Methodology for the Assessment of Confidence in Safety Margin for Small Break Loss of Coolant Accident Sequences

Energy Technology Data Exchange (ETDEWEB)

Nagrale, D. B.; Prasad, M.; Rao, R. S.; Gaikwad, A.J., E-mail: avinashg@aerb.gov.in [Nuclear Safety Analysis Division, Atomic Energy Regulatory Board, Mumbai (India)

2014-10-15

Deterministic Safety Analysis and Probabilistic Safety Assessment (PSA) analyses are used concurrently to assess the Nuclear Power Plant (NPP) safety. The conventional deterministic analysis is conservative. The best estimate plus uncertainty analysis is increasingly being used for deterministic calculation in NPPs. The PSA methodology aims to be as realistic as possible while integrating information about accident phenomena, plant design, operating practices, component reliability and human behaviour. The peak clad temperature (PCT) distribution provides an insight into the confidence in safety margin for an initiating event. The paper deals with the concept of calculating the peak clad temperature with 95 percent confidence and 95 percent probability (PCT{sub 95/95}) in small break loss of coolant accident (SBLOCA) and methodologies for assessing safety margin. Five input parameters mainly, nominal power level, decay power, fuel clad gap conductivity, fuel thermal conductivity and discharge coefficient, were selected. A Uniform probability density function was assigned to the uncertain parameters and these uncertainties are propagated using Latin Hypercube Sampling (LHS) technique. The sampled data for 5 parameters were randomly mixed by LHS to obtain 25 input sets. A non-core damage accident sequence was selected from the SBLOCA event tree of a typical VVER study to estimate the PCTs and safety margin. A Kolmogorov– Smirnov goodness-of-fit test was carried out for PCTs. The smallest value of safety margin would indicate the robustness of the system with 95% confidence and 95% probability. Regression analysis was also carried out using 1000 sample size for the estimating PCTs. Mean, variance and finally safety margin were analysed. (author)

We will be champions: Leaders' confidence in 'us' inspires team members' team confidence and performance.

Science.gov (United States)

Fransen, K; Steffens, N K; Haslam, S A; Vanbeselaere, N; Vande Broek, G; Boen, F

2016-12-01

The present research examines the impact of leaders' confidence in their team on the team confidence and performance of their teammates. In an experiment involving newly assembled soccer teams, we manipulated the team confidence expressed by the team leader (high vs neutral vs low) and assessed team members' responses and performance as they unfolded during a competition (i.e., in a first baseline session and a second test session). Our findings pointed to team confidence contagion such that when the leader had expressed high (rather than neutral or low) team confidence, team members perceived their team to be more efficacious and were more confident in the team's ability to win. Moreover, leaders' team confidence affected individual and team performance such that teams led by a highly confident leader performed better than those led by a less confident leader. Finally, the results supported a hypothesized mediational model in showing that the effect of leaders' confidence on team members' team confidence and performance was mediated by the leader's perceived identity leadership and members' team identification. In conclusion, the findings of this experiment suggest that leaders' team confidence can enhance members' team confidence and performance by fostering members' identification with the team. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Integration of multiple biological features yields high confidence human protein interactome.

Science.gov (United States)

Karagoz, Kubra; Sevimoglu, Tuba; Arga, Kazim Yalcin

2016-08-21

The biological function of a protein is usually determined by its physical interaction with other proteins. Protein-protein interactions (PPIs) are identified through various experimental methods and are stored in curated databases. The noisiness of the existing PPI data is evident, and it is essential that a more reliable data is generated. Furthermore, the selection of a set of PPIs at different confidence levels might be necessary for many studies. Although different methodologies were introduced to evaluate the confidence scores for binary interactions, a highly reliable, almost complete PPI network of Homo sapiens is not proposed yet. The quality and coverage of human protein interactome need to be improved to be used in various disciplines, especially in biomedicine. In the present work, we propose an unsupervised statistical approach to assign confidence scores to PPIs of H. sapiens. To achieve this goal PPI data from six different databases were collected and a total of 295,288 non-redundant interactions between 15,950 proteins were acquired. The present scoring system included the context information that was assigned to PPIs derived from eight biological attributes. A high confidence network, which included 147,923 binary interactions between 13,213 proteins, had scores greater than the cutoff value of 0.80, for which sensitivity, specificity, and coverage were 94.5%, 80.9%, and 82.8%, respectively. We compared the present scoring method with others for evaluation. Reducing the noise inherent in experimental PPIs via our scoring scheme increased the accuracy significantly. As it was demonstrated through the assessment of process and cancer subnetworks, this study allows researchers to construct and analyze context-specific networks via valid PPI sets and one can easily achieve subnetworks around proteins of interest at a specified confidence level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Statistical assignment of DNA sequences using Bayesian phylogenetics

DEFF Research Database (Denmark)

Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Huelsenbeck, John P.

2008-01-01

We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data...... that the method outperforms Blast searches as a measure of confidence and can help eliminate 80% of all false assignment based on best Blast hit. However, the most important advance of the method is that it provides statistically meaningful measures of confidence. We apply the method to a re......-analysis of previously published ancient DNA data and show that, with high statistical confidence, most of the published sequences are in fact of Neanderthal origin. However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA....

A machine learning model to determine the accuracy of variant calls in capture-based next generation sequencing.

Science.gov (United States)

van den Akker, Jeroen; Mishne, Gilad; Zimmer, Anjali D; Zhou, Alicia Y

2018-04-17

Next generation sequencing (NGS) has become a common technology for clinical genetic tests. The quality of NGS calls varies widely and is influenced by features like reference sequence characteristics, read depth, and mapping accuracy. With recent advances in NGS technology and software tools, the majority of variants called using NGS alone are in fact accurate and reliable. However, a small subset of difficult-to-call variants that still do require orthogonal confirmation exist. For this reason, many clinical laboratories confirm NGS results using orthogonal technologies such as Sanger sequencing. Here, we report the development of a deterministic machine-learning-based model to differentiate between these two types of variant calls: those that do not require confirmation using an orthogonal technology (high confidence), and those that require additional quality testing (low confidence). This approach allows reliable NGS-based calling in a clinical setting by identifying the few important variant calls that require orthogonal confirmation. We developed and tested the model using a set of 7179 variants identified by a targeted NGS panel and re-tested by Sanger sequencing. The model incorporated several signals of sequence characteristics and call quality to determine if a variant was identified at high or low confidence. The model was tuned to eliminate false positives, defined as variants that were called by NGS but not confirmed by Sanger sequencing. The model achieved very high accuracy: 99.4% (95% confidence interval: +/- 0.03%). It categorized 92.2% (6622/7179) of the variants as high confidence, and 100% of these were confirmed to be present by Sanger sequencing. Among the variants that were categorized as low confidence, defined as NGS calls of low quality that are likely to be artifacts, 92.1% (513/557) were found to be not present by Sanger sequencing. This work shows that NGS data contains sufficient characteristics for a machine-learning-based model to

A high confidence, manually validated human blood plasma protein reference set

DEFF Research Database (Denmark)

Schenk, Susann; Schoenhals, Gary J; de Souza, Gustavo

2008-01-01

BACKGROUND: The immense diagnostic potential of human plasma has prompted great interest and effort in cataloging its contents, exemplified by the Human Proteome Organization (HUPO) Plasma Proteome Project (PPP) pilot project. Due to challenges in obtaining a reliable blood plasma protein list......-trap-Fourier transform (LTQ-FT) and a linear ion trap-Orbitrap (LTQ-Orbitrap) for mass spectrometry (MS) analysis. Both instruments allow the measurement of peptide masses in the low ppm range. Furthermore, we employed a statistical score that allows database peptide identification searching using the products of two...... consecutive stages of tandem mass spectrometry (MS3). The combination of MS3 with very high mass accuracy in the parent peptide allows peptide identification with orders of magnitude more confidence than that typically achieved. RESULTS: Herein we established a high confidence set of 697 blood plasma proteins...

High resolution sequence stratigraphy in China

International Nuclear Information System (INIS)

Zhang Shangfeng; Zhang Changmin; Yin Yanshi; Yin Taiju

2008-01-01

Since high resolution sequence stratigraphy was introduced into China by DENG Hong-wen in 1995, it has been experienced two development stages in China which are the beginning stage of theory research and development of theory research and application, and the stage of theoretical maturity and widely application that is going into. It is proved by practices that high resolution sequence stratigraphy plays more and more important roles in the exploration and development of oil and gas in Chinese continental oil-bearing basin and the research field spreads to the exploration of coal mine, uranium mine and other strata deposits. However, the theory of high resolution sequence stratigraphy still has some shortages, it should be improved in many aspects. The authors point out that high resolution sequence stratigraphy should be characterized quantitatively and modelized by computer techniques. (authors)

Confidant Relations in Italy

Directory of Open Access Journals (Sweden)

Jenny Isaacs

2015-02-01

Full Text Available Confidants are often described as the individuals with whom we choose to disclose personal, intimate matters. The presence of a confidant is associated with both mental and physical health benefits. In this study, 135 Italian adults responded to a structured questionnaire that asked if they had a confidant, and if so, to describe various features of the relationship. The vast majority of participants (91% reported the presence of a confidant and regarded this relationship as personally important, high in mutuality and trust, and involving minimal lying. Confidants were significantly more likely to be of the opposite sex. Participants overall were significantly more likely to choose a spouse or other family member as their confidant, rather than someone outside of the family network. Familial confidants were generally seen as closer, and of greater value, than non-familial confidants. These findings are discussed within the context of Italian culture.

High-throughput sequence alignment using Graphics Processing Units

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Trapnell Cole

2007-12-01

Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

FRESCO: Referential compression of highly similar sequences.

Science.gov (United States)

Wandelt, Sebastian; Leser, Ulf

2013-01-01

In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing

Directory of Open Access Journals (Sweden)

Miri eMichaeli

2012-12-01

Full Text Available High throughput sequencing (HTS yields tens of thousands to millions of sequences that require a large amount of pre-processing work to clean various artifacts. Such cleaning cannot be performed manually. Existing programs are not suitable for immunoglobulin (Ig genes, which are variable and often highly mutated. This paper describes Ig-HTS-Cleaner (Ig High Throughput Sequencing Cleaner, a program containing a simple cleaning procedure that successfully deals with pre-processing of Ig sequences derived from HTS, and Ig-Indel-Identifier (Ig Insertion – Deletion Identifier, a program for identifying legitimate and artifact insertions and/or deletions (indels. Our programs were designed for analyzing Ig gene sequences obtained by 454 sequencing, but they are applicable to all types of sequences and sequencing platforms. Ig-HTS-Cleaner and Ig-Indel-Identifier have been implemented in Java and saved as executable JAR files, supported on Linux and MS Windows. No special requirements are needed in order to run the programs, except for correctly constructing the input files as explained in the text. The programs' performance has been tested and validated on real and simulated data sets.

Brain networks for confidence weighting and hierarchical inference during probabilistic learning.

Science.gov (United States)

Meyniel, Florent; Dehaene, Stanislas

2017-05-09

Learning is difficult when the world fluctuates randomly and ceaselessly. Classical learning algorithms, such as the delta rule with constant learning rate, are not optimal. Mathematically, the optimal learning rule requires weighting prior knowledge and incoming evidence according to their respective reliabilities. This "confidence weighting" implies the maintenance of an accurate estimate of the reliability of what has been learned. Here, using fMRI and an ideal-observer analysis, we demonstrate that the brain's learning algorithm relies on confidence weighting. While in the fMRI scanner, human adults attempted to learn the transition probabilities underlying an auditory or visual sequence, and reported their confidence in those estimates. They knew that these transition probabilities could change simultaneously at unpredicted moments, and therefore that the learning problem was inherently hierarchical. Subjective confidence reports tightly followed the predictions derived from the ideal observer. In particular, subjects managed to attach distinct levels of confidence to each learned transition probability, as required by Bayes-optimal inference. Distinct brain areas tracked the likelihood of new observations given current predictions, and the confidence in those predictions. Both signals were combined in the right inferior frontal gyrus, where they operated in agreement with the confidence-weighting model. This brain region also presented signatures of a hierarchical process that disentangles distinct sources of uncertainty. Together, our results provide evidence that the sense of confidence is an essential ingredient of probabilistic learning in the human brain, and that the right inferior frontal gyrus hosts a confidence-based statistical learning algorithm for auditory and visual sequences.

Brain networks for confidence weighting and hierarchical inference during probabilistic learning

Science.gov (United States)

Meyniel, Florent; Dehaene, Stanislas

2017-01-01

Learning is difficult when the world fluctuates randomly and ceaselessly. Classical learning algorithms, such as the delta rule with constant learning rate, are not optimal. Mathematically, the optimal learning rule requires weighting prior knowledge and incoming evidence according to their respective reliabilities. This “confidence weighting” implies the maintenance of an accurate estimate of the reliability of what has been learned. Here, using fMRI and an ideal-observer analysis, we demonstrate that the brain’s learning algorithm relies on confidence weighting. While in the fMRI scanner, human adults attempted to learn the transition probabilities underlying an auditory or visual sequence, and reported their confidence in those estimates. They knew that these transition probabilities could change simultaneously at unpredicted moments, and therefore that the learning problem was inherently hierarchical. Subjective confidence reports tightly followed the predictions derived from the ideal observer. In particular, subjects managed to attach distinct levels of confidence to each learned transition probability, as required by Bayes-optimal inference. Distinct brain areas tracked the likelihood of new observations given current predictions, and the confidence in those predictions. Both signals were combined in the right inferior frontal gyrus, where they operated in agreement with the confidence-weighting model. This brain region also presented signatures of a hierarchical process that disentangles distinct sources of uncertainty. Together, our results provide evidence that the sense of confidence is an essential ingredient of probabilistic learning in the human brain, and that the right inferior frontal gyrus hosts a confidence-based statistical learning algorithm for auditory and visual sequences. PMID:28439014

High-Throughput Block Optical DNA Sequence Identification.

Science.gov (United States)

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

2018-01-01

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

High-Throughput Next-Generation Sequencing of Polioviruses

Science.gov (United States)

Montmayeur, Anna M.; Schmidt, Alexander; Zhao, Kun; Magaña, Laura; Iber, Jane; Castro, Christina J.; Chen, Qi; Henderson, Elizabeth; Ramos, Edward; Shaw, Jing; Tatusov, Roman L.; Dybdahl-Sissoko, Naomi; Endegue-Zanga, Marie Claire; Adeniji, Johnson A.; Oberste, M. Steven; Burns, Cara C.

2016-01-01

ABSTRACT The poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random reverse transcription (RT), amplification, and the use of the Nextera XT DNA library preparation kit produced significantly better results than other preparations. The average viral reads per total reads, a measurement of efficiency, was as high as 84.2% ± 15.6%. PV genomes covering >99 to 100% of the reference length were obtained and validated with Sanger sequencing. A total of 52 PV genomes were generated, multiplexing as many as 64 samples in a single Illumina MiSeq run. This high-throughput, sequence-independent NGS approach facilitated the detection of a diverse range of PVs, especially for those in vaccine-derived polioviruses (VDPV), circulating VDPV, or immunodeficiency-related VDPV. In contrast to results from previous studies on other viruses, our results showed that filtration and nuclease treatment did not discernibly increase the sequencing efficiency of PV isolates. However, DNase treatment after nucleic acid extraction to remove host DNA significantly improved the sequencing results. This NGS method has been successfully implemented to generate PV genomes for molecular epidemiology of the most recent PV isolates. Additionally, the ability to obtain full PV genomes from FTA cards will aid in facilitating global poliovirus surveillance. PMID:27927929

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

DEFF Research Database (Denmark)

de Souza, S J; Camargo, A A; Briones, M R

2000-01-01

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central ...

Coronal oblique imaging of the knee: Can it increase radiologists' confidence in diagnosing posterior root meniscal tears?

International Nuclear Information System (INIS)

Casagranda, B.U.; Leeman, J.; Costello, J.M.; Rafiee, B.; Harner, C.D.

2013-01-01

Aim: To investigate the utility of the coronal oblique sequence in the interrogation of posterior root meniscal lesions. Materials and methods: Following international review board approval, 62 consecutive knee arthroscopy cases were referred to the musculoskeletal (MSK) radiologists from the same orthopaedic surgeon for imaging/surgical correlation of the posterior meniscal roots. Of 62 cases, 45 lateral and 46 medial menisci met the inclusion criteria. Imaging evaluation was performed with standard magnetic resonance imaging (MRI) sequences, including a coronal oblique proton density sequence. Two blinded fellowship-trained MSK radiologists independently evaluated the menisci on standard sequences indicating whether a tear was identified and then specifying a confidence score using a scale of 1–3 on each study interpreted. Immediately thereafter, the coronal oblique sequence was evaluated using the same method. Statistics were performed on meniscal lesions involving the posterior horn/root junction or isolated root tears comparing confidence scores. Results: Reader A identified nine posterior horn/root junction tears and 14 isolated root tears. Following the addition of the coronal oblique sequence, confidence scores increased in three of 14 (21.4%) isolated root tears. All three final reads were concordant with arthroscopy. Reader B identified 10 posterior horn/root junction tears and 19 isolated root tears. The confidence score increased in six cases: five of 19 (26.3%) isolated root tears and one of 10 (10%) posterior horn/root junction tears. All six final reads were concordant with arthroscopy. Kappa coefficients indicated near perfect agreement. Conclusion: The coronal oblique sequence increased reader confidence in nearly 24% of the posterior root cases identified in this series

Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence*

Science.gov (United States)

Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora; Wilfling, Florian; Stoehr, Gabriele; Mann, Matthias; Farese, Robert V.; Walther, Tobias C.

2013-01-01

Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues. PMID:23319140

Management of High-Throughput DNA Sequencing Projects: Alpheus.

Science.gov (United States)

Miller, Neil A; Kingsmore, Stephen F; Farmer, Andrew; Langley, Raymond J; Mudge, Joann; Crow, John A; Gonzalez, Alvaro J; Schilkey, Faye D; Kim, Ryan J; van Velkinburgh, Jennifer; May, Gregory D; Black, C Forrest; Myers, M Kathy; Utsey, John P; Frost, Nicholas S; Sugarbaker, David J; Bueno, Raphael; Gullans, Stephen R; Baxter, Susan M; Day, Steve W; Retzel, Ernest F

2008-12-26

High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and inter-related data and analysis. Alpheus is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multi-gigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystem's SOLiD (sequencing-by-ligation). Alpheus enables alignment to reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence. Alpheus is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymorphisms (SNPs), insertions/deletions (indels), premature stop codons, and splice isoforms. Variant detection is aided by the ability to filter variant calls based on consistency, expected allele frequency, sequence quality, coverage, and variant type in order to minimize false positives while maximizing the identification of true positives. Alpheus also enables comparisons of genes with variants between cases and controls or bulk segregant pools. Sequence-based differential expression comparisons can be developed, with data export to SAS JMP Genomics for statistical analysis.

Label-Driven Learning Framework: Towards More Accurate Bayesian Network Classifiers through Discrimination of High-Confidence Labels

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Yi Sun

2017-12-01

Full Text Available Bayesian network classifiers (BNCs have demonstrated competitive classification accuracy in a variety of real-world applications. However, it is error-prone for BNCs to discriminate among high-confidence labels. To address this issue, we propose the label-driven learning framework, which incorporates instance-based learning and ensemble learning. For each testing instance, high-confidence labels are first selected by a generalist classifier, e.g., the tree-augmented naive Bayes (TAN classifier. Then, by focusing on these labels, conditional mutual information is redefined to more precisely measure mutual dependence between attributes, thus leading to a refined generalist with a more reasonable network structure. To enable finer discrimination, an expert classifier is tailored for each high-confidence label. Finally, the predictions of the refined generalist and the experts are aggregated. We extend TAN to LTAN (Label-driven TAN by applying the proposed framework. Extensive experimental results demonstrate that LTAN delivers superior classification accuracy to not only several state-of-the-art single-structure BNCs but also some established ensemble BNCs at the expense of reasonable computation overhead.

Highly conserved non-coding sequences are associated with vertebrate development.

Directory of Open Access Journals (Sweden)

Adam Woolfe

2005-01-01

Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

Perceptual learning effect on decision and confidence thresholds.

Science.gov (United States)

Solovey, Guillermo; Shalom, Diego; Pérez-Schuster, Verónica; Sigman, Mariano

2016-10-01

Practice can enhance of perceptual sensitivity, a well-known phenomenon called perceptual learning. However, the effect of practice on subjective perception has received little attention. We approach this problem from a visual psychophysics and computational modeling perspective. In a sequence of visual search experiments, subjects significantly increased the ability to detect a "trained target". Before and after training, subjects performed two psychophysical protocols that parametrically vary the visibility of the "trained target": an attentional blink and a visual masking task. We found that confidence increased after learning only in the attentional blink task. Despite large differences in some observables and task settings, we identify common mechanisms for decision-making and confidence. Specifically, our behavioral results and computational model suggest that perceptual ability is independent of processing time, indicating that changes in early cortical representations are effective, and learning changes decision criteria to convey choice and confidence. Copyright © 2016 Elsevier Inc. All rights reserved.

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

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Courdy Samir J

2008-12-01

Full Text Available Abstract Background High throughput signature sequencing holds many promises, one of which is the ready identification of in vivo transcription factor binding sites, histone modifications, changes in chromatin structure and patterns of DNA methylation across entire genomes. In these experiments, chromatin immunoprecipitation is used to enrich for particular DNA sequences of interest and signature sequencing is used to map the regions to the genome (ChIP-Seq. Elucidation of these sites of DNA-protein binding/modification are proving instrumental in reconstructing networks of gene regulation and chromatin remodelling that direct development, response to cellular perturbation, and neoplastic transformation. Results Here we present a package of algorithms and software that makes use of control input data to reduce false positives and estimate confidence in ChIP-Seq peaks. Several different methods were compared using two simulated spike-in datasets. Use of control input data and a normalized difference score were found to more than double the recovery of ChIP-Seq peaks at a 5% false discovery rate (FDR. Moreover, both a binomial p-value/q-value and an empirical FDR were found to predict the true FDR within 2–3 fold and are more reliable estimators of confidence than a global Poisson p-value. These methods were then used to reanalyze Johnson et al.'s neuron-restrictive silencer factor (NRSF ChIP-Seq data without relying on extensive qPCR validated NRSF sites and the presence of NRSF binding motifs for setting thresholds. Conclusion The methods developed and tested here show considerable promise for reducing false positives and estimating confidence in ChIP-Seq data without any prior knowledge of the chIP target. They are part of a larger open source package freely available from http://useq.sourceforge.net/.

Confidence Building Strategies in the Public Schools.

Science.gov (United States)

Achilles, C. M.; And Others

1985-01-01

Data from the Phi Delta Kappa Commission on Public Confidence in Education indicate that "high-confidence" schools make greater use of marketing and public relations strategies. Teacher attitudes were ranked first and administrator attitudes second by 409 respondents for both gain and loss of confidence in schools. (MLF)

Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

DEFF Research Database (Denmark)

Alquezar-Planas, David E; Fordyce, Sarah Louise

2012-01-01

Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure...... that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred...

Beyond hypercorrection: remembering corrective feedback for low-confidence errors.

Science.gov (United States)

Griffiths, Lauren; Higham, Philip A

2018-02-01

Correcting errors based on corrective feedback is essential to successful learning. Previous studies have found that corrections to high-confidence errors are better remembered than low-confidence errors (the hypercorrection effect). The aim of this study was to investigate whether corrections to low-confidence errors can also be successfully retained in some cases. Participants completed an initial multiple-choice test consisting of control, trick and easy general-knowledge questions, rated their confidence after answering each question, and then received immediate corrective feedback. After a short delay, they were given a cued-recall test consisting of the same questions. In two experiments, we found high-confidence errors to control questions were better corrected on the second test compared to low-confidence errors - the typical hypercorrection effect. However, low-confidence errors to trick questions were just as likely to be corrected as high-confidence errors. Most surprisingly, we found that memory for the feedback and original responses, not confidence or surprise, were significant predictors of error correction. We conclude that for some types of material, there is an effortful process of elaboration and problem solving prior to making low-confidence errors that facilitates memory of corrective feedback.

Directed PCR-free engineering of highly repetitive DNA sequences

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Preissler Steffen

2011-09-01

Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

Exome Sequence Analysis of 14 Families With High Myopia

DEFF Research Database (Denmark)

Kloss, Bethany A.; Tompson, Stuart W.; Whisenhunt, Kristina N.

2017-01-01

Purpose: To identify causal gene mutations in 14 families with autosomal dominant (AD) high myopia using exome sequencing. Methods: Select individuals from 14 large Caucasian families with high myopia were exome sequenced. Gene variants were filtered to identify potential pathogenic changes. Sang...

Bayesian Correlation Analysis for Sequence Count Data.

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Daniel Sánchez-Taltavull

Full Text Available Evaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities' measurements based on high-throughput sequencing data. These entities could be different genes or miRNAs whose expression is measured by RNA-seq, different transcription factors or histone marks whose expression is measured by ChIP-seq, or even combinations of different types of entities. Our Bayesian formulation accounts for both measured signal levels and uncertainty in those levels, due to varying sequencing depth in different experiments and to varying absolute levels of individual entities, both of which affect the precision of the measurements. In comparison with a traditional Pearson correlation analysis, we show that our Bayesian correlation analysis retains high correlations when measurement confidence is high, but suppresses correlations when measurement confidence is low-especially for entities with low signal levels. In addition, we consider the influence of priors on the Bayesian correlation estimate. Perhaps surprisingly, we show that naive, uniform priors on entities' signal levels can lead to highly biased correlation estimates, particularly when different experiments have widely varying sequencing depths. However, we propose two alternative priors that provably mitigate this problem. We also prove that, like traditional Pearson correlation, our Bayesian correlation calculation constitutes a kernel in the machine learning sense, and thus can be used as a similarity measure in any kernel-based machine learning algorithm. We demonstrate our approach on two RNA-seq datasets and one miRNA-seq dataset.

Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation

DEFF Research Database (Denmark)

Czaban, Adrian; Sharma, Sapna; Byrne, Stephen

2015-01-01

species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family...... clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity...... enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some...

Near-complete genome sequencing of swine vesicular disease virus using the Roche GS FLX sequencing platform

DEFF Research Database (Denmark)

Nielsen, Sandra Cathrine Abel; Bruhn, Christian Anders Wathne; Samaniego Castruita, Jose Alfredo

2014-01-01

Swine vesicular disease virus (SVDV) is an enterovirus that is both genetically and antigenically closely related to human coxsackievirus B5 within the Picornaviridae family. SVDV is the causative agent of a highly contagious (though rarely fatal) vesicular disease in pigs. We report a rapid method...... with significant genetic distances within the same species of viruses. All reference mappings used an iterative method to avoid bias. Further verification was achieved through phylogenetic analysis against published SVDV genomes and additional Enterovirus B sequences. This approach allows high confidence...

Consumer confidence or the business cycle

DEFF Research Database (Denmark)

Møller, Stig Vinther; Nørholm, Henrik; Rangvid, Jesper

2014-01-01

Answer: The business cycle. We show that consumer confidence and the output gap both excess returns on stocks in many European countries: When the output gap is positive (the economy is doing well), expected returns are low, and when consumer confidence is high, expected returns are also low...

An evaluation of Comparative Genome Sequencing (CGS by comparing two previously-sequenced bacterial genomes

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Herring Christopher D

2007-08-01

Full Text Available Abstract Background With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected. Results In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence. Conclusion CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

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Jason D Thompson

Full Text Available Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Science.gov (United States)

Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre

2012-01-01

Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Effect of spotters on state anxiety and self-confidence during maximal squatting among male high school athletes

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Drew Rykert

2017-09-01

Full Text Available The ideal performance state is manifested by psychological and physiological efficiency. The psychological effects of anxiety and self-confidence has been shown to alter the efficiency of performance. This study attempted to identify the state anxiety and self-confidence of high school athletes just prior to a one repetition maximum (1-RM back squat and determine if the number of spotters affects an athlete’s level of state anxiety and/or self-confidence. Male high school athletes (10th and 11th grades were randomly separated into two experimental groups who performed the 1-RM back squat (BSQ with either 1 spotter (1SG: n=52 or 3 spotters (3SG: n=54. Following a dynamic warm-up period and several progressive BSQ warm-up sets, and just prior to attempts at a 1-RM BSQ, the participants completed the revised Competitive State Anxiety Inventory-2 (CSAI-2R. The CSAI-2R included the number of spotters (1 or 3 that would be present during the subsequent 1-RM BSQ attempts. The CSAI-2R is a17-question instrument with three subscales (self-confidence, somatic anxiety, and cognitive anxiety. The subscale scores were compared between the 1SG and 3SG with an independent t-test (alpha≤0.05. None of the subscales (self-confidence, somatic anxiety, and cognitive anxiety were significantly different between the 1SG and 3SG experimental groups (p>0.05. Within the parameters of this study, the number of spotters present during the execution of the 1-RM BSQ had no practical or statistical impact on self-confidence, somatic anxiety, and cognitive anxiety. Coaches and athletes could use this information in the training environment in order to make best use of personnel (assigned to spotting tasks, physical resources (ex. squat racks, and time management.

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

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Li Kelvin

2012-11-01

Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

Confidence improvement of disosal safety bydevelopement of a safety case for high-level radioactive waste disposal

Energy Technology Data Exchange (ETDEWEB)

Baik, Min Hoon; Ko, Nak Youl; Jeong, Jong Tae; Kim, Kyung Su [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2016-12-15

Many countries have developed a safety case suitable to their own countries in order to improve the confidence of disposal safety in deep geological disposal of high-level radioactive waste as well as to develop a disposal program and obtain its license. This study introduces and summarizes the meaning, necessity, and development process of the safety case for radioactive waste disposal. The disposal safety is also discussed in various aspects of the safety case. In addition, the status of safety case development in the foreign countries is briefly introduced for Switzerland, Japan, the United States of America, Sweden, and Finland. The strategy for the safety case development that is being developed by KAERI is also briefly introduced. Based on the safety case, we analyze the efforts necessary to improve confidence in disposal safety for high-level radioactive waste. Considering domestic situations, we propose and discuss some implementing methods for the improvement of disposal safety, such as construction of a reliable information database, understanding of processes related to safety, reduction of uncertainties in safety assessment, communication with stakeholders, and ensuring justice and transparency. This study will contribute to the understanding of the safety case for deep geological disposal and to improving confidence in disposal safety through the development of the safety case in Korea for the disposal of high-level radioactive waste.

Highly multiplexed targeted DNA sequencing from single nuclei.

Science.gov (United States)

Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

2016-02-01

Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

Spatio-Spectral Method for Estimating Classified Regions with High Confidence using MODIS Data

International Nuclear Information System (INIS)

Katiyal, Anuj; Rajan, Dr K S

2014-01-01

In studies like change analysis, the availability of very high resolution (VHR)/high resolution (HR) imagery for a particular period and region is a challenge due to the sensor revisit times and high cost of acquisition. Therefore, most studies prefer lower resolution (LR) sensor imagery with frequent revisit times, in addition to their cost and computational advantages. Further, the classification techniques provide us a global estimate of the class accuracy, which limits its utility if the accuracy is low. In this work, we focus on the sub-classification problem of LR images and estimate regions of higher confidence than the global classification accuracy within its classified region. The spectrally classified data was mined into spatially clustered regions and further refined and processed using statistical measures to arrive at local high confidence regions (LHCRs), for every class. Rabi season MODIS data of January 2006 and 2007 was used for this study and the evaluation of LHCR was done using the APLULC 2005 classified data. For Jan-2007, the global class accuracies for water bodies (WB), forested regions (FR) and Kharif crops and barren lands (KB) were 89%, 71.7% and 71.23% respectively, while the respective LHCRs had accuracies of 96.67%, 89.4% and 80.9% covering an area of 46%, 29% and 14.5% of the initially classified areas. Though areas are reduced, LHCRs with higher accuracies help in extracting more representative class regions. Identification of such regions can facilitate in improving the classification time and processing for HR images when combined with the more frequently acquired LR imagery, isolate pure vs. mixed/impure pixels and as training samples locations for HR imagery

Exome sequencing identifies ZNF644 mutations in high myopia.

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Yi Shi

2011-06-01

Full Text Available Myopia is the most common ocular disorder worldwide, and high myopia in particular is one of the leading causes of blindness. Genetic factors play a critical role in the development of myopia, especially high myopia. Recently, the exome sequencing approach has been successfully used for the disease gene identification of Mendelian disorders. Here we show a successful application of exome sequencing to identify a gene for an autosomal dominant disorder, and we have identified a gene potentially responsible for high myopia in a monogenic form. We captured exomes of two affected individuals from a Han Chinese family with high myopia and performed sequencing analysis by a second-generation sequencer with a mean coverage of 30× and sufficient depth to call variants at ∼97% of each targeted exome. The shared genetic variants of these two affected individuals in the family being studied were filtered against the 1000 Genomes Project and the dbSNP131 database. A mutation A672G in zinc finger protein 644 isoform 1 (ZNF644 was identified as being related to the phenotype of this family. After we performed sequencing analysis of the exons in the ZNF644 gene in 300 sporadic cases of high myopia, we identified an additional five mutations (I587V, R680G, C699Y, 3'UTR+12 C>G, and 3'UTR+592 G>A in 11 different patients. All these mutations were absent in 600 normal controls. The ZNF644 gene was expressed in human retinal and retinal pigment epithelium (RPE. Given that ZNF644 is predicted to be a transcription factor that may regulate genes involved in eye development, mutation may cause the axial elongation of eyeball found in high myopia patients. Our results suggest that ZNF644 might be a causal gene for high myopia in a monogenic form.

Ancient Human Genome Sequence of an Extinct Palaeo-Eskimo

DEFF Research Database (Denmark)

Rasmussen, Morten; Li, Yingrui; Lindgreen, Stinus

2010-01-01

We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome...... possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence...

Exome sequencing generates high quality data in non-target regions

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Guo Yan

2012-05-01

Full Text Available Abstract Background Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of DNA fragments from the capture process fall outside target regions, and sequence data for positions outside target regions have been mostly ignored after alignment. Result We performed whole exome sequencing on 22 subjects using Agilent SureSelect capture reagent and 6 subjects using Illumina TrueSeq capture reagent. We also downloaded sequencing data for 6 subjects from the 1000 Genomes Project Pilot 3 study. Using these data, we examined the quality of SNPs detected outside target regions by computing consistency rate with genotypes obtained from SNP chips or the Hapmap database, transition-transversion (Ti/Tv ratio, and percentage of SNPs inside dbSNP. For all three platforms, we obtained high-quality SNPs outside target regions, and some far from target regions. In our Agilent SureSelect data, we obtained 84,049 high-quality SNPs outside target regions compared to 65,231 SNPs inside target regions (a 129% increase. For our Illumina TrueSeq data, we obtained 222,171 high-quality SNPs outside target regions compared to 95,818 SNPs inside target regions (a 232% increase. For the data from the 1000 Genomes Project, we obtained 7,139 high-quality SNPs outside target regions compared to 1,548 SNPs inside target regions (a 461% increase. Conclusions These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data. These data should not be ignored in genetic epidemiology studies.

The effect of Think Pair Share (TPS) using scientific approach on students’ self-confidence and mathematical problem-solving

Science.gov (United States)

Rifa’i, A.; Lestari, H. P.

2018-03-01

This study was designed to know the effects of Think Pair Share using Scientific Approach on students' self-confidence and mathematical problem-solving. Quasi-experimental with pre-test post-test non-equivalent group method was used as a basis for design this study. Self-confidence questionnaire and problem-solving test have been used for measurement of the two variables. Two classes of the first grade in religious senior high school (MAN) in Indonesia were randomly selected for this study. Teaching sequence and series from mathematics book at control group in the traditional way and at experiment group has been in TPS using scientific approach learning method. For data analysis regarding students’ problem-solving skill and self-confidence, One-Sample t-Test, Independent Sample t-Test, and Multivariate of Variance (MANOVA) were used. The results showed that (1) TPS using a scientific approach and traditional learning had positive effects (2) TPS using scientific approach learning in comparative with traditional learning had a more significant effect on students’ self-confidence and problem-solving skill.

Confidence-building and Canadian leadership

International Nuclear Information System (INIS)

Cleminson, F.R.

1998-01-01

Confidence-building has come into its own as a 'tool of choice' in facilitating the non-proliferation, arms control and disarmament (NACD) agenda, whether regional or global. From the Middle East Peace Process (MEPP) to the ASEAN Intersessional Group on Confidence-Building (ARF ISG on CBMS), confidence-building has assumed a central profile in regional terms. In the Four Power Talks begun in Geneva on December 9, 1997, the United States identified confidence-building as one of two subject areas for initial discussion as part of a structured peace process between North and South Korea. Thus, with CBMs assuming such a high profile internationally, it seems prudent for Canadians to pause and take stock of the significant role which Canada has already played in the conceptual development of the process over the last two decades. Since the Helsinki accords of 1975, Canada has developed a significant expertise in this area through an unbroken series of original, basic research projects. These have contributed to defining the process internationally from concept to implementation. Today, these studies represent a solid and unique Departmental investment in basic research from which to draw in meeting Canada's current commitments to multilateral initiatives in the area of confidence-building and to provide a 'step up' in terms of future-oriented leadership. (author)

Frontline nurse managers' confidence and self-efficacy.

Science.gov (United States)

Van Dyk, Jennifer; Siedlecki, Sandra L; Fitzpatrick, Joyce J

2016-05-01

This study was focused on determining relationships between confidence levels and self-efficacy among nurse managers. Frontline nurse managers have a pivotal role in delivering high-quality patient care while managing the associated costs and resources. The competency and skill of nurse managers affect every aspect of patient care and staff well-being as nurse managers are largely responsible for creating work environments in which clinical nurses are able to provide high-quality, patient-centred, holistic care. A descriptive, correlational survey design was used; 85 nurse managers participated. Years in a formal leadership role and confidence scores were found to be significant predictors of self-efficacy scores. Experience as a nurse manager is an important component of confidence and self-efficacy. There is a need to develop educational programmes for nurse managers to enhance their self-confidence and self-efficacy, and to maintain experienced nurse managers in the role. © 2016 John Wiley & Sons Ltd.

Weighting Mean and Variability during Confidence Judgments

Science.gov (United States)

de Gardelle, Vincent; Mamassian, Pascal

2015-01-01

Humans can not only perform some visual tasks with great precision, they can also judge how good they are in these tasks. However, it remains unclear how observers produce such metacognitive evaluations, and how these evaluations might be dissociated from the performance in the visual task. Here, we hypothesized that some stimulus variables could affect confidence judgments above and beyond their impact on performance. In a motion categorization task on moving dots, we manipulated the mean and the variance of the motion directions, to obtain a low-mean low-variance condition and a high-mean high-variance condition with matched performances. Critically, in terms of confidence, observers were not indifferent between these two conditions. Observers exhibited marked preferences, which were heterogeneous across individuals, but stable within each observer when assessed one week later. Thus, confidence and performance are dissociable and observers’ confidence judgments put different weights on the stimulus variables that limit performance. PMID:25793275

A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis

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Aditi Sengupta

2016-03-01

Full Text Available Amplicon-based sequencing strategies that include 16S rRNA and functional genes, alongside “meta-omics” analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to “who” is present in the environment and “what” they are doing. Next-generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high-throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high-throughput amplicon-based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high-throughput microbial DNA sequencing and sequences analysis.

Concerns and developmental needs of highly confident and less ...

African Journals Online (AJOL)

The development of this study was based on three assumptions, namely 1) that coaching efficacy (confidence specific to the task of coaching) impacts the performance of coaches, 2) that coaching efficacy is influenced by the individual's procedural and declarative knowledge on coaching, and 3) that coaches do their work ...

Using the confidence interval confidently.

Science.gov (United States)

Hazra, Avijit

2017-10-01

Biomedical research is seldom done with entire populations but rather with samples drawn from a population. Although we work with samples, our goal is to describe and draw inferences regarding the underlying population. It is possible to use a sample statistic and estimates of error in the sample to get a fair idea of the population parameter, not as a single value, but as a range of values. This range is the confidence interval (CI) which is estimated on the basis of a desired confidence level. Calculation of the CI of a sample statistic takes the general form: CI = Point estimate ± Margin of error, where the margin of error is given by the product of a critical value (z) derived from the standard normal curve and the standard error of point estimate. Calculation of the standard error varies depending on whether the sample statistic of interest is a mean, proportion, odds ratio (OR), and so on. The factors affecting the width of the CI include the desired confidence level, the sample size and the variability in the sample. Although the 95% CI is most often used in biomedical research, a CI can be calculated for any level of confidence. A 99% CI will be wider than 95% CI for the same sample. Conflict between clinical importance and statistical significance is an important issue in biomedical research. Clinical importance is best inferred by looking at the effect size, that is how much is the actual change or difference. However, statistical significance in terms of P only suggests whether there is any difference in probability terms. Use of the CI supplements the P value by providing an estimate of actual clinical effect. Of late, clinical trials are being designed specifically as superiority, non-inferiority or equivalence studies. The conclusions from these alternative trial designs are based on CI values rather than the P value from intergroup comparison.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

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Jonas Binladen

2007-02-01

Full Text Available The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences. Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis.We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%. Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial

Regional Competition for Confidence: Features of Formation

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Irina Svyatoslavovna Vazhenina

2016-09-01

Full Text Available The increase in economic independence of the regions inevitably leads to an increase in the quality requirements of the regional economic policy. The key to successful regional policy, both during its development and implementation, is the understanding of the necessity of gaining confidence (at all levels, and the inevitable participation in the competition for confidence. The importance of confidence in the region is determined by its value as a competitive advantage in the struggle for partners, resources and tourists, and attracting investments. In today’s environment the focus of governments, regions and companies on long-term cooperation is clearly expressed, which is impossible without a high level of confidence between partners. Therefore, the most important competitive advantages of territories are intangible assets such as an attractive image and a good reputation, which builds up confidence of the population and partners. The higher the confidence in the region is, the broader is the range of potential partners, the larger is the planning horizon of long-term concerted action, the better are the chances of acquiring investment, the higher is the level of competitive immunity of the territories. The article defines competition for confidence as purposeful behavior of a market participant in economic environment, aimed at acquiring specific intangible competitive advantage – the confidence of the largest possible number of other market actors. The article also highlights the specifics of confidence as a competitive goal, presents factors contributing to the destruction of confidence, proposes a strategy to fight for confidence as a program of four steps, considers the factors which integrate regional confidence and offers several recommendations for the establishment of effective regional competition for confidence

Technical Report on Modeling for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

Energy Technology Data Exchange (ETDEWEB)

McLoughlin, K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2016-01-11

The overall aim of this project is to develop a software package, called MetaQuant, that can determine the constituents of a complex microbial sample and estimate their relative abundances by analysis of metagenomic sequencing data. The goal for Task 1 is to create a generative model describing the stochastic process underlying the creation of sequence read pairs in the data set. The stages in this generative process include the selection of a source genome sequence for each read pair, with probability dependent on its abundance in the sample. The other stages describe the evolution of the source genome from its nearest common ancestor with a reference genome, breakage of the source DNA into short fragments, and the errors in sequencing the ends of the fragments to produce read pairs.

Confidence-building and Canadian leadership

Energy Technology Data Exchange (ETDEWEB)

Cleminson, F.R. [Dept. of Foreign Affairs and International Trade, Verification, Non-Proliferation, Arms Control and Disarmament Div (IDA), Ottawa, Ontario (Canada)

1998-07-01

Confidence-building has come into its own as a 'tool of choice' in facilitating the non-proliferation, arms control and disarmament (NACD) agenda, whether regional or global. From the Middle East Peace Process (MEPP) to the ASEAN Intersessional Group on Confidence-Building (ARF ISG on CBMS), confidence-building has assumed a central profile in regional terms. In the Four Power Talks begun in Geneva on December 9, 1997, the United States identified confidence-building as one of two subject areas for initial discussion as part of a structured peace process between North and South Korea. Thus, with CBMs assuming such a high profile internationally, it seems prudent for Canadians to pause and take stock of the significant role which Canada has already played in the conceptual development of the process over the last two decades. Since the Helsinki accords of 1975, Canada has developed a significant expertise in this area through an unbroken series of original, basic research projects. These have contributed to defining the process internationally from concept to implementation. Today, these studies represent a solid and unique Departmental investment in basic research from which to draw in meeting Canada's current commitments to multilateral initiatives in the area of confidence-building and to provide a 'step up' in terms of future-oriented leadership. (author)

High throughput 16S rRNA gene amplicon sequencing

DEFF Research Database (Denmark)

Nierychlo, Marta; Larsen, Poul; Jørgensen, Mads Koustrup

S rRNA gene amplicon sequencing has been developed over the past few years and is now ready to use for more comprehensive studies related to plant operation and optimization thanks to short analysis time, low cost, high throughput, and high taxonomic resolution. In this study we show how 16S r......RNA gene amplicon sequencing can be used to reveal factors of importance for the operation of full-scale nutrient removal plants related to settling problems and floc properties. Using optimized DNA extraction protocols, indexed primers and our in-house Illumina platform, we prepared multiple samples...... be correlated to the presence of the species that are regarded as “strong” and “weak” floc formers. In conclusion, 16S rRNA gene amplicon sequencing provides a high throughput approach for a rapid and cheap community profiling of activated sludge that in combination with multivariate statistics can be used...

Application of high-throughput DNA sequencing in phytopathology.

Science.gov (United States)

Studholme, David J; Glover, Rachel H; Boonham, Neil

2011-01-01

The new sequencing technologies are already making a big impact in academic research on medically important microbes and may soon revolutionize diagnostics, epidemiology, and infection control. Plant pathology also stands to gain from exploiting these opportunities. This manuscript reviews some applications of these high-throughput sequencing methods that are relevant to phytopathology, with emphasis on the associated computational and bioinformatics challenges and their solutions. Second-generation sequencing technologies have recently been exploited in genomics of both prokaryotic and eukaryotic plant pathogens. They are also proving to be useful in diagnostics, especially with respect to viruses. Copyright © 2011 by Annual Reviews. All rights reserved.

Data on electrical energy conservation using high efficiency motors for the confidence bounds using statistical techniques.

Science.gov (United States)

Shaikh, Muhammad Mujtaba; Memon, Abdul Jabbar; Hussain, Manzoor

2016-09-01

In this article, we describe details of the data used in the research paper "Confidence bounds for energy conservation in electric motors: An economical solution using statistical techniques" [1]. The data presented in this paper is intended to show benefits of high efficiency electric motors over the standard efficiency motors of similar rating in the industrial sector of Pakistan. We explain how the data was collected and then processed by means of formulas to show cost effectiveness of energy efficient motors in terms of three important parameters: annual energy saving, cost saving and payback periods. This data can be further used to construct confidence bounds for the parameters using statistical techniques as described in [1].

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data.

Science.gov (United States)

Massouras, Andreas; Decouttere, Frederik; Hens, Korneel; Deplancke, Bart

2010-07-01

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users.

A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius.

Directory of Open Access Journals (Sweden)

Ceiridwen J Edwards

Full Text Available BACKGROUND: The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY: DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer. In total, 289.9 megabases (22.48% of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS: For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously

A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius).

LENUS (Irish Health Repository)

Edwards, Ceiridwen J

2010-01-01

BACKGROUND: The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY: DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+\\/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS: For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified

Probabilistic Methods for Processing High-Throughput Sequencing Signals

DEFF Research Database (Denmark)

Sørensen, Lasse Maretty

High-throughput sequencing has the potential to answer many of the big questions in biology and medicine. It can be used to determine the ancestry of species, to chart complex ecosystems and to understand and diagnose disease. However, going from raw sequencing data to biological or medical insig....... By estimating the genotypes on a set of candidate variants obtained from both a standard mapping-based approach as well as de novo assemblies, we are able to find considerably more structural variation than previous studies...... for reconstructing transcript sequences from RNA sequencing data. The method is based on a novel sparse prior distribution over transcript abundances and is markedly more accurate than existing approaches. The second chapter describes a new method for calling genotypes from a fixed set of candidate variants....... The method queries the reads using a graph representation of the variants and hereby mitigates the reference-bias that characterise standard genotyping methods. In the last chapter, we apply this method to call the genotypes of 50 deeply sequencing parent-offspring trios from the GenomeDenmark project...

Sources of PCR-induced distortions in high-throughput sequencing data sets

Science.gov (United States)

Kebschull, Justus M.; Zador, Anthony M.

2015-01-01

PCR permits the exponential and sequence-specific amplification of DNA, even from minute starting quantities. PCR is a fundamental step in preparing DNA samples for high-throughput sequencing. However, there are errors associated with PCR-mediated amplification. Here we examine the effects of four important sources of error—bias, stochasticity, template switches and polymerase errors—on sequence representation in low-input next-generation sequencing libraries. We designed a pool of diverse PCR amplicons with a defined structure, and then used Illumina sequencing to search for signatures of each process. We further developed quantitative models for each process, and compared predictions of these models to our experimental data. We find that PCR stochasticity is the major force skewing sequence representation after amplification of a pool of unique DNA amplicons. Polymerase errors become very common in later cycles of PCR but have little impact on the overall sequence distribution as they are confined to small copy numbers. PCR template switches are rare and confined to low copy numbers. Our results provide a theoretical basis for removing distortions from high-throughput sequencing data. In addition, our findings on PCR stochasticity will have particular relevance to quantification of results from single cell sequencing, in which sequences are represented by only one or a few molecules. PMID:26187991

Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

Directory of Open Access Journals (Sweden)

Takeru Nakazato

Full Text Available 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.

Food skills confidence and household gatekeepers' dietary practices.

Science.gov (United States)

Burton, Melissa; Reid, Mike; Worsley, Anthony; Mavondo, Felix

2017-01-01

Household food gatekeepers have the potential to influence the food attitudes and behaviours of family members, as they are mainly responsible for food-related tasks in the home. The aim of this study was to determine the role of gatekeepers' confidence in food-related skills and nutrition knowledge on food practices in the home. An online survey was completed by 1059 Australian dietary gatekeepers selected from the Global Market Insite (GMI) research database. Participants responded to questions about food acquisition and preparation behaviours, the home eating environment, perceptions and attitudes towards food, and demographics. Two-step cluster analysis was used to identify groups based on confidence regarding food skills and nutrition knowledge. Chi-square tests and one-way ANOVAs were used to compare the groups on the dependent variables. Three groups were identified: low confidence, moderate confidence and high confidence. Gatekeepers in the highest confidence group were significantly more likely to report lower body mass index (BMI), and indicate higher importance of fresh food products, vegetable prominence in meals, product information use, meal planning, perceived behavioural control and overall diet satisfaction. Gatekeepers in the lowest confidence group were significantly more likely to indicate more perceived barriers to healthy eating, report more time constraints and more impulse purchasing practices, and higher convenience ingredient use. Other smaller associations were also found. Household food gatekeepers with high food skills confidence were more likely to engage in several healthy food practices, while those with low food skills confidence were more likely to engage in unhealthy food practices. Food education strategies aimed at building food-skills and nutrition knowledge will enable current and future gatekeepers to make healthier food decisions for themselves and for their families. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tracking TCRβ sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region

Directory of Open Access Journals (Sweden)

Mark W Robinson

2016-04-01

Full Text Available To maintain a persistent infection viruses such as hepatitis C virus (HCV employ a range of mechanisms that subvert protective T cell responses. The suppression of antigen-specific T cell responses by HCV hinders efforts to profile T cell responses during chronic infection and antiviral therapy. Conventional methods of detecting antigen-specific T cells utilise either antigen stimulation (e.g. ELISpot, proliferation assays, cytokine production or antigen-loaded tetramer staining. This limits the ability to profile T cell responses during chronic infection due to suppressed effector function and the requirement for prior knowledge of antigenic viral peptide sequences. Recently high-throughput sequencing (HTS technologies have been developed for the analysis of T cell repertoires. In the present study we have assessed the feasibility of HTS of the TCRβ complementarity determining region (CDR3 to track T cell expansions in an antigen-independent manner. Using sequential blood samples from HCV-infected individuals undergoing anti-viral therapy we were able to measure the population frequencies of >35,000 TCRβ sequence clonotypes in each individual over the course of 12 weeks. TRBV/TRBJ gene segment usage varied markedly between individuals but remained relatively constant within individuals across the course of therapy. Despite this stable TRBV/TRBJ gene segment usage, a number of TCRβ sequence clonotypes showed dramatic changes in read frequency. These changes could not be linked to therapy outcomes in the present study however the TCRβ CDR3 sequences with the largest fold changes did include sequences with identical TRBV/TRBJ gene segment usage and high joining region homology to previously published CDR3 sequences from HCV-specific T cells targeting the HLA-B*0801-restricted 1395HSKKKCDEL1403 and HLA-A*0101–restricted 1435ATDALMTGY1443 epitopes. The pipeline developed in this proof of concept study provides a platform for the design of

Technical Report: Benchmarking for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

Energy Technology Data Exchange (ETDEWEB)

McLoughlin, K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2016-01-22

The software application “MetaQuant” was developed by our group at Lawrence Livermore National Laboratory (LLNL). It is designed to profile microbial populations in a sample using data from whole-genome shotgun (WGS) metagenomic DNA sequencing. Several other metagenomic profiling applications have been described in the literature. We ran a series of benchmark tests to compare the performance of MetaQuant against that of a few existing profiling tools, using real and simulated sequence datasets. This report describes our benchmarking procedure and results.

Communicating the Benefits of a Full Sequence of High School Science Courses

Science.gov (United States)

Nicholas, Catherine Marie

2014-01-01

High school students are generally uninformed about the benefits of enrolling in a full sequence of science courses, therefore only about a third of our nation's high school graduates have completed the science sequence of Biology, Chemistry and Physics. The lack of students completing a full sequence of science courses contributes to the deficit…

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

DEFF Research Database (Denmark)

Binladen, Jonas; Gilbert, M Thomas P; Bollback, Jonathan P

2007-01-01

BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine...... primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution...

Scrutinizing virus genome termini by high-throughput sequencing.

Directory of Open Access Journals (Sweden)

Shasha Li

Full Text Available Analysis of genomic terminal sequences has been a major step in studies on viral DNA replication and packaging mechanisms. However, traditional methods to study genome termini are challenging due to the time-consuming protocols and their inefficiency where critical details are lost easily. Recent advances in next generation sequencing (NGS have enabled it to be a powerful tool to study genome termini. In this study, using NGS we sequenced one iridovirus genome and twenty phage genomes and confirmed for the first time that the high frequency sequences (HFSs found in the NGS reads are indeed the terminal sequences of viral genomes. Further, we established a criterion to distinguish the type of termini and the viral packaging mode. We also obtained additional terminal details such as terminal repeats, multi-termini, asymmetric termini. With this approach, we were able to simultaneously detect details of the genome termini as well as obtain the complete sequence of bacteriophage genomes. Theoretically, this application can be further extended to analyze larger and more complicated genomes of plant and animal viruses. This study proposed a novel and efficient method for research on viral replication, packaging, terminase activity, transcription regulation, and metabolism of the host cell.

Recall Latencies, Confidence, and Output Positions of True and False Memories: Implications for Recall and Metamemory Theories

Science.gov (United States)

Jou, Jerwen

2008-01-01

Recall latency, recall accuracy rate, and recall confidence were examined in free recall as a function of recall output serial position using a modified Deese-Roediger-McDermott paradigm to test a strength-based theory against the dual-retrieval process theory of recall output sequence. The strength theory predicts the item output sequence to be…

Phylogenetic Trees From Sequences

Science.gov (United States)

Ryvkin, Paul; Wang, Li-San

In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.

Science.gov (United States)

Sato, Yukuto; Kojima, Kaname; Nariai, Naoki; Yamaguchi-Kabata, Yumi; Kawai, Yosuke; Takahashi, Mamoru; Mimori, Takahiro; Nagasaki, Masao

2014-08-08

Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved. The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures.

The impact of MRI sequence on tumour staging and gross tumour volume delineation in squamous cell carcinoma of the anal canal

International Nuclear Information System (INIS)

Prezzi, Davide; Mandegaran, Ramin; Gourtsoyianni, Sofia; Owczarczyk, Katarzyna; Gaya, Andrew; Glynne-Jones, Robert; Goh, Vicky

2018-01-01

To compare maximum tumour diameter (MTD) and gross tumour volume (GTV) measurements between T 2 -weighted (T 2 -w) and diffusion-weighted (DWI) MRI in squamous cell carcinoma of the anal canal (SCCA) and assess sequence impact on tumour (T) staging. Second, to evaluate interobserver agreement and reader delineation confidence. The staging MRI scans of 45 SCCA patients (25 females) were assessed retrospectively by two independent radiologists (0 and 5 years' experience of anal cancer MRI). MTD and GTV were delineated on both T 2 -w and high-b-value DWI images and compared between sequences; T staging was derived from MTD. Interobserver agreement was assessed and delineation confidence scored (1 to 5) by each observer. GTV and MTD were significantly and systematically lower on DWI versus T 2 -w sequences by 14.80%/9.98% (MTD) and 29.70%/12.25% (GTV) for each reader, respectively, causing T staging discordances in approximately a quarter of cases. Bland-Altman limits of agreement were narrower and intraclass correlation coefficients higher for DWI. Delineation confidence was greater on DWI: 40/42 cases were scored confidently (4 or 5) by each reader, respectively, versus 31/36 cases based on T 2 -w images. Sequence selection affects SCCA measurements and T stage. DWI yields higher interobserver agreement and greater tumour delineation confidence. (orig.)

The Relationship Between Eyewitness Confidence and Identification Accuracy: A New Synthesis.

Science.gov (United States)

Wixted, John T; Wells, Gary L

2017-05-01

The U.S. legal system increasingly accepts the idea that the confidence expressed by an eyewitness who identified a suspect from a lineup provides little information as to the accuracy of that identification. There was a time when this pessimistic assessment was entirely reasonable because of the questionable eyewitness-identification procedures that police commonly employed. However, after more than 30 years of eyewitness-identification research, our understanding of how to properly conduct a lineup has evolved considerably, and the time seems ripe to ask how eyewitness confidence informs accuracy under more pristine testing conditions (e.g., initial, uncontaminated memory tests using fair lineups, with no lineup administrator influence, and with an immediate confidence statement). Under those conditions, mock-crime studies and police department field studies have consistently shown that, for adults, (a) confidence and accuracy are strongly related and (b) high-confidence suspect identifications are remarkably accurate. However, when certain non-pristine testing conditions prevail (e.g., when unfair lineups are used), the accuracy of even a high-confidence suspect ID is seriously compromised. Unfortunately, some jurisdictions have not yet made reforms that would create pristine testing conditions and, hence, our conclusions about the reliability of high-confidence identifications cannot yet be applied to those jurisdictions. However, understanding the information value of eyewitness confidence under pristine testing conditions can help the criminal justice system to simultaneously achieve both of its main objectives: to exonerate the innocent (by better appreciating that initial, low-confidence suspect identifications are error prone) and to convict the guilty (by better appreciating that initial, high-confidence suspect identifications are surprisingly accurate under proper testing conditions).

Confidence assessment. Site-descriptive modelling SDM-Site Laxemar

International Nuclear Information System (INIS)

2009-06-01

The objective of this report is to assess the confidence that can be placed in the Laxemar site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Laxemar). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface-based investigations or more usefully by explorations underground made during construction of the repository. Procedures for this assessment have been progressively refined during the course of the site descriptive modelling, and applied to all previous versions of the Forsmark and Laxemar site descriptive models. They include assessment of whether all relevant data have been considered and understood, identification of the main uncertainties and their causes, possible alternative models and their handling, and consistency between disciplines. The assessment then forms the basis for an overall confidence statement. The confidence in the Laxemar site descriptive model, based on the data available at the conclusion of the surface based site investigations, has been assessed by exploring: - Confidence in the site characterization data base, - remaining issues and their handling, - handling of alternatives, - consistency between disciplines and - main reasons for confidence and lack of confidence in the model. Generally, the site investigation database is of high quality, as assured by the quality procedures applied. It is judged that the Laxemar site descriptive model has an overall high level of confidence. Because of the relatively robust geological model that describes the site, the overall confidence in the Laxemar Site Descriptive model is judged to be high, even though details of the spatial variability remain unknown. The overall reason for this confidence is the wide spatial distribution of the data and the consistency between

Confidence assessment. Site-descriptive modelling SDM-Site Laxemar

Energy Technology Data Exchange (ETDEWEB)

2008-12-15

The objective of this report is to assess the confidence that can be placed in the Laxemar site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Laxemar). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface-based investigations or more usefully by explorations underground made during construction of the repository. Procedures for this assessment have been progressively refined during the course of the site descriptive modelling, and applied to all previous versions of the Forsmark and Laxemar site descriptive models. They include assessment of whether all relevant data have been considered and understood, identification of the main uncertainties and their causes, possible alternative models and their handling, and consistency between disciplines. The assessment then forms the basis for an overall confidence statement. The confidence in the Laxemar site descriptive model, based on the data available at the conclusion of the surface based site investigations, has been assessed by exploring: - Confidence in the site characterization data base, - remaining issues and their handling, - handling of alternatives, - consistency between disciplines and - main reasons for confidence and lack of confidence in the model. Generally, the site investigation database is of high quality, as assured by the quality procedures applied. It is judged that the Laxemar site descriptive model has an overall high level of confidence. Because of the relatively robust geological model that describes the site, the overall confidence in the Laxemar Site Descriptive model is judged to be high, even though details of the spatial variability remain unknown. The overall reason for this confidence is the wide spatial distribution of the data and the consistency between

Contrasting Academic Behavioural Confidence in Mexican and European Psychology Students

Science.gov (United States)

Ochoa, Alma Rosa Aguila; Sander, Paul

2012-01-01

Introduction: Research with the Academic Behavioural Confidence scale using European students has shown that students have high levels of confidence in their academic abilities. It is generally accepted that people in more collectivist cultures have more realistic confidence levels in contrast to the overconfidence seen in individualistic European…

Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data

DEFF Research Database (Denmark)

Rask, Thomas Salhøj; Petersen, Bent; Chen, Donald S.

2016-01-01

. The new basecalling method described here, named Multipass, implements a probabilistic framework for working with the raw flowgrams obtained by pyrosequencing. For each sequence variant Multipass calculates the likelihood and nucleotide sequence of several most likely sequences given the flowgram data....... This probabilistic approach enables integration of basecalling into a larger model where other parameters can be incorporated, such as the likelihood for observing a full-length open reading frame at the targeted region. We apply the method to 454 amplicon pyrosequencing data obtained from a malaria virulence gene...... family, where Multipass generates 20 % more error-free sequences than current state of the art methods, and provides sequence characteristics that allow generation of a set of high confidence error-free sequences. This novel method can be used to increase accuracy of existing and future amplicon...

Self Confidence Spillovers and Motivated Beliefs

DEFF Research Database (Denmark)

Banerjee, Ritwik; Gupta, Nabanita Datta; Villeval, Marie Claire

that success when competing in a task increases the performers’ self-confidence and competitiveness in the subsequent task. We also find that such spillovers affect the self-confidence of low-status individuals more than that of high-status individuals. Receiving good news under Affirmative Action, however......Is success in a task used strategically by individuals to motivate their beliefs prior to taking action in a subsequent, unrelated, task? Also, is the distortion of beliefs reinforced for individuals who have lower status in society? Conducting an artefactual field experiment in India, we show...

SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

Science.gov (United States)

Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver

2012-07-15

In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.

The application of the high throughput sequencing technology in the transposable elements.

Science.gov (United States)

Liu, Zhen; Xu, Jian-hong

2015-09-01

High throughput sequencing technology has dramatically improved the efficiency of DNA sequencing, and decreased the costs to a great extent. Meanwhile, this technology usually has advantages of better specificity, higher sensitivity and accuracy. Therefore, it has been applied to the research on genetic variations, transcriptomics and epigenomics. Recently, this technology has been widely employed in the studies of transposable elements and has achieved fruitful results. In this review, we summarize the application of high throughput sequencing technology in the fields of transposable elements, including the estimation of transposon content, preference of target sites and distribution, insertion polymorphism and population frequency, identification of rare copies, transposon horizontal transfers as well as transposon tagging. We also briefly introduce the major common sequencing strategies and algorithms, their advantages and disadvantages, and the corresponding solutions. Finally, we envision the developing trends of high throughput sequencing technology, especially the third generation sequencing technology, and its application in transposon studies in the future, hopefully providing a comprehensive understanding and reference for related scientific researchers.

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

Directory of Open Access Journals (Sweden)

Allard Marc W

2012-01-01

Full Text Available Abstract Background Next-Generation Sequencing (NGS is increasingly being used as a molecular epidemiologic tool for discerning ancestry and traceback of the most complicated, difficult to resolve bacterial pathogens. Making a linkage between possible food sources and clinical isolates requires distinguishing the suspected pathogen from an environmental background and placing the variation observed into the wider context of variation occurring within a serovar and among other closely related foodborne pathogens. Equally important is the need to validate these high resolution molecular tools for use in molecular epidemiologic traceback. Such efforts include the examination of strain cluster stability as well as the cumulative genetic effects of sub-culturing on these clusters. Numerous isolates of S. Montevideo were shot-gun sequenced including diverse lineage representatives as well as numerous replicate clones to determine how much variability is due to bias, sequencing error, and or the culturing of isolates. All new draft genomes were compared to 34 S. Montevideo isolates previously published during an NGS-based molecular epidemiological case study. Results Intraserovar lineages of S. Montevideo differ by thousands of SNPs, that are only slightly less than the number of SNPs observed between S. Montevideo and other distinct serovars. Much less variability was discovered within an individual S. Montevideo clade implicated in a recent foodborne outbreak as well as among individual NGS replicates. These findings were similar to previous reports documenting homopolymeric and deletion error rates with the Roche 454 GS Titanium technology. In no case, however, did variability associated with sequencing methods or sample preparations create inconsistencies with our current phylogenetic results or the subsequent molecular epidemiological evidence gleaned from these data. Conclusions Implementation of a validated pipeline for NGS data acquisition and

Randomness confidence bands of fractal scaling exponents for financial price returns

International Nuclear Information System (INIS)

Ibarra-Valdez, C.; Alvarez, J.; Alvarez-Ramirez, J.

2016-01-01

Highlights: • A robust test for randomness of price returns is proposed. • The DFA scaling exponent is contrasted against confidence bands for random sequences. • The size of the band depends of the sequence length. • Crude oil and USA stock markets have been rarely inefficient. - Abstract: The weak-form of the efficient market hypothesis (EMH) establishes that price returns behave as a pure random process and so their outcomes cannot be forecasted. The detrended fluctuation analysis (DFA) has been widely used to test the weak-form of the EMH by showing that time series of price returns are serially uncorrelated. In this case, the DFA scaling exponent exhibits deviations from the theoretical value of 0.5. This work considers the test of the EMH for DFA implementation on a sliding window, which is an approach that is intended to monitor the evolution of markets. Under these conditions, the scaling exponent exhibits important variations over the scrutinized period that can offer valuable insights in the behavior of the market provided the estimated scaling value is kept within strict statistical tests to verify the presence or not of serial correlations in the price returns. In this work, the statistical tests are based on comparing the estimated scaling exponent with the values obtained from pure Gaussian sequences with the length of the real time series. In this way, the presence of serial correlations can be guaranteed only in terms of the confidence bands of a pure Gaussian process. The crude oil (WTI) and the USA stock (DJIA) markets are used to illustrate the methodology.

Raising Confident Kids

Science.gov (United States)

... First Aid & Safety Doctors & Hospitals Videos Recipes for Kids Kids site Sitio para niños How the Body ... Videos for Educators Search English Español Raising Confident Kids KidsHealth / For Parents / Raising Confident Kids What's in ...

Highly accurate sequence imputation enables precise QTL mapping in Brown Swiss cattle.

Science.gov (United States)

Frischknecht, Mirjam; Pausch, Hubert; Bapst, Beat; Signer-Hasler, Heidi; Flury, Christine; Garrick, Dorian; Stricker, Christian; Fries, Ruedi; Gredler-Grandl, Birgit

2017-12-29

Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required. In this study we evaluated the accuracy of imputation from high density chips to whole genome sequence data in Brown Swiss cattle. Using four popular imputation programs (Beagle, FImpute, Impute2, Minimac) and various compositions of reference panels, the accuracy of the imputed sequence variant genotypes was high and differences between the programs and scenarios were small. We imputed sequence variant genotypes for more than 1600 Brown Swiss bulls and performed genome-wide association studies for milk fat percentage at two stages of lactation. We found one and three quantitative trait loci for early and late lactation fat content, respectively. Known causal variants that were imputed from the sequenced reference panel were among the most significantly associated variants of the genome-wide association study. Our study demonstrates that whole-genome sequence information can be imputed at high accuracy in cattle populations. Using imputed sequence variant genotypes in genome-wide association studies may facilitate causal variant detection.

Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).

Science.gov (United States)

Cantsilieris, Stuart; Stessman, Holly A; Shendure, Jay; Eichler, Evan E

2017-01-01

Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.

Individuals with high obsessive-compulsive tendencies or undermined confidence rely more on external proxies to access their internal states.

Science.gov (United States)

Zhang, Zhongming; Wang, Mengyun; Miao, Xiaocui; Li, Yijuan; Hitchman, Glenn; Yuan, Zhen

2017-03-01

The Seeking Proxies for Internal States (SPIS) hypothesis predicts that obsessive-compulsive disorder (OCD) is associated with a deficit in subjective convictions, which may lead to a reliance on external substitutes for the perceptions of an individual's internal states. Two well-designed studies were performed for the present work that adopted a false bio-feedback procedure in a muscle tension task to examine the SPIS hypothesis. The false bio-feedback paradigm was used to investigate our hypothesis. NeXus-10 Mark II hardware and V2011 BioTrace + software (Mind Media B.V., Herten, Netherlands) were utilized to measure the muscle tension of the flexor carpiulnaris muscle, which characterized the target's internal state. In addition, false EMG changes were recorded and displayed on a computer monitor and were considered external proxies. Study 1 demonstrated that the participants with high obsessive-compulsive (OC) tendencies were more affected by the false bio-feedback and exhibited lower confidence in their judgments regarding their muscle tension compared with the participants with low OC tendencies. These findings indicate that subjects with high OC tendencies were more influenced by self-perception effects. In contrast, the subjects in the undermined confidence group in Study 2 were more easily influenced by the false bio-feedback compared with the control group, which suggests that the subjects in the undermined confidence group were more affected by self-perception effects. We did not combine the undermined confidence with OC tendencies or OCD symptoms in our paradigm to investigate their joint effects on self-perception. Our findings provide further evidence that supports the SPIS hypothesis, which indicates that OC tendencies and the confidence in an individual's recognition of internal states appear to have similar effects on the assessment of internal states and reliance on proxies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Impaired action self-monitoring and cognitive confidence among ultra-high risk for psychosis and first-episode psychosis patients.

Science.gov (United States)

Gawęda, Ł; Li, E; Lavoie, S; Whitford, T J; Moritz, S; Nelson, B

2018-01-01

Self-monitoring biases and overconfidence in incorrect judgments have been suggested as playing a role in schizophrenia spectrum disorders. Little is known about whether self-monitoring biases may contribute to early risk factors for psychosis. In this study, action self-monitoring (i.e., discrimination between imagined and performed actions) was investigated, along with confidence in judgments among ultra-high risk (UHR) for psychosis individuals and first-episode psychosis (FEP) patients. Thirty-six UHR for psychosis individuals, 25 FEP patients and 33 healthy controls (CON) participated in the study. Participants were assessed with the Action memory task. Simple actions were presented to participants verbally or non-verbally. Some actions were required to be physically performed and others were imagined. Participants were asked whether the action was presented verbally or non-verbally (action presentation type discrimination), and whether the action was performed or imagined (self-monitoring). Confidence self-ratings related to self-monitoring responses were obtained. The analysis of self-monitoring revealed that both UHR and FEP groups misattributed imagined actions as being performed (i.e., self-monitoring errors) significantly more often than the CON group. There were no differences regarding performed actions as being imagined. UHR and FEP groups made their false responses with higher confidence in their judgments than the CON group. There were no group differences regarding discrimination between the types of actions presented (verbal vs non-verbal). A specific type of self-monitoring bias (i.e., misattributing imagined actions with performed actions), accompanied by high confidence in this judgment, may be a risk factor for the subsequent development of a psychotic disorder. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing.

Science.gov (United States)

Yamamoto, F; Höglund, B; Fernandez-Vina, M; Tyan, D; Rastrou, M; Williams, T; Moonsamy, P; Goodridge, D; Anderson, M; Erlich, H A; Holcomb, C L

2015-12-01

Compared to Sanger sequencing, next-generation sequencing offers advantages for high resolution HLA genotyping including increased throughput, lower cost, and reduced genotype ambiguity. Here we describe an enhancement of the Roche 454 GS GType HLA genotyping assay to provide very high resolution (VHR) typing, by the addition of 8 primer pairs to the original 14, to genotype 11 HLA loci. These additional amplicons help resolve common and well-documented alleles and exclude commonly found null alleles in genotype ambiguity strings. Simplification of workflow to reduce the initial preparation effort using early pooling of amplicons or the Fluidigm Access Array™ is also described. Performance of the VHR assay was evaluated on 28 well characterized cell lines using Conexio Assign MPS software which uses genomic, rather than cDNA, reference sequence. Concordance was 98.4%; 1.6% had no genotype assignment. Of concordant calls, 53% were unambiguous. To further assess the assay, 59 clinical samples were genotyped and results compared to unambiguous allele assignments obtained by prior sequence-based typing supplemented with SSO and/or SSP. Concordance was 98.7% with 58.2% as unambiguous calls; 1.3% could not be assigned. Our results show that the amplicon-based VHR assay is robust and can replace current Sanger methodology. Together with software enhancements, it has the potential to provide even higher resolution HLA typing. Copyright © 2015. Published by Elsevier Inc.

Binning sequences using very sparse labels within a metagenome

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Halgamuge Saman K

2008-04-01

Full Text Available Abstract Background In metagenomic studies, a process called binning is necessary to assign contigs that belong to multiple species to their respective phylogenetic groups. Most of the current methods of binning, such as BLAST, k-mer and PhyloPythia, involve assigning sequence fragments by comparing sequence similarity or sequence composition with already-sequenced genomes that are still far from comprehensive. We propose a semi-supervised seeding method for binning that does not depend on knowledge of completed genomes. Instead, it extracts the flanking sequences of highly conserved 16S rRNA from the metagenome and uses them as seeds (labels to assign other reads based on their compositional similarity. Results The proposed seeding method is implemented on an unsupervised Growing Self-Organising Map (GSOM, and called Seeded GSOM (S-GSOM. We compared it with four well-known semi-supervised learning methods in a preliminary test, separating random-length prokaryotic sequence fragments sampled from the NCBI genome database. We identified the flanking sequences of the highly conserved 16S rRNA as suitable seeds that could be used to group the sequence fragments according to their species. S-GSOM showed superior performance compared to the semi-supervised methods tested. Additionally, S-GSOM may also be used to visually identify some species that do not have seeds. The proposed method was then applied to simulated metagenomic datasets using two different confidence threshold settings and compared with PhyloPythia, k-mer and BLAST. At the reference taxonomic level Order, S-GSOM outperformed all k-mer and BLAST results and showed comparable results with PhyloPythia for each of the corresponding confidence settings, where S-GSOM performed better than PhyloPythia in the ≥ 10 reads datasets and comparable in the ≥ 8 kb benchmark tests. Conclusion In the task of binning using semi-supervised learning methods, results indicate S-GSOM to be the best of

On the optimal trimming of high-throughput mRNA sequence data

Directory of Open Access Journals (Sweden)

Matthew D MacManes

2014-01-01

Full Text Available The widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in functional biology and adaptation have used these technologies to sequence mRNA transcriptomes of specific tissues, which in turn are often compared to other tissues, or other individuals with different phenotypes. While these techniques are extremely powerful, careful attention to data quality is required. In particular, because high-throughput sequencing is more error-prone than traditional Sanger sequencing, quality trimming of sequence reads should be an important step in all data processing pipelines. While several software packages for quality trimming exist, no general guidelines for the specifics of trimming have been developed. Here, using empirically derived sequence data, I provide general recommendations regarding the optimal strength of trimming, specifically in mRNA-Seq studies. Although very aggressive quality trimming is common, this study suggests that a more gentle trimming, specifically of those nucleotides whose Phred score < 2 or < 5, is optimal for most studies across a wide variety of metrics.

In-situ high resolution particle sampling by large time sequence inertial spectrometry

International Nuclear Information System (INIS)

Prodi, V.; Belosi, F.

1990-09-01

In situ sampling is always preferred, when possible, because of the artifacts that can arise when the aerosol has to flow through long sampling lines. On the other hand, the amount of possible losses can be calculated with some confidence only when the size distribution can be measured with a sufficient precision and the losses are not too large. This makes it desirable to sample directly in the vicinity of the aerosol source or containment. High temperature sampling devices with a detailed aerodynamic separation are extremely useful to this purpose. Several measurements are possible with the inertial spectrometer (INSPEC), but not with cascade impactors or cyclones. INSPEC - INertial SPECtrometer - has been conceived to measure the size distribution of aerosols by separating the particles while airborne according to their size and collecting them on a filter. It consists of a channel of rectangular cross-section with a 90 degree bend. Clean air is drawn through the channel, with a thin aerosol sheath injected close to the inner wall. Due to the bend, the particles are separated according to their size, leaving the original streamline by a distance which is a function of particle inertia and resistance, i.e. of aerodynamic diameter. The filter collects all the particles of the same aerodynamic size at the same distance from the inlet, in a continuous distribution. INSPEC particle separation at high temperature (up to 800 C) has been tested with Zirconia particles as calibration aerosols. The feasibility study has been concerned with resolution and time sequence sampling capabilities under high temperature (700 C)

Nurse leader certification preparation: how are confidence levels impacted?

Science.gov (United States)

Junger, Stacey; Trinkle, Nicole; Hall, Norma

2016-09-01

The aim was to examine the effect of a nurse leader certification preparation course on the confidence levels of the participants. Limited literature is available regarding nurse leader development and certifications. Barriers exist related to lack of confidence, high cost, time and lack of access to a preparation course. Nurse leaders (n = 51) completed a pre- and post-survey addressing confidence levels of participants related to the topics addressed in the nurse leader certification preparation course. There were statistically significant increases in confidence levels related to all course content for the participants. At the time of the study, there were 31.4% of participants intending to sit for the certification examination, and 5 of the 51 participants successfully sat for and passed the examination. A nurse leader certification preparation course increases confidence levels of the participants and removes barriers, thereby increasing the number of certifications obtained. The health-care climate is increasingly complex and nurse leaders need the expertise to navigate the ever-changing health-care environment. Certification in a specialty, such as leadership, serves as an indicator of a high level of competence in the field. © 2016 John Wiley & Sons Ltd.

Learning from the coffee shop: increasing junior high school students’ self-confidence through contextual learning based on local culture of Aceh

Science.gov (United States)

Sarmini; Supriono, A.; Ridwan

2018-01-01

Teachers should be able to provide meaningful learning, create a fun learning, and encourage the self-confidence of students. The reality is learning in Junior High School still teacher-centered learning that results the level of self-confidence of students is low. Pre-action showed 30% of students do not have self-confidence. The research aims to improve the self-confidence of students through contextual learning in the course from the social studies of Aceh based on the local culture. This type of research is classroom action research that conducted in two cycles. The research focus is the students’ responses. The coffee shop is a source of learning social studies. Students Involved in the coffee shop interact with villagers who have made the coffee shop as social media. Students participate meetings to address issues of rural villagers. The coffee shop as a public share with characteristics of particularly subject as a gathering place for many people regardless of social strata, convey information, chat, and informal atmosphere that stimulates self-confidence.

Using high-throughput barcode sequencing to efficiently map connectomes.

Science.gov (United States)

Peikon, Ian D; Kebschull, Justus M; Vagin, Vasily V; Ravens, Diana I; Sun, Yu-Chi; Brouzes, Eric; Corrêa, Ivan R; Bressan, Dario; Zador, Anthony M

2017-07-07

The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence-an RNA 'barcode'-which is targeted to the synapse using engineered proteins. Barcodes in pre- and postsynaptic neurons are then associated through protein-protein crosslinking across the synapse, extracted from the tissue, and joined into a form suitable for sequencing. Although our failure to develop an efficient barcode joining scheme precludes the widespread application of this approach, we expect that with further development SYNseq will enable tracing of complex circuits at high speed and low cost. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins

Energy Technology Data Exchange (ETDEWEB)

Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry (Poland); Sanderova, Hana; Krasny, Libor [Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria, Department of Bacteriology (Czech Republic)

2012-04-15

Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using {delta} subunit (20 kDa) of Bacillus subtilis RNA polymerase that has an 81-amino acid disordered part containing various repetitive sequences.

Diverse interpretations of confidence building

International Nuclear Information System (INIS)

Macintosh, J.

1998-01-01

This paper explores the variety of operational understandings associated with the term 'confidence building'. Collectively, these understandings constitute what should be thought of as a 'family' of confidence building approaches. This unacknowledged and generally unappreciated proliferation of operational understandings that function under the rubric of confidence building appears to be an impediment to effective policy. The paper's objective is to analyze these different understandings, stressing the important differences in their underlying assumptions. In the process, the paper underlines the need for the international community to clarify its collective thinking about what it means when it speaks of 'confidence building'. Without enhanced clarity, it will be unnecessarily difficult to employ the confidence building approach effectively due to the lack of consistent objectives and common operating assumptions. Although it is not the intention of this paper to promote a particular account of confidence building, dissecting existing operational understandings should help to identify whether there are fundamental elements that define what might be termed 'authentic' confidence building. Implicit here is the view that some operational understandings of confidence building may diverge too far from consensus models to count as meaningful members of the confidence building family. (author)

Chinese Management Research Needs Self-Confidence but not Over-confidence

DEFF Research Database (Denmark)

Li, Xin; Ma, Li

2018-01-01

Chinese management research aims to contribute to global management knowledge by offering rigorous and innovative theories and practical recommendations both for managing in China and outside. However, two seemingly opposite directions that researchers are taking could prove detrimental......-confidence, limiting theoretical innovation and practical relevance. Yet going in the other direction of overly indigenous research reflects over-confidence, often isolating the Chinese management research from the mainstream academia and at times, even becoming anti-science. A more integrated approach of conducting...... to the healthy development of Chinese management research. We argue that the two directions share a common ground that lies in the mindset regarding the confidence in the work on and from China. One direction of simply following the American mainstream on academic rigor demonstrates a lack of self...

Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples.

Science.gov (United States)

Yin, Yuxin; Lan, James H; Nguyen, David; Valenzuela, Nicole; Takemura, Ping; Bolon, Yung-Tsi; Springer, Brianna; Saito, Katsuyuki; Zheng, Ying; Hague, Tim; Pasztor, Agnes; Horvath, Gyorgy; Rigo, Krisztina; Reed, Elaine F; Zhang, Qiuheng

2016-01-01

Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA. Multiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C) from promotor to 3' UTR. Class II genes (DRB1, DQB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML) format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing. Using this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%), 92 rare alleles (0.091%) and 42 exon novelties (0.042%). Long

Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples.

Directory of Open Access Journals (Sweden)

Yuxin Yin

Full Text Available Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT, HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP registry donors using long-range PCR by next generation sequencing (NGS approach on buccal swab DNA.Multiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C from promotor to 3' UTR. Class II genes (DRB1, DQB1 were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing.Using this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%, 92 rare alleles (0.091% and 42 exon novelties (0.042%.Long

Diagnosing Anomalous Network Performance with Confidence

Energy Technology Data Exchange (ETDEWEB)

Settlemyer, Bradley W [ORNL; Hodson, Stephen W [ORNL; Kuehn, Jeffery A [ORNL; Poole, Stephen W [ORNL

2011-04-01

Variability in network performance is a major obstacle in effectively analyzing the throughput of modern high performance computer systems. High performance interconnec- tion networks offer excellent best-case network latencies; how- ever, highly parallel applications running on parallel machines typically require consistently high levels of performance to adequately leverage the massive amounts of available computing power. Performance analysts have usually quantified network performance using traditional summary statistics that assume the observational data is sampled from a normal distribution. In our examinations of network performance, we have found this method of analysis often provides too little data to under- stand anomalous network performance. Our tool, Confidence, instead uses an empirically derived probability distribution to characterize network performance. In this paper we describe several instances where the Confidence toolkit allowed us to understand and diagnose network performance anomalies that we could not adequately explore with the simple summary statis- tics provided by traditional measurement tools. In particular, we examine a multi-modal performance scenario encountered with an Infiniband interconnection network and we explore the performance repeatability on the custom Cray SeaStar2 interconnection network after a set of software and driver updates.

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

Science.gov (United States)

de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

2000-01-01

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

Directory of Open Access Journals (Sweden)

Sarah M Hykin

Full Text Available For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles, attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp. We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

Science.gov (United States)

Hykin, Sarah M; Bi, Ke; McGuire, Jimmy A

2015-01-01

For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for

The Effects of Game-Based Learning on Mathematical Confidence and Performance: High Ability vs. Low Ability

Science.gov (United States)

Ku, Oskar; Chen, Sherry Y.; Wu, Denise H.; Lao, Andrew C. C.; Chan, Tak-Wai

2014-01-01

Many students possess low confidence toward learning mathematics, which, in turn, may lead them to give up pursuing more mathematics knowledge. Recently, game-based learning (GBL) is regarded as a potential means in improving students' confidence. Thus, this study tried to promote students' confidence toward mathematics by using GBL. In addition,…

Confidence in Alternative Dispute Resolution: Experience from Switzerland

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Christof Schwenkel

2014-06-01

Full Text Available Alternative Dispute Resolution plays a crucial role in the justice system of Switzerland. With the unified Swiss Code of Civil Procedure, it is required that each litigation session shall be preceded by an attempt at conciliation before a conciliation authority. However, there has been little research on conciliation authorities and the public's perception of the authorities. This paper looks at public confidence in conciliation authorities and provides results of a survey conducted with more than 3,400 participants. This study found that public confidence in Swiss conciliation authorities is generally high, exceeds the ratings for confidence in cantonal governments and parliaments, but is lower than confidence in courts.Since the institutional models of the conciliation authorities (meaning the organization of the authorities and the selection of the conciliators differ widely between the 26 Swiss cantons, the influence of the institutional models on public confidence is analyzed. Contrary to assumptions based on New Institutional-ism approaches, this study reports that the institutional models do not impact public confidence. Also, the relationship between a participation in an election of justices of the peace or conciliators and public confidence in these authorities is found to be at most very limited (and negative. Similar to common findings on courts, the results show that general contacts with conciliation authorities decrease public confidence in these institutions whereas a positive experience with a conciliation authority leads to more confidence.The Study was completed as part of the research project 'Basic Research into Court Management in Switzerland', supported by the Swiss National Science Foundation (SNSF. Christof Schwenkel is a PhD student at the University of Lucerne and a research associate and project manager at Interface Policy Studies. A first version of this article was presented at the 2013 European Group for Public

Whole Genome Sequencing of Enterovirus species C Isolates by High-throughput Sequencing: Development of Generic Primers

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Maël Bessaud

2016-08-01

Full Text Available Enteroviruses are among the most common viruses infecting humans and can cause diverse clinical syndromes ranging from minor febrile illness to severe and potentially fatal diseases. Enterovirus species C (EV-C consists of more than 20 types, among which the 3 serotypes of polioviruses, the etiological agents of poliomyelitis, are included. Biodiversity and evolution of EV-C genomes are shaped by frequent recombination events. Therefore, identification and characterization of circulating EV-C strains require the sequencing of different genomic regions.A simple method was developed to sequence quickly the entire genome of EV-C isolates. Four overlapping fragments were produced separately by RT-PCR performed with generic primers. The four amplicons were then pooled and purified prior to be sequenced by high-throughput technique.The method was assessed on a panel of EV-Cs belonging to a wide-range of types. It can be used to determine full-length genome sequences through de novo assembly of thousands of reads. It was also able to discriminate reads from closely related viruses in mixtures.By decreasing the workload compared to classical Sanger-based techniques, this method will serve as a precious tool for sequencing large panels of EV-Cs isolated in cell cultures during environmental surveillance or from patients, including vaccine-derived polioviruses.

Fast high-resolution MR imaging using the snapshot-FLASH MR sequence

International Nuclear Information System (INIS)

Matthaei, D.; Haase, A.; Henrich, D.; Duhmke, E.

1990-01-01

Snapshot, fast low-angle short (FLASH) MR imaging using an accelerated FLASH-MR sequence provides MR images with measuring times far below 1 second. The short TE of this sequence prevents susceptibility artifacts in gradient-echo imaging. In this paper variations of the sequence are shown that provide high resolution images with T1-weighted IR, T2-weighted SE, and chemical shift (CHESS) contrast sequences. METHODS AND MATERIALS: A whole-body 2-T system (Bruker-Medizintechnik) were used in combination with a 60-cm gradient system (providing gradient strength of 5 mT/m) to study healthy volunteers. The measuring time for a 256 x 256 image matrix was 800 msec. This sequence has been used in combination with T1-weighted IR, T2-weighted SE, and CHESS variations

Sequencing of 50 human exomes reveals adaptation to high altitude

DEFF Research Database (Denmark)

Yi, Xin; Liang, Yu; Huerta-Sanchez, Emilia

2010-01-01

Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which repres...... in genetic adaptation to high altitude.......Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which...... represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency...

Protein-Level Integration Strategy of Multiengine MS Spectra Search Results for Higher Confidence and Sequence Coverage.

Science.gov (United States)

Zhao, Panpan; Zhong, Jiayong; Liu, Wanting; Zhao, Jing; Zhang, Gong

2017-12-01

Multiple search engines based on various models have been developed to search MS/MS spectra against a reference database, providing different results for the same data set. How to integrate these results efficiently with minimal compromise on false discoveries is an open question due to the lack of an independent, reliable, and highly sensitive standard. We took the advantage of the translating mRNA sequencing (RNC-seq) result as a standard to evaluate the integration strategies of the protein identifications from various search engines. We used seven mainstream search engines (Andromeda, Mascot, OMSSA, X!Tandem, pFind, InsPecT, and ProVerB) to search the same label-free MS data sets of human cell lines Hep3B, MHCCLM3, and MHCC97H from the Chinese C-HPP Consortium for Chromosomes 1, 8, and 20. As expected, the union of seven engines resulted in a boosted false identification, whereas the intersection of seven engines remarkably decreased the identification power. We found that identifications of at least two out of seven engines resulted in maximizing the protein identification power while minimizing the ratio of suspicious/translation-supported identifications (STR), as monitored by our STR index, based on RNC-Seq. Furthermore, this strategy also significantly improves the peptides coverage of the protein amino acid sequence. In summary, we demonstrated a simple strategy to significantly improve the performance for shotgun mass spectrometry by protein-level integrating multiple search engines, maximizing the utilization of the current MS spectra without additional experimental work.

Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries.

Science.gov (United States)

Lam, Kathy N; Hall, Michael W; Engel, Katja; Vey, Gregory; Cheng, Jiujun; Neufeld, Josh D; Charles, Trevor C

2014-01-01

High-throughput sequencing methods have been instrumental in the growing field of metagenomics, with technological improvements enabling greater throughput at decreased costs. Nonetheless, the economy of high-throughput sequencing cannot be fully leveraged in the subdiscipline of functional metagenomics. In this area of research, environmental DNA is typically cloned to generate large-insert libraries from which individual clones are isolated, based on specific activities of interest. Sequence data are required for complete characterization of such clones, but the sequencing of a large set of clones requires individual barcode-based sample preparation; this can become costly, as the cost of clone barcoding scales linearly with the number of clones processed, and thus sequencing a large number of metagenomic clones often remains cost-prohibitive. We investigated a hybrid Sanger/Illumina pooled sequencing strategy that omits barcoding altogether, and we evaluated this strategy by comparing the pooled sequencing results to reference sequence data obtained from traditional barcode-based sequencing of the same set of clones. Using identity and coverage metrics in our evaluation, we show that pooled sequencing can generate high-quality sequence data, without producing problematic chimeras. Though caveats of a pooled strategy exist and further optimization of the method is required to improve recovery of complete clone sequences and to avoid circumstances that generate unrecoverable clone sequences, our results demonstrate that pooled sequencing represents an effective and low-cost alternative for sequencing large sets of metagenomic clones.

A systematic review of maternal confidence for physiologic birth: characteristics of prenatal care and confidence measurement.

Science.gov (United States)

Avery, Melissa D; Saftner, Melissa A; Larson, Bridget; Weinfurter, Elizabeth V

2014-01-01

Because a focus on physiologic labor and birth has reemerged in recent years, care providers have the opportunity in the prenatal period to help women increase confidence in their ability to give birth without unnecessary interventions. However, most research has only examined support for women during labor. The purpose of this systematic review was to examine the research literature for information about prenatal care approaches that increase women's confidence for physiologic labor and birth and tools to measure that confidence. Studies were reviewed that explored any element of a pregnant woman's interaction with her prenatal care provider that helped build confidence in her ability to labor and give birth. Timing of interaction with pregnant women included during pregnancy, labor and birth, and the postpartum period. In addition, we looked for studies that developed a measure of women's confidence related to labor and birth. Outcome measures included confidence or similar concepts, descriptions of components of prenatal care contributing to maternal confidence for birth, and reliability and validity of tools measuring confidence. The search of MEDLINE, CINAHL, PsycINFO, and Scopus databases provided a total of 893 citations. After removing duplicates and articles that did not meet inclusion criteria, 6 articles were included in the review. Three relate to women's confidence for labor during the prenatal period, and 3 describe tools to measure women's confidence for birth. Research about enhancing women's confidence for labor and birth was limited to qualitative studies. Results suggest that women desire information during pregnancy and want to use that information to participate in care decisions in a relationship with a trusted provider. Further research is needed to develop interventions to help midwives and physicians enhance women's confidence in their ability to give birth and to develop a tool to measure confidence for use during prenatal care. © 2014 by

Growing confidence, building skills | IDRC - International ...

International Development Research Centre (IDRC) Digital Library (Canada)

In 2012 Rashid explored the influence of think tanks on policy in Bangladesh, as well as their relationships with international donors and media. In 2014, he explored two-way student exchanges between Canadian and ... his IDRC experience “gave me the confidence to conduct high quality research in social sciences.”.

A robust, simple genotyping-by-sequencing (GBS approach for high diversity species.

Directory of Open Access Journals (Sweden)

Robert J Elshire

Full Text Available Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs. This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM and barley (Oregon Wolfe Barley recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

Sources of sport confidence, imagery type and performance among competitive athletes: the mediating role of sports confidence.

Science.gov (United States)

Levy, A R; Perry, J; Nicholls, A R; Larkin, D; Davies, J

2015-01-01

This study explored the mediating role of sport confidence upon (1) sources of sport confidence-performance relationship and (2) imagery-performance relationship. Participants were 157 competitive athletes who completed state measures of confidence level/sources, imagery type and performance within one hour after competition. Among the current sample, confirmatory factor analysis revealed appropriate support for the nine-factor SSCQ and the five-factor SIQ. Mediational analysis revealed that sport confidence had a mediating influence upon the achievement source of confidence-performance relationship. In addition, both cognitive and motivational imagery types were found to be important sources of confidence, as sport confidence mediated imagery type- performance relationship. Findings indicated that athletes who construed confidence from their own achievements and report multiple images on a more frequent basis are likely to benefit from enhanced levels of state sport confidence and subsequent performance.

Teachers and Counselors: Building Math Confidence in Schools

Directory of Open Access Journals (Sweden)

Joseph M. Furner

2017-08-01

Full Text Available Mathematics teachers need to take on the role of counselors in addressing the math anxious in today's math classrooms. This paper looks at the impact math anxiety has on the future of young adults in our high-tech society. Teachers and professional school counselors are encouraged to work together to prevent and reduce math anxiety. It is important that all students feel confident in their ability to do mathematics in an age that relies so heavily on problem solving, technology, science, and mathematics. It really is a school's obligation to see that their students value and feel confident in their ability to do math, because ultimately a child's life: all decisions they will make and careers choices may be determined based on their disposition toward mathematics. This paper raises some interesting questions and provides some strategies (See Appendix A for teachers and counselors for addressing the issue of math anxiety while discussing the importance of developing mathematically confident young people for a high-tech world of STEM.

Alignment of high-throughput sequencing data inside in-memory databases.

Science.gov (United States)

Firnkorn, Daniel; Knaup-Gregori, Petra; Lorenzo Bermejo, Justo; Ganzinger, Matthias

2014-01-01

In times of high-throughput DNA sequencing techniques, performance-capable analysis of DNA sequences is of high importance. Computer supported DNA analysis is still an intensive time-consuming task. In this paper we explore the potential of a new In-Memory database technology by using SAP's High Performance Analytic Appliance (HANA). We focus on read alignment as one of the first steps in DNA sequence analysis. In particular, we examined the widely used Burrows-Wheeler Aligner (BWA) and implemented stored procedures in both, HANA and the free database system MySQL, to compare execution time and memory management. To ensure that the results are comparable, MySQL has been running in memory as well, utilizing its integrated memory engine for database table creation. We implemented stored procedures, containing exact and inexact searching of DNA reads within the reference genome GRCh37. Due to technical restrictions in SAP HANA concerning recursion, the inexact matching problem could not be implemented on this platform. Hence, performance analysis between HANA and MySQL was made by comparing the execution time of the exact search procedures. Here, HANA was approximately 27 times faster than MySQL which means, that there is a high potential within the new In-Memory concepts, leading to further developments of DNA analysis procedures in the future.

Analysis of high-throughput sequencing and annotation strategies for phage genomes.

Directory of Open Access Journals (Sweden)

Matthew R Henn

Full Text Available BACKGROUND: Bacterial viruses (phages play a critical role in shaping microbial populations as they influence both host mortality and horizontal gene transfer. As such, they have a significant impact on local and global ecosystem function and human health. Despite their importance, little is known about the genomic diversity harbored in phages, as methods to capture complete phage genomes have been hampered by the lack of knowledge about the target genomes, and difficulties in generating sufficient quantities of genomic DNA for sequencing. Of the approximately 550 phage genomes currently available in the public domain, fewer than 5% are marine phage. METHODOLOGY/PRINCIPAL FINDINGS: To advance the study of phage biology through comparative genomic approaches we used marine cyanophage as a model system. We compared DNA preparation methodologies (DNA extraction directly from either phage lysates or CsCl purified phage particles, and sequencing strategies that utilize either Sanger sequencing of a linker amplification shotgun library (LASL or of a whole genome shotgun library (WGSL, or 454 pyrosequencing methods. We demonstrate that genomic DNA sample preparation directly from a phage lysate, combined with 454 pyrosequencing, is best suited for phage genome sequencing at scale, as this method is capable of capturing complete continuous genomes with high accuracy. In addition, we describe an automated annotation informatics pipeline that delivers high-quality annotation and yields few false positives and negatives in ORF calling. CONCLUSIONS/SIGNIFICANCE: These DNA preparation, sequencing and annotation strategies enable a high-throughput approach to the burgeoning field of phage genomics.

Consumer’s and merchant’s confidence in internet payments

Directory of Open Access Journals (Sweden)

Franc Bračun

2003-01-01

Full Text Available Performing payment transactions over the Internet is becoming increasingly important. Whenever one interacts with others, he or she faces the problem of uncertainty because in interacting with others, one makes him or herself vulnerable, i.e. one can be betrayed. Thus, perceived risk and confidence are of fundamental importance in electronic payment transactions. A higher risk leads to greater hesitance about entering into a business relationship with a high degree of uncertainty; and therefore, to an increased need for confidence. This paper has two objectives. First, it aims to introduce and test a theoretical model that predicts consumer and merchant acceptance of the Internet payment solution by explaining the complex set of relationships among the key factors influencing confidence in electronic payment transactions. Second, the paper attempts to shed light on the complex interrelationship among confidence, control and perceived risk. An empirical study was conducted to test the proposed model using data from consumers and merchants in Slovenia. The results show how perceived risk dimensions and post-transaction control influence consumer’s and merchant’s confidence in electronic payment transactions, and the impact of confidence on the adoption of mass-market on-line payment solutions.

Building Public Confidence in Nuclear Activities

International Nuclear Information System (INIS)

Isaacs, T

2002-01-01

Achieving public acceptance has become a central issue in discussions regarding the future of nuclear power and associated nuclear activities. Effective public communication and public participation are often put forward as the key building blocks in garnering public acceptance. A recent international workshop in Finland provided insights into other features that might also be important to building and sustaining public confidence in nuclear activities. The workshop was held in Finland in close cooperation with Finnish stakeholders. This was most appropriate because of the recent successes in achieving positive decisions at the municipal, governmental, and Parliamentary levels, allowing the Finnish high-level radioactive waste repository program to proceed, including the identification and approval of a proposed candidate repository site. Much of the workshop discussion appropriately focused on the roles of public participation and public communications in building public confidence. It was clear that well constructed and implemented programs of public involvement and communication and a sense of fairness were essential in building the extent of public confidence needed to allow the repository program in Finland to proceed. It was also clear that there were a number of other elements beyond public involvement that contributed substantially to the success in Finland to date. And, in fact, it appeared that these other factors were also necessary to achieving the Finnish public acceptance. In other words, successful public participation and communication were necessary but not sufficient. What else was important? Culture, politics, and history vary from country to country, providing differing contexts for establishing and maintaining public confidence. What works in one country will not necessarily be effective in another. Nonetheless, there appear to be certain elements that might be common to programs that are successful in sustaining public confidence and some of

Building Public Confidence in Nuclear Activities

International Nuclear Information System (INIS)

Isaacs, T

2002-01-01

Achieving public acceptance has become a central issue in discussions regarding the future of nuclear power and associated nuclear activities. Effective public communication and public participation are often put forward as the key building blocks in garnering public acceptance. A recent international workshop in Finland provided insights into other features that might also be important to building and sustaining public confidence in nuclear activities. The workshop was held in Finland in close cooperation with Finnish stakeholders. This was most appropriate because of the recent successes in achieving positive decisions at the municipal, governmental, and Parliamentary levels, allowing the Finnish high-level radioactive waste repository program to proceed, including the identification and approval of a proposed candidate repository site Much of the workshop discussion appropriately focused on the roles of public participation and public communications in building public confidence. It was clear that well constructed and implemented programs of public involvement and communication and a sense of fairness were essential in building the extent of public confidence needed to allow the repository program in Finland to proceed. It was also clear that there were a number of other elements beyond public involvement that contributed substantially to the success in Finland to date. And, in fact, it appeared that these other factors were also necessary to achieving the Finnish public acceptance. In other words, successful public participation and communication were necessary but not sufficient. What else was important? Culture, politics, and history vary from country to country, providing differing contexts for establishing and maintaining public confidence. What works in one country will not necessarily be effective in another. Nonetheless, there appear to be certain elements that might be common to programs that are successful in sustaining public confidence, and some of

Alan Greenspan, the confidence strategy

Directory of Open Access Journals (Sweden)

Edwin Le Heron

2006-12-01

Full Text Available To evaluate the Greenspan era, we nevertheless need to address three questions: Is his success due to talent or just luck? Does he have a system of monetary policy or is he himself the system? What will be his legacy? Greenspan was certainly lucky, but he was also clairvoyant. Above all, he has developed a profoundly original monetary policy. His confidence strategy is clearly opposed to the credibility strategy developed in central banks and the academic milieu after 1980, but also inflation targeting, which today constitutes the mainstream monetary policy regime. The question of his legacy seems more nuanced. However, Greenspan will remain 'for a considerable period of time' a highly heterodox and original central banker. His political vision, his perception of an uncertain world, his pragmatism and his openness form the structure of a powerful alternative system, the confidence strategy, which will leave its mark on the history of monetary policy.

ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.

Science.gov (United States)

Luo, Guan-Zheng; Yang, Wei; Ma, Ying-Ke; Wang, Xiu-Jie

2014-02-01

Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets. ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.

Communicating the Benefits of a Full Sequence of High School Science Courses

Science.gov (United States)

Nicholas, Catherine Marie

High school students are generally uninformed about the benefits of enrolling in a full sequence of science courses, therefore only about a third of our nation's high school graduates have completed the science sequence of Biology, Chemistry and Physics. The lack of students completing a full sequence of science courses contributes to the deficit in the STEM degree production rate needed to fill the demand of the current job market and remain competitive as a nation. The purpose of the study was to make a difference in the number of students who have access to information about the benefits of completing a full sequence of science courses. This dissertation study employed qualitative research methodology to gain a broad perspective of staff through a questionnaire and document review and then a deeper understanding through semi-structured interview protocol. The data revealed that a universal sequence of science courses in the high school district did not exist. It also showed that not all students had access to all science courses; students were sorted and tracked according to prerequisites that did not necessarily match the skill set needed for the courses. In addition, the study showed a desire for more support and direction from the district office. It was also apparent that there was a disconnect that existed between who staff members believed should enroll in a full sequence of science courses and who actually enrolled. Finally, communication about science was shown to occur mainly through counseling and peers. A common science sequence, detracking of science courses, increased communication about the postsecondary and academic benefits of a science education, increased district direction and realistic mathematics alignment were all discussed as solutions to the problem.

Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

Energy Technology Data Exchange (ETDEWEB)

Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Department of Radiology, Zurich (Switzerland); Espinosa, Norman [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Orthopedic Surgery, Zurich (Switzerland)

2017-08-15

To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

International Nuclear Information System (INIS)

Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja; Espinosa, Norman

2017-01-01

To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

Droplet Digital™ PCR Next-Generation Sequencing Library QC Assay.

Science.gov (United States)

Heredia, Nicholas J

2018-01-01

Digital PCR is a valuable tool to quantify next-generation sequencing (NGS) libraries precisely and accurately. Accurately quantifying NGS libraries enable accurate loading of the libraries on to the sequencer and thus improve sequencing performance by reducing under and overloading error. Accurate quantification also benefits users by enabling uniform loading of indexed/barcoded libraries which in turn greatly improves sequencing uniformity of the indexed/barcoded samples. The advantages gained by employing the Droplet Digital PCR (ddPCR™) library QC assay includes the precise and accurate quantification in addition to size quality assessment, enabling users to QC their sequencing libraries with confidence.

Self-confidence and metacognitive processes

Directory of Open Access Journals (Sweden)

Kleitman Sabina

2005-01-01

Full Text Available This paper examines the status of Self-confidence trait. Two studies strongly suggest that Self-confidence is a component of metacognition. In the first study, participants (N=132 were administered measures of Self-concept, a newly devised Memory and Reasoning Competence Inventory (MARCI, and a Verbal Reasoning Test (VRT. The results indicate a significant relationship between confidence ratings on the VRT and the Reasoning component of MARCI. The second study (N=296 employed an extensive battery of cognitive tests and several metacognitive measures. Results indicate the presence of robust Self-confidence and Metacognitive Awareness factors, and a significant correlation between them. Self-confidence taps not only processes linked to performance on items that have correct answers, but also beliefs about events that may never occur.

Increasing Product Confidence-Shifting Paradigms.

Science.gov (United States)

Phillips, Marla; Kashyap, Vishal; Cheung, Mee-Shew

2015-01-01

Leaders in the pharmaceutical, medical device, and food industries expressed a unilateral concern over product confidence throughout the total product lifecycle, an unsettling fact for these leaders to manage given that their products affect the lives of millions of people each year. Fueled by the heparin incident of intentional adulteration in 2008, initial efforts for increasing product confidence were focused on improving the confidence of incoming materials, with a belief that supplier performance must be the root cause. As in the heparin case, concern over supplier performance extended deep into the supply chain to include suppliers of the suppliers-which is often a blind spot for pharmaceutical, device, and food manufacturers. Resolved to address the perceived lack of supplier performance, these U.S. Food and Drug Administration (FDA)-regulated industries began to adopt the supplier relationship management strategy, developed by the automotive industry, that emphasizes "management" of suppliers for the betterment of the manufacturers. Current product and supplier management strategies, however, have not led to a significant improvement in product confidence. As a result of the enduring concern by industry leaders over the lack of product confidence, Xavier University launched the Integrity of Supply Initiative in 2012 with a team of industry leaders and FDA officials. Through a methodical research approach, data generated by the pharmaceutical, medical device, and food manufacturers surprisingly pointed to themselves as a source of the lack of product confidence, and revealed that manufacturers either unknowingly increase the potential for error or can control/prevent many aspects of product confidence failure. It is only through this paradigm shift that manufacturers can work collaboratively with their suppliers as equal partners, instead of viewing their suppliers as "lesser" entities needing to be controlled. The basis of this shift provides manufacturers

"Joint Workshop on High Confidence Medical Devices, Software, and Systems (HCMDSS) and Medical Device Plug-and-Play (MD PnP) Interoperability"

National Research Council Canada - National Science Library

Goldman, Julian M

2008-01-01

Partial support was requested from TATRC, with joint funding from NSF, for a joint workshop to bring together the synergistic efforts and communities of the High Confidence Medical Devices, Software, and Systems (HCMDSS...

Confidence in Assessment of Lumbar Spondylolysis Using Three-Dimensional Volumetric T2-Weighted MRI Compared With Limited Field of View, Decreased-Dose CT.

Science.gov (United States)

Delavan, Joshua Adam; Stence, Nicholas V; Mirsky, David M; Gralla, Jane; Fadell, Michael F

2016-07-01

Limited z-axis-coverage computed tomography (CT) to evaluate for pediatric lumbar spondylolysis, altering the technique such that the dose to the patient is comparable or lower than radiographs, is currently used at our institution. The objective of the study was to determine whether volumetric 3-dimensional fast spin echo magnetic resonance imaging (3D MRI) can provide equal or greater diagnostic accuracy compared with limited CT in the diagnosis of pediatric lumbar spondylolysis without ionizing radiation. Volumetric 3D MRI can provide equal or greater diagnostic accuracy compared with low-dose CT for pediatric lumbar spondylolysis without ionizing radiation. Clinical review. Level 2. Three pediatric neuroradiologists evaluated 2-dimensional (2D) MRI, 2D + 3D MRI, and limited CT examinations in 42 pediatric patients who obtained imaging for low back pain and suspected spondylolysis. As there is no gold standard for the diagnosis of spondylolysis besides surgery, interobserver agreement and degree of confidence were compared to determine which modality is preferable. Decreased-dose CT provided a greater level of agreement than 2D MRI and 2D + 3D MRI. The kappa for rater agreement with 2D MRI, 2D + 3D MRI, and CT was 0.19, 0.32, and 1.0, respectively. All raters agreed in 31%, 40%, and 100% of cases with 2D MRI, 2D + 3D MRI, and CT. Lack of confidence was significantly lower with CT (0%) than with 2D MRI (30%) and 2D + 3D MRI (25%). For diagnosing spondylolysis, radiologist agreement and confidence trended toward improvement with the addition of a volumetric 3D MRI sequence to standard 2D MRI sequences compared with 2D MRI alone; however, agreement and confidence remain significantly greater using decreased-dose CT when compared with either MRI acquisition. Decreased-dose CT of the lumbar spine remains the optimal examination to confirm a high suspicion of spondylolysis, with dose essentially equivalent to radiographs. If clinical symptoms are not classic for

High-throughput Sequencing Based Immune Repertoire Study during Infectious Disease

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Dongni Hou

2016-08-01

Full Text Available The selectivity of the adaptive immune response is based on the enormous diversity of T and B cell antigen-specific receptors. The immune repertoire, the collection of T and B cells with functional diversity in the circulatory system at any given time, is dynamic and reflects the essence of immune selectivity. In this article, we review the recent advances in immune repertoire study of infectious diseases that achieved by traditional techniques and high-throughput sequencing techniques. High-throughput sequencing techniques enable the determination of complementary regions of lymphocyte receptors with unprecedented efficiency and scale. This progress in methodology enhances the understanding of immunologic changes during pathogen challenge, and also provides a basis for further development of novel diagnostic markers, immunotherapies and vaccines.

The determination of high-resolution spatio-temporal glacier motion fields from time-lapse sequences

Science.gov (United States)

Schwalbe, Ellen; Maas, Hans-Gerd

2017-12-01

This paper presents a comprehensive method for the determination of glacier surface motion vector fields at high spatial and temporal resolution. These vector fields can be derived from monocular terrestrial camera image sequences and are a valuable data source for glaciological analysis of the motion behaviour of glaciers. The measurement concepts for the acquisition of image sequences are presented, and an automated monoscopic image sequence processing chain is developed. Motion vector fields can be derived with high precision by applying automatic subpixel-accuracy image matching techniques on grey value patterns in the image sequences. Well-established matching techniques have been adapted to the special characteristics of the glacier data in order to achieve high reliability in automatic image sequence processing, including the handling of moving shadows as well as motion effects induced by small instabilities in the camera set-up. Suitable geo-referencing techniques were developed to transform image measurements into a reference coordinate system.The result of monoscopic image sequence analysis is a dense raster of glacier surface point trajectories for each image sequence. Each translation vector component in these trajectories can be determined with an accuracy of a few centimetres for points at a distance of several kilometres from the camera. Extensive practical validation experiments have shown that motion vector and trajectory fields derived from monocular image sequences can be used for the determination of high-resolution velocity fields of glaciers, including the analysis of tidal effects on glacier movement, the investigation of a glacier's motion behaviour during calving events, the determination of the position and migration of the grounding line and the detection of subglacial channels during glacier lake outburst floods.

Effects of informed consent for individual genome sequencing on relevant knowledge.

Science.gov (United States)

Kaphingst, K A; Facio, F M; Cheng, M-R; Brooks, S; Eidem, H; Linn, A; Biesecker, B B; Biesecker, L G

2012-11-01

Increasing availability of individual genomic information suggests that patients will need knowledge about genome sequencing to make informed decisions, but prior research is limited. In this study, we examined genome sequencing knowledge before and after informed consent among 311 participants enrolled in the ClinSeq™ sequencing study. An exploratory factor analysis of knowledge items yielded two factors (sequencing limitations knowledge; sequencing benefits knowledge). In multivariable analysis, high pre-consent sequencing limitations knowledge scores were significantly related to education [odds ratio (OR): 8.7, 95% confidence interval (CI): 2.45-31.10 for post-graduate education, and OR: 3.9; 95% CI: 1.05, 14.61 for college degree compared with less than college degree] and race/ethnicity (OR: 2.4, 95% CI: 1.09, 5.38 for non-Hispanic Whites compared with other racial/ethnic groups). Mean values increased significantly between pre- and post-consent for the sequencing limitations knowledge subscale (6.9-7.7, p benefits knowledge subscale (7.0-7.5, p < 0.0001); increase in knowledge did not differ by sociodemographic characteristics. This study highlights gaps in genome sequencing knowledge and underscores the need to target educational efforts toward participants with less education or from minority racial/ethnic groups. The informed consent process improved genome sequencing knowledge. Future studies could examine how genome sequencing knowledge influences informed decision making. © 2012 John Wiley & Sons A/S.

The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences.

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Fabian König

Full Text Available The monoclonal antibody S9.6 is a widely-used tool to purify, analyse and quantify R-loop structures in cells. A previous study using the surface plasmon resonance technology and a single-chain variable fragment (scFv of S9.6 showed high affinity (0.6 nM for DNA-RNA and also a high affinity (2.7 nM for RNA-RNA hybrids. We used the microscale thermophoresis method allowing surface independent interaction studies and electromobility shift assays to evaluate additional RNA-DNA hybrid sequences and to quantify the binding affinities of the S9.6 antibody with respect to distinct sequences and their GC-content. Our results confirm high affinity binding to previously analysed sequences, but reveals that binding affinities are highly sequence specific. Our study presents R-loop sequences that independent of GC-content and in different sequence variations exhibit either no binding, binding affinities in the micromolar range and as well high affinity binding in the nanomolar range. Our study questions the usefulness of the S9.6 antibody in the quantitative analysis of R-loop sequences in vivo.

Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

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Christian M. Tobias

2008-11-01

Full Text Available The development of genomic resources for switchgrass ( L., a perennial NAD-malic enzyme type C grass, is required to enable molecular breeding and biotechnological approaches for improving its value as a forage and bioenergy crop. Expressed sequence tag (EST sequencing is one method that can quickly sample gene inventories and produce data suitable for marker development or analysis of tissue-specific patterns of expression. Toward this goal, three cDNA libraries from callus, crown, and seedling tissues of ‘Kanlow’ switchgrass were end-sequenced to generate a total of 61,585 high-quality ESTs from 36,565 separate clones. Seventy-three percent of the assembled consensus sequences could be aligned with the sorghum [ (L. Moench] genome at a -value of <1 × 10, indicating a high degree of similarity. Sixty-five percent of the ESTs matched with gene ontology molecular terms, and 3.3% of the sequences were matched with genes that play potential roles in cell-wall biogenesis. The representation in the three libraries of gene families known to be associated with C photosynthesis, cellulose and β-glucan synthesis, phenylpropanoid biosynthesis, and peroxidase activity indicated likely roles for individual family members. Pairwise comparisons of synonymous codon substitutions were used to assess genome sequence diversity and indicated an overall similarity between the two genome copies present in the tetraploid. Identification of EST–simple sequence repeat markers and amplification on two individual parents of a mapping population yielded an average of 2.18 amplicons per individual, and 35% of the markers produced fragment length polymorphisms.

The Model Confidence Set

DEFF Research Database (Denmark)

Hansen, Peter Reinhard; Lunde, Asger; Nason, James M.

The paper introduces the model confidence set (MCS) and applies it to the selection of models. A MCS is a set of models that is constructed such that it will contain the best model with a given level of confidence. The MCS is in this sense analogous to a confidence interval for a parameter. The MCS......, beyond the comparison of models. We apply the MCS procedure to two empirical problems. First, we revisit the inflation forecasting problem posed by Stock and Watson (1999), and compute the MCS for their set of inflation forecasts. Second, we compare a number of Taylor rule regressions and determine...... the MCS of the best in terms of in-sample likelihood criteria....

Integration testing through reusing representative unit test cases for high-confidence medical software.

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Shin, Youngsul; Choi, Yunja; Lee, Woo Jin

2013-06-01

As medical software is getting larger-sized, complex, and connected with other devices, finding faults in integrated software modules gets more difficult and time consuming. Existing integration testing typically takes a black-box approach, which treats the target software as a black box and selects test cases without considering internal behavior of each software module. Though it could be cost-effective, this black-box approach cannot thoroughly test interaction behavior among integrated modules and might leave critical faults undetected, which should not happen in safety-critical systems such as medical software. This work anticipates that information on internal behavior is necessary even for integration testing to define thorough test cases for critical software and proposes a new integration testing method by reusing test cases used for unit testing. The goal is to provide a cost-effective method to detect subtle interaction faults at the integration testing phase by reusing the knowledge obtained from unit testing phase. The suggested approach notes that the test cases for the unit testing include knowledge on internal behavior of each unit and extracts test cases for the integration testing from the test cases for the unit testing for a given test criteria. The extracted representative test cases are connected with functions under test using the state domain and a single test sequence to cover the test cases is produced. By means of reusing unit test cases, the tester has effective test cases to examine diverse execution paths and find interaction faults without analyzing complex modules. The produced test sequence can have test coverage as high as the unit testing coverage and its length is close to the length of optimal test sequences. Copyright © 2013 Elsevier Ltd. All rights reserved.

Confidence in Numerical Simulations

International Nuclear Information System (INIS)

Hemez, Francois M.

2015-01-01

This PowerPoint presentation offers a high-level discussion of uncertainty, confidence and credibility in scientific Modeling and Simulation (M&S). It begins by briefly evoking M&S trends in computational physics and engineering. The first thrust of the discussion is to emphasize that the role of M&S in decision-making is either to support reasoning by similarity or to ''forecast,'' that is, make predictions about the future or extrapolate to settings or environments that cannot be tested experimentally. The second thrust is to explain that M&S-aided decision-making is an exercise in uncertainty management. The three broad classes of uncertainty in computational physics and engineering are variability and randomness, numerical uncertainty and model-form uncertainty. The last part of the discussion addresses how scientists ''think.'' This thought process parallels the scientific method where by a hypothesis is formulated, often accompanied by simplifying assumptions, then, physical experiments and numerical simulations are performed to confirm or reject the hypothesis. ''Confidence'' derives, not just from the levels of training and experience of analysts, but also from the rigor with which these assessments are performed, documented and peer-reviewed.

Investigating the psychological resilience, self-confidence and problem-solving skills of midwife candidates.

Science.gov (United States)

Ertekin Pinar, Sukran; Yildirim, Gulay; Sayin, Neslihan

2018-05-01

The high level of psychological resilience, self-confidence and problem solving skills of midwife candidates play an important role in increasing the quality of health care and in fulfilling their responsibilities towards patients. This study was conducted to investigate the psychological resilience, self-confidence and problem-solving skills of midwife candidates. It is a convenience descriptive quantitative study. Students who study at Health Sciences Faculty in Turkey's Central Anatolia Region. Midwife candidates (N = 270). In collection of data, the Personal Information Form, Psychological Resilience Scale for Adults (PRSA), Self-Confidence Scale (SCS), and Problem Solving Inventory (PSI) were used. There was a negatively moderate-level significant relationship between the Problem Solving Inventory scores and the Psychological Resilience Scale for Adults scores (r = -0.619; p = 0.000), and between Self-Confidence Scale scores (r = -0.524; p = 0.000). There was a positively moderate-level significant relationship between the Psychological Resilience Scale for Adults scores and the Self-Confidence Scale scores (r = 0.583; p = 0.000). There was a statistically significant difference (p Problem Solving Inventory and the Psychological Resilience Scale for Adults scores according to getting support in a difficult situation. As psychological resilience and self-confidence levels increase, problem-solving skills increase; additionally, as self-confidence increases, psychological resilience increases too. Psychological resilience, self-confidence, and problem-solving skills of midwife candidates in their first-year of studies are higher than those who are in their fourth year. Self-confidence and psychological resilience of midwife candidates aged between 17 and 21, self-confidence and problem solving skills of residents of city centers, psychological resilience of those who perceive their monthly income as sufficient are high

Frequency-locked pulse sequencer for high-frame-rate monochromatic tissue motion imaging.

Science.gov (United States)

Azar, Reza Zahiri; Baghani, Ali; Salcudean, Septimiu E; Rohling, Robert

2011-04-01

To overcome the inherent low frame rate of conventional ultrasound, we have previously presented a system that can be implemented on conventional ultrasound scanners for high-frame-rate imaging of monochromatic tissue motion. The system employs a sector subdivision technique in the sequencer to increase the acquisition rate. To eliminate the delays introduced during data acquisition, a motion phase correction algorithm has also been introduced to create in-phase displacement images. Previous experimental results from tissue- mimicking phantoms showed that the system can achieve effective frame rates of up to a few kilohertz on conventional ultrasound systems. In this short communication, we present a new pulse sequencing strategy that facilitates high-frame-rate imaging of monochromatic motion such that the acquired echo signals are inherently in-phase. The sequencer uses the knowledge of the excitation frequency to synchronize the acquisition of the entire imaging plane to that of an external exciter. This sequencing approach eliminates any need for synchronization or phase correction and has applications in tissue elastography, which we demonstrate with tissue-mimicking phantoms. © 2011 IEEE

Thought confidence as a determinant of persuasion: the self-validation hypothesis.

Science.gov (United States)

Petty, Richard E; Briñol, Pablo; Tormala, Zakary L

2002-05-01

Previous research in the domain of attitude change has described 2 primary dimensions of thinking that impact persuasion processes and outcomes: the extent (amount) of thinking and the direction (valence) of issue-relevant thought. The authors examined the possibility that another, more meta-cognitive aspect of thinking is also important-the degree of confidence people have in their own thoughts. Four studies test the notion that thought confidence affects the extent of persuasion. When positive thoughts dominate in response to a message, increasing confidence in those thoughts increases persuasion, but when negative thoughts dominate, increasing confidence decreases persuasion. In addition, using self-reported and manipulated thought confidence in separate studies, the authors provide evidence that the magnitude of the attitude-thought relationship depends on the confidence people have in their thoughts. Finally, the authors also show that these self-validation effects are most likely in situations that foster high amounts of information processing activity.

Centroid based clustering of high throughput sequencing reads based on n-mer counts.

Science.gov (United States)

Solovyov, Alexander; Lipkin, W Ian

2013-09-08

Many problems in computational biology require alignment-free sequence comparisons. One of the common tasks involving sequence comparison is sequence clustering. Here we apply methods of alignment-free comparison (in particular, comparison using sequence composition) to the challenge of sequence clustering. We study several centroid based algorithms for clustering sequences based on word counts. Study of their performance shows that using k-means algorithm with or without the data whitening is efficient from the computational point of view. A higher clustering accuracy can be achieved using the soft expectation maximization method, whereby each sequence is attributed to each cluster with a specific probability. We implement an open source tool for alignment-free clustering. It is publicly available from github: https://github.com/luscinius/afcluster. We show the utility of alignment-free sequence clustering for high throughput sequencing analysis despite its limitations. In particular, it allows one to perform assembly with reduced resources and a minimal loss of quality. The major factor affecting performance of alignment-free read clustering is the length of the read.

Confidence in critical care nursing.

Science.gov (United States)

Evans, Jeanne; Bell, Jennifer L; Sweeney, Annemarie E; Morgan, Jennifer I; Kelly, Helen M

2010-10-01

The purpose of the study was to gain an understanding of the nursing phenomenon, confidence, from the experience of nurses in the nursing subculture of critical care. Leininger's theory of cultural care diversity and universality guided this qualitative descriptive study. Questions derived from the sunrise model were used to elicit nurses' perspectives about cultural and social structures that exist within the critical care nursing subculture and the influence that these factors have on confidence. Twenty-eight critical care nurses from a large Canadian healthcare organization participated in semistructured interviews about confidence. Five themes arose from the descriptions provided by the participants. The three themes, tenuously navigating initiation rituals, deliberately developing holistic supportive relationships, and assimilating clinical decision-making rules were identified as social and cultural factors related to confidence. The remaining two themes, preserving a sense of security despite barriers and accommodating to diverse challenges, were identified as environmental factors related to confidence. Practice and research implications within the culture of critical care nursing are discussed in relation to each of the themes.

Professional confidence: a concept analysis.

Science.gov (United States)

Holland, Kathlyn; Middleton, Lyn; Uys, Leana

2012-03-01

Professional confidence is a concept that is frequently used and or implied in occupational therapy literature, but often without specifying its meaning. Rodgers's Model of Concept Analysis was used to analyse the term "professional confidence". Published research obtained from a federated search in four health sciences databases was used to inform the concept analysis. The definitions, attributes, antecedents, and consequences of professional confidence as evidenced in the literature are discussed. Surrogate terms and related concepts are identified, and a model case of the concept provided. Based on the analysis, professional confidence can be described as a dynamic, maturing personal belief held by a professional or student. This includes an understanding of and a belief in the role, scope of practice, and significance of the profession, and is based on their capacity to competently fulfil these expectations, fostered through a process of affirming experiences. Developing and fostering professional confidence should be nurtured and valued to the same extent as professional competence, as the former underpins the latter, and both are linked to professional identity.

Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria.

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Jeffrey R Johansen

Full Text Available A highly divergent 16S rRNA gene was found in one of the five ribosomal operons present in a species complex currently circumscribed as Scytonema hyalinum (Nostocales, Cyanobacteria using clone libraries. If 16S rRNA sequence macroheterogeneity among ribosomal operons due to insertions, deletions or truncation is excluded, the sequence heterogeneity observed in S. hyalinum was the highest observed in any prokaryotic species thus far (7.3-9.0%. The secondary structure of the 16S rRNA molecules encoded by the two divergent operons was nearly identical, indicating possible functionality. The 23S rRNA gene was examined for a few strains in this complex, and it was also found to be highly divergent from the gene in Type 2 operons (8.7%, and likewise had nearly identical secondary structure between the Type 1 and Type 2 operons. Furthermore, the 16S-23S ITS showed marked differences consistent between operons among numerous strains. Both operons have promoter sequences that satisfy consensus requirements for functional prokaryotic transcription initiation. Horizontal gene transfer from another unknown heterocytous cyanobacterium is considered the most likely explanation for the origin of this molecule, but does not explain the ultimate origin of this sequence, which is very divergent from all 16S rRNA sequences found thus far in cyanobacteria. The divergent sequence is highly conserved among numerous strains of S. hyalinum, suggesting adaptive advantage and selective constraint of the divergent sequence.

Two sides of the same coin : Monetary incentives concurrently improve and bias confidence judgments

NARCIS (Netherlands)

Lebreton, Maël; Langdon, Shari; Slieker, Matthijs J; Nooitgedacht, Jip S; Goudriaan, Anna E; Denys, D.; van Holst, Ruth J; Luigjes, Judy

2018-01-01

Decisions are accompanied by a feeling of confidence, that is, a belief about the decision being correct. Confidence accuracy is critical, notably in high-stakes situations such as medical or financial decision-making. We investigated how incentive motivation influences confidence accuracy by

Categorizing Biases in High-Confidence High-Throughput Protein-Protein Interaction Data Sets*

Science.gov (United States)

Yu, Xueping; Ivanic, Joseph; Memišević, Vesna; Wallqvist, Anders; Reifman, Jaques

2011-01-01

We characterized and evaluated the functional attributes of three yeast high-confidence protein-protein interaction data sets derived from affinity purification/mass spectrometry, protein-fragment complementation assay, and yeast two-hybrid experiments. The interacting proteins retrieved from these data sets formed distinct, partially overlapping sets with different protein-protein interaction characteristics. These differences were primarily a function of the deployed experimental technologies used to recover these interactions. This affected the total coverage of interactions and was especially evident in the recovery of interactions among different functional classes of proteins. We found that the interaction data obtained by the yeast two-hybrid method was the least biased toward any particular functional characterization. In contrast, interacting proteins in the affinity purification/mass spectrometry and protein-fragment complementation assay data sets were over- and under-represented among distinct and different functional categories. We delineated how these differences affected protein complex organization in the network of interactions, in particular for strongly interacting complexes (e.g. RNA and protein synthesis) versus weak and transient interacting complexes (e.g. protein transport). We quantified methodological differences in detecting protein interactions from larger protein complexes, in the correlation of protein abundance among interacting proteins, and in their connectivity of essential proteins. In the latter case, we showed that minimizing inherent methodology biases removed many of the ambiguous conclusions about protein essentiality and protein connectivity. We used these findings to rationalize how biological insights obtained by analyzing data sets originating from different sources sometimes do not agree or may even contradict each other. An important corollary of this work was that discrepancies in biological insights did not

Multiple Teaching Approaches, Teaching Sequence and Concept Retention in High School Physics Education

Science.gov (United States)

Fogarty, Ian; Geelan, David

2013-01-01

Students in 4 Canadian high school physics classes completed instructional sequences in two key physics topics related to motion--Straight Line Motion and Newton's First Law. Different sequences of laboratory investigation, teacher explanation (lecture) and the use of computer-based scientific visualizations (animations and simulations) were…

Sequence of a cDNA encoding turtle high mobility group 1 protein.

Science.gov (United States)

Zheng, Jifang; Hu, Bi; Wu, Duansheng

2005-07-01

In order to understand sequence information about turtle HMG1 gene, a cDNA encoding HMG1 protein of the Chinese soft-shell turtle (Pelodiscus sinensis) was amplified by RT-PCR from kidney total RNA, and was cloned, sequenced and analyzed. The results revealed that the open reading frame (ORF) of turtle HMG1 cDNA is 606 bp long. The ORF codifies 202 amino acid residues, from which two DNA-binding domains and one polyacidic region are derived. The DNA-binding domains share higher amino acid identity with homologues sequences of chicken (96.5%) and mammalian (74%) than homologues sequence of rainbow trout (67%). The polyacidic region shows 84.6% amino acid homology with the equivalent region of chicken HMG1 cDNA. Turtle HMG1 protein contains 3 Cys residues located at completely conserved positions. Conservation in sequence and structure suggests that the functions of turtle HMG1 cDNA may be highly conserved during evolution. To our knowledge, this is the first report of HMG1 cDNA sequence in any reptilian.

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis

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Thiele Bernhard

2011-05-01

Full Text Available Abstract Background Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4 variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Methods Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Results Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%, and defining a minority cutoff of 5%, the results were concordant in all but one isolate. Conclusions The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

Science.gov (United States)

Däumer, Martin; Kaiser, Rolf; Klein, Rolf; Lengauer, Thomas; Thiele, Bernhard; Thielen, Alexander

2011-05-13

Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4) variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS) detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%), and defining a minority cutoff of 5%, the results were concordant in all but one isolate. The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

SOCIAL MEDIA – VITAL INSTRUMENT IN GAINING CONSUMERS CONFIDENCE

Directory of Open Access Journals (Sweden)

Mirela-Cristina VOICU

2016-06-01

Full Text Available Given that, currently, the consumer has become more demanding and organizations face some of the greatest challenges due to the economic climate of recent years, the need to build and cultivate strong relationships has become vital not only for the company's success but also for its survival. And solid relationships are built over time through confidence. Trust is one of the most important elements in the process of purchasing and consumer loyalty; it is difficult to obtain but easy to lose. Companies that are enjoying a high degree of confidence benefit from best quotations for their shares, higher profits and a better retention of the best employees. The effects of the lack of confidence are obvious (unsatisfied consumers, lost sales and very expensive for the company. In this context, through the following paper we seek to bring more understanding on how a company can gain the confidence of consumers given that the forms of communication that consumers prefer and that are gaining momentum currently, are taking place online, especially in the social media.

High Throughput Sequencing for Detection of Foodborne Pathogens

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Camilla Sekse

2017-10-01

Full Text Available High-throughput sequencing (HTS is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic “natural” strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.

High-throughput sequencing of three Lemnoideae (duckweeds chloroplast genomes from total DNA.

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Wenqin Wang

Full Text Available BACKGROUND: Chloroplast genomes provide a wealth of information for evolutionary and population genetic studies. Chloroplasts play a particularly important role in the adaption for aquatic plants because they float on water and their major surface is exposed continuously to sunlight. The subfamily of Lemnoideae represents such a collection of aquatic species that because of photosynthesis represents one of the fastest growing plant species on earth. METHODS: We sequenced the chloroplast genomes from three different genera of Lemnoideae, Spirodela polyrhiza, Wolffiella lingulata and Wolffia australiana by high-throughput DNA sequencing of genomic DNA using the SOLiD platform. Unfractionated total DNA contains high copies of plastid DNA so that sequences from the nucleus and mitochondria can easily be filtered computationally. Remaining sequence reads were assembled into contiguous sequences (contigs using SOLiD software tools. Contigs were mapped to a reference genome of Lemna minor and gaps, selected by PCR, were sequenced on the ABI3730xl platform. CONCLUSIONS: This combinatorial approach yielded whole genomic contiguous sequences in a cost-effective manner. Over 1,000-time coverage of chloroplast from total DNA were reached by the SOLiD platform in a single spot on a quadrant slide without purification. Comparative analysis indicated that the chloroplast genome was conserved in gene number and organization with respect to the reference genome of L. minor. However, higher nucleotide substitution, abundant deletions and insertions occurred in non-coding regions of these genomes, indicating a greater genomic dynamics than expected from the comparison of other related species in the Pooideae. Noticeably, there was no transition bias over transversion in Lemnoideae. The data should have immediate applications in evolutionary biology and plant taxonomy with increased resolution and statistical power.

High signals in the uterine cervix on T2-weighted MRI sequences

International Nuclear Information System (INIS)

Graef, De M.; Karam, R.; Daclin, P.Y.; Rouanet, J.P.; Juhan, V.; Maubon, A.J.

2003-01-01

The aim of this pictorial review was to illustrate the normal cervix appearance on T2-weighted images, and give a review of common or less common disorders of the uterine cervix that appear as high signal intensity lesions on T2-weighted sequences. Numerous aetiologies dominated by cervical cancer are reviewed and discussed. This gamut is obviously incomplete; however, radiologists who perform MR women's imaging should perform T2-weighted sequences in the sagittal plane regardless of the indication for pelvic MR. Those sequences will diagnose some previously unknown cervical cancers as well as many other unknown cervical or uterine lesions. (orig.)

Decision time and confidence predict choosers' identification performance in photographic showups

Science.gov (United States)

Sagana, Anna; Sporer, Siegfried L.; Wixted, John T.

2018-01-01

In vast contrast to the multitude of lineup studies that report on the link between decision time, confidence, and identification accuracy, only a few studies looked at these associations for showups, with results varying widely across studies. We therefore set out to test the individual and combined value of decision time and post-decision confidence for diagnosing the accuracy of positive showup decisions using confidence-accuracy characteristic curves and Bayesian analyses. Three-hundred-eighty-four participants viewed a stimulus event and were subsequently presented with two showups which could be target-present or target-absent. As expected, we found a negative decision time-accuracy and a positive post-decision confidence-accuracy correlation for showup selections. Confidence-accuracy characteristic curves demonstrated the expected additive effect of combining both postdictors. Likewise, Bayesian analyses, taking into account all possible target-presence base rate values showed that fast and confident identification decisions were more diagnostic than slow or less confident decisions, with the combination of both being most diagnostic for postdicting accurate and inaccurate decisions. The postdictive value of decision time and post-decision confidence was higher when the prior probability that the suspect is the perpetrator was high compared to when the prior probability that the suspect is the perpetrator was low. The frequent use of showups in practice emphasizes the importance of these findings for court proceedings. Overall, these findings support the idea that courts should have most trust in showup identifications that were made fast and confidently, and least in showup identifications that were made slowly and with low confidence. PMID:29346394

High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA.

Science.gov (United States)

Kebschull, Justus M; Garcia da Silva, Pedro; Reid, Ashlan P; Peikon, Ian D; Albeanu, Dinu F; Zador, Anthony M

2016-09-07

Neurons transmit information to distant brain regions via long-range axonal projections. In the mouse, area-to-area connections have only been systematically mapped using bulk labeling techniques, which obscure the diverse projections of intermingled single neurons. Here we describe MAPseq (Multiplexed Analysis of Projections by Sequencing), a technique that can map the projections of thousands or even millions of single neurons by labeling large sets of neurons with random RNA sequences ("barcodes"). Axons are filled with barcode mRNA, each putative projection area is dissected, and the barcode mRNA is extracted and sequenced. Applying MAPseq to the locus coeruleus (LC), we find that individual LC neurons have preferred cortical targets. By recasting neuroanatomy, which is traditionally viewed as a problem of microscopy, as a problem of sequencing, MAPseq harnesses advances in sequencing technology to permit high-throughput interrogation of brain circuits. Copyright © 2016 Elsevier Inc. All rights reserved.

Workshop on confidence limits. Proceedings

International Nuclear Information System (INIS)

James, F.; Lyons, L.; Perrin, Y.

2000-01-01

The First Workshop on Confidence Limits was held at CERN on 17-18 January 2000. It was devoted to the problem of setting confidence limits in difficult cases: number of observed events is small or zero, background is larger than signal, background not well known, and measurements near a physical boundary. Among the many examples in high-energy physics are searches for the Higgs, searches for neutrino oscillations, B s mixing, SUSY, compositeness, neutrino masses, and dark matter. Several different methods are on the market: the CL s methods used by the LEP Higgs searches; Bayesian methods; Feldman-Cousins and modifications thereof; empirical and combined methods. The Workshop generated considerable interest, and attendance was finally limited by the seating capacity of the CERN Council Chamber where all the sessions took place. These proceedings contain all the papers presented, as well as the full text of the discussions after each paper and of course the last session which was a discussion session. The list of participants and the 'required reading', which was expected to be part of the prior knowledge of all participants, are also included. (orig.)

Subfamily logos: visualization of sequence deviations at alignment positions with high information content

Directory of Open Access Journals (Sweden)

Beitz Eric

2006-06-01

Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

[Sources of leader's confidence in organizations].

Science.gov (United States)

Ikeda, Hiroshi; Furukawa, Hisataka

2006-04-01

The purpose of this study was to examine the sources of confidence that organization leaders had. As potential sources of the confidence, we focused on fulfillment of expectations made by self and others, reflection on good as well as bad job experiences, and awareness of job experiences in terms of commonality, differentiation, and multiple viewpoints. A questionnaire was administered to 170 managers of Japanese companies. Results were as follows: First, confidence in leaders was more strongly related to fulfillment of expectations made by self and others than reflection on and awareness of job experiences. Second, the confidence was weakly related to internal processing of job experiences, in the form of commonality awareness and reflection on good job experiences. And finally, years of managerial experiences had almost no relation to the confidence. These findings suggested that confidence in leaders was directly acquired from fulfillment of expectations made by self and others, rather than indirectly through internal processing of job experiences. Implications of the findings for leadership training were also discussed.

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

Science.gov (United States)

Inagaki, Soichi; Henry, Isabelle M; Lieberman, Meric C; Comai, Luca

2015-01-01

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination

Science.gov (United States)

Warwood, Stacey; van Dongen, Bart; Kitchener, Andrew C.; Manning, Phillip L.

2017-01-01

A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr Tyrannosaurus rex fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr Brachylophosaurus canadensis fossil were reported that have remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, Struthio camelus. The resulting LC–MS/MS data were found to match all of the proposed sequences for both the original Tyrannosaurus and Brachylophosaurus studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated. PMID:28566488

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

Science.gov (United States)

Kou, Qinghe; Jiang, Jiao; Guo, Shaogui; Zhang, Haiying; Hou, Wenju; Zou, Xiaohua; Sun, Honghe; Gong, Guoyi; Levi, Amnon; Xu, Yong

2012-01-01

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits. PMID:22247776

Two sides of the same coin: Monetary incentives concurrently improve and bias confidence judgments.

Science.gov (United States)

Lebreton, Maël; Langdon, Shari; Slieker, Matthijs J; Nooitgedacht, Jip S; Goudriaan, Anna E; Denys, Damiaan; van Holst, Ruth J; Luigjes, Judy

2018-05-01

Decisions are accompanied by a feeling of confidence, that is, a belief about the decision being correct. Confidence accuracy is critical, notably in high-stakes situations such as medical or financial decision-making. We investigated how incentive motivation influences confidence accuracy by combining a perceptual task with a confidence incentivization mechanism. By varying the magnitude and valence (gains or losses) of monetary incentives, we orthogonalized their motivational and affective components. Corroborating theories of rational decision-making and motivation, our results first reveal that the motivational value of incentives improves aspects of confidence accuracy. However, in line with a value-confidence interaction hypothesis, we further show that the affective value of incentives concurrently biases confidence reports, thus degrading confidence accuracy. Finally, we demonstrate that the motivational and affective effects of incentives differentially affect how confidence builds on perceptual evidence. Together, these findings may provide new hints about confidence miscalibration in healthy or pathological contexts.

Two sides of the same coin: Monetary incentives concurrently improve and bias confidence judgments

Science.gov (United States)

Lebreton, Maël; Slieker, Matthijs J.; Nooitgedacht, Jip S.; van Holst, Ruth J.; Luigjes, Judy

2018-01-01

Decisions are accompanied by a feeling of confidence, that is, a belief about the decision being correct. Confidence accuracy is critical, notably in high-stakes situations such as medical or financial decision-making. We investigated how incentive motivation influences confidence accuracy by combining a perceptual task with a confidence incentivization mechanism. By varying the magnitude and valence (gains or losses) of monetary incentives, we orthogonalized their motivational and affective components. Corroborating theories of rational decision-making and motivation, our results first reveal that the motivational value of incentives improves aspects of confidence accuracy. However, in line with a value-confidence interaction hypothesis, we further show that the affective value of incentives concurrently biases confidence reports, thus degrading confidence accuracy. Finally, we demonstrate that the motivational and affective effects of incentives differentially affect how confidence builds on perceptual evidence. Together, these findings may provide new hints about confidence miscalibration in healthy or pathological contexts. PMID:29854944

On-line confidence monitoring during decision making.

Science.gov (United States)

Dotan, Dror; Meyniel, Florent; Dehaene, Stanislas

2018-02-01

Humans can readily assess their degree of confidence in their decisions. Two models of confidence computation have been proposed: post hoc computation using post-decision variables and heuristics, versus online computation using continuous assessment of evidence throughout the decision-making process. Here, we arbitrate between these theories by continuously monitoring finger movements during a manual sequential decision-making task. Analysis of finger kinematics indicated that subjects kept separate online records of evidence and confidence: finger deviation continuously reflected the ongoing accumulation of evidence, whereas finger speed continuously reflected the momentary degree of confidence. Furthermore, end-of-trial finger speed predicted the post-decisional subjective confidence rating. These data indicate that confidence is computed on-line, throughout the decision process. Speed-confidence correlations were previously interpreted as a post-decision heuristics, whereby slow decisions decrease subjective confidence, but our results suggest an adaptive mechanism that involves the opposite causality: by slowing down when unconfident, participants gain time to improve their decisions. Copyright © 2017 Elsevier B.V. All rights reserved.

Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations.

Science.gov (United States)

Reid-Bayliss, Kate S; Loeb, Lawrence A

2017-08-29

Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.

The impact of simulation sequencing on perceived clinical decision making.

Science.gov (United States)

Woda, Aimee; Hansen, Jamie; Paquette, Mary; Topp, Robert

2017-09-01

An emerging nursing education trend is to utilize simulated learning experiences as a means to optimize competency and decision making skills. The purpose of this study was to examine differences in students' perception of clinical decision making and clinical decision making-related self-confidence and anxiety based on the sequence (order) in which they participated in a block of simulated versus hospital-based learning experiences. A quasi-experimental crossover design was used. Between and within group differences were found relative to self-confidence with the decision making process. When comparing groups, at baseline the simulation followed by hospital group had significantly higher self-confidence scores, however, at 14-weeks both groups were not significantly different. Significant within group differences were found in the simulation followed by hospital group only, demonstrating a significant decrease in clinical decision making related anxiety across the semester. Finally, there were no significant difference in; perceived clinical decision making within or between the groups at the two measurement points. Preliminary findings suggest that simulated learning experiences can be offered with alternating sequences without impacting the process, anxiety or confidence with clinical decision making. This study provides beginning evidence to guide curriculum development and allow flexibility based on student needs and available resources. Copyright © 2017. Published by Elsevier Ltd.

SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data

Science.gov (United States)

Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the subset of paired-end sequences that pass quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc). All modules are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, Windows). The program suite relies on a compiled Python extension module to perform paired-end alignments. Instructions for compiling the extension from source code are provided in the documentation. Users who do not have Python installed on their computers or who do not have the ability to compile software also may choose to download packaged executable files. These files include all Python scripts, a copy of the compiled extension module, and a minimal installation of Python in a single binary executable. See program documentation for more information.

How do regulators measure public confidence?

International Nuclear Information System (INIS)

Schmitt, A.; Besenyei, E.

2006-01-01

The conclusions and recommendations of this session can be summarized this way. - There are some important elements of confidence: visibility, satisfaction, credibility and reputation. The latter can consist of trust, positive image and knowledge of the role the organisation plays. A good reputation is hard to achieve but easy to lose. - There is a need to define what public confidence is and what to measure. The difficulty is that confidence is a matter of perception of the public, so what we try to measure is the perception. - It is controversial how to take into account the results of confidence measurement because of the influence of the context. It is not an exact science, results should be examined cautiously and surveys should be conducted frequently, at least every two years. - Different experiences were explained: - Quantitative surveys - among the general public or more specific groups like the media; - Qualitative research - with test groups and small panels; - Semi-quantitative studies - among stakeholders who have regular contracts with the regulatory body. It is not clear if the results should be shared with the public or just with other authorities and governmental organisations. - Efforts are needed to increase visibility, which is a prerequisite for confidence. - A practical example of organizing an emergency exercise and an information campaign without taking into account the real concerns of the people was given to show how public confidence can be decreased. - We learned about a new method - the so-called socio-drama - which addresses another issue also connected to confidence - the notion of understanding between stakeholders around a nuclear site. It is another way of looking at confidence in a more restricted group. (authors)

Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery.

Directory of Open Access Journals (Sweden)

Randi Holm Jensen

Full Text Available Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing.

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

Science.gov (United States)

Yang, Yaping; Muzny, Donna M.; Reid, Jeffrey G.; Bainbridge, Matthew N.; Willis, Alecia; Ward, Patricia A.; Braxton, Alicia; Beuten, Joke; Xia, Fan; Niu, Zhiyv; Hardison, Matthew; Person, Richard; Bekheirnia, Mir Reza; Leduc, Magalie S.; Kirby, Amelia; Pham, Peter; Scull, Jennifer; Wang, Min; Ding, Yan; Plon, Sharon E.; Lupski, James R.; Beaudet, Arthur L.; Gibbs, Richard A.; Eng, Christine M.

2014-01-01

BACKGROUND Whole-exome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders. METHODS We developed technical, bioinformatic, interpretive, and validation pipelines for whole-exome sequencing in a certified clinical laboratory to identify sequence variants underlying disease phenotypes in patients. RESULTS We present data on the first 250 probands for whom referring physicians ordered whole-exome sequencing. Patients presented with a range of phenotypes suggesting potential genetic causes. Approximately 80% were children with neurologic pheno-types. Insurance coverage was similar to that for established genetic tests. We identified 86 mutated alleles that were highly likely to be causative in 62 of the 250 patients, achieving a 25% molecular diagnostic rate (95% confidence interval, 20 to 31). Among the 62 patients, 33 had autosomal dominant disease, 16 had auto-somal recessive disease, and 9 had X-linked disease. A total of 4 probands received two nonoverlapping molecular diagnoses, which potentially challenged the clinical diagnosis that had been made on the basis of history and physical examination. A total of 83% of the autosomal dominant mutant alleles and 40% of the X-linked mutant alleles occurred de novo. Recurrent clinical phenotypes occurred in patients with mutations that were highly likely to be causative in the same genes and in different genes responsible for genetically heterogeneous disorders. CONCLUSIONS Whole-exome sequencing identified the underlying genetic defect in 25% of consecutive patients referred for evaluation of a possible genetic condition. (Funded by the National Human Genome Research Institute.) PMID:24088041

A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex.

Science.gov (United States)

Armour, Sean M; Bennett, Eric J; Braun, Craig R; Zhang, Xiao-Yong; McMahon, Steven B; Gygi, Steven P; Harper, J Wade; Sinclair, David A

2013-04-01

Although many functions and targets have been attributed to the histone and protein deacetylase SIRT1, a comprehensive analysis of SIRT1 binding proteins yielding a high-confidence interaction map has not been established. Using a comparative statistical analysis of binding partners, we have assembled a high-confidence SIRT1 interactome. Employing this method, we identified the deubiquitinating enzyme ubiquitin-specific protease 22 (USP22), a component of the deubiquitinating module (DUBm) of the SAGA transcriptional coactivating complex, as a SIRT1-interacting partner. We found that this interaction is highly specific, requires the ZnF-UBP domain of USP22, and is disrupted by the inactivating H363Y mutation within SIRT1. Moreover, we show that USP22 is acetylated on multiple lysine residues and that alteration of a single lysine (K129) within the ZnF-UBP domain is sufficient to alter interaction of the DUBm with the core SAGA complex. Furthermore, USP22-mediated recruitment of SIRT1 activity promotes the deacetylation of individual SAGA complex components. Our results indicate an important role of SIRT1-mediated deacetylation in regulating the formation of DUBm subcomplexes within the larger SAGA complex.

The Great Recession and confidence in homeownership

OpenAIRE

Anat Bracha; Julian Jamison

2013-01-01

Confidence in homeownership shifts for those who personally experienced real estate loss during the Great Recession. Older Americans are confident in the value of homeownership. Younger Americans are less confident.

Social media sentiment and consumer confidence

OpenAIRE

Daas, Piet J.H.; Puts, Marco J.H.

2014-01-01

Changes in the sentiment of Dutch public social media messages were compared with changes in monthly consumer confidence over a period of three-and-a-half years, revealing that both were highly correlated (up to r = 0.9) and that both series cointegrated. This phenomenon is predominantly affected by changes in the sentiment of all Dutch public Facebook messages. The inclusion of various selections of public Twitter messages improved this association and the response to changes in sentiment. G...

Chemistry, the Central Science? The History of the High School Science Sequence

Science.gov (United States)

Sheppard, Keith; Robbins, Dennis M.

2005-01-01

Chemistry became the ''central science'' not by design but by accident in the US high schools. The three important factors, which had their influence on the high school science, are sequenced and their impact on the development of US science education, are mentioned.

Get your high-quality low-cost genome sequence

NARCIS (Netherlands)

Faino, L.; Thomma, B.P.H.J.

2014-01-01

The study of whole-genome sequences has become essential for almost all branches of biological research. Next-generation sequencing (NGS) has revolutionized the scalability, speed, and resolution of sequencing and brought genomic science within reach of academic laboratories that study non-model

Sequence assembly

DEFF Research Database (Denmark)

Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

2009-01-01

Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq).

Science.gov (United States)

Preston, Jessica L; Royall, Ariel E; Randel, Melissa A; Sikkink, Kristin L; Phillips, Patrick C; Johnson, Eric A

2016-06-14

Polymorphic loci exist throughout the genomes of a population and provide the raw genetic material needed for a species to adapt to changes in the environment. The minor allele frequencies of rare Single Nucleotide Polymorphisms (SNPs) within a population have been difficult to track with Next-Generation Sequencing (NGS), due to the high error rate of standard methods such as Illumina sequencing. We have developed a wet-lab protocol and variant-calling method that identifies both sequencing and PCR errors, called Paired-End Low Error Sequencing (PELE-Seq). To test the specificity and sensitivity of the PELE-Seq method, we sequenced control E. coli DNA libraries containing known rare alleles present at frequencies ranging from 0.2-0.4 % of the total reads. PELE-Seq had higher specificity and sensitivity than standard libraries. We then used PELE-Seq to characterize rare alleles in a Caenorhabditis remanei nematode worm population before and after laboratory adaptation, and found that minor and rare alleles can undergo large changes in frequency during lab-adaptation. We have developed a method of rare allele detection that mitigates both sequencing and PCR errors, called PELE-Seq. PELE-Seq was evaluated using control E. coli populations and was then used to compare a wild C. remanei population to a lab-adapted population. The PELE-Seq method is ideal for investigating the dynamics of rare alleles in a broad range of reduced-representation sequencing methods, including targeted amplicon sequencing, RAD-Seq, ddRAD, and GBS. PELE-Seq is also well-suited for whole genome sequencing of mitochondria and viruses, and for high-throughput rare mutation screens.

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

Science.gov (United States)

Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike; Khan, Arifa S

2018-01-01

Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have

Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods.

Science.gov (United States)

Mu, John C; Tootoonchi Afshar, Pegah; Mohiyuddin, Marghoob; Chen, Xi; Li, Jian; Bani Asadi, Narges; Gerstein, Mark B; Wong, Wing H; Lam, Hugo Y K

2015-09-28

A high-confidence, comprehensive human variant set is critical in assessing accuracy of sequencing algorithms, which are crucial in precision medicine based on high-throughput sequencing. Although recent works have attempted to provide such a resource, they still do not encompass all major types of variants including structural variants (SVs). Thus, we leveraged the massive high-quality Sanger sequences from the HuRef genome to construct by far the most comprehensive gold set of a single individual, which was cross validated with deep Illumina sequencing, population datasets, and well-established algorithms. It was a necessary effort to completely reanalyze the HuRef genome as its previously published variants were mostly reported five years ago, suffering from compatibility, organization, and accuracy issues that prevent their direct use in benchmarking. Our extensive analysis and validation resulted in a gold set with high specificity and sensitivity. In contrast to the current gold sets of the NA12878 or HS1011 genomes, our gold set is the first that includes small variants, deletion SVs and insertion SVs up to a hundred thousand base-pairs. We demonstrate the utility of our HuRef gold set to benchmark several published SV detection tools.

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

Directory of Open Access Journals (Sweden)

Soichi Inagaki

Full Text Available Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

The need for high-quality whole-genome sequence databases in microbial forensics.

Science.gov (United States)

Sjödin, Andreas; Broman, Tina; Melefors, Öjar; Andersson, Gunnar; Rasmusson, Birgitta; Knutsson, Rickard; Forsman, Mats

2013-09-01

Microbial forensics is an important part of a strengthened capability to respond to biocrime and bioterrorism incidents to aid in the complex task of distinguishing between natural outbreaks and deliberate acts. The goal of a microbial forensic investigation is to identify and criminally prosecute those responsible for a biological attack, and it involves a detailed analysis of the weapon--that is, the pathogen. The recent development of next-generation sequencing (NGS) technologies has greatly increased the resolution that can be achieved in microbial forensic analyses. It is now possible to identify, quickly and in an unbiased manner, previously undetectable genome differences between closely related isolates. This development is particularly relevant for the most deadly bacterial diseases that are caused by bacterial lineages with extremely low levels of genetic diversity. Whole-genome analysis of pathogens is envisaged to be increasingly essential for this purpose. In a microbial forensic context, whole-genome sequence analysis is the ultimate method for strain comparisons as it is informative during identification, characterization, and attribution--all 3 major stages of the investigation--and at all levels of microbial strain identity resolution (ie, it resolves the full spectrum from family to isolate). Given these capabilities, one bottleneck in microbial forensics investigations is the availability of high-quality reference databases of bacterial whole-genome sequences. To be of high quality, databases need to be curated and accurate in terms of sequences, metadata, and genetic diversity coverage. The development of whole-genome sequence databases will be instrumental in successfully tracing pathogens in the future.

A microarray-based genotyping and genetic mapping approach for highly heterozygous outcrossing species enables localization of a large fraction of the unassembled Populus trichocarpa genome sequence.

Science.gov (United States)

Drost, Derek R; Novaes, Evandro; Boaventura-Novaes, Carolina; Benedict, Catherine I; Brown, Ryan S; Yin, Tongming; Tuskan, Gerald A; Kirst, Matias

2009-06-01

Microarrays have demonstrated significant power for genome-wide analyses of gene expression, and recently have also revolutionized the genetic analysis of segregating populations by genotyping thousands of loci in a single assay. Although microarray-based genotyping approaches have been successfully applied in yeast and several inbred plant species, their power has not been proven in an outcrossing species with extensive genetic diversity. Here we have developed methods for high-throughput microarray-based genotyping in such species using a pseudo-backcross progeny of 154 individuals of Populus trichocarpa and P. deltoides analyzed with long-oligonucleotide in situ-synthesized microarray probes. Our analysis resulted in high-confidence genotypes for 719 single-feature polymorphism (SFP) and 1014 gene expression marker (GEM) candidates. Using these genotypes and an established microsatellite (SSR) framework map, we produced a high-density genetic map comprising over 600 SFPs, GEMs and SSRs. The abundance of gene-based markers allowed us to localize over 35 million base pairs of previously unplaced whole-genome shotgun (WGS) scaffold sequence to putative locations in the genome of P. trichocarpa. A high proportion of sampled scaffolds could be verified for their placement with independently mapped SSRs, demonstrating the previously un-utilized power that high-density genotyping can provide in the context of map-based WGS sequence reassembly. Our results provide a substantial contribution to the continued improvement of the Populus genome assembly, while demonstrating the feasibility of microarray-based genotyping in a highly heterozygous population. The strategies presented are applicable to genetic mapping efforts in all plant species with similarly high levels of genetic diversity.

Combining Amplification Typing of L1 Active Subfamilies (ATLAS) with High-Throughput Sequencing.

Science.gov (United States)

Rahbari, Raheleh; Badge, Richard M

2016-01-01

With the advent of new generations of high-throughput sequencing technologies, the catalog of human genome variants created by retrotransposon activity is expanding rapidly. However, despite these advances in describing L1 diversity and the fact that L1 must retrotranspose in the germline or prior to germline partitioning to be evolutionarily successful, direct assessment of de novo L1 retrotransposition in the germline or early embryogenesis has not been achieved for endogenous L1 elements. A direct study of de novo L1 retrotransposition into susceptible loci within sperm DNA (Freeman et al., Hum Mutat 32(8):978-988, 2011) suggested that the rate of L1 retrotransposition in the germline is much lower than previously estimated (ATLAS L1 display technique (Badge et al., Am J Hum Genet 72(4):823-838, 2003) to investigate de novo L1 retrotransposition in human genomes. In this chapter, we describe how we combined a high-coverage ATLAS variant with high-throughput sequencing, achieving 11-25× sequence depth per single amplicon, to study L1 retrotransposition in whole genome amplified (WGA) DNAs.

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

Science.gov (United States)

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.

Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis.

Science.gov (United States)

Guo, Yan; Dai, Yulin; Yu, Hui; Zhao, Shilin; Samuels, David C; Shyr, Yu

2017-03-01

Analyses of high throughput sequencing data starts with alignment against a reference genome, which is the foundation for all re-sequencing data analyses. Each new release of the human reference genome has been augmented with improved accuracy and completeness. It is presumed that the latest release of human reference genome, GRCh38 will contribute more to high throughput sequencing data analysis by providing more accuracy. But the amount of improvement has not yet been quantified. We conducted a study to compare the genomic analysis results between the GRCh38 reference and its predecessor GRCh37. Through analyses of alignment, single nucleotide polymorphisms, small insertion/deletions, copy number and structural variants, we show that GRCh38 offers overall more accurate analysis of human sequencing data. More importantly, GRCh38 produced fewer false positive structural variants. In conclusion, GRCh38 is an improvement over GRCh37 not only from the genome assembly aspect, but also yields more reliable genomic analysis results. Copyright © 2017. Published by Elsevier Inc.

The Relationship between a Women's Leadership Development Program and Participant Self-Confidence

Science.gov (United States)

Jennings, Janelle Perron

2009-01-01

According to Lundeberg, Fox, and Punccohar (1994), the reason that there are fewer women in certain professions is because of a lack of self-confidence. In a review of the literature, they found studies reporting a lack of self-confidence in sixth-grade girls, high school students, and women in undergraduate and graduate school. In her work on…

Parallel Sequencing of Expressed Sequence Tags from Two Complementary DNA Libraries for High and Low Phosphorus Adaptation in Common Beans

Directory of Open Access Journals (Sweden)

Matthew W. Blair

2011-11-01

Full Text Available Expressed sequence tags (ESTs have proven useful for gene discovery in many crops. In this work, our objective was to construct complementary DNA (cDNA libraries from root tissues of common beans ( L. grown under low and high P hydroponic conditions and to conduct EST sequencing and comparative analyses of the libraries. Expressed sequence tag analysis of 3648 clones identified 2372 unigenes, of which 1591 were annotated as known genes while a total of 465 unigenes were not associated with any known gene. Unigenes with hits were categorized according to biological processes, molecular function, and cellular compartmentalization. Given the young tissue used to make the root libraries, genes for catalytic activity and binding were highly expressed. Comparisons with previous root EST sequencing and between the two libraries made here resulted in a set of genes to study further for differential gene expression and adaptation to low P, such as a 14 kDa praline-rich protein, a metallopeptidase, tonoplast intrinsic protein, adenosine triphosphate (ATP citrate synthase, and cell proliferation genes expressed in the low P treated plants. Given that common beans are often grown on acid soils of the tropics and subtropics that are usually low in P these genes and the two parallel libraries will be useful for selection for better uptake of this essential macronutrient. The importance of EST generation for common bean root tissues under low P and other abiotic soil stresses is also discussed.

A new sieving matrix for DNA sequencing, genotyping and mutation detection and high-throughput genotyping with a 96-capillary array system

Energy Technology Data Exchange (ETDEWEB)

Gao, David [Iowa State Univ., Ames, IA (United States)

1999-11-08

Capillary electrophoresis has been widely accepted as a fast separation technique in DNA analysis. In this dissertation, a new sieving matrix is described for DNA analysis, especially DNA sequencing, genetic typing and mutation detection. A high-throughput 96 capillary array electrophoresis system was also demonstrated for simultaneous multiple genotyping. The authors first evaluated the influence of different capillary coatings on the performance of DNA sequencing. A bare capillary was compared with a DB-wax, an FC-coated and a polyvinylpyrrolidone dynamically coated capillary with PEO as sieving matrix. It was found that covalently-coated capillaries had no better performance than bare capillaries while PVP coating provided excellent and reproducible results. The authors also developed a new sieving Matrix for DNA separation based on commercially available poly(vinylpyrrolidone) (PVP). This sieving matrix has a very low viscosity and an excellent self-coating effect. Successful separations were achieved in uncoated capillaries. Sequencing of M13mp18 showed good resolution up to 500 bases in treated PVP solution. Temperature gradient capillary electrophoresis and PVP solution was applied to mutation detection. A heteroduplex sample and a homoduplex reference were injected during a pair of continuous runs. A temperature gradient of 10 C with a ramp of 0.7 C/min was swept throughout the capillary. Detection was accomplished by laser induced fluorescence detection. Mutation detection was performed by comparing the pattern changes between the homoduplex and the heteroduplex samples. High throughput, high detection rate and easy operation were achieved in this system. They further demonstrated fast and reliable genotyping based on CTTv STR system by multiple-capillary array electrophoresis. The PCR products from individuals were mixed with pooled allelic ladder as an absolute standard and coinjected with a 96-vial tray. Simultaneous one-color laser-induced fluorescence

Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

Science.gov (United States)

Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

2014-09-18

Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.

Science.gov (United States)

Peng, Yu; Leung, Henry C M; Yiu, S M; Chin, Francis Y L

2012-06-01

Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs. We introduce the IDBA-UD algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths. Several non-trivial techniques have been employed to tackle the problems. Instead of using a simple threshold, we use multiple depthrelative thresholds to remove erroneous k-mers in both low-depth and high-depth regions. The technique of local assembly with paired-end information is used to solve the branch problem of low-depth short repeat regions. To speed up the process, an error correction step is conducted to correct reads of high-depth regions that can be aligned to highconfident contigs. Comparison of the performances of IDBA-UD and existing assemblers (Velvet, Velvet-SC, SOAPdenovo and Meta-IDBA) for different datasets, shows that IDBA-UD can reconstruct longer contigs with higher accuracy. The IDBA-UD toolkit is available at our website http://www.cs.hku.hk/~alse/idba_ud

Method for critical software event execution reliability in high integrity software

Energy Technology Data Exchange (ETDEWEB)

Kidd, M.E. [Sandia National Labs., Albuquerque, NM (United States)

1997-11-01

This report contains viewgraphs on a method called SEER, which provides a high level of confidence that critical software driven event execution sequences faithfully exceute in the face of transient computer architecture failures in both normal and abnormal operating environments.

Confidence Leak in Perceptual Decision Making.

Science.gov (United States)

Rahnev, Dobromir; Koizumi, Ai; McCurdy, Li Yan; D'Esposito, Mark; Lau, Hakwan

2015-11-01

People live in a continuous environment in which the visual scene changes on a slow timescale. It has been shown that to exploit such environmental stability, the brain creates a continuity field in which objects seen seconds ago influence the perception of current objects. What is unknown is whether a similar mechanism exists at the level of metacognitive representations. In three experiments, we demonstrated a robust intertask confidence leak-that is, confidence in one's response on a given task or trial influencing confidence on the following task or trial. This confidence leak could not be explained by response priming or attentional fluctuations. Better ability to modulate confidence leak predicted higher capacity for metacognition as well as greater gray matter volume in the prefrontal cortex. A model based on normative principles from Bayesian inference explained the results by postulating that observers subjectively estimate the perceptual signal strength in a stable environment. These results point to the existence of a novel metacognitive mechanism mediated by regions in the prefrontal cortex. © The Author(s) 2015.

Applications of High Throughput Nucleotide Sequencing

DEFF Research Database (Denmark)

Waage, Johannes Eichler

equally large demands in data handling, analysis and interpretation, perhaps defining the modern challenge of the computational biologist of the post-genomic era. The first part of this thesis consists of a general introduction to the history, common terms and challenges of next generation sequencing......-sequencing, a study of the effects on alternative RNA splicing of KO of the nonsense mediated RNA decay system in Mus, using digital gene expression and a custom-built exon-exon junction mapping pipeline is presented (article I). Evolved from this work, a Bioconductor package, spliceR, for classifying alternative...

Evolutionary growth process of highly conserved sequences in vertebrate genomes.

Science.gov (United States)

Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

2012-08-01

Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

Errors and Predictors of Confidence in Condom Use amongst Young Australians Attending a Music Festival

OpenAIRE

Hall, Karina M.; Brieger, Daniel G.; De Silva, Sukhita H.; Pfister, Benjamin F.; Youlden, Daniel J.; John-Leader, Franklin; Pit, Sabrina W.

2016-01-01

Objectives. To determine the confidence and ability to use condoms correctly and consistently and the predictors of confidence in young Australians attending a festival. Methods. 288 young people aged 18 to 29 attending a mixed-genre music festival completed a survey measuring demographics, self-reported confidence using condoms, ability to use condoms, and issues experienced when using condoms in the past 12 months. Results. Self-reported confidence using condoms was high (77%). Multivariate...

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.

Science.gov (United States)

Vetrovský, Tomáš; Baldrian, Petr; Morais, Daniel; Berger, Bonnie

2018-02-14

Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems. SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4GB of data. SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://www.biomed.cas.cz/mbu/lbwrf/seed/ as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions. daniel.morais@biomed.cas.cz. Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press.

Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

Directory of Open Access Journals (Sweden)

Zhao Patrick X

2011-07-01

Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most common type of sequence variation among plants and are often functionally important. We describe the use of 454 technology and high resolution melting analysis (HRM for high throughput SNP discovery in tetraploid alfalfa (Medicago sativa L., a species with high economic value but limited genomic resources. Results The alfalfa genotypes selected from M. sativa subsp. sativa var. 'Chilean' and M. sativa subsp. falcata var. 'Wisfal', which differ in water stress sensitivity, were used to prepare cDNA from tissue of clonally-propagated plants grown under either well-watered or water-stressed conditions, and then pooled for 454 sequencing. Based on 125.2 Mb of raw sequence, a total of 54,216 unique sequences were obtained including 24,144 tentative consensus (TCs sequences and 30,072 singletons, ranging from 100 bp to 6,662 bp in length, with an average length of 541 bp. We identified 40,661 candidate SNPs distributed throughout the genome. A sample of candidate SNPs were evaluated and validated using high resolution melting (HRM analysis. A total of 3,491 TCs harboring 20,270 candidate SNPs were located on the M. truncatula (MT 3.5.1 chromosomes. Gene Ontology assignments indicate that sequences obtained cover a broad range of GO categories. Conclusions We describe an efficient method to identify thousands of SNPs distributed throughout the alfalfa genome covering a broad range of GO categories. Validated SNPs represent valuable molecular marker resources that can be used to enhance marker density in linkage maps, identify potential factors involved in heterosis and genetic variation, and as tools for association mapping and genomic selection in alfalfa.

Towards confidence in transport safety

International Nuclear Information System (INIS)

Robison, R.W.

1992-01-01

The U.S. Department of Energy (US DOE) plans to demonstrate to the public that high-level waste can be transported safely to the proposed repository. The author argues US DOE should begin now to demonstrate its commitment to safety by developing an extraordinary safety program for nuclear cargo it is now shipping. The program for current shipments should be developed with State, Tribal, and local officials. Social scientists should be involved in evaluating the effect of the safety program on public confidence. The safety program developed in cooperation with western states for shipments to the Waste Isolation Pilot plant is a good basis for designing that extraordinary safety program

High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq).

Science.gov (United States)

Jiao, Yang; Li, Ran; Wu, Chao; Ding, Yibin; Liu, Yanning; Jia, Danmei; Wang, Lifeng; Xu, Xiang; Zhu, Jing; Zheng, Min; Jia, Junling

2018-01-15

Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine. Here, we present a cost-efficient Saturated Tiling Capture Sequencing (STC-Seq) approach to capturing 14 HLA class I and II genes. The highly efficient capture (an approximately 23,000-fold enrichment) of these genes allows for simplified allele calling. Tests on five genes (HLA-A/B/C/DRB1/DQB1) from 31 human samples and 351 datasets using STC-Seq showed results that were 98% consistent with the known two sets of digitals (field1 and field2) genotypes. Additionally, STC can capture genomic DNA fragments longer than 3 kb from HLA loci, making the library compatible with the third-generation sequencing. STC-Seq is a highly accurate and cost-efficient method for HLA typing which can be used to facilitate the establishment of population-based HLA databases for the precision and transplantation medicine.

Targeting Low Career Confidence Using the Career Planning Confidence Scale

Science.gov (United States)

McAuliffe, Garrett; Jurgens, Jill C.; Pickering, Worth; Calliotte, James; Macera, Anthony; Zerwas, Steven

2006-01-01

The authors describe the development and validation of a test of career planning confidence that makes possible the targeting of specific problem issues in employment counseling. The scale, developed using a rational process and the authors' experience with clients, was tested for criterion-related validity against 2 other measures. The scale…

Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.

Science.gov (United States)

Morse, Alison M; Calabro, Kaitlyn R; Fear, Justin M; Bloom, David C; McIntyre, Lauren M

2017-08-16

High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines. Here, we evaluate two approaches for the identification of genetic variants in HSV1 strains using Illumina short read sequencing data. The first, a reference-based approach, identifies variants from reads aligned to a reference sequence and the second, a de novo assembly approach, identifies variants from reads aligned to de novo assembled consensus sequences. Of critical importance for both approaches is the reduction in the number of low complexity regions through the construction of a non-redundant reference genome. We compared variants identified in the two methods. Our results indicate that approximately 85% of variants are identified regardless of the approach. The reference-based approach to variant discovery captures an additional 15% representing variants divergent from the HSV1 reference possibly due to viral passage. Reference-based approaches are significantly less labor-intensive and identify variants across the genome where de novo assembly-based approaches are limited to regions where contigs have been successfully assembled. In addition, regions of poor quality assembly can lead to false variant identification in de novo consensus sequences. For viruses with a well-assembled reference genome, a reference-based approach is recommended.

A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination.

Science.gov (United States)

Buckley, Michael; Warwood, Stacey; van Dongen, Bart; Kitchener, Andrew C; Manning, Phillip L

2017-05-31

A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr Tyrannosaurus rex fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr Brachylophosaurus canadensis fossil were reported that have remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, Struthio camelus The resulting LC-MS/MS data were found to match all of the proposed sequences for both the original Tyrannosaurus and Brachylophosaurus studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated. © 2017 The Authors.

Analysis of quality raw data of second generation sequencers with Quality Assessment Software.

Science.gov (United States)

Ramos, Rommel Tj; Carneiro, Adriana R; Baumbach, Jan; Azevedo, Vasco; Schneider, Maria Pc; Silva, Artur

2011-04-18

Second generation technologies have advantages over Sanger; however, they have resulted in new challenges for the genome construction process, especially because of the small size of the reads, despite the high degree of coverage. Independent of the program chosen for the construction process, DNA sequences are superimposed, based on identity, to extend the reads, generating contigs; mismatches indicate a lack of homology and are not included. This process improves our confidence in the sequences that are generated. We developed Quality Assessment Software, with which one can review graphs showing the distribution of quality values from the sequencing reads. This software allow us to adopt more stringent quality standards for sequence data, based on quality-graph analysis and estimated coverage after applying the quality filter, providing acceptable sequence coverage for genome construction from short reads. Quality filtering is a fundamental step in the process of constructing genomes, as it reduces the frequency of incorrect alignments that are caused by measuring errors, which can occur during the construction process due to the size of the reads, provoking misassemblies. Application of quality filters to sequence data, using the software Quality Assessment, along with graphing analyses, provided greater precision in the definition of cutoff parameters, which increased the accuracy of genome construction.

Confidence rating of marine eutrophication assessments

DEFF Research Database (Denmark)

Murray, Ciarán; Andersen, Jesper Harbo; Kaartokallio, Hermanni

2011-01-01

of the 'value' of the indicators on which the primary assessment is made. Such secondary assessment of confidence represents a first step towards linking status classification with information regarding their accuracy and precision and ultimately a tool for improving or targeting actions to improve the health......This report presents the development of a methodology for assessing confidence in eutrophication status classifications. The method can be considered as a secondary assessment, supporting the primary assessment of eutrophication status. The confidence assessment is based on a transparent scoring...

HTSeq--a Python framework to work with high-throughput sequencing data.

Science.gov (United States)

Anders, Simon; Pyl, Paul Theodor; Huber, Wolfgang

2015-01-15

A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard workflows, custom scripts are needed. We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes. HTSeq is released as an open-source software under the GNU General Public Licence and available from http://www-huber.embl.de/HTSeq or from the Python Package Index at https://pypi.python.org/pypi/HTSeq. © The Author 2014. Published by Oxford University Press.

Empowerment as Interactions that Generate Self-Confidence

DEFF Research Database (Denmark)

Poder, Poul

2010-01-01

to address this gap in understanding by theorizing how confidence and other positive emotions contribute to personal agency, which is an essential aspect of the empowerment process.                       It is generally understood that confidence – meaning faith in oneself as opposed to conceit or arrogance...... by particular social interactions that promote recognition and access to relevant resources for action. Drawing on emotion-focused sociological theory about agency and emotional energy, and Fredrickson’s ‘build and broaden’ theory of positive emotions, I argue that the focus on consciousness and intentionality...... as the defining features of human agency has led us to downplay the fact that agency is primarily an emotional phenomenon. As such, it is also dynamic and situational, since it is highly dependent on interactions that engender emotional energy and positive emotions that fuel and widen agency. As an example...

Extraction of High Molecular Weight DNA from Fungal Rust Spores for Long Read Sequencing.

Science.gov (United States)

Schwessinger, Benjamin; Rathjen, John P

2017-01-01

Wheat rust fungi are complex organisms with a complete life cycle that involves two different host plants and five different spore types. During the asexual infection cycle on wheat, rusts produce massive amounts of dikaryotic urediniospores. These spores are dikaryotic (two nuclei) with each nucleus containing one haploid genome. This dikaryotic state is likely to contribute to their evolutionary success, making them some of the major wheat pathogens globally. Despite this, most published wheat rust genomes are highly fragmented and contain very little haplotype-specific sequence information. Current long-read sequencing technologies hold great promise to provide more contiguous and haplotype-phased genome assemblies. Long reads are able to span repetitive regions and phase structural differences between the haplomes. This increased genome resolution enables the identification of complex loci and the study of genome evolution beyond simple nucleotide polymorphisms. Long-read technologies require pure high molecular weight DNA as an input for sequencing. Here, we describe a DNA extraction protocol for rust spores that yields pure double-stranded DNA molecules with molecular weight of >50 kilo-base pairs (kbp). The isolated DNA is of sufficient purity for PacBio long-read sequencing, but may require additional purification for other sequencing technologies such as Nanopore and 10× Genomics.

Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing

DEFF Research Database (Denmark)

Vinner, Lasse; Mourier, Tobias; Friis-Nielsen, Jens

2015-01-01

-stringency in-solution hybridization method enables detection of discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral...... sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer...

High Performance Systolic Array Core Architecture Design for DNA Sequencer

Directory of Open Access Journals (Sweden)

Saiful Nurdin Dayana

2018-01-01

Full Text Available This paper presents a high performance systolic array (SA core architecture design for Deoxyribonucleic Acid (DNA sequencer. The core implements the affine gap penalty score Smith-Waterman (SW algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA and improved in the core area by 90% reduction.

Exploring sequence characteristics related to high-level production of secreted proteins in Aspergillus niger.

Directory of Open Access Journals (Sweden)

Bastiaan A van den Berg

Full Text Available Protein sequence features are explored in relation to the production of over-expressed extracellular proteins by fungi. Knowledge on features influencing protein production and secretion could be employed to improve enzyme production levels in industrial bioprocesses via protein engineering. A large set, over 600 homologous and nearly 2,000 heterologous fungal genes, were overexpressed in Aspergillus niger using a standardized expression cassette and scored for high versus no production. Subsequently, sequence-based machine learning techniques were applied for identifying relevant DNA and protein sequence features. The amino-acid composition of the protein sequence was found to be most predictive and interpretation revealed that, for both homologous and heterologous gene expression, the same features are important: tyrosine and asparagine composition was found to have a positive correlation with high-level production, whereas for unsuccessful production, contributions were found for methionine and lysine composition. The predictor is available online at http://bioinformatics.tudelft.nl/hipsec. Subsequent work aims at validating these findings by protein engineering as a method for increasing expression levels per gene copy.

A problem with double-blind photospread procedures: photospread administrators use one eyewitness's confidence to influence the identification of another eyewitness.

Science.gov (United States)

Douglass, Amy Bradfield; Smith, Caroline; Fraser-Thill, Rebecca

2005-10-01

In Experiment 1, photospread administrators (PAs, N = 50) showed a target-absent photospread to a confederate eyewitness (CW), who was randomly assigned to identify one photo with either high or low confidence. PAs subsequently administered the same target-absent photospread to participant eyewitnesses (PWs, N = 50), all of whom had viewed a live staged crime 1 week earlier. CWs were rated by the PAs as significantly more confident in the high-confidence condition versus low-confidence condition. More importantly, the confidence of the CW affected the identification decision of the PW. In the low-confidence condition, the photo identified by the CW was identified by the PW significantly more than the other photos; there was no significant difference in photo choice in the high-confidence condition. In spite of the obvious influence exerted in the low-confidence condition, observers were not able to detect bias in the photospread procedures. A second experiment was conducted to test a post-hoc explanation for the results of Experiment 1: PAs exerted influence in the low-confidence condition because they perceived the task as more difficult for the eyewitness than in the high-confidence condition. Independent observers (N = 84) rated the difficulty of the confederate's task as higher in the low-confidence condition compared with the high-confidence condition, suggesting that expectations of task difficulty might be driving the effect observed in Experiment 1. Results support recommendations for double-blind photospreads and emphasize that the same investigator should not administer photo lineups to multiple eyewitnesses in an investigation.

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Science.gov (United States)

Edgar, Robert C

2004-01-01

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

Assessment of risk to wildlife from ionising radiation: can initial screening tiers be used with a high level of confidence?

International Nuclear Information System (INIS)

Beresford, N A; Barnett, C L; Hosseini, A; Brown, J E; Cailes, C; Copplestone, D; Beaugelin-Seiller, K

2010-01-01

A number of models are being used to assess the potential environmental impact of releases of radioactivity. These often use a tiered assessment structure whose first tier is designed to be highly conservative and simple to use. An aim of using this initial tier is to identify sites of negligible concern and to remove them from further consideration with a high degree of confidence. In this paper we compare the screening assessment outputs of three freely available models. The outputs of these models varied considerably in terms of estimated risk quotient (RQ) and the radionuclide-organism combinations identified as being the most limiting. A number of factors are identified as contributing to this variability: values of transfer parameters (concentration ratios and K d ) used; organisms considered; different input options and how these are utilised in the assessment; assumptions as regards secular equilibrium; geometries and exposure scenarios. This large variation in RQ values between models means that the level of confidence required by users is not achieved. We recommend that the factors contributing to the variation in screening assessments be subjected to further investigation so that they can be more fully understood and assessors (and those reviewing assessment outputs) can better justify and evaluate the results obtained.

Errors and Predictors of Confidence in Condom Use amongst Young Australians Attending a Music Festival.

Science.gov (United States)

Hall, Karina M; Brieger, Daniel G; De Silva, Sukhita H; Pfister, Benjamin F; Youlden, Daniel J; John-Leader, Franklin; Pit, Sabrina W

2016-01-01

Objectives . To determine the confidence and ability to use condoms correctly and consistently and the predictors of confidence in young Australians attending a festival. Methods . 288 young people aged 18 to 29 attending a mixed-genre music festival completed a survey measuring demographics, self-reported confidence using condoms, ability to use condoms, and issues experienced when using condoms in the past 12 months. Results . Self-reported confidence using condoms was high (77%). Multivariate analyses showed confidence was associated with being male ( P < 0.001) and having had five or more lifetime sexual partners ( P = 0.038). Reading packet instructions was associated with increased condom use confidence ( P = 0.011). Amongst participants who had used a condom in the last year, 37% had experienced the condom breaking and 48% had experienced the condom slipping off during intercourse and 51% when withdrawing the penis after sex. Conclusion . This population of young people are experiencing high rates of condom failures and are using them inconsistently or incorrectly, demonstrating the need to improve attitudes, behaviour, and knowledge about correct and consistent condom usage. There is a need to empower young Australians, particularly females, with knowledge and confidence in order to improve condom use self-efficacy.

Application of high-throughput sequencing in understanding human oral microbiome related with health and disease

OpenAIRE

Chen, Hui; Jiang, Wen

2014-01-01

The oral microbiome is one of most diversity habitat in the human body and they are closely related with oral health and disease. As the technique developing,, high throughput sequencing has become a popular approach applied for oral microbial analysis. Oral bacterial profiles have been studied to explore the relationship between microbial diversity and oral diseases such as caries and periodontal disease. This review describes the application of high-throughput sequencing for characterizati...

Communicating Low-Probability High-Consequence Risk, Uncertainty and Expert Confidence: Induced Seismicity of Deep Geothermal Energy and Shale Gas.

Science.gov (United States)

Knoblauch, Theresa A K; Stauffacher, Michael; Trutnevyte, Evelina

2018-04-01

Subsurface energy activities entail the risk of induced seismicity including low-probability high-consequence (LPHC) events. For designing respective risk communication, the scientific literature lacks empirical evidence of how the public reacts to different written risk communication formats about such LPHC events and to related uncertainty or expert confidence. This study presents findings from an online experiment (N = 590) that empirically tested the public's responses to risk communication about induced seismicity and to different technology frames, namely deep geothermal energy (DGE) and shale gas (between-subject design). Three incrementally different formats of written risk communication were tested: (i) qualitative, (ii) qualitative and quantitative, and (iii) qualitative and quantitative with risk comparison. Respondents found the latter two the easiest to understand, the most exact, and liked them the most. Adding uncertainty and expert confidence statements made the risk communication less clear, less easy to understand and increased concern. Above all, the technology for which risks are communicated and its acceptance mattered strongly: respondents in the shale gas condition found the identical risk communication less trustworthy and more concerning than in the DGE conditions. They also liked the risk communication overall less. For practitioners in DGE or shale gas projects, the study shows that the public would appreciate efforts in describing LPHC risks with numbers and optionally risk comparisons. However, there seems to be a trade-off between aiming for transparency by disclosing uncertainty and limited expert confidence, and thereby decreasing clarity and increasing concern in the view of the public. © 2017 Society for Risk Analysis.

Changing job seekers' image perceptions during recruitment visits: the moderating role of belief confidence.

Science.gov (United States)

Slaughter, Jerel E; Cable, Daniel M; Turban, Daniel B

2014-11-01

The purpose of this study was to understand how an important construct in social psychology-confidence in one's beliefs-could both (a) influence the effectiveness of organizations' recruiting processes and (b) be changed during recruitment. Using a sample of recruits to a branch of the United States military, the authors studied belief confidence before and after recruits' formal visits to the organization's recruiting stations. Personal sources of information had a stronger influence on recruits' belief confidence than impersonal sources. Moreover, recruits' confidence in their initial beliefs affected how perceptions of the recruiter changed their employer images. Among participants with low-initial confidence, the relation between recruitment experiences and employer images was positive and linear across the whole range of recruitment experiences. Among recruits with high-initial confidence, however, the recruitment experience-image relationship was curvilinear, such that recruitment experiences were related to images only at more positive recruitment experiences. The relationship between recruitment experiences and changes in belief confidence was also curvilinear, such that only more positive recruitment experiences led to changes in confidence. These results indicate not only that belief confidence influences the effectiveness of recruiting efforts but also that recruiting efforts can influence belief confidence. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

Confidence bands for inverse regression models

International Nuclear Information System (INIS)

Birke, Melanie; Bissantz, Nicolai; Holzmann, Hajo

2010-01-01

We construct uniform confidence bands for the regression function in inverse, homoscedastic regression models with convolution-type operators. Here, the convolution is between two non-periodic functions on the whole real line rather than between two periodic functions on a compact interval, since the former situation arguably arises more often in applications. First, following Bickel and Rosenblatt (1973 Ann. Stat. 1 1071–95) we construct asymptotic confidence bands which are based on strong approximations and on a limit theorem for the supremum of a stationary Gaussian process. Further, we propose bootstrap confidence bands based on the residual bootstrap and prove consistency of the bootstrap procedure. A simulation study shows that the bootstrap confidence bands perform reasonably well for moderate sample sizes. Finally, we apply our method to data from a gel electrophoresis experiment with genetically engineered neuronal receptor subunits incubated with rat brain extract

Impact of an Advanced Cardiac Life Support Simulation Laboratory Experience on Pharmacy Student Confidence and Knowledge.

Science.gov (United States)

Maxwell, Whitney D; Mohorn, Phillip L; Haney, Jason S; Phillips, Cynthia M; Lu, Z Kevin; Clark, Kimberly; Corboy, Alex; Ragucci, Kelly R

2016-10-25

Objective. To assess the impact of an advanced cardiac life support (ACLS) simulation on pharmacy student confidence and knowledge. Design. Third-year pharmacy students participated in a simulation experience that consisted of team roles training, high-fidelity ACLS simulations, and debriefing. Students completed a pre/postsimulation confidence and knowledge assessment. Assessment. Overall, student knowledge assessment scores and student confidence scores improved significantly. Student confidence and knowledge changes from baseline were not significantly correlated. Conversely, a significant, weak positive correlation between presimulation studying and both presimulation confidence and presimulation knowledge was discovered. Conclusions. Overall, student confidence and knowledge assessment scores in ACLS significantly improved from baseline; however, student confidence and knowledge were not significantly correlated.

Targeted DNA Methylation Analysis by High Throughput Sequencing in Porcine Peri-attachment Embryos

OpenAIRE

MORRILL, Benson H.; COX, Lindsay; WARD, Anika; HEYWOOD, Sierra; PRATHER, Randall S.; ISOM, S. Clay

2013-01-01

Abstract The purpose of this experiment was to implement and evaluate the effectiveness of a next-generation sequencing-based method for DNA methylation analysis in porcine embryonic samples. Fourteen discrete genomic regions were amplified by PCR using bisulfite-converted genomic DNA derived from day 14 in vivo-derived (IVV) and parthenogenetic (PA) porcine embryos as template DNA. Resulting PCR products were subjected to high-throughput sequencing using the Illumina Genome Analyzer IIx plat...

Nuclear power: restoring public confidence

International Nuclear Information System (INIS)

Arnold, L.

1986-01-01

The paper concerns a one day conference on nuclear power organised by the Centre for Science Studies and Science Policy, Lancaster, April 1986. Following the Chernobyl reactor accident, the conference concentrated on public confidence in nuclear power. Causes of lack of public confidence, public perceptions of risk, and the effect of Chernobyl in the United Kingdom, were all discussed. A Select Committee on the Environment examined the problems of radioactive waste disposal. (U.K.)

Effect of False Confidence on Asset Allocation Decisions of Households

Directory of Open Access Journals (Sweden)

Swarn Chatterjee

2014-01-01

Full Text Available This paper investigates whether false confidence, as characterized by a high level of personal mastery and a low level of intelligence (IQ, results in frequent investor trading and subsequent investor wealth erosion across time. Using the National Longitudinal Survey (NLSY79, change in wealth and asset allocation across time is modeled as a function of various behavioral, socio-economic and demographic variables drawn from prior literature.  Findings of this research reveal that false confidence is indeed a predictor of trading activity in individual investment assets, and it also has a negative impact on individual wealth creation across time.

Confidence assessment. Site descriptive modelling SDM-Site Forsmark

International Nuclear Information System (INIS)

2008-09-01

The objective of this report is to assess the confidence that can be placed in the Forsmark site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Forsmark). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface based investigations or more usefully by explorations underground made during construction of the repository. The confidence in the Forsmark site descriptive model, based on the data available at the conclusion of the surface-based site investigations, have been assessed by exploring: Confidence in the site characterisation data base; Key remaining issues and their handling; Handling of alternative models; Consistency between disciplines; and, Main reasons for confidence and lack of confidence in the model. It is generally found that the key aspects of importance for safety assessment and repository engineering of the Forsmark site descriptive model are associated with a high degree of confidence. Because of the robust geological model that describes the site, the overall confidence in Forsmark site descriptive model is judged to be high. While some aspects have lower confidence this lack of confidence is handled by providing wider uncertainty ranges, bounding estimates and/or alternative models. Most, but not all, of the low confidence aspects have little impact on repository engineering design or for long-term safety. Poor precision in the measured data are judged to have limited impact on uncertainties on the site descriptive model, with the exceptions of inaccuracy in determining the position of some boreholes at depth in 3-D space, as well as the poor precision of the orientation of BIPS images in some boreholes, and the poor precision of stress data determined by overcoring at the locations where the pre

Rapid detection of SMARCB1 sequence variation using high resolution melting

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Ashley David M

2009-12-01

Full Text Available Abstract Background Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM, for detecting sequence variations in SMARCB1. Methods Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. Results The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4% showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA. A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. Conclusions This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to

Rapid detection of SMARCB1 sequence variation using high resolution melting

International Nuclear Information System (INIS)

Dagar, Vinod; Chow, Chung-Wo; Ashley, David M; Algar, Elizabeth M

2009-01-01

Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1. Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening

Exploring fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing

Science.gov (United States)

Zhang, Xiao-Yong; Wang, Guang-Hua; Xu, Xin-Ya; Nong, Xu-Hua; Wang, Jie; Amin, Muhammad; Qi, Shu-Hua

2016-10-01

The present study investigated the fungal diversity in four different deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS1). A total of 40,297 fungal ITS1 sequences clustered into 420 operational taxonomic units (OTUs) with 97% sequence similarity and 170 taxa were recovered from these sediments. Most ITS1 sequences (78%) belonged to the phylum Ascomycota, followed by Basidiomycota (17.3%), Zygomycota (1.5%) and Chytridiomycota (0.8%), and a small proportion (2.4%) belonged to unassigned fungal phyla. Compared with previous studies on fungal diversity of sediments from deep-sea environments by culture-dependent approach and clone library analysis, the present result suggested that Illumina sequencing had been dramatically accelerating the discovery of fungal community of deep-sea sediments. Furthermore, our results revealed that Sordariomycetes was the most diverse and abundant fungal class in this study, challenging the traditional view that the diversity of Sordariomycetes phylotypes was low in the deep-sea environments. In addition, more than 12 taxa accounted for 21.5% sequences were found to be rarely reported as deep-sea fungi, suggesting the deep-sea sediments from Okinawa Trough harbored a plethora of different fungal communities compared with other deep-sea environments. To our knowledge, this study is the first exploration of the fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing.

Markovian Model in High Order Sequence Prediction From Log-Motif Patterns in Agbada Paralic Section, Niger Delta, Nigeria

International Nuclear Information System (INIS)

Olabode, S. O.; Adekoya, J. A.

2002-01-01

Markovian model in the elucidation of high order sequence was applied to repetitive events of regressive and transgressive phases in the Agbada paralic section Niger Delta. The repetitive events are made up of delta front, delta topset and fluvio-deltaic sediments. The sediments consist of sands, sandstones, siltstones and shales in various proportions. Five wells: MN1, AA1, NP2, NP6 and NP8 were studied.Summary of biostratigraphic report and well log-motif patterns was used to delineate the third order depositional sequences in the wells.Various Markovian properties - observed transition frequency matrix, observed transition probability matrix, fixed probability vector, expected random matrix (randomised transition matrix) and difference matrix were determined for stacked high order sequence (high frequency cyclic events) nested within the third-order sequences using the log-motif patterns for the various sand bodies and shales. Flow diagrams were constructed for each of the depositional sequences to know the likely occurrence of number of cycles.Upward transition matrix between the log-motif patterns and flow diagram to elucidate cyclicity show that the overall regressive sequence of the Niger Delta has been modified by deltaic depositional elements and fluctuations in sea level. The predictions of higher order sequence within third order sequences from Markovian Properties provide good basis for correlation within the depositional sequences. The model has also been used to decipher the dominant depositional processes during the formation of the sequences. Discrete reservoir intervals and seal potentials within the sequences were also predicted from the flow diagrams constructed

Organic labbeling systems and consumer confidence

OpenAIRE

Sønderskov, Kim Mannemar; Daugbjerg, Carsten

2009-01-01

A research analysis suggests that a state certification and labelling system creates confidence in organic labelling systems and consequently green consumerism. Danish consumers have higher levels of confidence in the labelling system than consumers in countries where the state plays a minor role in labelling and certification.

False memories and memory confidence in borderline patients.

Science.gov (United States)

Schilling, Lisa; Wingenfeld, Katja; Spitzer, Carsten; Nagel, Matthias; Moritz, Steffen

2013-12-01

Mixed results have been obtained regarding memory in patients with borderline personality disorder (BPD). Prior reports and anecdotal evidence suggests that patients with BPD are prone to false memories but this assumption has to been put to firm empirical test, yet. Memory accuracy and confidence was assessed in 20 BPD patients and 22 healthy controls using a visual variant of the false memory (Deese-Roediger-McDermott) paradigm which involved a negative and a positive-valenced picture. Groups did not differ regarding veridical item recognition. Importantly, patients did not display more false memories than controls. At trend level, borderline patients rated more items as new with high confidence compared to healthy controls. The results tentatively suggest that borderline patients show uncompromised visual memory functions and display no increased susceptibility for distorted memories. Copyright © 2013 Elsevier Ltd. All rights reserved.

Identification of High Confidence Nuclear Forensics Signatures. Results of a Coordinated Research Project and Related Research

International Nuclear Information System (INIS)

2017-08-01

The results of a Coordinated Research Project and related research on the identification of high confidence nuclear forensic isotopic, chemical and physical data characteristics, or signatures, provides information on signatures that can help identify the origin and history of nuclear and other radioactive material encountered out of regulatory control. This research report compiles findings from investigations of materials obtained from throughout the nuclear fuel cycle to include radioactive sources. The report further provides recent results used to identify, analyse in the laboratory, predict and interpret these signatures relative to the requirements of a nuclear forensics examination. The report describes some of the controls on the incorporation and persistence of these signatures in these materials as well as their potential use in a national system of identification to include a national nuclear forensics library.

Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome.

Science.gov (United States)

Neuer-Nitsche, B; Lu, X N; Werner, D

1988-09-12

The major portion of the eukaryotic genome consists of various categories of repetitive DNA sequences which have been studied with respect to their base compositions, organizations, copy numbers, transcription and species specificities; their biological roles, however, are still unclear. A novel quality of a highly repetitive mouse DNA sequence is described which points to a functional role: All copies (approximately 50,000 per haploid genome) of this DNA sequence reside on genomic Alu I DNA fragments each associated with nuclear polypeptides that are not released from DNA by proteinase K, SDS and phenol extraction. By this quality the repetitive DNA sequence is classified as a member of the sub-set of DNA sequences involved in tight DNA-polypeptide complexes which have been previously shown to be components of the subnuclear structure termed 'nuclear matrix'. From these results it has to be concluded that the repetitive DNA sequence characterized in this report represents or comprises a signal for a large number of site specific attachment points of the mouse genome in the nuclear matrix.

Characterizing ncRNAs in human pathogenic protists using high-throughput sequencing technology

Directory of Open Access Journals (Sweden)

Lesley Joan Collins

2011-12-01

Full Text Available ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, snoRNAs and long ncRNAs on a genomic scale making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases.

Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology

Science.gov (United States)

Collins, Lesley Joan

2011-01-01

ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, small nucleolar RNAs (snoRNAs), and long ncRNAs on a genomic scale, making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational, and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases. PMID:22303390

Search for high confidence AGN candidates and its counterparts in the Fermi-LAT unassociated sample using machine learning

Energy Technology Data Exchange (ETDEWEB)

Einecke, Sabrina [Technical University Dortmund (Germany); Doert, Marlene [Ruhr-University Bochum (Germany)

2016-07-01

The third Fermi-LAT source catalog (3FGL) is the deepest all-sky survey in gamma-rays and comprises 3033 point sources. While for 2023 sources plausible associations have been found, 1010 remain unassociated. A search for active galactic nuclei (AGN) will help to reduce the number of unassociated sources, and will increase our knowledge of the population of gamma-ray emitting AGN. Several machine learning approaches applied to Fermi data have shown the capability of this method. The extension to multiwavelength data improves these studies, and at the same time offers the possibility to determine the most likely corresponding counterpart. As the 95% confidence region of the localization by the Fermi measurement is in the order of several arcminutes, generally multiple point sources at different wavelengths are located within this region and the association is ambiguous. To figure out the most likely counterpart, the associated sample is used to train machine learning classifiers as e.g. the random forest. Therefore, all possible combinations of the Fermi measurement and the measurements at a second wavelength are considered for a particular source. In this talk, the statistical model to obtain high confidence AGN counterpart candidates is described as well as the validation of the model to estimate the performance.

Applications of high-throughput sequencing to chromatin structure and function in mammals

OpenAIRE

Dunham, Ian

2009-01-01

High-throughput DNA sequencing approaches have enabled direct interrogation of chromatin samples from mammalian cells. We are beginning to develop a genome-wide description of nuclear function during development, but further data collection, refinement, and integration are needed.

Metacognitive Confidence Increases with, but Does Not Determine, Visual Perceptual Learning.

Science.gov (United States)

Zizlsperger, Leopold; Kümmel, Florian; Haarmeier, Thomas

2016-01-01

While perceptual learning increases objective sensitivity, the effects on the constant interaction of the process of perception and its metacognitive evaluation have been rarely investigated. Visual perception has been described as a process of probabilistic inference featuring metacognitive evaluations of choice certainty. For visual motion perception in healthy, naive human subjects here we show that perceptual sensitivity and confidence in it increased with training. The metacognitive sensitivity-estimated from certainty ratings by a bias-free signal detection theoretic approach-in contrast, did not. Concomitant 3Hz transcranial alternating current stimulation (tACS) was applied in compliance with previous findings on effective high-low cross-frequency coupling subserving signal detection. While perceptual accuracy and confidence in it improved with training, there were no statistically significant tACS effects. Neither metacognitive sensitivity in distinguishing between their own correct and incorrect stimulus classifications, nor decision confidence itself determined the subjects' visual perceptual learning. Improvements of objective performance and the metacognitive confidence in it were rather determined by the perceptual sensitivity at the outset of the experiment. Post-decision certainty in visual perceptual learning was neither independent of objective performance, nor requisite for changes in sensitivity, but rather covaried with objective performance. The exact functional role of metacognitive confidence in human visual perception has yet to be determined.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

Directory of Open Access Journals (Sweden)

Wang Nian

2012-08-01

Full Text Available Abstract Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.

Communication confidence in persons with aphasia.

Science.gov (United States)

Babbitt, Edna M; Cherney, Leora R

2010-01-01

Communication confidence is a construct that has not been explored in the aphasia literature. Recently, national and international organizations have endorsed broader assessment methods that address quality of life and include participation, activity, and impairment domains as well as psychosocial areas. Individuals with aphasia encounter difficulties in all these areas on a daily basis in living with a communication disorder. Improvements are often reflected in narratives that are not typically included in standard assessments. This article illustrates how a new instrument measuring communication confidence might fit into a broad assessment framework and discusses the interaction of communication confidence, autonomy, and self-determination for individuals living with aphasia.

Fragility estimation for seismically isolated nuclear structures by high confidence low probability of failure values and bi-linear regression

International Nuclear Information System (INIS)

Carausu, A.

1996-01-01

A method for the fragility estimation of seismically isolated nuclear power plant structure is proposed. The relationship between the ground motion intensity parameter (e.g. peak ground velocity or peak ground acceleration) and the response of isolated structures is expressed in terms of a bi-linear regression line, whose coefficients are estimated by the least-square method in terms of available data on seismic input and structural response. The notion of high confidence low probability of failure (HCLPF) value is also used for deriving compound fragility curves for coupled subsystems. (orig.)

On Bayesian treatment of systematic uncertainties in confidence interval calculation

CERN Document Server

Tegenfeldt, Fredrik

2005-01-01

In high energy physics, a widely used method to treat systematic uncertainties in confidence interval calculations is based on combining a frequentist construction of confidence belts with a Bayesian treatment of systematic uncertainties. In this note we present a study of the coverage of this method for the standard Likelihood Ratio (aka Feldman & Cousins) construction for a Poisson process with known background and Gaussian or log-Normal distributed uncertainties in the background or signal efficiency. For uncertainties in the signal efficiency of upto 40 % we find over-coverage on the level of 2 to 4 % depending on the size of uncertainties and the region in signal space. Uncertainties in the background generally have smaller effect on the coverage. A considerable smoothing of the coverage curves is observed. A software package is presented which allows fast calculation of the confidence intervals for a variety of assumptions on shape and size of systematic uncertainties for different nuisance paramete...

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

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Walid Mottawea

2018-05-01

Full Text Available Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella. In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S. Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.

High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs

DEFF Research Database (Denmark)

Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus

2016-01-01

Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards...

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.

Science.gov (United States)

Sasagawa, Yohei; Danno, Hiroki; Takada, Hitomi; Ebisawa, Masashi; Tanaka, Kaori; Hayashi, Tetsutaro; Kurisaki, Akira; Nikaido, Itoshi

2018-03-09

High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in the reaction steps make it possible to effectively convert initial reads to UMI counts, at a rate of 30-50%, and detect more genes. To demonstrate the power of Quartz-Seq2, we analyzed approximately 10,000 transcriptomes from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.

CONFIDENCE LEVELS AND/VS. STATISTICAL HYPOTHESIS TESTING IN STATISTICAL ANALYSIS. CASE STUDY

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ILEANA BRUDIU

2009-05-01

Full Text Available Estimated parameters with confidence intervals and testing statistical assumptions used in statistical analysis to obtain conclusions on research from a sample extracted from the population. Paper to the case study presented aims to highlight the importance of volume of sample taken in the study and how this reflects on the results obtained when using confidence intervals and testing for pregnant. If statistical testing hypotheses not only give an answer "yes" or "no" to some questions of statistical estimation using statistical confidence intervals provides more information than a test statistic, show high degree of uncertainty arising from small samples and findings build in the "marginally significant" or "almost significant (p very close to 0.05.

Sex differences in confidence influence patterns of conformity.

Science.gov (United States)

Cross, Catharine P; Brown, Gillian R; Morgan, Thomas J H; Laland, Kevin N

2017-11-01

Lack of confidence in one's own ability can increase the likelihood of relying on social information. Sex differences in confidence have been extensively investigated in cognitive tasks, but implications for conformity have not been directly tested. Here, we tested the hypothesis that, in a task that shows sex differences in confidence, an indirect effect of sex on social information use will also be evident. Participants (N = 168) were administered a mental rotation (MR) task or a letter transformation (LT) task. After providing an answer, participants reported their confidence before seeing the responses of demonstrators and being allowed to change their initial answer. In the MR, but not the LT, task, women showed lower levels of confidence than men, and confidence mediated an indirect effect of sex on the likelihood of switching answers. These results provide novel, experimental evidence that confidence is a general explanatory mechanism underpinning susceptibility to social influences. Our results have implications for the interpretation of the wider literature on sex differences in conformity. © 2016 The British Psychological Society.

Comprehensive Plan for Public Confidence in Nuclear Regulator

International Nuclear Information System (INIS)

Choi, Kwang Sik; Choi, Young Sung; Kim, Ho ki

2008-01-01

Public confidence in nuclear regulator has been discussed internationally. Public trust or confidence is needed for achieving regulatory goal of assuring nuclear safety to the level that is acceptable by the public or providing public ease for nuclear safety. In Korea, public ease or public confidence has been suggested as major policy goal in the 'Nuclear regulatory policy direction' annually announced. This paper reviews theory of trust, its definitions and defines nuclear safety regulation, elements of public trust or public confidence developed based on the study conducted so far. Public ease model developed and 10 measures for ensuring public confidence are also presented and future study directions are suggested

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

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Debnath Bhattacharyya

2013-01-01

Full Text Available 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.

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

Science.gov (United States)

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

The relationship between fundamental movement skill proficiency and physical self-confidence among adolescents.

Science.gov (United States)

McGrane, Bronagh; Belton, Sarahjane; Powell, Danielle; Issartel, Johann

2017-09-01

This study aims to assess fundamental movement skill (FMS) proficiency, physical self-confidence levels, and the relationship between these variables and gender differences among adolescents. Three hundred and ninety five adolescents aged 13.78 years (SD = ±1.2) from 20 schools were involved in this study. The Test of Gross Motor Development-2nd Edition (TGMD), TGMD-2 and Victorian Skills Manual were used to assess 15 FMS. Participants' physical self-confidence was also assessed using a valid skill-specific scale. A significant correlation was observed between FMS proficiency and physical self-confidence for females only (r = 0.305, P < 0.001). Males rated themselves as having significantly higher physical self-confidence levels than females (P = 0.001). Males scored significantly higher than females in FMS proficiency (P < 0.05), and the lowest physical self-confidence group were significantly less proficient at FMS than the medium (P < 0.001) and high physical self-confidence groups (P < 0.05). This information not only highlights those in need of assistance to develop their FMS but will also facilitate in the development of an intervention which aims to improve physical self-confidence and FMS proficiency.

Simultaneous confidence bands for the integrated hazard function

OpenAIRE

Dudek, Anna; Gocwin, Maciej; Leskow, Jacek

2006-01-01

The construction of the simultaneous confidence bands for the integrated hazard function is considered. The Nelson--Aalen estimator is used. The simultaneous confidence bands based on bootstrap methods are presented. Two methods of construction of such confidence bands are proposed. The weird bootstrap method is used for resampling. Simulations are made to compare the actual coverage probability of the bootstrap and the asymptotic simultaneous confidence bands. It is shown that the equal--tai...

Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data

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William H Thiel

2016-01-01

Full Text Available Development of RNA and DNA aptamers for diagnostic and therapeutic applications is a rapidly growing field. Aptamers are identified through iterative rounds of selection in a process termed SELEX (Systematic Evolution of Ligands by EXponential enrichment. High-throughput sequencing (HTS revolutionized the modern SELEX process by identifying millions of aptamer sequences across multiple rounds of aptamer selection. However, these vast aptamer HTS datasets necessitated bioinformatics techniques. Herein, we describe a semiautomated approach to analyze aptamer HTS datasets using the Galaxy Project, a web-based open source collection of bioinformatics tools that were originally developed to analyze genome, exome, and transcriptome HTS data. Using a series of Workflows created in the Galaxy webserver, we demonstrate efficient processing of aptamer HTS data and compilation of a database of unique aptamer sequences. Additional Workflows were created to characterize the abundance and persistence of aptamer sequences within a selection and to filter sequences based on these parameters. A key advantage of this approach is that the online nature of the Galaxy webserver and its graphical interface allow for the analysis of HTS data without the need to compile code or install multiple programs.

Formal Learning Sequences and Progression in the Studio: A Framework for Digital Design Education

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Pontus Wärnestål

2016-02-01

Full Text Available This paper examines how to leverage the design studio learning environment throughout long-term Digital Design education in order to support students to progress from tactical, well-defined, device-centric routine design, to confidently design sustainable solutions for strategic, complex, problems for a wide range of devices and platforms in the digital space. We present a framework derived from literature on design, creativity, and theories on learning that: (a implements a theory of formal learning sequences as a user-centered design process in the studio; and (b describes design challenge progressions in the design studio environment modeled in seven dimensions. The framework can be used as a tool for designing, evaluating, and communicating course progressions within – and between series of – design studio courses. This approach is evaluated by implementing a formal learning sequence framework in a series of design studio courses that progress in an undergraduate design-oriented Informatics program. Reflections from students, teachers, and external clients indicate high student motivation and learning goal achievement, high teacher satisfaction and skill development, and high satisfaction among external clients.

Screening of whole genome sequences identified high-impact variants for stallion fertility.

Science.gov (United States)

Schrimpf, Rahel; Gottschalk, Maren; Metzger, Julia; Martinsson, Gunilla; Sieme, Harald; Distl, Ottmar

2016-04-14

Stallion fertility is an economically important trait due to the increase of artificial insemination in horses. The availability of whole genome sequence data facilitates identification of rare high-impact variants contributing to stallion fertility. The aim of our study was to genotype rare high-impact variants retrieved from next-generation sequencing (NGS)-data of 11 horses in order to unravel harmful genetic variants in large samples of stallions. Gene ontology (GO) terms and search results from public databases were used to obtain a comprehensive list of human und mice genes predicted to participate in the regulation of male reproduction. The corresponding equine orthologous genes were searched in whole genome sequence data of seven stallions and four mares and filtered for high-impact genetic variants using SnpEFF, SIFT and Polyphen 2 software. All genetic variants with the missing homozygous mutant genotype were genotyped on 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. Mixed linear model analysis was employed for an association analysis with de-regressed estimated breeding values of the paternal component of the pregnancy rate per estrus (EBV-PAT). We screened next generation sequenced data of whole genomes from 11 horses for equine genetic variants in 1194 human and mice genes involved in male fertility and linked through common gene ontology (GO) with male reproductive processes. Variants were filtered for high-impact on protein structure and validated through SIFT and Polyphen 2. Only those genetic variants were followed up when the homozygote mutant genotype was missing in the detection sample comprising 11 horses. After this filtering process, 17 single nucleotide polymorphism (SNPs) were left. These SNPs were genotyped in 337 fertile stallions of 19 breeds using KASP genotyping assays or PCR-RFLP. An association analysis in 216 Hanoverian stallions revealed a significant association of the splice-site disruption variant

High-fidelity target sequencing of individual molecules identified using barcode sequences: de novo detection and absolute quantitation of mutations in plasma cell-free DNA from cancer patients.

Science.gov (United States)

Kukita, Yoji; Matoba, Ryo; Uchida, Junji; Hamakawa, Takuya; Doki, Yuichiro; Imamura, Fumio; Kato, Kikuya

2015-08-01

Circulating tumour DNA (ctDNA) is an emerging field of cancer research. However, current ctDNA analysis is usually restricted to one or a few mutation sites due to technical limitations. In the case of massively parallel DNA sequencers, the number of false positives caused by a high read error rate is a major problem. In addition, the final sequence reads do not represent the original DNA population due to the global amplification step during the template preparation. We established a high-fidelity target sequencing system of individual molecules identified in plasma cell-free DNA using barcode sequences; this system consists of the following two steps. (i) A novel target sequencing method that adds barcode sequences by adaptor ligation. This method uses linear amplification to eliminate the errors introduced during the early cycles of polymerase chain reaction. (ii) The monitoring and removal of erroneous barcode tags. This process involves the identification of individual molecules that have been sequenced and for which the number of mutations have been absolute quantitated. Using plasma cell-free DNA from patients with gastric or lung cancer, we demonstrated that the system achieved near complete elimination of false positives and enabled de novo detection and absolute quantitation of mutations in plasma cell-free DNA. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

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Monson-Miller Jennifer

2012-02-01

Full Text Available Abstract Background The availability of low cost sequencing has spurred its application to discovery and typing of variation, including variation induced by mutagenesis. Mutation discovery is challenging as it requires a substantial amount of sequencing and analysis to detect very rare changes and distinguish them from noise. Also challenging are the cases when the organism of interest has not been sequenced or is highly divergent from the reference. Results We describe the development of a simple method for reduced representation sequencing. Input DNA was digested with a single restriction enzyme and ligated to Y adapters modified to contain a sequence barcode and to provide a compatible overhang for ligation. We demonstrated the efficiency of this method at SNP discovery using rice and arabidopsis. To test its suitability for the discovery of very rare SNP, one control and three mutagenized rice individuals (1, 5 and 10 mM sodium azide were used to prepare genomic libraries for Illumina sequencers by ligating barcoded adapters to NlaIII restriction sites. For genome-dependent discovery 15-30 million of 80 base reads per individual were aligned to the reference sequence achieving individual sequencing coverage from 7 to 15×. We identified high-confidence base changes by comparing sequences across individuals and identified instances consistent with mutations, i.e. changes that were found in a single treated individual and were solely GC to AT transitions. For genome-independent discovery 70-mers were extracted from the sequence of the control individual and single-copy sequence was identified by comparing the 70-mers across samples to evaluate copy number and variation. This de novo "genome" was used to align the reads and identify mutations as above. Covering approximately 1/5 of the 380 Mb genome of rice we detected mutation densities ranging from 0.6 to 4 per Mb of diploid DNA depending on the mutagenic treatment. Conclusions The

Maternal Confidence for Physiologic Childbirth: A Concept Analysis.

Science.gov (United States)

Neerland, Carrie E

2018-06-06

Confidence is a term often used in research literature and consumer media in relation to birth, but maternal confidence has not been clearly defined, especially as it relates to physiologic labor and birth. The aim of this concept analysis was to define maternal confidence in the context of physiologic labor and childbirth. Rodgers' evolutionary method was used to identify attributes, antecedents, and consequences of maternal confidence for physiologic birth. Databases searched included Ovid MEDLINE, CINAHL, PsycINFO, and Sociological Abstracts from the years 1995 to 2015. A total of 505 articles were retrieved, using the search terms pregnancy, obstetric care, prenatal care, and self-efficacy and the keyword confidence. Articles were identified for in-depth review and inclusion based on whether the term confidence was used or assessed in relationship to labor and/or birth. In addition, a hand search of the reference lists of the selected articles was performed. Twenty-four articles were reviewed in this concept analysis. We define maternal confidence for physiologic birth as a woman's belief that physiologic birth can be achieved, based on her view of birth as a normal process and her belief in her body's innate ability to birth, which is supported by social support, knowledge, and information founded on a trusted relationship with a maternity care provider in an environment where the woman feels safe. This concept analysis advances the concept of maternal confidence for physiologic birth and provides new insight into how women's confidence for physiologic birth might be enhanced during the prenatal period. Further investigation of confidence for physiologic birth across different cultures is needed to identify cultural differences in constructions of the concept. © 2018 by the American College of Nurse-Midwives.

Self-Confidence in the Hospitality Industry

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Michael Oshins

2014-02-01

Full Text Available Few industries rely on self-confidence to the extent that the hospitality industry does because guests must feel welcome and that they are in capable hands. This article examines the results of hundreds of student interviews with industry professionals at all levels to determine where the majority of the hospitality industry gets their self-confidence.

Confidence and trust: empirical investigations for the Netherlands and the financial sector

OpenAIRE

Mosch, Robert; Prast, Henriëtte

2010-01-01

This paper reviews the state of confidence and trust in the Netherlands, with special attention to the financial sector. An attempt has been made to identify the factors that determine individual trust and confidence and to uncover connections between the various variables. Based on surveys over the period 2003-2006, the data show that interpersonal trust in the Netherlands - the extent to which the Dutch trust each other - is high from both an international and an historical perspective. Peo...

Re-thinking accountability: trust versus confidence in medical practice.

Science.gov (United States)

Checkland, K; Marshall, M; Harrison, S

2004-04-01

In seeking to prevent a reoccurrence of scandals such as that involving cardiac surgery in Bristol, the UK government has adopted a model of regulation that uses rules and surveillance as a way of both improving the quality of care delivered and increasing confidence in healthcare institutions. However, this approach may actually act to reduce confidence and trust while also reducing the moral motivation of practitioners. Accountability in health care is discussed, and it is suggested that openness about the difficult dilemmas that arise when practitioners have a duty to be accountable to more than one audience may be an alternative means of restoring trust. A greater emphasis on the sharing of information between individual health professionals and their patients would increase trust and would allow patients to hold their doctors to account for the quality of care they receive. Concentrating more on developing trust by the sharing of information and less on the futile search for complete confidence in systems and rules may improve the quality of care delivered while also nurturing the moral motivation of professionals upon which the delivery of high quality health care depends.

Believing in "us": exploring leaders' capacity to enhance team confidence and performance by building a sense of shared social identity.

Science.gov (United States)

Fransen, Katrien; Haslam, S Alexander; Steffens, Niklas K; Vanbeselaere, Norbert; De Cuyper, Bert; Boen, Filip

2015-03-01

The present study examined the impact of athlete leaders' perceived confidence on their teammates' confidence and performance. Male basketball players (N = 102) participated in groups of 4. To manipulate leaders' team confidence, the appointed athlete leader of each newly formed basketball team (a confederate) expressed either high or low team confidence. The results revealed an effect of team confidence contagion such that team members had greater team confidence when the leader expressed high (rather than low) confidence in the team's success. Second, the present study sought to explain the mechanisms through which this contagion occurs. In line with the social identity approach to leadership, structural equation modeling demonstrated that this effect was partially mediated by team members' increased team identification. Third, findings indicated that when leaders expressed high team confidence, team members' performance increased during the test, but when leaders expressed low confidence, team members' performance decreased. Athlete leaders thus have the capacity to shape team members' confidence--and hence their performance--in both positive and negative ways. In particular, by showing that they believe in "our team," leaders are able not only to make "us" a psychological reality, but also to transform "us" into an effective operational unit. PsycINFO Database Record (c) 2015 APA, all rights reserved.

ADAM SMITH: THE INVISIBLE HAND OR CONFIDENCE

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Fernando Luis, Gache

2010-01-01

Full Text Available In 1776 Adam Smith raised the matter that an invisible hand was the one which moved the markets to obtain its efficiency. Despite in the present paper we are going to raise the hypothesis, that this invisible hand is in fact the confidence that each person feels when he is going to do business. That in addition it is unique, because it is different from the confidence of the others and that is a variable nonlinear that essentially is ligatured to respective personal histories. For that we are going to take as its bases the paper by Leopoldo Abadía (2009, with respect to the financial economy crisis that happened in 2007-2008, to evidence the form in which confidence operates. Therefore the contribution that we hope to do with this paper is to emphasize that, the level of confidence of the different actors, is the one which really moves the markets, (therefore the economy and that the crisis of the subprime mortgages is a confidence crisis at world-wide level.

Exome Sequencing Identifies Potential Risk Variants for Mendelian Disorders at High Prevalence in Qatar

Science.gov (United States)

Rodriguez-Flores, Juan L.; Fakhro, Khalid; Hackett, Neil R.; Salit, Jacqueline; Fuller, Jennifer; Agosto-Perez, Francisco; Gharbiah, Maey; Malek, Joel A.; Zirie, Mahmoud; Jayyousi, Amin; Badii, Ramin; Al-Marri, Ajayeb Al-Nabet; Chouchane, Lotfi; Stadler, Dora J.; Hunter-Zinck, Haley; Mezey, Jason G.; Crystal, Ronald G.

2013-01-01

Exome sequencing of families of related individuals has been highly successful in identifying genetic polymorphisms responsible for Mendelian disorders. Here, we demonstrate the value of the reverse approach, where we use exome sequencing of a sample of unrelated individuals to analyze allele frequencies of known causal mutations for Mendelian diseases. We sequenced the exomes of 100 individuals representing the three major genetic subgroups of the Qatari population (Q1 Bedouin, Q2 Persian-South Asian, Q3 African) and identified 37 variants in 33 genes with effects on 36 clinically significant Mendelian diseases. These include variants not present in 1000 Genomes and variants at high frequency when compared to 1000 Genomes populations. Several of these Mendelian variants were only segregating in one Qatari subpopulation, where the observed subpopulation specificity trends were confirmed in an independent population of 386 Qataris. Pre-marital genetic screening in Qatar tests for only 4 out of the 37, such that this study provides a set of Mendelian disease variants with potential impact on the epidemiological profile of the population that could be incorporated into the testing program if further experimental and clinical characterization confirms high penetrance. PMID:24123366

High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic.

Science.gov (United States)

Sealfon, Rachel; Gire, Stephen; Ellis, Crystal; Calderwood, Stephen; Qadri, Firdausi; Hensley, Lisa; Kellis, Manolis; Ryan, Edward T; LaRocque, Regina C; Harris, Jason B; Sabeti, Pardis C

2012-09-11

Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x); four of the seven isolates were previously sequenced. Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961), 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways. Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic

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Sealfon Rachel

2012-09-01

Full Text Available Abstract Background Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x; four of the seven isolates were previously sequenced. Results Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961, 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways. Conclusions Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

Bronchoscopic Lung Cryobiopsy Increases Diagnostic Confidence in the Multidisciplinary Diagnosis of Idiopathic Pulmonary Fibrosis.

Science.gov (United States)

Tomassetti, Sara; Wells, Athol U; Costabel, Ulrich; Cavazza, Alberto; Colby, Thomas V; Rossi, Giulio; Sverzellati, Nicola; Carloni, Angelo; Carretta, Elisa; Buccioli, Matteo; Tantalocco, Paola; Ravaglia, Claudia; Gurioli, Christian; Dubini, Alessandra; Piciucchi, Sara; Ryu, Jay H; Poletti, Venerino

2016-04-01

Surgical lung biopsy is often required for a confident multidisciplinary diagnosis of idiopathic pulmonary fibrosis (IPF). Alternative, less-invasive biopsy methods, such as bronchoscopic lung cryobiopsy (BLC), are highly desirable. To address the impact of BLC on diagnostic confidence in the multidisciplinary diagnosis of IPF. In this cross-sectional study we selected 117 patients with fibrotic interstitial lung disease without a typical usual interstitial pneumonia pattern on high-resolution computed tomography. All cases underwent lung biopsies: 58 were BLC, and 59 were surgical lung biopsy (SLB). Two clinicians, two radiologists, and two pathologists sequentially reviewed clinical-radiologic findings and biopsy results, recording at each step in the process their diagnostic impressions and confidence levels. We observed a major increase in diagnostic confidence after the addition of BLC, similar to SLB (from 29 to 63%, P = 0.0003 and from 30 to 65%, P = 0.0016 of high confidence IPF diagnosis, in the BLC group and SLB group, respectively). The overall interobserver agreement in IPF diagnosis was similar for both approaches (BLC overall kappa, 0.96; SLB overall kappa, 0.93). IPF was the most frequent diagnosis (50 and 39% in the BLC and SLB group, respectively; P = 0.23). After the addition of histopathologic information, 17% of cases in the BLC group and 19% of cases in the SLB group, mostly idiopathic nonspecific interstitial pneumonia and hypersensitivity pneumonitis, were reclassified as IPF. BLC is a new biopsy method that has a meaningful impact on diagnostic confidence in the multidisciplinary diagnosis of interstitial lung disease and may prove useful in the diagnosis of IPF. This study provides a robust rationale for future studies investigating the diagnostic accuracy of BLC compared with SLB.

Study on high-resolution sequence stratigraphy framework of uranium-hosting rock series in Qianjiadian sag

International Nuclear Information System (INIS)

Chen Fanghong; Zhang Mingyu

2005-01-01

The ore-hosting Yaojia Formation is composed of a set of braided stream medium-fine grained sediments. Guided by the basic theory of high-resolution sequence stratigraphy, and based on the core observation, the analysis of chemical composition of rocks, and data of natural potential logging and apparent resistivity logging, the authors have set up the high-resolution sequence stratigraphy framework of the ore-hosting Yaojia Formation, and discussed the relation of the stratigraphic structure of the middle cycle, as well as the paleotopography, the micro-facies to the formation of uranium deposit. (authors)

A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites

DEFF Research Database (Denmark)

Uren, Anthony G; Mikkers, Harald; Kool, Jaap

2009-01-01

sites has been a major limitation to performing screens on this scale. Here we present a method for the high-throughput isolation of insertion sites using a highly efficient splinkerette-PCR method coupled with capillary or 454 sequencing. This protocol includes a description of the procedure for DNA......Insertional mutagens such as viruses and transposons are a useful tool for performing forward genetic screens in mice to discover cancer genes. These screens are most effective when performed using hundreds of mice; however, until recently, the cost-effective isolation and sequencing of insertion...

High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

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Weiguo Hou

2018-05-01

Full Text Available Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length encoding the cyanophage gp23 major capsid protein (MCP. Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92% belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts

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Ouyang Shu

2005-09-01

Full Text Available Abstract Background The Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation across the Solanaceae. The availability of large collections of Expressed Sequence Tags (ESTs for the Solanaceae now provides the opportunity to assess sequence conservation and divergence on a genomic scale. Results All available ESTs and Expressed Transcripts (ETs, 449,224 sequences for six Solanaceae species (potato, tomato, pepper, petunia, tobacco and Nicotiana benthamiana, were clustered and assembled into gene indices. Examination of gene ontologies revealed that the transcripts within the gene indices encode a similar suite of biological processes. Although the ESTs and ETs were derived from a variety of tissues, 55–81% of the sequences had significant similarity at the nucleotide level with sequences among the six species. Putative orthologs could be identified for 28–58% of the sequences. This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species. 16–19% of the transcripts within the six Solanaceae gene indices did not have matches among Solanaceae, Arabidopsis, rice or 21 other plant gene indices. Conclusion Results from this genome scale analysis confirmed a high level of sequence conservation at the nucleotide level of the coding sequence among Solanaceae. Additionally, the results indicated that part of the Solanaceae transcriptome is likely to be unique for each species.

The cognitive approach on self-confidence of the girl students with academic failure

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Ommolbanin Sheibani

2011-01-01

Full Text Available Background: The consequences of behavior attributed to external factors as chance, luck or help of other people are effective on one's self confidence and educational improvement. The aim of this study is to assess the effect of teaching “locus of control” on the basis of cognitive approach on Yazd high school students' self confidence.Materials and Method: This descriptive analytic research is done as an experimental project by using pre-test and post-test method on 15 first-grade high school students in Yazd city during 1387-88 educational year. The participants were chosen by the multistage cluster random sampling. Fifteen students were also chosen as the control group. The instruments used in this research were Eysenk self confidence test and also the “locus of control” teaching program. A t-test was used for the statistical analysis of the present study.Results: The results of the statistical analyses showed that there is a significant difference between the experimental and control group (p=0.01 in increasing the self confidence. Also the results of the t-test revealed that there is no significant difference in the educational improvement of the experimental group before and after teaching “locus of control”.Conclusion: According to this study, teaching “locus of control” on the basis of the cognitive approach has a significant effect on the self confidence but it doesn't have any positive effect on educational improvement

Trust, confidence, and the 2008 global financial crisis.

Science.gov (United States)

Earle, Timothy C

2009-06-01

The 2008 global financial crisis has been compared to a "once-in-a-century credit tsunami," a disaster in which the loss of trust and confidence played key precipitating roles and the recovery from which will require the restoration of these crucial factors. Drawing on the analogy between the financial crisis and environmental and technological hazards, recent research on the role of trust and confidence in the latter is used to provide a perspective on the former. Whereas "trust" and "confidence" are used interchangeably and without explicit definition in most discussions of the financial crisis, this perspective uses the TCC model of cooperation to clearly distinguish between the two and to demonstrate how this distinction can lead to an improved understanding of the crisis. The roles of trust and confidence-both in precipitation and in possible recovery-are discussed for each of the three major sets of actors in the crisis, the regulators, the banks, and the public. The roles of trust and confidence in the larger context of risk management are also examined; trust being associated with political approaches, confidence with technical. Finally, the various stances that government can take with regard to trust-such as supportive or skeptical-are considered. Overall, it is argued that a clear understanding of trust and confidence and a close examination of the specific, concrete circumstances of a crisis-revealing when either trust or confidence is appropriate-can lead to useful insights for both recovery and prevention of future occurrences.

Scoring protein relationships in functional interaction networks predicted from sequence data.

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Gaston K Mazandu

Full Text Available UNLABELLED: The abundance of diverse biological data from various sources constitutes a rich source of knowledge, which has the power to advance our understanding of organisms. This requires computational methods in order to integrate and exploit these data effectively and elucidate local and genome wide functional connections between protein pairs, thus enabling functional inferences for uncharacterized proteins. These biological data are primarily in the form of sequences, which determine functions, although functional properties of a protein can often be predicted from just the domains it contains. Thus, protein sequences and domains can be used to predict protein pair-wise functional relationships, and thus contribute to the function prediction process of uncharacterized proteins in order to ensure that knowledge is gained from sequencing efforts. In this work, we introduce information-theoretic based approaches to score protein-protein functional interaction pairs predicted from protein sequence similarity and conserved protein signature matches. The proposed schemes are effective for data-driven scoring of connections between protein pairs. We applied these schemes to the Mycobacterium tuberculosis proteome to produce a homology-based functional network of the organism with a high confidence and coverage. We use the network for predicting functions of uncharacterised proteins. AVAILABILITY: Protein pair-wise functional relationship scores for Mycobacterium tuberculosis strain CDC1551 sequence data and python scripts to compute these scores are available at http://web.cbio.uct.ac.za/~gmazandu/scoringschemes.

Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS).

Science.gov (United States)

Lou, Tzu-Fang; Weidmann, Chase A; Killingsworth, Jordan; Tanaka Hall, Traci M; Goldstrohm, Aaron C; Campbell, Zachary T

2017-04-15

RNA-binding proteins (RBPs) collaborate to control virtually every aspect of RNA function. Tremendous progress has been made in the area of global assessment of RBP specificity using next-generation sequencing approaches both in vivo and in vitro. Understanding how protein-protein interactions enable precise combinatorial regulation of RNA remains a significant problem. Addressing this challenge requires tools that can quantitatively determine the specificities of both individual proteins and multimeric complexes in an unbiased and comprehensive way. One approach utilizes in vitro selection, high-throughput sequencing, and sequence-specificity landscapes (SEQRS). We outline a SEQRS experiment focused on obtaining the specificity of a multi-protein complex between Drosophila RBPs Pumilio (Pum) and Nanos (Nos). We discuss the necessary controls in this type of experiment and examine how the resulting data can be complemented with structural and cell-based reporter assays. Additionally, SEQRS data can be integrated with functional genomics data to uncover biological function. Finally, we propose extensions of the technique that will enhance our understanding of multi-protein regulatory complexes assembled onto RNA. Copyright © 2016 Elsevier Inc. All rights reserved.

CoLIde: A bioinformatics tool for CO-expression based small RNA Loci Identification using high-throughput sequencing data

OpenAIRE

Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

2013-01-01

Small RNAs (sRNAs) are 20–25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the...

The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains

DEFF Research Database (Denmark)

Nistelberger, H. M.; Smith, O.; Wales, Nathan

2016-01-01

. It has been suggested that high-throughput sequencing (HTS) technologies coupled with DNA enrichment techniques may overcome some of these limitations. Here we report the findings of HTS and target enrichment on four important archaeological crops (barley, grape, maize and rice) performed in three...... lightly-charred maize cob. Even with target enrichment, this sample failed to yield adequate data required to address fundamental questions in archaeology and biology. We further reanalysed part of an existing dataset on charred plant material, and found all purported endogenous DNA sequences were likely...

Algorithms for mapping high-throughput DNA sequences

DEFF Research Database (Denmark)

Frellsen, Jes; Menzel, Peter; Krogh, Anders

2014-01-01

of data generation, new bioinformatics approaches have been developed to cope with the large amount of sequencing reads obtained in these experiments. In this chapter, we first introduce HTS technologies and their usage in molecular biology and discuss the problem of mapping sequencing reads...... to their genomic origin. We then in detail describe two approaches that offer very fast heuristics to solve the mapping problem in a feasible runtime. In particular, we describe the BLAT algorithm, and we give an introduction to the Burrows-Wheeler Transform and the mapping algorithms based on this transformation....

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

Science.gov (United States)

Adalsteinsson, Viktor A; Ha, Gavin; Freeman, Samuel S; Choudhury, Atish D; Stover, Daniel G; Parsons, Heather A; Gydush, Gregory; Reed, Sarah C; Rotem, Denisse; Rhoades, Justin; Loginov, Denis; Livitz, Dimitri; Rosebrock, Daniel; Leshchiner, Ignaty; Kim, Jaegil; Stewart, Chip; Rosenberg, Mara; Francis, Joshua M; Zhang, Cheng-Zhong; Cohen, Ofir; Oh, Coyin; Ding, Huiming; Polak, Paz; Lloyd, Max; Mahmud, Sairah; Helvie, Karla; Merrill, Margaret S; Santiago, Rebecca A; O'Connor, Edward P; Jeong, Seong H; Leeson, Rachel; Barry, Rachel M; Kramkowski, Joseph F; Zhang, Zhenwei; Polacek, Laura; Lohr, Jens G; Schleicher, Molly; Lipscomb, Emily; Saltzman, Andrea; Oliver, Nelly M; Marini, Lori; Waks, Adrienne G; Harshman, Lauren C; Tolaney, Sara M; Van Allen, Eliezer M; Winer, Eric P; Lin, Nancy U; Nakabayashi, Mari; Taplin, Mary-Ellen; Johannessen, Cory M; Garraway, Levi A; Golub, Todd R; Boehm, Jesse S; Wagle, Nikhil; Getz, Gad; Love, J Christopher; Meyerson, Matthew

2017-11-06

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

49 CFR 1103.23 - Confidences of a client.

Science.gov (United States)

2010-10-01

... 49 Transportation 8 2010-10-01 2010-10-01 false Confidences of a client. 1103.23 Section 1103.23... Responsibilities Toward A Client § 1103.23 Confidences of a client. (a) The practitioner's duty to preserve his client's confidence outlasts the practitioner's employment by the client, and this duty extends to the...

Curling for Confidence: Psychophysical Benefits of Curling for Older Adults.

Science.gov (United States)

Stone, Rachael C; Rakhamilova, Zina; Gage, William H; Baker, Joseph

2018-04-01

While physical activity is increasingly promoted for older adults, there is a paucity of sport promotion, which has distinct benefits from exercise and remains stereotypically associated with younger age. Curling is a moderately intense and safe sport that continues to gain popularity; however, no research has investigated psychophysical benefits of curling for older adults. The present study compares high-experience (20+ years; n = 63) and low-experience (<20 years; n = 53) curlers (aged 60+ years) with older adult noncurlers (n = 44) on measures of daily functionality, balance confidence, and perceptions of the aging process. While no significant differences were found between high- and low-experience curlers, any level of experience reported significantly better functionality, physical confidence, and aging attitudes compared to noncurlers (p ≤ .05). Although further research is necessary, the results suggest that any level of curling experience can enhance older adult psychophysical well-being, and warrants consideration for physical activity promotion and falls prevention programs.

Validation of self - confidence scale for clean urinary intermittent self - catheterization for patients and health - caregivers.

Science.gov (United States)

Biaziolo, Cintia Fernandes Baccarin; Mazzo, Alessandra; Martins, José Carlos Amado; Jorge, Beatriz Maria; Batista, Rui Carlos Negrão; Tucci, Silvio Júnior

2017-01-01

To validate a measurement instrument for clean intermittent self-catheterization for patients and health-caregivers. Methodological study of instrument validation performed at a Rehabilitation Center in a University hospital for patients submitted to clean intermittent self-catheterization and their health-caregivers. Following ethical criteria, data were collected during interview with nurse staff using a Likert question form containing 16 items with 5 points each: "no confidence"=1, "little confidence"=2, "confident"=3, "very confident"=4 and "completely confident"=5. Questionnaire called "Self- Confident Scale for Clean Intermittent Self-catheterization" (SCSCISC) was constructed based on literature and previously validated (appearance and content). The instrument was validated by 122 patients and 119 health-caregivers, in a proportion of 15:1. It was observed a good linear association and sample adequacy KMO 0.931 and X2=2881.63, p<0.001. Anti-image matrix showed high values at diagonal suggesting inclusion of all factors. Screen plot analysis showed a suggestion of items maintenance in a single set. It was observed high correlation of all items with the total, alpha-Cronbach 0.944. The same results were obtained in subsamples of patients and health-caregivers. The instrument showed good psychometric adequacy corroborating its use for evaluation of self-confidence during clean intermittent self-catheterization. Copyright® by the International Brazilian Journal of Urology.

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

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Yandell Mark

2010-07-01

Full Text Available Abstract Background In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24. The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda. Results We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (≥ 75% nucleotide identity elsewhere in the genome, but only 23% have identical copies (99% identity. The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome. Conclusions This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is

The effectiveness of collaborative problem based physics learning (CPBPL) model to improve student’s self-confidence on physics learning

Science.gov (United States)

Prahani, B. K.; Suprapto, N.; Suliyanah; Lestari, N. A.; Jauhariyah, M. N. R.; Admoko, S.; Wahyuni, S.

2018-03-01

In the previous research, Collaborative Problem Based Physic Learning (CPBPL) model has been developed to improve student’s science process skills, collaborative problem solving, and self-confidence on physics learning. This research is aimed to analyze the effectiveness of CPBPL model towards the improvement of student’s self-confidence on physics learning. This research implemented quasi experimental design on 140 senior high school students who were divided into 4 groups. Data collection was conducted through questionnaire, observation, and interview. Self-confidence measurement was conducted through Self-Confidence Evaluation Sheet (SCES). The data was analyzed using Wilcoxon test, n-gain, and Kruskal Wallis test. Result shows that: (1) There is a significant score improvement on student’s self-confidence on physics learning (α=5%), (2) n-gain value student’s self-confidence on physics learning is high, and (3) n-gain average student’s self-confidence on physics learning was consistent throughout all groups. It can be concluded that CPBPL model is effective to improve student’s self-confidence on physics learning.

High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

Science.gov (United States)

van Koningsbruggen, Silvana; Gierlinski, Marek; Schofield, Pietá; Martin, David; Barton, Geoffey J; Ariyurek, Yavuz; den Dunnen, Johan T; Lamond, Angus I

2010-11-01

The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs.

Science.gov (United States)

Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus; Morling, Niels

2016-01-01

Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates automation of DNA sequencing.

High levels of diversity characterize mandrill (Mandrillus sphinx) Mhc-DRB sequences.

Science.gov (United States)

Abbott, Kristin M; Wickings, E Jean; Knapp, Leslie A

2006-08-01

The major histocompatibility complex (MHC) is highly polymorphic in most primate species studied thus far. The rhesus macaque (Macaca mulatta) has been studied extensively and the Mhc-DRB region demonstrates variability similar to humans. The extent of MHC diversity is relatively unknown for other Old World monkeys (OWM), especially among genera other than Macaca. A molecular survey of the Mhc-DRB region in mandrills (Mandrillus sphinx) revealed extensive variability, suggesting that other OWMs may also possess high levels of Mhc-DRB polymorphism. In the present study, 33 Mhc-DRB loci were identified from only 13 animals. Eleven were wild-born and presumed to be unrelated and two were captive-born twins. Two to seven different sequences were identified for each individual, suggesting that some mandrills may have as many as four Mhc-DRB loci on a single haplotype. From these sequences, representatives of at least six Mhc-DRB loci or lineages were identified. As observed in other primates, some new lineages may have arisen through the process of gene conversion. These findings indicate that mandrills have Mhc-DRB diversity not unlike rhesus macaques and humans.

Quantum-Sequencing: Fast electronic single DNA molecule sequencing

Science.gov (United States)

Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

2014-03-01

A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

ACHIEVEMENT GOALS AND INTENSIVITY OF PHYSICAL ACTIVITY DURING FREE PLAY IN CHILDREN: THE MODERATING ROLE OF PERCEIVED SPORT CONFIDENCE

Directory of Open Access Journals (Sweden)

R. Lochbaum Marc

2015-11-01

Full Text Available Purpose: to examine the moderating role of sport confidence and resultant the achievement goal profile with physical activity intensity during free play. Material: participants were 28 children participating in an after-school program. The 28 children completed measures of task and ego goal orientations and sport confidence two weeks prior to having their heart rate monitored during a free play session. Results: indicated that children with high sport confidence were characterized ( p 1.10 by higher task and ego orientations and average heart rate over the course of the free play session when compared to the low sport confidence children. The moderate sport confidence children were not significantly different than the other groups expect for ego orientation though effect sizes indicated this group tended towards being more similar to the high sport confidence group. The results were confounded as all children in the low sport confidence condition were girls. Conclusions: Sport confidence moderates physical activity intensity during free play in children and is characterized by a higher ego orientation and generally higher task orientation. But given all of the low confident children were females, intervention work is needed at early ages with girls to build sport confidence and motivations for both goal orientations to hopefully increase physical activity intensity during free play.

Digital PCR provides sensitive and absolute calibration for high throughput sequencing

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Fan H Christina

2009-03-01

Full Text Available Abstract Background Next-generation DNA sequencing on the 454, Solexa, and SOLiD platforms requires absolute calibration of the number of molecules to be sequenced. This requirement has two unfavorable consequences. First, large amounts of sample-typically micrograms-are needed for library preparation, thereby limiting the scope of samples which can be sequenced. For many applications, including metagenomics and the sequencing of ancient, forensic, and clinical samples, the quantity of input DNA can be critically limiting. Second, each library requires a titration sequencing run, thereby increasing the cost and lowering the throughput of sequencing. Results We demonstrate the use of digital PCR to accurately quantify 454 and Solexa sequencing libraries, enabling the preparation of sequencing libraries from nanogram quantities of input material while eliminating costly and time-consuming titration runs of the sequencer. We successfully sequenced low-nanogram scale bacterial and mammalian DNA samples on the 454 FLX and Solexa DNA sequencing platforms. This study is the first to definitively demonstrate the successful sequencing of picogram quantities of input DNA on the 454 platform, reducing the sample requirement more than 1000-fold without pre-amplification and the associated bias and reduction in library depth. Conclusion The digital PCR assay allows absolute quantification of sequencing libraries, eliminates uncertainties associated with the construction and application of standard curves to PCR-based quantification, and with a coefficient of variation close to 10%, is sufficiently precise to enable direct sequencing without titration runs.

Evidence for a confidence-accuracy relationship in memory for same- and cross-race faces.

Science.gov (United States)

Nguyen, Thao B; Pezdek, Kathy; Wixted, John T

2017-12-01

Discrimination accuracy is usually higher for same- than for cross-race faces, a phenomenon known as the cross-race effect (CRE). According to prior research, the CRE occurs because memories for same- and cross-race faces rely on qualitatively different processes. However, according to a continuous dual-process model of recognition memory, memories that rely on qualitatively different processes do not differ in recognition accuracy when confidence is equated. Thus, although there are differences in overall same- and cross-race discrimination accuracy, confidence-specific accuracy (i.e., recognition accuracy at a particular level of confidence) may not differ. We analysed datasets from four recognition memory studies on same- and cross-race faces to test this hypothesis. Confidence ratings reliably predicted recognition accuracy when performance was above chance levels (Experiments 1, 2, and 3) but not when performance was at chance levels (Experiment 4). Furthermore, at each level of confidence, confidence-specific accuracy for same- and cross-race faces did not significantly differ when overall performance was above chance levels (Experiments 1, 2, and 3) but significantly differed when overall performance was at chance levels (Experiment 4). Thus, under certain conditions, high-confidence same-race and cross-race identifications may be equally reliable.

Multishot versus single-shot pulse sequences in very high field fMRI: a comparison using retinotopic mapping.

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Jascha D Swisher

Full Text Available High-resolution functional MRI is a leading application for very high field (7 Tesla human MR imaging. Though higher field strengths promise improvements in signal-to-noise ratios (SNR and BOLD contrast relative to fMRI at 3 Tesla, these benefits may be partially offset by accompanying increases in geometric distortion and other off-resonance effects. Such effects may be especially pronounced with the single-shot EPI pulse sequences typically used for fMRI at standard field strengths. As an alternative, one might consider multishot pulse sequences, which may lead to somewhat lower temporal SNR than standard EPI, but which are also often substantially less susceptible to off-resonance effects. Here we consider retinotopic mapping of human visual cortex as a practical test case by which to compare examples of these sequence types for high-resolution fMRI at 7 Tesla. We performed polar angle retinotopic mapping at each of 3 isotropic resolutions (2.0, 1.7, and 1.1 mm using both accelerated single-shot 2D EPI and accelerated multishot 3D gradient-echo pulse sequences. We found that single-shot EPI indeed led to greater temporal SNR and contrast-to-noise ratios (CNR than the multishot sequences. However, additional distortion correction in postprocessing was required in order to fully realize these advantages, particularly at higher resolutions. The retinotopic maps produced by both sequence types were qualitatively comparable, and showed equivalent test/retest reliability. Thus, when surface-based analyses are planned, or in other circumstances where geometric distortion is of particular concern, multishot pulse sequences could provide a viable alternative to single-shot EPI.

Diagnosing lung nodules on oncologic MR/PET imaging: Comparison of fast T1-weighted sequences and influence of image acquisition in inspiration and expiration breath-hold

Energy Technology Data Exchange (ETDEWEB)

Schwenzer, Nina F.; Seith, Ferdinand; Gatidis, Sergios; Brendle, Cornelia; Schmidt, Holger; Pfannenberg, Christina A; LaFougère, Christian; Nikolaou, Konstantin; Schraml, Christina [University Hospital of Tuebingen, Tuebingen (Germany)

2016-09-15

First, to investigate the diagnostic performance of fast T1-weighted sequences for lung nodule evaluation in oncologic magnetic resonance (MR)/positron emission tomography (PET). Second, to evaluate the influence of image acquisition in inspiration and expiration breath-hold on diagnostic performance. The study was approved by the local Institutional Review Board. PET/CT and MR/PET of 44 cancer patients were evaluated by 2 readers. PET/CT included lung computed tomography (CT) scans in inspiration and expiration (CTin, CTex). MR/PET included Dixon sequence for attenuation correction and fast T1-weighted volumetric interpolated breath-hold examination (VIBE) sequences (volume interpolated breath-hold examination acquired in inspiration [VIBEin], volume interpolated breath-hold examination acquired in expiration [VIBEex]). Diagnostic performance was analyzed for lesion-, lobe-, and size-dependence. Diagnostic confidence was evaluated (4-point Likert-scale; 1 = high). Jackknife alternative free-response receiver-operating characteristic (JAFROC) analysis was performed. Seventy-six pulmonary lesions were evaluated. Lesion-based detection rates were: CTex, 77.6%; VIBEin, 53.3%; VIBEex, 51.3%; and Dixon, 22.4%. Lobe-based detection rates were: CTex, 89.6%; VIBEin, 58.3%; VIBEex, 60.4%; and Dixon, 31.3%. In contrast to CT, inspiration versus expiration did not alter diagnostic performance in VIBE sequences. Diagnostic confidence was best for VIBEin and CTex and decreased in VIBEex and Dixon (1.2 ± 0.6; 1.2 ± 0.7; 1.5 ± 0.9; 1.7 ± 1.1, respectively). The JAFROC figure-of-merit of Dixon was significantly lower. All patients with malignant lesions were identified by CTex, VIBEin, and VIBEex, while 3 patients were false-negative in Dixon. Fast T1-weighted VIBE sequences allow for identification of patients with malignant pulmonary lesions. The Dixon sequence is not recommended for lung nodule evaluation in oncologic MR/PET patients. In contrast to CT, inspiration versus

Diagnosing Lung Nodules on Oncologic MR/PET Imaging: Comparison of Fast T1-Weighted Sequences and Influence of Image Acquisition in Inspiration and Expiration Breath-Hold

Energy Technology Data Exchange (ETDEWEB)

Schwenzer, Nina F.; Seith, Ferdinand; Gatidis, Sergios [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Brendle, Cornelia [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Department of Diagnostic and Interventional Neuroradiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Schmidt, Holger; Pfannenberg, Christina A. [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Fougère, Christian la [Department of Nuclear Medicine, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Nikolaou, Konstantin; Schraml, Christina [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany)

2016-11-01

First, to investigate the diagnostic performance of fast T1-weighted sequences for lung nodule evaluation in oncologic magnetic resonance (MR)/positron emission tomography (PET). Second, to evaluate the influence of image acquisition in inspiration and expiration breath-hold on diagnostic performance. The study was approved by the local Institutional Review Board. PET/CT and MR/PET of 44 cancer patients were evaluated by 2 readers. PET/CT included lung computed tomography (CT) scans in inspiration and expiration (CTin, CTex). MR/PET included Dixon sequence for attenuation correction and fast T1-weighted volumetric interpolated breath-hold examination (VIBE) sequences (volume interpolated breath-hold examination acquired in inspiration [VIBEin], volume interpolated breath-hold examination acquired in expiration [VIBEex]). Diagnostic performance was analyzed for lesion-, lobe-, and size-dependence. Diagnostic confidence was evaluated (4-point Likert-scale; 1 = high). Jackknife alternative free-response receiver-operating characteristic (JAFROC) analysis was performed. Seventy-six pulmonary lesions were evaluated. Lesion-based detection rates were: CTex, 77.6%; VIBEin, 53.3%; VIBEex, 51.3%; and Dixon, 22.4%. Lobe-based detection rates were: CTex, 89.6%; VIBEin, 58.3%; VIBEex, 60.4%; and Dixon, 31.3%. In contrast to CT, inspiration versus expiration did not alter diagnostic performance in VIBE sequences. Diagnostic confidence was best for VIBEin and CTex and decreased in VIBEex and Dixon (1.2 ± 0.6; 1.2 ± 0.7; 1.5 ± 0.9; 1.7 ± 1.1, respectively). The JAFROC figure-of-merit of Dixon was significantly lower. All patients with malignant lesions were identified by CTex, VIBEin, and VIBEex, while 3 patients were false-negative in Dixon. Fast T1-weighted VIBE sequences allow for identification of patients with malignant pulmonary lesions. The Dixon sequence is not recommended for lung nodule evaluation in oncologic MR/PET patients. In contrast to CT, inspiration versus

Music educators : their artistry and self-confidence

NARCIS (Netherlands)

Lion-Slovak, Brigitte; Stöger, Christine; Smilde, Rineke; Malmberg, Isolde; de Vugt, Adri

2013-01-01

How does artistic identity influence the self-confidence of music educators? What is the interconnection between the artistic and the teacher identity? What is actually meant by artistic identity in music education? What is a fruitful environment for the development of artistic self-confidence of

Financial Literacy, Confidence and Financial Advice Seeking

NARCIS (Netherlands)

Kramer, Marc M.

2016-01-01

We find that people with higher confidence in their own financial literacy are less likely to seek financial advice, but no relation between objective measures of literacy and advice seeking. The negative association between confidence and advice seeking is more pronounced among wealthy households.

Confidence building in implementation of geological disposal

International Nuclear Information System (INIS)

Umeki, Hiroyuki

2004-01-01

Long-term safety of the disposal system should be demonstrated to the satisfaction of the stakeholders. Convincing arguments are therefore required that instil in the stakeholders confidence in the safety of a particular concept for the siting and design of a geological disposal, given the uncertainties that inevitably exist in its a priori description and in its evolution. The step-wise approach associated with making safety case at each stage is a key to building confidence in the repository development programme. This paper discusses aspects and issues on confidence building in the implementation of HLW disposal in Japan. (author)

Continuous- and Discrete-Time Stimulus Sequences for High Stimulus Rate Paradigm in Evoked Potential Studies

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Tao Wang

2013-01-01

Full Text Available To obtain reliable transient auditory evoked potentials (AEPs from EEGs recorded using high stimulus rate (HSR paradigm, it is critical to design the stimulus sequences of appropriate frequency properties. Traditionally, the individual stimulus events in a stimulus sequence occur only at discrete time points dependent on the sampling frequency of the recording system and the duration of stimulus sequence. This dependency likely causes the implementation of suboptimal stimulus sequences, sacrificing the reliability of resulting AEPs. In this paper, we explicate the use of continuous-time stimulus sequence for HSR paradigm, which is independent of the discrete electroencephalogram (EEG recording system. We employ simulation studies to examine the applicability of the continuous-time stimulus sequences and the impacts of sampling frequency on AEPs in traditional studies using discrete-time design. Results from these studies show that the continuous-time sequences can offer better frequency properties and improve the reliability of recovered AEPs. Furthermore, we find that the errors in the recovered AEPs depend critically on the sampling frequencies of experimental systems, and their relationship can be fitted using a reciprocal function. As such, our study contributes to the literature by demonstrating the applicability and advantages of continuous-time stimulus sequences for HSR paradigm and by revealing the relationship between the reliability of AEPs and sampling frequencies of the experimental systems when discrete-time stimulus sequences are used in traditional manner for the HSR paradigm.

Possession of ATM Sequence Variants as Predictor for Late Normal Tissue Responses in Breast Cancer Patients Treated With Radiotherapy

International Nuclear Information System (INIS)

Ho, Alice Y.; Fan, Grace; Atencio, David P.; Green, Sheryl; Formenti, Silvia C.; Haffty, Bruce G.; Iyengar, Preetha B.A.; Bernstein, Jonine L.; Stock, Richard G.; Cesaretti, Jamie A.; Rosenstein, Barry S.

2007-01-01

Purpose: The ATM gene product is a central component of cell cycle regulation and genomic surveillance. We hypothesized that DNA sequence alterations in ATM predict for adverse effects after external beam radiotherapy for early breast cancer. Methods and Materials: A total of 131 patients with a minimum of 2 years follow-up who had undergone breast-conserving surgery and adjuvant radiotherapy were screened for sequence alterations in ATM using DNA from blood lymphocytes. Genetic variants were identified using denaturing high performance liquid chromatography. The Radiation Therapy Oncology Group late morbidity scoring schemes for skin and subcutaneous tissues were applied to quantify the radiation-induced effects. Results: Of the 131 patients, 51 possessed ATM sequence alterations located within exons or in short intron regions flanking each exon that encompass putative splice site regions. Of these 51 patients, 21 (41%) exhibited a minimum of a Grade 2 late radiation response. In contrast, of the 80 patients without an ATM sequence variation, only 18 (23%) had radiation-induced adverse responses, for an odds ratio of 2.4 (95% confidence interval, 1.1-5.2). Fifteen patients were heterozygous for the G→A polymorphism at nucleotide 5557, which causes substitution of asparagine for aspartic acid at position 1853 of the ATM protein. Of these 15 patients, 8 (53%) exhibited a Grade 2-4 late response compared with 31 (27%) of the 116 patients without this alteration, for an odds ratio of 3.1 (95% confidence interval, 1.1-9.4). Conclusion: Sequence variants located in the ATM gene, in particular the 5557 G→A polymorphism, may predict for late adverse radiation responses in breast cancer patients

A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing.

Science.gov (United States)

Chen, Shi-Yi; Deng, Feilong; Jia, Xianbo; Li, Cao; Lai, Song-Jia

2017-08-09

It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus). We totally obtain 36,186 high-confidence transcripts from 14,474 genic loci, among which more than 23% of genic loci and 66% of isoforms have not been annotated yet within the current reference genome. Furthermore, about 17% of transcripts are computationally revealed to be non-coding RNAs. Up to 24,797 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events are detected within this de novo constructed transcriptome, respectively. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of rabbit genome.

[Study on Microbial Diversity of Peri-implantitis Subgingival by High-throughput Sequencing].

Science.gov (United States)

Li, Zhi-jie; Wang, Shao-guo; Li, Yue-hong; Tu, Dong-xiang; Liu, Shi-yun; Nie, Hong-bing; Li, Zhi-qiang; Zhang, Ju-mei

2015-07-01

To study microbial diversity of peri-implantitis subgingival with high-throughput sequencing, and investigate microbiological etiology of peri-implantitis. Subgingival plaques were sampled from the patients with peri-implantitis (D group) and non-peri-implantitis subjects (N group). The microbiological diversity of the subgingival plaques was detected by sequencing V4 region of 16S rRNA with Illumina Miseq platform. The diversity of the community structure was analyzed using Mothur software. A total of 156 507 gene sequences were detected in nine samples and 4 402 operational taxonomic units (OTUs) were found. Selenomonas, Pseudomonas, and Fusobacterium were dominant bacteria in D group, while Fusobacterium, Veillonella and Streptococcus were dominant bacteria in N group. Differences between peri-implantitis and non-peri-implantitis bacterial communities were observed at all phylogenetic levels by LEfSe, which was also found in PcoA test. The occurrence of peri-implantitis is not only related to periodontitis pathogenic microbe, but also related with the changes of oral microbial community structure. Treponema, Herbaspirillum, Butyricimonas and Phaeobacte may be closely related to the occurrence and development of peri-implantitis.

Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.

Directory of Open Access Journals (Sweden)

Kui Lin

2014-01-01

Full Text Available Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.

Sequencing and characterization of the guppy (Poecilia reticulata transcriptome

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Rodd F Helen

2011-04-01

Full Text Available Abstract Background Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs, and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA-sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in

Highly accurate fluorogenic DNA sequencing with information theory-based error correction.

Science.gov (United States)

Chen, Zitian; Zhou, Wenxiong; Qiao, Shuo; Kang, Li; Duan, Haifeng; Xie, X Sunney; Huang, Yanyi

2017-12-01

Eliminating errors in next-generation DNA sequencing has proved challenging. Here we present error-correction code (ECC) sequencing, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory-based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. We show that, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%, ECC sequencing provides single-end, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine.

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles.

Science.gov (United States)

Gadala-Maria, Daniel; Yaari, Gur; Uduman, Mohamed; Kleinstein, Steven H

2015-02-24

Individual variation in germline and expressed B-cell immunoglobulin (Ig) repertoires has been associated with aging, disease susceptibility, and differential response to infection and vaccination. Repertoire properties can now be studied at large-scale through next-generation sequencing of rearranged Ig genes. Accurate analysis of these repertoire-sequencing (Rep-Seq) data requires identifying the germline variable (V), diversity (D), and joining (J) gene segments used by each Ig sequence. Current V(D)J assignment methods work by aligning sequences to a database of known germline V(D)J segment alleles. However, existing databases are likely to be incomplete and novel polymorphisms are hard to differentiate from the frequent occurrence of somatic hypermutations in Ig sequences. Here we develop a Tool for Ig Genotype Elucidation via Rep-Seq (TIgGER). TIgGER analyzes mutation patterns in Rep-Seq data to identify novel V segment alleles, and also constructs a personalized germline database containing the specific set of alleles carried by a subject. This information is then used to improve the initial V segment assignments from existing tools, like IMGT/HighV-QUEST. The application of TIgGER to Rep-Seq data from seven subjects identified 11 novel V segment alleles, including at least one in every subject examined. These novel alleles constituted 13% of the total number of unique alleles in these subjects, and impacted 3% of V(D)J segment assignments. These results reinforce the highly polymorphic nature of human Ig V genes, and suggest that many novel alleles remain to be discovered. The integration of TIgGER into Rep-Seq processing pipelines will increase the accuracy of V segment assignments, thus improving B-cell repertoire analyses.

Confidence and self-attribution bias in an artificial stock market

Science.gov (United States)

Bertella, Mario A.; Pires, Felipe R.; Rego, Henio H. A.; Vodenska, Irena; Stanley, H. Eugene

2017-01-01

Using an agent-based model we examine the dynamics of stock price fluctuations and their rates of return in an artificial financial market composed of fundamentalist and chartist agents with and without confidence. We find that chartist agents who are confident generate higher price and rate of return volatilities than those who are not. We also find that kurtosis and skewness are lower in our simulation study of agents who are not confident. We show that the stock price and confidence index—both generated by our model—are cointegrated and that stock price affects confidence index but confidence index does not affect stock price. We next compare the results of our model with the S&P 500 index and its respective stock market confidence index using cointegration and Granger tests. As in our model, we find that stock prices drive their respective confidence indices, but that the opposite relationship, i.e., the assumption that confidence indices drive stock prices, is not significant. PMID:28231255

Psychometric properties of the communication Confidence Rating Scale for Aphasia (CCRSA): phase 1.

Science.gov (United States)

Cherney, Leora R; Babbitt, Edna M; Semik, Patrick; Heinemann, Allen W

2011-01-01

Confidence is a construct that has not been explored previously in aphasia research. We developed the Communication Confidence Rating Scale for Aphasia (CCRSA) to assess confidence in communicating in a variety of activities and evaluated its psychometric properties using rating scale (Rasch) analysis. The CCRSA was administered to 21 individuals with aphasia before and after participation in a computer-based language therapy study. Person reliability of the 8-item CCRSA was .77. The 5-category rating scale demonstrated monotonic increases in average measures from low to high ratings. However, one item ("I follow news, sports, stories on TV/movies") misfit the construct defined by the other items (mean square infit = 1.69, item-measure correlation = .41). Deleting this item improved reliability to .79; the 7 remaining items demonstrated excellent fit to the underlying construct, although there was a modest ceiling effect in this sample. Pre- to posttreatment changes on the 7-item CCRSA measure were statistically significant using a paired samples t test. Findings support the reliability and sensitivity of the CCRSA in assessing participants' self-report of communication confidence. Further evaluation of communication confidence is required with larger and more diverse samples.

Improved realism of confidence for an episodic memory event

Directory of Open Access Journals (Sweden)

Sandra Buratti

2012-09-01

Full Text Available We asked whether people can make their confidence judgments more realistic (accurate by adjusting them, with the aim of improving the relationship between the level of confidence and the correctness of the answer. This adjustment can be considered to include a so-called second-order metacognitive judgment. The participants first gave confidence judgments about their answers to questions about a video clip they had just watched. Next, they attempted to increase their accuracy by identifying confidence judgments in need of adjustment and then modifying them. The participants managed to increase their metacognitive realism, thus decreasing their absolute bias and improving their calibration, although the effects were small. We also examined the relationship between confidence judgments that were adjusted and the retrieval fluency and the phenomenological memory quality participants experienced when first answering the questions; this quality was one of either Remember (associated with concrete, vivid details or Know (associated with a feeling of familiarity. Confidence judgments associated with low retrieval fluency and the memory quality of knowing were modified more often. In brief, our results provide evidence that people can improve the realism of their confidence judgments, mainly by decreasing their confidence for incorrect answers. Thus, this study supports the conclusion that people can perform successful second-order metacognitive judgments.

High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak

Directory of Open Access Journals (Sweden)

Trout-Yakel Keri M

2010-02-01

Full Text Available Abstract Background A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. Subtyping of outbreak-associated isolates using pulsed-field gel electrophoresis (PFGE revealed two similar but distinct AscI PFGE patterns. High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. Results The chromosomes were collinear, but differences included 28 single nucleotide polymorphisms (SNPs and three indels, including a 33 kbp prophage that accounted for the observed difference in AscI PFGE patterns. The distribution of these traits was assessed within further clinical, environmental and food isolates associated with the outbreak, and this comparison indicated that three distinct, but highly related strains may have been involved in this nationwide outbreak. Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes. Conclusions High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology.

Interpretation of Confidence Interval Facing the Conflict

Science.gov (United States)

Andrade, Luisa; Fernández, Felipe

2016-01-01

As literature has reported, it is usual that university students in statistics courses, and even statistics teachers, interpret the confidence level associated with a confidence interval as the probability that the parameter value will be between the lower and upper interval limits. To confront this misconception, class activities have been…

Deciphering the Resistome of the Widespread Pseudomonas aeruginosa Sequence Type 175 International High-Risk Clone through Whole-Genome Sequencing.

Science.gov (United States)

Cabot, Gabriel; López-Causapé, Carla; Ocampo-Sosa, Alain A; Sommer, Lea M; Domínguez, María Ángeles; Zamorano, Laura; Juan, Carlos; Tubau, Fe; Rodríguez, Cristina; Moyà, Bartolomé; Peña, Carmen; Martínez-Martínez, Luis; Plesiat, Patrick; Oliver, Antonio

2016-12-01

Whole-genome sequencing (WGS) was used for the characterization of the frequently extensively drug resistant (XDR) Pseudomonas aeruginosa sequence type 175 (ST175) high-risk clone. A total of 18 ST175 isolates recovered from 8 different Spanish hospitals were analyzed; 4 isolates from 4 different French hospitals were included for comparison. The typical resistance profile of ST175 included penicillins, cephalosporins, monobactams, carbapenems, aminoglycosides, and fluoroquinolones. In the phylogenetic analysis, the four French isolates clustered together with two isolates from one of the Spanish regions. Sequence variation was analyzed for 146 chromosomal genes related to antimicrobial resistance, and horizontally acquired genes were explored using online databases. The resistome of ST175 was determined mainly by mutational events; resistance traits common to all or nearly all of the strains included specific ampR mutations leading to ampC overexpression, specific mutations in oprD conferring carbapenem resistance, or a mexZ mutation leading to MexXY overexpression. All isolates additionally harbored an aadB gene conferring gentamicin and tobramycin resistance. Several other resistance traits were specific to certain geographic areas, such as a streptomycin resistance gene, aadA13, detected in all four isolates from France and in the two isolates from the Cantabria region and a glpT mutation conferring fosfomycin resistance, detected in all but these six isolates. Finally, several unique resistance mutations were detected in single isolates; particularly interesting were those in genes encoding penicillin-binding proteins (PBP1A, PBP3, and PBP4). Thus, these results provide information valuable for understanding the genetic basis of resistance and the dynamics of the dissemination and evolution of high-risk clones. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Exome sequencing identifies highly recurrent MED12 somatic mutations in breast fibroadenoma.

Science.gov (United States)

Lim, Weng Khong; Ong, Choon Kiat; Tan, Jing; Thike, Aye Aye; Ng, Cedric Chuan Young; Rajasegaran, Vikneswari; Myint, Swe Swe; Nagarajan, Sanjanaa; Nasir, Nur Diyana Md; McPherson, John R; Cutcutache, Ioana; Poore, Gregory; Tay, Su Ting; Ooi, Wei Siong; Tan, Veronique Kiak Mien; Hartman, Mikael; Ong, Kong Wee; Tan, Benita K T; Rozen, Steven G; Tan, Puay Hoon; Tan, Patrick; Teh, Bin Tean

2014-08-01

Fibroadenomas are the most common breast tumors in women under 30 (refs. 1,2). Exome sequencing of eight fibroadenomas with matching whole-blood samples revealed recurrent somatic mutations solely in MED12, which encodes a Mediator complex subunit. Targeted sequencing of an additional 90 fibroadenomas confirmed highly frequent MED12 exon 2 mutations (58/98, 59%) that are probably somatic, with 71% of mutations occurring in codon 44. Using laser capture microdissection, we show that MED12 fibroadenoma mutations are present in stromal but not epithelial mammary cells. Expression profiling of MED12-mutated and wild-type fibroadenomas revealed that MED12 mutations are associated with dysregulated estrogen signaling and extracellular matrix organization. The fibroadenoma MED12 mutation spectrum is nearly identical to that of previously reported MED12 lesions in uterine leiomyoma but not those of other tumors. Benign tumors of the breast and uterus, both of which are key target tissues of estrogen, may thus share a common genetic basis underpinned by highly frequent and specific MED12 mutations.

Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform.

Science.gov (United States)

Monden, Yuki; Yamamoto, Ayaka; Shindo, Akiko; Tahara, Makoto

2014-10-01

In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LIb) in sweet potato. Using 38 cultivars, we identified 2,024 insertion sites in the two families with an Illumina MiSeq sequencing platform. Of these insertion sites, 91.4% appeared to be polymorphic among the cultivars and 376 cultivar-specific insertion sites were identified, which were converted directly into cultivar-specific sequence-characterized amplified region (SCAR) markers. A phylogenetic tree was constructed using these insertion sites, which corresponded well with known pedigree information, thereby indicating their suitability for genetic diversity studies. Thus, the genome-wide comparative analysis of active retrotransposon insertion sites using the bench-top MiSeq sequencing platform is highly effective for DNA fingerprinting without any requirement for whole genome sequence information. This approach may facilitate the development of practical polymerase chain reaction-based cultivar diagnostic system and could also be applied to the determination of genetic relationships. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Is consumer confidence an indicator of JSE performance?

OpenAIRE

Kamini Solanki; Yudhvir Seetharam

2014-01-01

While most studies examine the impact of business confidence on market performance, we instead focus on the consumer because consumer spending habits are a natural extension of trading activity on the equity market. This particular study examines investor sentiment as measured by the Consumer Confidence Index in South Africa and its effect on the Johannesburg Stock Exchange (JSE). We employ Granger causality tests to investigate the relationship across time between the Consumer Confidence Ind...

Automated side-chain model building and sequence assignment by template matching

International Nuclear Information System (INIS)

Terwilliger, Thomas C.

2002-01-01

A method for automated macromolecular side-chain model building and for aligning the sequence to the map is described. An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer

Confidence Interval Approximation For Treatment Variance In ...

African Journals Online (AJOL)

In a random effects model with a single factor, variation is partitioned into two as residual error variance and treatment variance. While a confidence interval can be imposed on the residual error variance, it is not possible to construct an exact confidence interval for the treatment variance. This is because the treatment ...

Feedback for reinforcement learning based brain-machine interfaces using confidence metrics

Science.gov (United States)

Prins, Noeline W.; Sanchez, Justin C.; Prasad, Abhishek

2017-06-01

Objective. For brain-machine interfaces (BMI) to be used in activities of daily living by paralyzed individuals, the BMI should be as autonomous as possible. One of the challenges is how the feedback is extracted and utilized in the BMI. Our long-term goal is to create autonomous BMIs that can utilize an evaluative feedback from the brain to update the decoding algorithm and use it intelligently in order to adapt the decoder. In this study, we show how to extract the necessary evaluative feedback from a biologically realistic (synthetic) source, use both the quantity and the quality of the feedback, and how that feedback information can be incorporated into a reinforcement learning (RL) controller architecture to maximize its performance. Approach. Motivated by the perception-action-reward cycle (PARC) in the brain which links reward for cognitive decision making and goal-directed behavior, we used a reward-based RL architecture named Actor-Critic RL as the model. Instead of using an error signal towards building an autonomous BMI, we envision to use a reward signal from the nucleus accumbens (NAcc) which plays a key role in the linking of reward to motor behaviors. To deal with the complexity and non-stationarity of biological reward signals, we used a confidence metric which was used to indicate the degree of feedback accuracy. This confidence was added to the Actor’s weight update equation in the RL controller architecture. If the confidence was high (>0.2), the BMI decoder used this feedback to update its parameters. However, when the confidence was low, the BMI decoder ignored the feedback and did not update its parameters. The range between high confidence and low confidence was termed as the ‘ambiguous’ region. When the feedback was within this region, the BMI decoder updated its weight at a lower rate than when fully confident, which was decided by the confidence. We used two biologically realistic models to generate synthetic data for MI (Izhikevich

Self-confidence of anglers in identification of freshwater sport fish

Science.gov (United States)

Chizinski, C.J.; Martin, D. R.; Pope, Kevin L.

2014-01-01

Although several studies have focused on how well anglers identify species using replicas and pictures, there has been no study assessing the confidence that can be placed in angler's ability to identify recreationally important fish. Understanding factors associated with low self-confidence will be useful in tailoring education programmes to improve self-confidence in identifying common species. The purposes of this assessment were to quantify the confidence of recreational anglers to identify 13 commonly encountered warm water fish species and to relate self-confidence to species availability and angler experience. Significant variation was observed in anglers self-confidence among species and levels of self-declared skill, with greater confidence associated with greater skill and with greater exposure. This study of angler self-confidence strongly highlights the need for educational programmes that target lower skilled anglers and the importance of teaching all anglers about less common species, regardless of skill level.

Fechner’s law in metacognition: a quantitative model of visual working memory confidence

Science.gov (United States)

van den Berg, Ronald; Yoo, Aspen H.; Ma, Wei Ji

2016-01-01

Although visual working memory (VWM) has been studied extensively, it is unknown how people form confidence judgments about their memories. Peirce (1878) speculated that Fechner’s law – which states that sensation is proportional to the logarithm of stimulus intensity – might apply to confidence reports. Based on this idea, we hypothesize that humans map the precision of their VWM contents to a confidence rating through Fechner’s law. We incorporate this hypothesis into the best available model of VWM encoding and fit it to data from a delayed-estimation experiment. The model provides an excellent account of human confidence rating distributions as well as the relation between performance and confidence. Moreover, the best-fitting mapping in a model with a highly flexible mapping closely resembles the logarithmic mapping, suggesting that no alternative mapping exists that accounts better for the data than Fechner's law. We propose a neural implementation of the model and find that this model also fits the behavioral data well. Furthermore, we find that jointly fitting memory errors and confidence ratings boosts the power to distinguish previously proposed VWM encoding models by a factor of 5.99 compared to fitting only memory errors. Finally, we show that Fechner's law also accounts for metacognitive judgments in a word recognition memory task, which is a first indication that it may be a general law in metacognition. Our work presents the first model to jointly account for errors and confidence ratings in VWM and could lay the groundwork for understanding the computational mechanisms of metacognition. PMID:28221087

Viral metagenomics: Analysis of begomoviruses by illumina high-throughput sequencing

KAUST Repository

Idris, Ali

2014-03-12

Traditional DNA sequencing methods are inefficient, lack the ability to discern the least abundant viral sequences, and ineffective for determining the extent of variability in viral populations. Here, populations of single-stranded DNA plant begomoviral genomes and their associated beta- and alpha-satellite molecules (virus-satellite complexes) (genus, Begomovirus; family, Geminiviridae) were enriched from total nucleic acids isolated from symptomatic, field-infected plants, using rolling circle amplification (RCA). Enriched virus-satellite complexes were subjected to Illumina-Next Generation Sequencing (NGS). CASAVA and SeqMan NGen programs were implemented, respectively, for quality control and for de novo and reference-guided contig assembly of viral-satellite sequences. The authenticity of the begomoviral sequences, and the reproducibility of the Illumina-NGS approach for begomoviral deep sequencing projects, were validated by comparing NGS results with those obtained using traditional molecular cloning and Sanger sequencing of viral components and satellite DNAs, also enriched by RCA or amplified by polymerase chain reaction. As the use of NGS approaches, together with advances in software development, make possible deep sequence coverage at a lower cost; the approach described herein will streamline the exploration of begomovirus diversity and population structure from naturally infected plants, irrespective of viral abundance. This is the first report of the implementation of Illumina-NGS to explore the diversity and identify begomoviral-satellite SNPs directly from plants naturally-infected with begomoviruses under field conditions. 2014 by the authors; licensee MDPI, Basel, Switzerland.

Viral Metagenomics: Analysis of Begomoviruses by Illumina High-Throughput Sequencing

Directory of Open Access Journals (Sweden)

Ali Idris

2014-03-01

Full Text Available Traditional DNA sequencing methods are inefficient, lack the ability to discern the least abundant viral sequences, and ineffective for determining the extent of variability in viral populations. Here, populations of single-stranded DNA plant begomoviral genomes and their associated beta- and alpha-satellite molecules (virus-satellite complexes (genus, Begomovirus; family, Geminiviridae were enriched from total nucleic acids isolated from symptomatic, field-infected plants, using rolling circle amplification (RCA. Enriched virus-satellite complexes were subjected to Illumina-Next Generation Sequencing (NGS. CASAVA and SeqMan NGen programs were implemented, respectively, for quality control and for de novo and reference-guided contig assembly of viral-satellite sequences. The authenticity of the begomoviral sequences, and the reproducibility of the Illumina-NGS approach for begomoviral deep sequencing projects, were validated by comparing NGS results with those obtained using traditional molecular cloning and Sanger sequencing of viral components and satellite DNAs, also enriched by RCA or amplified by polymerase chain reaction. As the use of NGS approaches, together with advances in software development, make possible deep sequence coverage at a lower cost; the approach described herein will streamline the exploration of begomovirus diversity and population structure from naturally infected plants, irrespective of viral abundance. This is the first report of the implementation of Illumina-NGS to explore the diversity and identify begomoviral-satellite SNPs directly from plants naturally-infected with begomoviruses under field conditions.

Model-free aftershock forecasts constructed from similar sequences in the past

Science.gov (United States)

van der Elst, N.; Page, M. T.

2017-12-01

The basic premise behind aftershock forecasting is that sequences in the future will be similar to those in the past. Forecast models typically use empirically tuned parametric distributions to approximate past sequences, and project those distributions into the future to make a forecast. While parametric models do a good job of describing average outcomes, they are not explicitly designed to capture the full range of variability between sequences, and can suffer from over-tuning of the parameters. In particular, parametric forecasts may produce a high rate of "surprises" - sequences that land outside the forecast range. Here we present a non-parametric forecast method that cuts out the parametric "middleman" between training data and forecast. The method is based on finding past sequences that are similar to the target sequence, and evaluating their outcomes. We quantify similarity as the Poisson probability that the observed event count in a past sequence reflects the same underlying intensity as the observed event count in the target sequence. Event counts are defined in terms of differential magnitude relative to the mainshock. The forecast is then constructed from the distribution of past sequences outcomes, weighted by their similarity. We compare the similarity forecast with the Reasenberg and Jones (RJ95) method, for a set of 2807 global aftershock sequences of M≥6 mainshocks. We implement a sequence-specific RJ95 forecast using a global average prior and Bayesian updating, but do not propagate epistemic uncertainty. The RJ95 forecast is somewhat more precise than the similarity forecast: 90% of observed sequences fall within a factor of two of the median RJ95 forecast value, whereas the fraction is 85% for the similarity forecast. However, the surprise rate is much higher for the RJ95 forecast; 10% of observed sequences fall in the upper 2.5% of the (Poissonian) forecast range. The surprise rate is less than 3% for the similarity forecast. The similarity

Effects of postidentification feedback on eyewitness identification and nonidentification confidence.

Science.gov (United States)

Semmler, Carolyn; Brewer, Neil; Wells, Gary L

2004-04-01

Two experiments investigated new dimensions of the effect of confirming feedback on eyewitness identification confidence using target-absent and target-present lineups and (previously unused) unbiased witness instructions (i.e., "offender not present" option highlighted). In Experiment 1, participants viewed a crime video and were later asked to try to identify the thief from an 8-person target-absent photo array. Feedback inflated witness confidence for both mistaken identifications and correct lineup rejections. With target-present lineups in Experiment 2, feedback inflated confidence for correct and mistaken identifications and lineup rejections. Although feedback had no influence on the confidence-accuracy correlation, it produced clear overconfidence. Confidence inflation varied with the confidence measure reference point (i.e., retrospective vs. current confidence) and identification response latency.

Increasing Classroom Compliance: Using a High-Probability Command Sequence with Noncompliant Students

Science.gov (United States)

Axelrod, Michael I.; Zank, Amber J.

2012-01-01

Noncompliance is one of the most problematic behaviors within the school setting. One strategy to increase compliance of noncompliant students is a high-probability command sequence (HPCS; i.e., a set of simple commands in which an individual is likely to comply immediately prior to the delivery of a command that has a lower probability of…

Confidence Intervals from Normalized Data: A correction to Cousineau (2005

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Richard D. Morey

2008-09-01

Full Text Available Presenting confidence intervals around means is a common method of expressing uncertainty in data. Loftus and Masson (1994 describe confidence intervals for means in within-subjects designs. These confidence intervals are based on the ANOVA mean squared error. Cousineau (2005 presents an alternative to the Loftus and Masson method, but his method produces confidence intervals that are smaller than those of Loftus and Masson. I show why this is the case and offer a simple correction that makes the expected size of Cousineau confidence intervals the same as that of Loftus and Masson confidence intervals.

Discovery of viruses and virus-like pathogens in pistachio using high-throughput sequencing

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Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of 60 trees including clonal UCB-1 hybrid rootstock (P. atlantica × P. integerrima) identif...

Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making.

Science.gov (United States)

Aitchison, Laurence; Bang, Dan; Bahrami, Bahador; Latham, Peter E

2015-10-01

Humans stand out from other animals in that they are able to explicitly report on the reliability of their internal operations. This ability, which is known as metacognition, is typically studied by asking people to report their confidence in the correctness of some decision. However, the computations underlying confidence reports remain unclear. In this paper, we present a fully Bayesian method for directly comparing models of confidence. Using a visual two-interval forced-choice task, we tested whether confidence reports reflect heuristic computations (e.g. the magnitude of sensory data) or Bayes optimal ones (i.e. how likely a decision is to be correct given the sensory data). In a standard design in which subjects were first asked to make a decision, and only then gave their confidence, subjects were mostly Bayes optimal. In contrast, in a less-commonly used design in which subjects indicated their confidence and decision simultaneously, they were roughly equally likely to use the Bayes optimal strategy or to use a heuristic but suboptimal strategy. Our results suggest that, while people's confidence reports can reflect Bayes optimal computations, even a small unusual twist or additional element of complexity can prevent optimality.

Registered nurse leadership style and confidence in delegation.

Science.gov (United States)

Saccomano, Scott J; Pinto-Zipp, Genevieve

2011-05-01

  Leadership and confidence in delegation are two important explanatory constructs of nursing practice. The relationship between these constructs, however, is not clearly understood. To be successful in their roles as leaders, regardless of their experience, registered nurses (RNs) need to understand how to best delegate. The present study explored and described the relationship between RN leadership styles, demographic variables and confidence in delegation in a community teaching hospital. Utilizing a cross-sectional survey design, RNs employed in one acute care hospital completed questionnaires that measured leadership style [Path-Goal Leadership Questionnaire (PGLQ)] and confidence in delegating patient care tasks [Confidence and Intent to Delegate Scale (CIDS)]. Contrary to expectations, the data did not confirm a relationship between confidence in delegating tasks to unlicensed assistive personnel (UAPs) and leadership style. Nurses who were diploma or associate degree prepared were initially less confident in delegating tasks to UAPs as compared with RNs holding a bachelor's degree or higher. Further, after 5 years of clinical nursing experience, nurses with less educational experience reported more confidence in delegating tasks as compared with RNs with more educational experience. The lack of a relationship between leadership style and confidence in delegating patient care tasks were discussed in terms of the PGLQ classification criteria and hospital unit differences. As suggested by the significant two-way interaction between educational preparation and clinical nursing experience, changes in the nurse's confidence in delegating patient care tasks to UAPs was a dynamic changing variable that resulted from the interplay between amount of educational preparation and years of clinical nursing experience in this population of nurses. Clearly, generalizability of these findings to nurses outside the US is questionable, thus nurse managers must be familiar

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

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Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

2015-05-01

Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

Detecting Disease in Radiographs with Intuitive Confidence

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Stefan Jaeger

2015-01-01

Full Text Available This paper argues in favor of a specific type of confidence for use in computer-aided diagnosis and disease classification, namely, sine/cosine values of angles represented by points on the unit circle. The paper shows how this confidence is motivated by Chinese medicine and how sine/cosine values are directly related with the two forces Yin and Yang. The angle for which sine and cosine are equal (45° represents the state of equilibrium between Yin and Yang, which is a state of nonduality that indicates neither normality nor abnormality in terms of disease classification. The paper claims that the proposed confidence is intuitive and can be readily understood by physicians. The paper underpins this thesis with theoretical results in neural signal processing, stating that a sine/cosine relationship between the actual input signal and the perceived (learned input is key to neural learning processes. As a practical example, the paper shows how to use the proposed confidence values to highlight manifestations of tuberculosis in frontal chest X-rays.

Confidence mediates the sex difference in mental rotation performance.

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Estes, Zachary; Felker, Sydney

2012-06-01

On tasks that require the mental rotation of 3-dimensional figures, males typically exhibit higher accuracy than females. Using the most common measure of mental rotation (i.e., the Mental Rotations Test), we investigated whether individual variability in confidence mediates this sex difference in mental rotation performance. In each of four experiments, the sex difference was reliably elicited and eliminated by controlling or manipulating participants' confidence. Specifically, confidence predicted performance within and between sexes (Experiment 1), rendering confidence irrelevant to the task reliably eliminated the sex difference in performance (Experiments 2 and 3), and manipulating confidence significantly affected performance (Experiment 4). Thus, confidence mediates the sex difference in mental rotation performance and hence the sex difference appears to be a difference of performance rather than ability. Results are discussed in relation to other potential mediators and mechanisms, such as gender roles, sex stereotypes, spatial experience, rotation strategies, working memory, and spatial attention.

Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

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Zdepski Anna

2011-05-01

Full Text Available Abstract Background High throughput sequencing (HTS technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR. We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.

Aging and Confidence Judgments in Item Recognition

Science.gov (United States)

Voskuilen, Chelsea; Ratcliff, Roger; McKoon, Gail

2018-01-01

We examined the effects of aging on performance in an item-recognition experiment with confidence judgments. A model for confidence judgments and response time (RTs; Ratcliff & Starns, 2013) was used to fit a large amount of data from a new sample of older adults and a previously reported sample of younger adults. This model of confidence…

BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data.

Science.gov (United States)

Chae, Heejoon; Rhee, Sungmin; Nephew, Kenneth P; Kim, Sun

2015-01-15

It is now well established that microRNAs (miRNAs) play a critical role in regulating gene expression in a sequence-specific manner, and genome-wide efforts are underway to predict known and novel miRNA targets. However, the integrated miRNA-mRNA analysis remains a major computational challenge, requiring powerful informatics systems and bioinformatics expertise. The objective of this study was to modify our widely recognized Web server for the integrated mRNA-miRNA analysis (MMIA) and its subsequent deployment on the Amazon cloud (BioVLAB-MMIA) to be compatible with high-throughput platforms, including next-generation sequencing (NGS) data (e.g. RNA-seq). We developed a new version called the BioVLAB-MMIA-NGS, deployed on both Amazon cloud and on a high-performance publicly available server called MAHA. By using NGS data and integrating various bioinformatics tools and databases, BioVLAB-MMIA-NGS offers several advantages. First, sequencing data is more accurate than array-based methods for determining miRNA expression levels. Second, potential novel miRNAs can be detected by using various computational methods for characterizing miRNAs. Third, because miRNA-mediated gene regulation is due to hybridization of an miRNA to its target mRNA, sequencing data can be used to identify many-to-many relationship between miRNAs and target genes with high accuracy. http://epigenomics.snu.ac.kr/biovlab_mmia_ngs/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The use of DNase I, buffer gradient gel, and 35S label for DNA sequencing

International Nuclear Information System (INIS)

Hong, G.F.

1987-01-01

The use of microcentrifuge tubes and mixing of sequencing reactions and brief centrifugation in racks rather than the original capillary tube method has made sequencing reactions relatively simple. Buffer gradient gels and 15 S label are simple means of increasing the rate of sequence analysis; they add little time to that required for determining the sequences of a given number of clones, need no elaborate equipment, and increase the amount of useful data per gel. The standard approach of running 2- and 4-hr gels generates about 300 bases of sequence. The above improvements allow the same number of bases to be read with more confidence from a single 50-cm gel for each clone sequenced due to the changed spacing between sharpened bands

High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform

DEFF Research Database (Denmark)

Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen; Rockenbauer, Eszter

2011-01-01

repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method...

Retirement Sequences of Older Americans: Moderately Destandardized and Highly Stratified Across Gender, Class, and Race.

Science.gov (United States)

Calvo, Esteban; Madero-Cabib, Ignacio; Staudinger, Ursula M

2017-06-06

A destandardization of labor-force patterns revolving around retirement has been observed in recent literature. It is unclear, however, to which degree and of which kind. This study looked at sequences rather than individual statuses or transitions and argued that differentiating older Americans' retirement sequences by type, order, and timing and considering gender, class, and race differences yields a less destandardized picture. Sequence analysis was employed to analyze panel data from the Health and Retirement Study (HRS) for 7,881 individuals observed 6 consecutive times between ages 60-61 and 70-71. As expected, types of retirement sequences were identified that cannot be subsumed under the conventional model of complete retirement from full-time employment around age 65. However, these retirement sequences were not entirely destandardized, as some irreversibility and age-grading persisted. Further, the degree of destandardization varied along gender, class, and race. Unconventional sequences were archetypal for middle-level educated individuals and Blacks. Also, sequences for women and individuals with lower education showed more unemployment and part-time jobs, and less age-grading. A sequence-analytic approach that models group differences uncovers misjudgments about the degree of destandardization of retirement sequences. When a continuous process is represented as individual transitions, the overall pattern of retirement sequences gets lost and appears destandardized. These patterns get further complicated by differences in social structures by gender, class, and race in ways that seem to reproduce advantages that men, more highly educated individuals, and Whites enjoy in numerous areas over the life course. © The Author 2017. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Maximum-confidence discrimination among symmetric qudit states

International Nuclear Information System (INIS)

Jimenez, O.; Solis-Prosser, M. A.; Delgado, A.; Neves, L.

2011-01-01

We study the maximum-confidence (MC) measurement strategy for discriminating among nonorthogonal symmetric qudit states. Restricting to linearly dependent and equally likely pure states, we find the optimal positive operator valued measure (POVM) that maximizes our confidence in identifying each state in the set and minimizes the probability of obtaining inconclusive results. The physical realization of this POVM is completely determined and it is shown that after an inconclusive outcome, the input states may be mapped into a new set of equiprobable symmetric states, restricted, however, to a subspace of the original qudit Hilbert space. By applying the MC measurement again onto this new set, we can still gain some information about the input states, although with less confidence than before. This leads us to introduce the concept of sequential maximum-confidence (SMC) measurements, where the optimized MC strategy is iterated in as many stages as allowed by the input set, until no further information can be extracted from an inconclusive result. Within each stage of this measurement our confidence in identifying the input states is the highest possible, although it decreases from one stage to the next. In addition, the more stages we accomplish within the maximum allowed, the higher will be the probability of correct identification. We will discuss an explicit example of the optimal SMC measurement applied in the discrimination among four symmetric qutrit states and propose an optical network to implement it.

Are You Sure? Confidence about the Satiating Capacity of a Food Affects Subsequent Food Intake.

Science.gov (United States)

Schiöth, Helgi B; Ferriday, Danielle; Davies, Sarah R; Benedict, Christian; Elmståhl, Helena; Brunstrom, Jeffrey M; Hogenkamp, Pleunie S

2015-06-24

Expectations about a food's satiating capacity predict self-selected portion size, food intake and food choice. However, two individuals might have a similar expectation, but one might be extremely confident while the other might be guessing. It is unclear whether confidence about an expectation affects adjustments in energy intake at a subsequent meal. In a randomized cross-over design, 24 subjects participated in three separate breakfast sessions, and were served a low-energy-dense preload (53 kcal/100 g), a high-energy-dense preload (94 kcal/100 g), or no preload. Subjects received ambiguous information about the preload's satiating capacity and rated how confident they were about their expected satiation before consuming the preload in its entirety. They were served an ad libitum test meal 30 min later. Confidence ratings were negatively associated with energy compensation after consuming the high-energy-dense preload (r = -0.61; p = 0.001). The same relationship was evident after consuming the low-energy-dense preload, but only after controlling for dietary restraint, hunger prior to, and liking of the test meal (p = 0.03). Our results suggest that confidence modifies short-term controls of food intake by affecting energy compensation. These results merit consideration because imprecise caloric compensation has been identified as a potential risk factor for a positive energy balance and weight gain.

Are You Sure? Confidence about the Satiating Capacity of a Food Affects Subsequent Food Intake

Directory of Open Access Journals (Sweden)

Helgi B. Schiöth

2015-06-01

Full Text Available Expectations about a food’s satiating capacity predict self-selected portion size, food intake and food choice. However, two individuals might have a similar expectation, but one might be extremely confident while the other might be guessing. It is unclear whether confidence about an expectation affects adjustments in energy intake at a subsequent meal. In a randomized cross-over design, 24 subjects participated in three separate breakfast sessions, and were served a low-energy-dense preload (53 kcal/100 g, a high-energy-dense preload (94 kcal/100 g, or no preload. Subjects received ambiguous information about the preload’s satiating capacity and rated how confident they were about their expected satiation before consuming the preload in its entirety. They were served an ad libitum test meal 30 min later. Confidence ratings were negatively associated with energy compensation after consuming the high-energy-dense preload (r = −0.61; p = 0.001. The same relationship was evident after consuming the low-energy-dense preload, but only after controlling for dietary restraint, hunger prior to, and liking of the test meal (p = 0.03. Our results suggest that confidence modifies short-term controls of food intake by affecting energy compensation. These results merit consideration because imprecise caloric compensation has been identified as a potential risk factor for a positive energy balance and weight gain.

Understanding public confidence in government to prevent terrorist attacks.

Energy Technology Data Exchange (ETDEWEB)

Baldwin, T. E.; Ramaprasad, A,; Samsa, M. E.; Decision and Information Sciences; Univ. of Illinois at Chicago

2008-04-02

A primary goal of terrorism is to instill a sense of fear and vulnerability in a population and to erode its confidence in government and law enforcement agencies to protect citizens against future attacks. In recognition of its importance, the Department of Homeland Security includes public confidence as one of the principal metrics used to assess the consequences of terrorist attacks. Hence, a detailed understanding of the variations in public confidence among individuals, terrorist event types, and as a function of time is critical to developing this metric. In this exploratory study, a questionnaire was designed, tested, and administered to small groups of individuals to measure public confidence in the ability of federal, state, and local governments and their public safety agencies to prevent acts of terrorism. Data was collected from three groups before and after they watched mock television news broadcasts portraying a smallpox attack, a series of suicide bomber attacks, a refinery explosion attack, and cyber intrusions on financial institutions, resulting in identity theft. Our findings are: (a) although the aggregate confidence level is low, there are optimists and pessimists; (b) the subjects are discriminating in interpreting the nature of a terrorist attack, the time horizon, and its impact; (c) confidence recovery after a terrorist event has an incubation period; and (d) the patterns of recovery of confidence of the optimists and the pessimists are different. These findings can affect the strategy and policies to manage public confidence after a terrorist event.

Functional Dissociation of Confident and Not-Confident Errors in the Spatial Delayed Response Task Demonstrates Impairments in Working Memory Encoding and Maintenance in Schizophrenia

Directory of Open Access Journals (Sweden)

Jutta S. Mayer

2018-05-01

Full Text Available Even though extensively investigated, the nature of working memory (WM deficits in patients with schizophrenia (PSZ is not yet fully understood. In particular, the contribution of different WM sub-processes to the severe WM deficit observed in PSZ is a matter of debate. So far, most research has focused on impaired WM maintenance. By analyzing different types of errors in a spatial delayed response task (DRT, we have recently demonstrated that incorrect yet confident responses (which we labeled as false memory errors rather than incorrect/not-confident responses reflect failures of WM encoding, which was also impaired in PSZ. In the present study, we provide further evidence for a functional dissociation between confident and not-confident errors by manipulating the demands on WM maintenance, i.e., the length over which information has to be maintained in WM. Furthermore, we investigate whether these functionally distinguishable WM processes are impaired in PSZ. Twenty-four PSZ and 24 demographically matched healthy controls (HC performed a spatial DRT in which the length of the delay period was varied between 1, 2, 4, and 6 s. In each trial, participants also rated their level of response confidence. Across both groups, longer delays led to increased rates of incorrect/not-confident responses, while incorrect/confident responses were not affected by delay length. This functional dissociation provides additional support for our proposal that false memory errors (i.e., confident errors reflect problems at the level of WM encoding, while not-confident errors reflect failures of WM maintenance. Schizophrenic patients showed increased numbers of both confident and not-confident errors, suggesting that both sub-processes of WM—encoding and maintenance—are impaired in schizophrenia. Combined with the delay length-dependent functional dissociation, we propose that these impairments in schizophrenic patients are functionally distinguishable.

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

Science.gov (United States)

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.

Effects of confidence and anxiety on flow state in competition.

Science.gov (United States)

Koehn, Stefan

2013-01-01

Confidence and anxiety are important variables that underlie the experience of flow in sport. Specifically, research has indicated that confidence displays a positive relationship and anxiety a negative relationship with flow. The aim of this study was to assess potential direct and indirect effects of confidence and anxiety dimensions on flow state in tennis competition. A sample of 59 junior tennis players completed measures of Competitive State Anxiety Inventory-2d and Flow State Scale-2. Following predictive analysis, results showed significant positive correlations between confidence (intensity and direction) and anxiety symptoms (only directional perceptions) with flow state. Standard multiple regression analysis indicated confidence as the only significant predictor of flow. The results confirmed a protective function of confidence against debilitating anxiety interpretations, but there were no significant interaction effects between confidence and anxiety on flow state.

Dead certain: confidence and conservatism predict aggression in simulated international crisis decision-making.

Science.gov (United States)

Johnson, Dominic D P; McDermott, Rose; Cowden, Jon; Tingley, Dustin

2012-03-01

Evolutionary psychologists have suggested that confidence and conservatism promoted aggression in our ancestral past, and that this may have been an adaptive strategy given the prevailing costs and benefits of conflict. However, in modern environments, where the costs and benefits of conflict can be very different owing to the involvement of mass armies, sophisticated technology, and remote leadership, evolved tendencies toward high levels of confidence and conservatism may continue to be a contributory cause of aggression despite leading to greater costs and fewer benefits. The purpose of this paper is to test whether confidence and conservatism are indeed associated with greater levels of aggression-in an explicitly political domain. We present the results of an experiment examining people's levels of aggression in response to hypothetical international crises (a hostage crisis, a counter-insurgency campaign, and a coup). Levels of aggression (which range from concession to negotiation to military attack) were significantly predicted by subjects' (1) confidence that their chosen policy would succeed, (2) score on a liberal-conservative scale, (3) political party affiliation, and (4) preference for the use of military force in real-world U.S. policy toward Iraq and Iran. We discuss the possible adaptive and maladaptive implications of confidence and conservatism for the prospects of war and peace in the modern world.

Use of high flip angle in T1-prepared FAST sequences for myocardial perfusion quantification

International Nuclear Information System (INIS)

Vallee, Jean-Paul; Ivancevic, Marko; Lazeyras, Francois; Didier, Dominique; Kasuboski, Larry; Chatelain, Pascal; Righetti, Alberto

2003-01-01

This study reports on the first use of high flip angle and radio-frequency (RF) spoiling in T1-prepared fast acquisition in steady state (FAST) sequence for myocardial perfusion in patients. T1 dynamic range was measured in vitro with a FAST, an RF FAST and a snapshot fast low-angle shot (FLASH) sequences with a 90 flip angle. Myocardial perfusion was then measured twice in 6 patients during the same MR session. The RF FAST and FLASH, but not the FAST sequence, demonstrated an extended T1 dynamic range; however, the FLASH images were degraded by artifacts not present on the RF FAST images. The myocardial perfusion indices K1 (first-order transfer constant from the blood to the myocardium for the Gd-DTPA) and Vd (distribution volume of Gd-DTPA in myocardium) did not differ significantly between the two injections. K1 was 0.48±0.12 ml/min g -1 and Vd was 12.5±2.9%. With an extended T1 dynamic range and the sensitivity required for myocardial perfusion quantification, the RF FAST sequence with a 90 flip angle outperformed the snapshot FLASH sequence in terms of image quality and the FAST sequence in terms of contrast dynamic range. (orig.)

Preservice teachers' perceived confidence in teaching school violence prevention.

Science.gov (United States)

Kandakai, Tina L; King, Keith A

2002-01-01

To examine preservice teachers' perceived confidence in teaching violence prevention and the potential effect of violence-prevention training on preservice teachers' confidence in teaching violence prevention. Six Ohio universities participated in the study. More than 800 undergraduate and graduate students completed surveys. Violence-prevention training, area of certification, and location of student- teaching placement significantly influenced preservice teachers' perceived confidence in teaching violence prevention. Violence-prevention training positively influences preservice teachers' confidence in teaching violence prevention. The results suggest that such training should be considered as a requirement for teacher preparation programs.

Building technical and social confidence in the safety of geological disposal in Japan

International Nuclear Information System (INIS)

Tochiyama, Osamu; Masuda, Sumio

2013-01-01

Geological disposal has been adopted as the most feasible option for the method of long-term management of high-level radioactive waste (HLW) in every country in the world, regardless of the pros and cons of the nuclear power generation. Building stakeholders’ confidence in safety of geological disposal is indispensable to reach the point where the implementation of geological disposal is accepted by the current generation. The safety case is a key input to build confidence in geological disposal stepwise as the program progresses and regarded to play an important role as a common platform in the communication among stakeholders. The aim of this paper is to review arguments relevant to building technical and social confidence in the progress of Japanese research and development activities as well as international discussions. (author)

Probing the Rare Biosphere of the North-West Mediterranean Sea: An Experiment with High Sequencing Effort.

Directory of Open Access Journals (Sweden)

Bibiana G Crespo

Full Text Available High-throughput sequencing (HTS techniques have suggested the existence of a wealth of species with very low relative abundance: the rare biosphere. We attempted to exhaustively map this rare biosphere in two water samples by performing an exceptionally deep pyrosequencing analysis (~500,000 final reads per sample. Species data were derived by a 97% identity criterion and various parametric distributions were fitted to the observed counts. Using the best-fitting Sichel distribution we estimate a total species richness of 1,568-1,669 (95% Credible Interval and 5,027-5,196 for surface and deep water samples respectively, implying that 84-89% of the total richness in those two samples was sequenced, and we predict that a quadrupling of the present sequencing effort would suffice to observe 90% of the total richness in both samples. Comparing the HTS results with a culturing approach we found that most of the cultured taxa were not obtained by HTS, despite the high sequencing effort. Culturing therefore remains a useful tool for uncovering marine bacterial diversity, in addition to its other uses for studying the ecology of marine bacteria.

Probing the Rare Biosphere of the North-West Mediterranean Sea: An Experiment with High Sequencing Effort.

Science.gov (United States)

Crespo, Bibiana G; Wallhead, Philip J; Logares, Ramiro; Pedrós-Alió, Carlos

2016-01-01

High-throughput sequencing (HTS) techniques have suggested the existence of a wealth of species with very low relative abundance: the rare biosphere. We attempted to exhaustively map this rare biosphere in two water samples by performing an exceptionally deep pyrosequencing analysis (~500,000 final reads per sample). Species data were derived by a 97% identity criterion and various parametric distributions were fitted to the observed counts. Using the best-fitting Sichel distribution we estimate a total species richness of 1,568-1,669 (95% Credible Interval) and 5,027-5,196 for surface and deep water samples respectively, implying that 84-89% of the total richness in those two samples was sequenced, and we predict that a quadrupling of the present sequencing effort would suffice to observe 90% of the total richness in both samples. Comparing the HTS results with a culturing approach we found that most of the cultured taxa were not obtained by HTS, despite the high sequencing effort. Culturing therefore remains a useful tool for uncovering marine bacterial diversity, in addition to its other uses for studying the ecology of marine bacteria.

Alternative confidence measure for local matching stereo algorithms

CSIR Research Space (South Africa)

Ndhlovu, T

2009-11-01

Full Text Available The authors present a confidence measure applied to individual disparity estimates in local matching stereo correspondence algorithms. It aims at identifying textureless areas, where most local matching algorithms fail. The confidence measure works...

People’s confidence in innovation: A component of the entrepreneurial mindset, embedded in gender and culture

DEFF Research Database (Denmark)

Ashourizadeh, Shayegheh; Hassannezhad Chavousi, Zohreh; Schøtt, Thomas

2014-01-01

People may have confidence in innovation, prone to try, buy and use new services and products. Expectedly, confidence in innovation is a component in the entrepreneurial mindset that promotes intention to become entrepreneur and is embedded in the micro-level context of gender and in the macro......-level context of culture. – People’s confidence in innovation is examined for a representative sample of 384,444 adults in 71 societies surveyed in the Global Entrepreneurship Monitor. – Linear modelling shows that people’s confidence in innovation is a component in the entrepreneurial mindset by being...... in innovation promotes entrepreneurial intention, as expected and the benefit is especially high for men and in traditional culture, as hypothesised....

Coping skills: role of trait sport confidence and trait anxiety.

Science.gov (United States)

Cresswell, Scott; Hodge, Ken

2004-04-01

The current research assesses relationships among coping skills, trait sport confidence, and trait anxiety. Two samples (n=47 and n=77) of international competitors from surf life saving (M=23.7 yr.) and touch rugby (M=26.2 yr.) completed the Athletic Coping Skills Inventory, Trait Sport Confidence Inventory, and Sport Anxiety Scale. Analysis yielded significant correlations amongst trait anxiety, sport confidence, and coping. Specifically confidence scores were positively associated with coping with adversity scores and anxiety scores were negatively associated. These findings support the inclusion of the personality characteristics of confidence and anxiety within the coping model presented by Hardy, Jones, and Gould, Researchers should be aware that confidence and anxiety may influence the coping processes of athletes.

High-resolution sequence stratigraphy and continental environmental evolution: An example from east-central Argentina

Science.gov (United States)

Beilinson, Elisa; Veiga, Gonzalo D.; Spalletti, Luis A.

2013-10-01

The aims of this contribution is to establish a high-resolution sequence stratigraphic scheme for the continental deposits that constitute the Punta San Andrés Alloformation (Plio-Pleistocene) in east-central Argentina, to analyze the basin fill evolution and to identify and assess the role that extrinsic factors such as climate and sea-level oscillations played during evolution of the unit. For the high-resolution sequence stratigraphical study of the Punta San Andrés Alloformation, high- and low-accommodation system tracts were defined mainly on the basis of the architectural elements present in the succession, also taking into account the relative degree of channel and floodplain deposits. Discontinuities and the nature of depositional systems generated during variations in accommodation helped identify two fourth-order high-accommodation system tracts and two fourth-order low-accommodation system tracts. At a third-order scale, the Punta San Andrés Alloformation may be interpreted as the progradation of continental depositional systems, characterized by a braided system in the proximal areas, and a low-sinuosity, single-channel system in the distal areas, defined by a high rate of sediment supply and discharge peaks which periodically flooded the plains and generated high aggradation rates during the late Pliocene and lower Pleistocene.

Identifying the bad guy in a lineup using confidence judgments under deadline pressure.

Science.gov (United States)

Brewer, Neil; Weber, Nathan; Wootton, David; Lindsay, D Stephen

2012-10-01

Eyewitness-identification tests often culminate in witnesses not picking the culprit or identifying innocent suspects. We tested a radical alternative to the traditional lineup procedure used in such tests. Rather than making a positive identification, witnesses made confidence judgments under a short deadline about whether each lineup member was the culprit. We compared this deadline procedure with the traditional sequential-lineup procedure in three experiments with retention intervals ranging from 5 min to 1 week. A classification algorithm that identified confidence criteria that optimally discriminated accurate from inaccurate decisions revealed that decision accuracy was 24% to 66% higher under the deadline procedure than under the traditional procedure. Confidence profiles across lineup stimuli were more informative than were identification decisions about the likelihood that an individual witness recognized the culprit or correctly recognized that the culprit was not present. Large differences between the maximum and the next-highest confidence value signaled very high accuracy. Future support for this procedure across varied conditions would highlight a viable alternative to the problematic lineup procedures that have traditionally been used by law enforcement.

Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features

KAUST Repository

Wang, Bing; Zhang, Jun; Chen, Peng; Ji, Zhiwei; Deng, Shuping; Li, Chi

2013-01-01

Background: Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale. IMMS becomes a powerful tool to analyzing complex mixtures, especially for the analysis of peptides in proteomics. The high-throughput nature of this technique provides a challenge for the identification of peptides in complex biological samples. As an important parameter, peptide drift time can be used for enhancing downstream data analysis in IMMS-based proteomics.Results: In this paper, a model is presented based on least square support vectors regression (LS-SVR) method to predict peptide ion drift time in IMMS from the sequence-based features of peptide. Four descriptors were extracted from peptide sequence to represent peptide ions by a 34-component vector. The parameters of LS-SVR were selected by a grid searching strategy, and a 10-fold cross-validation approach was employed for the model training and testing. Our proposed method was tested on three datasets with different charge states. The high prediction performance achieve demonstrate the effectiveness and efficiency of the prediction model.Conclusions: Our proposed LS-SVR model can predict peptide drift time from sequence information in relative high prediction accuracy by a test on a dataset of 595 peptides. This work can enhance the confidence of protein identification by combining with current protein searching techniques. 2013 Wang et al.; licensee BioMed Central Ltd.

Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features

KAUST Repository

Wang, Bing

2013-05-09

Background: Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale. IMMS becomes a powerful tool to analyzing complex mixtures, especially for the analysis of peptides in proteomics. The high-throughput nature of this technique provides a challenge for the identification of peptides in complex biological samples. As an important parameter, peptide drift time can be used for enhancing downstream data analysis in IMMS-based proteomics.Results: In this paper, a model is presented based on least square support vectors regression (LS-SVR) method to predict peptide ion drift time in IMMS from the sequence-based features of peptide. Four descriptors were extracted from peptide sequence to represent peptide ions by a 34-component vector. The parameters of LS-SVR were selected by a grid searching strategy, and a 10-fold cross-validation approach was employed for the model training and testing. Our proposed method was tested on three datasets with different charge states. The high prediction performance achieve demonstrate the effectiveness and efficiency of the prediction model.Conclusions: Our proposed LS-SVR model can predict peptide drift time from sequence information in relative high prediction accuracy by a test on a dataset of 595 peptides. This work can enhance the confidence of protein identification by combining with current protein searching techniques. 2013 Wang et al.; licensee BioMed Central Ltd.

Reclaim your creative confidence.

Science.gov (United States)

Kelley, Tom; Kelley, David

2012-12-01

Most people are born creative. But over time, a lot of us learn to stifle those impulses. We become warier of judgment, more cautious more analytical. The world seems to divide into "creatives" and "noncreatives," and too many people resign themselves to the latter category. And yet we know that creativity is essential to success in any discipline or industry. The good news, according to authors Tom Kelley and David Kelley of IDEO, is that we all can rediscover our creative confidence. The trick is to overcome the four big fears that hold most of us back: fear of the messy unknown, fear of judgment, fear of the first step, and fear of losing control. The authors use an approach based on the work of psychologist Albert Bandura in helping patients get over their snake phobias: You break challenges down into small steps and then build confidence by succeeding on one after another. Creativity is something you practice, say the authors, not just a talent you are born with.

Factors affecting midwives' confidence in intrapartum care: a phenomenological study.

Science.gov (United States)

Bedwell, Carol; McGowan, Linda; Lavender, Tina

2015-01-01

midwives are frequently the lead providers of care for women throughout labour and birth. In order to perform their role effectively and provide women with the choices they require midwives need to be confident in their practice. This study explores factors which may affect midwives' confidence in their practice. hermeneutic phenomenology formed the theoretical basis for the study. Prospective longitudinal data collection was completed using diaries and semi-structured interviews. Twelve midwives providing intrapartum care in a variety of settings were recruited to ensure a variety of experiences in different contexts were captured. the principal factor affecting workplace confidence, both positively and negatively, was the influence of colleagues. Perceived autonomy and a sense of familiarity could also enhance confidence. However, conflict in the workplace was a critical factor in reducing midwives' confidence. Confidence was an important, but fragile, phenomenon to midwives and they used a variety of coping strategies, emotional intelligence and presentation management to maintain it. this is the first study to highlight both the factors influencing midwives' workplace confidence and the strategies midwives employed to maintain their confidence. Confidence is important in maintaining well-being and workplace culture may play a role in explaining the current low morale within the midwifery workforce. This may have implications for women's choices and care. Support, effective leadership and education may help midwives develop and sustain a positive sense of confidence. Copyright © 2014 Elsevier Ltd. All rights reserved.

The specificity of memory for a highly trained finger movement sequence: Change the ending, change all.

Science.gov (United States)

Rozanov, Simon; Keren, Ofer; Karni, Avi

2010-05-17

How are highly trained movement sequences represented in long-term memory? Here we show that the gains attained in the performance of a well-trained sequence of finger movements can be expressed only when the order of the movements is exactly as practiced. Ten young adults were trained to perform a given 5-element sequence of finger-to-thumb opposition movements with their left hand. Movements were analyzed using video based tracking. Three weeks of training resulted, along with improved accuracy, in robustly shortened movement times as well as shorter finger-to-thumb touch times. However, there was little transfer of these gains in speed to the execution of the same component movements arranged in a new order. Moreover, even when the only change was the omission of the one before final movement of the trained sequence (Omit sequence), the initial movements of the sequence were significantly slowed down, although these movements were identical to the initial movements of the trained sequence. Our results support the notion that a well-trained sequence of finger movements can be represented, in the adult motor system, as a singular, co-articulated, unit of movement, in which even the initial component movements are contingent on the subsequent, anticipated, ones. Because of co-articulation related anticipatory effects, gains in fluency and accuracy acquired in training on a specific movement sequence cannot be expressed in full in the execution of the trained component movements or of a full segment of the trained sequence, if followed by a different ending segment. Copyright 2010. Published by Elsevier B.V.

nigerian students' self-confidence in responding to statements

African Journals Online (AJOL)

Temechegn

Altogether the test is made up of 40 items covering students' ability to recall definition ... confidence interval within which student have confidence in their choice of the .... is mentioned these equilibrium systems come to memory of the learner.

Conquering Credibility for Monetary Policy Under Sticky Confidence

Directory of Open Access Journals (Sweden)

Jaylson Jair da Silveira

2015-06-01

Full Text Available We derive a best-reply monetary policy when the confidence by price setters on the monetary authority’s commitment to price level targeting may be both incomplete and sticky. We find that complete confidence (or full credibility is not a necessary condition for the achievement of a price level target even when heterogeneity in firms’ price level expectations is endogenously time-varying and may emerge as a long-run equilibrium outcome. In fact, in the absence of exogenous perturbations to the dynamic of confidence building, it is the achievement of a price level target for long enough that, due to stickiness in the state of confidence, rather ensures the conquering of full credibility. This result has relevant implications for the conduct of monetary policy in pursuit of price stability. One implication is that setting a price level target matters more as a means to provide monetary policy with a sharper focus on price stability than as a device to conquer credibility. As regards the conquering of credibility for monetary policy, it turns out that actions speak louder than words, as the continuing achievement of price stability is what ultimately performs better as a confidence-building device.

Accurate molecular diagnosis of phenylketonuria and tetrahydrobiopterin-deficient hyperphenylalaninemias using high-throughput targeted sequencing

Science.gov (United States)

Trujillano, Daniel; Perez, Belén; González, Justo; Tornador, Cristian; Navarrete, Rosa; Escaramis, Georgia; Ossowski, Stephan; Armengol, Lluís; Cornejo, Verónica; Desviat, Lourdes R; Ugarte, Magdalena; Estivill, Xavier

2014-01-01

Genetic diagnostics of phenylketonuria (PKU) and tetrahydrobiopterin (BH4) deficient hyperphenylalaninemia (BH4DH) rely on methods that scan for known mutations or on laborious molecular tools that use Sanger sequencing. We have implemented a novel and much more efficient strategy based on high-throughput multiplex-targeted resequencing of four genes (PAH, GCH1, PTS, and QDPR) that, when affected by loss-of-function mutations, cause PKU and BH4DH. We have validated this approach in a cohort of 95 samples with the previously known PAH, GCH1, PTS, and QDPR mutations and one control sample. Pooled barcoded DNA libraries were enriched using a custom NimbleGen SeqCap EZ Choice array and sequenced using a HiSeq2000 sequencer. The combination of several robust bioinformatics tools allowed us to detect all known pathogenic mutations (point mutations, short insertions/deletions, and large genomic rearrangements) in the 95 samples, without detecting spurious calls in these genes in the control sample. We then used the same capture assay in a discovery cohort of 11 uncharacterized HPA patients using a MiSeq sequencer. In addition, we report the precise characterization of the breakpoints of four genomic rearrangements in PAH, including a novel deletion of 899 bp in intron 3. Our study is a proof-of-principle that high-throughput-targeted resequencing is ready to substitute classical molecular methods to perform differential genetic diagnosis of hyperphenylalaninemias, allowing the establishment of specifically tailored treatments a few days after birth. PMID:23942198

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics.

Science.gov (United States)

Timmermans, M J T N; Dodsworth, S; Culverwell, C L; Bocak, L; Ahrens, D; Littlewood, D T J; Pons, J; Vogler, A P

2010-11-01

Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags ('barcodes'). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three 'bait' sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species 'barcodes' that currently use the cox1 gene only.

Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

KAUST Repository

Black, PA

2015-10-24

Background Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. This study aimed to define a reliable cut-off for identification of low frequency sequence variants and to subsequently investigate genetic heterogeneity and the evolution of drug resistance in M. tuberculosis. Methods Genomic DNA was isolated from single colonies from 14 rifampicin mono-resistant M. tuberculosis isolates, as well as the primary cultures and follow up MDR cultures from two of these patients. The whole genomes of the M. tuberculosis isolates were sequenced using either the Illumina MiSeq or Illumina HiSeq platforms. Sequences were analysed with an in-house pipeline. Results Using next-generation sequencing in combination with Sanger sequencing and statistical analysis we defined a read frequency cut-off of 30 % to identify low frequency M. tuberculosis variants with high confidence. Using this cut-off we demonstrated a high rate of genetic diversity between single colonies isolated from one population, showing that by using the current sequencing technology, single colonies are not a true reflection of the genetic diversity within a whole population and vice versa. We further showed that numerous heterogeneous variants emerge and then disappear during the evolution of isoniazid resistance within individual patients. Our findings allowed us to formulate a model for the selective bottleneck which occurs during the course of infection, acting as a genomic purification event. Conclusions Our study demonstrated true levels of genetic diversity

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar.

Science.gov (United States)

Perry, George H; Reeves, Darryl; Melsted, Páll; Ratan, Aakrosh; Miller, Webb; Michelini, Katelyn; Louis, Edward E; Pritchard, Jonathan K; Mason, Christopher E; Gilad, Yoav

2012-01-01

We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ~3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ~2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ~10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage-a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests.

Simulation experience enhances physical therapist student confidence in managing a patient in the critical care environment.

Science.gov (United States)

Ohtake, Patricia J; Lazarus, Marcilene; Schillo, Rebecca; Rosen, Michael

2013-02-01

Rehabilitation of patients in critical care environments improves functional outcomes. This finding has led to increased implementation of intensive care unit (ICU) rehabilitation programs, including early mobility, and an associated increased demand for physical therapists practicing in ICUs. Unfortunately, many physical therapists report being inadequately prepared to work in this high-risk environment. Simulation provides focused, deliberate practice in safe, controlled learning environments and may be a method to initiate academic preparation of physical therapists for ICU practice. The purpose of this study was to examine the effect of participation in simulation-based management of a patient with critical illness in an ICU setting on levels of confidence and satisfaction in physical therapist students. A one-group, pretest-posttest, quasi-experimental design was used. Physical therapist students (N=43) participated in a critical care simulation experience requiring technical (assessing bed mobility and pulmonary status), behavioral (patient and interprofessional communication), and cognitive (recognizing a patient status change and initiating appropriate responses) skill performance. Student confidence and satisfaction were surveyed before and after the simulation experience. Students' confidence in their technical, behavioral, and cognitive skill performance increased from "somewhat confident" to "confident" following the critical care simulation experience. Student satisfaction was highly positive, with strong agreement the simulation experience was valuable, reinforced course content, and was a useful educational tool. Limitations of the study were the small sample from one university and a control group was not included. Incorporating a simulated, interprofessional critical care experience into a required clinical course improved physical therapist student confidence in technical, behavioral, and cognitive performance measures and was associated with high

The antecedents and belief-polarized effects of thought confidence.

Science.gov (United States)

Chou, Hsuan-Yi; Lien, Nai-Hwa; Liang, Kuan-Yu

2011-01-01

This article investigates 2 possible antecedents of thought confidence and explores the effects of confidence induced before or during ad exposure. The results of the experiments indicate that both consumers' dispositional optimism and spokesperson attractiveness have significant effects on consumers' confidence in thoughts that are generated after viewing the advertisement. Higher levels of thought confidence will influence the quality of the thoughts that people generate, lead to either positively or negatively polarized message processing, and therefore induce better or worse advertising effectiveness, depending on the valence of thoughts. The authors posit the belief-polarization hypothesis to explain these findings.

Applications of High-Throughput Nucleotide Sequencing (PhD)

DEFF Research Database (Denmark)

Waage, Johannes

equally large demands in data handling, analysis and interpretation, perhaps defining the modern challenge of the computational biologist of the post-genomic era. The first part of this thesis consists of a general introduction to the history, common terms and challenges of next generation sequencing......-sequencing, a study of the effects on alternative RNA splicing of KO of the nonsense mediated RNA decay system in Mus, using digital gene expression and a custom-built exon-exon junction mapping pipeline is presented (article I). Evolved from this work, a Bioconductor package, spliceR, for classifying alternative...

Imaging of cranial nerves with three-dimensional high resolution diffusion-weighted MR sequence based on SSFP technique

International Nuclear Information System (INIS)

Zhang Zhongwei; Chen Yingming; Meng Quanfei

2008-01-01

Objective: To depict the normal anatomy of cranial nerves in detail and define the exact relationships between cranial nerves and adjacent structures with three-dimensional high resolution diffusion-weighted MR sequence based on SSFP technique (3D DW-SSFP). Methods: 3D DW- SSFP sequence was performed and axial images were obtained in 12 healthy volunteers Post-processing techniques were used to generate images of cranial nerves, and the images acquired were compared with anatomical sections and diagrams of textbook. Results: In all subjects, 3D DW-SSFP sequence could produce homogeneous images and high contrast between the cranial nerves and other solid structures. The intracranial portions of all cranial nerves except olfactory nerve were identified; the extracranial portions of nerve Ⅱ-Ⅻ were identified in all subjects bilaterally. Conclusion: The 3D DW-SSFP sequence can characterize the normal MR appearance of cranial nerves and its branches and the ability to define the nerves may provide greater sensitivity and specificity in detecting abnormalities of craniofacial structure. (authors)

Sedimentology and High Resolution Sequence Stratigraphy of the Middle Jurassic Dhruma Formation Carbonates Outcrops in the Central Saudi Arabia

Science.gov (United States)

Yousif, Ibrahim; Abdullatif, Osman; Makkawi, Mohammed; Abdulghani, Waleed

2017-04-01

This study investigates the microfacies and sequence stratigraphic frame work of the Middle Jurassic Dhruma Formation in outcrops in central Saudi Arabia. The study contributes to the efforts to understand and enhance local and regional stratigraphic relationship and correlation of the Jurassic carbonate sequences and their significance to reservoir description and prediction in the subsurcae. The study describes and characterizes the sedimentology, microfacies and the stratigraphy of Dhruma Formation from outcrop sections having a total thickness of 70 m. Detailed microfacies and high-resolution stratigraphical analysis were carried out to determine microfacies, cyclicity, sequences and staking pattern. The study revealed ten lithofacies namely: oolitic grainstone,bioclastic oolitic grainstone, oolitic grapestone, bioclastic grainstone,foraminiferal packstone, echinoderm packstone, peloidal packstone to grainstone,skeletal wackestone to packstone, mudstone, and marlstone.These lithofacies were grouped into five lithofacies associations that deposited on a carbonate ramp setting. The depositional environment ranging from low energy lagoonal setting to high-energy shoals and banks to low energy outer ramp setting. Five high-resolution composite sequences have been defined and each sequence is composed at the bottom of intercalated mudstone/wackestone that passing up into grainstone lithofacies.The composite sequences range in thickness from 7 to 15 m, while the parasequences range from 0.5 to 1.5 m. The composite sequences extend laterally for a distance of more than 350 m. The overall composite section shows a shallowing upward succession of the 4th to the 5th order high-resolution sequences.The dominant lithofacies are the grainy ones, which constitute 30%, 50% and 80% of the studied sections. Furthermore, the parasequences thickness and their bio-components are increasing towards the top. The muddy lithofacies intensively affected the vertical continuity of the

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.

Science.gov (United States)

Yuan, Tiezheng; Huang, Xiaoyi; Dittmar, Rachel L; Du, Meijun; Kohli, Manish; Boardman, Lisa; Thibodeau, Stephen N; Wang, Liang

2014-03-05

RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers. We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification" includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module "mRNA identification" includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module "Target screening" provides expression profiling analyses and graphic visualization. The module "Self-testing" offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program's functionality. eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory.

Peptide Pattern Recognition for high-throughput protein sequence analysis and clustering

DEFF Research Database (Denmark)

Busk, Peter Kamp

2017-01-01

Large collections of protein sequences with divergent sequences are tedious to analyze for understanding their phylogenetic or structure-function relation. Peptide Pattern Recognition is an algorithm that was developed to facilitate this task but the previous version does only allow a limited...... number of sequences as input. I implemented Peptide Pattern Recognition as a multithread software designed to handle large numbers of sequences and perform analysis in a reasonable time frame. Benchmarking showed that the new implementation of Peptide Pattern Recognition is twenty times faster than...... the previous implementation on a small protein collection with 673 MAP kinase sequences. In addition, the new implementation could analyze a large protein collection with 48,570 Glycosyl Transferase family 20 sequences without reaching its upper limit on a desktop computer. Peptide Pattern Recognition...

Clinical Application of 3D-CISS MRI Sequences for Diagnosis and Surgical Planning of Spinal Arachnoid Diverticula and Adhesions in Dogs.

Science.gov (United States)

Tauro, Anna; Jovanovik, Jelena; Driver, Colin John; Rusbridge, Clare

2018-02-01

 Abnormalities within the spinal arachnoid space are often treated surgically, but they can be challenging to detect with conventional magnetic resonance imaging (MRI) sequences. 3D-CISS sequences are considered superior in evaluating structures surrounded by cerebrospinal fluid (CSF) due to the high signal-to-noise ratio, high contrast-to-noise ratio and intrinsic insensitivity to motion with minimal signal loss due to CSF pulsations. Our objective was to describe findings and advantages in adding 3D-CISS sequences to routine MRI in patients affected by spinal arachnoid diverticula (SAD) or arachnoid adhesions.  This article is a retrospective review of medical records of 19 dogs admitted at Fitzpatrick Referrals between 2013 and 2017 that were diagnosed with SAD and confirmed surgically. Inclusion criterions were the presence of clinical signs compatible with compressive myelopathy and an MRI diagnosis, which included the 3D-CISS sequence. Our database was searched for additional 19 dogs diagnosed with other spinal lesions other than SAD that had the same MR sequences. All MR images were anonymized and evaluated by two assessors.  3D-CISS sequence appears to improve confidence in diagnosing and surgical planning (Mann-Whitney U -test: p  CSF hydrodynamics and providing more anatomical details than conventional MRI sequences. The clinical data in combination with imaging findings would limit over interpretation, when concurrent pathology within the arachnoid space is present. Schattauer GmbH Stuttgart.

Bayesian reconstruction of photon interaction sequences for high-resolution PET detectors

Energy Technology Data Exchange (ETDEWEB)

Pratx, Guillem; Levin, Craig S [Molecular Imaging Program at Stanford, Department of Radiology, Stanford, CA (United States)], E-mail: cslevin@stanford.edu

2009-09-07

Realizing the full potential of high-resolution positron emission tomography (PET) systems involves accurately positioning events in which the annihilation photon deposits all its energy across multiple detector elements. Reconstructing the complete sequence of interactions of each photon provides a reliable way to select the earliest interaction because it ensures that all the interactions are consistent with one another. Bayesian estimation forms a natural framework to maximize the consistency of the sequence with the measurements while taking into account the physics of {gamma}-ray transport. An inherently statistical method, it accounts for the uncertainty in the measured energy and position of each interaction. An algorithm based on maximum a posteriori (MAP) was evaluated for computer simulations. For a high-resolution PET system based on cadmium zinc telluride detectors, 93.8% of the recorded coincidences involved at least one photon multiple-interactions event (PMIE). The MAP estimate of the first interaction was accurate for 85.2% of the single photons. This represents a two-fold reduction in the number of mispositioned events compared to minimum pair distance, a simpler yet efficient positioning method. The point-spread function of the system presented lower tails and higher peak value when MAP was used. This translated into improved image quality, which we quantified by studying contrast and spatial resolution gains.

An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data.

Science.gov (United States)

Azam, Sarwar; Rathore, Abhishek; Shah, Trushar M; Telluri, Mohan; Amindala, BhanuPrakash; Ruperao, Pradeep; Katta, Mohan A V S K; Varshney, Rajeev K

2014-01-01

Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone

Allele Re-sequencing Technologies

DEFF Research Database (Denmark)

Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

2013-01-01

The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

Male partner selectivity, romantic confidence, and media depictions of partner scarcity.

Science.gov (United States)

Taylor, Laramie D

2013-01-18

An experiment was conducted to explore the effects of exposure to partner scarcity or abundance messages on men's partner selectivity, romantic confidence, and self-assessed attractiveness. Undergraduate male participants watched a soap opera narrative featuring either two men competing over one potential female partner (partner scarcity) or two women competing over one potential male partner (partner abundance). Relative to control subjects, watching either narrative reduced romantic confidence. Experimental condition also affected partner selectivity and self-assessed attractiveness, though both effects were moderated by endorsement of traditional masculine ideology. Viewing the abundance narrative resulted in greater selectivity and self-assessed attractiveness for men high in endorsement of traditional masculinity but diminished selectivity and self-assessed attractiveness for men low in endorsement of traditional masculine identity.

Male Partner Selectivity, Romantic Confidence, and Media Depictions of Partner Scarcity

Directory of Open Access Journals (Sweden)

Laramie D. Taylor

2013-01-01

Full Text Available An experiment was conducted to explore the effects of exposure to partner scarcity or abundance messages on men's partner selectivity, romantic confidence, and self-assessed attractiveness. Undergraduate male participants watched a soap opera narrative featuring either two men competing over one potential female partner (partner scarcity or two women competing over one potential male partner (partner abundance. Relative to control subjects, watching either narrative reduced romantic confidence. Experimental condition also affected partner selectivity and self-assessed attractiveness, though both effects were moderated by endorsement of traditional masculine ideology. Viewing the abundance narrative resulted in greater selectivity and self-assessed attractiveness for men high in endorsement of traditional masculinity but diminished selectivity and self-assessed attractiveness for men low in endorsement of traditional masculine identity.

Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life

DEFF Research Database (Denmark)

Karst, Soeren M; Dueholm, Morten S; McIlroy, Simon J

2016-01-01

Ribosomal RNA (rRNA) genes are the consensus marker for determination of microbial diversity on the planet, invaluable in studies of evolution and, for the past decade, high-throughput sequencing of variable regions of ribosomal RNA genes has become the backbone of most microbial ecology studies...... (SSU) rRNA genes and synthetic long read sequencing by molecular tagging, to generate primer-free, full-length SSU rRNA gene sequences from all domains of life, with a median raw error rate of 0.17%. We generated thousands of full-length SSU rRNA sequences from five well-studied ecosystems (soil, human...... gut, fresh water, anaerobic digestion, and activated sludge) and obtained sequences covering all domains of life and the majority of all described phyla. Interestingly, 30% of all bacterial operational taxonomic units were novel, compared to the SILVA database (less than 97% similarity...

Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum

Directory of Open Access Journals (Sweden)

White Frank F

2011-07-01

Full Text Available Abstract Background Eight diverse sorghum (Sorghum bicolor L. Moench accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs. Two strategies were used for DNA library preparation. Missing SNP genotype data were imputed by local haplotype comparison. The effect of library type and genomic diversity on SNP discovery and imputation are evaluated. Results Alignment of eight genome equivalents (6 Gb to the public reference genome revealed 283,000 SNPs at ≥82% confirmation probability. Sequencing from libraries constructed to limit sequencing to start at defined restriction sites led to genotyping 10-fold more SNPs in all 8 accessions, and correctly imputing 11% more missing data, than from semirandom libraries. The SNP yield advantage of the reduced-representation method was less than expected, since up to one fifth of reads started at noncanonical restriction sites and up to one third of restriction sites predicted in silico to yield unique alignments were not sampled at near-saturation. For imputation accuracy, the availability of a genomically similar accession in the germplasm panel was more important than panel size or sequencing coverage. Conclusions A sequence quantity of 3 million 50-base reads per accession using a BsrFI library would conservatively provide satisfactory genotyping of 96,000 sorghum SNPs. For most reliable SNP-genotype imputation in shallowly sequenced genomes, germplasm panels should consist of pairs or groups of genomically similar entries. These results may help in designing strategies for economical genotyping-by-sequencing of large numbers of plant accessions.

Confidence in Numerical Simulations

Energy Technology Data Exchange (ETDEWEB)

Hemez, Francois M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-02-23

This PowerPoint presentation offers a high-level discussion of uncertainty, confidence and credibility in scientific Modeling and Simulation (M&S). It begins by briefly evoking M&S trends in computational physics and engineering. The first thrust of the discussion is to emphasize that the role of M&S in decision-making is either to support reasoning by similarity or to “forecast,” that is, make predictions about the future or extrapolate to settings or environments that cannot be tested experimentally. The second thrust is to explain that M&S-aided decision-making is an exercise in uncertainty management. The three broad classes of uncertainty in computational physics and engineering are variability and randomness, numerical uncertainty and model-form uncertainty. The last part of the discussion addresses how scientists “think.” This thought process parallels the scientific method where by a hypothesis is formulated, often accompanied by simplifying assumptions, then, physical experiments and numerical simulations are performed to confirm or reject the hypothesis. “Confidence” derives, not just from the levels of training and experience of analysts, but also from the rigor with which these assessments are performed, documented and peer-reviewed.

Non-Asymptotic Confidence Sets for Circular Means

Directory of Open Access Journals (Sweden)

Thomas Hotz

2016-10-01

Full Text Available The mean of data on the unit circle is defined as the minimizer of the average squared Euclidean distance to the data. Based on Hoeffding’s mass concentration inequalities, non-asymptotic confidence sets for circular means are constructed which are universal in the sense that they require no distributional assumptions. These are then compared with asymptotic confidence sets in simulations and for a real data set.

Prediction of Toxin Genes from Chinese Yellow Catfish Based on Transcriptomic and Proteomic Sequencing

Directory of Open Access Journals (Sweden)

Bing Xie

2016-04-01

Full Text Available Fish venom remains a virtually untapped resource. There are so few fish toxin sequences for reference, which increases the difficulty to study toxins from venomous fish and to develop efficient and fast methods to dig out toxin genes or proteins. Here, we utilized Chinese yellow catfish (Pelteobagrus fulvidraco as our research object, since it is a representative species in Siluriformes with its venom glands embedded in the pectoral and dorsal fins. In this study, we set up an in-house toxin database and a novel toxin-discovering protocol to dig out precise toxin genes by combination of transcriptomic and proteomic sequencing. Finally, we obtained 15 putative toxin proteins distributed in five groups, namely Veficolin, Ink toxin, Adamalysin, Za2G and CRISP toxin. It seems that we have developed a novel bioinformatics method, through which we could identify toxin proteins with high confidence. Meanwhile, these toxins can also be useful for comparative studies in other fish and development of potential drugs.

High-throughput sequencing of nematode communities from total soil DNA extractions

DEFF Research Database (Denmark)

Sapkota, Rumakanta; Nicolaisen, Mogens

2015-01-01

nematodes without the need for enrichment was developed. Using this strategy on DNA templates from a set of 22 agricultural soils, we obtained 64.4% sequences of nematode origin in total, whereas the remaining sequences were almost entirely from other metazoans. The nematode sequences were derived from...... in previous sequence-based studies are not nematode specific but also amplify other groups of organisms such as fungi and plantae, and thus require a nematode enrichment step that may introduce biases. Results: In this study an amplification strategy which selectively amplifies a fragment of the SSU from...... a broad taxonomic range and most sequences were from nematode taxa that have previously been found to be abundant in soil such as Tylenchida, Rhabditida, Dorylaimida, Triplonchida and Araeolaimida. Conclusions: Our amplification and sequencing strategy for assessing nematode diversity was able to collect...

Water imaging (hydrography) in the fetus: the value of a heavily T2-weighted sequence

Energy Technology Data Exchange (ETDEWEB)

Kline-Fath, Beth M.; Calvo-Garcia, Maria A.; O' Hara, Sara M.; Racadio, Judy M. [University of Cincinnati Medical Center, Department of Radiology, Cincinnati Children' s Hospital Medical Center, Cincinnati, OH (United States)

2007-02-15

Since the development of fast imaging sequences, MR has proved to be a helpful tool in the evaluation of fetal pathology. Because of the high water content of fetal tissues and pathology, hydrography imaging (MR fetography) can provide additional diagnostic information. To demonstrate the benefit of MR fetography in fetal imaging. From 2004 to 2005, 126 fetal MR examinations were performed for evaluation of an abnormality depicted on an antenatal sonogram. Single-shot fast spin-echo MR imaging and MR fetography were performed through the area of fetal pathology. The two studies were retrospectively compared. The primary diagnosis was not changed with the addition of MR fetography. New findings, particularly in the kidneys and spine, were identified in 9% of the patients. When fetal pathology was of high water content (80% patients), the MR fetography imaging increased diagnostic confidence. In 11% of the patients, those with cardiovascular or low water pathology, the MR fetography was not beneficial. The mainstay of fetal imaging is currently the HASTE and SSFSE sequences. However, MR fetography is an excellent adjunct that highlights fetal pathology by reinforcing the diagnosis, identifying additional findings, and providing high-contrast high-resolution images that are helpful when counseling clinicians and patients. (orig.)

Asteroseismic measurement of surface-to-core rotation in a main-sequence star*

Directory of Open Access Journals (Sweden)

Kurtz Donald W.

2015-01-01

Full Text Available We have discovered rotationally split core g-mode triplets and surface p-mode triplets and quintuplets in a terminal age main-sequence A star, KIC 11145123, that shows both δ Sct p-mode pulsations and γ Dor g-mode pulsations. This gives the first robust determination of the rotation of the deep core and surface of a main-sequence star, essentially model-independently. We find its rotation to be nearly uniform with a period near 100 d, but we show with high confidence that the surface rotates slightly faster than the core. A strong angular momentum transfer mechanism must be operating to produce the nearly rigid rotation, and a mechanism other than viscosity must be operating to produce a more rapidly rotating surface than core. Our asteroseismic result, along with previous asteroseismic constraints on internal rotation in some B stars, and measurements of internal rotation in some subgiant, giant and white dwarf stars, has made angular momentum transport in stars throughout their lifetimes an observational science.

Methodology for building confidence measures

Science.gov (United States)

Bramson, Aaron L.

2004-04-01

This paper presents a generalized methodology for propagating known or estimated levels of individual source document truth reliability to determine the confidence level of a combined output. Initial document certainty levels are augmented by (i) combining the reliability measures of multiply sources, (ii) incorporating the truth reinforcement of related elements, and (iii) incorporating the importance of the individual elements for determining the probability of truth for the whole. The result is a measure of confidence in system output based on the establishing of links among the truth values of inputs. This methodology was developed for application to a multi-component situation awareness tool under development at the Air Force Research Laboratory in Rome, New York. Determining how improvements in data quality and the variety of documents collected affect the probability of a correct situational detection helps optimize the performance of the tool overall.

The relationship between confidence in charitable organizations and volunteering revisited

NARCIS (Netherlands)

Bekkers, René H.F.P.; Bowman, Woods

2009-01-01

Confidence in charitable organizations (charitable confidence) would seem to be an important prerequisite for philanthropic behavior. Previous research relying on cross-sectional data has suggested that volunteering promotes charitable confidence and vice versa. This research note, using new

Disconnections Between Teacher Expectations and Student Confidence in Bioethics

Science.gov (United States)

Hanegan, Nikki L.; Price, Laura; Peterson, Jeremy

2008-09-01

This study examines how student practice of scientific argumentation using socioscientific bioethics issues affects both teacher expectations of students’ general performance and student confidence in their own work. When teachers use bioethical issues in the classroom students can gain not only biology content knowledge but also important decision-making skills. Learning bioethics through scientific argumentation gives students opportunities to express their ideas, formulate educated opinions and value others’ viewpoints. Research has shown that science teachers’ expectations of student success and knowledge directly influence student achievement and confidence levels. Our study analyzes pre-course and post-course surveys completed by students enrolled in a university level bioethics course ( n = 111) and by faculty in the College of Biology and Agriculture faculty ( n = 34) based on their perceptions of student confidence. Additionally, student data were collected from classroom observations and interviews. Data analysis showed a disconnect between faculty and students perceptions of confidence for both knowledge and the use of science argumentation. Student reports of their confidence levels regarding various bioethical issues were higher than faculty reports. A further disconnect showed up between students’ preferred learning styles and the general faculty’s common teaching methods; students learned more by practicing scientific argumentation than listening to traditional lectures. Students who completed a bioethics course that included practice in scientific argumentation, significantly increased their confidence levels. This study suggests that professors’ expectations and teaching styles influence student confidence levels in both knowledge and scientific argumentation.

Risk of Breast Cancer with CXCR4-using HIV Defined by V3-Loop Sequencing