as a monolayer to the air–water interface (indicating unfolding of DAMP4 to give a chain of four connected DAMP1 molecules), with a concentration ratio equal to that in the bulk. This suggests the overall free energy of adsorption is equal despite differences in size and bulk structure. At small interfacial extensional strains, only molecule packing influenced the stress response. At larger strains, the effect of size became apparent, with DAMP4 registering a higher stress response and interfacial elasticity. When both components were present at the interface, most stress-dissipating movement was achieved by DAMP1. This work thus provides insights into the role of proteins' molecular size and structure on their interfacial properties, and the designed sequences introduced here can serve as effective tools for interfacial studies of proteins and polymers. PMID:23303222

Distinguishing thrust sequences in gravity-driven fold and thrust belts

NASA Astrophysics Data System (ADS)

Alsop, G. I.; Weinberger, R.; Marco, S.

2018-04-01

Piggyback or foreland-propagating thrust sequences, where younger thrusts develop in the footwalls of existing thrusts, are generally assumed to be the typical order of thrust development in most orogenic settings. However, overstep or 'break-back' sequences, where later thrusts develop above and in the hangingwalls of earlier thrusts, may potentially form during cessation of movement in gravity-driven mass transport deposits (MTDs). In this study, we provide a detailed outcrop-based analysis of such an overstep thrust sequence developed in an MTD in the southern Dead Sea Basin. Evidence that may be used to discriminate overstep thrusting from piggyback thrust sequences within the gravity-driven fold and thrust belt includes upright folds and forethrusts that are cut by younger overlying thrusts. Backthrusts form ideal markers that are also clearly offset and cut by overlying younger forethrusts. Portions of the basal detachment to the thrust system are folded and locally imbricated in footwall synclines below forethrust ramps, and these geometries also support an overstep sequence. However, new 'short-cut' basal detachments develop below these synclines, indicating that movement continued on the basal detachment rather than it being abandoned as in classic overstep sequences. Further evidence for 'synchronous thrusting', where movement on more than one thrust occurs at the same time, is provided by displacement patterns on sequences of thrust ramp imbricates that systematically increases downslope towards the toe of the MTD. Older thrusts that initiate downslope in the broadly overstep sequence continue to move and therefore accrue greater displacements during synchronous thrusting. Our study provides a template to help distinguish different thrust sequences in both orogenic settings and gravity-driven surficial systems, with displacement patterns potentially being imaged in seismic sections across offshore MTDs.

Critical Reflection as a Rationalistic Ideal

ERIC Educational Resources Information Center

van Woerkom, Marianne

2010-01-01

There is a growing interest in the concept of critical reflection in the adult learning and management literature. In this article, the author examines four different intellectual traditions that inform the use of the term "critical reflection" on the different ideals they express and the different definitions of critical reflection they use. On…

Derivation of the Ideal Gas Law

ERIC Educational Resources Information Center

Laugier, Alexander; Garai, Jozsef

2007-01-01

Undergraduate and graduate physics and chemistry books usually state that combining the gas laws results in the ideal gas law. Leaving the derivation to the students implies that this should be a simple task, most likely a substitution. Boyle's law, Charles's law, and the Avogadro's principle are given under certain conditions; therefore, direct…

Realizing a Rasch measurement through instructionally- sequenced domains of test items.

NASA Astrophysics Data System (ADS)

Schulz, E. Matthew

2016-11-01

This paper presents results from a project in which instructionally-sequenced domains were defined for purposes of constructing measures that that conform to an ideal in Guttman scaling and Rasch measurement. A fundamental idea in these measurement systems is that every person higher on the measurement scale can do everything that lower-level persons can do, plus at least one more thing. This idea has had limited application in educational measurement due to the stochastic nature of item response data and the sheer number of items needed to obtain reliable measures. However, it has been shown by Schulz, Lee, and Mullen [1] that this ideal can be can be realized at a higher level of abstraction - when items within a content strand are aggregated into a small number of domains that are ordered in instructional timing and difficulty. The present paper shows how this was done, and the results, in an achievement level setting project for the 2007 Grade 12 NAEP Economics Assessment.

Simulation of Cold Flow in a Truncated Ideal Nozzle with Film Cooling

NASA Technical Reports Server (NTRS)

Braman, Kalen; Ruf, Joseph

2015-01-01

Flow transients during rocket start-up and shut-down can lead to significant side loads on rocket nozzles. The capability to estimate these side loads computationally can streamline the nozzle design process. Towards this goal, the flow in a truncated ideal contour (TIC) nozzle has been simulated for a range of nozzle pressure ratios (NPRs) aimed to match a series of cold flow experiments performed at the NASA MSFC Nozzle Test Facility. These simulations were performed with varying turbulence model choices and with four different versions of the TIC nozzle model geometry, each of which was created with a different simplification to the test article geometry.

Enhanced learning of natural visual sequences in newborn chicks.

PubMed

Wood, Justin N; Prasad, Aditya; Goldman, Jason G; Wood, Samantha M W

2016-07-01

To what extent are newborn brains designed to operate over natural visual input? To address this question, we used a high-throughput controlled-rearing method to examine whether newborn chicks (Gallus gallus) show enhanced learning of natural visual sequences at the onset of vision. We took the same set of images and grouped them into either natural sequences (i.e., sequences showing different viewpoints of the same real-world object) or unnatural sequences (i.e., sequences showing different images of different real-world objects). When raised in virtual worlds containing natural sequences, newborn chicks developed the ability to recognize familiar images of objects. Conversely, when raised in virtual worlds containing unnatural sequences, newborn chicks' object recognition abilities were severely impaired. In fact, the majority of the chicks raised with the unnatural sequences failed to recognize familiar images of objects despite acquiring over 100 h of visual experience with those images. Thus, newborn chicks show enhanced learning of natural visual sequences at the onset of vision. These results indicate that newborn brains are designed to operate over natural visual input.

A Three-Dimensional Approach and Open Source Structure for the Design and Experimentation of Teaching-Learning Sequences: The case of friction

NASA Astrophysics Data System (ADS)

Besson, Ugo; Borghi, Lidia; De Ambrosis, Anna; Mascheretti, Paolo

2010-07-01

We have developed a teaching-learning sequence (TLS) on friction based on a preliminary study involving three dimensions: an analysis of didactic research on the topic, an overview of usual approaches, and a critical analysis of the subject, considered also in its historical development. We found that mostly the usual presentations do not take into account the complexity of friction as it emerges from scientific research, may reinforce some inaccurate students' conceptions, and favour a limited vision of friction phenomena. The TLS we propose begins by considering a wide range of friction phenomena to favour an initial motivation and a broader view of the topic and then develops a path of interrelated observations, experiments, and theoretical aspects. It proposes the use of structural models, involving visual representations and stimulating intuition, aimed at helping students build mental models of friction mechanisms. To facilitate the reproducibility in school contexts, the sequence is designed as an open source structure, with a core of contents, conceptual correlations and methodological choices, and a cloud of elements that can be re-designed by teachers. The sequence has been tested in teacher education and in upper secondary school, and has shown positive results in overcoming student difficulties and stimulating richer reasoning based on the structural models we suggested. The proposed path has modified the teachers' view of the topic, producing a motivation to change their traditional presentations. The open structure of the sequence has facilitated its implementation by teachers in school in coherence with the rationale of the proposal.

Evaluation of high-intensity focused ultrasound ablation for uterine fibroids: an IDEAL prospective exploration study.

PubMed

Chen, J; Li, Y; Wang, Z; McCulloch, P; Hu, L; Chen, W; Liu, G; Li, J; Lang, J

2018-02-01

To evaluate the clinical outcomes of high-intensity focused ultrasound (HIFU) and surgery in treating uterine fibroids, and prepare for a definitive randomised trial. Prospective multicentre patient choice cohort study (IDEAL Exploratory study) of HIFU, myomectomy or hysterectomy for treating symptomatic uterine fibroids. 20 Chinese hospitals. 2411 Chinese women with symptomatic fibroids. Prospective non-randomised cohort study with learning curve analysis (IDEAL Stage 2b Prospective Exploration Study). Complications, hospital stay, return to normal activities, and quality of life (measured with UFS-Qol and SF-36 at baseline, 6 and 12 months), and need for further treatment. Quality-of-life outcomes were adjusted using regression modelling. HIFU treatment quality was evaluated using LC-CUSUM to identify operator learning curves. A health economic analysis of costs was performed. 1353 women received HIFU, 472 hysterectomy and 586 myomectomy. HIFU patients were significantly younger (P < 0.001), slimmer (P < 0.001), better educated (P < 0.001), and wealthier (P = 0.002) than surgery patients. Both UFS and QoL improved more rapidly after HIFU than after surgery (P = 0.002 and P = 0.001, respectively at 6 months), but absolute differences were small. Major adverse events occurred in 3 (0.2%) of HIFU and in 133 (12.6%) of surgical cases (P < 0.001). Median time for hospital stay was 4 days (interquartile range, 0-5 days), 10 days (interquartile range, 8-12.5 days) and 8 days (interquartile range, 7-10 days). HIFU caused substantially less morbidity than surgery, with similar longer-term QoL. Despite group baseline differences and lack of blinding, these findings support the need for a randomised controlled trial (RCT) of HIFU treatment for fibroids. The IDEAL Exploratory design facilitated RCT protocol development. HIFU had much better short-term outcomes than surgery for fibroids in 2411-patient Chinese IDEAL format study. © 2017 Royal College of Obstetricians and

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

PubMed Central

2011-01-01

Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/. PMID:21385349

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

PubMed

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

Karl Jaspers on the disease entity: Kantian ideas and Weberian ideal types.

PubMed

Walker, Chris

2014-09-01

Jaspers' nosology is indebted to Immanuel Kant's theory of knowledge. He drew the distinction of form and content from the Transcendental Analytic of Kant's Critique of Pure Reason. The distinction is universal to all knowledge, including psychopathology. Individual experience is constituted by a form or category of the Understanding to give a determinate or knowable object classified into the generic type of a real disease entity. The application of form and content is limited by the boundaries of experience. Beyond this boundary are wholes whose conception requires Ideas of reason drawn from the Transcendental Dialectic. Wholes are regulated by Ideas of reason to give an object or schema of the Idea collected into ideal types of an ideal typical disease entity. Jaspers drew ideal types from Max Weber's social theory. He anticipated that, as knowledge advanced, ideal typical disease entities would become real disease entities. By 1920, this had been the destiny of general paralysis as knowledge of its neuropathology, serology and microbiology emerged. As he presented the final edition of General Psychopathology in 1946, Jaspers was anticipating the transition of schizophrenia from ideal typical to real disease entity. Almost 70 years later, with knowledge of its aetiology still unclear, schizophrenia remains marooned as an ideal typical disease entity - still awaiting that crucial advance! © The Author(s) 2014.

Using genetic prediction from known complex disease Loci to guide the design of next-generation sequencing experiments.

PubMed

Jostins, Luke; Levine, Adam P; Barrett, Jeffrey C

2013-01-01

A central focus of complex disease genetics after genome-wide association studies (GWAS) is to identify low frequency and rare risk variants, which may account for an important fraction of disease heritability unexplained by GWAS. A profusion of studies using next-generation sequencing are seeking such risk alleles. We describe how already-known complex trait loci (largely from GWAS) can be used to guide the design of these new studies by selecting cases, controls, or families who are most likely to harbor undiscovered risk alleles. We show that genetic risk prediction can select unrelated cases from large cohorts who are enriched for unknown risk factors, or multiply-affected families that are more likely to harbor high-penetrance risk alleles. We derive the frequency of an undiscovered risk allele in selected cases and controls, and show how this relates to the variance explained by the risk score, the disease prevalence and the population frequency of the risk allele. We also describe a new method for informing the design of sequencing studies using genetic risk prediction in large partially-genotyped families using an extension of the Inside-Outside algorithm for inference on trees. We explore several study design scenarios using both simulated and real data, and show that in many cases genetic risk prediction can provide significant increases in power to detect low-frequency and rare risk alleles. The same approach can also be used to aid discovery of non-genetic risk factors, suggesting possible future utility of genetic risk prediction in conventional epidemiology. Software implementing the methods in this paper is available in the R package Mangrove.

Generic Science Skills Enhancement of Students through Implementation of IDEAL Problem Solving Model on Genetic Information Course

NASA Astrophysics Data System (ADS)

Zirconia, A.; Supriyanti, F. M. T.; Supriatna, A.

2018-04-01

This study aims to determine generic science skills enhancement of students through implementation of IDEAL problem-solving model on genetic information course. Method of this research was mixed method, with pretest-posttest nonequivalent control group design. Subjects of this study were chemistry students enrolled in biochemistry course, consisted of 22 students in the experimental class and 19 students in control class. The instrument in this study was essayed involves 6 indicators generic science skills such as indirect observation, causality thinking, logical frame, self-consistent thinking, symbolic language, and developing concept. The results showed that genetic information course using IDEAL problem-solving model have been enhancing generic science skills in low category with of 20,93%. Based on result for each indicator, showed that there are indicators of generic science skills classified in the high category.

Optimization of sequence alignment for simple sequence repeat regions.

PubMed

Jighly, Abdulqader; Hamwieh, Aladdin; Ogbonnaya, Francis C

2011-07-20

Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs) mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs).SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type.When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic phylogenic relationship.

Sensitive and Specific Target Sequences Selected from Retrotransposons of Schistosoma japonicum for the Diagnosis of Schistosomiasis

PubMed Central

Xu, Jing; Zhu, Xing-Quan; Wang, Sheng-Yue; Xia, Chao-Ming

2012-01-01

Background Schistosomiasis japonica is a serious debilitating and sometimes fatal disease. Accurate diagnostic tests play a key role in patient management and control of the disease. However, currently available diagnostic methods are not ideal, and the detection of the parasite DNA in blood samples has turned out to be one of the most promising tools for the diagnosis of schistosomiasis. In our previous investigations, a 230-bp sequence from the highly repetitive retrotransposon SjR2 was identified and it showed high sensitivity and specificity for detecting Schistosoma japonicum DNA in the sera of rabbit model and patients. Recently, 29 retrotransposons were found in S. japonicum genome by our group. The present study highlighted the key factors for selecting a new perspective sensitive target DNA sequence for the diagnosis of schistosomiasis, which can serve as example for other parasitic pathogens. Methodology/Principal Findings In this study, we demonstrated that the key factors based on the bioinformatic analysis for selecting target sequence are the higher genome proportion, repetitive complete copies and partial copies, and active ESTs than the others in the chromosome genome. New primers based on 25 novel retrotransposons and SjR2 were designed and their sensitivity and specificity for detecting S. japonicum DNA were compared. The results showed that a new 303-bp sequence from non-long terminal repeat (LTR) retrotransposon (SjCHGCS19) had high sensitivity and specificity. The 303-bp target sequence was amplified from the sera of rabbit model at 3 d post-infection by nested-PCR and it became negative at 17 weeks post-treatment. Furthermore, the percentage sensitivity of the nested-PCR was 97.67% in 43 serum samples of S. japonicum-infected patients. Conclusions/Significance Our findings highlighted the key factors based on the bioinformatic analysis for selecting target sequence from S. japonicum genome, which provide basis for establishing powerful

The Heat Capacity of Ideal Gases

ERIC Educational Resources Information Center

Scott, Robert L.

2006-01-01

The heat capacity of an ideal gas has been shown to be calculable directly by statistical mechanics if the energies of the quantum states are known. However, unless one makes careful calculations, it is not easy for a student to understand the qualitative results. Why there are maxima (and occasionally minima) in heat capacity-temperature curves…

Ideal gas behavior of a strongly coupled complex (dusty) plasma.

PubMed

Oxtoby, Neil P; Griffith, Elias J; Durniak, Céline; Ralph, Jason F; Samsonov, Dmitry

2013-07-05

In a laboratory, a two-dimensional complex (dusty) plasma consists of a low-density ionized gas containing a confined suspension of Yukawa-coupled plastic microspheres. For an initial crystal-like form, we report ideal gas behavior in this strongly coupled system during shock-wave experiments. This evidence supports the use of the ideal gas law as the equation of state for soft crystals such as those formed by dusty plasmas.

IDEAL 3D spoiled gradient echo of the articular cartilage of the knee on 3.0 T MRI: a comparison with conventional 3.0 T fast spin-echo T2 fat saturation image.

PubMed

Han, Chul Hee; Park, Hee Jin; Lee, So Yeon; Chung, Eun Chul; Choi, Seon Hyeong; Yun, Ji Sup; Rho, Myung Ho

2015-12-01

Many two-dimensional (2D) morphologic cartilage imaging sequences have disadvantages such as long acquisition time, inadequate spatial resolution, suboptimal tissue contrast, and image degradation secondary to artifacts. IDEAL imaging can overcome these disadvantages. To compare sound-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and quality of two different methods of imaging that include IDEAL 3D SPGR and 3.0-T FSE T2 fat saturation (FS) imaging and to evaluate the utility of IDEAL 3D SPGR for knee joint imaging. SNR and CNR of the patellar and femoral cartilages were measured and calculated. Two radiologists performed subjective scoring of all images for three measures: general image quality, FS, and cartilage evaluation. SNR and CNR values were compared by paired Student's t-tests. Mean SNRs of patellar and femoral cartilages were 90% and 66% higher, respectively, for IDEAL 3D SPGR. CNRs of patellar cartilages and joint fluids were 2.4 times higher for FSE T2 FS, and CNR between the femoral cartilage and joint fluid was 2.2 times higher for FSE T2 FS. General image quality and FS were superior using FSE T2 FS compared to those of IDEAL 3D SPGR imaging according to both readers, while cartilage evaluation was superior using IDEAL 3D SPGR. Additionally, cartilage injuries were more prominent in IDEAL 3D SPGR than in FSE T2FS according to both readers. IDEAL 3D SPGR images show excellent visualization of patellar and femoral cartilages in 3.0 T and can compensate for the weaknesses of FSE T2 FS in the evaluation of cartilage injuries. © The Foundation Acta Radiologica 2014.

Sequence information signal processor for local and global string comparisons

DOEpatents

Peterson, John C.; Chow, Edward T.; Waterman, Michael S.; Hunkapillar, Timothy J.

1997-01-01

A sequence information signal processing integrated circuit chip designed to perform high speed calculation of a dynamic programming algorithm based upon the algorithm defined by Waterman and Smith. The signal processing chip of the present invention is designed to be a building block of a linear systolic array, the performance of which can be increased by connecting additional sequence information signal processing chips to the array. The chip provides a high speed, low cost linear array processor that can locate highly similar global sequences or segments thereof such as contiguous subsequences from two different DNA or protein sequences. The chip is implemented in a preferred embodiment using CMOS VLSI technology to provide the equivalent of about 400,000 transistors or 100,000 gates. Each chip provides 16 processing elements, and is designed to provide 16 bit, two's compliment operation for maximum score precision of between -32,768 and +32,767. It is designed to provide a comparison between sequences as long as 4,194,304 elements without external software and between sequences of unlimited numbers of elements with the aid of external software. Each sequence can be assigned different deletion and insertion weight functions. Each processor is provided with a similarity measure device which is independently variable. Thus, each processor can contribute to maximum value score calculation using a different similarity measure.

Group Design Problems in Engineering Design Graphics.

ERIC Educational Resources Information Center

Kelley, David

2001-01-01

Describes group design techniques used within the engineering design graphics sequence at Western Washington University. Engineering and design philosophies such as concurrent engineering place an emphasis on group collaboration for the solving of design problems. (Author/DDR)

Individual deals within teams: Investigating the role of relative i-deals for employee performance.

PubMed

Vidyarthi, Prajya R; Singh, Satvir; Erdogan, Berrin; Chaudhry, Anjali; Posthuma, Richard; Anand, Smriti

2016-11-01

The authors extend i-deals theory to an individual-within-a-team context. Drawing upon social comparison theory, they contend that individuals will react to their own i-deals within the context of group members' i-deals. Therefore, they examine the role of relative i-deals (an individual's i-deals relative to the team's average) in relation to employee performance. Furthermore, integrating social comparison theory with social identity theory the authors assert that the behavioral outcomes of relative i-deals are influenced by the team's social and structural attributes of team orientation and task interdependence. Finally, they contend that the perceptions of one's relative standing with the leader, or leader-member exchange social comparison (LMXSC), mediate the i-deals-outcome relationship in groups with low team orientation and task interdependence. Results of multilevel modeling using time-lagged data from 321 employees nested in 46 teams demonstrated that the positive relationship between relative i-deals and employee performance was stronger in groups with low team orientation and task interdependence, and the mediation effect of LMXSC was stronger in teams with low rather than high team orientation. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Bayesian Ideal Types: Integration of Psychometric Data for Visually Impaired Persons.

ERIC Educational Resources Information Center

Jones, W. P.

1991-01-01

A model is proposed for the clinical synthesis of data from psychological tests of persons with visual impairments. The model integrates the concepts of the ideal type and Bayesian probability and compares actual test scores with ideal scores through use of a pattern similarity coefficient. A pilot study with Business Enterprise Program operators…

An ideal observer analysis of visual working memory.

PubMed

Sims, Chris R; Jacobs, Robert A; Knill, David C

2012-10-01

Limits in visual working memory (VWM) strongly constrain human performance across many tasks. However, the nature of these limits is not well understood. In this article we develop an ideal observer analysis of human VWM by deriving the expected behavior of an optimally performing but limited-capacity memory system. This analysis is framed around rate-distortion theory, a branch of information theory that provides optimal bounds on the accuracy of information transmission subject to a fixed information capacity. The result of the ideal observer analysis is a theoretical framework that provides a task-independent and quantitative definition of visual memory capacity and yields novel predictions regarding human performance. These predictions are subsequently evaluated and confirmed in 2 empirical studies. Further, the framework is general enough to allow the specification and testing of alternative models of visual memory (e.g., how capacity is distributed across multiple items). We demonstrate that a simple model developed on the basis of the ideal observer analysis-one that allows variability in the number of stored memory representations but does not assume the presence of a fixed item limit-provides an excellent account of the empirical data and further offers a principled reinterpretation of existing models of VWM. PsycINFO Database Record (c) 2012 APA, all rights reserved.

An Ideal Observer Analysis of Visual Working Memory

PubMed Central

Sims, Chris R.; Jacobs, Robert A.; Knill, David C.

2013-01-01

Limits in visual working memory (VWM) strongly constrain human performance across many tasks. However, the nature of these limits is not well understood. In this paper we develop an ideal observer analysis of human visual working memory, by deriving the expected behavior of an optimally performing, but limited-capacity memory system. This analysis is framed around rate–distortion theory, a branch of information theory that provides optimal bounds on the accuracy of information transmission subject to a fixed information capacity. The result of the ideal observer analysis is a theoretical framework that provides a task-independent and quantitative definition of visual memory capacity and yields novel predictions regarding human performance. These predictions are subsequently evaluated and confirmed in two empirical studies. Further, the framework is general enough to allow the specification and testing of alternative models of visual memory (for example, how capacity is distributed across multiple items). We demonstrate that a simple model developed on the basis of the ideal observer analysis—one which allows variability in the number of stored memory representations, but does not assume the presence of a fixed item limit—provides an excellent account of the empirical data, and further offers a principled re-interpretation of existing models of visual working memory. PMID:22946744

Doctor-patient communication in a Southeast Asian setting: the conflict between ideal and reality.

PubMed

Claramita, Mora; Utarini, Adi; Soebono, Hardyanto; Van Dalen, Jan; Van der Vleuten, Cees

2011-03-01

Doctor-patient communication has been extensively studied in non-Western contexts and in relation to patients' cultural and education backgrounds. This study explores the perceived ideal communication style for doctor-patient consultations and the reality of actual practice in a Southeast Asian context. We conducted the study in a teaching hospital in Indonesia, using a qualitative and a quantitative design. In-depth interviews were conducted with ten internal medicine specialists, ten internal medicine residents, 16 patients in two groups based on education level and ten most senior medical students. The contributions of doctors and patients to the communication during consultations were observed and rated quantitatively by thirty internal medicine residents, 393 patients with different educational backgrounds and ten senior medical students. The 'informed and shared decision making' is the central observation in this quantitative study. The results of the interviews showed that Southeast Asian stakeholders are in favor of a partnership style of communication and revealed barriers to achieving this: doctors and patients are not prepared for a participatory style and high patient load due to an inefficient health care system does not allow sufficient time for this type of communication. The results of the quantitative study showed a sharp contrast between observed and ideal communication styles. A paternalistic style seems to prevail, irrespective of patients' educational background. We found a sharp conflict between ideal and reality concerning doctor-patient communication in a Southeast Asian context. Further studies should examine ways to change the prevailing communication style in the desired direction.

Exploring the Professional Ideals of Christian Teachers from Conservative Protestant Schools in the Netherlands

ERIC Educational Resources Information Center

Boele-de Bruin, H. L.; de Muynck, A.

2018-01-01

Professional ideals arise from personal worldviews and specify teachers' professional identities. This study aimed to explore how faith is present in the professional ideals of Christian teachers. The professional ideals of 107 Dutch teachers from conservative Protestant primary and secondary schools were explored using an open-ended…

Leveraging Failure in Design Research

ERIC Educational Resources Information Center

Lobato, Joanne; Walters, C. David; Hohensee, Charles; Gruver, John; Diamond, Jaime Marie

2015-01-01

Even in the resource-rich, more ideal conditions of many design-based classroom interventions, unexpected events can lead to disappointing results in student learning. However, if later iterations in a design research study are more successful, the previous failures can provide opportunities for comparisons to reveal subtle differences in…

Reversible second-order conditional sequences in incidental sequence learning tasks.

PubMed

Pasquali, Antoine; Cleeremans, Axel; Gaillard, Vinciane

2018-06-01

In sequence learning tasks, participants' sensitivity to the sequential structure of a series of events often overshoots their ability to express relevant knowledge intentionally, as in generation tasks that require participants to produce either the next element of a sequence (inclusion) or a different element (exclusion). Comparing generation performance under inclusion and exclusion conditions makes it possible to assess the respective influences of conscious and unconscious learning. Recently, two main concerns have been expressed concerning such tasks. First, it is often difficult to design control sequences in such a way that they enable clear comparisons with the training material. Second, it is challenging to ask participants to perform appropriately under exclusion instructions, for the requirement to exclude familiar responses often leads them to adopt degenerate strategies (e.g., pushing on the same key all the time), which then need to be specifically singled out as invalid. To overcome both concerns, we introduce reversible second-order conditional (RSOC) sequences and show (a) that they elicit particularly strong transfer effects, (b) that dissociation of implicit and explicit influences becomes possible thanks to the removal of salient transitions in RSOCs, and (c) that exclusion instructions can be greatly simplified without losing sensitivity.

The Role of Idealization in Science and Its Implications for Science Education

NASA Astrophysics Data System (ADS)

Niaz, Mansoor

1999-06-01

The main objective of this article is to study the role of empirical evidence in the interpretation of psychological and epistemological aspects of Piagetian theory. According to Galilean methodology, after having asked the right question, a scientist could experimentally vary one impediment, and observe what happens to the dependent variable, as it approaches the ideal limiting case. Following Galileo's idealization, scientific laws being epistemological constructions do not describe the behavior of actual bodies. It is plausible to suggest that just as Galileo's ideal law can be observed only when all the impediment variables approach zero, similarly individuals in the real world have various `impediments' and it is only when these impediments are gradually removed by experimental manipulation that the real performance of individuals can approximate the competence of Piaget's epistemic subject (ideal knower). Finally, evidence is presented to the effect that by experimentally manipulating the impediment variables (e.g., Pascual-Leone's M-demand and Witkin's perceptual field effect of a task), performance of the real subjects approximates the competence of the ideal epistemic subject, which leads to the construction of a neo-Piagetian epistemological theory.

An ideal sealed source life-cycle

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

Tompkins, Joseph Andrew

2009-01-01

system they we have today. This regulation created a new regulatory framework seen as promising at the time. However, now they recognize that, despite the good intentions, the NIJWP/85 has not solved any source disposition problems. The answer to these sealed source disposition problems is to adopt a philosophy to correct these regulatory issues, determine an interim solution, execute that solution until there is a minimal backlog of sources to deal with, and then let the mechanisms they have created solve this problem into the foreseeable future. The primary philosophical tenet of the ideal sealed source life cycle follows. You do not allow the creation (or importation) of any source whose use cannot be justified, which cannot be affordably shipped, or that does not have a well-delinated and affordable disposition pathway. The path forward dictates that we fix the problem by embracing the Ideal Source Life cycle. In figure 1, we can see some of the elements of the ideal source life cycle. The life cycle is broken down into four portions, manufacture, use, consolidation, and disposition. These four arbitrary elements allow them to focus on the ideal life cycle phases that every source should go through between manufacture and final disposition. As we examine the various phases of the sealed source life cycle, they pick specific examples and explore the adoption of the ideal life cycle model.« less

American Citizens’ Views of an Ideal Pig Farm

PubMed Central

Sato, Patrycia; Hötzel, Maria J.; von Keyserlingk, Marina A.G.

2017-01-01

Simple Summary The public, who also make up the largest proportion of consumers of animal products, often criticize farm animal industries in regards to their care and handling of farm animals. The U.S. swine industry has not been exempt from such criticisms. The aim of this study was to explore the views of the people not affiliated with the swine industry on what they perceived to be the ideal pig/pork farm, and their associated reasons. Through an online survey, participants were invited to respond to the following open-ended question: “What do you consider to be an ideal pig/pork farm and why are these characteristics important to you?”. Respondents considered animal care, profitability, farm size, compliance with sanitary, environmental rules and regulations, farm cleanliness and sanitary standards, and workers’ rights and welfare important, but also raised concerns relating to pigs’ quality of life including space to move, feeding, contact with outdoors or nature, absence of pain, suffering and mistreatment. Perspectives were also raised regarding the ideal farm as a profitable business operation, clean, and with optimal sanitary conditions. Respondents also emphasized naturalness, frequently stating that pigs should have access to the outdoors, and rejected the use of hormones, antibiotics, and other chemicals for the purposes of increasing production. Abstract Food animal production practices are often cited as having negative animal welfare consequences. The U.S. swine industry has not been exempt from such criticisms. Little is known, however, about how lay citizens who are not actively engaged in agricultural discussions, think about swine production. Thus, the aim of this study was to explore the views of people not affiliated with the swine industry on what they perceived to be the ideal pig/pork farm, and their associated reasons. Through an online survey, participants were invited to respond to the following open-ended question: “What do

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

PubMed Central

Ramos, Antonio M.; Crooijmans, Richard P. M. A.; Affara, Nabeel A.; Amaral, Andreia J.; Archibald, Alan L.; Beever, Jonathan E.; Bendixen, Christian; Churcher, Carol; Clark, Richard; Dehais, Patrick; Hansen, Mark S.; Hedegaard, Jakob; Hu, Zhi-Liang; Kerstens, Hindrik H.; Law, Andy S.; Megens, Hendrik-Jan; Milan, Denis; Nonneman, Danny J.; Rohrer, Gary A.; Rothschild, Max F.; Smith, Tim P. L.; Schnabel, Robert D.; Van Tassell, Curt P.; Taylor, Jeremy F.; Wiedmann, Ralph T.; Schook, Lawrence B.; Groenen, Martien A. M.

2009-01-01

Background The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. Conclusions/Significance Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs. PMID:19654876

Differential molar heat capacities to test ideal solubility estimations.

PubMed

Neau, S H; Bhandarkar, S V; Hellmuth, E W

1997-05-01

Calculation of the ideal solubility of a crystalline solute in a liquid solvent requires knowledge of the difference in the molar heat capacity at constant pressure of the solid and the supercooled liquid forms of the solute, delta Cp. Since this parameter is not usually known, two assumptions have been used to simplify the expression. The first is that delta Cp can be considered equal to zero; the alternate assumption is that the molar entropy of fusion, delta Sf, is an estimate of delta Cp. Reports claiming the superiority of one assumption over the other, on the basis of calculations done using experimentally determined parameters, have appeared in the literature. The validity of the assumptions in predicting the ideal solubility of five structurally unrelated compounds of pharmaceutical interest, with melting points in the range 420 to 470 K, was evaluated in this study. Solid and liquid heat capacities of each compound near its melting point were determined using differential scanning calorimetry. Linear equations describing the heat capacities were extrapolated to the melting point to generate the differential molar heat capacity. Linear data were obtained for both crystal and liquid heat capacities of sample and test compounds. For each sample, ideal solubility at 298 K was calculated and compared to the two estimates generated using literature equations based on the differential molar heat capacity assumptions. For the compounds studied, delta Cp was not negligible and was closer to delta Sf than to zero. However, neither of the two assumptions was valid for accurately estimating the ideal solubility as given by the full equation.

Theory and Simulation of Real and Ideal Magnetohydrodynamic Turbulence

NASA Technical Reports Server (NTRS)

Shebalin, John V.

2004-01-01

Incompressible, homogeneous magnetohydrodynamic (MHD) turbulence consists of fluctuating vorticity and magnetic fields, which are represented in terms of their Fourier coefficients. Here, a set of five Fourier spectral transform method numerical simulations of two-dimensional (2-D) MHD turbulence on a 512(sup 2) grid is described. Each simulation is a numerically realized dynamical system consisting of Fourier modes associated with wave vectors k, with integer components, such that k = |k| less than or equal to k(sub max). The simulation set consists of one ideal (non-dissipative) case and four real (dissipative) cases. All five runs had equivalent initial conditions. The dimensions of the dynamical systems associated with these cases are the numbers of independent real and imaginary parts of the Fourier modes. The ideal simulation has a dimension of 366104, while each real simulation has a dimension of 411712. The real runs vary in magnetic Prandtl number P(sub M), with P(sub M) is a member of {0.1, 0.25, 1, 4}. In the results presented here, all runs have been taken to a simulation time of t = 25. Although ideal and real Fourier spectra are quite different at high k, they are similar at low values of k. Their low k behavior indicates the existence of broken symmetry and coherent structure in real MHD turbulence, similar to what exists in ideal MHD turbulence. The value of PM strongly affects the ratio of kinetic to magnetic energy and energy dissipation (which is mostly ohmic). The relevance of these results to 3-D Navier-Stokes and MHD turbulence is discussed.

A Multidimensional Ideal Point Item Response Theory Model for Binary Data

ERIC Educational Resources Information Center

Maydeu-Olivares, Albert; Hernandez, Adolfo; McDonald, Roderick P.

2006-01-01

We introduce a multidimensional item response theory (IRT) model for binary data based on a proximity response mechanism. Under the model, a respondent at the mode of the item response function (IRF) endorses the item with probability one. The mode of the IRF is the ideal point, or in the multidimensional case, an ideal hyperplane. The model…

40 CFR 1065.645 - Amount of water in an ideal gas.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 34 2012-07-01 2012-07-01 false Amount of water in an ideal gas. 1065.645 Section 1065.645 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.645 Amount of water in an ideal gas. This section describes how to...

40 CFR 1065.645 - Amount of water in an ideal gas.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 34 2013-07-01 2013-07-01 false Amount of water in an ideal gas. 1065.645 Section 1065.645 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.645 Amount of water in an ideal gas. This section describes how to...

40 CFR 1065.645 - Amount of water in an ideal gas.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 33 2011-07-01 2011-07-01 false Amount of water in an ideal gas. 1065.645 Section 1065.645 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS ENGINE-TESTING PROCEDURES Calculations and Data Requirements § 1065.645 Amount of water in an ideal gas. This section describes how to...

Toward an Ideal Senior High School Governance Structure.

ERIC Educational Resources Information Center

Treslan, D. L.

1979-01-01

This paper delineates six attributes of an ideal high school governance structure: respect, freedom, rationality, flexibility, equality, and involvement of staff and students in the decision-making process. (Author/SJL)

Ideal for Whom? A Cultural Analysis of Ideal Worker Norms in Higher Education and Student Affairs Graduate Programs

ERIC Educational Resources Information Center

Sallee, Margaret W.

2016-01-01

This chapter explores the consequences of ideal worker norms for graduate student-parents in higher education and student affairs programs. Using Schein's (2004) levels of culture as a conceptual lens, this chapter considers the ways that programmatic structures and interactions with faculty and peers reflect and reproduce a culture across…

Ideal walking dynamics via a gauged NJL model

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

Rantaharju, Jarno; Pica, Claudio; Sannino, Francesco

According to the ideal walking technicolor paradigm, large mass anomalous dimensions arise in gauged Nambu–Jona-Lasinio (NJL) models when the four-fermion coupling is sufficiently strong to induce spontaneous symmetry breaking in an otherwise conformal gauge theory. Therefore, we study the SU(2) gauged NJL model with two adjoint fermions using lattice simulations. The model is in an infrared conformal phase at small NJL coupling while it displays a chirally broken phase at large NJL couplings. In the infrared conformal phase, we find that the mass anomalous dimension varies with the NJL coupling, reaching γm ~ 1 close to the chiral symmetry breakingmore » transition, de facto making the present model the first explicit realization of the ideal walking scenario.« less

Ideal walking dynamics via a gauged NJL model

DOE PAGES

Rantaharju, Jarno; Pica, Claudio; Sannino, Francesco

2017-07-25

According to the ideal walking technicolor paradigm, large mass anomalous dimensions arise in gauged Nambu–Jona-Lasinio (NJL) models when the four-fermion coupling is sufficiently strong to induce spontaneous symmetry breaking in an otherwise conformal gauge theory. Therefore, we study the SU(2) gauged NJL model with two adjoint fermions using lattice simulations. The model is in an infrared conformal phase at small NJL coupling while it displays a chirally broken phase at large NJL couplings. In the infrared conformal phase, we find that the mass anomalous dimension varies with the NJL coupling, reaching γm ~ 1 close to the chiral symmetry breakingmore » transition, de facto making the present model the first explicit realization of the ideal walking scenario.« less

Hyperpolarized (129) Xe imaging of the rat lung using spiral IDEAL.

PubMed

Doganay, Ozkan; Wade, Trevor; Hegarty, Elaine; McKenzie, Charles; Schulte, Rolf F; Santyr, Giles E

2016-08-01

To implement and optimize a single-shot spiral encoding strategy for rapid 2D IDEAL projection imaging of hyperpolarized (Hp) (129) Xe in the gas phase, and in the pulmonary tissue (PT) and red blood cells (RBCs) compartments of the rat lung, respectively. A theoretical and experimental point spread function analysis was used to optimize the spiral k-space read-out time in a phantom. Hp (129) Xe IDEAL images from five healthy rats were used to: (i) optimize flip angles by a Bloch equation analysis using measured kinetics of gas exchange and (ii) investigate the feasibility of the approach to characterize the exchange of Hp (129) Xe. A read-out time equal to approximately 1.8 × T2* was found to provide the best trade-off between spatial resolution and signal-to-noise ratio (SNR). Spiral IDEAL approaches that use the entire dissolved phase magnetization should give an SNR improvement of a factor of approximately three compared with Cartesian approaches with similar spatial resolution. The IDEAL strategy allowed imaging of gas, PT, and RBC compartments with sufficient SNR and temporal resolution to permit regional gas exchange measurements in healthy rats. Single-shot spiral IDEAL imaging of gas, PT and RBC compartments and gas exchange is feasible in rat lung using Hp (129) Xe. Magn Reson Med 76:566-576, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

An Idealized, Single Radial Swirler, Lean-Direct-Injection (LDI) Concept Meshing Script

NASA Technical Reports Server (NTRS)

Iannetti, Anthony C.; Thompson, Daniel

2008-01-01

To easily study combustor design parameters using computational fluid dynamics codes (CFD), a Gridgen Glyph-based macro (based on the Tcl scripting language) dubbed BladeMaker has been developed for the meshing of an idealized, single radial swirler, lean-direct-injection (LDI) combustor. BladeMaker is capable of taking in a number of parameters, such as blade width, blade tilt with respect to the perpendicular, swirler cup radius, and grid densities, and producing a three-dimensional meshed radial swirler with a can-annular (canned) combustor. This complex script produces a data format suitable for but not specific to the National Combustion Code (NCC), a state-of-the-art CFD code developed for reacting flow processes.

Ideal gender identity related to parent images and locus of control: Jungian and social learning perspectives.

PubMed

Shimoda, Hiroko; Keskinen, Soili

2004-06-01

In this research, we wanted to clarify how gender images are different or invariant and related to parents, attributes, and the attitude of controlling life (locus of control) in two cultural contexts, Japan and Finland. For this purpose, students' ideal gender images, consisting of ideal mother, female, father and male images, and parents' similarity to the four ideal gender images were studied in 135 Japanese and 119 Finnish university students. Major findings were (a) Japanese students' ideal gender images were more stereotypic than those of Finnish students; (b) students' ideal mother image and parents' similarity to the ideal mother image were related only to their sex, which supports Jung's theory; (c) students socially learned other ideal gender images, but these did not fit with expectation from social learning theory; (d) Japanese students' mothers are models or examples of gender images, but Finnish male students did not seem to base their ideal gender images on their parents. Implication of measures was discussed.

Do the Particles of an Ideal Gas Collide?

ERIC Educational Resources Information Center

Lesk, Arthur M.

1974-01-01

Describes the collisional properties as a logically essential component of the ideal gas model since an actual intraparticle process cannot support observable anisotropic velocity distributions without collisions taken into account. (CC)

Computer-Aided TRIZ Ideality and Level of Invention Estimation Using Natural Language Processing and Machine Learning

NASA Astrophysics Data System (ADS)

Adams, Christopher; Tate, Derrick

Patent textual descriptions provide a wealth of information that can be used to understand the underlying design approaches that result in the generation of novel and innovative technology. This article will discuss a new approach for estimating Degree of Ideality and Level of Invention metrics from the theory of inventive problem solving (TRIZ) using patent textual information. Patent text includes information that can be used to model both the functions performed by a design and the associated costs and problems that affect a design’s value. The motivation of this research is to use patent data with calculation of TRIZ metrics to help designers understand which combinations of system components and functions result in creative and innovative design solutions. This article will discuss in detail methods to estimate these TRIZ metrics using natural language processing and machine learning with the use of neural networks.

Maximizing overall liking results in a superior product to minimizing deviations from ideal ratings: an optimization case study with coffee-flavored milk

PubMed Central

Li, Bangde; Hayes, John E.; Ziegler, Gregory R.

2015-01-01

In just-about-right (JAR) scaling and ideal scaling, attribute delta (i.e., “Too Little” or “Too Much”) reflects a subject’s dissatisfaction level for an attribute relative to their hypothetical ideal. Dissatisfaction (attribute delta) is a different construct from consumer acceptability, operationalized as liking. Therefore, we hypothesized minimizing dissatisfaction and maximizing liking would yield different optimal formulations. The objective of this research was to compare product optimization strategies, i.e. maximizing liking vis-à-vis minimizing dissatisfaction. Coffee-flavored dairy beverages (n = 20) were formulated using a fractional mixture design that constrained the proportions of coffee extract, milk, sucrose, and water. Participants (n = 388) were randomly assigned to one of three research conditions, where they evaluated 4 of the 20 samples using an incomplete block design. Samples were rated for overall liking and for intensity of the attributes sweetness, milk flavor, thickness and coffee flavor. Where appropriate, measures of overall product quality (Ideal_Delta and JAR_Delta) were calculated as the sum of the absolute values of the four attribute deltas. Optimal formulations were estimated by: a) maximizing liking; b) minimizing Ideal_Delta; or c) minimizing JAR_Delta. A validation study was conducted to evaluate product optimization models. Participants indicated a preference for a coffee-flavored dairy beverage with more coffee extract and less milk and sucrose in the dissatisfaction model compared to the formula obtained by maximizing liking. That is, when liking was optimized, participants generally liked a weaker, milkier and sweeter coffee-flavored dairy beverage. Predicted liking scores were validated in a subsequent experiment, and the optimal product formulated to maximize liking was significantly preferred to that formulated to minimize dissatisfaction by a paired preference test. These findings are consistent with the view

Rational Design of Small Molecules Targeting Oncogenic Noncoding RNAs from Sequence.

PubMed

Disney, Matthew D; Angelbello, Alicia J

2016-12-20

The discovery of RNA catalysis in the 1980s and the dissemination of the human genome sequence at the start of this century inspired investigations of the regulatory roles of noncoding RNAs in biology. In fact, the Encyclopedia of DNA Elements (ENCODE) project has shown that only 1-2% of the human genome encodes protein, yet 75% is transcribed into RNA. Functional studies both preceding and following the ENCODE project have shown that these noncoding RNAs have important roles in regulating gene expression, developmental timing, and other critical functions. RNA's diverse roles are often a consequence of the various folds that it adopts. The single-stranded nature of the biopolymer enables it to adopt intramolecular folds with noncanonical pairings to lower its free energy. These folds can be scaffolds to bind proteins or to form frameworks to interact with other RNAs. Not surprisingly, dysregulation of certain noncoding RNAs has been shown to be causative of disease. Given this as the background, it is easy to see why it would be useful to develop methods that target RNA and manipulate its biology in rational and predictable ways. The antisense approach has afforded strategies to target RNAs via Watson-Crick base pairing and has typically focused on targeting partially unstructured regions of RNA. Small molecule strategies to target RNA would be desirable not only because compounds could be lead optimized via medicinal chemistry but also because structured regions within an RNA of interest could be targeted to directly interfere with RNA folds that contribute to disease. Additionally, small molecules have historically been the most successful drug candidates. Until recently, the ability to design small molecules that target non-ribosomal RNAs has been elusive, creating the perception that they are "undruggable". In this Account, approaches to demystify targeting RNA with small molecules are described. Rather than bulk screening for compounds that bind to singular

Ideal cardiovascular health and psychosocial risk factors among Finnish female municipal workers.

PubMed

Veromaa, Veera; Kautiainen, Hannu; Saxen, Ulla; Malmberg-Ceder, Kirsi; Bergman, Elina; Korhonen, Päivi E

2017-02-01

Ideal cardiovascular health has been defined by the American Heart Association as the absence of disease and the presence of seven key health factors and behaviours. However, little is known about the mental aspects associated with ideal cardiovascular health metrics. The objective of this study was to assess the relationships between psychosocial risk factors and ideal cardiovascular health metrics among Finnish women at municipal work units. A cross-sectional study was conducted in Finland among 732 female employees (mean±SD age 48±10 years) from ten work units in 2014. Ideal cardiovascular health metrics were evaluated with a physical examination, laboratory tests, medical history and self-administrated questionnaires. Psychosocial risk factors (social isolation, stress, depressive symptoms, anxiety, hostility and type D personality) were assessed with core questions as suggested by the European Society of Cardiology. The prevalence of having 5-7 ideal cardiovascular health metrics was 183 (25.0%), of whom 54.1% had at least one psychosocial risk factor. Anxiety (31.3%), work stress (30.7%) and type D personality (26.1%) were the most prevalent of the psychosocial risk factors. The prevalence of depressive symptoms ( p<0.001) and type D personality ( p=0.049) decreased linearly according to the sum of ideal cardiovascular health metrics after adjustment for age and years of education. Even women with good cardiovascular health are affected by psychosocial risk factors at municipal work units. Although the association is possibly bidirectional, screening and treating depression and dealing with type D personality might be crucial in improving cardiovascular health among women.

The predictive validity of ideal partner preferences: a review and meta-analysis.

PubMed

Eastwick, Paul W; Luchies, Laura B; Finkel, Eli J; Hunt, Lucy L

2014-05-01

A central element of interdependence theory is that people have standards against which they compare their current outcomes, and one ubiquitous standard in the mating domain is the preference for particular attributes in a partner (ideal partner preferences). This article reviews research on the predictive validity of ideal partner preferences and presents a new integrative model that highlights when and why ideals succeed or fail to predict relational outcomes. Section 1 examines predictive validity by reviewing research on sex differences in the preference for physical attractiveness and earning prospects. Men and women reliably differ in the extent to which these qualities affect their romantic evaluations of hypothetical targets. Yet a new meta-analysis spanning the attraction and relationships literatures (k = 97) revealed that physical attractiveness predicted romantic evaluations with a moderate-to-strong effect size (r = ∼.40) for both sexes, and earning prospects predicted romantic evaluations with a small effect size (r = ∼.10) for both sexes. Sex differences in the correlations were small (r difference = .03) and uniformly nonsignificant. Section 2 reviews research on individual differences in ideal partner preferences, drawing from several theoretical traditions to explain why ideals predict relational evaluations at different relationship stages. Furthermore, this literature also identifies alternative measures of ideal partner preferences that have stronger predictive validity in certain theoretically sensible contexts. Finally, a discussion highlights a new framework for conceptualizing the appeal of traits, the difference between live and hypothetical interactions, and the productive interplay between mating research and broader psychological theories.

Patients respond more positively to physicians who focus on their ideal affect.

PubMed

Sims, Tamara; Tsai, Jeanne L

2015-06-01

Previous findings suggest that patients choose physicians whose affective focus matches how they ideally want to feel (Sims et al., 2014). For instance, the more people wanted to feel excitement, the more likely they were to hypothetically choose a new physician who promoted excitement. What remains unknown is whether this match shapes how patients actually respond to physicians after being assigned to them (i.e., whether they adhere to physicians' recommendations more and evaluate physicians more positively). To this end, community adults reported their global ideal affect and actual affect (how they ideally want to feel and actually feel during a typical week, respectively), and were randomly assigned to receive health recommendations from either a physician who expressed and promoted high arousal positive states (HAP) (e.g., excitement), or one who expressed and promoted low arousal positive states (LAP) (e.g., calm). For the next 5 days, participants reported their daily adherence to the recommendations and their daily ideal and actual affect. At the end of the week, participants evaluated their physician. As predicted, the more participants wanted to feel HAP, the more they adhered to the "HAP-focused" physician's recommendations, and the more participants wanted to feel LAP, the more they adhered to the "LAP-focused" physician's recommendations. Participants also evaluated their physician more positively when his affective focus matched their ideal affect. Neither global nor daily actual affect systematically predicted how patients responded to their physicians. These findings suggest that patients respond better to physicians whose affective focus matches their ideal affect. (c) 2015 APA, all rights reserved).

Patients Respond More Positively to Physicians Who Focus on Their Ideal Affect

PubMed Central

Sims, Tamara; Tsai, Jeanne L.

2014-01-01

Previous findings suggest that patients choose physicians whose affective focus matches how they ideally want to feel (Sims et al., 2014). For instance, the more people wanted to feel excitement, the more likely they were to hypothetically choose a new physician who promoted excitement. What remains unknown is whether this match shapes how patients actually respond to physicians after being assigned to them (i.e., whether they adhere to physicians’ recommendations more and evaluate physicians more positively). To this end, community adults reported their global ideal affect and actual affect (how they ideally want to feel and actually feel during a typical week, respectively), and were randomly assigned to receive health recommendations from either a physician who expressed and promoted high arousal positive states (HAP) (e.g., excitement), or one who expressed and promoted low arousal positive states (LAP) (e.g., calm). For the next five days, participants reported their daily adherence to the recommendations and their daily ideal and actual affect. At the end of the week, participants evaluated their physician. As predicted, the more participants wanted to feel HAP, the more they adhered to the “HAP-focused” physician’s recommendations, and the more participants wanted to feel LAP, the more they adhered to the “LAP-focused” physician’s recommendations. Participants also evaluated their physician more positively when his affective focus matched their ideal affect. Neither global nor daily actual affect systematically predicted how patients responded to their physicians. These findings suggest that patients respond better to physicians whose affective focus matches their ideal affect. PMID:25313670

Associations between Sexual Abstinence Ideals, Religiosity, and Alcohol Abstinence: A Longitudinal Study of Finnish Twins

PubMed Central

Winter, Torsten; Karvonen, Sakari; Rose, Richard J.

2016-01-01

We analyzed prevalence and stability of attitudes endorsing sexual abstinence ideals from late adolescence into early adulthood and studied associations of these attitudes with religiosity and alcohol abstinence in a sexually liberal Nordic society. Our population-based sample of Finnish twins permitted comparisons of co-twins concordant for religiosity but discordant for drinking to evaluate the association of sexual abstinence ideals with alcohol abstinence, controlling for household environment. From age 17 to 24, endorsement of sexual abstinence as a romantic ideal declined from 25% to 15%. Religiosity and alcohol abstinence correlated, both separately and together, with endorsing sexual abstinence. Abstinence ideals were associated with literal belief in fundamental tenets of the Bible. The association of sexual abstinence ideals with alcohol abstinence was confirmed in within-family comparisons of co-twins discordant for drinking but concordant for religiosity. Alcohol-abstinent twins were significantly more likely than their non-alcohol-abstinent twin siblings to endorse sexual abstinence ideals; that result suggests the association of sexual abstinence ideals with abstaining from alcohol is not explained by unmeasured confounds in familial background and structure. Our longitudinal results and analyses of discordant twins suggest that attitudes toward sexual abstinence ideals are embedded within other conservative attitudes and behaviors. PMID:23301620

The influence of family context on life, educational and occupational ideal among middle school students in China.

PubMed

Yao, Benxian; Zhang, Ling; Zhen, Rui; Zhou, Xiao

2016-06-01

This study examined the relationship between family context of middle school students on their educational and occupational ideals. Middle school students (N = 2000) responded to questions assessing family location, family structure, parental educational level and family economic status, as well as to the Middle School Students' Ideals Questionnaire. Multivariate analysis of variance indicated that life, educational and occupational ideals of female students and students in lower grades were higher than that of male students and students in higher grades. Regression analysis indicated that paternal education level have a positive association with educational and occupational ideals, but not life ideals, and family economic status have a positive relation to life ideals, but not educational and occupational ideals. Moreover, the interaction between family economic status and family location has a negative association with students' life, educational and occupational ideals. These results suggest that different factors predicted different ideals of adolescents, and that family economic status had a negative moderating effect on the relationship between family location and ideals of students. © 2015 International Union of Psychological Science.