Integration of Temporal and Ordinal Information During Serial Interception Sequence Learning

PubMed Central

Gobel, Eric W.; Sanchez, Daniel J.; Reber, Paul J.

2011-01-01

The expression of expert motor skills typically involves learning to perform a precisely timed sequence of movements (e.g., language production, music performance, athletic skills). Research examining incidental sequence learning has previously relied on a perceptually-cued task that gives participants exposure to repeating motor sequences but does not require timing of responses for accuracy. Using a novel perceptual-motor sequence learning task, learning a precisely timed cued sequence of motor actions is shown to occur without explicit instruction. Participants learned a repeating sequence through practice and showed sequence-specific knowledge via a performance decrement when switched to an unfamiliar sequence. In a second experiment, the integration of representation of action order and timing sequence knowledge was examined. When either action order or timing sequence information was selectively disrupted, performance was reduced to levels similar to completely novel sequences. Unlike prior sequence-learning research that has found timing information to be secondary to learning action sequences, when the task demands require accurate action and timing information, an integrated representation of these types of information is acquired. These results provide the first evidence for incidental learning of fully integrated action and timing sequence information in the absence of an independent representation of action order, and suggest that this integrative mechanism may play a material role in the acquisition of complex motor skills. PMID:21417511

Why Children Are Left Behind and What We Can Do about It.

ERIC Educational Resources Information Center

Reigeluth, Charles M.; Beatty, Brian J.

2003-01-01

Proposes four main reasons that children are left behind in schools: unmet needs, lack of motivation, lack of foundation and prior knowledge, and lack of support for learning. Discusses Maslow's hierarch of needs; partnerships with parents; connecting to student interests; insisting on mastery; curriculum sequencing; brain-based research; and…

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake

USGS Publications Warehouse

Castoe, Todd A.; Poole, Alexander W.; de Koning, A. P. Jason; Jones, Kenneth L.; Tomback, Diana F.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Lance, Stacey L.; Streicher, Jeffrey W.; Smith, Eric N.; Pollock, David D.

2012-01-01

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

Rapid microsatellite identification from illumina paired-end genomic sequencing in two birds and a snake

USGS Publications Warehouse

Castoe, T.A.; Poole, A.W.; de Koning, A. P. J.; Jones, K.L.; Tomback, D.F.; Oyler-McCance, S.J.; Fike, J.A.; Lance, S.L.; Streicher, J.W.; Smith, E.N.; Pollock, D.D.

2012-01-01

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample - a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable. ?? 2012 Castoe et al.

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.

PubMed

Castoe, Todd A; Poole, Alexander W; de Koning, A P Jason; Jones, Kenneth L; Tomback, Diana F; Oyler-McCance, Sara J; Fike, Jennifer A; Lance, Stacey L; Streicher, Jeffrey W; Smith, Eric N; Pollock, David D

2012-01-01

Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample--a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

The Fallacy of Composition: Prospective Mathematics Teachers' Use of Logical Fallacies

ERIC Educational Resources Information Center

Chernoff, Egan J.; Russell, Gale L.

2012-01-01

The purpose of this article is to address the lack of research on teachers' knowledge of probability. As has been the case in prior research, we asked prospective mathematics teachers to determine which of the presented sequences of coin flips was least likely to occur. However, instead of using the traditional perspectives of heuristic and…

The influence of prior knowledge on the retrieval-directed function of note taking in prior knowledge activation.

PubMed

Wetzels, Sandra A J; Kester, Liesbeth; van Merriënboer, Jeroen J G; Broers, Nick J

2011-06-01

Prior knowledge activation facilitates learning. Note taking during prior knowledge activation (i.e., note taking directed at retrieving information from memory) might facilitate the activation process by enabling learners to build an external representation of their prior knowledge. However, taking notes might be less effective in supporting prior knowledge activation if available prior knowledge is limited. This study investigates the effects of the retrieval-directed function of note taking depending on learners' level of prior knowledge. It is hypothesized that the effectiveness of note taking is influenced by the amount of prior knowledge learners already possess. Sixty-one high school students participated in this study. A prior knowledge test was used to ascertain differences in level of prior knowledge and assign participants to a low or a high prior knowledge group. A 2×2 factorial design was used to investigate the effects of note taking during prior knowledge activation (yes, no) depending on learners' level of prior knowledge (low, high) on mental effort, performance, and mental efficiency. Note taking during prior knowledge activation lowered mental effort and increased mental efficiency for high prior knowledge learners. For low prior knowledge learners, note taking had the opposite effect on mental effort and mental efficiency. The effects of the retrieval-directed function of note taking are influenced by learners' level of prior knowledge. Learners with high prior knowledge benefit from taking notes while activating prior knowledge, whereas note taking has no beneficial effects for learners with limited prior knowledge. ©2010 The British Psychological Society.

Preferences for learning different types of genome sequencing results among young breast cancer patients: Role of psychological and clinical factors.

PubMed

Kaphingst, Kimberly A; Ivanovich, Jennifer; Lyons, Sarah; Biesecker, Barbara; Dresser, Rebecca; Elrick, Ashley; Matsen, Cindy; Goodman, Melody

2018-01-29

The growing importance of genome sequencing means that patients will increasingly face decisions regarding what results they would like to learn. The present study examined psychological and clinical factors that might affect these preferences. 1,080 women diagnosed with breast cancer at age 40 or younger completed an online survey. We assessed their interest in learning various types of genome sequencing results: risk of preventable disease or unpreventable disease, cancer treatment response, uncertain meaning, risk to relatives' health, and ancestry/physical traits. Multivariable logistic regression was used to examine whether being "very" interested in each result type was associated with clinical factors: BRCA1/2 mutation status, prior genetic testing, family history of breast cancer, and psychological factors: cancer recurrence worry, genetic risk worry, future orientation, health information orientation, and genome sequencing knowledge. The proportion of respondents who were very interested in learning each type of result ranged from 16% to 77%. In all multivariable models, those who were very interested in learning a result type had significantly higher knowledge about sequencing benefits, greater genetic risks worry, and stronger health information orientation compared to those with less interest (p-values < .05). Our findings indicate that high interest in return of various types of genome sequencing results was more closely related to psychological factors. Shared decision-making approaches that increase knowledge about genome sequencing and incorporate patient preferences for health information and learning about genetic risks may help support patients' informed choices about learning different types of sequencing results. © Society of Behavioral Medicine 2018.

A Fast Variant of 1H Spectroscopic U-FLARE Imaging Using Adjusted Chemical Shift Phase Encoding

NASA Astrophysics Data System (ADS)

Ebel, Andreas; Dreher, Wolfgang; Leibfritz, Dieter

2000-02-01

So far, fast spectroscopic imaging (SI) using the U-FLARE sequence has provided metabolic maps indirectly via Fourier transformation (FT) along the chemical shift (CS) dimension and subsequent peak integration. However, a large number of CS encoding steps Nω is needed to cover the spectral bandwidth and to achieve sufficient spectral resolution for peak integration even if the number of resonance lines is small compared to Nω and even if only metabolic images are of interest and not the spectra in each voxel. Other reconstruction algorithms require extensive prior knowledge, starting values, and/or model functions. An adjusted CS phase encoding scheme (APE) can be used to overcome these drawbacks. It incorporates prior knowledge only about the resonance frequencies present in the sample. Thus, Nω can be reduced by a factor of 4 for many 1H in vivo studies while no spectra have to be reconstructed, and no additional user interaction, prior knowledge, starting values, or model function are required. Phantom measurements and in vivo experiments on rat brain have been performed at 4.7 T to test the feasibility of the method for proton SI.

What are they up to? The role of sensory evidence and prior knowledge in action understanding.

PubMed

Chambon, Valerian; Domenech, Philippe; Pacherie, Elisabeth; Koechlin, Etienne; Baraduc, Pierre; Farrer, Chlöé

2011-02-18

Explaining or predicting the behaviour of our conspecifics requires the ability to infer the intentions that motivate it. Such inferences are assumed to rely on two types of information: (1) the sensory information conveyed by movement kinematics and (2) the observer's prior expectations--acquired from past experience or derived from prior knowledge. However, the respective contribution of these two sources of information is still controversial. This controversy stems in part from the fact that "intention" is an umbrella term that may embrace various sub-types each being assigned different scopes and targets. We hypothesized that variations in the scope and target of intentions may account for variations in the contribution of visual kinematics and prior knowledge to the intention inference process. To test this hypothesis, we conducted four behavioural experiments in which participants were instructed to identify different types of intention: basic intentions (i.e. simple goal of a motor act), superordinate intentions (i.e. general goal of a sequence of motor acts), or social intentions (i.e. intentions accomplished in a context of reciprocal interaction). For each of the above-mentioned intentions, we varied (1) the amount of visual information available from the action scene and (2) participant's prior expectations concerning the intention that was more likely to be accomplished. First, we showed that intentional judgments depend on a consistent interaction between visual information and participant's prior expectations. Moreover, we demonstrated that this interaction varied according to the type of intention to be inferred, with participant's priors rather than perceptual evidence exerting a greater effect on the inference of social and superordinate intentions. The results are discussed by appealing to the specific properties of each type of intention considered and further interpreted in the light of a hierarchical model of action representation.

Computationally modeling interpersonal trust.

PubMed

Lee, Jin Joo; Knox, W Bradley; Wormwood, Jolie B; Breazeal, Cynthia; Desteno, David

2013-01-01

We present a computational model capable of predicting-above human accuracy-the degree of trust a person has toward their novel partner by observing the trust-related nonverbal cues expressed in their social interaction. We summarize our prior work, in which we identify nonverbal cues that signal untrustworthy behavior and also demonstrate the human mind's readiness to interpret those cues to assess the trustworthiness of a social robot. We demonstrate that domain knowledge gained from our prior work using human-subjects experiments, when incorporated into the feature engineering process, permits a computational model to outperform both human predictions and a baseline model built in naiveté of this domain knowledge. We then present the construction of hidden Markov models to investigate temporal relationships among the trust-related nonverbal cues. By interpreting the resulting learned structure, we observe that models built to emulate different levels of trust exhibit different sequences of nonverbal cues. From this observation, we derived sequence-based temporal features that further improve the accuracy of our computational model. Our multi-step research process presented in this paper combines the strength of experimental manipulation and machine learning to not only design a computational trust model but also to further our understanding of the dynamics of interpersonal trust.

Automatic seed selection for segmentation of liver cirrhosis in laparoscopic sequences

NASA Astrophysics Data System (ADS)

Sinha, Rahul; Marcinczak, Jan Marek; Grigat, Rolf-Rainer

2014-03-01

For computer aided diagnosis based on laparoscopic sequences, image segmentation is one of the basic steps which define the success of all further processing. However, many image segmentation algorithms require prior knowledge which is given by interaction with the clinician. We propose an automatic seed selection algorithm for segmentation of liver cirrhosis in laparoscopic sequences which assigns each pixel a probability of being cirrhotic liver tissue or background tissue. Our approach is based on a trained classifier using SIFT and RGB features with PCA. Due to the unique illumination conditions in laparoscopic sequences of the liver, a very low dimensional feature space can be used for classification via logistic regression. The methodology is evaluated on 718 cirrhotic liver and background patches that are taken from laparoscopic sequences of 7 patients. Using a linear classifier we achieve a precision of 91% in a leave-one-patient-out cross-validation. Furthermore, we demonstrate that with logistic probability estimates, seeds with high certainty of being cirrhotic liver tissue can be obtained. For example, our precision of liver seeds increases to 98.5% if only seeds with more than 95% probability of being liver are used. Finally, these automatically selected seeds can be used as priors in Graph Cuts which is demonstrated in this paper.

Improving transmission efficiency of large sequence alignment/map (SAM) files.

PubMed

Sakib, Muhammad Nazmus; Tang, Jijun; Zheng, W Jim; Huang, Chin-Tser

2011-01-01

Research in bioinformatics primarily involves collection and analysis of a large volume of genomic data. Naturally, it demands efficient storage and transfer of this huge amount of data. In recent years, some research has been done to find efficient compression algorithms to reduce the size of various sequencing data. One way to improve the transmission time of large files is to apply a maximum lossless compression on them. In this paper, we present SAMZIP, a specialized encoding scheme, for sequence alignment data in SAM (Sequence Alignment/Map) format, which improves the compression ratio of existing compression tools available. In order to achieve this, we exploit the prior knowledge of the file format and specifications. Our experimental results show that our encoding scheme improves compression ratio, thereby reducing overall transmission time significantly.

Whole-exome sequencing, without prior linkage, identifies a mutation in LAMB3 as a cause of dominant hypoplastic amelogenesis imperfecta.

PubMed

Poulter, James A; El-Sayed, Walid; Shore, Roger C; Kirkham, Jennifer; Inglehearn, Chris F; Mighell, Alan J

2014-01-01

The conventional approach to identifying the defective gene in a family with an inherited disease is to find the disease locus through family studies. However, the rapid development and decreasing cost of next generation sequencing facilitates a more direct approach. Here, we report the identification of a frameshift mutation in LAMB3 as a cause of dominant hypoplastic amelogenesis imperfecta (AI). Whole-exome sequencing of three affected family members and subsequent filtering of shared variants, without prior genetic linkage, sufficed to identify the pathogenic variant. Simultaneous analysis of multiple family members confirms segregation, enhancing the power to filter the genetic variation found and leading to rapid identification of the pathogenic variant. LAMB3 encodes a subunit of Laminin-5, one of a family of basement membrane proteins with essential functions in cell growth, movement and adhesion. Homozygous LAMB3 mutations cause junctional epidermolysis bullosa (JEB) and enamel defects are seen in JEB cases. However, to our knowledge, this is the first report of dominant AI due to a LAMB3 mutation in the absence of JEB.

SFM: A novel sequence-based fusion method for disease genes identification and prioritization.

PubMed

Yousef, Abdulaziz; Moghadam Charkari, Nasrollah

2015-10-21

The identification of disease genes from human genome is of great importance to improve diagnosis and treatment of disease. Several machine learning methods have been introduced to identify disease genes. However, these methods mostly differ in the prior knowledge used to construct the feature vector for each instance (gene), the ways of selecting negative data (non-disease genes) where there is no investigational approach to find them and the classification methods used to make the final decision. In this work, a novel Sequence-based fusion method (SFM) is proposed to identify disease genes. In this regard, unlike existing methods, instead of using a noisy and incomplete prior-knowledge, the amino acid sequence of the proteins which is universal data has been carried out to present the genes (proteins) into four different feature vectors. To select more likely negative data from candidate genes, the intersection set of four negative sets which are generated using distance approach is considered. Then, Decision Tree (C4.5) has been applied as a fusion method to combine the results of four independent state-of the-art predictors based on support vector machine (SVM) algorithm, and to make the final decision. The experimental results of the proposed method have been evaluated by some standard measures. The results indicate the precision, recall and F-measure of 82.6%, 85.6% and 84, respectively. These results confirm the efficiency and validity of the proposed method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Engagement and communication among participants in the ClinSeq Genomic Sequencing Study.

PubMed

Hooker, Gillian W; Umstead, Kendall L; Lewis, Katie L; Koehly, Laura K; Biesecker, Leslie G; Biesecker, Barbara B

2017-01-01

As clinical genome sequencing expand its reach, understanding how individuals engage with this process are of critical importance. In this study, we aimed to describe internal engagement and its correlates among a ClinSeq cohort of adults consented to genome sequencing and receipt of results. This study was framed using the precaution adoption process model (PAPM), in which knowledge predicts engagement and engagement predicts subsequent behaviors. Prior to receipt of sequencing results, 630 participants in the study completed a baseline survey. Engagement was assessed as the frequency with which participants thought about their participation in ClinSeq since enrollment. Results were consistent with the PAPM: those with higher genomics knowledge reported higher engagement (r = 0.13, P = 0.001) and those who were more engaged reported more frequent communication with their physicians (r = 0.28, P < 0.001) and family members (r = 0.35, P < 0.001) about ClinSeq. Characteristics of those with higher engagement included poorer overall health (r = -0.13, P = 0.002), greater seeking of health information (r = 0.16, P < 0.001), and more recent study enrollment (r = -0.21, P < 0.001). These data support the importance of internal engagement in communication related to genomic sequencing.Genet Med 19 1, 98-103.

Exploiting Genome Structure in Association Analysis

PubMed Central

Kim, Seyoung

2014-01-01

Abstract A genome-wide association study involves examining a large number of single-nucleotide polymorphisms (SNPs) to identify SNPs that are significantly associated with the given phenotype, while trying to reduce the false positive rate. Although haplotype-based association methods have been proposed to accommodate correlation information across nearby SNPs that are in linkage disequilibrium, none of these methods directly incorporated the structural information such as recombination events along chromosome. In this paper, we propose a new approach called stochastic block lasso for association mapping that exploits prior knowledge on linkage disequilibrium structure in the genome such as recombination rates and distances between adjacent SNPs in order to increase the power of detecting true associations while reducing false positives. Following a typical linear regression framework with the genotypes as inputs and the phenotype as output, our proposed method employs a sparsity-enforcing Laplacian prior for the regression coefficients, augmented by a first-order Markov process along the sequence of SNPs that incorporates the prior information on the linkage disequilibrium structure. The Markov-chain prior models the structural dependencies between a pair of adjacent SNPs, and allows us to look for association SNPs in a coupled manner, combining strength from multiple nearby SNPs. Our results on HapMap-simulated datasets and mouse datasets show that there is a significant advantage in incorporating the prior knowledge on linkage disequilibrium structure for marker identification under whole-genome association. PMID:21548809

Prior Knowledge Facilitates Mutual Gaze Convergence and Head Nodding Synchrony in Face-to-face Communication

PubMed Central

Thepsoonthorn, C.; Yokozuka, T.; Miura, S.; Ogawa, K.; Miyake, Y.

2016-01-01

As prior knowledge is claimed to be an essential key to achieve effective education, we are interested in exploring whether prior knowledge enhances communication effectiveness. To demonstrate the effects of prior knowledge, mutual gaze convergence and head nodding synchrony are observed as indicators of communication effectiveness. We conducted an experiment on lecture task between lecturer and student under 2 conditions: prior knowledge and non-prior knowledge. The students in prior knowledge condition were provided the basic information about the lecture content and were assessed their understanding by the experimenter before starting the lecture while the students in non-prior knowledge had none. The result shows that the interaction in prior knowledge condition establishes significantly higher mutual gaze convergence (t(15.03) = 6.72, p < 0.0001; α = 0.05, n = 20) and head nodding synchrony (t(16.67) = 1.83, p = 0.04; α = 0.05, n = 19) compared to non-prior knowledge condition. This study reveals that prior knowledge facilitates mutual gaze convergence and head nodding synchrony. Furthermore, the interaction with and without prior knowledge can be evaluated by measuring or observing mutual gaze convergence and head nodding synchrony. PMID:27910902

Prior Knowledge Facilitates Mutual Gaze Convergence and Head Nodding Synchrony in Face-to-face Communication.

PubMed

Thepsoonthorn, C; Yokozuka, T; Miura, S; Ogawa, K; Miyake, Y

2016-12-02

As prior knowledge is claimed to be an essential key to achieve effective education, we are interested in exploring whether prior knowledge enhances communication effectiveness. To demonstrate the effects of prior knowledge, mutual gaze convergence and head nodding synchrony are observed as indicators of communication effectiveness. We conducted an experiment on lecture task between lecturer and student under 2 conditions: prior knowledge and non-prior knowledge. The students in prior knowledge condition were provided the basic information about the lecture content and were assessed their understanding by the experimenter before starting the lecture while the students in non-prior knowledge had none. The result shows that the interaction in prior knowledge condition establishes significantly higher mutual gaze convergence (t(15.03) = 6.72, p < 0.0001; α = 0.05, n = 20) and head nodding synchrony (t(16.67) = 1.83, p = 0.04; α = 0.05, n = 19) compared to non-prior knowledge condition. This study reveals that prior knowledge facilitates mutual gaze convergence and head nodding synchrony. Furthermore, the interaction with and without prior knowledge can be evaluated by measuring or observing mutual gaze convergence and head nodding synchrony.

The effects of activating prior topic and metacognitive knowledge on text comprehension scores.

PubMed

Kostons, Danny; van der Werf, Greetje

2015-09-01

Research on prior knowledge activation has consistently shown that activating learners' prior knowledge has beneficial effects on learning. If learners activate their prior knowledge, this activated knowledge serves as a framework for establishing relationships between the knowledge they already possess and new information provided to them. Thus far, prior knowledge activation has dealt primarily with topic knowledge in specific domains. Students, however, likely also possess at least some metacognitive knowledge useful in those domains, which, when activated, should aid in the deployment of helpful strategies during reading. In this study, we investigated the effects of both prior topic knowledge activation (PTKA) and prior metacognitive knowledge activation (PMKA) on text comprehension scores. Eighty-eight students in primary education were randomly distributed amongst the conditions of the 2 × 2 (PTKA yes/no × PMKA yes/no) designed experiment. Results show that activating prior metacognitive knowledge had a beneficial effect on text comprehension, whereas activating prior topic knowledge, after correcting for the amount of prior knowledge, did not. Most studies deal with explicit instruction of metacognitive knowledge, but our results show that this may not be necessary, specifically in the case of students who already have some metacognitive knowledge. However, existing metacognitive knowledge needs to be activated in order for students to make better use of this knowledge. © 2015 The British Psychological Society.

What Are They Up To? The Role of Sensory Evidence and Prior Knowledge in Action Understanding

PubMed Central

Chambon, Valerian; Domenech, Philippe; Pacherie, Elisabeth; Koechlin, Etienne; Baraduc, Pierre; Farrer, Chlöé

2011-01-01

Explaining or predicting the behaviour of our conspecifics requires the ability to infer the intentions that motivate it. Such inferences are assumed to rely on two types of information: (1) the sensory information conveyed by movement kinematics and (2) the observer's prior expectations – acquired from past experience or derived from prior knowledge. However, the respective contribution of these two sources of information is still controversial. This controversy stems in part from the fact that “intention” is an umbrella term that may embrace various sub-types each being assigned different scopes and targets. We hypothesized that variations in the scope and target of intentions may account for variations in the contribution of visual kinematics and prior knowledge to the intention inference process. To test this hypothesis, we conducted four behavioural experiments in which participants were instructed to identify different types of intention: basic intentions (i.e. simple goal of a motor act), superordinate intentions (i.e. general goal of a sequence of motor acts), or social intentions (i.e. intentions accomplished in a context of reciprocal interaction). For each of the above-mentioned intentions, we varied (1) the amount of visual information available from the action scene and (2) participant's prior expectations concerning the intention that was more likely to be accomplished. First, we showed that intentional judgments depend on a consistent interaction between visual information and participant's prior expectations. Moreover, we demonstrated that this interaction varied according to the type of intention to be inferred, with participant's priors rather than perceptual evidence exerting a greater effect on the inference of social and superordinate intentions. The results are discussed by appealing to the specific properties of each type of intention considered and further interpreted in the light of a hierarchical model of action representation. PMID:21364992

Plant genotyping using fluorescently tagged inter-simple sequence repeats (ISSRs): basic principles and methodology.

PubMed

Prince, Linda M

2015-01-01

Inter-simple sequence repeat PCR (ISSR-PCR) is a fast, inexpensive genotyping technique based on length variation in the regions between microsatellites. The method requires no species-specific prior knowledge of microsatellite location or composition. Very small amounts of DNA are required, making this method ideal for organisms of conservation concern, or where the quantity of DNA is extremely limited due to organism size. ISSR-PCR can be highly reproducible but requires careful attention to detail. Optimization of DNA extraction, fragment amplification, and normalization of fragment peak heights during fluorescent detection are critical steps to minimizing the downstream time spent verifying and scoring the data.

Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies

PubMed Central

Santiago-Rodriguez, Tasha M.; Luciani, Stefania; Toranzos, Gary A.; Marota, Isolina; Giuffra, Valentina; Cano, Raul J.

2017-01-01

Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacterial diversity as compared to the Inca mummies when using 16S ribosomal (rRNA) gene amplicon sequencing, but both groups showed bacterial and fungal taxa when using shotgun metagenomic sequencing that may resemble both the thanatomicrobiome and extant human gut microbiomes. Identification of sequences associated with plants, animals, and carbohydrate-active enzymes (CAZymes) may provide further insights into the dietary habits of Inca and Italian nobility mummies. Putative antibiotic-resistance genes in the Inca and Italian nobility mummies support a human gut resistome prior to the antibiotic therapy era. The higher proportion of putative antibiotic-resistance genes in the Inca compared to Italian nobility mummies may support the hypotheses that a greater exposure to the environment may result in a greater acquisition of antibiotic-resistance genes. The present study adds knowledge of the microbiome resulting from the process of mummification of the human gut, insights of ancient dietary habits, and the preserved putative human gut resistome prior the antibiotic therapy era. PMID:29112136

Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies.

PubMed

Santiago-Rodriguez, Tasha M; Fornaciari, Gino; Luciani, Stefania; Toranzos, Gary A; Marota, Isolina; Giuffra, Valentina; Cano, Raul J

2017-11-07

Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacterial diversity as compared to the Inca mummies when using 16S ribosomal (rRNA) gene amplicon sequencing, but both groups showed bacterial and fungal taxa when using shotgun metagenomic sequencing that may resemble both the thanatomicrobiome and extant human gut microbiomes. Identification of sequences associated with plants, animals, and carbohydrate-active enzymes (CAZymes) may provide further insights into the dietary habits of Inca and Italian nobility mummies. Putative antibiotic-resistance genes in the Inca and Italian nobility mummies support a human gut resistome prior to the antibiotic therapy era. The higher proportion of putative antibiotic-resistance genes in the Inca compared to Italian nobility mummies may support the hypotheses that a greater exposure to the environment may result in a greater acquisition of antibiotic-resistance genes. The present study adds knowledge of the microbiome resulting from the process of mummification of the human gut, insights of ancient dietary habits, and the preserved putative human gut resistome prior the antibiotic therapy era.

A general strategy for cloning viroids and other small circular RNAs that uses minimal amounts of template and does not require prior knowledge of its sequence.

PubMed

Navarro, B; Daròs, J A; Flores, R

1996-01-01

Two PCR-based methods are described for obtaining clones of small circular RNAs of unknown sequence and for which only minute amounts are available. To avoid introducing any assumption about the RNA sequence, synthesis of the cDNAs is initiated with random primers. The cDNA population is then PCR-amplified using a primer whose sequence is present at both sides of the cDNAs, since they have been obtained with random hexamers and then a linker with the sequence of the PCR primer has been ligated to their termini, or because the cDNAs have been synthesized with an oligonucleotide that contains the sequence of the PCR primer at its 5' end and six randomized positions at its 3' end. The procedures need only approximately 50 ng of purified RNA template. The reasons for the emergence of cloning artifacts and precautions to avoid them are discussed.

The Influence of Prior Knowledge on the Retrieval-Directed Function of Note Taking in Prior Knowledge Activation

ERIC Educational Resources Information Center

Wetzels, Sandra A. J.; Kester, Liesbeth; van Merrienboer, Jeroen J. G.; Broers, Nick J.

2011-01-01

Background: Prior knowledge activation facilitates learning. Note taking during prior knowledge activation (i.e., note taking directed at retrieving information from memory) might facilitate the activation process by enabling learners to build an external representation of their prior knowledge. However, taking notes might be less effective in…

Cognitive Dissonance as an Instructional Tool for Understanding Chemical Representations

NASA Astrophysics Data System (ADS)

Corradi, David; Clarebout, Geraldine; Elen, Jan

2015-10-01

Previous research on multiple external representations (MER) indicates that sequencing representations (compared with presenting them as a whole) can, in some cases, increase conceptual understanding if there is interference between internal and external representations. We tested this mechanism by sequencing different combinations of scientific and abstract chemical representations and presenting them to 133 learners with low prior knowledge of the represented domain. The results provide insight into three separate mechanisms of learning with MER. (1) A memory (number of ideas reproduced) and (2) an accuracy (correctness of these ideas) effects occur when two representations are presented in a sequence. An accuracy and a (3) redundancy (number of redundant ideas remembered) effects occur when three representations are presented in a sequence. A necessary precondition for these effects is that descriptive formats are placed before depictive formats. The identified effects are analyzed in terms of the concept of cognitive dissonance.

Advanced Virus Detection Technologies Interest Group (AVDTIG): Efforts on High Throughput Sequencing (HTS) for Virus Detection.

PubMed

Khan, Arifa S; Vacante, Dominick A; Cassart, Jean-Pol; Ng, Siemon H S; Lambert, Christophe; Charlebois, Robert L; King, Kathryn E

Several nucleic-acid based technologies have recently emerged with capabilities for broad virus detection. One of these, high throughput sequencing, has the potential for novel virus detection because this method does not depend upon prior viral sequence knowledge. However, the use of high throughput sequencing for testing biologicals poses greater challenges as compared to other newly introduced tests due to its technical complexities and big data bioinformatics. Thus, the Advanced Virus Detection Technologies Users Group was formed as a joint effort by regulatory and industry scientists to facilitate discussions and provide a forum for sharing data and experiences using advanced new virus detection technologies, with a focus on high throughput sequencing technologies. The group was initiated as a task force that was coordinated by the Parenteral Drug Association and subsequently became the Advanced Virus Detection Technologies Interest Group to continue efforts for using new technologies for detection of adventitious viruses with broader participation, including international government agencies, academia, and technology service providers. © PDA, Inc. 2016.

Self-Organizing Hidden Markov Model Map (SOHMMM).

PubMed

Ferles, Christos; Stafylopatis, Andreas

2013-12-01

A hybrid approach combining the Self-Organizing Map (SOM) and the Hidden Markov Model (HMM) is presented. The Self-Organizing Hidden Markov Model Map (SOHMMM) establishes a cross-section between the theoretic foundations and algorithmic realizations of its constituents. The respective architectures and learning methodologies are fused in an attempt to meet the increasing requirements imposed by the properties of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein chain molecules. The fusion and synergy of the SOM unsupervised training and the HMM dynamic programming algorithms bring forth a novel on-line gradient descent unsupervised learning algorithm, which is fully integrated into the SOHMMM. Since the SOHMMM carries out probabilistic sequence analysis with little or no prior knowledge, it can have a variety of applications in clustering, dimensionality reduction and visualization of large-scale sequence spaces, and also, in sequence discrimination, search and classification. Two series of experiments based on artificial sequence data and splice junction gene sequences demonstrate the SOHMMM's characteristics and capabilities. Copyright © 2013 Elsevier Ltd. All rights reserved.

An artificial intelligence approach fit for tRNA gene studies in the era of big sequence data.

PubMed

Iwasaki, Yuki; Abe, Takashi; Wada, Kennosuke; Wada, Yoshiko; Ikemura, Toshimichi

2017-09-12

Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide compositions as high-dimensional data, we have previously modified the conventional self-organizing map (SOM) for genome informatics and established BLSOM, which can analyze more than ten million sequences simultaneously. Here, we develop BLSOM specialized for tRNA genes (tDNAs) that can cluster (self-organize) more than one million microbial tDNAs according to their cognate amino acid solely depending on tetra- and pentanucleotide compositions. This unsupervised clustering can reveal combinatorial oligonucleotide motifs that are responsible for the amino acid-dependent clustering, as well as other functionally and structurally important consensus motifs, which have been evolutionarily conserved. BLSOM is also useful for identifying tDNAs as phylogenetic markers for special phylotypes. When we constructed BLSOM with 'species-unknown' tDNAs from metagenomic sequences plus 'species-known' microbial tDNAs, a large portion of metagenomic tDNAs self-organized with species-known tDNAs, yielding information on microbial communities in environmental samples. BLSOM can also enhance accuracy in the tDNA database obtained from big sequence data. This unsupervised data mining should become important for studying numerous functionally unclear RNAs obtained from a wide range of organisms.

A motif detection and classification method for peptide sequences using genetic programming.

PubMed

Tomita, Yasuyuki; Kato, Ryuji; Okochi, Mina; Honda, Hiroyuki

2008-08-01

An exploration of common rules (property motifs) in amino acid sequences has been required for the design of novel sequences and elucidation of the interactions between molecules controlled by the structural or physical environment. In the present study, we developed a new method to search property motifs that are common in peptide sequence data. Our method comprises the following two characteristics: (i) the automatic determination of the position and length of common property motifs by calculating the physicochemical similarity of amino acids, and (ii) the quick and effective exploration of motif candidates that discriminates the positives and negatives by the introduction of genetic programming (GP). Our method was evaluated by two types of model data sets. First, the intentionally buried property motifs were searched in the artificially derived peptide data containing intentionally buried property motifs. As a result, the expected property motifs were correctly extracted by our algorithm. Second, the peptide data that interact with MHC class II molecules were analyzed as one of the models of biologically active peptides with buried motifs in various lengths. Twofold MHC class II binding peptides were identified with the rule using our method, compared to the existing scoring matrix method. In conclusion, our GP based motif searching approach enabled to obtain knowledge of functional aspects of the peptides without any prior knowledge.

Prior-knowledge Fitting of Accelerated Five-dimensional Echo Planar J-resolved Spectroscopic Imaging: Effect of Nonlinear Reconstruction on Quantitation.

PubMed

Iqbal, Zohaib; Wilson, Neil E; Thomas, M Albert

2017-07-24

1 H Magnetic Resonance Spectroscopic imaging (SI) is a powerful tool capable of investigating metabolism in vivo from mul- tiple regions. However, SI techniques are time consuming, and are therefore difficult to implement clinically. By applying non-uniform sampling (NUS) and compressed sensing (CS) reconstruction, it is possible to accelerate these scans while re- taining key spectral information. One recently developed method that utilizes this type of acceleration is the five-dimensional echo planar J-resolved spectroscopic imaging (5D EP-JRESI) sequence, which is capable of obtaining two-dimensional (2D) spectra from three spatial dimensions. The prior-knowledge fitting (ProFit) algorithm is typically used to quantify 2D spectra in vivo, however the effects of NUS and CS reconstruction on the quantitation results are unknown. This study utilized a simulated brain phantom to investigate the errors introduced through the acceleration methods. Errors (normalized root mean square error >15%) were found between metabolite concentrations after twelve-fold acceleration for several low concentra- tion (<2 mM) metabolites. The Cramér Rao lower bound% (CRLB%) values, which are typically used for quality control, were not reflective of the increased quantitation error arising from acceleration. Finally, occipital white (OWM) and gray (OGM) human brain matter were quantified in vivo using the 5D EP-JRESI sequence with eight-fold acceleration.

The critical success factors and impact of prior knowledge to nursing students when transferring nursing knowledge during nursing clinical practise.

PubMed

Tsai, Ming-Tien; Tsai, Ling-Long

2005-11-01

Nursing practise plays an important role in transferring nursing knowledge to nursing students. From the related literature review, prior knowledge will affect how learners gain new knowledge. There has been no direct examination of the prior knowledge interaction effect on students' performance and its influence on nursing students when evaluating the knowledge transfer success factors. This study explores (1) the critical success factors in transferring nursing knowledge, (2) the impact of prior knowledge when evaluating the success factors for transferring nursing knowledge. This research utilizes in-depth interviews to probe the initial success factor phase. A total of 422 valid questionnaires were conducted by the authors. The data were analysed by comparing the mean score and t-test between two groups. Seventeen critical success factors were identified by the two groups of students. Twelve items were selected to examine the diversity in the two groups. Students with prior knowledge were more independent than the other group. They also preferred self-directed learning over students without prior knowledge. Students who did not have prior knowledge were eager to take every opportunity to gain experience and more readily adopted new knowledge.

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.

PubMed Central

Drummond, Alexei J; Nicholls, Geoff K; Rodrigo, Allen G; Solomon, Wiremu

2002-01-01

Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used to describe the time structure of the ancestral tree. We recover information about the unknown true ancestral coalescent tree, population size, and the overall mutation rate from temporally spaced data, that is, from nucleotide sequences gathered at different times, from different individuals, in an evolving haploid population. We briefly discuss the methodological implications and show what can be inferred, in various practically relevant states of prior knowledge. We develop extensions for exponentially growing population size and joint estimation of substitution model parameters. We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences. PMID:12136032

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.

PubMed

Drummond, Alexei J; Nicholls, Geoff K; Rodrigo, Allen G; Solomon, Wiremu

2002-07-01

Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used to describe the time structure of the ancestral tree. We recover information about the unknown true ancestral coalescent tree, population size, and the overall mutation rate from temporally spaced data, that is, from nucleotide sequences gathered at different times, from different individuals, in an evolving haploid population. We briefly discuss the methodological implications and show what can be inferred, in various practically relevant states of prior knowledge. We develop extensions for exponentially growing population size and joint estimation of substitution model parameters. We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences.

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

PubMed

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.

Individual differences in adult foreign language learning: the mediating effect of metalinguistic awareness.

PubMed

Brooks, Patricia J; Kempe, Vera

2013-02-01

In this study, we sought to identify cognitive predictors of individual differences in adult foreign-language learning and to test whether metalinguistic awareness mediated the observed relationships. Using a miniature language-learning paradigm, adults (N = 77) learned Russian vocabulary and grammar (gender agreement and case marking) over six 1-h sessions, completing tasks that encouraged attention to phrases without explicitly teaching grammatical rules. The participants' ability to describe the Russian gender and case-marking patterns mediated the effects of nonverbal intelligence and auditory sequence learning on grammar learning and generalization. Hence, even under implicit-learning conditions, individual differences stemmed from explicit metalinguistic awareness of the underlying grammar, which, in turn, was linked to nonverbal intelligence and auditory sequence learning. Prior knowledge of languages with grammatical gender (predominantly Spanish) predicted learning of gender agreement. Transfer of knowledge of gender from other languages to Russian was not mediated by awareness, which suggests that transfer operates through an implicit process akin to structural priming.

On the way toward systems biology of Aspergillus fumigatus infection.

PubMed

Albrecht, Daniela; Kniemeyer, Olaf; Mech, Franziska; Gunzer, Matthias; Brakhage, Axel; Guthke, Reinhard

2011-06-01

Pathogenicity of Aspergillus fumigatus is multifactorial. Thus, global studies are essential for the understanding of the infection process. Therefore, a data warehouse was established where genome sequence, transcriptome and proteome data are stored. These data are analyzed for the elucidation of virulence determinants. The data analysis workflow starts with pre-processing including imputing of missing values and normalization. Last step is the identification of differentially expressed genes/proteins as interesting candidates for further analysis, in particular for functional categorization and correlation studies. Sequence data and other prior knowledge extracted from databases are integrated to support the inference of gene regulatory networks associated with pathogenicity. This knowledge-assisted data analysis aims at establishing mathematical models with predictive strength to assist further experimental work. Recently, first steps were done to extend the integrative data analysis and computational modeling by evaluating spatio-temporal data (movies) that monitor interactions of A. fumigatus morphotypes (e.g. conidia) with host immune cells. Copyright © 2011 Elsevier GmbH. All rights reserved.

SVS: data and knowledge integration in computational biology.

PubMed

Zycinski, Grzegorz; Barla, Annalisa; Verri, Alessandro

2011-01-01

In this paper we present a framework for structured variable selection (SVS). The main concept of the proposed schema is to take a step towards the integration of two different aspects of data mining: database and machine learning perspective. The framework is flexible enough to use not only microarray data, but other high-throughput data of choice (e.g. from mass spectrometry, microarray, next generation sequencing). Moreover, the feature selection phase incorporates prior biological knowledge in a modular way from various repositories and is ready to host different statistical learning techniques. We present a proof of concept of SVS, illustrating some implementation details and describing current results on high-throughput microarray data.

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

PubMed Central

2017-01-01

Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package. PMID:29107980

Effects of Prior Knowledge on Memory: Implications for Education

ERIC Educational Resources Information Center

Shing, Yee Lee; Brod, Garvin

2016-01-01

The encoding, consolidation, and retrieval of events and facts form the basis for acquiring new skills and knowledge. Prior knowledge can enhance those memory processes considerably and thus foster knowledge acquisition. But prior knowledge can also hinder knowledge acquisition, in particular when the to-be-learned information is inconsistent with…

Evidence of repeated wildfires prior to human occupation on San Nicolas Island, California

USGS Publications Warehouse

Pigati, Jeffrey S.; McGeehin, John P.; Skipp, Gary L.; Muhs, Daniel R.

2014-01-01

Understanding how early humans on the California Channel Islands might have changed local fire regimes requires a baseline knowledge of the frequency of natural wildfires on the islands prior to human occupation. A sedimentary sequence that was recently discovered in a small canyon on San Nicolas Island contains evidence of at least 24 burn events that date to between ~37 and 25 ka (thousands of calibrated 14C years before present), well before humans entered North America. The evidence includes abundant macroscopic charcoal, blackened sediments, and discrete packages of oxidized, reddish-brown sediments that are similar in appearance to sedimentary features called “fire areas” on Santa Rosa Island and elsewhere. Massive fine-grained sediments that contain the burn evidence are interpreted as sheetwash deposits and are interbedded with coarse-grained, clast-supported alluvial sediments and matrix supported sands, pebbles, and cobbles that represent localized debris flows. These sedimentary sequences suggest that the catchment area above our study site underwent multiple cycles of relative quiescence that were interrupted by fire and followed by slope instability and mass wasting events. Our 14C-based chronology dates these cycles to well before the arrival of humans on the Channel Islands and shows that natural wildfires occurred here, at a minimum, every 300–500 years prior to human occupation.

The Effects of Prior Knowledge Activation on Free Recall and Study Time Allocation.

ERIC Educational Resources Information Center

Machiels-Bongaerts, Maureen; And Others

The effects of mobilizing prior knowledge on information processing were studied. Two hypotheses, the cognitive set-point hypothesis and the selective attention hypothesis, try to account for the facilitation effects of prior knowledge activation. These hypotheses predict different recall patterns as a result of mobilizing prior knowledge. In…

Deepening Understanding of Prior Knowledge: What Diverse First-Generation College Students in the U.S. Can Teach Us

ERIC Educational Resources Information Center

Castillo-Montoya, Milagros

2017-01-01

Educational research indicates that teachers revealing and utilizing students' prior knowledge supports students' academic learning. Yet, the variation in students' prior knowledge is not fully known. To better understand students' prior knowledge, I drew on sociocultural learning theories to examine racially and ethnically diverse college…

Novice and expert teachers' conceptions of learners' prior knowledge

NASA Astrophysics Data System (ADS)

Meyer, Helen

2004-11-01

This study presents comparative case studies of preservice and first-year teachers' and expert teachers' conceptions of the concept of prior knowledge. Kelly's (The Psychology of Personal Construct, New York: W.W. Norton, 1955) theory of personal constructs as discussed by Akerson, Flick, and Lederman (Journal of Research in Science Teaching, 2000, 37, 363-385) in relationship to prior knowledge underpins the study. Six teachers were selected to participate in the case studies based upon their level experience teaching science and their willingness to take part. The comparative case studies of the novice and expert teachers provide insights into (a) how novice and expert teachers understand the concept of prior knowledge and (b) how they use this knowledge to make instructional decisions. Data collection consisted of interviews, classroom observations, and document analysis. Findings suggest that novice teachers hold insufficient conceptions of prior knowledge and its role in instruction to effectively implement constructivist teaching practices. While expert teachers hold a complex conception of prior knowledge and make use of their students' prior knowledge in significant ways during instruction. A second finding was an apparent mismatch between the novice teachers' beliefs about their urban students' life experiences and prior knowledge and the wealth of knowledge the expert teachers found to draw upon.

Use of Elaborative Interrogation to Help Students Acquire Information Consistent with Prior Knowledge and Information Inconsistent with Prior Knowledge.

ERIC Educational Resources Information Center

Woloshyn, Vera E.; And Others

1994-01-01

Thirty-two factual statements, half consistent and half not consistent with subjects' prior knowledge, were processed by 140 sixth and seventh graders. Half were directed to use elaborative interrogation (using prior knowledge) to answer why each statement was true. Across all memory measures, elaborative interrogation subjects performed better…

Brief Report: Teachers' Awareness of the Relationship between Prior Knowledge and New Learning

ERIC Educational Resources Information Center

Journal for Research in Mathematics Education, 2016

2016-01-01

The author examined the degree to which experienced teachers are aware of the relationship between prior knowledge and new learning. Interviews with teachers revealed that they were explicitly aware of when students made connections between prior knowledge and new learning, when they applied their prior knowledge to new contexts, and when they…

"Dare I Ask?": Eliciting Prior Knowledge and Its Implications for Teaching and Learning

ERIC Educational Resources Information Center

Dávila, Liv Thorstensson

2015-01-01

This article examines high school teachers' engagement of newcomer English learner students' prior knowledge. Three central research questions guided this study: 1) To what extent do teachers function as mediators of their students' prior knowledge? 2) What goes into teachers' thinking about how and when to elicit prior knowledge? and 3) How do…

Implicit Learning in Science: Activating and Suppressing Scientific Intuitions to Enhance Conceptual Change

NASA Astrophysics Data System (ADS)

Wang, Jeremy Yi-Ming

This dissertation examines the thesis that implicit learning plays a role in learning about scientific phenomena, and subsequently, in conceptual change. Decades of research in learning science demonstrate that a primary challenge of science education is overcoming prior, naive knowledge of natural phenomena in order to gain scientific understanding. Until recently, a key assumption of this research has been that to develop scientific understanding, learners must abandon their prior scientific intuitions and replace them with scientific concepts. However, a growing body of research shows that scientific intuitions persist, even among science experts. This suggests that naive intuitions are suppressed, not supplanted, as learners gain scientific understanding. The current study examines two potential roles of implicit learning processes in the development of scientific knowledge. First, implicit learning is a source of cognitive structures that impede science learning. Second, tasks that engage implicit learning processes can be employed to activate and suppress prior intuitions, enhancing the likelihood that scientific concepts are adopted and applied. This second proposal is tested in two experiments that measure training-induced changes in intuitive and conceptual knowledge related to sinking and floating objects in water. In Experiment 1, an implicit learning task was developed to examine whether implicit learning can induce changes in performance on near and far transfer tasks. The results of this experiment provide evidence that implicit learning tasks activate and suppress scientific intuitions. Experiment 2 examined the effects of combining implicit learning with traditional, direct instruction to enhance explicit learning of science concepts. This experiment demonstrates that sequencing implicit learning task before and after direct instruction has different effects on intuitive and conceptual knowledge. Together, these results suggest a novel approach for enhancing learning for conceptual change in science education.

Predictive top-down integration of prior knowledge during speech perception.

PubMed

Sohoglu, Ediz; Peelle, Jonathan E; Carlyon, Robert P; Davis, Matthew H

2012-06-20

A striking feature of human perception is that our subjective experience depends not only on sensory information from the environment but also on our prior knowledge or expectations. The precise mechanisms by which sensory information and prior knowledge are integrated remain unclear, with longstanding disagreement concerning whether integration is strictly feedforward or whether higher-level knowledge influences sensory processing through feedback connections. Here we used concurrent EEG and MEG recordings to determine how sensory information and prior knowledge are integrated in the brain during speech perception. We manipulated listeners' prior knowledge of speech content by presenting matching, mismatching, or neutral written text before a degraded (noise-vocoded) spoken word. When speech conformed to prior knowledge, subjective perceptual clarity was enhanced. This enhancement in clarity was associated with a spatiotemporal profile of brain activity uniquely consistent with a feedback process: activity in the inferior frontal gyrus was modulated by prior knowledge before activity in lower-level sensory regions of the superior temporal gyrus. In parallel, we parametrically varied the level of speech degradation, and therefore the amount of sensory detail, so that changes in neural responses attributable to sensory information and prior knowledge could be directly compared. Although sensory detail and prior knowledge both enhanced speech clarity, they had an opposite influence on the evoked response in the superior temporal gyrus. We argue that these data are best explained within the framework of predictive coding in which sensory activity is compared with top-down predictions and only unexplained activity propagated through the cortical hierarchy.

Relations among conceptual knowledge, procedural knowledge, and procedural flexibility in two samples differing in prior knowledge.

PubMed

Schneider, Michael; Rittle-Johnson, Bethany; Star, Jon R

2011-11-01

Competence in many domains rests on children developing conceptual and procedural knowledge, as well as procedural flexibility. However, research on the developmental relations between these different types of knowledge has yielded unclear results, in part because little attention has been paid to the validity of the measures or to the effects of prior knowledge on the relations. To overcome these problems, we modeled the three constructs in the domain of equation solving as latent factors and tested (a) whether the predictive relations between conceptual and procedural knowledge were bidirectional, (b) whether these interrelations were moderated by prior knowledge, and (c) how both constructs contributed to procedural flexibility. We analyzed data from 2 measurement points each from two samples (Ns = 228 and 304) of middle school students who differed in prior knowledge. Conceptual and procedural knowledge had stable bidirectional relations that were not moderated by prior knowledge. Both kinds of knowledge contributed independently to procedural flexibility. The results demonstrate how changes in complex knowledge structures contribute to competence development.

The Influence of Prior Knowledge on Memory: A Developmental Cognitive Neuroscience Perspective

PubMed Central

Brod, Garvin; Werkle-Bergner, Markus; Shing, Yee Lee

2013-01-01

Across ontogenetic development, individuals gather manifold experiences during which they detect regularities in their environment and thereby accumulate knowledge. This knowledge is used to guide behavior, make predictions, and acquire further new knowledge. In this review, we discuss the influence of prior knowledge on memory from both the psychology and the emerging cognitive neuroscience literature and provide a developmental perspective on this topic. Recent neuroscience findings point to a prominent role of the medial prefrontal cortex (mPFC) and of the hippocampus (HC) in the emergence of prior knowledge and in its application during the processes of successful memory encoding, consolidation, and retrieval. We take the lateral PFC into consideration as well and discuss changes in both medial and lateral PFC and HC across development and postulate how these may be related to the development of the use of prior knowledge for remembering. For future direction, we argue that, to measure age differential effects of prior knowledge on memory, it is necessary to distinguish the availability of prior knowledge from its accessibility and use. PMID:24115923

When generating answers benefits arithmetic skill: the importance of prior knowledge.

PubMed

Rittle-Johnson, Bethany; Kmicikewycz, Alexander Oleksij

2008-09-01

People remember information better if they generate the information while studying rather than read the information. However, prior research has not investigated whether this generation effect extends to related but unstudied items and has not been conducted in classroom settings. We compared third graders' success on studied and unstudied multiplication problems after they spent a class period generating answers to problems or reading the answers from a calculator. The effect of condition interacted with prior knowledge. Students with low prior knowledge had higher accuracy in the generate condition, but as prior knowledge increased, the advantage of generating answers decreased. The benefits of generating answers may extend to unstudied items and to classroom settings, but only for learners with low prior knowledge.

An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences.

PubMed

Pollier, Jacob; González-Guzmán, Miguel; Ardiles-Diaz, Wilson; Geelen, Danny; Goossens, Alain

2011-01-01

cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis. A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts. The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.

The Effects of the Timing of Isolated FFI on the Explicit Knowledge and Written Accuracy of Learners with Different Prior Knowledge of the Linguistic Target

ERIC Educational Resources Information Center

Shintani, Natsuko

2017-01-01

This study examines the effects of the timing of explicit instruction (EI) on grammatical accuracy. A total of 123 learners were divided into two groups: those with some productive knowledge of past-counterfactual conditionals (+Prior Knowledge) and those without such knowledge (-Prior Knowledge). Each group was divided into four conditions. Two…

Active Prior Tactile Knowledge Transfer for Learning Tactual Properties of New Objects

PubMed Central

Feng, Di

2018-01-01

Reusing the tactile knowledge of some previously-explored objects (prior objects) helps us to easily recognize the tactual properties of new objects. In this paper, we enable a robotic arm equipped with multi-modal artificial skin, like humans, to actively transfer the prior tactile exploratory action experiences when it learns the detailed physical properties of new objects. These experiences, or prior tactile knowledge, are built by the feature observations that the robot perceives from multiple sensory modalities, when it applies the pressing, sliding, and static contact movements on objects with different action parameters. We call our method Active Prior Tactile Knowledge Transfer (APTKT), and systematically evaluated its performance by several experiments. Results show that the robot improved the discrimination accuracy by around 10% when it used only one training sample with the feature observations of prior objects. By further incorporating the predictions from the observation models of prior objects as auxiliary features, our method improved the discrimination accuracy by over 20%. The results also show that the proposed method is robust against transferring irrelevant prior tactile knowledge (negative knowledge transfer). PMID:29466300

Defining personal utility in genomics: A Delphi study.

PubMed

Kohler, J N; Turbitt, E; Lewis, K L; Wilfond, B S; Jamal, L; Peay, H L; Biesecker, L G; Biesecker, B B

2017-09-01

Individual genome sequencing results are valued by patients in ways distinct from clinical utility. Such outcomes have been described as components of "personal utility," a concept that broadly encompasses patient-endorsed benefits, that is operationally defined as non-clinical outcomes. No empirical delineation of these outcomes has been reported. To address this gap, we administered a Delphi survey to adult participants in a National Institute of Health (NIH) clinical exome study to extract the most highly endorsed outcomes constituting personal utility. Forty research participants responded to a Delphi survey to rate 35 items identified by a systematic literature review of personal utility. Two rounds of ranking resulted in 24 items that represented 14 distinct elements of personal utility. Elements most highly endorsed by participants were: increased self-knowledge, knowledge of "the condition," altruism, and anticipated coping. Our findings represent the first systematic effort to delineate elements of personal utility that may be used to anticipate participant expectation and inform genetic counseling prior to sequencing. The 24 items reported need to be studied further in additional clinical genome sequencing studies to assess generalizability in other populations. Further research will help to understand motivations and to predict the meaning and use of results. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Applying Standard Interfaces to a Process-Control Language

NASA Technical Reports Server (NTRS)

Berthold, Richard T.

2005-01-01

A method of applying open-operating-system standard interfaces to the NASA User Interface Language (UIL) has been devised. UIL is a computing language that can be used in monitoring and controlling automated processes: for example, the Timeliner computer program, written in UIL, is a general-purpose software system for monitoring and controlling sequences of automated tasks in a target system. In providing the major elements of connectivity between UIL and the target system, the present method offers advantages over the prior method. Most notably, unlike in the prior method, the software description of the target system can be made independent of the applicable compiler software and need not be linked to the applicable executable compiler image. Also unlike in the prior method, it is not necessary to recompile the source code and relink the source code to a new executable compiler image. Abstraction of the description of the target system to a data file can be defined easily, with intuitive syntax, and knowledge of the source-code language is not needed for the definition.

Knowledge Structures of Entering Computer Networking Students and Their Instructors

ERIC Educational Resources Information Center

DiCerbo, Kristen E.

2007-01-01

Students bring prior knowledge to their learning experiences. This prior knowledge is known to affect how students encode and later retrieve new information learned. Teachers and content developers can use information about students' prior knowledge to create more effective lessons and materials. In many content areas, particularly the sciences,…

Nudging toward Inquiry: Awakening and Building upon Prior Knowledge

ERIC Educational Resources Information Center

Fontichiaro, Kristin, Comp.

2010-01-01

"Prior knowledge" (sometimes called schema or background knowledge) is information one already knows that helps him/her make sense of new information. New learning builds on existing prior knowledge. In traditional reporting-style research projects, students bypass this crucial step and plow right into answer-finding. It's no wonder that many…

Methods for determining the genetic affinity of microorganisms and viruses

NASA Technical Reports Server (NTRS)

Fox, George E. (Inventor); Willson, III, Richard C. (Inventor); Zhang, Zhengdong (Inventor)

2012-01-01

Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism.

Mind wandering during film comprehension: The role of prior knowledge and situational interest.

PubMed

Kopp, Kristopher; Mills, Caitlin; D'Mello, Sidney

2016-06-01

This study assessed the occurrence and factors that influence mind wandering (MW) in the domain of film comprehension. The cascading model of inattention assumes that a stronger mental representation (i.e., a situation model) during comprehension results in less MW. Accordingly, a suppression hypothesis suggests that MW would decrease as a function of having the knowledge of the plot of a film prior to viewing, because the prior-knowledge would help to strengthen the situation model during comprehension. Furthermore, an interest-moderation hypothesis would predict that the suppression effect of prior-knowledge would only emerge when there was interest in viewing the film. In the current experiment, 108 participants either read a short story that depicted the plot (i.e., prior-knowledge condition) or read an unrelated story of equal length (control condition) prior to viewing the short film (32.5 minutes) entitled The Red Balloon. Participants self-reported their interest in viewing the film immediately before the film was presented. MW was tracked using a self-report method targeting instances of MW with metacognitive awareness. Participants in the prior-knowledge condition reported less MW compared with the control condition, thereby supporting the suppression hypothesis. MW also decreased over the duration of the film, but only for those with prior-knowledge of the film. Finally, prior-knowledge effects on MW were only observed when interest was average or high, but not when interest was low.

The effects of learning on event-related potential correlates of musical expectancy.

PubMed

Carrión, Ricardo E; Bly, Benjamin Martin

2008-09-01

Musical processing studies have shown that unexpected endings in familiar musical sequences produce extended latencies of the P300 component. The present study sought to identify event-related potential (ERP) correlates of musical expectancy by entraining participants with rule-governed chord sequences and testing whether unexpected endings created similar responses. Two experiments were conducted in which participants performed grammaticality classifications without training (Experiment 1) and with training (Experiment 2). In both experiments, deviant chords differing in instrumental timbre elicited a MMN/P3a waveform complex. Violations related to learned patterns elicited an early right anterior negativity and P3b. Latency and amplitude of peak components were modulated by the physical characteristics of the chords, expectations due to prior knowledge of musical harmony, and contextually defined expectations developed through entrainment.

A Sequence-Independent Strategy for Detection and Cloning of Circular DNA Virus Genomes by Using Multiply Primed Rolling-Circle Amplification

PubMed Central

Rector, Annabel; Tachezy, Ruth; Van Ranst, Marc

2004-01-01

The discovery of novel viruses has often been accomplished by using hybridization-based methods that necessitate the availability of a previously characterized virus genome probe or knowledge of the viral nucleotide sequence to construct consensus or degenerate PCR primers. In their natural replication cycle, certain viruses employ a rolling-circle mechanism to propagate their circular genomes, and multiply primed rolling-circle amplification (RCA) with φ29 DNA polymerase has recently been applied in the amplification of circular plasmid vectors used in cloning. We employed an isothermal RCA protocol that uses random hexamer primers to amplify the complete genomes of papillomaviruses without the need for prior knowledge of their DNA sequences. We optimized this RCA technique with extracted human papillomavirus type 16 (HPV-16) DNA from W12 cells, using a real-time quantitative PCR assay to determine amplification efficiency, and obtained a 2.4 × 104-fold increase in HPV-16 DNA concentration. We were able to clone the complete HPV-16 genome from this multiply primed RCA product. The optimized protocol was subsequently applied to a bovine fibropapillomatous wart tissue sample. Whereas no papillomavirus DNA could be detected by restriction enzyme digestion of the original sample, multiply primed RCA enabled us to obtain a sufficient amount of papillomavirus DNA for restriction enzyme analysis, cloning, and subsequent sequencing of a novel variant of bovine papillomavirus type 1. The multiply primed RCA method allows the discovery of previously unknown papillomaviruses, and possibly also other circular DNA viruses, without a priori sequence information. PMID:15113879

Assessing the Previous Economic Knowledge of Beginning Students in Germany: Implications for Teaching Economics in Basic Courses

ERIC Educational Resources Information Center

Happ, Roland; Förster, Manuel; Zlatkin-Troitschanskaia, Olga; Carstensen, Vivian

2016-01-01

Study-related prior knowledge plays a decisive role in business and economics degree courses. Prior knowledge has a significant influence on knowledge acquisition in higher education, and teachers need information on it to plan their introductory courses accordingly. Very few studies have been conducted of first-year students' prior economic…

Time-specific contribution of the supplementary motor area to intermanual transfer of procedural knowledge

PubMed Central

Perez, MA; Tanaka, S; Wise, SP; Willingham, DT; Cohen, LG

2008-01-01

The supplementary motor area (SMA) makes a crucial contribution to intermanual transfer: the ability to use one hand to perform a skill practiced and learned with the other hand. However, the timing of this contribution relative to movement remains unknown. Here, 33 healthy volunteers performed a 12-item sequence in the serial reaction time task (SRTT). During training, each participant responded to a sequence of visual cues presented at 1 Hz by pressing one of 4 keys with their right hand. The measure of intermanual transfer was response time (RT) during repetition of the trained sequence with the left hand, which was at rest during learning. Participants were divided into 3 groups, which did not differ in their learning rates or amounts. In 2 groups, 1 Hz repetitive transcranial magnetic stimulation (rTMS) induced transient virtual lesions of the SMA during training, either 100 ms before each cue (the premovement group) or during each key press (the movement group). The third group received sham stimulation (the sham group). After training with the right hand, RTs for performance with the left (transfer) hand were longer for the premovement group than for the movement or sham groups. Thus SMA’s most crucial contribution to intermanual transfer occurs in the interval between movements, when the memory of a prior movement plays a role in encoding specific sequences. These results provide insight into frontal-lobe contributions to procedural knowledge. PMID:18815252

The Effects of Prior-knowledge and Online Learning Approaches on Students' Inquiry and Argumentation Abilities

NASA Astrophysics Data System (ADS)

Yang, Wen-Tsung; Lin, Yu-Ren; She, Hsiao-Ching; Huang, Kai-Yi

2015-07-01

This study investigated the effects of students' prior science knowledge and online learning approaches (social and individual) on their learning with regard to three topics: science concepts, inquiry, and argumentation. Two science teachers and 118 students from 4 eighth-grade science classes were invited to participate in this research. Students in each class were divided into three groups according to their level of prior science knowledge; they then took either our social- or individual-based online science learning program. The results show that students in the social online argumentation group performed better in argumentation and online argumentation learning. Qualitative analysis indicated that the students' social interactions benefited the co-construction of sound arguments and the accurate understanding of science concepts. In constructing arguments, students in the individual online argumentation group were limited to knowledge recall and self-reflection. High prior-knowledge students significantly outperformed low prior-knowledge students in all three aspects of science learning. However, the difference in inquiry and argumentation performance between low and high prior-knowledge students decreased with the progression of online learning topics.

Explanation and Prior Knowledge Interact to Guide Learning

ERIC Educational Resources Information Center

Williams, Joseph J.; Lombrozo, Tania

2013-01-01

How do explaining and prior knowledge contribute to learning? Four experiments explored the relationship between explanation and prior knowledge in category learning. The experiments independently manipulated whether participants were prompted to explain the category membership of study observations and whether category labels were informative in…

An improved pulse sequence and inversion algorithm of T2 spectrum

NASA Astrophysics Data System (ADS)

Ge, Xinmin; Chen, Hua; Fan, Yiren; Liu, Juntao; Cai, Jianchao; Liu, Jianyu

2017-03-01

The nuclear magnetic resonance transversal relaxation time is widely applied in geological prospecting, both in laboratory and downhole environments. However, current methods used for data acquisition and inversion should be reformed to characterize geological samples with complicated relaxation components and pore size distributions, such as samples of tight oil, gas shale, and carbonate. We present an improved pulse sequence to collect transversal relaxation signals based on the CPMG (Carr, Purcell, Meiboom, and Gill) pulse sequence. The echo spacing is not constant but varies in different windows, depending on prior knowledge or customer requirements. We use the entropy based truncated singular value decomposition (TSVD) to compress the ill-posed matrix and discard small singular values which cause the inversion instability. A hybrid algorithm combining the iterative TSVD and a simultaneous iterative reconstruction technique is implemented to reach the global convergence and stability of the inversion. Numerical simulations indicate that the improved pulse sequence leads to the same result as CPMG, but with lower echo numbers and computational time. The proposed method is a promising technique for geophysical prospecting and other related fields in future.

Detecting novel genes with sparse arrays

PubMed Central

Haiminen, Niina; Smit, Bart; Rautio, Jari; Vitikainen, Marika; Wiebe, Marilyn; Martinez, Diego; Chee, Christine; Kunkel, Joe; Sanchez, Charles; Nelson, Mary Anne; Pakula, Tiina; Saloheimo, Markku; Penttilä, Merja; Kivioja, Teemu

2014-01-01

Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods and tiling arrays can be used to find genes without prior information and they have demonstrated that novel genes can still be found from extensively studied model organisms. Unfortunately, these methods are expensive and thus are not easily applicable, e.g., to finding genes that are expressed only in very specific conditions. We demonstrate a method for finding novel genes with sparse arrays, applying it on the 33.9 Mb genome of the filamentous fungus Trichoderma reesei. Our computational method does not require normalisations between arrays and it takes into account the multiple-testing problem typical for analysis of microarray data. In contrast to tiling arrays, that use overlapping probes, only one 25mer microarray oligonucleotide probe was used for every 100 b. Thus, only relatively little space on a microarray slide was required to cover the intergenic regions of a genome. The analysis was done as a by-product of a conventional microarray experiment with no additional costs. We found at least 23 good candidates for novel transcripts that could code for proteins and all of which were expressed at high levels. Candidate genes were found to neighbour ire1 and cre1 and many other regulatory genes. Our simple, low-cost method can easily be applied to finding novel species-specific genes without prior knowledge of their sequence properties. PMID:20691772

The Importance of Prior Knowledge.

ERIC Educational Resources Information Center

Cleary, Linda Miller

1989-01-01

Recounts a college English teacher's experience of reading and rereading Noam Chomsky, building up a greater store of prior knowledge. Argues that Frank Smith provides a theory for the importance of prior knowledge and Chomsky's work provided a personal example with which to interpret and integrate that theory. (RS)

Genomic variation in macrophage-cultured European porcine reproductive and respiratory syndrome virus Olot/91 revealed using ultra-deep next generation sequencing.

PubMed

Lu, Zen H; Brown, Alexander; Wilson, Alison D; Calvert, Jay G; Balasch, Monica; Fuentes-Utrilla, Pablo; Loecherbach, Julia; Turner, Frances; Talbot, Richard; Archibald, Alan L; Ait-Ali, Tahar

2014-03-04

Porcine Reproductive and Respiratory Syndrome (PRRS) is a disease of major economic impact worldwide. The etiologic agent of this disease is the PRRS virus (PRRSV). Increasing evidence suggest that microevolution within a coexisting quasispecies population can give rise to high sequence heterogeneity in PRRSV. We developed a pipeline based on the ultra-deep next generation sequencing approach to first construct the complete genome of a European PRRSV, strain Olot/9, cultured on macrophages and then capture the rare variants representative of the mixed quasispecies population. Olot/91 differs from the reference Lelystad strain by about 5% and a total of 88 variants, with frequencies as low as 1%, were detected in the mixed population. These variants included 16 non-synonymous variants concentrated in the genes encoding structural and nonstructural proteins; including Glycoprotein 2a and 5. Using an ultra-deep sequencing methodology, the complete genome of Olot/91 was constructed without any prior knowledge of the sequence. Rare variants that constitute minor fractions of the heterogeneous PRRSV population could successfully be detected to allow further exploration of microevolutionary events.

Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity

PubMed Central

Jia, Yi; Huan, Jun; Buhr, Vincent; Zhang, Jintao; Carayannopoulos, Leonidas N

2009-01-01

Background Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or "midnight-" zones where pair-wise sequence identities to known sequences fall below 25% and sequence-based functional annotations often fail. Results Here we report a novel graph database mining method and demonstrate its application to protein structure pattern identification and structure classification. The biologic motivation of our study is to recognize common structure patterns in "immunoevasins", proteins mediating virus evasion of host immune defense. Our experimental study, using both viral and non-viral proteins, demonstrates the efficiency and efficacy of the proposed method. Conclusion We present a theoretic framework, offer a practical software implementation for incorporating prior domain knowledge, such as substitution matrices as studied here, and devise an efficient algorithm to identify approximate matched frequent subgraphs. By doing so, we significantly expanded the analytical power of sophisticated data mining algorithms in dealing with large volume of complicated and noisy protein structure data. And without loss of generality, choice of appropriate compatibility matrices allows our method to be easily employed in domains where subgraph labels have some uncertainty. PMID:19208148

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

PubMed Central

Lipinski, Leszek; Dziembowski, Andrzej

2018-01-01

Abstract Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples. PlasFlow can recover plasmid sequences from assembled metagenomes without any prior knowledge of the taxonomical or functional composition of samples with an accuracy up to 96%. It can also recover sequences of both circular and linear plasmids and can perform initial taxonomical classification of sequences. Compared to other currently available tools, PlasFlow demonstrated significantly better performance on test datasets. Analysis of two samples from heavy metal-contaminated microbial mats revealed that plasmids may constitute an important fraction of their metagenomes and carry genes involved in heavy-metal homeostasis, proving the pivotal role of plasmids in microorganism adaptation to environmental conditions. PMID:29346586

Infants learn better from left to right: a directional bias in infants' sequence learning.

PubMed

Bulf, Hermann; de Hevia, Maria Dolores; Gariboldi, Valeria; Macchi Cassia, Viola

2017-05-26

A wealth of studies show that human adults map ordered information onto a directional spatial continuum. We asked whether mapping ordinal information into a directional space constitutes an early predisposition, already functional prior to the acquisition of symbolic knowledge and language. While it is known that preverbal infants represent numerical order along a left-to-right spatial continuum, no studies have investigated yet whether infants, like adults, organize any kind of ordinal information onto a directional space. We investigated whether 7-month-olds' ability to learn high-order rule-like patterns from visual sequences of geometric shapes was affected by the spatial orientation of the sequences (left-to-right vs. right-to-left). Results showed that infants readily learn rule-like patterns when visual sequences were presented from left to right, but not when presented from right to left. This result provides evidence that spatial orientation critically determines preverbal infants' ability to perceive and learn ordered information in visual sequences, opening to the idea that a left-to-right spatially organized mental representation of ordered dimensions might be rooted in biologically-determined constraints on human brain development.

Exploring expectation effects in EMDR: does prior treatment knowledge affect the degrading effects of eye movements on memories?

PubMed Central

Littel, Marianne; van Schie, Kevin; van den Hout, Marcel A.

2017-01-01

ABSTRACT Background: Eye movement desensitization and reprocessing (EMDR) is an effective psychological treatment for posttraumatic stress disorder. Recalling a memory while simultaneously making eye movements (EM) decreases a memory’s vividness and/or emotionality. It has been argued that non-specific factors, such as treatment expectancy and experimental demand, may contribute to the EMDR’s effectiveness. Objective: The present study was designed to test whether expectations about the working mechanism of EMDR would alter the memory attenuating effects of EM. Two experiments were conducted. In Experiment 1, we examined the effects of pre-existing (non-manipulated) knowledge of EMDR in participants with and without prior knowledge. In Experiment 2, we experimentally manipulated prior knowledge by providing participants without prior knowledge with correct or incorrect information about EMDR’s working mechanism. Method: Participants in both experiments recalled two aversive, autobiographical memories during brief sets of EM (Recall+EM) or keeping eyes stationary (Recall Only). Before and after the intervention, participants scored their memories on vividness and emotionality. A Bayesian approach was used to compare two competing hypotheses on the effects of (existing/given) prior knowledge: (1) Prior (correct) knowledge increases the effects of Recall+EM vs. Recall Only, vs. (2) prior knowledge does not affect the effects of Recall+EM. Results: Recall+EM caused greater reductions in memory vividness and emotionality than Recall Only in all groups, including the incorrect information group. In Experiment 1, both hypotheses were supported by the data: prior knowledge boosted the effects of EM, but only modestly. In Experiment 2, the second hypothesis was clearly supported over the first: providing knowledge of the underlying mechanism of EMDR did not alter the effects of EM. Conclusions: Recall+EM appears to be quite robust against the effects of prior expectations. As Recall+EM is the core component of EMDR, expectancy effects probably contribute little to the effectiveness of EMDR treatment. PMID:29038685

ElemeNT: a computational tool for detecting core promoter elements.

PubMed

Sloutskin, Anna; Danino, Yehuda M; Orenstein, Yaron; Zehavi, Yonathan; Doniger, Tirza; Shamir, Ron; Juven-Gershon, Tamar

2015-01-01

Core promoter elements play a pivotal role in the transcriptional output, yet they are often detected manually within sequences of interest. Here, we present 2 contributions to the detection and curation of core promoter elements within given sequences. First, the Elements Navigation Tool (ElemeNT) is a user-friendly web-based, interactive tool for prediction and display of putative core promoter elements and their biologically-relevant combinations. Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs). ElemeNT's predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions. ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence. These resources, freely accessible at http://lifefaculty.biu.ac.il/gershon-tamar/index.php/resources, facilitate the identification of core promoter elements as active contributors to gene expression.

Calculus Instructors' Responses to Prior Knowledge Errors

ERIC Educational Resources Information Center

Talley, Jana Renee

2009-01-01

This study investigates the responses to prior knowledge errors that Calculus I instructors make when assessing students. Prior knowledge is operationalized as any skill or understanding that a student needs to successfully navigate through a Calculus I course. A two part qualitative study consisting of student exams and instructor interviews was…

Signaling Text-Picture Relations in Multimedia Learning: The Influence of Prior Knowledge

ERIC Educational Resources Information Center

Richter, Juliane; Scheiter, Katharina; Eitel, Alexander

2018-01-01

Multimedia integration signals highlight correspondences between text and pictures with the aim of supporting learning from multimedia. A recent meta-analysis revealed that only learners with low domain-specific prior knowledge benefit from multimedia integration signals. To more thoroughly investigate the influence of prior knowledge on the…

Menarche: Prior Knowledge and Experience.

ERIC Educational Resources Information Center

Skandhan, K. P.; And Others

1988-01-01

Recorded menstruation information among 305 young women in India, assessing the differences between those who did and did not have knowledge of menstruation prior to menarche. Those with prior knowledge considered menarche to be a normal physiological function and had a higher rate of regularity, lower rate of dysmenorrhea, and earlier onset of…

Preparing learners with partly incorrect intuitive prior knowledge for learning

PubMed Central

Ohst, Andrea; Fondu, Béatrice M. E.; Glogger, Inga; Nückles, Matthias; Renkl, Alexander

2014-01-01

Learners sometimes have incoherent and fragmented intuitive prior knowledge that is (partly) “incompatible” with the to-be-learned contents. Such knowledge in pieces can cause conceptual disorientation and cognitive overload while learning. We hypothesized that a pre-training intervention providing a generalized schema as a structuring framework for such knowledge in pieces would support (re)organizing-processes of prior knowledge and thus reduce unnecessary cognitive load during subsequent learning. Fifty-six student teachers participated in the experiment. A framework group underwent a pre-training intervention providing a generalized, categorical schema for categorizing primary learning strategies and related but different strategies as a cognitive framework for (re-)organizing their prior knowledge. Our control group received comparable factual information but no framework. Afterwards, all participants learned about primary learning strategies. The framework group claimed to possess higher levels of interest and self-efficacy, achieved higher learning outcomes, and learned more efficiently. Hence, providing a categorical framework can help overcome the barrier of incorrect prior knowledge in pieces. PMID:25071638

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data.

PubMed

Parker, Nicolas J; Parker, Andrew G

2008-04-18

The advent of pyrophosphate sequencing makes large volumes of sequencing data available at a lower cost than previously possible. However, the short read lengths are difficult to assemble and the large dataset is difficult to handle. During the sequencing of a virus from the tsetse fly, Glossina pallidipes, we found the need for tools to search quickly a set of reads for near exact text matches. A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of de novo assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads. Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data set; investigating homopolymer lengths, repeat regions and polymorphisms; and resolving inserted bases caused by incomplete chain extension. The additional information contained in a pyrophosphate sequencing data set beyond a basic assembly is difficult to access due to a lack of tools. The set of simple tools presented here would allow anyone with basic computer skills and a standard PC to access this information.

Using Hypermedia: Effects of Prior Knowledge and Goal Strength.

ERIC Educational Resources Information Center

Last, David A.; O'Donnell, Angela M.; Kelly, Anthony E.

The influences of a student's prior knowledge and desired goal on the difficulties and benefits associated with using hypertext were examined in this study. Participants, 12 students from an undergraduate course in educational psychology, were assigned to either the low or high prior knowledge category. Within these two groups, subjects were…

The Role of Prior Knowledge in Learning from Analogies in Science Texts

ERIC Educational Resources Information Center

Braasch, Jason L. G.; Goldman, Susan R.

2010-01-01

Two experiments examined whether inconsistent effects of analogies in promoting new content learning from text are related to prior knowledge of the analogy "per se." In Experiment 1, college students who demonstrated little understanding of weather systems and different levels of prior knowledge (more vs. less) of an analogous everyday…

Neural Mechanisms for Integrating Prior Knowledge and Likelihood in Value-Based Probabilistic Inference

PubMed Central

Ting, Chih-Chung; Yu, Chia-Chen; Maloney, Laurence T.

2015-01-01

In Bayesian decision theory, knowledge about the probabilities of possible outcomes is captured by a prior distribution and a likelihood function. The prior reflects past knowledge and the likelihood summarizes current sensory information. The two combined (integrated) form a posterior distribution that allows estimation of the probability of different possible outcomes. In this study, we investigated the neural mechanisms underlying Bayesian integration using a novel lottery decision task in which both prior knowledge and likelihood information about reward probability were systematically manipulated on a trial-by-trial basis. Consistent with Bayesian integration, as sample size increased, subjects tended to weigh likelihood information more compared with prior information. Using fMRI in humans, we found that the medial prefrontal cortex (mPFC) correlated with the mean of the posterior distribution, a statistic that reflects the integration of prior knowledge and likelihood of reward probability. Subsequent analysis revealed that both prior and likelihood information were represented in mPFC and that the neural representations of prior and likelihood in mPFC reflected changes in the behaviorally estimated weights assigned to these different sources of information in response to changes in the environment. Together, these results establish the role of mPFC in prior-likelihood integration and highlight its involvement in representing and integrating these distinct sources of information. PMID:25632152

Incorporating prior knowledge induced from stochastic differential equations in the classification of stochastic observations.

PubMed

Zollanvari, Amin; Dougherty, Edward R

2016-12-01

In classification, prior knowledge is incorporated in a Bayesian framework by assuming that the feature-label distribution belongs to an uncertainty class of feature-label distributions governed by a prior distribution. A posterior distribution is then derived from the prior and the sample data. An optimal Bayesian classifier (OBC) minimizes the expected misclassification error relative to the posterior distribution. From an application perspective, prior construction is critical. The prior distribution is formed by mapping a set of mathematical relations among the features and labels, the prior knowledge, into a distribution governing the probability mass across the uncertainty class. In this paper, we consider prior knowledge in the form of stochastic differential equations (SDEs). We consider a vector SDE in integral form involving a drift vector and dispersion matrix. Having constructed the prior, we develop the optimal Bayesian classifier between two models and examine, via synthetic experiments, the effects of uncertainty in the drift vector and dispersion matrix. We apply the theory to a set of SDEs for the purpose of differentiating the evolutionary history between two species.

Supervised Learning for Dynamical System Learning.

PubMed

Hefny, Ahmed; Downey, Carlton; Gordon, Geoffrey J

2015-01-01

Recently there has been substantial interest in spectral methods for learning dynamical systems. These methods are popular since they often offer a good tradeoff between computational and statistical efficiency. Unfortunately, they can be difficult to use and extend in practice: e.g., they can make it difficult to incorporate prior information such as sparsity or structure. To address this problem, we present a new view of dynamical system learning: we show how to learn dynamical systems by solving a sequence of ordinary supervised learning problems, thereby allowing users to incorporate prior knowledge via standard techniques such as L 1 regularization. Many existing spectral methods are special cases of this new framework, using linear regression as the supervised learner. We demonstrate the effectiveness of our framework by showing examples where nonlinear regression or lasso let us learn better state representations than plain linear regression does; the correctness of these instances follows directly from our general analysis.

The Effect of Prior Knowledge Activation on Text Recall: An Investigation of Two Conflicting Hypotheses.

ERIC Educational Resources Information Center

Machiels-Bongaerts, Maureen; And Others

Two hypotheses, the cognitive capacity hypothesis and the selective attention hypothesis, try to account for the facilitation effects of prior knowledge activation. They appear to be mutually exclusive since they predict different recall patterns as a result of prior knowledge activation. This study was designed to determine whether the two…

Understanding the Role of Prior Knowledge in a Multimedia Learning Application

ERIC Educational Resources Information Center

Rias, Riaza Mohd; Zaman, Halimah Badioze

2013-01-01

This study looked at the effects that individual differences in prior knowledge have on student understanding in learning with multimedia in a computer science subject. Students were identified as having either low or high prior knowledge from a series of questions asked in a survey conducted at the Faculty of Computer and Mathematical Sciences at…

A Fuzzy-Based Prior Knowledge Diagnostic Model with Multiple Attribute Evaluation

ERIC Educational Resources Information Center

Lin, Yi-Chun; Huang, Yueh-Min

2013-01-01

Prior knowledge is a very important part of teaching and learning, as it affects how instructors and students interact with the learning materials. In general, tests are used to assess students' prior knowledge. Nevertheless, conventional testing approaches usually assign only an overall score to each student, and this may mean that students are…

Probabilistic models for neural populations that naturally capture global coupling and criticality

PubMed Central

2017-01-01

Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality. PMID:28926564

When does prior knowledge disproportionately benefit older adults’ memory?

PubMed Central

Badham, Stephen P.; Hay, Mhairi; Foxon, Natasha; Kaur, Kiran; Maylor, Elizabeth A.

2016-01-01

ABSTRACT Material consistent with knowledge/experience is generally more memorable than material inconsistent with knowledge/experience – an effect that can be more extreme in older adults. Four experiments investigated knowledge effects on memory with young and older adults. Memory for familiar and unfamiliar proverbs (Experiment 1) and for common and uncommon scenes (Experiment 2) showed similar knowledge effects across age groups. Memory for person-consistent and person-neutral actions (Experiment 3) showed a greater benefit of prior knowledge in older adults. For cued recall of related and unrelated word pairs (Experiment 4), older adults benefited more from prior knowledge only when it provided uniquely useful additional information beyond the episodic association itself. The current data and literature suggest that prior knowledge has the age-dissociable mnemonic properties of (1) improving memory for the episodes themselves (age invariant), and (2) providing conceptual information about the tasks/stimuli extrinsically to the actual episodic memory (particularly aiding older adults). PMID:26473767

Is an Illustration Always Worth Ten Thousand Words? Effects of Prior Knowledge, Learning Style and Multimedia Illustrations on Text Comprehension.

ERIC Educational Resources Information Center

Ollerenshaw, Alison; Aidman, Eugene; Kidd, Garry

1997-01-01

This study examined comprehension in four groups of undergraduates under text only, multimedia, and two diagram conditions of text supplementation. Results indicated that effects of text supplementation are mediated by prior knowledge and learning style: multimedia appears more beneficial to surface learners with little prior knowledge and makes…

Effects of Prior Knowledge in Mathematics on Learner-Interface Interactions in a Learning-by-Teaching Intelligent Tutoring System

ERIC Educational Resources Information Center

Bringula, Rex P.; Basa, Roselle S.; Dela Cruz, Cecilio; Rodrigo, Ma. Mercedes T.

2016-01-01

This study attempted to determine the influence of prior knowledge in mathematics of students on learner-interface interactions in a learning-by-teaching intelligent tutoring system. One hundred thirty-nine high school students answered a pretest (i.e., the prior knowledge in mathematics) and a posttest. In between the pretest and posttest, they…

The Effect of the States of Prior Knowledge on Question Answering.

ERIC Educational Resources Information Center

Holmes, Betty C.

A study was conducted to gain insight into the question answering abilities of good and poor readers by comparing how well they answered questions when their prior knowledge was at two different levels (high, low) and in four different states. These states of prior knowledge consisted of the ways in which answers to the questions were stored in…

Learning from Instructional Animations: How Does Prior Knowledge Mediate the Effect of Visual Cues?

ERIC Educational Resources Information Center

Arslan-Ari, I.

2018-01-01

The purpose of this study was to investigate the effects of cueing and prior knowledge on learning and mental effort of students studying an animation with narration. This study employed a 2 (no cueing vs. visual cueing) × 2 (low vs. high prior knowledge) between-subjects factorial design. The results revealed a significant interaction effect…

Predicting fifth-grade students' understanding of ecological science concepts with motivational and cognitive variables

NASA Astrophysics Data System (ADS)

Alao, Solomon

The need to identify factors that contribute to students' understanding of ecological concepts has been widely expressed in recent literature. The purpose of this study was to investigate the relationship between fifth grade students' prior knowledge, learning strategies, interest, and learning goals and their conceptual understanding of ecological science concepts. Subject were 72 students from three fifth grade classrooms located in a metropolitan area of the eastern United States. Students completed the goal commitment, interest, and strategy use questionnaire (GISQ), and a knowledge test designed to assess their prior knowledge and conceptual understanding of ecological science concepts. The learning goals scale assessed intentions to try to learn and understand ecological concepts. The interest scale assessed the feeling and value-related valences that students ascribed to science and ecological science concepts. The strategy use scale assessed the use of two cognitive strategies (monitoring and elaboration). The knowledge test assessed students' understanding of ecological concepts (the relationship between living organisms and their environment). Scores on all measures were examined for gender differences; no significant gender differences were observed. The motivational and cognitive variables contributed to students' understanding of ecological concepts. After accounting for interest, learning goals, and strategy use, prior knowledge accounted for 28% of the total variance in conceptual understanding. After accounting for prior knowledge, interest, learning goals, and strategy use explained 7%, 6%, and 4% of the total variance in conceptual understanding, respectively. More importantly, these variables were interrelated to each other and to conceptual understanding. After controlling for prior knowledge, learning goals, and strategy use, interest did not predict the variance in conceptual understanding. After controlling for prior knowledge, interest, and strategy use, learning goals did not predict the variance in conceptual understanding. And, after controlling for prior knowledge, interest, and learning goals, strategy use did not predict the variance in conceptual understanding. Results of this study indicated that prior knowledge, interest, learning goals, and strategy use should be included in theoretical models design to explain and to predict fifth grade students' understanding of ecological concepts. Results of this study further suggested that curriculum developers and science teachers need to take fifth grade students' prior knowledge of ecological concepts, interest in science and ecological concepts; intentions to learn and understand ecological concepts, and use of cognitive strategies into account when designing instructional contexts to support these students' understanding of ecological concepts.

The relation between prior knowledge and students' collaborative discovery learning processes

NASA Astrophysics Data System (ADS)

Gijlers, Hannie; de Jong, Ton

2005-03-01

In this study we investigate how prior knowledge influences knowledge development during collaborative discovery learning. Fifteen dyads of students (pre-university education, 15-16 years old) worked on a discovery learning task in the physics field of kinematics. The (face-to-face) communication between students was recorded and the interaction with the environment was logged. Based on students' individual judgments of the truth-value and testability of a series of domain-specific propositions, a detailed description of the knowledge configuration for each dyad was created before they entered the learning environment. Qualitative analyses of two dialogues illustrated that prior knowledge influences the discovery learning processes, and knowledge development in a pair of students. Assessments of student and dyad definitional (domain-specific) knowledge, generic (mathematical and graph) knowledge, and generic (discovery) skills were related to the students' dialogue in different discovery learning processes. Results show that a high level of definitional prior knowledge is positively related to the proportion of communication regarding the interpretation of results. Heterogeneity with respect to generic prior knowledge was positively related to the number of utterances made in the discovery process categories hypotheses generation and experimentation. Results of the qualitative analyses indicated that collaboration between extremely heterogeneous dyads is difficult when the high achiever is not willing to scaffold information and work in the low achiever's zone of proximal development.

From protein sequence to dynamics and disorder with DynaMine.

PubMed

Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim F

2013-01-01

Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine--a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.

Identifying Differentially Abundant Metabolic Pathways in Metagenomic Datasets

NASA Astrophysics Data System (ADS)

Liu, Bo; Pop, Mihai

Enabled by rapid advances in sequencing technology, metagenomic studies aim to characterize entire communities of microbes bypassing the need for culturing individual bacterial members. One major goal of such studies is to identify specific functional adaptations of microbial communities to their habitats. Here we describe a powerful analytical method (MetaPath) that can identify differentially abundant pathways in metagenomic data-sets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge. We show that MetaPath outperforms other common approaches when evaluated on simulated datasets. We also demonstrate the power of our methods in analyzing two, publicly available, metagenomic datasets: a comparison of the gut microbiome of obese and lean twins; and a comparison of the gut microbiome of infant and adult subjects. We demonstrate that the subpathways identified by our method provide valuable insights into the biological activities of the microbiome.

The Influence of Self-Regulated Learning and Prior Knowledge on Knowledge Acquisition in Computer-Based Learning Environments

ERIC Educational Resources Information Center

Bernacki, Matthew

2010-01-01

This study examined how learners construct textbase and situation model knowledge in hypertext computer-based learning environments (CBLEs) and documented the influence of specific self-regulated learning (SRL) tactics, prior knowledge, and characteristics of the learner on posttest knowledge scores from exposure to a hypertext. A sample of 160…

A novel method based on new adaptive LVQ neural network for predicting protein-protein interactions from protein sequences.

PubMed

Yousef, Abdulaziz; Moghadam Charkari, Nasrollah

2013-11-07

Protein-Protein interaction (PPI) is one of the most important data in understanding the cellular processes. Many interesting methods have been proposed in order to predict PPIs. However, the methods which are based on the sequence of proteins as a prior knowledge are more universal. In this paper, a sequence-based, fast, and adaptive PPI prediction method is introduced to assign two proteins to an interaction class (yes, no). First, in order to improve the presentation of the sequences, twelve physicochemical properties of amino acid have been used by different representation methods to transform the sequence of protein pairs into different feature vectors. Then, for speeding up the learning process and reducing the effect of noise PPI data, principal component analysis (PCA) is carried out as a proper feature extraction algorithm. Finally, a new and adaptive Learning Vector Quantization (LVQ) predictor is designed to deal with different models of datasets that are classified into balanced and imbalanced datasets. The accuracy of 93.88%, 90.03%, and 89.72% has been found on S. cerevisiae, H. pylori, and independent datasets, respectively. The results of various experiments indicate the efficiency and validity of the method. © 2013 Published by Elsevier Ltd.

Does prior domain-specific content knowledge influence students' recall of arguments surrounding interdisciplinary topics?

PubMed

Schmidt, Hiemke K; Rothgangel, Martin; Grube, Dietmar

2017-12-01

Awareness of various arguments can help interactants present opinions, stress points, and build counterarguments during discussions. At school, some topics are taught in a way that students learn to accumulate knowledge and gather arguments, and later employ them during debates. Prior knowledge may facilitate recalling information on well structured, fact-based topics, but does it facilitate recalling arguments during discussions on complex, interdisciplinary topics? We assessed the prior knowledge in domains related to a bioethical topic of 277 students from Germany (approximately 15 years old), their interest in the topic, and their general knowledge. The students read a text with arguments for and against prenatal diagnostics and tried to recall the arguments one week later and again six weeks later. Prior knowledge in various domains related to the topic individually and separately helped students recall the arguments. These relationships were independent of students' interest in the topic and their general knowledge. Copyright © 2017 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Prior Knowledge Guides Speech Segregation in Human Auditory Cortex.

PubMed

Wang, Yuanye; Zhang, Jianfeng; Zou, Jiajie; Luo, Huan; Ding, Nai

2018-05-18

Segregating concurrent sound streams is a computationally challenging task that requires integrating bottom-up acoustic cues (e.g. pitch) and top-down prior knowledge about sound streams. In a multi-talker environment, the brain can segregate different speakers in about 100 ms in auditory cortex. Here, we used magnetoencephalographic (MEG) recordings to investigate the temporal and spatial signature of how the brain utilizes prior knowledge to segregate 2 speech streams from the same speaker, which can hardly be separated based on bottom-up acoustic cues. In a primed condition, the participants know the target speech stream in advance while in an unprimed condition no such prior knowledge is available. Neural encoding of each speech stream is characterized by the MEG responses tracking the speech envelope. We demonstrate that an effect in bilateral superior temporal gyrus and superior temporal sulcus is much stronger in the primed condition than in the unprimed condition. Priming effects are observed at about 100 ms latency and last more than 600 ms. Interestingly, prior knowledge about the target stream facilitates speech segregation by mainly suppressing the neural tracking of the non-target speech stream. In sum, prior knowledge leads to reliable speech segregation in auditory cortex, even in the absence of reliable bottom-up speech segregation cue.

Clinical genomics information management software linking cancer genome sequence and clinical decisions.

PubMed

Watt, Stuart; Jiao, Wei; Brown, Andrew M K; Petrocelli, Teresa; Tran, Ben; Zhang, Tong; McPherson, John D; Kamel-Reid, Suzanne; Bedard, Philippe L; Onetto, Nicole; Hudson, Thomas J; Dancey, Janet; Siu, Lillian L; Stein, Lincoln; Ferretti, Vincent

2013-09-01

Using sequencing information to guide clinical decision-making requires coordination of a diverse set of people and activities. In clinical genomics, the process typically includes sample acquisition, template preparation, genome data generation, analysis to identify and confirm variant alleles, interpretation of clinical significance, and reporting to clinicians. We describe a software application developed within a clinical genomics study, to support this entire process. The software application tracks patients, samples, genomic results, decisions and reports across the cohort, monitors progress and sends reminders, and works alongside an electronic data capture system for the trial's clinical and genomic data. It incorporates systems to read, store, analyze and consolidate sequencing results from multiple technologies, and provides a curated knowledge base of tumor mutation frequency (from the COSMIC database) annotated with clinical significance and drug sensitivity to generate reports for clinicians. By supporting the entire process, the application provides deep support for clinical decision making, enabling the generation of relevant guidance in reports for verification by an expert panel prior to forwarding to the treating physician. Copyright © 2013 Elsevier Inc. All rights reserved.

Basic Skills Resource Center: Report on the Preliminary Research Findings

DTIC Science & Technology

1985-01-01

indicates that the higher the level of processing , the greater the comprehension and recall. This is true of word lists ( Craik & Lockhart , 1972) as well as... Levels of Processing Principle 9 Content-Driven Strategy/Skills Instruction Principle 10 Instruction, Content, and Prior Knowledge Principle 11 Sequencing...34 Ws 1.’t) 0 U) 14 C0 W u w. C -0.0 C) a. I-s U) w~ 0 4) 0 C "q’ 01 .0 0c 414U >4 0.4 F 0 to 0)0 IvJ0 04Cu B-13 Principle 8 ( Levels of Processing ) The

Contribution of prior semantic knowledge to new episodic learning in amnesia.

PubMed

Kan, Irene P; Alexander, Michael P; Verfaellie, Mieke

2009-05-01

We evaluated whether prior semantic knowledge would enhance episodic learning in amnesia. Subjects studied prices that are either congruent or incongruent with prior price knowledge for grocery and household items and then performed a forced-choice recognition test for the studied prices. Consistent with a previous report, healthy controls' performance was enhanced by price knowledge congruency; however, only a subset of amnesic patients experienced the same benefit. Whereas patients with relatively intact semantic systems, as measured by an anatomical measure (i.e., lesion involvement of anterior and lateral temporal lobes), experienced a significant congruency benefit, patients with compromised semantic systems did not experience a congruency benefit. Our findings suggest that when prior knowledge structures are intact, they can support acquisition of new episodic information by providing frameworks into which such information can be incorporated.

Assessment of knowledge transfer in the context of biomechanics

NASA Astrophysics Data System (ADS)

Hutchison, Randolph E.

The dynamic act of knowledge transfer, or the connection of a student's prior knowledge to features of a new problem, could be considered one of the primary goals of education. Yet studies highlight more instances of failure than success. This dissertation focuses on how knowledge transfer takes place during individual problem solving, in classroom settings and during group work. Through the lens of dynamic transfer, or how students connect prior knowledge to problem features, this qualitative study focuses on a methodology to assess transfer in the context of biomechanics. The first phase of this work investigates how a pedagogical technique based on situated cognition theory affects students' ability to transfer knowledge gained in a biomechanics class to later experiences both in and out of the classroom. A post-class focus group examined events the students remembered from the class, what they learned from them, and how they connected them to later relevant experiences inside and outside the classroom. These results were triangulated with conceptual gains evaluated through concept inventories and pre- and post- content tests. Based on these results, the next two phases of the project take a more in-depth look at dynamic knowledge transfer during independent problem-solving and group project interactions, respectively. By categorizing prior knowledge (Source Tools), problem features (Target Tools) and the connections between them, results from the second phase of this study showed that within individual problem solving, source tools were almost exclusively derived from "propagated sources," i.e. those based on an authoritative source. This differs from findings in the third phase of the project, in which a mixture of "propagated" sources and "fabricated" sources, i.e. those based on student experiences, were identified within the group project work. This methodology is effective at assessing knowledge transfer in the context of biomechanics through evidence of the ability to identify differing patterns of how different students apply prior knowledge and make new connections between prior knowledge and current problem features in different learning situations. Implications for the use of this methodology include providing insight into not only students' prior knowledge, but also how they connect this prior knowledge to problem features (i.e. dynamic knowledge transfer). It also allows the identification of instances in which external input from other students or the instructor prompted knowledge transfer to take place. The use of this dynamic knowledge transfer lens allows the addressing of gaps in student understanding, and permits further investigations of techniques that increase instances of successful knowledge transfer.

Scalable Learning for Geostatistics and Speaker Recognition

DTIC Science & Technology

2011-01-01

of prior knowledge of the model or due to improved robustness requirements). Both these methods have their own advantages and disadvantages. The use...application. If the data is well-correlated and low-dimensional, any prior knowledge available on the data can be used to build a parametric model. In the...absence of prior knowledge , non-parametric methods can be used. If the data is high-dimensional, PCA based dimensionality reduction is often the first

SU-E-J-71: Spatially Preserving Prior Knowledge-Based Treatment Planning

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

Wang, H; Xing, L

2015-06-15

Purpose: Prior knowledge-based treatment planning is impeded by the use of a single dose volume histogram (DVH) curve. Critical spatial information is lost from collapsing the dose distribution into a histogram. Even similar patients possess geometric variations that becomes inaccessible in the form of a single DVH. We propose a simple prior knowledge-based planning scheme that extracts features from prior dose distribution while still preserving the spatial information. Methods: A prior patient plan is not used as a mere starting point for a new patient but rather stopping criteria are constructed. Each structure from the prior patient is partitioned intomore » multiple shells. For instance, the PTV is partitioned into an inner, middle, and outer shell. Prior dose statistics are then extracted for each shell and translated into the appropriate Dmin and Dmax parameters for the new patient. Results: The partitioned dose information from a prior case has been applied onto 14 2-D prostate cases. Using prior case yielded final DVHs that was comparable to manual planning, even though the DVH for the prior case was different from the DVH for the 14 cases. Solely using a single DVH for the entire organ was also performed for comparison but showed a much poorer performance. Different ways of translating the prior dose statistics into parameters for the new patient was also tested. Conclusion: Prior knowledge-based treatment planning need to salvage the spatial information without transforming the patients on a voxel to voxel basis. An efficient balance between the anatomy and dose domain is gained through partitioning the organs into multiple shells. The use of prior knowledge not only serves as a starting point for a new case but the information extracted from the partitioned shells are also translated into stopping criteria for the optimization problem at hand.« less

Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of the Legume Crop Species Lupinus angustifolius L

PubMed Central

Zheng, Zequn; Zhang, Qisen; Zhou, Gaofeng; Sweetingham, Mark W.; Howieson, John G.; Li, Chengdao

2013-01-01

Lupin (Lupinus angustifolius L.) is the most recently domesticated crop in major agricultural cultivation. Its seeds are high in protein and dietary fibre, but low in oil and starch. Medical and dietetic studies have shown that consuming lupin-enriched food has significant health benefits. We report the draft assembly from a whole genome shotgun sequencing dataset for this legume species with 26.9x coverage of the genome, which is predicted to contain 57,807 genes. Analysis of the annotated genes with metabolic pathways provided a partial understanding of some key features of lupin, such as the amino acid profile of storage proteins in seeds. Furthermore, we applied the NGS-based RAD-sequencing technology to obtain 8,244 sequence-defined markers for anchoring the genomic sequences. A total of 4,214 scaffolds from the genome sequence assembly were aligned into the genetic map. The combination of the draft assembly and a sequence-defined genetic map made it possible to locate and study functional genes of agronomic interest. The identification of co-segregating SNP markers, scaffold sequences and gene annotation facilitated the identification of a candidate R gene associated with resistance to the major lupin disease anthracnose. We demonstrated that the combination of medium-depth genome sequencing and a high-density genetic linkage map by application of NGS technology is a cost-effective approach to generating genome sequence data and a large number of molecular markers to study the genomics, genetics and functional genes of lupin, and to apply them to molecular plant breeding. This strategy does not require prior genome knowledge, which potentiates its application to a wide range of non-model species. PMID:23734219

Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L.

PubMed

Yang, Huaan; Tao, Ye; Zheng, Zequn; Zhang, Qisen; Zhou, Gaofeng; Sweetingham, Mark W; Howieson, John G; Li, Chengdao

2013-01-01

Lupin (Lupinus angustifolius L.) is the most recently domesticated crop in major agricultural cultivation. Its seeds are high in protein and dietary fibre, but low in oil and starch. Medical and dietetic studies have shown that consuming lupin-enriched food has significant health benefits. We report the draft assembly from a whole genome shotgun sequencing dataset for this legume species with 26.9x coverage of the genome, which is predicted to contain 57,807 genes. Analysis of the annotated genes with metabolic pathways provided a partial understanding of some key features of lupin, such as the amino acid profile of storage proteins in seeds. Furthermore, we applied the NGS-based RAD-sequencing technology to obtain 8,244 sequence-defined markers for anchoring the genomic sequences. A total of 4,214 scaffolds from the genome sequence assembly were aligned into the genetic map. The combination of the draft assembly and a sequence-defined genetic map made it possible to locate and study functional genes of agronomic interest. The identification of co-segregating SNP markers, scaffold sequences and gene annotation facilitated the identification of a candidate R gene associated with resistance to the major lupin disease anthracnose. We demonstrated that the combination of medium-depth genome sequencing and a high-density genetic linkage map by application of NGS technology is a cost-effective approach to generating genome sequence data and a large number of molecular markers to study the genomics, genetics and functional genes of lupin, and to apply them to molecular plant breeding. This strategy does not require prior genome knowledge, which potentiates its application to a wide range of non-model species.

Learning from the Mars Rover Mission: Scientific Discovery, Learning and Memory

NASA Technical Reports Server (NTRS)

Linde, Charlotte

2005-01-01

Purpose: Knowledge management for space exploration is part of a multi-generational effort. Each mission builds on knowledge from prior missions, and learning is the first step in knowledge production. This paper uses the Mars Exploration Rover mission as a site to explore this process. Approach: Observational study and analysis of the work of the MER science and engineering team during rover operations, to investigate how learning occurs, how it is recorded, and how these representations might be made available for subsequent missions. Findings: Learning occurred in many areas: planning science strategy, using instrumen?s within the constraints of the martian environment, the Deep Space Network, and the mission requirements; using software tools effectively; and running two teams on Mars time for three months. This learning is preserved in many ways. Primarily it resides in individual s memories. It is also encoded in stories, procedures, programming sequences, published reports, and lessons learned databases. Research implications: Shows the earliest stages of knowledge creation in a scientific mission, and demonstrates that knowledge management must begin with an understanding of knowledge creation. Practical implications: Shows that studying learning and knowledge creation suggests proactive ways to capture and use knowledge across multiple missions and generations. Value: This paper provides a unique analysis of the learning process of a scientific space mission, relevant for knowledge management researchers and designers, as well as demonstrating in detail how new learning occurs in a learning organization.

Studying Functions of All Yeast Genes Simultaneously

NASA Technical Reports Server (NTRS)

Stolc, Viktor; Eason, Robert G.; Poumand, Nader; Herman, Zelek S.; Davis, Ronald W.; Anthony Kevin; Jejelowo, Olufisayo

2006-01-01

A method of studying the functions of all the genes of a given species of microorganism simultaneously has been developed in experiments on Saccharomyces cerevisiae (commonly known as baker's or brewer's yeast). It is already known that many yeast genes perform functions similar to those of corresponding human genes; therefore, by facilitating understanding of yeast genes, the method may ultimately also contribute to the knowledge needed to treat some diseases in humans. Because of the complexity of the method and the highly specialized nature of the underlying knowledge, it is possible to give only a brief and sketchy summary here. The method involves the use of unique synthetic deoxyribonucleic acid (DNA) sequences that are denoted as DNA bar codes because of their utility as molecular labels. The method also involves the disruption of gene functions through deletion of genes. Saccharomyces cerevisiae is a particularly powerful experimental system in that multiple deletion strains easily can be pooled for parallel growth assays. Individual deletion strains recently have been created for 5,918 open reading frames, representing nearly all of the estimated 6,000 genetic loci of Saccharomyces cerevisiae. Tagging of each deletion strain with one or two unique 20-nucleotide sequences enables identification of genes affected by specific growth conditions, without prior knowledge of gene functions. Hybridization of bar-code DNA to oligonucleotide arrays can be used to measure the growth rate of each strain over several cell-division generations. The growth rate thus measured serves as an index of the fitness of the strain.

Nonparametric Combinatorial Sequence Models

NASA Astrophysics Data System (ADS)

Wauthier, Fabian L.; Jordan, Michael I.; Jojic, Nebojsa

This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This paper presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three sequence datasets which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution induced by the prior. By integrating out the posterior our method compares favorably to leading binding predictors.

Comfort and experience with online learning: trends over nine years and associations with knowledge.

PubMed

Cook, David A; Thompson, Warren G

2014-07-01

Some evidence suggests that attitude toward computer-based instruction is an important determinant of success in online learning. We sought to determine how comfort using computers and perceptions of prior online learning experiences have changed over the past decade, and how these associate with learning outcomes. Each year from 2003-2011 we conducted a prospective trial of online learning. As part of each year's study, we asked medicine residents about their comfort using computers and if their previous experiences with online learning were favorable. We assessed knowledge using a multiple-choice test. We used regression to analyze associations and changes over time. 371 internal medicine and family medicine residents participated. Neither comfort with computers nor perceptions of prior online learning experiences showed a significant change across years (p > 0.61), with mean comfort rating 3.96 (maximum 5 = very comfortable) and mean experience rating 4.42 (maximum 6 = strongly agree [favorable]). Comfort showed no significant association with knowledge scores (p = 0.39) but perceptions of prior experiences did, with a 1.56% rise in knowledge score for a 1-point rise in experience score (p = 0.02). Correlations among comfort, perceptions of prior experiences, and number of prior experiences were all small and not statistically significant. Comfort with computers and perceptions of prior experience with online learning remained stable over nine years. Prior good experiences (but not comfort with computers) demonstrated a modest association with knowledge outcomes, suggesting that prior course satisfaction may influence subsequent learning.

Small Stories for Learning: A Sociocultural Analysis of Children's Participation in Informal Science Education

NASA Astrophysics Data System (ADS)

Desjardins, Elia Nelson

2011-12-01

This dissertation examines the ways children use language to construct scientific knowledge in designed informal learning environments such as museums, aquariums, and zoos, with particular attention to autobiographical storytelling. This study takes as its foundation cultural-historical activity theory, defining learning as increased participation in meaningful, knowledge-based activity. It aims to improve experience design in informal learning environments by facilitating and building upon language interactions that are already in use by learners in these contexts. Fieldwork consists of audio recordings of individual children aged 4--12 as they explored a museum of science and technology with their families. Recordings were transcribed and coded according to the activity (task) and context (artifact/exhibit) in which the child was participating during each sequence of utterances. Additional evidence is provided by supplemental interviews with museum educators. Analysis suggests that short autobiographical stories can provide opportunities for learners to access metacognitive knowledge, for educators to assess learners' prior experience and knowledge, and for designers to engage affective pathways in order to increase participation that is both active and contemplative. Design implications are discussed and a design proposal for a distributed informal learning environment is presented.

Anatomy-guided joint tissue segmentation and topological correction for 6-month infant brain MRI with risk of autism.

PubMed

Wang, Li; Li, Gang; Adeli, Ehsan; Liu, Mingxia; Wu, Zhengwang; Meng, Yu; Lin, Weili; Shen, Dinggang

2018-06-01

Tissue segmentation of infant brain MRIs with risk of autism is critically important for characterizing early brain development and identifying biomarkers. However, it is challenging due to low tissue contrast caused by inherent ongoing myelination and maturation. In particular, at around 6 months of age, the voxel intensities in both gray matter and white matter are within similar ranges, thus leading to the lowest image contrast in the first postnatal year. Previous studies typically employed intensity images and tentatively estimated tissue probabilities to train a sequence of classifiers for tissue segmentation. However, the important prior knowledge of brain anatomy is largely ignored during the segmentation. Consequently, the segmentation accuracy is still limited and topological errors frequently exist, which will significantly degrade the performance of subsequent analyses. Although topological errors could be partially handled by retrospective topological correction methods, their results may still be anatomically incorrect. To address these challenges, in this article, we propose an anatomy-guided joint tissue segmentation and topological correction framework for isointense infant MRI. Particularly, we adopt a signed distance map with respect to the outer cortical surface as anatomical prior knowledge, and incorporate such prior information into the proposed framework to guide segmentation in ambiguous regions. Experimental results on the subjects acquired from National Database for Autism Research demonstrate the effectiveness to topological errors and also some levels of robustness to motion. Comparisons with the state-of-the-art methods further demonstrate the advantages of the proposed method in terms of both segmentation accuracy and topological correctness. © 2018 Wiley Periodicals, Inc.

7 CFR 275.2 - State agency responsibilities.

Code of Federal Regulations, 2014 CFR

2014-01-01

...: (i) Data collection through management evaluation (ME) reviews and quality control (QC) reviews; (ii... knowledge of either the household or the decision under review. Where there is prior knowledge, the reviewer must disqualify her/himself. Prior knowledge is defined as having: (1) Taken any part in the decision...

7 CFR 275.2 - State agency responsibilities.

Code of Federal Regulations, 2011 CFR

2011-01-01

...: (i) Data collection through management evaluation (ME) reviews and quality control (QC) reviews; (ii... knowledge of either the household or the decision under review. Where there is prior knowledge, the reviewer must disqualify her/himself. Prior knowledge is defined as having: (1) Taken any part in the decision...

7 CFR 275.2 - State agency responsibilities.

Code of Federal Regulations, 2013 CFR

2013-01-01

...: (i) Data collection through management evaluation (ME) reviews and quality control (QC) reviews; (ii... knowledge of either the household or the decision under review. Where there is prior knowledge, the reviewer must disqualify her/himself. Prior knowledge is defined as having: (1) Taken any part in the decision...

7 CFR 275.2 - State agency responsibilities.

Code of Federal Regulations, 2012 CFR

2012-01-01

...: (i) Data collection through management evaluation (ME) reviews and quality control (QC) reviews; (ii... knowledge of either the household or the decision under review. Where there is prior knowledge, the reviewer must disqualify her/himself. Prior knowledge is defined as having: (1) Taken any part in the decision...

7 CFR 275.2 - State agency responsibilities.

Code of Federal Regulations, 2010 CFR

2010-01-01

...: (i) Data collection through management evaluation (ME) reviews and quality control (QC) reviews; (ii... knowledge of either the household or the decision under review. Where there is prior knowledge, the reviewer must disqualify her/himself. Prior knowledge is defined as having: (1) Taken any part in the decision...

Performing the unexplainable: Implicit task performance reveals individually reliable sequence learning without explicit knowledge

PubMed Central

Sanchez, Daniel J.; Gobel, Eric W.; Reber, Paul J.

2015-01-01

Memory-impaired patients express intact implicit perceptual–motor sequence learning, but it has been difficult to obtain a similarly clear dissociation in healthy participants. When explicit memory is intact, participants acquire some explicit knowledge and performance improvements from implicit learning may be subtle. Therefore, it is difficult to determine whether performance exceeds what could be expected on the basis of the concomitant explicit knowledge. Using a challenging new sequence-learning task, robust implicit learning was found in healthy participants with virtually no associated explicit knowledge. Participants trained on a repeating sequence that was selected randomly from a set of five. On a performance test of all five sequences, performance was best on the trained sequence, and two-thirds of the participants exhibited individually reliable improvement (by chi-square analysis). Participants could not reliably indicate which sequence had been trained by either recognition or recall. Only by expressing their knowledge via performance were participants able to indicate which sequence they had learned. PMID:21169570

A Knowledge-Based Arrangement of Prototypical Neural Representation Prior to Experience Contributes to Selectivity in Upcoming Knowledge Acquisition.

PubMed

Kurashige, Hiroki; Yamashita, Yuichi; Hanakawa, Takashi; Honda, Manabu

2018-01-01

Knowledge acquisition is a process in which one actively selects a piece of information from the environment and assimilates it with prior knowledge. However, little is known about the neural mechanism underlying selectivity in knowledge acquisition. Here we executed a 2-day human experiment to investigate the involvement of characteristic spontaneous activity resembling a so-called "preplay" in selectivity in sentence comprehension, an instance of knowledge acquisition. On day 1, we presented 10 sentences (prior sentences) that were difficult to understand on their own. On the following day, we first measured the resting-state functional magnetic resonance imaging (fMRI). Then, we administered a sentence comprehension task using 20 new sentences (posterior sentences). The posterior sentences were also difficult to understand on their own, but some could be associated with prior sentences to facilitate their understanding. Next, we measured the posterior sentence-induced fMRI to identify the neural representation. From the resting-state fMRI, we extracted the appearances of activity patterns similar to the neural representations for posterior sentences. Importantly, the resting-state fMRI was measured before giving the posterior sentences, and thus such appearances could be considered as preplay-like or prototypical neural representations. We compared the intensities of such appearances with the understanding of posterior sentences. This gave a positive correlation between these two variables, but only if posterior sentences were associated with prior sentences. Additional analysis showed the contribution of the entorhinal cortex, rather than the hippocampus, to the correlation. The present study suggests that prior knowledge-based arrangement of neural activity before an experience contributes to the active selection of information to be learned. Such arrangement prior to an experience resembles preplay activity observed in the rodent brain. In terms of knowledge acquisition, the present study leads to a new view of the brain (or more precisely of the brain's knowledge) as an autopoietic system in which the brain (or knowledge) selects what it should learn by itself, arranges preplay-like activity as a position for the new information in advance, and actively reorganizes itself.

A Knowledge-Based Arrangement of Prototypical Neural Representation Prior to Experience Contributes to Selectivity in Upcoming Knowledge Acquisition

PubMed Central

Kurashige, Hiroki; Yamashita, Yuichi; Hanakawa, Takashi; Honda, Manabu

2018-01-01

Knowledge acquisition is a process in which one actively selects a piece of information from the environment and assimilates it with prior knowledge. However, little is known about the neural mechanism underlying selectivity in knowledge acquisition. Here we executed a 2-day human experiment to investigate the involvement of characteristic spontaneous activity resembling a so-called “preplay” in selectivity in sentence comprehension, an instance of knowledge acquisition. On day 1, we presented 10 sentences (prior sentences) that were difficult to understand on their own. On the following day, we first measured the resting-state functional magnetic resonance imaging (fMRI). Then, we administered a sentence comprehension task using 20 new sentences (posterior sentences). The posterior sentences were also difficult to understand on their own, but some could be associated with prior sentences to facilitate their understanding. Next, we measured the posterior sentence-induced fMRI to identify the neural representation. From the resting-state fMRI, we extracted the appearances of activity patterns similar to the neural representations for posterior sentences. Importantly, the resting-state fMRI was measured before giving the posterior sentences, and thus such appearances could be considered as preplay-like or prototypical neural representations. We compared the intensities of such appearances with the understanding of posterior sentences. This gave a positive correlation between these two variables, but only if posterior sentences were associated with prior sentences. Additional analysis showed the contribution of the entorhinal cortex, rather than the hippocampus, to the correlation. The present study suggests that prior knowledge-based arrangement of neural activity before an experience contributes to the active selection of information to be learned. Such arrangement prior to an experience resembles preplay activity observed in the rodent brain. In terms of knowledge acquisition, the present study leads to a new view of the brain (or more precisely of the brain’s knowledge) as an autopoietic system in which the brain (or knowledge) selects what it should learn by itself, arranges preplay-like activity as a position for the new information in advance, and actively reorganizes itself. PMID:29662446

Self-Explanation in the Domain of Statistics: An Expertise Reversal Effect

ERIC Educational Resources Information Center

Leppink, Jimmie; Broers, Nick J.; Imbos, Tjaart; van der Vleuten, Cees P. M.; Berger, Martijn P. F.

2012-01-01

This study investigated the effects of four instructional methods on cognitive load, propositional knowledge, and conceptual understanding of statistics, for low prior knowledge students and for high prior knowledge students. The instructional methods were (1) a reading-only control condition, (2) answering open-ended questions, (3) answering…

The proteome: structure, function and evolution

PubMed Central

Fleming, Keiran; Kelley, Lawrence A; Islam, Suhail A; MacCallum, Robert M; Muller, Arne; Pazos, Florencio; Sternberg, Michael J.E

2006-01-01

This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family. PMID:16524832

Comfort and experience with online learning: trends over nine years and associations with knowledge

PubMed Central

2014-01-01

Background Some evidence suggests that attitude toward computer-based instruction is an important determinant of success in online learning. We sought to determine how comfort using computers and perceptions of prior online learning experiences have changed over the past decade, and how these associate with learning outcomes. Methods Each year from 2003–2011 we conducted a prospective trial of online learning. As part of each year’s study, we asked medicine residents about their comfort using computers and if their previous experiences with online learning were favorable. We assessed knowledge using a multiple-choice test. We used regression to analyze associations and changes over time. Results 371 internal medicine and family medicine residents participated. Neither comfort with computers nor perceptions of prior online learning experiences showed a significant change across years (p > 0.61), with mean comfort rating 3.96 (maximum 5 = very comfortable) and mean experience rating 4.42 (maximum 6 = strongly agree [favorable]). Comfort showed no significant association with knowledge scores (p = 0.39) but perceptions of prior experiences did, with a 1.56% rise in knowledge score for a 1-point rise in experience score (p = 0.02). Correlations among comfort, perceptions of prior experiences, and number of prior experiences were all small and not statistically significant. Conclusions Comfort with computers and perceptions of prior experience with online learning remained stable over nine years. Prior good experiences (but not comfort with computers) demonstrated a modest association with knowledge outcomes, suggesting that prior course satisfaction may influence subsequent learning. PMID:24985690

Middle school students' knowledge of autism.

PubMed

Campbell, Jonathan M; Barger, Brian D

2011-06-01

Authors examined 1,015 middle school students' knowledge of autism using a single item of prior awareness and a 10-item Knowledge of Autism (KOA) scale. The KOA scale was designed to assess students' knowledge of the course, etiology, and symptoms associated with autism. Less than half of students (46.1%) reported having heard of autism; however, most students correctly responded that autism was a chronic condition that was not communicable. Students reporting prior awareness of autism scored higher on 9 of 10 KOA scale items when compared to their naïve counterparts. Prior awareness of autism and KOA scores also differed across schools. A more detailed understanding of developmental changes in students' knowledge of autism should improve peer educational interventions.

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

PubMed Central

DeBlasio, Dan

2013-01-01

Abstract We develop a novel and general approach to estimating the accuracy of multiple sequence alignments without knowledge of a reference alignment, and use our approach to address a new task that we call parameter advising: the problem of choosing values for alignment scoring function parameters from a given set of choices to maximize the accuracy of a computed alignment. For protein alignments, we consider twelve independent features that contribute to a quality alignment. An accuracy estimator is learned that is a polynomial function of these features; its coefficients are determined by minimizing its error with respect to true accuracy using mathematical optimization. Compared to prior approaches for estimating accuracy, our new approach (a) introduces novel feature functions that measure nonlocal properties of an alignment yet are fast to evaluate, (b) considers more general classes of estimators beyond linear combinations of features, and (c) develops new regression formulations for learning an estimator from examples; in addition, for parameter advising, we (d) determine the optimal parameter set of a given cardinality, which specifies the best parameter values from which to choose. Our estimator, which we call Facet (for “feature-based accuracy estimator”), yields a parameter advisor that on the hardest benchmarks provides more than a 27% improvement in accuracy over the best default parameter choice, and for parameter advising significantly outperforms the best prior approaches to assessing alignment quality. PMID:23489379

Relationship of prior knowledge and working engineers' learning preferences: implications for designing effective instruction

NASA Astrophysics Data System (ADS)

Baukal, Charles E.; Ausburn, Lynna J.

2017-05-01

Continuing engineering education (CEE) is important to ensure engineers maintain proficiency over the life of their careers. However, relatively few studies have examined designing effective training for working engineers. Research has indicated that both learner instructional preferences and prior knowledge can impact the learning process, but it has not established if these factors are interrelated. The study reported here considered relationships of prior knowledge and three aspects of learning preferences of working engineers at a manufacturing company: learning strategy choices, verbal-visual cognitive styles, and multimedia preferences. Prior knowledge was not found to be significantly related to engineers' learning preferences, indicating independence of effects of these variables on learning. The study also examined relationships of this finding to the Multimedia Cone of Abstraction and implications for its use as an instructional design tool for CEE.

Exploring the Impact of Prior Knowledge and Appropriate Feedback on Students' Perceived Cognitive Load and Learning Outcomes: Animation-based earthquakes instruction

NASA Astrophysics Data System (ADS)

Yeh, Ting-Kuang; Tseng, Kuan-Yun; Cho, Chung-Wen; Barufaldi, James P.; Lin, Mei-Shin; Chang, Chun-Yen

2012-07-01

The aim of this study was to develop an animation-based curriculum and to evaluate the effectiveness of animation-based instruction; the report involved the assessment of prior knowledge and the appropriate feedback approach, for the purpose of reducing perceived cognitive load and improving learning. The curriculum was comprised of five subunits designed to teach the 'Principles of Earthquakes.' Each subunit consisted of three modules: evaluation of prior knowledge with/without in-time feedback; animation-based instruction; and evaluation of learning outcomes with feedback. The 153 participants consisted of 10th grade high-school students. Seventy-eight students participated in the animation-based instruction, involving assessment of prior knowledge and appropriate feedback mechanism (APA group). A total of 75 students participated in animation-based learning that did not take into account their prior knowledge (ANPA group). The effectiveness of the instruction was then evaluated by using a Science Conception Test (SCT), a self-rating cognitive load questionnaire (CLQ), as well as a structured interview. The results indicated that: (1) Students' perceived cognitive load was reduced effectively through improving their prior knowledge by providing appropriate feedback. (2) When students perceived lower levels of cognitive load, they showed better learning outcome. The result of this study revealed that students of the APA group showed better performance than those of the ANPA group in an open-ended question. Furthermore, students' perceived cognitive load was negatively associated with their learning outcomes.

Investigating the Effectiveness of Inquiry-Based Instruction on Students with Different Prior Knowledge and Reading Abilities

ERIC Educational Resources Information Center

Wang, Jing-Ru; Wang, Yuh-Chao; Tai, Hsin-Jung; Chen, Wen-Ju

2010-01-01

This study examined the differential impacts of an inquiry-based instruction on conceptual changes across levels of prior knowledge and reading ability. The instrument emphasized four simultaneously important components: conceptual knowledge, reading ability, attitude toward science, and learning environment. Although the learning patterns and…

The Relation between Prior Knowledge and Students' Collaborative Discovery Learning Processes

ERIC Educational Resources Information Center

Gijlers, Hannie; de Jong, Ton

2005-01-01

In this study we investigate how prior knowledge influences knowledge development during collaborative discovery learning. Fifteen dyads of students (pre-university education, 15-16 years old) worked on a discovery learning task in the physics field of kinematics. The (face-to-face) communication between students was recorded and the interaction…

Prior Knowledge and Story Processing: Integration, Selection, and Variation. Technical Report No. 138.

ERIC Educational Resources Information Center

Spiro, Rand J.

Psychological research concerning several aspects of the relationship between existing knowledge schemata and the processing of text is summarized in this report. The first section is concerned with dynamic processes of story understanding, with emphasis on the integration of information. The role of prior knowledge in accommodating parts of…

Preparation for College General Chemistry: More than Just a Matter of Content Knowledge Acquisition

ERIC Educational Resources Information Center

Cracolice, Mark S.; Busby, Brittany D.

2015-01-01

This study investigates the potential of five factors that may be predictive of success in college general chemistry courses: prior knowledge of common alternate conceptions, intelligence, scientific reasoning ability, proportional reasoning ability, and attitude toward chemistry. We found that both prior knowledge and scientific reasoning ability…

Third-Grade Students' Mental Models of Energy Expenditure during Exercise

ERIC Educational Resources Information Center

Pasco, Denis; Ennis, Catherine D.

2015-01-01

Background: Students' prior knowledge plays an important role in learning new knowledge. In physical education (PE) and physical activity settings, studies have confirmed the role of students' prior knowledge. According to Placek and Griffin, these studies demonstrate that: "our students are not empty balls waiting to be filled with knowledge…

Mathematics understanding and anxiety in collaborative teaching

NASA Astrophysics Data System (ADS)

Ansari, B. I.; Wahyu, N.

2017-12-01

This study aims to examine students’ mathematical understanding and anxiety using collaborative teaching. The sample consists of 51 students in the 7th-grade of MTs N Jeureula, one of the Islamic public junior high schools in Jeureula, Aceh, Indonesia. A test of mathematics understanding was administered to the students twice during the period of two months. The result suggests that there is a significant increase in mathematical understanding in the pre-test and post-test. We categorized the students into the high, intermediate, and low level of prior mathematics knowledge. In the high-level prior knowledge, there is no difference of mathematical understanding between the experiment and control group. Meanwhile, in the intermediate and low level of prior knowledge, there is a significant difference of mathematical understanding between the experiment and control group. The mathematics anxiety is at an intermediate level in the experiment class and at a high level in the control group. There is no interaction between the learning model and the students’ prior knowledge towards the mathematical understanding, but there are interactions towards the mathematics anxiety. It indicates that the collaborative teaching model and the students’ prior knowledge do not simultaneously impacts on the mathematics understanding but the mathematics anxiety.

A knowledge engineering approach to recognizing and extracting sequences of nucleic acids from scientific literature.

PubMed

García-Remesal, Miguel; Maojo, Victor; Crespo, José

2010-01-01

In this paper we present a knowledge engineering approach to automatically recognize and extract genetic sequences from scientific articles. To carry out this task, we use a preliminary recognizer based on a finite state machine to extract all candidate DNA/RNA sequences. The latter are then fed into a knowledge-based system that automatically discards false positives and refines noisy and incorrectly merged sequences. We created the knowledge base by manually analyzing different manuscripts containing genetic sequences. Our approach was evaluated using a test set of 211 full-text articles in PDF format containing 3134 genetic sequences. For such set, we achieved 87.76% precision and 97.70% recall respectively. This method can facilitate different research tasks. These include text mining, information extraction, and information retrieval research dealing with large collections of documents containing genetic sequences.

Developmental Change in the Influence of Domain-General Abilities and Domain-Specific Knowledge on Mathematics Achievement: An Eight-Year Longitudinal Study

PubMed Central

Geary, David C.; Nicholas, Alan; Li, Yaoran; Sun, Jianguo

2016-01-01

The contributions of domain-general abilities and domain-specific knowledge to subsequent mathematics achievement were longitudinally assessed (n = 167) through 8th grade. First grade intelligence and working memory and prior grade reading achievement indexed domain-general effects and domain-specific effects were indexed by prior grade mathematics achievement and mathematical cognition measures of prior grade number knowledge, addition skills, and fraction knowledge. Use of functional data analysis enabled grade-by-grade estimation of overall domain-general and domain-specific effects on subsequent mathematics achievement, the relative importance of individual domain-general and domain-specific variables on this achievement, and linear and non-linear across-grade estimates of these effects. The overall importance of domain-general abilities for subsequent achievement was stable across grades, with working memory emerging as the most important domain-general ability in later grades. The importance of prior mathematical competencies on subsequent mathematics achievement increased across grades, with number knowledge and arithmetic skills critical in all grades and fraction knowledge in later grades. Overall, domain-general abilities were more important than domain-specific knowledge for mathematics learning in early grades but general abilities and domain-specific knowledge were equally important in later grades. PMID:28781382

Integrated rare variant-based risk gene prioritization in disease case-control sequencing studies.

PubMed

Lin, Jhih-Rong; Zhang, Quanwei; Cai, Ying; Morrow, Bernice E; Zhang, Zhengdong D

2017-12-01

Rare variants of major effect play an important role in human complex diseases and can be discovered by sequencing-based genome-wide association studies. Here, we introduce an integrated approach that combines the rare variant association test with gene network and phenotype information to identify risk genes implicated by rare variants for human complex diseases. Our data integration method follows a 'discovery-driven' strategy without relying on prior knowledge about the disease and thus maintains the unbiased character of genome-wide association studies. Simulations reveal that our method can outperform a widely-used rare variant association test method by 2 to 3 times. In a case study of a small disease cohort, we uncovered putative risk genes and the corresponding rare variants that may act as genetic modifiers of congenital heart disease in 22q11.2 deletion syndrome patients. These variants were missed by a conventional approach that relied on the rare variant association test alone.

The impact of reward and punishment on skill learning depends on task demands

PubMed Central

Steel, Adam; Silson, Edward H.; Stagg, Charlotte J.; Baker, Chris I.

2016-01-01

Reward and punishment motivate behavior, but it is unclear exactly how they impact skill performance and whether the effect varies across skills. The present study investigated the effect of reward and punishment in both a sequencing skill and a motor skill context. Participants trained on either a sequencing skill (serial reaction time task) or a motor skill (force-tracking task). Skill knowledge was tested immediately after training, and again 1 hour, 24–48 hours, and 30 days after training. We found a dissociation of the effects of reward and punishment on the tasks, primarily reflecting the impact of punishment. While punishment improved serial reaction time task performance, it impaired force-tracking task performance. In contrast to prior literature, neither reward nor punishment benefitted memory retention, arguing against the common assumption that reward ubiquitously benefits skill retention. Collectively, these results suggest that punishment impacts skilled behavior more than reward in a complex, task dependent fashion. PMID:27786302

The impact of reward and punishment on skill learning depends on task demands.

PubMed

Steel, Adam; Silson, Edward H; Stagg, Charlotte J; Baker, Chris I

2016-10-27

Reward and punishment motivate behavior, but it is unclear exactly how they impact skill performance and whether the effect varies across skills. The present study investigated the effect of reward and punishment in both a sequencing skill and a motor skill context. Participants trained on either a sequencing skill (serial reaction time task) or a motor skill (force-tracking task). Skill knowledge was tested immediately after training, and again 1 hour, 24-48 hours, and 30 days after training. We found a dissociation of the effects of reward and punishment on the tasks, primarily reflecting the impact of punishment. While punishment improved serial reaction time task performance, it impaired force-tracking task performance. In contrast to prior literature, neither reward nor punishment benefitted memory retention, arguing against the common assumption that reward ubiquitously benefits skill retention. Collectively, these results suggest that punishment impacts skilled behavior more than reward in a complex, task dependent fashion.

Prior schemata transfer as an account for assessing the intuitive use of new technology.

PubMed

Fischer, Sandrine; Itoh, Makoto; Inagaki, Toshiyuki

2015-01-01

New devices are considered intuitive when they allow users to transfer prior knowledge. Drawing upon fundamental psychology experiments that distinguish prior knowledge transfer from new schema induction, a procedure was specified for assessing intuitive use. This procedure was tested with 31 participants who, prior to using an on-board computer prototype, studied its screenshots in reading vs. schema induction conditions. Distinct patterns of transfer or induction resulted for features of the prototype whose functions were familiar or unfamiliar, respectively. Though moderated by participants' cognitive style, these findings demonstrated a means for quantitatively assessing transfer of prior knowledge as the operation that underlies intuitive use. Implications for interface evaluation and design, as well as potential improvements to the procedure, are discussed. Copyright © 2014 Elsevier Ltd and The Ergonomics Society. All rights reserved.

How Prior Knowledge and Colour Contrast Interfere Visual Search Processes in Novice Learners: An Eye Tracking Study

ERIC Educational Resources Information Center

Sonmez, Duygu; Altun, Arif; Mazman, Sacide Guzin

2012-01-01

This study investigates how prior content knowledge and prior exposure to microscope slides on the phases of mitosis effect students' visual search strategies and their ability to differentiate cells that are going through any phases of mitosis. Two different sets of microscope slide views were used for this purpose; with high and low colour…

Identification of Boolean Network Models From Time Series Data Incorporating Prior Knowledge.

PubMed

Leifeld, Thomas; Zhang, Zhihua; Zhang, Ping

2018-01-01

Motivation: Mathematical models take an important place in science and engineering. A model can help scientists to explain dynamic behavior of a system and to understand the functionality of system components. Since length of a time series and number of replicates is limited by the cost of experiments, Boolean networks as a structurally simple and parameter-free logical model for gene regulatory networks have attracted interests of many scientists. In order to fit into the biological contexts and to lower the data requirements, biological prior knowledge is taken into consideration during the inference procedure. In the literature, the existing identification approaches can only deal with a subset of possible types of prior knowledge. Results: We propose a new approach to identify Boolean networks from time series data incorporating prior knowledge, such as partial network structure, canalizing property, positive and negative unateness. Using vector form of Boolean variables and applying a generalized matrix multiplication called the semi-tensor product (STP), each Boolean function can be equivalently converted into a matrix expression. Based on this, the identification problem is reformulated as an integer linear programming problem to reveal the system matrix of Boolean model in a computationally efficient way, whose dynamics are consistent with the important dynamics captured in the data. By using prior knowledge the number of candidate functions can be reduced during the inference. Hence, identification incorporating prior knowledge is especially suitable for the case of small size time series data and data without sufficient stimuli. The proposed approach is illustrated with the help of a biological model of the network of oxidative stress response. Conclusions: The combination of efficient reformulation of the identification problem with the possibility to incorporate various types of prior knowledge enables the application of computational model inference to systems with limited amount of time series data. The general applicability of this methodological approach makes it suitable for a variety of biological systems and of general interest for biological and medical research.

Executive Functions as Moderators of the Worked Example Effect: When Shifting Is More Important than Working Memory Capacity

ERIC Educational Resources Information Center

Schwaighofer, Matthias; Bühner, Markus; Fischer, Frank

2016-01-01

Worked examples have proven to be effective for knowledge acquisition compared with problem solving, particularly when prior knowledge is low (e.g., Kalyuga, 2007). However, in addition to prior knowledge, executive functions and fluid intelligence might be potential moderators of the effectiveness of worked examples. The present study examines…

Can Prior Knowledge Hurt Text Comprehension? An Answer Borrowed from Plato, Aristotle, and Descartes.

ERIC Educational Resources Information Center

Friedman, Lawrence B.

Taking a philosophical approach based on what Plato, Aristotle, and Descartes said about knowledge, this paper addresses some of the murkiness in the conceptual space surrounding the issue of whether prior knowledge does or does not facilitate text comprehension. Specifically, the paper first develops a non-exhaustive typology of cases in which…

Effects of Activation of Prior Knowledge on the Recall of a Clinical Case.

ERIC Educational Resources Information Center

Schmidt, Henk G.; Boshuizen, Henny P. A.

A study investigated the known phenomenon of "intermediate effect" in which medical students with an intermediate amount of knowledge and experience demonstrate higher amounts of recall of the text of a medical case than either experienced clinicians or novices. In this study the amount of activation of prior knowledge was controlled by…

Effect of Altered Prior Knowledge on Passage Recall.

ERIC Educational Resources Information Center

Langer, Judith A.; Nicolich, Mark

A study was conducted to determine: (1) the relationships between prior knowledge and passage recall; (2) the effect of a prereading activity (PReP) on available knowledge; and (3) the effect of the PReP activity on total comprehension scores. The subjects were 161 sixth grade students from a middle class suburban Long Island, New York, public…

Does Teaching Experience Matter? Examining Biology Teachers' Prior Knowledge for Teaching in an Alternative Certification Program

ERIC Educational Resources Information Center

Friedrichsen, Patricia J.; Abell, Sandra K.; Pareja, Enrique M.; Brown, Patrick L.; Lankford, Deanna M.; Volkmann, Mark J.

2009-01-01

Alternative certification programs (ACPs) have been proposed as a viable way to address teacher shortages, yet we know little about how teacher knowledge develops within such programs. The purpose of this study was to investigate prior knowledge for teaching among students entering an ACP, comparing individuals with teaching experience to those…

The Importance of Prior Knowledge when Comparing Examples: Influences on Conceptual and Procedural Knowledge of Equation Solving

ERIC Educational Resources Information Center

Rittle-Johnson, Bethany; Star, Jon R.; Durkin, Kelley

2009-01-01

Comparing multiple examples typically supports learning and transfer in laboratory studies and is considered a key feature of high-quality mathematics instruction. This experimental study investigated the importance of prior knowledge in learning from comparison. Seventh- and 8th-grade students (N = 236) learned to solve equations by comparing…

Ascertainment-adjusted parameter estimation approach to improve robustness against misspecification of health monitoring methods

NASA Astrophysics Data System (ADS)

Juesas, P.; Ramasso, E.

2016-12-01

Condition monitoring aims at ensuring system safety which is a fundamental requirement for industrial applications and that has become an inescapable social demand. This objective is attained by instrumenting the system and developing data analytics methods such as statistical models able to turn data into relevant knowledge. One difficulty is to be able to correctly estimate the parameters of those methods based on time-series data. This paper suggests the use of the Weighted Distribution Theory together with the Expectation-Maximization algorithm to improve parameter estimation in statistical models with latent variables with an application to health monotonic under uncertainty. The improvement of estimates is made possible by incorporating uncertain and possibly noisy prior knowledge on latent variables in a sound manner. The latent variables are exploited to build a degradation model of dynamical system represented as a sequence of discrete states. Examples on Gaussian Mixture Models, Hidden Markov Models (HMM) with discrete and continuous outputs are presented on both simulated data and benchmarks using the turbofan engine datasets. A focus on the application of a discrete HMM to health monitoring under uncertainty allows to emphasize the interest of the proposed approach in presence of different operating conditions and fault modes. It is shown that the proposed model depicts high robustness in presence of noisy and uncertain prior.

Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.

PubMed

Chamrad, Daniel C; Körting, Gerhard; Schäfer, Heike; Stephan, Christian; Thiele, Herbert; Apweiler, Rolf; Meyer, Helmut E; Marcus, Katrin; Blüggel, Martin

2006-09-01

A novel software tool named PTM-Explorer has been applied to LC-MS/MS datasets acquired within the Human Proteome Organisation (HUPO) Brain Proteome Project (BPP). PTM-Explorer enables automatic identification of peptide MS/MS spectra that were not explained in typical sequence database searches. The main focus was detection of PTMs, but PTM-Explorer detects also unspecific peptide cleavage, mass measurement errors, experimental modifications, amino acid substitutions, transpeptidation products and unknown mass shifts. To avoid a combinatorial problem the search is restricted to a set of selected protein sequences, which stem from previous protein identifications using a common sequence database search. Prior to application to the HUPO BPP data, PTM-Explorer was evaluated on excellently manually characterized and evaluated LC-MS/MS data sets from Alpha-A-Crystallin gel spots obtained from mouse eye lens. Besides various PTMs including phosphorylation, a wealth of experimental modifications and unspecific cleavage products were successfully detected, completing the primary structure information of the measured proteins. Our results indicate that a large amount of MS/MS spectra that currently remain unidentified in standard database searches contain valuable information that can only be elucidated using suitable software tools.

What You Know Can Hurt You: Effects of Age and Prior Knowledge on the Accuracy of Judgments of Learning

PubMed Central

Toth, Jeffrey P.; Daniels, Karen A.; Solinger, Lisa A.

2011-01-01

How do aging and prior knowledge affect memory and metamemory? We explored this question in the context of a dual-process approach to Judgments of Learning (JOLs) which require people to predict their ability to remember information at a later time. Young and older adults (n's = 36, mean ages = 20.2 & 73.1) studied the names of actors that were famous in the 1950s or 1990s, providing a JOL for each. Recognition memory for studied and unstudied actors was then assessed using a Recollect/Know/No-Memory (R/K/N) judgment task. Results showed that prior knowledge increased recollection in both age groups such that older adults recollected significantly more 1950s actors than younger adults. Also, for both age groups and both decades, actors judged R at test garnered significantly higher JOLs at study than actors judged K or N. However, while the young showed benefits of prior knowledge on relative JOL accuracy, older adults did not, showing lower levels of JOL accuracy for 1950s actors despite having higher recollection for, and knowledge about, those actors. Overall, the data suggest that prior knowledge can be a double-edged sword, increasing the availability of details that can support later recollection, but also increasing non-diagnostic feelings of familiarity that can reduce the accuracy of memory predictions. PMID:21480715

Exploiting rice-sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map.

PubMed

Ramu, P; Kassahun, B; Senthilvel, S; Ashok Kumar, C; Jayashree, B; Folkertsma, R T; Reddy, L Ananda; Kuruvinashetti, M S; Haussmann, B I G; Hash, C T

2009-11-01

The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag (EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50 homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using parental pairs of two existing sorghum mapping populations. About 28% of these new markers detected polymorphism in this 4-entry panel. A subset of 55 polymorphic EST-derived SSR markers were mapped onto the existing skeleton map of a recombinant inbred population derived from cross N13 x E 36-1, which is segregating for Striga resistance and the stay-green component of terminal drought tolerance. These new EST-derived SSR markers mapped across all 10 sorghum linkage groups, mostly to regions expected based on prior knowledge of rice-sorghum synteny. The ESTs from which these markers were derived were then mapped in silico onto the aligned sorghum genome sequence, and 88% of the best hits corresponded to linkage-based positions. This study demonstrates the utility of comparative genomic information in targeted development of markers to fill gaps in linkage maps of related crop species for which sufficient genomic tools are not available.

Effects of Teacher Use of Analogies on Achievement of High School Biology Students with Varying Levels of Cognitive Ability and Prior Knowledge.

ERIC Educational Resources Information Center

Burns, Joseph C.; Okey, James R.

This study investigated the effects of analogy-based and conventional lecture-based instructional strategies on the achievement of four classes of high school biology students (N=123). Prior to treatment, students were assessed for cognitive ability and prior knowledge of the analogy vehicle. The analogy-based treatment consisted of teacher…

The impact of curiosity on learning during a school field trip to the zoo

NASA Astrophysics Data System (ADS)

Carlin, Kerry Ann

1999-11-01

This study was designed to examine (a) differences in cognitive learning as a result of a zoo field trip, (b) if the trip to the zoo had an impact on epistemic curiosity, (c) the role epistemic curiosity plays in learning, (d) the effect of gender, race, prior knowledge and prior visitation to the zoo on learning and epistemic curiosity, (e) participants' affect for the zoo animals, and (f) if prior visitation to the zoo contributes to prior knowledge. Ninety-six fourth and fifth grade children completed curiosity, cognitive, and affective written tests before and after a field trip to the Lowery Park Zoo in Tampa, Florida. The data showed that students were very curious about zoo animals. Dependent T-tests indicated no significant difference between pretest and posttest curiosity levels. The trip did not influence participants' curiosity levels. Multiple regression analysis was used to determine the relationship between the dependent variable, curiosity, and the independent variables, gender, race, prior knowledge, and prior visitation. No significant differences were found. Dependent T-tests indicated no significant difference between pretest and posttest cognitive scores. The field trip to the zoo did not cause an increase in participants' knowledge. However, participants did learn on the trip. After the field trip, participants identified more animals displayed by the zoo than they did before. Also, more animals were identified by species and genus names after the trip than before. These differences were significant (alpha = .05). Multiple regression analysis was used to determine the relationship between the dependent variable, posttest cognitive performance, and the independent variables, curiosity, gender, race, prior knowledge, and prior visitation. A significant difference was found for prior knowledge (alpha = .05). No significant differences were found for the other independent variables. Chi-square tests of significance indicated significant differences (alpha = .05) in preferences for types of animals and preference for animals by gender. Significant differences (alpha = .05) were also found between the reasons why animals were preferred. Differences occurred between animals that were liked and disliked, between genders, and between the pretest and the posttest.

An investigation of multitasking information behavior and the influence of working memory and flow

NASA Astrophysics Data System (ADS)

Alexopoulou, Peggy; Hepworth, Mark; Morris, Anne

2015-02-01

This study explored the multitasking information behaviour of Web users and how this is influenced by working memory, flow and Personal, Artefact and Task characteristics, as described in the PAT model. The research was exploratory using a pragmatic, mixed method approach. Thirty University students participated; 10 psychologists, 10 accountants and 10 mechanical engineers. The data collection tools used were: pre and post questionnaires, a working memory test, a flow state scale test, audio-visual data, web search logs, think aloud data, observation, and the critical decision method. All participants searched information on the Web for four topics: two for which they had prior knowledge and two more without prior knowledge. Perception of task complexity was found to be related to working memory. People with low working memory reported a significant increase in task complexity after they had completed information searching tasks for which they had no prior knowledge, this was not the case for tasks with prior knowledge. Regarding flow and task complexity, the results confirmed the suggestion of the PAT model (Finneran and Zhang, 2003), which proposed that a complex task can lead to anxiety and low flow levels as well as to perceived challenge and high flow levels. However, the results did not confirm the suggestion of the PAT model regarding the characteristics of web search systems and especially perceived vividness. All participants experienced high vividness. According to the PAT model, however, only people with high flow should experience high levels of vividness. Flow affected the degree of change of knowledge of the participants. People with high flow gained more knowledge for tasks without prior knowledge rather than people with low flow. Furthermore, accountants felt that tasks without prior knowledge were less complex at the end of the web seeking procedure than psychologists and mechanical engineers. Finally, the three disciplines appeared to differ regarding the multitasking information behaviour characteristics such as queries, web search sessions and opened tabs/windows.

Powerful Learning Tools for ELLs: Using Native Language, Familiar Examples, and Concept Mapping to Teach English Language Learners

ERIC Educational Resources Information Center

Dong, Yu Ren

2013-01-01

This article highlights how English language learners' (ELLs) prior knowledge can be used to help learn science vocabulary. The article explains that the concept of prior knowledge needs to encompass the ELL student's native language, previous science learning, native literacy skills, and native cultural knowledge and life experiences.…

Teachers' Beliefs about the Role of Prior Language Knowledge in Learning and How These Influence Teaching Practices

ERIC Educational Resources Information Center

De Angelis, Gessica

2011-01-01

The present study was developed to assess teachers' beliefs on (1) the role of prior language knowledge in language learning; (2) the perceived usefulness of language knowledge in modern society; and (3) the teaching practices to be used with multilingual students. Subjects were 176 secondary schoolteachers working in Italy (N = 103), Austria (N =…

Maple

NASA Astrophysics Data System (ADS)

Nicolaides, Roy A.; Walkington, Noel J.

1996-06-01

A knowledge of one or more high level symbolic mathematics programs is rapidly becoming a necessity for mathematics users from all fields of science. The aim of this book is to provide a solid grounding in Maple, one of the best known of these programs. The authors combine efficiency and economy of exposition with a complete coverage of Maple. The book has twelve chapters, of which eight are completely accessible to anyone who has completed calculus and linear sequences as taught in American universities. These chapters cover the great majority of Maple's capabilities. There are also three chapters on Maple programming that can be read without prior programming experience, although knowledge of a high level programming language (Basic, Fortran, C etc.) will help. There is also a chapter on some relevant aspects of algebra. Above all, the book allows the reader to extract value from Maple without wasting time and effort in the learning process. It is the fastest track to expertise for Maple users in mathematics and computer science.

Modifying Cookbook Labs.

ERIC Educational Resources Information Center

Clark, Robert, L.; Clough, Michael P.; Berg, Craig A.

2000-01-01

Modifies an extended lab activity from a cookbook approach for determining the percent mass of water in copper sulfate pentahydrate crystals to one which incorporates students' prior knowledge, engenders active mental struggling with prior knowledge and new experiences, and encourages metacognition. (Contains 12 references.) (ASK)

Knowledge Modeling in Prior Art Search

NASA Astrophysics Data System (ADS)

Graf, Erik; Frommholz, Ingo; Lalmas, Mounia; van Rijsbergen, Keith

This study explores the benefits of integrating knowledge representations in prior art patent retrieval. Key to the introduced approach is the utilization of human judgment available in the form of classifications assigned to patent documents. The paper first outlines in detail how a methodology for the extraction of knowledge from such an hierarchical classification system can be established. Further potential ways of integrating this knowledge with existing Information Retrieval paradigms in a scalable and flexible manner are investigated. Finally based on these integration strategies the effectiveness in terms of recall and precision is evaluated in the context of a prior art search task for European patents. As a result of this evaluation it can be established that in general the proposed knowledge expansion techniques are particularly beneficial to recall and, with respect to optimizing field retrieval settings, further result in significant precision gains.

Conceptual issues in Bayesian divergence time estimation

PubMed Central

2016-01-01

Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’. PMID:27325831

Conceptual issues in Bayesian divergence time estimation.

PubMed

Rannala, Bruce

2016-07-19

Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. © 2016 The Author(s).

Generalized species sampling priors with latent Beta reinforcements

PubMed Central

Airoldi, Edoardo M.; Costa, Thiago; Bassetti, Federico; Leisen, Fabrizio; Guindani, Michele

2014-01-01

Many popular Bayesian nonparametric priors can be characterized in terms of exchangeable species sampling sequences. However, in some applications, exchangeability may not be appropriate. We introduce a novel and probabilistically coherent family of non-exchangeable species sampling sequences characterized by a tractable predictive probability function with weights driven by a sequence of independent Beta random variables. We compare their theoretical clustering properties with those of the Dirichlet Process and the two parameters Poisson-Dirichlet process. The proposed construction provides a complete characterization of the joint process, differently from existing work. We then propose the use of such process as prior distribution in a hierarchical Bayes modeling framework, and we describe a Markov Chain Monte Carlo sampler for posterior inference. We evaluate the performance of the prior and the robustness of the resulting inference in a simulation study, providing a comparison with popular Dirichlet Processes mixtures and Hidden Markov Models. Finally, we develop an application to the detection of chromosomal aberrations in breast cancer by leveraging array CGH data. PMID:25870462

Sequencing in SLA: Phonological Memory, Chunking, and Points of Order.

ERIC Educational Resources Information Center

Ellis, Nick C.

1996-01-01

Argues that much of language acquisition is sequence learning and that the resultant long-term knowledge base of language sequences serves as the database for grammar acquisition. The article also proposes mechanisms to analyze sequence information that result in knowledge of underlying grammar. (184 references) (Author/CK)

Discovery of Undefined Protein Crosslinking Chemistry: A Comprehensive Methodology Utilizing 18O-labeling and Mass Spectrometry

PubMed Central

Liu, Min; Zhang, Zhongqi; Zang, Tianzhu; Spahr, Chris; Cheetham, Janet; Ren, Da; Sunny Zhou, Zhaohui

2013-01-01

Characterization of protein crosslinking, particularly without prior knowledge of the chemical nature and site of crosslinking, poses a significant challenge due to their intrinsic structural complexity and the lack of a comprehensive analytical approach. Towards this end, we have developed a generally applicable workflow—XChem-Finder that involves four stages. (1) Detection of crosslinked peptides via 18O-labeling at C-termini. (2) Determination of the putative partial sequences of each crosslinked peptide pair using a fragment ion mass database search against known protein sequences coupled with a de novo sequence tag search. (3) Extension to full sequences based on protease specificity, the unique combination of mass, and other constraints. (4) Deduction of crosslinking chemistry and site. The mass difference between the sum of two putative full-length peptides and the crosslinked peptide provides the formulas (elemental composition analysis) for the functional groups involved in each cross- linking. Combined with sequence restraint from MS/MS data, plausible crosslinking chemistry and site were inferred, and ultimately, confirmed by matching with all data. Applying our approach to a stressed IgG2 antibody, ten cross-linked peptides were discovered and found to be connected via thioether originating from disulfides at locations that had not been previously recognized. Furthermore, once the crosslink chemistry was revealed, a targeted crosslink search yielded four additional crosslinked peptides that all contain the C-terminus of the light chain. PMID:23634697

Effects of Prior Economic Education, Native Language, and Gender on Economic Knowledge of First-Year Students in Higher Education. A Comparative Study between Germany and the USA

ERIC Educational Resources Information Center

Brückner, Sebastian; Förster, Manuel; Zlatkin-Troitschanskaia, Olga; Walstad, William B.

2015-01-01

The assessment of university students' economic knowledge has become an increasingly important research area within and across countries. Particularly, the different influences of prior education, native language, and gender as some of the main prerequisites on students' economic knowledge have been highlighted since long. However, the findings…

Fuzzy-based propagation of prior knowledge to improve large-scale image analysis pipelines

PubMed Central

Mikut, Ralf

2017-01-01

Many automatically analyzable scientific questions are well-posed and a variety of information about expected outcomes is available a priori. Although often neglected, this prior knowledge can be systematically exploited to make automated analysis operations sensitive to a desired phenomenon or to evaluate extracted content with respect to this prior knowledge. For instance, the performance of processing operators can be greatly enhanced by a more focused detection strategy and by direct information about the ambiguity inherent in the extracted data. We present a new concept that increases the result quality awareness of image analysis operators by estimating and distributing the degree of uncertainty involved in their output based on prior knowledge. This allows the use of simple processing operators that are suitable for analyzing large-scale spatiotemporal (3D+t) microscopy images without compromising result quality. On the foundation of fuzzy set theory, we transform available prior knowledge into a mathematical representation and extensively use it to enhance the result quality of various processing operators. These concepts are illustrated on a typical bioimage analysis pipeline comprised of seed point detection, segmentation, multiview fusion and tracking. The functionality of the proposed approach is further validated on a comprehensive simulated 3D+t benchmark data set that mimics embryonic development and on large-scale light-sheet microscopy data of a zebrafish embryo. The general concept introduced in this contribution represents a new approach to efficiently exploit prior knowledge to improve the result quality of image analysis pipelines. The generality of the concept makes it applicable to practically any field with processing strategies that are arranged as linear pipelines. The automated analysis of terabyte-scale microscopy data will especially benefit from sophisticated and efficient algorithms that enable a quantitative and fast readout. PMID:29095927

Language knowledge and event knowledge in language use.

PubMed

Willits, Jon A; Amato, Michael S; MacDonald, Maryellen C

2015-05-01

This paper examines how semantic knowledge is used in language comprehension and in making judgments about events in the world. We contrast knowledge gleaned from prior language experience ("language knowledge") and knowledge coming from prior experience with the world ("world knowledge"). In two corpus analyses, we show that previous research linking verb aspect and event representations have confounded language and world knowledge. Then, using carefully chosen stimuli that remove this confound, we performed four experiments that manipulated the degree to which language knowledge or world knowledge should be salient and relevant to performing a task, finding in each case that participants use the type of knowledge most appropriate to the task. These results provide evidence for a highly context-sensitive and interactionist perspective on how semantic knowledge is represented and used during language processing. Copyright © 2015. Published by Elsevier Inc.

Incorporating linguistic knowledge for learning distributed word representations.

PubMed

Wang, Yan; Liu, Zhiyuan; Sun, Maosong

2015-01-01

Combined with neural language models, distributed word representations achieve significant advantages in computational linguistics and text mining. Most existing models estimate distributed word vectors from large-scale data in an unsupervised fashion, which, however, do not take rich linguistic knowledge into consideration. Linguistic knowledge can be represented as either link-based knowledge or preference-based knowledge, and we propose knowledge regularized word representation models (KRWR) to incorporate these prior knowledge for learning distributed word representations. Experiment results demonstrate that our estimated word representation achieves better performance in task of semantic relatedness ranking. This indicates that our methods can efficiently encode both prior knowledge from knowledge bases and statistical knowledge from large-scale text corpora into a unified word representation model, which will benefit many tasks in text mining.

Incorporating Linguistic Knowledge for Learning Distributed Word Representations

PubMed Central

Wang, Yan; Liu, Zhiyuan; Sun, Maosong

2015-01-01

Combined with neural language models, distributed word representations achieve significant advantages in computational linguistics and text mining. Most existing models estimate distributed word vectors from large-scale data in an unsupervised fashion, which, however, do not take rich linguistic knowledge into consideration. Linguistic knowledge can be represented as either link-based knowledge or preference-based knowledge, and we propose knowledge regularized word representation models (KRWR) to incorporate these prior knowledge for learning distributed word representations. Experiment results demonstrate that our estimated word representation achieves better performance in task of semantic relatedness ranking. This indicates that our methods can efficiently encode both prior knowledge from knowledge bases and statistical knowledge from large-scale text corpora into a unified word representation model, which will benefit many tasks in text mining. PMID:25874581

Cognitive assessment and health education in children from two different cultures.

PubMed

Sivaramakrishnan, M; Arocha, J F; Patel, V L

1998-09-01

This paper presents research aimed at investigating high level comprehension and problem solving processes in children in two different countries, India and Colombia. To this end, we use a series of health-related cognitive tasks as assessment tools. In one study, we also examine children's performance on these cognitive tasks, in relation to their nutritional status and parasitic load. The ages of the children tested ranged from 2 through 14 years. The tasks were designed to assess comprehension of sequences, organization of concepts, understanding of health routines (hygiene practices) and evaluation of hypothesis and evidence. The results show that children approach the different tasks with a baggage of beliefs and local knowledge of the world which determines their reasoning process, their comprehension and their problems solving. The results are discussed in terms of cognitive assessment approaches, as applied to classroom instruction. Given that children construct their understanding of reality based on what they already know and that education does not take this into account, we recommend that assessment tools should be devised that can tap prior knowledge and understanding, such that this can be analyzed and understood in relation to knowledge taught in the classroom. Current educational assessment fails in such an endeavor.

Evaluating the Impact of a Multistrategy Inference Intervention for Middle-Grade Struggling Readers

PubMed Central

Elleman, Amy

2017-01-01

Purpose We examined the effectiveness of a multistrategy inference intervention designed to increase inference making and reading comprehension for middle-grade struggling readers. Method A total of 66 middle-grade struggling readers were randomized to treatment (n = 33) and comparison (n = 33) conditions. Students in the treatment group received explicit instruction in 4 inference strategies (i.e., clarification using text clues; activating and using prior knowledge; understanding character perspectives and author's purpose; answering inferential questions). In addition, narrative and informational texts were carefully chosen and sequenced to build requisite background knowledge to form inferences. Intervention was delivered in small groups of 3 students for 10 days of instruction. Results One-way analysis of covariance models on outcome measures with the respective pretest scores as a covariate revealed significant gains on a proximal measure of Egyptian-content knowledge (g = 1.37) and on a standardized measure of reading comprehension—i.e., Wechsler Individual Achievement Test–Third Edition Reading Comprehension (g = 0.46). Conclusion The moderate effect on a standardized measure of reading comprehension provides preliminary evidence for the effectiveness of this multistrategy inference intervention in improving reading comprehension of middle-grade struggling readers. PMID:27776201

Control of gaze in natural environments: effects of rewards and costs, uncertainty and memory in target selection.

PubMed

Hayhoe, Mary M; Matthis, Jonathan Samir

2018-08-06

The development of better eye and body tracking systems, and more flexible virtual environments have allowed more systematic exploration of natural vision and contributed a number of insights. In natural visually guided behaviour, humans make continuous sequences of sensory-motor decisions to satisfy current goals, and the role of vision is to provide the relevant information in order to achieve those goals. This paper reviews the factors that control gaze in natural visually guided actions such as locomotion, including the rewards and costs associated with the immediate behavioural goals, uncertainty about the state of the world and prior knowledge of the environment. These general features of human gaze control may inform the development of artificial systems.

PLAN-IT: Knowledge-Based Mission Sequencing

NASA Astrophysics Data System (ADS)

Biefeld, Eric W.

1987-02-01

Mission sequencing consumes a large amount of time and manpower during a space exploration effort. Plan-It is a knowledge-based approach to assist in mission sequencing. Plan-It uses a combined frame and blackboard architecture. This paper reports on the approach implemented by Plan-It and the current applications of Plan-It for sequencing at NASA.

Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm.

PubMed

Zhang, ZhiZhuo; Chang, Cheng Wei; Hugo, Willy; Cheung, Edwin; Sung, Wing-Kin

2013-03-01

Although de novo motifs can be discovered through mining over-represented sequence patterns, this approach misses some real motifs and generates many false positives. To improve accuracy, one solution is to consider some additional binding features (i.e., position preference and sequence rank preference). This information is usually required from the user. This article presents a de novo motif discovery algorithm called SEME (sampling with expectation maximization for motif elicitation), which uses pure probabilistic mixture model to model the motif's binding features and uses expectation maximization (EM) algorithms to simultaneously learn the sequence motif, position, and sequence rank preferences without asking for any prior knowledge from the user. SEME is both efficient and accurate thanks to two important techniques: the variable motif length extension and importance sampling. Using 75 large-scale synthetic datasets, 32 metazoan compendium benchmark datasets, and 164 chromatin immunoprecipitation sequencing (ChIP-Seq) libraries, we demonstrated the superior performance of SEME over existing programs in finding transcription factor (TF) binding sites. SEME is further applied to a more difficult problem of finding the co-regulated TF (coTF) motifs in 15 ChIP-Seq libraries. It identified significantly more correct coTF motifs and, at the same time, predicted coTF motifs with better matching to the known motifs. Finally, we show that the learned position and sequence rank preferences of each coTF reveals potential interaction mechanisms between the primary TF and the coTF within these sites. Some of these findings were further validated by the ChIP-Seq experiments of the coTFs. The application is available online.

Filtering genetic variants and placing informative priors based on putative biological function.

PubMed

Friedrichs, Stefanie; Malzahn, Dörthe; Pugh, Elizabeth W; Almeida, Marcio; Liu, Xiao Qing; Bailey, Julia N

2016-02-03

High-density genetic marker data, especially sequence data, imply an immense multiple testing burden. This can be ameliorated by filtering genetic variants, exploiting or accounting for correlations between variants, jointly testing variants, and by incorporating informative priors. Priors can be based on biological knowledge or predicted variant function, or even be used to integrate gene expression or other omics data. Based on Genetic Analysis Workshop (GAW) 19 data, this article discusses diversity and usefulness of functional variant scores provided, for example, by PolyPhen2, SIFT, or RegulomeDB annotations. Incorporating functional scores into variant filters or weights and adjusting the significance level for correlations between variants yielded significant associations with blood pressure traits in a large family study of Mexican Americans (GAW19 data set). Marker rs218966 in gene PHF14 and rs9836027 in MAP4 significantly associated with hypertension; additionally, rare variants in SNUPN significantly associated with systolic blood pressure. Variant weights strongly influenced the power of kernel methods and burden tests. Apart from variant weights in test statistics, prior weights may also be used when combining test statistics or to informatively weight p values while controlling false discovery rate (FDR). Indeed, power improved when gene expression data for FDR-controlled informative weighting of association test p values of genes was used. Finally, approaches exploiting variant correlations included identity-by-descent mapping and the optimal strategy for joint testing rare and common variants, which was observed to depend on linkage disequilibrium structure.

Estimating the effect of lay knowledge and prior contact with pulmonary TB patients, on health-belief model in a high-risk pulmonary TB transmission population.

PubMed

Zein, Rizqy Amelia; Suhariadi, Fendy; Hendriani, Wiwin

2017-01-01

The research aimed to investigate the effect of lay knowledge of pulmonary tuberculosis (TB) and prior contact with pulmonary TB patients on a health-belief model (HBM) as well as to identify the social determinants that affect lay knowledge. Survey research design was conducted, where participants were required to fill in a questionnaire, which measured HBM and lay knowledge of pulmonary TB. Research participants were 500 residents of Semampir, Asemrowo, Bubutan, Pabean Cantian, and Simokerto districts, where the risk of pulmonary TB transmission is higher than other districts in Surabaya. Being a female, older in age, and having prior contact with pulmonary TB patients significantly increase the likelihood of having a higher level of lay knowledge. Lay knowledge is a substantial determinant to estimate belief in the effectiveness of health behavior and personal health threat. Prior contact with pulmonary TB patients is able to explain the belief in the effectiveness of a health behavior, yet fails to estimate participants' belief in the personal health threat. Health authorities should prioritize males and young people as their main target groups in a pulmonary TB awareness campaign. The campaign should be able to reconstruct people's misconception about pulmonary TB, thereby bringing around the health-risk perception so that it is not solely focused on improving lay knowledge.

The positive and negative consequences of multiple-choice testing.

PubMed

Roediger, Henry L; Marsh, Elizabeth J

2005-09-01

Multiple-choice tests are commonly used in educational settings but with unknown effects on students' knowledge. The authors examined the consequences of taking a multiple-choice test on a later general knowledge test in which students were warned not to guess. A large positive testing effect was obtained: Prior testing of facts aided final cued-recall performance. However, prior testing also had negative consequences. Prior reading of a greater number of multiple-choice lures decreased the positive testing effect and increased production of multiple-choice lures as incorrect answers on the final test. Multiple-choice testing may inadvertently lead to the creation of false knowledge.

Report of the International Commission on Earthquake Forecasting for Civil Protection (Invited)

NASA Astrophysics Data System (ADS)

Jordan, T. H.

2009-12-01

The destructive L’Aquila earthquake of 6 April 2009 (Mw 6.3) illustrates the challenges of operational earthquake forecasting. The earthquake ruptured a mapped normal fault in a region identified by long-term forecasting models as one of the most seismically dangerous in Italy; it was the strongest of a rich sequence that started several months earlier and included a M3.9 foreshock less than five hours prior to the mainshock. According to widely circulated news reports, the earthquake had been predicted by a local resident using unpublished radon-based techniques, provoking a public controversy prior to the event that intensified in its wake. Several weeks after the earthquake, the Italian Department of Civil Protection appointed an international commission with the mandate to report on the current state of knowledge of prediction and forecasting and guidelines for operational utilization. The commission included geoscientists from China, France, Germany, Greece, Italy, Japan, Russia, United Kingdom, and United States with experience in earthquake forecasting and prediction. This presentation by the chair of the commission will report on its findings and recommendations.

Community of Priors: A Bayesian Approach to Consensus Building

ERIC Educational Resources Information Center

Hara, Motoaki

2010-01-01

Despite having drawn from empirical evidence and cumulative prior expertise in the formulation of research questions as well as study design, each study is treated as a stand-alone product rather than positioned within a sequence of cumulative evidence. While results of prior studies are typically cited within the body of prior literature review,…

RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit.

PubMed

Garcia-Seco, Daniel; Zhang, Yang; Gutierrez-Mañero, Francisco J; Martin, Cathie; Ramos-Solano, Beatriz

2015-01-22

There is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limiting gene discovery and the breeding of improved varieties. De novo RNA-seq of ripe blackberries grown under field conditions was performed using Illumina Hiseq 2000. Almost 9 billion nucleotide bases were sequenced in total. Following assembly, 42,062 consensus sequences were detected. For functional annotation, 33,040 (NR), 32,762 (NT), 21,932 (Swiss-Prot), 20,134 (KEGG), 13,676 (COG), 24,168 (GO) consensus sequences were annotated using different databases; in total 34,552 annotated sequences were identified. For protein prediction analysis, the number of coding DNA sequences (CDS) that mapped to the protein database was 32,540. Non redundant (NR), annotation showed that 25,418 genes (73.5%) has the highest similarity with Fragaria vesca subspecies vesca. Reanalysis was undertaken by aligning the reads with this reference genome for a deeper analysis of the transcriptome. We demonstrated that de novo assembly, using Trinity and later annotation with Blast using different databases, were complementary to alignment to the reference sequence using SOAPaligner/SOAP2. The Fragaria reference genome belongs to a species in the same family as blackberry (Rosaceae) but to a different genus. Since blackberries are tetraploids, the possibility of artefactual gene chimeras resulting from mis-assembly was tested with one of the genes sequenced by RNAseq, Chalcone Synthase (CHS). cDNAs encoding this protein were cloned and sequenced. Primers designed to the assembled sequences accurately distinguished different contigs, at least for chalcone synthase genes. We prepared and analysed transcriptome data from ripe blackberries, for which prior genomic information was limited. This new sequence information will improve the knowledge of this important and healthy fruit, providing an invaluable new tool for biological research.

Processing and memory of information presented in narrative or expository texts.

PubMed

Wolfe, Michael B W; Woodwyk, Joshua M

2010-09-01

Previous research suggests that narrative and expository texts differ in the extent to which they prompt students to integrate to-be-learned content with relevant prior knowledge during comprehension. We expand on previous research by examining on-line processing and representation in memory of to-be-learned content that is embedded in narrative or expository texts. We are particularly interested in how differences in the use of relevant prior knowledge leads to differences in terms of levels of discourse representation (textbase vs. situation model). A total of 61 university undergraduates in Expt 1, and 160 in Expt 2. In Expt 1, subjects thought out loud while comprehending circulatory system content embedded in a narrative or expository text, followed by free recall of text content. In Expt 2, subjects read silently and completed a sentence recognition task to assess memory. In Expt 1, subjects made more associations to prior knowledge while reading the expository text, and recalled more content. Content recall was also correlated with amount of relevant prior knowledge for subjects who read the expository text but not the narrative text. In Expt 2, subjects reading the expository text (compared to the narrative text) had a weaker textbase representation of the to-be-learned content, but a marginally stronger situation model. Results suggest that in terms of to-be-learned content, expository texts trigger students to utilize relevant prior knowledge more than narrative texts.

Characterization of GM events by insert knowledge adapted re-sequencing approaches

PubMed Central

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-01-01

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events. PMID:24088728

Characterization of GM events by insert knowledge adapted re-sequencing approaches.

PubMed

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-10-03

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.

Language knowledge and event knowledge in language use

PubMed Central

Willits, Jon A.; Amato, Michael S.; MacDonald, Maryellen C.

2018-01-01

This paper examines how semantic knowledge is used in language comprehension and in making judgments about events in the world. We contrast knowledge gleaned from prior language experience (“language knowledge”) and knowledge coming from prior experience with the world (“world knowledge”). In two corpus analyses, we show that previous research linking verb aspect and event representations have confounded language and world knowledge. Then, using carefully chosen stimuli that remove this confound, we performed four experiments that manipulated the degree to which language knowledge or world knowledge should be salient and relevant to performing a task, finding in each case that participants use the type of knowledge most appropriate to the task. These results provide evidence for a highly context-sensitive and interactionist perspective on how semantic knowledge is represented and used during language processing. PMID:25791750

An empirical Bayes approach to network recovery using external knowledge.

PubMed

Kpogbezan, Gino B; van der Vaart, Aad W; van Wieringen, Wessel N; Leday, Gwenaël G R; van de Wiel, Mark A

2017-09-01

Reconstruction of a high-dimensional network may benefit substantially from the inclusion of prior knowledge on the network topology. In the case of gene interaction networks such knowledge may come for instance from pathway repositories like KEGG, or be inferred from data of a pilot study. The Bayesian framework provides a natural means of including such prior knowledge. Based on a Bayesian Simultaneous Equation Model, we develop an appealing Empirical Bayes (EB) procedure that automatically assesses the agreement of the used prior knowledge with the data at hand. We use variational Bayes method for posterior densities approximation and compare its accuracy with that of Gibbs sampling strategy. Our method is computationally fast, and can outperform known competitors. In a simulation study, we show that accurate prior data can greatly improve the reconstruction of the network, but need not harm the reconstruction if wrong. We demonstrate the benefits of the method in an analysis of gene expression data from GEO. In particular, the edges of the recovered network have superior reproducibility (compared to that of competitors) over resampled versions of the data. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

78 FR 29071 - Assessment of Mediation and Arbitration Procedures

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-17

... proceeding. Program participants in the new arbitration program will have prior knowledge of the issues to be... final rules, all parties opting into the arbitration program will have full prior knowledge that these... including discovery, the submission of evidence, and the treatment of confidential information, and the...

Teaching Practice: A Perspective on Inter-Text and Prior Knowledge

ERIC Educational Resources Information Center

Costley, Kevin C.; West, Howard G.

2012-01-01

The use of teaching practices that involve intertextual relationship discovery in today's elementary classrooms is increasingly essential to the success of young learners of reading. Teachers must constantly strive to expand their perspective of how to incorporate the dialogue included in prior knowledge assessment. Teachers must also consider how…

Elaborative-Interrogation and Prior-Knowledge Effects on Learning of Facts.

ERIC Educational Resources Information Center

Woloshyn, Vera E.; And Others

1992-01-01

The differences among elaborative-interrogation, reading-to-understand, and no-exposure control conditions with familiar domain material in contrast to unfamiliar domain material were studied for 50 Canadian and 50 west German undergraduates. Results provide evidence of effects of both elaborative interrogation and prior knowledge on learning.…

Effects of Example Variability and Prior Knowledge in How Students Learn to Solve Equations

ERIC Educational Resources Information Center

Guo, Jian-Peng; Yang, Ling-Yan; Ding, Yi

2014-01-01

Researchers have consistently demonstrated that multiple examples are better than one example in facilitating learning because the comparison evoked by multiple examples supports learning and transfer. However, research outcomes are unclear regarding the effects of example variability and prior knowledge on learning from comparing multiple…

Relationship of Students' Prior Knowledge and Order of Questions on Tests to Students' Test Scores.

ERIC Educational Resources Information Center

Papp, Klara K.; And Others

1987-01-01

A study examined whether students beginning a cell biology course with prior knowledge of its three areas (genetics, histology, and biochemistry) would retain that advantage throughout the course and whether achievement was influenced by the order of questions in a test. (MSE)

The Impact of Prior Programming Knowledge on Lecture Attendance and Final Exam

ERIC Educational Resources Information Center

Veerasamy, Ashok Kumar; D'Souza, Daryl; Lindén, Rolf; Laakso, Mikko-Jussi

2018-01-01

In this article, we report the results of the impact of prior programming knowledge (PPK) on lecture attendance (LA) and on subsequent final programming exam performance in a university level introductory programming course. This study used Spearman's rank correlation coefficient, multiple regression, Kruskal-Wallis, and Bonferroni correction…

Composing Knowledge: Writing, Rhetoric, and Reflection in Prior Learning Assessment

ERIC Educational Resources Information Center

Leaker, Cathy; Ostman, Heather

2010-01-01

In this article, we argue that prior learning assessment (PLA) essays manifest a series of issues central to composition research and practice: they foreground the "contact zone" between the unauthorized writer, institutional power, and the articulation of knowledge claims; they reinforce the central role of a multifaceted approach to…

Using Analogies to Facilitate Conceptual Change in Mathematics Learning

ERIC Educational Resources Information Center

Vamvakoussi, Xenia

2017-01-01

The problem of adverse effects of prior knowledge in mathematics learning has been amply documented and theorized by mathematics educators as well as cognitive/developmental psychologists. This problem emerges when students' prior knowledge about a mathematical notion comes in contrast with new information coming from instruction, giving rise to…

Specific Previous Experience Affects Perception of Harmony and Meter

ERIC Educational Resources Information Center

Creel, Sarah C.

2011-01-01

Prior knowledge shapes our experiences, but which prior knowledge shapes which experiences? This question is addressed in the domain of music perception. Three experiments were used to determine whether listeners activate specific musical memories during music listening. Each experiment provided listeners with one of two musical contexts that was…

Pre-Test Assessment

ERIC Educational Resources Information Center

Berry, Thomas

2008-01-01

Pre-tests are a non-graded assessment tool used to determine pre-existing subject knowledge. Typically pre-tests are administered prior to a course to determine knowledge baseline, but here they are used to test students prior to topical material coverage throughout the course. While counterintuitive, the pre-tests cover material the student is…

A multi-run chemistry module for the production of [18F]FDG

NASA Astrophysics Data System (ADS)

Sipe, B.; Murphy, M.; Best, B.; Zigler, S.; Lim, J.; Dorman, E.; Mangner, T.; Weichelt, M.

2001-07-01

We have developed a new chemistry module for the production of up to four batches of [18F]FDG. Prior to starting a batch sequence, the module automatically performs a series of self-diagnostic tests, including a reagent detection sequence. The module then executes a user-defined production sequence followed by an automated process to rinse tubing, valves, and the reaction vessel prior to the next production sequence. Process feedback from the module is provided to a graphical user interface by mass flow controllers, radiation detectors, a pressure switch, a pressure transducer, and an IR temperature sensor. This paper will describe the module, the operating system, and the results of multi-site trials, including production data and quality control results.

The Interpretation of a Knowledge Claim in the Recognition of Prior Learning (RPL) and the Impact of This on RPL Practice

ERIC Educational Resources Information Center

de Graaff, Frederika

2014-01-01

The question addressed in this paper is: what does a knowledge claim consist of in the context of the Recognition of Prior Learning (RPL)? The research comprises a case study of RPL applicants' entry into a postgraduate diploma (a fourth-year programme) in project management. The focus is on the knowledge claims made as part of the RPL application…

Destination pluto: New horizons performance during the approach phase

NASA Astrophysics Data System (ADS)

Flanigan, Sarah H.; Rogers, Gabe D.; Guo, Yanping; Kirk, Madeline N.; Weaver, Harold A.; Owen, William M.; Jackman, Coralie D.; Bauman, Jeremy; Pelletier, Frederic; Nelson, Derek; Stanbridge, Dale; Dumont, Phillip J.; Williams, Bobby; Stern, S. Alan; Olkin, Cathy B.; Young, Leslie A.; Ennico, Kimberly

2016-11-01

The New Horizons spacecraft began its journey to the Pluto-Charon system on January 19, 2006 on-board an Atlas V rocket from Cape Canaveral, Florida. As the first mission in NASA's New Frontiers program, the objective of the New Horizons mission is to perform the first exploration of ice dwarfs in the Kuiper Belt, extending knowledge of the solar system to include the icy "third zone" for the first time. Arriving at the correct time and correct position relative to Pluto on July 14, 2015 depended on the successful execution of a carefully choreographed sequence of events. The Core command sequence, which was developed and optimized over multiple years and included the highest-priority science observations during the closest approach period, was contingent on precise navigation to the Pluto-Charon system and nominal performance of the guidance and control (G&C) subsystem. The flyby and gravity assist of Jupiter on February 28, 2007 was critical in placing New Horizons on the path to Pluto. Once past Jupiter, trajectory correction maneuvers (TCMs) became the sole source of trajectory control since the spacecraft did not encounter any other planetary bodies along its flight path prior to Pluto. During the Pluto approach phase, which formally began on January 15, 2015, optical navigation images were captured primarily with the Long Range Reconnaissance Imager to refine spacecraft and Pluto-Charon system trajectory knowledge, which in turn was used to design TCMs. Orbit determination solutions were also used to update the spacecraft's on-board trajectory knowledge throughout the approach phase. Nominal performance of the G&C subsystem, accurate TCM designs, and high-quality orbit determination solutions resulted in final Pluto-relative B-plane arrival conditions that facilitated a successful first reconnaissance of the Pluto-Charon system.

Creating illusions of knowledge: learning errors that contradict prior knowledge.

PubMed

Fazio, Lisa K; Barber, Sarah J; Rajaram, Suparna; Ornstein, Peter A; Marsh, Elizabeth J

2013-02-01

Most people know that the Pacific is the largest ocean on Earth and that Edison invented the light bulb. Our question is whether this knowledge is stable, or if people will incorporate errors into their knowledge bases, even if they have the correct knowledge stored in memory. To test this, we asked participants general-knowledge questions 2 weeks before they read stories that contained errors (e.g., "Franklin invented the light bulb"). On a later general-knowledge test, participants reproduced story errors despite previously answering the questions correctly. This misinformation effect was found even for questions that were answered correctly on the initial test with the highest level of confidence. Furthermore, prior knowledge offered no protection against errors entering the knowledge base; the misinformation effect was equivalent for previously known and unknown facts. Errors can enter the knowledge base even when learners have the knowledge necessary to catch the errors. 2013 APA, all rights reserved

Age differences in suggestibility to contradictions of demonstrated knowledge: the influence of prior knowledge.

PubMed

Umanath, Sharda

2016-11-01

People maintain intact general knowledge into very old age and use it to support remembering. Interestingly, when older and younger adults encounter errors that contradict general knowledge, older adults suffer fewer memorial consequences: Older adults use fewer recently-encountered errors as answers for later knowledge questions. Why do older adults show this reduced suggestibility, and what role does their intact knowledge play? In three experiments, I examined suggestibility following exposure to errors in fictional stories that contradict general knowledge. Older adults consistently demonstrated more prior knowledge than younger adults but also gained access to even more across time. Additionally, they did not show a reduction in new learning from the stories, indicating lesser involvement of episodic memory failures. Critically, when knowledge was stably accessible, older adults relied more heavily on that knowledge compared to younger adults, resulting in reduced suggestibility. Implications for the broader role of knowledge in aging are discussed.

Attentional load and implicit sequence learning.

PubMed

Shanks, David R; Rowland, Lee A; Ranger, Mandeep S

2005-06-01

A widely employed conceptualization of implicit learning hypothesizes that it makes minimal demands on attentional resources. This conjecture was investigated by comparing learning under single-task and dual-task conditions in the sequential reaction time (SRT) task. Participants learned probabilistic sequences, with dual-task participants additionally having to perform a counting task using stimuli that were targets in the SRT display. Both groups were then tested for sequence knowledge under single-task (Experiments 1 and 2) or dual-task (Experiment 3) conditions. Participants also completed a free generation task (Experiments 2 and 3) under inclusion or exclusion conditions to determine if sequence knowledge was conscious or unconscious in terms of its access to intentional control. The experiments revealed that the secondary task impaired sequence learning and that sequence knowledge was consciously accessible. These findings disconfirm both the notion that implicit learning is able to proceed normally under conditions of divided attention, and that the acquired knowledge is inaccessible to consciousness. A unitary framework for conceptualizing implicit and explicit learning is proposed.

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

PubMed Central

Jun, Goo; Flickinger, Matthew; Hetrick, Kurt N.; Romm, Jane M.; Doheny, Kimberly F.; Abecasis, Gonçalo R.; Boehnke, Michael; Kang, Hyun Min

2012-01-01

DNA sample contamination is a serious problem in DNA sequencing studies and may result in systematic genotype misclassification and false positive associations. Although methods exist to detect and filter out cross-species contamination, few methods to detect within-species sample contamination are available. In this paper, we describe methods to identify within-species DNA sample contamination based on (1) a combination of sequencing reads and array-based genotype data, (2) sequence reads alone, and (3) array-based genotype data alone. Analysis of sequencing reads allows contamination detection after sequence data is generated but prior to variant calling; analysis of array-based genotype data allows contamination detection prior to generation of costly sequence data. Through a combination of analysis of in silico and experimentally contaminated samples, we show that our methods can reliably detect and estimate levels of contamination as low as 1%. We evaluate the impact of DNA contamination on genotype accuracy and propose effective strategies to screen for and prevent DNA contamination in sequencing studies. PMID:23103226

Microfluidic droplet enrichment for targeted sequencing

PubMed Central

Eastburn, Dennis J.; Huang, Yong; Pellegrino, Maurizio; Sciambi, Adam; Ptáček, Louis J.; Abate, Adam R.

2015-01-01

Targeted sequence enrichment enables better identification of genetic variation by providing increased sequencing coverage for genomic regions of interest. Here, we report the development of a new target enrichment technology that is highly differentiated from other approaches currently in use. Our method, MESA (Microfluidic droplet Enrichment for Sequence Analysis), isolates genomic DNA fragments in microfluidic droplets and performs TaqMan PCR reactions to identify droplets containing a desired target sequence. The TaqMan positive droplets are subsequently recovered via dielectrophoretic sorting, and the TaqMan amplicons are removed enzymatically prior to sequencing. We demonstrated the utility of this approach by generating an average 31.6-fold sequence enrichment across 250 kb of targeted genomic DNA from five unique genomic loci. Significantly, this enrichment enabled a more comprehensive identification of genetic polymorphisms within the targeted loci. MESA requires low amounts of input DNA, minimal prior locus sequence information and enriches the target region without PCR bias or artifacts. These features make it well suited for the study of genetic variation in a number of research and diagnostic applications. PMID:25873629

MRAC Control with Prior Model Knowledge for Asymmetric Damaged Aircraft

PubMed Central

Zhang, Jing

2015-01-01

This paper develops a novel state-tracking multivariable model reference adaptive control (MRAC) technique utilizing prior knowledge of plant models to recover control performance of an asymmetric structural damaged aircraft. A modification of linear model representation is given. With prior knowledge on structural damage, a polytope linear parameter varying (LPV) model is derived to cover all concerned damage conditions. An MRAC method is developed for the polytope model, of which the stability and asymptotic error convergence are theoretically proved. The proposed technique reduces the number of parameters to be adapted and thus decreases computational cost and requires less input information. The method is validated by simulations on NASA generic transport model (GTM) with damage. PMID:26180839

Event-related potential correlates of declarative and non-declarative sequence knowledge.

PubMed

Ferdinand, Nicola K; Rünger, Dennis; Frensch, Peter A; Mecklinger, Axel

2010-07-01

The goal of the present study was to demonstrate that declarative and non-declarative knowledge acquired in an incidental sequence learning task contributes differentially to memory retrieval and leads to dissociable ERP signatures in a recognition memory task. For this purpose, participants performed a sequence learning task and were classified as verbalizers, partial verbalizers, or nonverbalizers according to their ability to verbally report the systematic response sequence. Thereafter, ERPs were recorded in a recognition memory task time-locked to sequence triplets that were either part of the previously learned sequence or not. Although all three groups executed old sequence triplets faster than new triplets in the recognition memory task, qualitatively distinct ERP patterns were found for participants with and without reportable knowledge. Verbalizers and, to a lesser extent, partial verbalizers showed an ERP correlate of recollection for parts of the incidentally learned sequence. In contrast, nonverbalizers showed a different ERP effect with a reverse polarity that might reflect priming. This indicates that an ensemble of qualitatively different processes is at work when declarative and non-declarative sequence knowledge is retrieved. By this, our findings favor a multiple-systems view postulating that explicit and implicit learning are supported by different and functionally independent systems. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Application of Sequence-Dependent Electrophoresis Fingerprinting in Exploring Biodiversity and Population Dynamics of Human Intestinal Microbiota: What Can Be Revealed?

PubMed Central

Huys, Geert; Vanhoutte, Tom; Vandamme, Peter

2008-01-01

Sequence-dependent electrophoresis (SDE) fingerprinting techniques such as denaturing gradient gel electrophoresis (DGGE) have become commonplace in the field of molecular microbial ecology. The success of the SDE technology lays in the fact that it allows visualization of the predominant members of complex microbial ecosystems independent of their culturability and without prior knowledge on the complexity and diversity of the ecosystem. Mainly using the prokaryotic 16S rRNA gene as PCR amplification target, SDE-based community fingerprinting turned into one of the leading molecular tools to unravel the diversity and population dynamics of human intestinal microbiota. The first part of this review covers the methodological concept of SDE fingerprinting and the technical hurdles for analyzing intestinal samples. Subsequently, the current state-of-the-art of DGGE and related techniques to analyze human intestinal microbiota from healthy individuals and from patients with intestinal disorders is surveyed. In addition, the applicability of SDE analysis to monitor intestinal population changes upon nutritional or therapeutic interventions is critically evaluated. PMID:19277102

The kinetics and location of intra-host HIV evolution to evade cellular immunity are predictable

NASA Astrophysics Data System (ADS)

Barton, John; Goonetilleke, Nilu; Butler, Thomas; Walker, Bruce; McMichael, Andrew; Chakraborty, Arup

Human immunodeficiency virus (HIV) evolves within infected persons to escape targeting and clearance by the host immune system, thereby preventing effective immune control of infection. Knowledge of the timing and pathways of escape that result in loss of control of the virus could aid in the design of effective strategies to overcome the challenge of viral diversification and immune escape. We combined methods from statistical physics and evolutionary dynamics to predict the course of in vivo viral sequence evolution in response to T cell-mediated immune pressure in a cohort of 17 persons with acute HIV infection. Our predictions agree well with both the location of documented escape mutations and the clinically observed time to escape. We also find that that the mutational pathways to escape depend on the viral sequence background due to epistatic interactions. The ability to predict escape pathways, and the duration over which control is maintained by specific immune responses prior to escape, could be exploited for the rational design of immunotherapeutic strategies that may enable long-term control of HIV infection.

What's your number? The effects of trial order on the one-target advantage.

PubMed

Bested, Stephen R; Khan, Michael A; Lawrence, Gavin P; Tremblay, Luc

2018-05-01

When moving our upper-limb towards a single target, movement times are typically shorter than when movement to a second target is required. This is known as the one-target advantage. Most studies that have demonstrated the one-target advantage have employed separate trial blocks for the one- and two-segment movements. To test if the presence of the one-target advantage depends on advance knowledge of the number of segments, the present study investigated whether the one-target advantage would emerge under different trial orders/sequences. One- and two-segment responses were organized in blocked (i.e., 1-1-1, 2-2-2), alternating (i.e., 1-2-1-2-1-2), and random (i.e., 1-1-2-1-2-2) trial sequences. Similar to previous studies, where only blocked schedules have typically been utilized, the one-target advantage emerged during the blocked and alternate conditions, but not in the random condition. This finding indicates that the one-target advantage is contingent on participants knowing the number of movement segments prior to stimulus onset. Copyright © 2018 Elsevier B.V. All rights reserved.

Hubby and Lewontin on Protein Variation in Natural Populations: When Molecular Genetics Came to the Rescue of Population Genetics.

PubMed

Charlesworth, Brian; Charlesworth, Deborah; Coyne, Jerry A; Langley, Charles H

2016-08-01

The 1966 GENETICS papers by John Hubby and Richard Lewontin were a landmark in the study of genome-wide levels of variability. They used the technique of gel electrophoresis of enzymes and proteins to study variation in natural populations of Drosophila pseudoobscura, at a set of loci that had been chosen purely for technical convenience, without prior knowledge of their levels of variability. Together with the independent study of human populations by Harry Harris, this seminal study provided the first relatively unbiased picture of the extent of genetic variability in protein sequences within populations, revealing that many genes had surprisingly high levels of diversity. These papers stimulated a large research program that found similarly high electrophoretic variability in many different species and led to statistical tools for interpreting the data in terms of population genetics processes such as genetic drift, balancing and purifying selection, and the effects of selection on linked variants. The current use of whole-genome sequences in studies of variation is the direct descendant of this pioneering work. Copyright © 2016 by the Genetics Society of America.

Epigenetic priors for identifying active transcription factor binding sites.

PubMed

Cuellar-Partida, Gabriel; Buske, Fabian A; McLeay, Robert C; Whitington, Tom; Noble, William Stafford; Bailey, Timothy L

2012-01-01

Accurate knowledge of the genome-wide binding of transcription factors in a particular cell type or under a particular condition is necessary for understanding transcriptional regulation. Using epigenetic data such as histone modification and DNase I, accessibility data has been shown to improve motif-based in silico methods for predicting such binding, but this approach has not yet been fully explored. We describe a probabilistic method for combining one or more tracks of epigenetic data with a standard DNA sequence motif model to improve our ability to identify active transcription factor binding sites (TFBSs). We convert each data type into a position-specific probabilistic prior and combine these priors with a traditional probabilistic motif model to compute a log-posterior odds score. Our experiments, using histone modifications H3K4me1, H3K4me3, H3K9ac and H3K27ac, as well as DNase I sensitivity, show conclusively that the log-posterior odds score consistently outperforms a simple binary filter based on the same data. We also show that our approach performs competitively with a more complex method, CENTIPEDE, and suggest that the relative simplicity of the log-posterior odds scoring method makes it an appealing and very general method for identifying functional TFBSs on the basis of DNA and epigenetic evidence. FIMO, part of the MEME Suite software toolkit, now supports log-posterior odds scoring using position-specific priors for motif search. A web server and source code are available at http://meme.nbcr.net. Utilities for creating priors are at http://research.imb.uq.edu.au/t.bailey/SD/Cuellar2011. t.bailey@uq.edu.au Supplementary data are available at Bioinformatics online.

Prospective regularization design in prior-image-based reconstruction

NASA Astrophysics Data System (ADS)

Dang, Hao; Siewerdsen, Jeffrey H.; Webster Stayman, J.

2015-12-01

Prior-image-based reconstruction (PIBR) methods leveraging patient-specific anatomical information from previous imaging studies and/or sequences have demonstrated dramatic improvements in dose utilization and image quality for low-fidelity data. However, a proper balance of information from the prior images and information from the measurements is required (e.g. through careful tuning of regularization parameters). Inappropriate selection of reconstruction parameters can lead to detrimental effects including false structures and failure to improve image quality. Traditional methods based on heuristics are subject to error and sub-optimal solutions, while exhaustive searches require a large number of computationally intensive image reconstructions. In this work, we propose a novel method that prospectively estimates the optimal amount of prior image information for accurate admission of specific anatomical changes in PIBR without performing full image reconstructions. This method leverages an analytical approximation to the implicitly defined PIBR estimator, and introduces a predictive performance metric leveraging this analytical form and knowledge of a particular presumed anatomical change whose accurate reconstruction is sought. Additionally, since model-based PIBR approaches tend to be space-variant, a spatially varying prior image strength map is proposed to optimally admit changes everywhere in the image (eliminating the need to know change locations a priori). Studies were conducted in both an ellipse phantom and a realistic thorax phantom emulating a lung nodule surveillance scenario. The proposed method demonstrated accurate estimation of the optimal prior image strength while achieving a substantial computational speedup (about a factor of 20) compared to traditional exhaustive search. Moreover, the use of the proposed prior strength map in PIBR demonstrated accurate reconstruction of anatomical changes without foreknowledge of change locations in phantoms where the optimal parameters vary spatially by an order of magnitude or more. In a series of studies designed to explore potential unknowns associated with accurate PIBR, optimal prior image strength was found to vary with attenuation differences associated with anatomical change but exhibited only small variations as a function of the shape and size of the change. The results suggest that, given a target change attenuation, prospective patient-, change-, and data-specific customization of the prior image strength can be performed to ensure reliable reconstruction of specific anatomical changes.

Potentiation in young infants: The origin of the prior knowledge effect?

PubMed Central

Barr, Rachel; Rovee-Collier, Carolyn; Learmonth, Amy

2011-01-01

In two experiments with 6-month-old infants, we found that prior learning of an operant task (remembered for 2 weeks) mediated new learning of a modeling event (remembered for only 1 day) and increased its recall. Infants first learned to associate lever pressing with moving a toy train housed in a large box. One or 2 weeks later, three target actions were modeled on a hand puppet while the train box (a retrieval cue) was in view. Merely retrieving the train memory strengthened it, and simultaneously pairing its retrieved memory with the modeled actions potentiated their learning and recall. When paired 1 week later, deferred imitation increased from 1 day to 4 weeks; when paired 2 weeks later, it increased from 1 day to 6 weeks. The striking parallels between potentiated learning in infants and the prior knowledge effect in adults suggests that the prior knowledge effect originates in early infancy. PMID:21264602

When Relationships Depicted Diagrammatically Conflict with Prior Knowledge: An Investigation of Students' Interpretations of Evolutionary Trees

ERIC Educational Resources Information Center

Novick, Laura R.; Catley, Kefyn M.

2014-01-01

Science is an important domain for investigating students' responses to information that contradicts their prior knowledge. In previous studies of this topic, this information was communicated verbally. The present research used diagrams, specifically trees (cladograms) depicting evolutionary relationships among taxa. Effects of college…

Building Knowledge through Portfolio Learning in Prior Learning Assessment and Recognition

ERIC Educational Resources Information Center

Conrad, Dianne

2008-01-01

It is important for academic credibility that the process of prior learning assessment and recognition (PLAR) keeps learning and knowledge as its foundational tenets. Doing so ensures PLAR's recognition as a fertile ground for learners' cognitive and personal growth. In many postsecondary venues, PLAR is often misunderstood and confused with…

Temporal Learning in 4 1/2- and 6-Year-Old Children: Role of Instructions and Prior Knowledge.

ERIC Educational Resources Information Center

Droit, Sylvie; And Others

1990-01-01

Examined the role of prior temporal knowledge of 4 1/2- and 6-year-olds through the use of high-rate, interval, and minimal instructions in a fixed-interval training schedule. Determined that the subjects' learning depended on their verbal self-control skills. (BC)

Understanding the Complexities of Prior Knowledge

ERIC Educational Resources Information Center

Soiferman, L. Karen

2014-01-01

The purpose of the study was to gain an understanding of the kinds of prior knowledge students bring with them from high school as it relates to the conventions of writing that they are expected to follow in ARTS 1110 Introduction to University. The research questions were "Can first-year students taking the Arts 1110 Introduction to…

An Effectiveness Index and Profile for Instructional Media.

ERIC Educational Resources Information Center

Bond, Jack H.

A scale was developed for judging the relative value of various media in teaching children. Posttest scores were partitioned into several components: error, prior knowledge, guessing, and gain from the learning exercise. By estimating the amounts of prior knowledge, guessing, and error, and then subtracting these from the total score, an index of…

Making Connections in Math: Activating a Prior Knowledge Analogue Matters for Learning

ERIC Educational Resources Information Center

Sidney, Pooja G.; Alibali, Martha W.

2015-01-01

This study investigated analogical transfer of conceptual structure from a prior-knowledge domain to support learning in a new domain of mathematics: division by fractions. Before a procedural lesson on division by fractions, fifth and sixth graders practiced with a surface analogue (other operations on fractions) or a structural analogue (whole…

An Investigation of the Relationships between Prior Knowledge and Vocabulary Development with Culturally Diverse Students.

ERIC Educational Resources Information Center

Karbon, Jacqueline C.

Using a semantic mapping technique for vocabulary instruction, a study explored how children of diverse groups bring different cultural backgrounds and prior knowledge to tasks involved in learning new words. The study was conducted in three sixth-grade classrooms--one containing rural Native American (especially Menominee) children, another…

The Influence of Prior Knowledge on Perception and Action: Relationships to Autistic Traits

ERIC Educational Resources Information Center

Buckingham, Gavin; Michelakakis, Elizabeth Evgenia; Rajendran, Gnanathusharan

2016-01-01

Autism is characterised by a range of perceptual and sensorimotor deficits, which might be related to abnormalities in how autistic individuals use prior knowledge. We investigated this proposition in a large non-clinical population in the context of the size-weight illusion, where individual's expectations about object weight influence their…

Interplay of Prior Knowledge, Self-Regulation and Motivation in Complex Multimedia Learning Environments

ERIC Educational Resources Information Center

Song, H. S.; Kalet, A. L.; Plass, J. L.

2016-01-01

This study examined the direct and indirect effects of medical clerkship students' prior knowledge, self-regulation and motivation on learning performance in complex multimedia learning environments. The data from 386 medical clerkship students from six medical schools were analysed using structural equation modeling. The structural model revealed…

Effects of Students' Prior Knowledge on Scientific Reasoning in Density.

ERIC Educational Resources Information Center

Yang, Il-Ho; Kwon, Yong-Ju; Kim, Young-Shin; Jang, Myoung-Duk; Jeong, Jin-Woo; Park, Kuk-Tae

2002-01-01

Investigates the effects of students' prior knowledge on the scientific reasoning processes of performing the task of controlling variables with computer simulation and identifies a number of problems that students encounter in scientific discovery. Involves (n=27) 5th grade students and (n=33) 7th grade students. Indicates that students' prior…

Relationship of Prior Knowledge and Working Engineers' Learning Preferences: Implications for Designing Effective Instruction

ERIC Educational Resources Information Center

Baukal, Charles E.; Ausburn, Lynna J.

2017-01-01

Continuing engineering education (CEE) is important to ensure engineers maintain proficiency over the life of their careers. However, relatively few studies have examined designing effective training for working engineers. Research has indicated that both learner instructional preferences and prior knowledge can impact the learning process, but it…

The Influence of Prior Knowledge and Viewing Repertoire on Learning from Video

ERIC Educational Resources Information Center

de Boer, Jelle; Kommers, Piet A. M.; de Brock, Bert; Tolboom, Jos

2016-01-01

Video is increasingly used as an instructional tool. It is therefore becoming more important to improve learning of students from video. We investigated whether student learning effects are influenced through an instruction about other viewing behaviours, and whether these learning effects depend on their prior knowledge. In a controlled…

Prior Knowledge and Online Inquiry-Based Science Reading: Evidence from Eye Tracking

ERIC Educational Resources Information Center

Ho, Hsin Ning Jessie; Tsai, Meng-Jung; Wang, Ching-Yeh; Tsai, Chin-Chung

2014-01-01

This study employed eye-tracking technology to examine how students with different levels of prior knowledge process text and data diagrams when reading a web-based scientific report. Students' visual behaviors were tracked and recorded when they read a report demonstrating the relationship between the greenhouse effect and global climate…

Students' Achievement in Relation to Reasoning Ability, Prior Knowledge and Gender

ERIC Educational Resources Information Center

Yenilmez, Ayse; Sungur, Semra; Tekkaya, Ceren

2006-01-01

This study investigated students' achievement regarding photosynthesis and respiration in plants in relation to reasoning ability, prior knowledge and gender. A total of 117 eighth-grade students participated in the study. Test of logical thinking and the two-tier multiple choice tests were administered to determine students' reasoning ability and…

The Effectiveness of Using Incorrect Examples to Support Learning about Decimal Magnitude

ERIC Educational Resources Information Center

Durkin, Kelley; Rittle-Johnson, Bethany

2012-01-01

Comparing common mathematical errors to correct examples may facilitate learning, even for students with limited prior domain knowledge. We examined whether studying incorrect and correct examples was more effective than studying two correct examples across prior knowledge levels. Fourth- and fifth-grade students (N = 74) learned about decimal…

Students' inductive reasoning skills and the relevance of prior knowledge: an exploratory study with a computer-based training course on the topic of acne vulgaris.

PubMed

Horn-Ritzinger, Sabine; Bernhardt, Johannes; Horn, Michael; Smolle, Josef

2011-04-01

The importance of inductive instruction in medical education is increasingly growing. Little is known about the relevance of prior knowledge regarding students' inductive reasoning abilities. The purpose is to evaluate this inductive teaching method as a means of fostering higher levels of learning and to explore how individual differences in prior knowledge (high [HPK] vs. low [LPK]) contribute to students' inductive reasoning skills. Twenty-six LPK and 18 HPK students could train twice with an interactive computer-based training object to discover the underlying concept before doing the final comprehension check. Students had a median of 76.9% of correct answers in the first, 90.9% in the second training, and answered 92% of the final assessment questions correctly. More important, 86% of all students succeeded with inductive learning, among them 83% of the HPK students and 89% of the LPK students. Prior knowledge did not predict performance on overall comprehension. This inductive instructional strategy fostered students' deep approaches to learning in a time-effective way.

Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction.

PubMed

Palmer, Lance E; Dejori, Mathaeus; Bolanos, Randall; Fasulo, Daniel

2010-01-15

With the rapid expansion of DNA sequencing databases, it is now feasible to identify relevant information from prior sequencing projects and completed genomes and apply it to de novo sequencing of new organisms. As an example, this paper demonstrates how such extra information can be used to improve de novo assemblies by augmenting the overlapping step. Finding all pairs of overlapping reads is a key task in many genome assemblers, and to this end, highly efficient algorithms have been developed to find alignments in large collections of sequences. It is well known that due to repeated sequences, many aligned pairs of reads nevertheless do not overlap. But no overlapping algorithm to date takes a rigorous approach to separating aligned but non-overlapping read pairs from true overlaps. We present an approach that extends the Minimus assembler by a data driven step to classify overlaps as true or false prior to contig construction. We trained several different classification models within the Weka framework using various statistics derived from overlaps of reads available from prior sequencing projects. These statistics included percent mismatch and k-mer frequencies within the overlaps as well as a comparative genomics score derived from mapping reads to multiple reference genomes. We show that in real whole-genome sequencing data from the E. coli and S. aureus genomes, by providing a curated set of overlaps to the contigging phase of the assembler, we nearly doubled the median contig length (N50) without sacrificing coverage of the genome or increasing the number of mis-assemblies. Machine learning methods that use comparative and non-comparative features to classify overlaps as true or false can be used to improve the quality of a sequence assembly.

Relationship of resident characteristics, attitudes, prior training and clinical knowledge to communication skills performance.

PubMed

Laidlaw, Toni Suzuki; Kaufman, David M; MacLeod, Heather; van Zanten, Sander; Simpson, David; Wrixon, William

2006-01-01

A substantial body of literature demonstrates that communication skills in medicine can be taught and retained through teaching and practice. Considerable evidence also reveals that characteristics such as gender, age, language and attitudes affect communication skills performance. Our study examined the characteristics, attitudes and prior communication skills training of residents to determine the relationship of each to patient-doctor communication. The relationship between communication skills proficiency and clinical knowledge application (biomedical and ethical) was also examined through the use of doctor-developed clinical content checklists, as very little research has been conducted in this area. A total of 78 first- and second-year residents across all departments at Dalhousie Medical School participated in a videotaped 4-station objective structured clinical examination presenting a range of communication and clinical knowledge challenges. A variety of instruments were used to gather information and assess performance. Two expert raters evaluated the videotapes. Significant relationships were observed between resident characteristics, prior communication skills training, clinical knowledge and communication skills performance. Females, younger residents and residents with English as first language scored significantly higher, as did residents with prior communication skills training. A significant positive relationship was found between the clinical content checklist and communication performance. Gender was the only characteristic related significantly to attitudes. Gender, age, language and prior communication skills training are related to communication skills performance and have implications for resident education. The positive relationship between communication skills proficiency and clinical knowledge application is important and should be explored further.

The construction of causal schemes: learning mechanisms at the knowledge level.

PubMed

diSessa, Andrea A

2014-06-01

This work uses microgenetic study of classroom learning to illuminate (1) the role of pre-instructional student knowledge in the construction of normative scientific knowledge, and (2) the learning mechanisms that drive change. Three enactments of an instructional sequence designed to lead to a scientific understanding of thermal equilibration are used as data sources. Only data from a scaffolded student inquiry preceding introduction of a normative model were used. Hence, the study involves nearly autonomous student learning. In two classes, students developed stable and socially shared explanations ("causal schemes") for understanding thermal equilibration. One case resulted in a near-normative understanding, while the other resulted in a non-normative "alternative conception." The near-normative case seems to be a particularly clear example wherein the constructed causal scheme is a composition of previously documented naïve conceptions. Detailed prior description of these naive elements allows a much better than usual view of the corresponding details of change during construction of the new scheme. A list of candidate mechanisms that can account for observed change is presented. The non-normative construction seems also to be a composition, albeit of a different structural form, using a different (although similar) set of naïve elements. This article provides one of very few high-resolution process analyses showing the productive use of naïve knowledge in learning. © 2014 Cognitive Science Society, Inc.

Nursing Student Perceptions Regarding Simulation Experience Sequencing.

PubMed

Woda, Aimee A; Gruenke, Theresa; Alt-Gehrman, Penny; Hansen, Jamie

2016-09-01

The use of simulated learning experiences (SLEs) have increased within nursing curricula with positive learning outcomes for nursing students. The purpose of this study is to explore nursing students' perceptions of their clinical decision making (CDM) related to the block sequencing of different patient care experiences, SLEs versus hospital-based learning experiences (HLEs). A qualitative descriptive design used open-ended survey questions to generate information about the block sequencing of SLEs and its impact on nursing students' perceived CDM. Three themes emerged from the data: Preexperience Anxiety, Real-Time Decision Making, and Increased Patient Care Experiences. Nursing students identified that having SLEs prior to HLEs provided several benefits. Even when students preferred SLEs prior to HLEs, the sequence did not impact their CDM. This suggests that alternating block sequencing can be used without impacting the students' perceptions of their ability to make decisions. [J Nurs Educ. 2016;55(9):528-532.]. Copyright 2016, SLACK Incorporated.

Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

PubMed

Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

2015-12-01

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid.

PubMed

Spooner, David M; Ruess, Holly; Iorizzo, Massimo; Senalik, Douglas; Simon, Philipp

2017-02-01

We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences. We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid ( Dc MP). Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus . Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named Dc MP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations. Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus , (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid. © 2017 Spooner et al. Published by the Botanical Society of America. This work is licensed under a Creative Commons public domain license (CC0 1.0).

Learning builds on learning: Infants' use of native language sound patterns to learn words

PubMed Central

Graf Estes, Katharine

2014-01-01

The present research investigated how infants apply prior knowledge of environmental regularities to support new learning. The experiments tested whether infants could exploit experience with native language (English) phonotactic patterns to facilitate associating sounds with meanings during word learning. Fourteen-month-olds heard fluent speech that contained cues for detecting target words; they were embedded in sequences that occur across word boundaries. A separate group heard the target words embedded without word boundary cues. Infants then participated in an object label-learning task. With the opportunity to use native language patterns to segment the target words, infants subsequently learned the labels. Without this experience, infants failed. Novice word learners can take advantage of early learning about sounds scaffold lexical development. PMID:24980741

Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae):Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid

USDA-ARS?s Scientific Manuscript database

We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results to prior phylogenetic results using plastid, nuclear, and mitochondrial DNA sequences. We obtained, using Illumina sequencing, full plastid sequences of 37 accessions of 20 Daucus taxa and outgrou...

Prior Knowledge Activation: How Different Concept Mapping Tasks Lead to Substantial Differences in Cognitive Processes, Learning Outcomes, and Perceived Self-Efficacy

ERIC Educational Resources Information Center

Gurlitt, Johannes; Renkl, Alexander

2010-01-01

Two experiments investigated the effects of characteristic features of concept mapping used for prior knowledge activation. Characteristic demands of concept mapping include connecting lines representing the relationships between concepts and labeling these lines, specifying the type of the semantic relationships. In the first experiment,…

Concept Development and Meaningful Learning among Electrical Engineering Students Engaged in a Problem-Based Laboratory Experience

ERIC Educational Resources Information Center

Bledsoe, Karen E.; Flick, Lawrence

2012-01-01

This phenomenographic study documented changes in student-held electrical concepts the development of meaningful learning among students with both low and high prior knowledge within a problem-based learning (PBL) undergraduate electrical engineering course. This paper reports on four subjects: two with high prior knowledge and two with low prior…

Formative Assessment Pre-Test to Identify College Students' Prior Knowledge, Misconceptions and Learning Difficulties in Biology

ERIC Educational Resources Information Center

Lazarowitz, Reuven; Lieb, Carl

2006-01-01

A formative assessment pretest was administered to undergraduate students at the beginning of a science course in order to find out their prior knowledge, misconceptions and learning difficulties on the topic of the human respiratory system and energy issues. Those findings could provide their instructors with the valuable information required in…

The Influence of Prior Knowledge, Peer Review, Age, and Gender in Online Philosophy Discussions

ERIC Educational Resources Information Center

Cuddy, Lucas Stebbins

2016-01-01

Using a primarily experimental design, this study investigated whether discussion boards in online community college philosophy classes can be designed in the Blackboard course management system to lead to higher order thinking. Discussions were designed using one of two teaching techniques: the activation of prior knowledge or the use of peer…

Thai University Students' Prior Knowledge about P-Waves Generated during Particle Motion

ERIC Educational Resources Information Center

Rakkapao, Suttida; Arayathanikul, Kwan; Pananont, Passakorn

2009-01-01

The goal of this study is to identify Thai students' prior knowledge about particle motion when P-waves arrive. This existing idea significantly influences what and how students learn in the classroom. The data were collected via conceptual open-ended questions designed by the researchers and through explanatory follow-up interviews. Participants…

The Interpretation of Cellular Transport Graphics by Students with Low and High Prior Knowledge

ERIC Educational Resources Information Center

Cook, Michelle; Carter, Glenda; Wiebe, Eric N.

2008-01-01

The purpose of this study was to examine how prior knowledge of cellular transport influenced how high school students in the USA viewed and interpreted graphic representations of this topic. The participants were Advanced Placement Biology students (n = 65); each participant had previously taken a biology course in high school. After assessing…

The Effects of Prior-Knowledge and Online Learning Approaches on Students' Inquiry and Argumentation Abilities

ERIC Educational Resources Information Center

Yang, Wen-Tsung; Lin, Yu-Ren; She, Hsiao-Ching; Huang, Kai-Yi

2015-01-01

This study investigated the effects of students' prior science knowledge and online learning approaches (social and individual) on their learning with regard to three topics: science concepts, inquiry, and argumentation. Two science teachers and 118 students from 4 eighth-grade science classes were invited to participate in this research. Students…

Python Environment for Bayesian Learning: Inferring the Structure of Bayesian Networks from Knowledge and Data

PubMed Central

Shah, Abhik; Woolf, Peter

2009-01-01

Summary In this paper, we introduce pebl, a Python library and application for learning Bayesian network structure from data and prior knowledge that provides features unmatched by alternative software packages: the ability to use interventional data, flexible specification of structural priors, modeling with hidden variables and exploitation of parallel processing. PMID:20161541

The Instructional Effectiveness of Animated Signaling among Learners with High and Low Prior Knowledge

ERIC Educational Resources Information Center

Li, Shanshan

2012-01-01

The purpose of this study was to investigate the instructional effectiveness of animated signals among learners with high and low prior knowledge. Each of the two treatments was presented with animated instruction either with signals or without signals on the content of how an airplane achieves lift. Subjects were eighty-seven undergraduate…

A Fair and Balanced Look at the News: What Affects Memory for Controversial Arguments?

ERIC Educational Resources Information Center

Wiley, J.

2005-01-01

This research demonstrates how prior knowledge may allow for qualitative differences in representation of texts about controversial issues. People often experience a memory bias in favor of information with which they agree. In several experiments it was found that individuals with high prior knowledge about the topic were better able to recall…

Prior Knowledge Influence on Self-Explanation Effectiveness when Solving Problems: An Exploratory Study in Science Learning

ERIC Educational Resources Information Center

Ionas, Ioan Gelu; Cernusca, Dan; Collier, Harvest L.

2012-01-01

This exploratory study presents the outcomes of using self-explanation to improve learners' performance in solving basic chemistry problems. The results of the randomized experiment show the existence of a moderation effect between prior knowledge and the level of support self-explanation provides to learners, suggestive of a synergistic effect…

The Impact of Learner's Prior Knowledge on Their Use of Chemistry Computer Simulations: A Case Study

ERIC Educational Resources Information Center

Liu, Han-Chin; Andre, Thomas; Greenbowe, Thomas

2008-01-01

It is complicated to design a computer simulation that adapts to students with different characteristics. This study documented cases that show how college students' prior chemistry knowledge level affected their interaction with peers and their approach to solving problems with the use of computer simulations that were designed to learn…

Feedback Both Helps and Hinders Learning: The Causal Role of Prior Knowledge

ERIC Educational Resources Information Center

Fyfe, Emily R.; Rittle-Johnson, Bethany

2016-01-01

Feedback can be a powerful learning tool, but its effects vary widely. Research has suggested that learners' prior knowledge may moderate the effects of feedback; however, no causal link has been established. In Experiment 1, we randomly assigned elementary school children (N = 108) to a condition based on a crossing of 2 factors: induced strategy…

The Effect of Prior Knowledge and Feedback Type Design on Student Achievement and Satisfaction in Introductory Accounting

ERIC Educational Resources Information Center

Campbell, Donald P.

2013-01-01

This study investigated the effect of student prior knowledge and feedback type on student achievement and satisfaction in an introductory managerial accounting course using computer-based formative assessment tools. The study involved a redesign of the existing Job Order Costing unit using the ADDIE model of instructional design. The…

Activating Junior Secondary School Students' Prior Knowledge for the Development of Vocabulary, Concepts and Mathematics through Instructional Strategies

ERIC Educational Resources Information Center

Oyinloye, Olu; Popoola, Abiodun A.

2013-01-01

This paper investigates the activation of students' prior knowledge for the development of vocabulary, concepts and mathematics. It has been observed that many secondary school students are not performing well in the examination conducted by the West African Examinations Council and National Examinations Council of Nigeria. The situation became…

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

NASA Astrophysics Data System (ADS)

Li, Na; Black, John B.

2016-10-01

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

Mechanisms underlying comprehension of health information in adulthood: the roles of prior knowledge and working memory capacity.

PubMed

Soederberg Miller, Lisa M; Gibson, Tanja N; Applegate, Elizabeth A; de Dios, Jeannette

2011-07-01

Prior knowledge, working memory capacity (WMC), and conceptual integration (attention allocated to integrating concepts in text) are critical within many contexts; however, their impact on the acquisition of health information (i.e. learning) is relatively unexplored.We examined how these factors impact learning about nutrition within a cross-sectional study of adults ages 18 to 81. Results showed that conceptual integration mediated the effects of knowledge and WMC on learning, confirming that attention to concepts while reading is important for learning about health. We also found that when knowledge was controlled, age declines in learning increased, suggesting that knowledge mitigates the effects of age on learning about nutrition.

Pharmaceutical pictograms: a model for development and testing for comprehension and utility.

PubMed

Montagne, Michael

2013-01-01

With concerns about the medication literacy skills of patients comes the need to develop various types of information materials that will enhance understanding and drug use. To review pictogram development projects and to propose a model for pharmaceutical pictogram development and testing for comprehension and use. Previous efforts in developing specific types of pictograms in engineering and safety as well as in health care and pharmacy are collected and summarized in terms of level of comprehension and recall. The impact of pictogram-enhanced medication information materials on knowledge acquisition, information retention, and adherence is assessed. Pictograms are a key component in re-designing medication information to improve comprehension, recall, and adherence. Many types of pictograms still produce low levels of comprehension and the impact of pictograms on medication knowledge is inconsistent. Prior training through patient counseling on the intended meaning and use of pictograms greatly increases their effectiveness. A model for the development and testing of pictograms and pictogram sequences for comprehension and use in medication information is presented and discussed. Copyright © 2013 Elsevier Inc. All rights reserved.

Examining the Gender Gap in Introductory Physics

NASA Astrophysics Data System (ADS)

Kost, Lauren; Pollock, Steven; Finkelstein, Noah

2009-05-01

Our previous research[1] showed that despite the use of interactive engagement techniques in the introductory physics course, the gap in performance between males and females on a mechanics conceptual learning survey persisted from pre- to post-test, at our institution. Such findings were counter to previously published work[2]. Follow-up studies[3] identified correlations between student performance on the conceptual learning survey and students' prior physics and math knowledge and their incoming attitudes and beliefs about physics and learning physics. The results indicate that the gender gap at our institution is predominantly associated with differences in males' and females' previous physics and math knowledge, and attitudes and beliefs. Our current work extends these results in two ways: 1) we look at the gender gap in the second semester of the introductory sequence and find results similar to those in the first semester course and 2) we identify ways in which males and females differentially experience several aspects of the introductory course. [1] Pollock, et al, Phys Rev: ST: PER 3, 010107. [2] Lorenzo, et al, Am J Phys 74, 118. [3] Kost, et al, PERC Proceedings 2008.

How Incidental Sequence Learning Creates Reportable Knowledge: The Role of Unexpected Events

ERIC Educational Resources Information Center

Runger, Dennis; Frensch, Peter A.

2008-01-01

Research on incidental sequence learning typically is concerned with the characteristics of implicit or nonconscious learning. In this article, the authors aim to elucidate the cognitive mechanisms that contribute to the generation of explicit, reportable sequence knowledge. According to the unexpected-event hypothesis (P. A. Frensch, H. Haider,…

Event-Related Potential Correlates of Declarative and Non-Declarative Sequence Knowledge

ERIC Educational Resources Information Center

Ferdinand, Nicola K.; Runger, Dennis; Frensch, Peter A.; Mecklinger, Axel

2010-01-01

The goal of the present study was to demonstrate that declarative and non-declarative knowledge acquired in an incidental sequence learning task contributes differentially to memory retrieval and leads to dissociable ERP signatures in a recognition memory task. For this purpose, participants performed a sequence learning task and were classified…

Event-related potentials in response to violations of content and temporal event knowledge.

PubMed

Drummer, Janna; van der Meer, Elke; Schaadt, Gesa

2016-01-08

Scripts that store knowledge of everyday events are fundamentally important for managing daily routines. Content event knowledge (i.e., knowledge about which events belong to a script) and temporal event knowledge (i.e., knowledge about the chronological order of events in a script) constitute qualitatively different forms of knowledge. However, there is limited information about each distinct process and the time course involved in accessing content and temporal event knowledge. Therefore, we analyzed event-related potentials (ERPs) in response to either correctly presented event sequences or event sequences that contained a content or temporal error. We found an N400, which was followed by a posteriorly distributed P600 in response to content errors in event sequences. By contrast, we did not find an N400 but an anteriorly distributed P600 in response to temporal errors in event sequences. Thus, the N400 seems to be elicited as a response to a general mismatch between an event and the established event model. We assume that the expectancy violation of content event knowledge, as indicated by the N400, induces the collapse of the established event model, a process indicated by the posterior P600. The expectancy violation of temporal event knowledge is assumed to induce an attempt to reorganize the event model in working memory, a process indicated by the frontal P600. Copyright © 2015 Elsevier Ltd. All rights reserved.

Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing.

PubMed

Jäger, Marten; Ott, Claus-Eric; Grünhagen, Johannes; Hecht, Jochen; Schell, Hanna; Mundlos, Stefan; Duda, Georg N; Robinson, Peter N; Lienau, Jasmin

2011-03-24

The sheep is an important model organism for many types of medically relevant research, but molecular genetic experiments in the sheep have been limited by the lack of knowledge about ovine gene sequences. Prior to our study, mRNA sequences for only 1,556 partial or complete ovine genes were publicly available. Therefore, we developed a composite de novo transcriptome assembly method for next-generation sequence data to combine known ovine mRNA and EST sequences, mRNA sequences from mouse and cow, and sequences assembled de novo from short read RNA-Seq data into a composite reference transcriptome, and identified transcripts from over 12 thousand previously undescribed ovine genes. Gene expression analysis based on these data revealed substantially different expression profiles in standard versus delayed bone healing in an ovine tibial osteotomy model. Hundreds of transcripts were differentially expressed between standard and delayed healing and between the time points of the standard and delayed healing groups. We used the sheep sequences to design quantitative RT-PCR assays with which we validated the differential expression of 26 genes that had been identified by RNA-seq analysis. A number of clusters of characteristic expression profiles could be identified, some of which showed striking differences between the standard and delayed healing groups. Gene Ontology (GO) analysis showed that the differentially expressed genes were enriched in terms including extracellular matrix, cartilage development, contractile fiber, and chemokine activity. Our results provide a first atlas of gene expression profiles and differentially expressed genes in standard and delayed bone healing in a large-animal model and provide a number of clues as to the shifts in gene expression that underlie delayed bone healing. In the course of our study, we identified transcripts of 13,987 ovine genes, including 12,431 genes for which no sequence information was previously available. This information will provide a basis for future molecular research involving the sheep as a model organism.

Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing

PubMed Central

2011-01-01

Background The sheep is an important model organism for many types of medically relevant research, but molecular genetic experiments in the sheep have been limited by the lack of knowledge about ovine gene sequences. Results Prior to our study, mRNA sequences for only 1,556 partial or complete ovine genes were publicly available. Therefore, we developed a composite de novo transcriptome assembly method for next-generation sequence data to combine known ovine mRNA and EST sequences, mRNA sequences from mouse and cow, and sequences assembled de novo from short read RNA-Seq data into a composite reference transcriptome, and identified transcripts from over 12 thousand previously undescribed ovine genes. Gene expression analysis based on these data revealed substantially different expression profiles in standard versus delayed bone healing in an ovine tibial osteotomy model. Hundreds of transcripts were differentially expressed between standard and delayed healing and between the time points of the standard and delayed healing groups. We used the sheep sequences to design quantitative RT-PCR assays with which we validated the differential expression of 26 genes that had been identified by RNA-seq analysis. A number of clusters of characteristic expression profiles could be identified, some of which showed striking differences between the standard and delayed healing groups. Gene Ontology (GO) analysis showed that the differentially expressed genes were enriched in terms including extracellular matrix, cartilage development, contractile fiber, and chemokine activity. Conclusions Our results provide a first atlas of gene expression profiles and differentially expressed genes in standard and delayed bone healing in a large-animal model and provide a number of clues as to the shifts in gene expression that underlie delayed bone healing. In the course of our study, we identified transcripts of 13,987 ovine genes, including 12,431 genes for which no sequence information was previously available. This information will provide a basis for future molecular research involving the sheep as a model organism. PMID:21435219

Discovery of DNA viruses in wild-caught mosquitoes using small RNA high throughput sequencing.

PubMed

Ma, Maijuan; Huang, Yong; Gong, Zhengda; Zhuang, Lu; Li, Cun; Yang, Hong; Tong, Yigang; Liu, Wei; Cao, Wuchun

2011-01-01

Mosquito-borne infectious diseases pose a severe threat to public health in many areas of the world. Current methods for pathogen detection and surveillance are usually dependent on prior knowledge of the etiologic agents involved. Hence, efficient approaches are required for screening wild mosquito populations to detect known and unknown pathogens. In this study, we explored the use of Next Generation Sequencing to identify viral agents in wild-caught mosquitoes. We extracted total RNA from different mosquito species from South China. Small 18-30 bp length RNA molecules were purified, reverse-transcribed into cDNA and sequenced using Illumina GAIIx instrumentation. Bioinformatic analyses to identify putative viral agents were conducted and the results confirmed by PCR. We identified a non-enveloped single-stranded DNA densovirus in the wild-caught Culex pipiens molestus mosquitoes. The majority of the viral transcripts (.>80% of the region) were covered by the small viral RNAs, with a few peaks of very high coverage obtained. The +/- strand sequence ratio of the small RNAs was approximately 7∶1, indicating that the molecules were mainly derived from the viral RNA transcripts. The small viral RNAs overlapped, enabling contig assembly of the viral genome sequence. We identified some small RNAs in the reverse repeat regions of the viral 5'- and 3' -untranslated regions where no transcripts were expected. Our results demonstrate for the first time that high throughput sequencing of small RNA is feasible for identifying viral agents in wild-caught mosquitoes. Our results show that it is possible to detect DNA viruses by sequencing the small RNAs obtained from insects, although the underlying mechanism of small viral RNA biogenesis is unclear. Our data and those of other researchers show that high throughput small RNA sequencing can be used for pathogen surveillance in wild mosquito vectors.

A schema theory analysis of students' think aloud protocols in an STS biology context

NASA Astrophysics Data System (ADS)

Quinlan, Catherine Louise

This dissertation study is a conglomerate of the fields of Science Education and Applied Cognitive Psychology. The goal of this study is to determine what organizational features and knowledge representation patterns high school students exhibit over time for issues pertinent to science and society. Participants are thirteen tenth grade students in a diverse suburban-urban classroom in a northeastern state. Students' think alouds are recorded, pre-, post-, and late-post treatment. Treatment consists of instruction in three Science, Technology, and Society (STS) biology issues, namely the human genome project, nutrition and health, and stem cell research. Coding and analyses are performed using Marshall's knowledge representations---identification knowledge, elaboration knowledge, planning knowledge, and execution knowledge, as well as qualitative research analysis methods. Schema theory, information processing theory, and other applied cognitive theory provide a framework in which to understand and explain students' schema descriptions and progressions over time. The results show that students display five organizational features in their identification and elaboration knowledge. Students also fall into one of four categories according to if they display prior schema or no prior schema, and their orientation "for" or "against," some of the issues. Students with prior schema and orientation "against" display the most robust schema descriptions and schema progressions. Those with no prior schemas and orientation "against" show very modest schema progressions best characterized by their keyword searches. This study shows the importance in considering not only students' integrated schemas but also their individual schemes. A role for the use of a more schema-based instruction that scaffolds student learning is implicated.

Knowledge-based processing for aircraft flight control

NASA Technical Reports Server (NTRS)

Painter, John H.

1991-01-01

The purpose is to develop algorithms and architectures for embedding artificial intelligence in aircraft guidance and control systems. With the approach adopted, AI-computing is used to create an outer guidance loop for driving the usual aircraft autopilot. That is, a symbolic processor monitors the operation and performance of the aircraft. Then, based on rules and other stored knowledge, commands are automatically formulated for driving the autopilot so as to accomplish desired flight operations. The focus is on developing a software system which can respond to linguistic instructions, input in a standard format, so as to formulate a sequence of simple commands to the autopilot. The instructions might be a fairly complex flight clearance, input either manually or by data-link. Emphasis is on a software system which responds much like a pilot would, employing not only precise computations, but, also, knowledge which is less precise, but more like common-sense. The approach is based on prior work to develop a generic 'shell' architecture for an AI-processor, which may be tailored to many applications by describing the application in appropriate processor data bases (libraries). Such descriptions include numerical models of the aircraft and flight control system, as well as symbolic (linguistic) descriptions of flight operations, rules, and tactics.

Perceptual learning of degraded speech by minimizing prediction error.

PubMed

Sohoglu, Ediz; Davis, Matthew H

2016-03-22

Human perception is shaped by past experience on multiple timescales. Sudden and dramatic changes in perception occur when prior knowledge or expectations match stimulus content. These immediate effects contrast with the longer-term, more gradual improvements that are characteristic of perceptual learning. Despite extensive investigation of these two experience-dependent phenomena, there is considerable debate about whether they result from common or dissociable neural mechanisms. Here we test single- and dual-mechanism accounts of experience-dependent changes in perception using concurrent magnetoencephalographic and EEG recordings of neural responses evoked by degraded speech. When speech clarity was enhanced by prior knowledge obtained from matching text, we observed reduced neural activity in a peri-auditory region of the superior temporal gyrus (STG). Critically, longer-term improvements in the accuracy of speech recognition following perceptual learning resulted in reduced activity in a nearly identical STG region. Moreover, short-term neural changes caused by prior knowledge and longer-term neural changes arising from perceptual learning were correlated across subjects with the magnitude of learning-induced changes in recognition accuracy. These experience-dependent effects on neural processing could be dissociated from the neural effect of hearing physically clearer speech, which similarly enhanced perception but increased rather than decreased STG responses. Hence, the observed neural effects of prior knowledge and perceptual learning cannot be attributed to epiphenomenal changes in listening effort that accompany enhanced perception. Instead, our results support a predictive coding account of speech perception; computational simulations show how a single mechanism, minimization of prediction error, can drive immediate perceptual effects of prior knowledge and longer-term perceptual learning of degraded speech.

Perceptual learning of degraded speech by minimizing prediction error

PubMed Central

Sohoglu, Ediz

2016-01-01

Human perception is shaped by past experience on multiple timescales. Sudden and dramatic changes in perception occur when prior knowledge or expectations match stimulus content. These immediate effects contrast with the longer-term, more gradual improvements that are characteristic of perceptual learning. Despite extensive investigation of these two experience-dependent phenomena, there is considerable debate about whether they result from common or dissociable neural mechanisms. Here we test single- and dual-mechanism accounts of experience-dependent changes in perception using concurrent magnetoencephalographic and EEG recordings of neural responses evoked by degraded speech. When speech clarity was enhanced by prior knowledge obtained from matching text, we observed reduced neural activity in a peri-auditory region of the superior temporal gyrus (STG). Critically, longer-term improvements in the accuracy of speech recognition following perceptual learning resulted in reduced activity in a nearly identical STG region. Moreover, short-term neural changes caused by prior knowledge and longer-term neural changes arising from perceptual learning were correlated across subjects with the magnitude of learning-induced changes in recognition accuracy. These experience-dependent effects on neural processing could be dissociated from the neural effect of hearing physically clearer speech, which similarly enhanced perception but increased rather than decreased STG responses. Hence, the observed neural effects of prior knowledge and perceptual learning cannot be attributed to epiphenomenal changes in listening effort that accompany enhanced perception. Instead, our results support a predictive coding account of speech perception; computational simulations show how a single mechanism, minimization of prediction error, can drive immediate perceptual effects of prior knowledge and longer-term perceptual learning of degraded speech. PMID:26957596

The Role of Specificity, Targeted Learning Activities, and Prior Knowledge for the Effects of Relevance Instructions

ERIC Educational Resources Information Center

Roelle, Julian; Lehmkuhl, Nina; Beyer, Martin-Uwe; Berthold, Kirsten

2015-01-01

In 2 experiments we examined the role of (a) specificity, (b) the type of targeted learning activities, and (c) learners' prior knowledge for the effects of relevance instructions on learning from instructional explanations. In Experiment 1, we recruited novices regarding the topic of atomic structure (N = 80) and found that "specific"…

Effects of Prior Knowledge of Topics and the Instructional Objectives on Students' Achievement in Literature-in-English

ERIC Educational Resources Information Center

Mbah, Blessing Akaraka

2015-01-01

This study investigated the effects of prior knowledge of topics with their instructional objectives on senior secondary school class two (SS II) students. The study was carried out in Abakaliki Education Zone of Ebonyi State, Nigeria. The design of the study is quasi experimental of pretest-posttest of non-equivalent control group. Two research…

Polite Web-Based Intelligent Tutors: Can They Improve Learning in Classrooms?

ERIC Educational Resources Information Center

McLaren, Bruce M.; DeLeeuw, Krista E.; Mayer, Richard E.

2011-01-01

Should an intelligent software tutor be polite, in an effort to motivate and cajole students to learn, or should it use more direct language? If it should be polite, under what conditions? In a series of studies in different contexts (e.g., lab versus classroom) with a variety of students (e.g., low prior knowledge versus high prior knowledge),…

"She Has to Drink Blood of the Snake": Culture and Prior Knowledge in Science|Health Education

ERIC Educational Resources Information Center

Bricker, Leah A.; Reeve, Suzanne; Bell, Philip

2014-01-01

In this analysis, we argue that science education should attend more deeply to youths' cultural resources and practices (e.g. material, social, and intellectual). Inherent in our argument is a call for revisiting conceptions of "prior knowledge" to theorize how people make sense of the complex ecologies of experience, ideas, and cultural…

Effects of Different Types of True-False Questions on Memory Awareness and Long-Term Retention

ERIC Educational Resources Information Center

Schaap, Lydia; Verkoeijen, Peter; Schmidt, Henk

2014-01-01

This study investigated the effects of two different true-false questions on memory awareness and long-term retention of knowledge. Participants took four subsequent knowledge tests on curriculum learning material that they studied at different retention intervals prior to the start of this study (i.e. prior to the first test). At the first and…

Effects of Prior Knowledge and Concept-Map Structure on Disorientation, Cognitive Load, and Learning

ERIC Educational Resources Information Center

Amadieu, Franck; van Gog, Tamara; Paas, Fred; Tricot, Andre; Marine, Claudette

2009-01-01

This study explored the effects of prior knowledge (high vs. low; HPK and LPK) and concept-map structure (hierarchical vs. network; HS and NS) on disorientation, cognitive load, and learning from non-linear documents on "the infection process of a retrograde virus (HIV)". Participants in the study were 24 adults. Overall subjective ratings of…

Relevant Prior Knowledge Moderates the Effect of Elaboration during Small Group Discussion on Academic Achievement

ERIC Educational Resources Information Center

Van Blankenstein, Floris M.; Dolmans, Diana H. J. M.; Van der Vleuten, Cees P. M.; Schmidt, Henk G.

2013-01-01

This study set out to test whether relevant prior knowledge would moderate a positive effect on academic achievement of elaboration during small-group discussion. In a 2 × 2 experimental design, 66 undergraduate students observed a video showing a small-group problem-based discussion about thunder and lightning. In the video, a teacher asked…

The Mediation Effect of In-Game Performance between Prior Knowledge and Posttest Score. CRESST Report 819

ERIC Educational Resources Information Center

Kerr, Deirdre; Chung, Gregory K. W. K.

2012-01-01

Though video games are commonly considered to hold great potential as learning environments, their effectiveness as a teaching tool has yet to be determined. One reason for this is that researchers often run into the problem of multicollinearity between prior knowledge, in-game performance, and posttest scores, thereby making the determination of…

Developmental Change in the Influence of Domain-General Abilities and Domain-Specific Knowledge on Mathematics Achievement: An Eight-Year Longitudinal Study

ERIC Educational Resources Information Center

Geary, David C.; Nicholas, Alan; Li, Yaoran; Sun, Jianguo

2017-01-01

The contributions of domain-general abilities and domain-specific knowledge to subsequent mathematics achievement were longitudinally assessed (n = 167) through 8th grade. First grade intelligence and working memory and prior grade reading achievement indexed domain-general effects, and domain-specific effects were indexed by prior grade…

Blended Learning Based on Schoology: Effort of Improvement Learning Outcome and Practicum Chance in Vocational High School

ERIC Educational Resources Information Center

Irawan, Vincentius Tjandra; Sutadji, Eddy; Widiyanti

2017-01-01

The aims of this study were to determine: (1) the differences in learning outcome between Blended Learning based on Schoology and Problem-Based Learning, (2) the differences in learning outcome between students with prior knowledge of high, medium, and low, and (3) the interaction between Blended Learning based on Schoology and prior knowledge to…

Why is a Pomegranate an Apple? The Role of Shape, Taxonomic Relatedness, and Prior Lexical Knowledge in Children's Overextensions of "Apple" and "Dog."

ERIC Educational Resources Information Center

Gelman, Susan A.; Croft, William; Fu, Panfang; Clausner, Timothy; Gottfried, Gail

1998-01-01

Examined how object shape, taxonomic relatedness, and prior lexical knowledge influenced children's overextensions (e.g., referring to pomegranates as apples). Researchers presented items that disentangled the three factors and used a novel comprehension task where children could indicate negative exemplars. Error patterns differed by task and by…

Building dynamical models from data and prior knowledge: the case of the first period-doubling bifurcation.

PubMed

Aguirre, Luis Antonio; Furtado, Edgar Campos

2007-10-01

This paper reviews some aspects of nonlinear model building from data with (gray box) and without (black box) prior knowledge. The model class is very important because it determines two aspects of the final model, namely (i) the type of nonlinearity that can be accurately approximated and (ii) the type of prior knowledge that can be taken into account. Such features are usually in conflict when it comes to choosing the model class. The problem of model structure selection is also reviewed. It is argued that such a problem is philosophically different depending on the model class and it is suggested that the choice of model class should be performed based on the type of a priori available. A procedure is proposed to build polynomial models from data on a Poincaré section and prior knowledge about the first period-doubling bifurcation, for which the normal form is also polynomial. The final models approximate dynamical data in a least-squares sense and, by design, present the first period-doubling bifurcation at a specified value of parameters. The procedure is illustrated by means of simulated examples.

Mixture class recovery in GMM under varying degrees of class separation: frequentist versus Bayesian estimation.

PubMed

Depaoli, Sarah

2013-06-01

Growth mixture modeling (GMM) represents a technique that is designed to capture change over time for unobserved subgroups (or latent classes) that exhibit qualitatively different patterns of growth. The aim of the current article was to explore the impact of latent class separation (i.e., how similar growth trajectories are across latent classes) on GMM performance. Several estimation conditions were compared: maximum likelihood via the expectation maximization (EM) algorithm and the Bayesian framework implementing diffuse priors, "accurate" informative priors, weakly informative priors, data-driven informative priors, priors reflecting partial-knowledge of parameters, and "inaccurate" (but informative) priors. The main goal was to provide insight about the optimal estimation condition under different degrees of latent class separation for GMM. Results indicated that optimal parameter recovery was obtained though the Bayesian approach using "accurate" informative priors, and partial-knowledge priors showed promise for the recovery of the growth trajectory parameters. Maximum likelihood and the remaining Bayesian estimation conditions yielded poor parameter recovery for the latent class proportions and the growth trajectories. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Using Genetic Programming with Prior Formula Knowledge to Solve Symbolic Regression Problem.

PubMed

Lu, Qiang; Ren, Jun; Wang, Zhiguang

2016-01-01

A researcher can infer mathematical expressions of functions quickly by using his professional knowledge (called Prior Knowledge). But the results he finds may be biased and restricted to his research field due to limitation of his knowledge. In contrast, Genetic Programming method can discover fitted mathematical expressions from the huge search space through running evolutionary algorithms. And its results can be generalized to accommodate different fields of knowledge. However, since GP has to search a huge space, its speed of finding the results is rather slow. Therefore, in this paper, a framework of connection between Prior Formula Knowledge and GP (PFK-GP) is proposed to reduce the space of GP searching. The PFK is built based on the Deep Belief Network (DBN) which can identify candidate formulas that are consistent with the features of experimental data. By using these candidate formulas as the seed of a randomly generated population, PFK-GP finds the right formulas quickly by exploring the search space of data features. We have compared PFK-GP with Pareto GP on regression of eight benchmark problems. The experimental results confirm that the PFK-GP can reduce the search space and obtain the significant improvement in the quality of SR.

PRIOR-WK&E: Social Software for Policy Making in the Knowledge Society

NASA Astrophysics Data System (ADS)

Turón, Alberto; Aguarón, Juan; Escobar, María Teresa; Gallardo, Carolina; Moreno-Jiménez, José María; Salazar, José Luis

This paper presents a social software application denominated as PRIOR-WK&E. It has been developed by the Zaragoza Multicriteria Decision Making Group (GDMZ) with the aim of responding to the challenges of policy making in the Knowledge Society. Three specific modules have been added to PRIOR, the collaborative tool used by the research group (GDMZ) for considering the multicriteria selection of a discrete set of alternatives. The first module (W), that deals with multiactor decision making through the Web, and the second (K), that concerns the extraction and diffusion of knowledge related to the scientific resolution of the problem, were explained in [1]. The new application strengthens securitization and includes a third module (E) that evaluates the effectiveness of public administrations policy making.

Prior probability modulates anticipatory activity in category-specific areas.

PubMed

Trapp, Sabrina; Lepsien, Jöran; Kotz, Sonja A; Bar, Moshe

2016-02-01

Bayesian models are currently a dominant framework for describing human information processing. However, it is not clear yet how major tenets of this framework can be translated to brain processes. In this study, we addressed the neural underpinning of prior probability and its effect on anticipatory activity in category-specific areas. Before fMRI scanning, participants were trained in two behavioral sessions to learn the prior probability and correct order of visual events within a sequence. The events of each sequence included two different presentations of a geometric shape and one picture of either a house or a face, which appeared with either a high or a low likelihood. Each sequence was preceded by a cue that gave participants probabilistic information about which items to expect next. This allowed examining cue-related anticipatory modulation of activity as a function of prior probability in category-specific areas (fusiform face area and parahippocampal place area). Our findings show that activity in the fusiform face area was higher when faces had a higher prior probability. The finding of a difference between levels of expectations is consistent with graded, probabilistically modulated activity, but the data do not rule out the alternative explanation of a categorical neural response. Importantly, these differences were only visible during anticipation, and vanished at the time of stimulus presentation, calling for a functional distinction when considering the effects of prior probability. Finally, there were no anticipatory effects for houses in the parahippocampal place area, suggesting sensitivity to stimulus material when looking at effects of prediction.

Measuring Knowledge Elaboration Based on a Computer-Assisted Knowledge Map Analytical Approach to Collaborative Learning

ERIC Educational Resources Information Center

Zheng, Lanqin; Huang, Ronghuai; Hwang, Gwo-Jen; Yang, Kaicheng

2015-01-01

The purpose of this study is to quantitatively measure the level of knowledge elaboration and explore the relationships between prior knowledge of a group, group performance, and knowledge elaboration in collaborative learning. Two experiments were conducted to investigate the level of knowledge elaboration. The collaborative learning objective in…

Evaluation of the effect of polymorphism on G-quadruplex-ligand interaction by means of spectroscopic and chromatographic techniques

NASA Astrophysics Data System (ADS)

Benito, S.; Ferrer, A.; Benabou, S.; Aviñó, A.; Eritja, R.; Gargallo, R.

2018-05-01

Guanine-rich sequences may fold into highly ordered structures known as G-quadruplexes. Apart from the monomeric G-quadruplex, these sequences may form multimeric structures that are not usually considered when studying interaction with ligands. This work studies the interaction of a ligand, crystal violet, with three guanine-rich DNA sequences with the capacity to form multimeric structures. These sequences correspond to short stretches found near the promoter regions of c-kit and SMARCA4 genes. Instrumental techniques (circular dichroism, molecular fluorescence, size-exclusion chromatography and electrospray ionization mass spectrometry) and multivariate data analysis were used for this purpose. The polymorphism of G-quadruplexes was characterized prior to the interaction studies. The ligand was shown to interact preferentially with the monomeric G-quadruplex; the binding stoichiometry was 1:1 and the binding constant was in the order of 105 M-1 for all three sequences. The results highlight the importance of DNA treatment prior to interaction studies.

A Bayesian Assessment of Seismic Semi-Periodicity Forecasts

NASA Astrophysics Data System (ADS)

Nava, F.; Quinteros, C.; Glowacka, E.; Frez, J.

2016-01-01

Among the schemes for earthquake forecasting, the search for semi-periodicity during large earthquakes in a given seismogenic region plays an important role. When considering earthquake forecasts based on semi-periodic sequence identification, the Bayesian formalism is a useful tool for: (1) assessing how well a given earthquake satisfies a previously made forecast; (2) re-evaluating the semi-periodic sequence probability; and (3) testing other prior estimations of the sequence probability. A comparison of Bayesian estimates with updated estimates of semi-periodic sequences that incorporate new data not used in the original estimates shows extremely good agreement, indicating that: (1) the probability that a semi-periodic sequence is not due to chance is an appropriate estimate for the prior sequence probability estimate; and (2) the Bayesian formalism does a very good job of estimating corrected semi-periodicity probabilities, using slightly less data than that used for updated estimates. The Bayesian approach is exemplified explicitly by its application to the Parkfield semi-periodic forecast, and results are given for its application to other forecasts in Japan and Venezuela.

Superposing pure quantum states with partial prior information

NASA Astrophysics Data System (ADS)

Dogra, Shruti; Thomas, George; Ghosh, Sibasish; Suter, Dieter

2018-05-01

The principle of superposition is an intriguing feature of quantum mechanics, which is regularly exploited in many different circumstances. A recent work [M. Oszmaniec et al., Phys. Rev. Lett. 116, 110403 (2016), 10.1103/PhysRevLett.116.110403] shows that the fundamentals of quantum mechanics restrict the process of superimposing two unknown pure states, even though it is possible to superimpose two quantum states with partial prior knowledge. The prior knowledge imposes geometrical constraints on the choice of input states. We discuss an experimentally feasible protocol to superimpose multiple pure states of a d -dimensional quantum system and carry out an explicit experimental realization for two single-qubit pure states with partial prior information on a two-qubit NMR quantum information processor.

The Impacts of Virtual Manipulatives and Prior Knowledge on Geometry Learning Performance in Junior High School

ERIC Educational Resources Information Center

Lee, Chun-Yi; Chen, Ming-Jang

2014-01-01

Previous studies on the effects of virtual and physical manipulatives have failed to consider the impact of prior knowledge on the efficacy of manipulatives. This study focuses on the learning of plane geometry in junior high schools, including the sum of interior angles in polygons, the sum of exterior angles in polygons, and the properties of…

Exploring the Impact of Prior Knowledge and Appropriate Feedback on Students' Perceived Cognitive Load and Learning Outcomes: Animation-Based Earthquakes Instruction

ERIC Educational Resources Information Center

Yeh, Ting-Kuang; Tseng, Kuan-Yun; Cho, Chung-Wen; Barufaldi, James P.; Lin, Mei-Shin; Chang, Chun-Yen

2012-01-01

The aim of this study was to develop an animation-based curriculum and to evaluate the effectiveness of animation-based instruction; the report involved the assessment of prior knowledge and the appropriate feedback approach, for the purpose of reducing perceived cognitive load and improving learning. The curriculum was comprised of five subunits…

How Word Decoding, Vocabulary and Prior Topic Knowledge Predict Reading Comprehension. A Study of Language-Minority Students in Norwegian Fifth Grade Classrooms

ERIC Educational Resources Information Center

Rydland, Veslemoy; Aukrust, Vibeke Grover; Fulland, Helene

2012-01-01

This study examined the contribution of word decoding, first-language (L1) and second-language (L2) vocabulary and prior topic knowledge to L2 reading comprehension. For measuring reading comprehension we employed two different reading tasks: Woodcock Passage Comprehension and a researcher-developed content-area reading assignment (the Global…

The Effectiveness of Worked Examples Associated with Presentation Format and Prior Knowledge: A Web-Based Experiment

ERIC Educational Resources Information Center

Hsiao, E-Ling

2010-01-01

The aim of this study is to explore whether presentation format and prior knowledge affect the effectiveness of worked examples. The experiment was conducted through a specially designed online instrument. A 2X2X3 factorial before-and-after design was conducted. Three-way ANOVA was employed for data analysis. The result showed first, that prior…

Case-based reasoning for space applications: Utilization of prior experience in knowledge-based systems

NASA Technical Reports Server (NTRS)

King, James A.

1987-01-01

The goal is to explain Case-Based Reasoning as a vehicle to establish knowledge-based systems based on experimental reasoning for possible space applications. This goal will be accomplished through an examination of reasoning based on prior experience in a sample domain, and also through a presentation of proposed space applications which could utilize Case-Based Reasoning techniques.

Effects of Reading Ability, Prior Knowledge, Topic Interest, and Locus of Control on At-Risk College Students' Use of Graphic Organizers and Summarizing.

ERIC Educational Resources Information Center

Balajthy, Ernest; Weisberg, Renee

A study investigated the influence of key factors (general comprehension ability, prior knowledge of passage topic, interest in passage topic, and locus of control) on training at-risk college students in the use of graphic organizers as a cognitive learning strategy. Subjects, 60 college freshmen required to take a developmental reading/study…

Self-Monitoring and Knowledge-Building in Learning by Teaching

ERIC Educational Resources Information Center

Roscoe, Rod D.

2014-01-01

Prior research has established that learning by teaching depends upon peer tutors' engagement in knowledge-building, in which tutors integrate their knowledge and generate new knowledge through reasoning. However, many tutors adopt a "knowledge-telling bias" defined by shallow summarizing of source materials and didactic lectures.…

Lending a Helping Hand: Voluntary Engagement in Knowledge Sharing

ERIC Educational Resources Information Center

Mergel, Ines; Lazer, David; Binz-Scharf, Maria Christina

2008-01-01

Knowledge is essential for the functioning of every social system, especially for professionals in knowledge-intensive organisations. Since individuals do not possess all the work-related knowledge that they require, they turn to others in search for that knowledge. While prior research has mainly focused on antecedents and consequences of…

Science Literacy and Prior Knowledge of Astronomy MOOC Students

NASA Astrophysics Data System (ADS)

Impey, Chris David; Buxner, Sanlyn; Wenger, Matthew; Formanek, Martin

2018-01-01

Many of science classes offered on Coursera fall into fall into the category of general education or general interest classes for lifelong learners, including our own, Astronomy: Exploring Time and Space. Very little is known about the backgrounds and prior knowledge of these students. In this talk we present the results of a survey of our Astronomy MOOC students. We also compare these results to our previous work on undergraduate students in introductory astronomy courses. Survey questions examined student demographics and motivations as well as their science and information literacy (including basic science knowledge, interest, attitudes and beliefs, and where they get their information about science). We found that our MOOC students are different than the undergraduate students in more ways than demographics. Many MOOC students demonstrated high levels of science and information literacy. With a more comprehensive understanding of our students’ motivations and prior knowledge about science and how they get their information about science, we will be able to develop more tailored learning experiences for these lifelong learners.

Genome Sequencing and Analysis of Geographically Diverse Clinical Isolates of Herpes Simplex Virus 2

PubMed Central

Lamers, Susanna L.; Weiner, Brian; Ray, Stuart C.; Colgrove, Robert C.; Diaz, Fernando; Jing, Lichen; Wang, Kening; Saif, Sakina; Young, Sarah; Henn, Matthew; Laeyendecker, Oliver; Tobian, Aaron A. R.; Cohen, Jeffrey I.; Koelle, David M.; Quinn, Thomas C.; Knipe, David M.

2015-01-01

ABSTRACT Herpes simplex virus 2 (HSV-2), the principal causative agent of recurrent genital herpes, is a highly prevalent viral infection worldwide. Limited information is available on the amount of genomic DNA variation between HSV-2 strains because only two genomes have been determined, the HG52 laboratory strain and the newly sequenced SD90e low-passage-number clinical isolate strain, each from a different geographical area. In this study, we report the nearly complete genome sequences of 34 HSV-2 low-passage-number and laboratory strains, 14 of which were collected in Uganda, 1 in South Africa, 11 in the United States, and 8 in Japan. Our analyses of these genomes demonstrated remarkable sequence conservation, regardless of geographic origin, with the maximum nucleotide divergence between strains being 0.4% across the genome. In contrast, prior studies indicated that HSV-1 genomes exhibit more sequence diversity, as well as geographical clustering. Additionally, unlike HSV-1, little viral recombination between HSV-2 strains could be substantiated. These results are interpreted in light of HSV-2 evolution, epidemiology, and pathogenesis. Finally, the newly generated sequences more closely resemble the low-passage-number SD90e than HG52, supporting the use of the former as the new reference genome of HSV-2. IMPORTANCE Herpes simplex virus 2 (HSV-2) is a causative agent of genital and neonatal herpes. Therefore, knowledge of its DNA genome and genetic variability is central to preventing and treating genital herpes. However, only two full-length HSV-2 genomes have been reported. In this study, we sequenced 34 additional HSV-2 low-passage-number and laboratory viral genomes and initiated analysis of the genetic diversity of HSV-2 strains from around the world. The analysis of these genomes will facilitate research aimed at vaccine development, diagnosis, and the evaluation of clinical manifestations and transmission of HSV-2. This information will also contribute to our understanding of HSV evolution. PMID:26018166

Pyrosequencing®-Based Identification of Low-Frequency Mutations Enriched Through Enhanced-ice-COLD-PCR.

PubMed

How-Kit, Alexandre; Tost, Jörg

2015-01-01

A number of molecular diagnostic assays have been developed in the last years for mutation detection. Although these methods have become increasingly sensitive, most of them are incompatible with a sequencing-based readout and require prior knowledge of the mutation present in the sample. Consequently, coamplification at low denaturation (COLD)-PCR-based methods have been developed and combine a high analytical sensitivity due to mutation enrichment in the sample with the identification of known or unknown mutations by downstream sequencing experiments. Among these methods, the recently developed Enhanced-ice-COLD-PCR appeared as the most powerful method as it outperformed the other COLD-PCR-based methods in terms of the mutation enrichment and due to the simplicity of the experimental setup of the assay. Indeed, E-ice-COLD-PCR is very versatile as it can be used on all types of PCR platforms and is applicable to different types of samples including fresh frozen, FFPE, and plasma samples. The technique relies on the incorporation of an LNA containing blocker probe in the PCR reaction followed by selective heteroduplex denaturation enabling amplification of the mutant allele while amplification of the wild-type allele is prevented. Combined with Pyrosequencing(®), which is a very quantitative high-resolution sequencing technology, E-ice-COLD-PCR can detect and identify mutations with a limit of detection down to 0.01 %.

Absolute quantification of Medicago truncatula sucrose synthase isoforms and N-metabolism enzymes in symbiotic root nodules and the detection of novel nodule phosphoproteins by mass spectrometry

PubMed Central

Wienkoop, Stefanie; Larrainzar, Estíbaliz; Glinski, Mirko; González, Esther M.; Arrese-Igor, Cesar; Weckwerth, Wolfram

2008-01-01

Mass spectrometry (MS) has become increasingly important for tissue specific protein quantification at the isoform level, as well as for the analysis of protein post-translational regulation mechanisms and turnover rates. Thanks to the development of high accuracy mass spectrometers, peptide sequencing without prior knowledge of the amino acid sequence—de novo sequencing—can be performed. In this work, absolute quantification of a set of key enzymes involved in carbon and nitrogen metabolism in Medicago truncatula ‘Jemalong A17’ root nodules is presented. Among them, sucrose synthase (SuSy; EC 2.4.1.13), one of the central enzymes in sucrose cleavage in root nodules, has been further characterized and the relative phosphorylation state of the three most abundant isoforms has been quantified. De novo sequencing provided sequence information of a so far unidentified peptide, most probably belonging to SuSy2, the second most abundant isoform in M. truncatula root nodules. TiO2-phosphopeptide enrichment led to the identification of not only a phosphorylation site at Ser11 in SuSy1, but also of several novel phosphorylation sites present in other root nodule proteins such as alkaline invertase (AI; EC 3.2.1.26) and an RNA-binding protein. PMID:18772307

Experimental evolution reveals genome-wide spectrum and dynamics of mutations in the rice blast fungus, Magnaporthe oryzae.

PubMed

Jeon, Junhyun; Choi, Jaeyoung; Lee, Gir-Won; Dean, Ralph A; Lee, Yong-Hwan

2013-01-01

Knowledge on mutation processes is central to interpreting genetic analysis data as well as understanding the underlying nature of almost all evolutionary phenomena. However, studies on genome-wide mutational spectrum and dynamics in fungal pathogens are scarce, hindering our understanding of their evolution and biology. Here, we explored changes in the phenotypes and genome sequences of the rice blast fungus Magnaporthe oryzae during the forced in vitro evolution by weekly transfer of cultures on artificial media. Through combination of experimental evolution with high throughput sequencing technology, we found that mutations accumulate rapidly prior to visible phenotypic changes and that both genetic drift and selection seem to contribute to shaping mutational landscape, suggesting the buffering capacity of fungal genome against mutations. Inference of mutational effects on phenotypes through the use of T-DNA insertion mutants suggested that at least some of the DNA sequence mutations are likely associated with the observed phenotypic changes. Furthermore, our data suggest oxidative damages and UV as major sources of mutation during subcultures. Taken together, our work revealed important properties of original source of variation in the genome of the rice blast fungus. We believe that these results provide not only insights into stability of pathogenicity and genome evolution in plant pathogenic fungi but also a model in which evolution of fungal pathogens in natura can be comparatively investigated.

Automatic 3D reconstruction of electrophysiology catheters from two-view monoplane C-arm image sequences.

PubMed

Baur, Christoph; Milletari, Fausto; Belagiannis, Vasileios; Navab, Nassir; Fallavollita, Pascal

2016-07-01

Catheter guidance is a vital task for the success of electrophysiology interventions. It is usually provided through fluoroscopic images that are taken intra-operatively. The cardiologists, who are typically equipped with C-arm systems, scan the patient from multiple views rotating the fluoroscope around one of its axes. The resulting sequences allow the cardiologists to build a mental model of the 3D position of the catheters and interest points from the multiple views. We describe and compare different 3D catheter reconstruction strategies and ultimately propose a novel and robust method for the automatic reconstruction of 3D catheters in non-synchronized fluoroscopic sequences. This approach does not purely rely on triangulation but incorporates prior knowledge about the catheters. In conjunction with an automatic detection method, we demonstrate the performance of our method compared to ground truth annotations. In our experiments that include 20 biplane datasets, we achieve an average reprojection error of 0.43 mm and an average reconstruction error of 0.67 mm compared to gold standard annotation. In clinical practice, catheters suffer from complex motion due to the combined effect of heartbeat and respiratory motion. As a result, any 3D reconstruction algorithm via triangulation is imprecise. We have proposed a new method that is fully automatic and highly accurate to reconstruct catheters in three dimensions.

Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB)

NASA Astrophysics Data System (ADS)

Ghani, Nur Syatila Ab; Firdaus-Raih, Mohd

2018-04-01

The three-dimensional structure of a protein can provide insights regarding its function. Functional relationship between proteins can be inferred from fold and sequence similarities. In certain cases, sequence or fold comparison fails to conclude homology between proteins with similar mechanism. Since the structure is more conserved than the sequence, a constellation of functional residues can be similarly arranged among proteins of similar mechanism. Local structural similarity searches are able to detect such constellation of amino acids among distinct proteins, which can be useful to annotate proteins of unknown function. Detection of such patterns of amino acids on a large scale can increase the repertoire of important 3D motifs since available known 3D motifs currently, could not compensate the ever-increasing numbers of uncharacterized proteins to be annotated. Here, a computational platform for an automated detection of 3D motifs is described. A fuzzy-pattern searching algorithm derived from IMagine an Amino Acid 3D Arrangement search EnGINE (IMAAAGINE) was implemented to develop an automated method for searching of hypothetical patterns of amino acid side chains in Protein Data Bank (PDB), without the need for prior knowledge on related sequence or structure of pattern of interest. We present an example of the searches, which is the detection of a hypothetical pattern derived from known structural motif of C2H2 structural pattern from zinc fingers. The conservation of particular patterns of amino acid side chains in unrelated proteins is highlighted. This approach can act as a complementary method for available structure- and sequence-based platforms and may contribute in improving functional association between proteins.

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data.

PubMed

de Andrade, Roberto R S; Vaslin, Maite F S

2014-03-07

Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/.

SearchSmallRNA: a graphical interface tool for the assemblage of viral genomes using small RNA libraries data

PubMed Central

2014-01-01

Background Next-generation parallel sequencing (NGS) allows the identification of viral pathogens by sequencing the small RNAs of infected hosts. Thus, viral genomes may be assembled from host immune response products without prior virus enrichment, amplification or purification. However, mapping of the vast information obtained presents a bioinformatics challenge. Methods In order to by pass the need of line command and basic bioinformatics knowledge, we develop a mapping software with a graphical interface to the assemblage of viral genomes from small RNA dataset obtained by NGS. SearchSmallRNA was developed in JAVA language version 7 using NetBeans IDE 7.1 software. The program also allows the analysis of the viral small interfering RNAs (vsRNAs) profile; providing an overview of the size distribution and other features of the vsRNAs produced in infected cells. Results The program performs comparisons between each read sequenced present in a library and a chosen reference genome. Reads showing Hamming distances smaller or equal to an allowed mismatched will be selected as positives and used to the assemblage of a long nucleotide genome sequence. In order to validate the software, distinct analysis using NGS dataset obtained from HIV and two plant viruses were used to reconstruct viral whole genomes. Conclusions SearchSmallRNA program was able to reconstructed viral genomes using NGS of small RNA dataset with high degree of reliability so it will be a valuable tool for viruses sequencing and discovery. It is accessible and free to all research communities and has the advantage to have an easy-to-use graphical interface. Availability and implementation SearchSmallRNA was written in Java and is freely available at http://www.microbiologia.ufrj.br/ssrna/. PMID:24607237

Mapping the physical network of cellular interactions.

PubMed

Boisset, Jean-Charles; Vivié, Judith; Grün, Dominic; Muraro, Mauro J; Lyubimova, Anna; van Oudenaarden, Alexander

2018-05-21

A cell's function is influenced by the environment, or niche, in which it resides. Studies of niches usually require assumptions about the cell types present, which impedes the discovery of new cell types or interactions. Here we describe ProximID, an approach for building a cellular network based on physical cell interaction and single-cell mRNA sequencing, and show that it can be used to discover new preferential cellular interactions without prior knowledge of component cell types. ProximID found specific interactions between megakaryocytes and mature neutrophils and between plasma cells and myeloblasts and/or promyelocytes (precursors of neutrophils) in mouse bone marrow, and it identified a Tac1 + enteroendocrine cell-Lgr5 + stem cell interaction in small intestine crypts. This strategy can be used to discover new niches or preferential interactions in a variety of organs.

Rapid measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides.

PubMed

Barnwal, Ravi Pratap; Rout, Ashok K; Chary, Kandala V R; Atreya, Hanudatta S

2007-12-01

We present two NMR experiments, (3,2)D HNHA and (3,2)D HNHB, for rapid and accurate measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides based on the principle of G-matrix Fourier transform NMR spectroscopy and quantitative J-correlation. These experiments, which facilitate fast acquisition of three-dimensional data with high spectral/digital resolution and chemical shift dispersion, will provide renewed opportunities to utilize them for sequence specific resonance assignments, estimation/characterization of secondary structure with/without prior knowledge of resonance assignments, stereospecific assignment of prochiral groups and 3D structure determination, refinement and validation. Taken together, these experiments have a wide range of applications from structural genomics projects to studying structure and folding in polypeptides.

Fusion of Building Information and Range Imaging for Autonomous Location Estimation in Indoor Environments

PubMed Central

Kohoutek, Tobias K.; Mautz, Rainer; Wegner, Jan D.

2013-01-01

We present a novel approach for autonomous location estimation and navigation in indoor environments using range images and prior scene knowledge from a GIS database (CityGML). What makes this task challenging is the arbitrary relative spatial relation between GIS and Time-of-Flight (ToF) range camera further complicated by a markerless configuration. We propose to estimate the camera's pose solely based on matching of GIS objects and their detected location in image sequences. We develop a coarse-to-fine matching strategy that is able to match point clouds without any initial parameters. Experiments with a state-of-the-art ToF point cloud show that our proposed method delivers an absolute camera position with decimeter accuracy, which is sufficient for many real-world applications (e.g., collision avoidance). PMID:23435055

ESOC activities during the MIR de-orbit

NASA Astrophysics Data System (ADS)

Klinkrad, H.; Flury, W.; Hernández, C.; Landgraf, M.; Jehn, R.; Christ, U.; Sintoni, F.

2002-11-01

On March 23, 2001, MIR was de-orbited in a controlled fashion, following a successful mission of 15 years. The de-orbiting operations were conducted by the TsUP Mission Control Center, who also consulted entities outside Russia, in order to consolidate their knowledge on the MIR orbit and attitude prior to the initiation of the de-orbit sequence. The European Space Agency ESA through their operations centre ESOC was tasked to support the pre-entry analysis of TsUP by own results, and by routing of Russian and European data via a dedicated communications network. Analysis results produced by ESOC, and details on the data exchange will be highlighted in this paper. The MIR de-orbit and its assessed risk potential will also be compared with the re-entries of Skylab and Salyut-7/Kosmos-1686.

Atypical combinations and scientific impact.

PubMed

Uzzi, Brian; Mukherjee, Satyam; Stringer, Michael; Jones, Ben

2013-10-25

Novelty is an essential feature of creative ideas, yet the building blocks of new ideas are often embodied in existing knowledge. From this perspective, balancing atypical knowledge with conventional knowledge may be critical to the link between innovativeness and impact. Our analysis of 17.9 million papers spanning all scientific fields suggests that science follows a nearly universal pattern: The highest-impact science is primarily grounded in exceptionally conventional combinations of prior work yet simultaneously features an intrusion of unusual combinations. Papers of this type were twice as likely to be highly cited works. Novel combinations of prior work are rare, yet teams are 37.7% more likely than solo authors to insert novel combinations into familiar knowledge domains.

Automatized spleen segmentation in non-contrast-enhanced MR volume data using subject-specific shape priors

NASA Astrophysics Data System (ADS)

Gloger, Oliver; Tönnies, Klaus; Bülow, Robin; Völzke, Henry

2017-07-01

To develop the first fully automated 3D spleen segmentation framework derived from T1-weighted magnetic resonance (MR) imaging data and to verify its performance for spleen delineation and volumetry. This approach considers the issue of low contrast between spleen and adjacent tissue in non-contrast-enhanced MR images. Native T1-weighted MR volume data was performed on a 1.5 T MR system in an epidemiological study. We analyzed random subsamples of MR examinations without pathologies to develop and verify the spleen segmentation framework. The framework is modularized to include different kinds of prior knowledge into the segmentation pipeline. Classification by support vector machines differentiates between five different shape types in computed foreground probability maps and recognizes characteristic spleen regions in axial slices of MR volume data. A spleen-shape space generated by training produces subject-specific prior shape knowledge that is then incorporated into a final 3D level set segmentation method. Individually adapted shape-driven forces as well as image-driven forces resulting from refined foreground probability maps steer the level set successfully to the segment the spleen. The framework achieves promising segmentation results with mean Dice coefficients of nearly 0.91 and low volumetric mean errors of 6.3%. The presented spleen segmentation approach can delineate spleen tissue in native MR volume data. Several kinds of prior shape knowledge including subject-specific 3D prior shape knowledge can be used to guide segmentation processes achieving promising results.

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

ERIC Educational Resources Information Center

Dobozy, Eva

2012-01-01

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

The Role of "Creative Transfer" in Professional Transitions

ERIC Educational Resources Information Center

Triantafyllaki, Angeliki

2016-01-01

This paper discusses the concept of "knowledge transfer" in terms of expansion of prior knowledge, creativity and approaches to generating new knowledge. It explores professional transitions in which knowledge restructuring and identity reformation are pathways into greater work flexibility and adjustment. Two studies, exploring…

Effects of Process-Oriented and Product-Oriented Worked Examples and Prior Knowledge on Learner Problem Solving and Attitude: A Study in the Domain of Microeconomics

ERIC Educational Resources Information Center

Brooks, Christopher Darren

2009-01-01

The purpose of this study was to investigate the effectiveness of process-oriented and product-oriented worked example strategies and the mediating effect of prior knowledge (high versus low) on problem solving and learner attitude in the domain of microeconomics. In addition, the effect of these variables on learning efficiency as well as the…

Influence of Prior Knowledge and Interest on Fourth- and Fifth-Grade Passage Comprehension on the Qualitative Reading Inventory-4

ERIC Educational Resources Information Center

Clark, Mary Kristen; Kamhi, Alan G.

2014-01-01

Purpose: In 2 experiments, we examined the influence of prior knowledge and interest on 4th- and 5th-grade students' passage comprehension scores on the Qualitative Reading Inventory-4 (QRI-4) and 2 experimenter constructed passages. Method: In Experiment 1, 4th- and 5th-grade students were administered 4 Level 4 passages or 4 Level 5…

Effects of Type of Exploratory Strategy and Prior Knowledge on Middle School Students' Learning of Chemical Formulas from a 3D Role-Playing Game

ERIC Educational Resources Information Center

Chen, Ming-Puu; Wong, Yu-Ting; Wang, Li-Chun

2014-01-01

The purpose of this study was to examine the effects of the type of exploratory strategy and level of prior knowledge on middle school students' performance and motivation in learning chemical formulas via a 3D role-playing game (RPG). Two types of exploratory strategies-RPG exploratory with worked-example and RPG exploratory without…

Counting-On, Trading and Partitioning: Effects of Training and Prior Knowledge on Performance on Base-10 Tasks

ERIC Educational Resources Information Center

Saxton, Matthew; Cakir, Kadir

2006-01-01

Factors affecting performance on base-10 tasks were investigated in a series of four studies with a total of 453 children aged 5-7 years. Training in counting-on was found to enhance child performance on base-10 tasks (Studies 2, 3, and 4), while prior knowledge of counting-on (Study 1), trading (Studies 1 and 3), and partitioning (Studies 1 and…

Efficient Genotyping of KRAS Mutant Non-Small Cell Lung Cancer Using a Multiplexed Droplet Digital PCR Approach.

PubMed

Pender, Alexandra; Garcia-Murillas, Isaac; Rana, Sareena; Cutts, Rosalind J; Kelly, Gavin; Fenwick, Kerry; Kozarewa, Iwanka; Gonzalez de Castro, David; Bhosle, Jaishree; O'Brien, Mary; Turner, Nicholas C; Popat, Sanjay; Downward, Julian

2015-01-01

Droplet digital PCR (ddPCR) can be used to detect low frequency mutations in oncogene-driven lung cancer. The range of KRAS point mutations observed in NSCLC necessitates a multiplex approach to efficient mutation detection in circulating DNA. Here we report the design and optimisation of three discriminatory ddPCR multiplex assays investigating nine different KRAS mutations using PrimePCR™ ddPCR™ Mutation Assays and the Bio-Rad QX100 system. Together these mutations account for 95% of the nucleotide changes found in KRAS in human cancer. Multiplex reactions were optimised on genomic DNA extracted from KRAS mutant cell lines and tested on DNA extracted from fixed tumour tissue from a cohort of lung cancer patients without prior knowledge of the specific KRAS genotype. The multiplex ddPCR assays had a limit of detection of better than 1 mutant KRAS molecule in 2,000 wild-type KRAS molecules, which compared favourably with a limit of detection of 1 in 50 for next generation sequencing and 1 in 10 for Sanger sequencing. Multiplex ddPCR assays thus provide a highly efficient methodology to identify KRAS mutations in lung adenocarcinoma.

Efficient Genotyping of KRAS Mutant Non-Small Cell Lung Cancer Using a Multiplexed Droplet Digital PCR Approach

PubMed Central

Pender, Alexandra; Garcia-Murillas, Isaac; Rana, Sareena; Cutts, Rosalind J.; Kelly, Gavin; Fenwick, Kerry; Kozarewa, Iwanka; Gonzalez de Castro, David; Bhosle, Jaishree; O’Brien, Mary; Turner, Nicholas C.; Popat, Sanjay; Downward, Julian

2015-01-01

Droplet digital PCR (ddPCR) can be used to detect low frequency mutations in oncogene-driven lung cancer. The range of KRAS point mutations observed in NSCLC necessitates a multiplex approach to efficient mutation detection in circulating DNA. Here we report the design and optimisation of three discriminatory ddPCR multiplex assays investigating nine different KRAS mutations using PrimePCR™ ddPCR™ Mutation Assays and the Bio-Rad QX100 system. Together these mutations account for 95% of the nucleotide changes found in KRAS in human cancer. Multiplex reactions were optimised on genomic DNA extracted from KRAS mutant cell lines and tested on DNA extracted from fixed tumour tissue from a cohort of lung cancer patients without prior knowledge of the specific KRAS genotype. The multiplex ddPCR assays had a limit of detection of better than 1 mutant KRAS molecule in 2,000 wild-type KRAS molecules, which compared favourably with a limit of detection of 1 in 50 for next generation sequencing and 1 in 10 for Sanger sequencing. Multiplex ddPCR assays thus provide a highly efficient methodology to identify KRAS mutations in lung adenocarcinoma. PMID:26413866

New enzymes from environmental cassette arrays: Functional attributes of a phosphotransferase and an RNA-methyltransferase

PubMed Central

Nield, Blair S.; Willows, Robert D.; Torda, Andrew E.; Gillings, Michael R.; Holmes, Andrew J.; Nevalainen, K.M. Helena; Stokes, H.W.; Mabbutt, Bridget C.

2004-01-01

By targeting gene cassettes by polymerase chain reaction (PCR) directly from environmentally derived DNA, we are able to amplify entire open reading frames (ORFs) independently of prior sequence knowledge. Approximately 10% of the mobile genes recovered by these means can be attributed to known protein families. Here we describe the characterization of two ORFs which show moderate homology to known proteins: (1) an aminoglycoside phosphotransferase displaying 25% sequence identity with APH(7″) from Streptomyces hygroscopicus, and (2) an RNA methyltransferase sharing 25%–28% identity with a group of recently defined bacterial RNA methyltransferases distinct from the SpoU enzyme family. Our novel genes were expressed as recombinant products and assayed for appropriate enzyme activity. The aminoglycoside phosphotransferase displayed ATPase activity, consistent with the presence of characteristic Mg2+-binding residues. Unlike related APH(4) or APH(7″) enzymes, however, this activity was not enhanced by hygromycin B or kanamycin, suggesting the normal substrate to be a different aminoglycoside. The RNA methyltransferase contains sequence motifs of the RNA methyltransferase superfamily, and our recombinant version showed methyltransferase activity with RNA. Our data confirm that gene cassettes present in the environment encode folded enzymes with novel sequence variation and demonstrable catalytic activity. Our PCR approach (cassette PCR) may be used to identify a diverse range of ORFs from any environmental sample, as well as to directly access the gene pool found in mobile gene cassettes commonly associated with integrons. This gene pool can be accessed from both cultured and uncultured microbial samples as a source of new enzymes and proteins. PMID:15152095

New enzymes from environmental cassette arrays: functional attributes of a phosphotransferase and an RNA-methyltransferase.

PubMed

Nield, Blair S; Willows, Robert D; Torda, Andrew E; Gillings, Michael R; Holmes, Andrew J; Nevalainen, K M Helena; Stokes, H W; Mabbutt, Bridget C

2004-06-01

By targeting gene cassettes by polymerase chain reaction (PCR) directly from environmentally derived DNA, we are able to amplify entire open reading frames (ORFs) independently of prior sequence knowledge. Approximately 10% of the mobile genes recovered by these means can be attributed to known protein families. Here we describe the characterization of two ORFs which show moderate homology to known proteins: (1) an aminoglycoside phosphotransferase displaying 25% sequence identity with APH(7") from Streptomyces hygroscopicus, and (2) an RNA methyltransferase sharing 25%-28% identity with a group of recently defined bacterial RNA methyltransferases distinct from the SpoU enzyme family. Our novel genes were expressed as recombinant products and assayed for appropriate enzyme activity. The aminoglycoside phosphotransferase displayed ATPase activity, consistent with the presence of characteristic Mg(2+)-binding residues. Unlike related APH(4) or APH(7") enzymes, however, this activity was not enhanced by hygromycin B or kanamycin, suggesting the normal substrate to be a different aminoglycoside. The RNA methyltransferase contains sequence motifs of the RNA methyltransferase superfamily, and our recombinant version showed methyltransferase activity with RNA. Our data confirm that gene cassettes present in the environment encode folded enzymes with novel sequence variation and demonstrable catalytic activity. Our PCR approach (cassette PCR) may be used to identify a diverse range of ORFs from any environmental sample, as well as to directly access the gene pool found in mobile gene cassettes commonly associated with integrons. This gene pool can be accessed from both cultured and uncultured microbial samples as a source of new enzymes and proteins.

The Extension-Reduction Strategy: Activating Prior Knowledge

ERIC Educational Resources Information Center

Sloyer, Cliff W.

2004-01-01

A mathematical problem is solved using the extension-reduction or build it up-tear it down tactic. This technique is implemented in reviving students' earlier knowledge to enable them to apply this knowledge to solving new problems.

Interactive web-based learning modules prior to general medicine advanced pharmacy practice experiences.

PubMed

Isaacs, Alex N; Walton, Alison M; Nisly, Sarah A

2015-04-25

To implement and evaluate interactive web-based learning modules prior to advanced pharmacy practice experiences (APPEs) on inpatient general medicine. Three clinical web-based learning modules were developed for use prior to APPEs in 4 health care systems. The aim of the interactive modules was to strengthen baseline clinical knowledge before the APPE to enable the application of learned material through the delivery of patient care. For the primary endpoint, postassessment scores increased overall and for each individual module compared to preassessment scores. Postassessment scores were similar among the health care systems. The survey demonstrated positive student perceptions of this learning experience. Prior to inpatient general medicine APPEs, web-based learning enabled the standardization and assessment of baseline student knowledge across 4 health care systems.

Informative priors based on transcription factor structural class improve de novo motif discovery.

PubMed

Narlikar, Leelavati; Gordân, Raluca; Ohler, Uwe; Hartemink, Alexander J

2006-07-15

An important problem in molecular biology is to identify the locations at which a transcription factor (TF) binds to DNA, given a set of DNA sequences believed to be bound by that TF. In previous work, we showed that information in the DNA sequence of a binding site is sufficient to predict the structural class of the TF that binds it. In particular, this suggests that we can predict which locations in any DNA sequence are more likely to be bound by certain classes of TFs than others. Here, we argue that traditional methods for de novo motif finding can be significantly improved by adopting an informative prior probability that a TF binding site occurs at each sequence location. To demonstrate the utility of such an approach, we present priority, a powerful new de novo motif finding algorithm. Using data from TRANSFAC, we train three classifiers to recognize binding sites of basic leucine zipper, forkhead, and basic helix loop helix TFs. These classifiers are used to equip priority with three class-specific priors, in addition to a default prior to handle TFs of other classes. We apply priority and a number of popular motif finding programs to sets of yeast intergenic regions that are reported by ChIP-chip to be bound by particular TFs. priority identifies motifs the other methods fail to identify, and correctly predicts the structural class of the TF recognizing the identified binding sites. Supplementary material and code can be found at http://www.cs.duke.edu/~amink/.

Interplay between Content Knowledge and Scientific Argumentation

ERIC Educational Resources Information Center

Hakyolu, Hanife; Ogan-Bekiroglu, Feral

2016-01-01

This research study aimed to analyze the relationship between content knowledge and argumentation by examining students' prior subject matter knowledge and their production of arguments as well as by comparing students' arguments with their knowledge-in-use during scientific argumentation sessions. A correlational research design was carried out…

Creating Illusions of Knowledge: Learning Errors that Contradict Prior Knowledge

ERIC Educational Resources Information Center

Fazio, Lisa K.; Barber, Sarah J.; Rajaram, Suparna; Ornstein, Peter A.; Marsh, Elizabeth J.

2013-01-01

Most people know that the Pacific is the largest ocean on Earth and that Edison invented the light bulb. Our question is whether this knowledge is stable, or if people will incorporate errors into their knowledge bases, even if they have the correct knowledge stored in memory. To test this, we asked participants general-knowledge questions 2 weeks…

Estimating the cost of production stoppage

NASA Technical Reports Server (NTRS)

Delionback, L. M.

1979-01-01

Estimation model considers learning curve quantities, and time of break to forecast losses due to break in production schedule. Major parameters capable of predicting costs are number of units made prior to production sequence, length of production break, and slope of learning curve produced prior to break.

Profiles of Inconsistent Knowledge in Children's Pathways of Conceptual Change

ERIC Educational Resources Information Center

Schneider, Michael; Hardy, Ilonca

2013-01-01

Conceptual change requires learners to restructure parts of their conceptual knowledge base. Prior research has identified the fragmentation and the integration of knowledge as 2 important component processes of knowledge restructuring but remains unclear as to their relative importance and the time of their occurrence during development. Previous…

49 CFR 240.209 - Procedures for making the determination on knowledge.

Code of Federal Regulations, 2010 CFR

2010-10-01

... knowledge. 240.209 Section 240.209 Transportation Other Regulations Relating to Transportation (Continued... determination on knowledge. (a) Each railroad, prior to initially certifying or recertifying any person as an... with the requirements of § 240.125 of this part, demonstrated sufficient knowledge of the railroad's...

Activation of Background Knowledge for Inference Making: Effects on Reading Comprehension

ERIC Educational Resources Information Center

Elbro, Carsten; Buch-Iversen, Ida

2013-01-01

Failure to "activate" relevant, existing background knowledge may be a cause of poor reading comprehension. This failure may cause particular problems with inferences that depend heavily on prior knowledge. Conversely, teaching how to use background knowledge in the context of gap-filling inferences could improve reading comprehension in…

Building on prior knowledge without building it in.

PubMed

Hansen, Steven S; Lampinen, Andrew K; Suri, Gaurav; McClelland, James L

2017-01-01

Lake et al. propose that people rely on "start-up software," "causal models," and "intuitive theories" built using compositional representations to learn new tasks more efficiently than some deep neural network models. We highlight the many drawbacks of a commitment to compositional representations and describe our continuing effort to explore how the ability to build on prior knowledge and to learn new tasks efficiently could arise through learning in deep neural networks.

Smoothing Spline ANOVA Decomposition of Arbitrary Splines: An Application to Eye Movements in Reading

PubMed Central

Matuschek, Hannes; Kliegl, Reinhold; Holschneider, Matthias

2015-01-01

The Smoothing Spline ANOVA (SS-ANOVA) requires a specialized construction of basis and penalty terms in order to incorporate prior knowledge about the data to be fitted. Typically, one resorts to the most general approach using tensor product splines. This implies severe constraints on the correlation structure, i.e. the assumption of isotropy of smoothness can not be incorporated in general. This may increase the variance of the spline fit, especially if only a relatively small set of observations are given. In this article, we propose an alternative method that allows to incorporate prior knowledge without the need to construct specialized bases and penalties, allowing the researcher to choose the spline basis and penalty according to the prior knowledge of the observations rather than choosing them according to the analysis to be done. The two approaches are compared with an artificial example and with analyses of fixation durations during reading. PMID:25816246

Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data

PubMed Central

2014-01-01

Background High-throughput omics technologies have enabled the measurement of many genes or metabolites simultaneously. The resulting high dimensional experimental data poses significant challenges to transcriptomics and metabolomics data analysis methods, which may lead to spurious instead of biologically relevant results. One strategy to improve the results is the incorporation of prior biological knowledge in the analysis. This strategy is used to reduce the solution space and/or to focus the analysis on biological meaningful regions. In this article, we review a selection of these methods used in transcriptomics and metabolomics. We combine the reviewed methods in three groups based on the underlying mathematical model: exploratory methods, supervised methods and estimation of the covariance matrix. We discuss which prior knowledge has been used, how it is incorporated and how it modifies the mathematical properties of the underlying methods. PMID:25033193

Visual representations in science education: The influence of prior knowledge and cognitive load theory on instructional design principles

NASA Astrophysics Data System (ADS)

Cook, Michelle Patrick

2006-11-01

Visual representations are essential for communicating ideas in the science classroom; however, the design of such representations is not always beneficial for learners. This paper presents instructional design considerations providing empirical evidence and integrating theoretical concepts related to cognitive load. Learners have a limited working memory, and instructional representations should be designed with the goal of reducing unnecessary cognitive load. However, cognitive architecture alone is not the only factor to be considered; individual differences, especially prior knowledge, are critical in determining what impact a visual representation will have on learners' cognitive structures and processes. Prior knowledge can determine the ease with which learners can perceive and interpret visual representations in working memory. Although a long tradition of research has compared experts and novices, more research is necessary to fully explore the expert-novice continuum and maximize the potential of visual representations.

Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence.

PubMed

Setoh, Yin Xiang; Amarilla, Alberto A; Peng, Nias Y; Slonchak, Andrii; Periasamy, Parthiban; Figueiredo, Luiz T M; Aquino, Victor H; Khromykh, Alexander A

2018-01-01

Rocio virus (ROCV) is an arbovirus belonging to the genus Flavivirus, family Flaviviridae. We present an updated sequence of ROCV strain SPH 34675 (GenBank: AY632542.4), the only available full genome sequence prior to this study. Using next-generation sequencing of the entire genome, we reveal substantial sequence variation from the prototype sequence, with 30 nucleotide differences amounting to 14 amino acid changes, as well as significant changes to predicted 3'UTR RNA structures. Our results present an updated and corrected sequence of a potential emerging human-virulent flavivirus uniquely indigenous to Brazil (GenBank: MF461639).

Sleep Spindle Density Predicts the Effect of Prior Knowledge on Memory Consolidation

PubMed Central

Lambon Ralph, Matthew A.; Kempkes, Marleen; Cousins, James N.; Lewis, Penelope A.

2016-01-01

Information that relates to a prior knowledge schema is remembered better and consolidates more rapidly than information that does not. Another factor that influences memory consolidation is sleep and growing evidence suggests that sleep-related processing is important for integration with existing knowledge. Here, we perform an examination of how sleep-related mechanisms interact with schema-dependent memory advantage. Participants first established a schema over 2 weeks. Next, they encoded new facts, which were either related to the schema or completely unrelated. After a 24 h retention interval, including a night of sleep, which we monitored with polysomnography, participants encoded a second set of facts. Finally, memory for all facts was tested in a functional magnetic resonance imaging scanner. Behaviorally, sleep spindle density predicted an increase of the schema benefit to memory across the retention interval. Higher spindle densities were associated with reduced decay of schema-related memories. Functionally, spindle density predicted increased disengagement of the hippocampus across 24 h for schema-related memories only. Together, these results suggest that sleep spindle activity is associated with the effect of prior knowledge on memory consolidation. SIGNIFICANCE STATEMENT Episodic memories are gradually assimilated into long-term memory and this process is strongly influenced by sleep. The consolidation of new information is also influenced by its relationship to existing knowledge structures, or schemas, but the role of sleep in such schema-related consolidation is unknown. We show that sleep spindle density predicts the extent to which schemas influence the consolidation of related facts. This is the first evidence that sleep is associated with the interaction between prior knowledge and long-term memory formation. PMID:27030764

45 CFR 1616.3 - Qualifications.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Academic training and performance; (b) The nature and extent of prior legal experience; (c) Knowledge and understanding of the legal problems and needs of the poor; (d) Prior working experience in the client community...

A Study about Placement Support Using Semantic Similarity

ERIC Educational Resources Information Center

Katz, Marco; van Bruggen, Jan; Giesbers, Bas; Waterink, Wim; Eshuis, Jannes; Koper, Rob

2014-01-01

This paper discusses Latent Semantic Analysis (LSA) as a method for the assessment of prior learning. The Accreditation of Prior Learning (APL) is a procedure to offer learners an individualized curriculum based on their prior experiences and knowledge. The placement decisions in this process are based on the analysis of student material by domain…

The Effects of Feedback during Exploratory Mathematics Problem Solving: Prior Knowledge Matters

ERIC Educational Resources Information Center

Fyfe, Emily R.; Rittle-Johnson, Bethany; DeCaro, Marci S.

2012-01-01

Providing exploratory activities prior to explicit instruction can facilitate learning. However, the level of guidance provided during the exploration has largely gone unstudied. In this study, we examined the effects of 1 form of guidance, feedback, during exploratory mathematics problem solving for children with varying levels of prior domain…

Learners' strategies for reconstructing cognitive frameworks and navigating conceptual change from prior conception to consensual genetics knowledge

NASA Astrophysics Data System (ADS)

Parrott, Annette M.

Problem. Science teachers are charged with preparing students to become scientifically literate individuals. Teachers are given curriculum that specifies the knowledge that students should come away with; however, they are not necessarily aware of the knowledge with which the student arrives or how best to help them navigate between the two knowledge states. Educators must be aware, not only of where their students are conceptually, but how their students move from their prior knowledge and naive theories, to scientifically acceptable theories. The understanding of how students navigate this course has the potential to revolutionize educational practices. Methods. This study explored how five 9th grade biology students reconstructed their cognitive frameworks and navigated conceptual change from prior conception to consensual genetics knowledge. The research questions investigated were: (1) how do students in the process of changing their naive science theories to accepted science theories describe their journey from prior knowledge to current conception, and (2) what are the methods that students utilize to bridge the gap between alternate and consensual science conceptions to effect conceptual change. Qualitative and quantitative methods were employed to gather and analyze the data. In depth, semi-structured interviews formed the primary data for probing the context and details of students' conceptual change experience. Primary interview data was coded by thematic analysis. Results and discussion. This study revealed information about students' perceived roles in learning, the role of articulation in the conceptual change process, and ways in which a community of learners aids conceptual change. It was ascertained that students see their role in learning primarily as repeating information until they could add that information to their knowledge. Students are more likely to consider challenges to their conceptual frameworks and be more motivated to become active participants in constructing their knowledge when they are working collaboratively with peers instead of receiving instruction from their teacher. Articulation was found to be instrumental in aiding learners in identifying their alternate conceptions as well as in revisiting, investigating and reconstructing their conceptual frameworks. Based on the assumptions generated, suggestions were offered to inform pedagogical practice in support of the conceptual change process.

A Path Algorithm for Constrained Estimation

PubMed Central

Zhou, Hua; Lange, Kenneth

2013-01-01

Many least-square problems involve affine equality and inequality constraints. Although there are a variety of methods for solving such problems, most statisticians find constrained estimation challenging. The current article proposes a new path-following algorithm for quadratic programming that replaces hard constraints by what are called exact penalties. Similar penalties arise in l1 regularization in model selection. In the regularization setting, penalties encapsulate prior knowledge, and penalized parameter estimates represent a trade-off between the observed data and the prior knowledge. Classical penalty methods of optimization, such as the quadratic penalty method, solve a sequence of unconstrained problems that put greater and greater stress on meeting the constraints. In the limit as the penalty constant tends to ∞, one recovers the constrained solution. In the exact penalty method, squared penalties!are replaced by absolute value penalties, and the solution is recovered for a finite value of the penalty constant. The exact path-following method starts at the unconstrained solution and follows the solution path as the penalty constant increases. In the process, the solution path hits, slides along, and exits from the various constraints. Path following in Lasso penalized regression, in contrast, starts with a large value of the penalty constant and works its way downward. In both settings, inspection of the entire solution path is revealing. Just as with the Lasso and generalized Lasso, it is possible to plot the effective degrees of freedom along the solution path. For a strictly convex quadratic program, the exact penalty algorithm can be framed entirely in terms of the sweep operator of regression analysis. A few well-chosen examples illustrate the mechanics and potential of path following. This article has supplementary materials available online. PMID:24039382

A multistage motion vector processing method for motion-compensated frame interpolation.

PubMed

Huang, Ai- Mei; Nguyen, Truong Q

2008-05-01

In this paper, a novel, low-complexity motion vector processing algorithm at the decoder is proposed for motion-compensated frame interpolation or frame rate up-conversion. We address the problems of having broken edges and deformed structures in an interpolated frame by hierarchically refining motion vectors on different block sizes. Our method explicitly considers the reliability of each received motion vector and has the capability of preserving the structure information. This is achieved by analyzing the distribution of residual energies and effectively merging blocks that have unreliable motion vectors. The motion vector reliability information is also used as a prior knowledge in motion vector refinement using a constrained vector median filter to avoid choosing identical unreliable one. We also propose using chrominance information in our method. Experimental results show that the proposed scheme has better visual quality and is also robust, even in video sequences with complex scenes and fast motion.

Loop-mediated isothermal amplification (LAMP) assay-A rapid detection tool for identifying red fox (Vulpes vulpes) DNA in the carcasses of harbour porpoises (Phocoena phocoena).

PubMed

Heers, Teresa; van Neer, Abbo; Becker, André; Grilo, Miguel Luca; Siebert, Ursula; Abdulmawjood, Amir

2017-01-01

Carcasses of wild animals are often visited by different scavengers. However, determining which scavenger caused certain types of bite marks is particularly difficult and knowledge thereof is lacking. Therefore, a loop-mediated isothermal amplification (LAMP) assay (target sequence cytochrome b) was developed to detect red fox DNA in carcasses of harbour porpoises. The MSwab™ method for direct testing without prior DNA isolation was validated. As a detection device, the portable real-time fluorometer Genie® II was used, which yields rapid results and can be used in field studies without huge laboratory equipment. In addition to in vitro evaluation and validation, a stranded and scavenged harbour porpoise carcass was successfully examined for red fox DNA residues. The developed LAMP method is a valuable diagnostic tool for confirming presumable red fox bite wounds in harbour porpoises without further DNA isolation steps.

Automated feature detection and identification in digital point-ordered signals

DOEpatents

Oppenlander, Jane E.; Loomis, Kent C.; Brudnoy, David M.; Levy, Arthur J.

1998-01-01

A computer-based automated method to detect and identify features in digital point-ordered signals. The method is used for processing of non-destructive test signals, such as eddy current signals obtained from calibration standards. The signals are first automatically processed to remove noise and to determine a baseline. Next, features are detected in the signals using mathematical morphology filters. Finally, verification of the features is made using an expert system of pattern recognition methods and geometric criteria. The method has the advantage that standard features can be, located without prior knowledge of the number or sequence of the features. Further advantages are that standard features can be differentiated from irrelevant signal features such as noise, and detected features are automatically verified by parameters extracted from the signals. The method proceeds fully automatically without initial operator set-up and without subjective operator feature judgement.

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs

PubMed Central

LeGault, Laura H.; Dewey, Colin N.

2013-01-01

Motivation: Alternative splicing and other processes that allow for different transcripts to be derived from the same gene are significant forces in the eukaryotic cell. RNA-Seq is a promising technology for analyzing alternative transcripts, as it does not require prior knowledge of transcript structures or genome sequences. However, analysis of RNA-Seq data in the presence of genes with large numbers of alternative transcripts is currently challenging due to efficiency, identifiability and representation issues. Results: We present RNA-Seq models and associated inference algorithms based on the concept of probabilistic splice graphs, which alleviate these issues. We prove that our models are often identifiable and demonstrate that our inference methods for quantification and differential processing detection are efficient and accurate. Availability: Software implementing our methods is available at http://deweylab.biostat.wisc.edu/psginfer. Contact: cdewey@biostat.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23846746

The whole-genome landscape of medulloblastoma subtypes

PubMed Central

Northcott, Paul A.; Buchhalter, Ivo; Morrissy, A. Sorana; Hovestadt, Volker; Weischenfeldt, Joachim; Ehrenberger, Tobias; Groebner, Susanne; Segura-Wang, Maia; Zichner, Thomas; Rudneva, Vasilisa; Warnatz, Hans-Jörg; Sidiropoulos, Nikos; Phillips, Aaron H.; Schumacher, Steven; Kleinheinz, Kortine; Waszak, Sebastian M.; Erkek, Serap; Jones, David T.W.; Worst, Barbara C.; Kool, Marcel; Zapatka, Marc; Jäger, Natalie; Chavez, Lukas; Hutter, Barbara; Bieg, Matthias; Paramasivam, Nagarajan; Heinold, Michael; Gu, Zuguang; Ishaque, Naveed; Jäger-Schmidt, Christina; Imbusch, Charles D.; Jugold, Alke; Hübschmann, Daniel; Risch, Thomas; Amstislavskiy, Vyacheslav; Gonzalez, Francisco German Rodriguez; Weber, Ursula D.; Wolf, Stephan; Robinson, Giles W.; Zhou, Xin; Wu, Gang; Finkelstein, David; Liu, Yanling; Cavalli, Florence M.G.; Luu, Betty; Ramaswamy, Vijay; Wu, Xiaochong; Koster, Jan; Ryzhova, Marina; Cho, Yoon-Jae; Pomeroy, Scott L.; Herold-Mende, Christel; Schuhmann, Martin; Ebinger, Martin; Liau, Linda M.; Mora, Jaume; McLendon, Roger E.; Jabado, Nada; Kumabe, Toshihiro; Chuah, Eric; Ma, Yussanne; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen L.; Thiessen, Nina; Tse, Kane; Wong, Tina; Jones, Steven J.M.; Witt, Olaf; Milde, Till; Von Deimling, Andreas; Capper, David; Korshunov, Andrey; Yaspo, Marie-Laure; Kriwacki, Richard; Gajjar, Amar; Zhang, Jinghui; Beroukhim, Rameen; Fraenkel, Ernest; Korbel, Jan O.; Brors, Benedikt; Schlesner, Matthias; Eils, Roland; Marra, Marco A.; Pfister, Stefan M.; Taylor, Michael D.; Lichter, Peter

2018-01-01

Summary Current therapies for medulloblastoma (MB), a highly malignant childhood brain tumor, impose debilitating effects on the developing child, warranting deployment of molecularly targeted treatments with reduced toxicities. Prior studies failed to disclose the full spectrum of driver genes and molecular processes operative in MB subgroups. Herein, we detail the somatic landscape across 491 sequenced MBs and molecular heterogeneity amongst 1,256 epigenetically analyzed cases, identifying subgroup-specific driver alterations including previously unappreciated actionable targets. Driver mutations explained the majority of Group 3 and Group 4 patients, remarkably enhancing previous knowledge. Novel molecular subtypes were differentially enriched for specific driver events, including hotspot in-frame insertions targeting KBTBD4 and ‘enhancer hijacking’ driving PRDM6 activation. Thus, application of integrative genomics to an unprecedented cohort of clinical samples derived from a single childhood cancer entity disclosed a series of new cancer genes and biologically relevant subtype diversity that represent attractive therapeutic targets for treating MB patients. PMID:28726821

Spatio-temporal alignment of multiple sensors

NASA Astrophysics Data System (ADS)

Zhang, Tinghua; Ni, Guoqiang; Fan, Guihua; Sun, Huayan; Yang, Biao

2018-01-01

Aiming to achieve the spatio-temporal alignment of multi sensor on the same platform for space target observation, a joint spatio-temporal alignment method is proposed. To calibrate the parameters and measure the attitude of cameras, an astronomical calibration method is proposed based on star chart simulation and collinear invariant features of quadrilateral diagonal between the observed star chart. In order to satisfy a temporal correspondence and spatial alignment similarity simultaneously, the method based on the astronomical calibration and attitude measurement in this paper formulates the video alignment to fold the spatial and temporal alignment into a joint alignment framework. The advantage of this method is reinforced by exploiting the similarities and prior knowledge of velocity vector field between adjacent frames, which is calculated by the SIFT Flow algorithm. The proposed method provides the highest spatio-temporal alignment accuracy compared to the state-of-the-art methods on sequences recorded from multi sensor at different times.

Temporal dynamics of the knowledge-mediated visual disambiguation process in humans: a magnetoencephalography study.

PubMed

Urakawa, Tomokazu; Ogata, Katsuya; Kimura, Takahiro; Kume, Yuko; Tobimatsu, Shozo

2015-01-01

Disambiguation of a noisy visual scene with prior knowledge is an indispensable task of the visual system. To adequately adapt to a dynamically changing visual environment full of noisy visual scenes, the implementation of knowledge-mediated disambiguation in the brain is imperative and essential for proceeding as fast as possible under the limited capacity of visual image processing. However, the temporal profile of the disambiguation process has not yet been fully elucidated in the brain. The present study attempted to determine how quickly knowledge-mediated disambiguation began to proceed along visual areas after the onset of a two-tone ambiguous image using magnetoencephalography with high temporal resolution. Using the predictive coding framework, we focused on activity reduction for the two-tone ambiguous image as an index of the implementation of disambiguation. Source analysis revealed that a significant activity reduction was observed in the lateral occipital area at approximately 120 ms after the onset of the ambiguous image, but not in preceding activity (about 115 ms) in the cuneus when participants perceptually disambiguated the ambiguous image with prior knowledge. These results suggested that knowledge-mediated disambiguation may be implemented as early as approximately 120 ms following an ambiguous visual scene, at least in the lateral occipital area, and provided an insight into the temporal profile of the disambiguation process of a noisy visual scene with prior knowledge. © 2014 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Iterating between lessons on concepts and procedures can improve mathematics knowledge.

PubMed

Rittle-Johnson, Bethany; Koedinger, Kenneth

2009-09-01

Knowledge of concepts and procedures seems to develop in an iterative fashion, with increases in one type of knowledge leading to increases in the other type of knowledge. This suggests that iterating between lessons on concepts and procedures may improve learning. The purpose of the current study was to evaluate the instructional benefits of an iterative lesson sequence compared to a concepts-before-procedures sequence for students learning decimal place-value concepts and arithmetic procedures. In two classroom experiments, sixth-grade students from two schools participated (N=77 and 26). Students completed six decimal lessons on an intelligent-tutoring systems. In the iterative condition, lessons cycled between concept and procedure lessons. In the concepts-first condition, all concept lessons were presented before introducing the procedure lessons. In both experiments, students in the iterative condition gained more knowledge of arithmetic procedures, including ability to transfer the procedures to problems with novel features. Knowledge of concepts was fairly comparable across conditions. Finally, pre-test knowledge of one type predicted gains in knowledge of the other type across experiments. An iterative sequencing of lessons seems to facilitate learning and transfer, particularly of mathematical procedures. The findings support an iterative perspective for the development of knowledge of concepts and procedures.

Mitigating Information Overload: The Impact of Context-Based Approach to the Design of Tools for Intelligence Analysts

DTIC Science & Technology

2008-03-01

amount of arriving data, extract actionable information, and integrate it with prior knowledge. Add to that the pressures of today’s fusion center...information, and integrate it with prior knowledge. Add to that the pressures of today’s fusion center climate and it becomes clear that analysts, police... fusion centers, including specifics about how these problems manifest at the Illinois State Police (ISP) Statewide Terrorism and Intelligence Center

Improving phylogenetic analyses by incorporating additional information from genetic sequence databases.

PubMed

Liang, Li-Jung; Weiss, Robert E; Redelings, Benjamin; Suchard, Marc A

2009-10-01

Statistical analyses of phylogenetic data culminate in uncertain estimates of underlying model parameters. Lack of additional data hinders the ability to reduce this uncertainty, as the original phylogenetic dataset is often complete, containing the entire gene or genome information available for the given set of taxa. Informative priors in a Bayesian analysis can reduce posterior uncertainty; however, publicly available phylogenetic software specifies vague priors for model parameters by default. We build objective and informative priors using hierarchical random effect models that combine additional datasets whose parameters are not of direct interest but are similar to the analysis of interest. We propose principled statistical methods that permit more precise parameter estimates in phylogenetic analyses by creating informative priors for parameters of interest. Using additional sequence datasets from our lab or public databases, we construct a fully Bayesian semiparametric hierarchical model to combine datasets. A dynamic iteratively reweighted Markov chain Monte Carlo algorithm conveniently recycles posterior samples from the individual analyses. We demonstrate the value of our approach by examining the insertion-deletion (indel) process in the enolase gene across the Tree of Life using the phylogenetic software BALI-PHY; we incorporate prior information about indels from 82 curated alignments downloaded from the BAliBASE database.

Informative priors on fetal fraction increase power of the noninvasive prenatal screen.

PubMed

Xu, Hanli; Wang, Shaowei; Ma, Lin-Lin; Huang, Shuai; Liang, Lin; Liu, Qian; Liu, Yang-Yang; Liu, Ke-Di; Tan, Ze-Min; Ban, Hao; Guan, Yongtao; Lu, Zuhong

2017-11-09

PurposeNoninvasive prenatal screening (NIPS) sequences a mixture of the maternal and fetal cell-free DNA. Fetal trisomy can be detected by examining chromosomal dosages estimated from sequencing reads. The traditional method uses the Z-test, which compares a subject against a set of euploid controls, where the information of fetal fraction is not fully utilized. Here we present a Bayesian method that leverages informative priors on the fetal fraction.MethodOur Bayesian method combines the Z-test likelihood and informative priors of the fetal fraction, which are learned from the sex chromosomes, to compute Bayes factors. Bayesian framework can account for nongenetic risk factors through the prior odds, and our method can report individual positive/negative predictive values.ResultsOur Bayesian method has more power than the Z-test method. We analyzed 3,405 NIPS samples and spotted at least 9 (of 51) possible Z-test false positives.ConclusionBayesian NIPS is more powerful than the Z-test method, is able to account for nongenetic risk factors through prior odds, and can report individual positive/negative predictive values.Genetics in Medicine advance online publication, 9 November 2017; doi:10.1038/gim.2017.186.

The dynamics of fidelity over the time course of long-term memory.

PubMed

Persaud, Kimele; Hemmer, Pernille

2016-08-01

Bayesian models of cognition assume that prior knowledge about the world influences judgments. Recent approaches have suggested that the loss of fidelity from working to long-term (LT) memory is simply due to an increased rate of guessing (e.g. Brady, Konkle, Gill, Oliva, & Alvarez, 2013). That is, recall is the result of either remembering (with some noise) or guessing. This stands in contrast to Bayesian models of cognition while assume that prior knowledge about the world influences judgments, and that recall is a combination of expectations learned from the environment and noisy memory representations. Here, we evaluate the time course of fidelity in LT episodic memory, and the relative contribution of prior category knowledge and guessing, using a continuous recall paradigm. At an aggregate level, performance reflects a high rate of guessing. However, when aggregate data is partitioned by lag (i.e., the number of presentations from study to test), or is un-aggregated, performance appears to be more complex than just remembering with some noise and guessing. We implemented three models: the standard remember-guess model, a three-component remember-guess model, and a Bayesian mixture model and evaluated these models against the data. The results emphasize the importance of taking into account the influence of prior category knowledge on memory. Copyright © 2016 Elsevier Inc. All rights reserved.

Assessment of Knowledge Transfer in the Context of Biomechanics

ERIC Educational Resources Information Center

Hutchison, Randolph E.

2011-01-01

The dynamic act of knowledge transfer, or the connection of a student's prior knowledge to features of a new problem, could be considered one of the primary goals of education. Yet studies highlight more instances of failure than success. This dissertation focuses on how knowledge transfer takes place during individual problem solving, in…

New Knowledge Derived from Learned Knowledge: Functional-Anatomic Correlates of Stimulus Equivalence

ERIC Educational Resources Information Center

Schlund, Michael W.; Hoehn-Saric, Rudolf; Cataldo, Michael F.

2007-01-01

Forming new knowledge based on knowledge established through prior learning is a central feature of higher cognition that is captured in research on stimulus equivalence (SE). Numerous SE investigations show that reinforcing behavior under control of distinct sets of arbitrary conditional relations gives rise to stimulus control by new, "derived"…

They're Lovin' It: How Preschool Children Mediated Their Funds of Knowledge into Dramatic Play

ERIC Educational Resources Information Center

Karabon, Anne

2017-01-01

The funds of knowledge framework promotes connecting community contexts with curriculum aimed to activate children's prior knowledge. Typically, teachers determine what knowledge sources harmonise best with their existing programming, potentially omitting particular resources that may not align. Young children, on the other hand, can act as agents…

Methods and compositions for efficient nucleic acid sequencing

DOEpatents

Drmanac, Radoje

2006-07-04

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

Methods and compositions for efficient nucleic acid sequencing

DOEpatents

Drmanac, Radoje

2002-01-01

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

Is knowledge important? Empirical research on nuclear risk communication in two countries.

PubMed

Perko, Tanja; Zeleznik, Nadja; Turcanu, Catrinel; Thijssen, Peter

2012-06-01

Increasing audience knowledge is often set as a primary objective of risk communication efforts. But is it worthwhile focusing risk communication strategies solely on enhancing specific knowledge? The main research questions tackled in this paper were: (1) if prior audience knowledge related to specific radiation risks is influential for the perception of these risks and the acceptance of communicated messages and (2) if gender, attitudes, risk perception of other radiation risks, confidence in authorities, and living in the vicinity of nuclear/radiological installations may also play an important role in this matter. The goal of this study was to test empirically the mentioned predictors in two independent case studies in different countries. The first case study was an information campaign for iodine pre-distribution in Belgium (N = 1035). The second was the information campaign on long-term radioactive waste disposal in Slovenia (N = 1,200). In both cases, recurrent and intensive communication campaigns were carried out by the authorities aiming, among other things, at increasing specific audience knowledge. Results show that higher prior audience knowledge leads to more willingness to accept communicated messages, but it does not affect people’s perception of the specific risk communicated. In addition, the influence of prior audience knowledge on the acceptance of communicated messages is shown to be no stronger than that of general radiation risk perception. The results in both case studies suggest that effective risk communication has to focus not only on knowledge but also on other more heuristic predictors, such as risk perception or attitudes toward communicated risks.

Relations among Conceptual Knowledge, Procedural Knowledge, and Procedural Flexibility in Two Samples Differing in Prior Knowledge

ERIC Educational Resources Information Center

Schneider, Michael; Rittle-Johnson, Bethany; Star, Jon R.

2011-01-01

Competence in many domains rests on children developing conceptual and procedural knowledge, as well as procedural flexibility. However, research on the developmental relations between these different types of knowledge has yielded unclear results, in part because little attention has been paid to the validity of the measures or to the effects of…

A biological compression model and its applications.

PubMed

Cao, Minh Duc; Dix, Trevor I; Allison, Lloyd

2011-01-01

A biological compression model, expert model, is presented which is superior to existing compression algorithms in both compression performance and speed. The model is able to compress whole eukaryotic genomes. Most importantly, the model provides a framework for knowledge discovery from biological data. It can be used for repeat element discovery, sequence alignment and phylogenetic analysis. We demonstrate that the model can handle statistically biased sequences and distantly related sequences where conventional knowledge discovery tools often fail.

Order priors for Bayesian network discovery with an application to malware phylogeny

DOE PAGES

Oyen, Diane; Anderson, Blake; Sentz, Kari; ...

2017-09-15

Here, Bayesian networks have been used extensively to model and discover dependency relationships among sets of random variables. We learn Bayesian network structure with a combination of human knowledge about the partial ordering of variables and statistical inference of conditional dependencies from observed data. Our approach leverages complementary information from human knowledge and inference from observed data to produce networks that reflect human beliefs about the system as well as to fit the observed data. Applying prior beliefs about partial orderings of variables is an approach distinctly different from existing methods that incorporate prior beliefs about direct dependencies (or edges)more » in a Bayesian network. We provide an efficient implementation of the partial-order prior in a Bayesian structure discovery learning algorithm, as well as an edge prior, showing that both priors meet the local modularity requirement necessary for an efficient Bayesian discovery algorithm. In benchmark studies, the partial-order prior improves the accuracy of Bayesian network structure learning as well as the edge prior, even though order priors are more general. Our primary motivation is in characterizing the evolution of families of malware to aid cyber security analysts. For the problem of malware phylogeny discovery, we find that our algorithm, compared to existing malware phylogeny algorithms, more accurately discovers true dependencies that are missed by other algorithms.« less

Order priors for Bayesian network discovery with an application to malware phylogeny

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

Oyen, Diane; Anderson, Blake; Sentz, Kari

Here, Bayesian networks have been used extensively to model and discover dependency relationships among sets of random variables. We learn Bayesian network structure with a combination of human knowledge about the partial ordering of variables and statistical inference of conditional dependencies from observed data. Our approach leverages complementary information from human knowledge and inference from observed data to produce networks that reflect human beliefs about the system as well as to fit the observed data. Applying prior beliefs about partial orderings of variables is an approach distinctly different from existing methods that incorporate prior beliefs about direct dependencies (or edges)more » in a Bayesian network. We provide an efficient implementation of the partial-order prior in a Bayesian structure discovery learning algorithm, as well as an edge prior, showing that both priors meet the local modularity requirement necessary for an efficient Bayesian discovery algorithm. In benchmark studies, the partial-order prior improves the accuracy of Bayesian network structure learning as well as the edge prior, even though order priors are more general. Our primary motivation is in characterizing the evolution of families of malware to aid cyber security analysts. For the problem of malware phylogeny discovery, we find that our algorithm, compared to existing malware phylogeny algorithms, more accurately discovers true dependencies that are missed by other algorithms.« less

An investigation of prior knowledge in Automatic Music Transcription systems.

PubMed

Cazau, Dorian; Revillon, Guillaume; Krywyk, Julien; Adam, Olivier

2015-10-01

Automatic transcription of music is a long-studied research field with many operational systems available commercially. In this paper, a generic transcription system able to host various prior knowledge parameters has been developed, followed by an in-depth investigation of their impact on music transcription. Explicit links between musical knowledge and algorithmic formalism have been made. Musical knowledge covers classes of timbre, musicology, and playing style of an instrument repertoire. An evaluation sound corpus gathering musical pieces played by human performers from three different instrument repertoires, namely, classical piano, steel-string acoustic guitar, and the marovany zither from Madagascar, has been developed. The different components of musical knowledge have been successively incorporated in a complete transcription system, consisting mainly of a Probabilistic Latent Component Analysis algorithm post-processed with a Hidden Markov Model, and their impact on transcription results have been comparatively evaluated.

GeneCOST: a novel scoring-based prioritization framework for identifying disease causing genes.

PubMed

Ozer, Bugra; Sağıroğlu, Mahmut; Demirci, Hüseyin

2015-11-15

Due to the big data produced by next-generation sequencing studies, there is an evident need for methods to extract the valuable information gathered from these experiments. In this work, we propose GeneCOST, a novel scoring-based method to evaluate every gene for their disease association. Without any prior filtering and any prior knowledge, we assign a disease likelihood score to each gene in correspondence with their variations. Then, we rank all genes based on frequency, conservation, pedigree and detailed variation information to find out the causative reason of the disease state. We demonstrate the usage of GeneCOST with public and real life Mendelian disease cases including recessive, dominant, compound heterozygous and sporadic models. As a result, we were able to identify causative reason behind the disease state in top rankings of our list, proving that this novel prioritization framework provides a powerful environment for the analysis in genetic disease studies alternative to filtering-based approaches. GeneCOST software is freely available at www.igbam.bilgem.tubitak.gov.tr/en/softwares/genecost-en/index.html. buozer@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Prior knowledge-based approach for associating ...

EPA Pesticide Factsheets

Evaluating the potential human health and/or ecological risks associated with exposures to complex chemical mixtures in the ambient environment is one of the central challenges of chemical safety assessment and environmental protection. There is a need for approaches that can help to integrate chemical monitoring and bio-effects data to evaluate risks associated with chemicals present in the environment. We used prior knowledge about chemical-gene interactions to develop a knowledge assembly model for detected chemicals at five locations near two wastewater treatment plants. The assembly model was used to generate hypotheses about the biological impacts of the chemicals at each location. The hypotheses were tested using empirical hepatic gene expression data from fathead minnows exposed for 12 d at each location. Empirical gene expression data was also mapped to the assembly models to statistically evaluate the likelihood of a chemical contributing to the observed biological responses. The prior knowledge approach was able reasonably hypothesize the biological impacts at one site but not the other. Chemicals most likely contributing to the observed biological responses were identified at each location. Despite limitations to the approach, knowledge assembly models have strong potential for associating chemical occurrence with potential biological effects and providing a foundation for hypothesis generation to guide research and/or monitoring efforts relat

Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology

PubMed Central

2012-01-01

Background An important question in the analysis of biochemical data is that of identifying subsets of molecular variables that may jointly influence a biological response. Statistical variable selection methods have been widely used for this purpose. In many settings, it may be important to incorporate ancillary biological information concerning the variables of interest. Pathway and network maps are one example of a source of such information. However, although ancillary information is increasingly available, it is not always clear how it should be used nor how it should be weighted in relation to primary data. Results We put forward an approach in which biological knowledge is incorporated using informative prior distributions over variable subsets, with prior information selected and weighted in an automated, objective manner using an empirical Bayes formulation. We employ continuous, linear models with interaction terms and exploit biochemically-motivated sparsity constraints to permit exact inference. We show an example of priors for pathway- and network-based information and illustrate our proposed method on both synthetic response data and by an application to cancer drug response data. Comparisons are also made to alternative Bayesian and frequentist penalised-likelihood methods for incorporating network-based information. Conclusions The empirical Bayes method proposed here can aid prior elicitation for Bayesian variable selection studies and help to guard against mis-specification of priors. Empirical Bayes, together with the proposed pathway-based priors, results in an approach with a competitive variable selection performance. In addition, the overall procedure is fast, deterministic, and has very few user-set parameters, yet is capable of capturing interplay between molecular players. The approach presented is general and readily applicable in any setting with multiple sources of biological prior knowledge. PMID:22578440

A 3000-year record of ground-rupturing earthquakes along the central North Anatolian fault near Lake Ladik, Turkey

USGS Publications Warehouse

Fraser, J.; Pigati, J.S.; Hubert-Ferrari, A.; Vanneste, K.; Avsar, U.; Altinok, S.

2009-01-01

The North Anatolian fault (NAF) is a ???1500 km long, arcuate, dextral strike-slip fault zone in northern Turkey that extends from the Karliova triple junction to the Aegean Sea. East of Bolu, the fault zone exhibits evidence of a sequence of large (Mw >7) earthquakes that occurred during the twentieth century that displayed a migrating earthquake sequence from east to west. Prolonged human occupation in this region provides an extensive, but not exhaustive, historical record of large earthquakes prior to the twentieth century that covers much of the last 2000 yr. In this study, we extend our knowledge of rupture events in the region by evaluating the stratigraphy and chronology of sediments exposed in a paleoseismic trench across a splay of the NAF at Destek, ???6:5 km east of Lake Ladik (40.868?? N, 36.121?? E). The trenched fault strand forms an uphill-facing scarp and associated sediment trap below a small catchment area. The trench exposed a narrow fault zone that has juxtaposed a sequence of weakly defined paleosols interbedded with colluvium against highly fractured bedrock. We mapped magnetic susceptibility variations on the trench walls and found evidence for multiple visually unrecognized colluvial wedges. This technique was also used to constrain a predominantly dip-slip style of displacement on this fault splay. Sediments exposed in the trench were dated using both charcoal and terrestrial gastropod shells to constrain the timing of the earthquake events. While the gastropod shells consistently yielded 14 C ages that were too old (by ???900 yr), we obtained highly reliable 14 C ages from the charcoal by dating multiple components of the sample material. Our radiocarbon chronology constrains the timing of seven large earthquakes over the past 3000 yr prior to the 1943 Tosya earthquake, including event ages of (2?? error): A.D. 1437-1788, A.D. 1034-1321, A.D. 549-719, A.D. 17-585 (1-3 events), 35 B.C.-A.D. 28, 700-392 B.C., 912-596 B.C. Our results indicate an average interevent time of 385 166?? yr (1??).

Collaborative Knowledge Building with Wikis: The Impact of Redundancy and Polarity

ERIC Educational Resources Information Center

Moskaliuk, Johannes; Kimmerle, Joachim; Cress, Ulrike

2012-01-01

Wikis as shared digital artifacts may enable users to participate in processes of knowledge building. To what extent and with which quality knowledge building can take place is assumed to depend on the interrelation between people's prior knowledge and the information available in a wiki. In two experimental studies we examined the impact on…

The Effects of Prior Knowledge on Children's Memory and Suggestibility

ERIC Educational Resources Information Center

Elischberger, Holger B.

2005-01-01

In this study, 5- and 6-year-olds were read a story and asked to recall its details. Two independent factors-prestory knowledge and poststory suggestions-were crossed to examine the effects on children's story recall. The results indicated that prestory social knowledge about the story protagonist as well as academic knowledge relating to the…

Approaching Multidimensional Forms of Knowledge through Personal Meaning Mapping in Science Integrating Teaching outside the Classroom

ERIC Educational Resources Information Center

Hartmeyer, Rikke; Bølling, Mads; Bentsen, Peter

2017-01-01

Current research points to Personal Meaning Mapping (PMM) as a method useful in investigating students' prior and current science knowledge. However, studies investigating PMM as a method for exploring specific knowledge dimensions are lacking. Ensuring that students are able to access specific knowledge dimensions is important, especially in…

Topic-Specific Pedagogical Content Knowledge (TSPCK) in Redox and Electrochemistry of Experienced Teachers

ERIC Educational Resources Information Center

O'Brien, Stephanie

2017-01-01

Topic specific pedagogical content knowledge (TSPCK) is the basis by which knowledge of subject matter of a particular topic is conveyed to students. This includes students' prior knowledge, curricular saliency, what makes a topic easy or difficult to teach, representations, and teaching strategies. The goal of this study is to assess the…

Creating Connections: Using the Internet to Support Struggling Readers' Background Knowledge. Issues in Technology

ERIC Educational Resources Information Center

Karchmer, Rachel A.

2004-01-01

Background knowledge plays an important role in one?s ability to learn. We learn new knowledge by relating it to our prior knowledge, which in turn provides concrete understanding (Piaget, 1969). Rosenblatt (1996) explained, "The reader brings to the work personality traits, memories of past events, present needs and preoccupations, a…

Interplay of Secondary Pre-Service Teacher Content Knowledge (CK), Pedagogical Content Knowledge (PCK) and Attitudes Regarding Scientific Inquiry Teaching within Teacher Training

ERIC Educational Resources Information Center

Smit, Robbert; Weitzel, Holger; Blank, Robert; Rietz, Florian; Tardent, Josiane; Robin, Nicolas

2017-01-01

Background: Beginning teachers encounter several constraints with respect to scientific inquiry. Depending on their prior beliefs, knowledge and understanding, these constraints affect their teaching of inquiry. Purpose: To investigate quantitatively the longitudinal relationship between pre-service teachers' knowledge and attitudes on scientific…

Prior knowledge guided active modules identification: an integrated multi-objective approach.

PubMed

Chen, Weiqi; Liu, Jing; He, Shan

2017-03-14

Active module, defined as an area in biological network that shows striking changes in molecular activity or phenotypic signatures, is important to reveal dynamic and process-specific information that is correlated with cellular or disease states. A prior information guided active module identification approach is proposed to detect modules that are both active and enriched by prior knowledge. We formulate the active module identification problem as a multi-objective optimisation problem, which consists two conflicting objective functions of maximising the coverage of known biological pathways and the activity of the active module simultaneously. Network is constructed from protein-protein interaction database. A beta-uniform-mixture model is used to estimate the distribution of p-values and generate scores for activity measurement from microarray data. A multi-objective evolutionary algorithm is used to search for Pareto optimal solutions. We also incorporate a novel constraints based on algebraic connectivity to ensure the connectedness of the identified active modules. Application of proposed algorithm on a small yeast molecular network shows that it can identify modules with high activities and with more cross-talk nodes between related functional groups. The Pareto solutions generated by the algorithm provides solutions with different trade-off between prior knowledge and novel information from data. The approach is then applied on microarray data from diclofenac-treated yeast cells to build network and identify modules to elucidate the molecular mechanisms of diclofenac toxicity and resistance. Gene ontology analysis is applied to the identified modules for biological interpretation. Integrating knowledge of functional groups into the identification of active module is an effective method and provides a flexible control of balance between pure data-driven method and prior information guidance.

Inferring internal properties of Earth's core dynamics and their evolution from surface observations and a numerical geodynamo model

NASA Astrophysics Data System (ADS)

Aubert, J.; Fournier, A.

2011-10-01

Over the past decades, direct three-dimensional numerical modelling has been successfully used to reproduce the main features of the geodynamo. Here we report on efforts to solve the associated inverse problem, aiming at inferring the underlying properties of the system from the sole knowledge of surface observations and the first principle dynamical equations describing the convective dynamo. To this end we rely on twin experiments. A reference model time sequence is first produced and used to generate synthetic data, restricted here to the large-scale component of the magnetic field and its rate of change at the outer boundary. Starting from a different initial condition, a second sequence is next run and attempts are made to recover the internal magnetic, velocity and buoyancy anomaly fields from the sparse surficial data. In order to reduce the vast underdetermination of this problem, we use stochastic inversion, a linear estimation method determining the most likely internal state compatible with the observations and some prior knowledge, and we also implement a sequential evolution algorithm in order to invert time-dependent surface observations. The prior is the multivariate statistics of the numerical model, which are directly computed from a large number of snapshots stored during a preliminary direct run. The statistics display strong correlation between different harmonic degrees of the surface observations and internal fields, provided they share the same harmonic order, a natural consequence of the linear coupling of the governing dynamical equations and of the leading influence of the Coriolis force. Synthetic experiments performed with a weakly nonlinear model yield an excellent quantitative retrieval of the internal structure. In contrast, the use of a strongly nonlinear (and more realistic) model results in less accurate static estimations, which in turn fail to constrain the unobserved small scales in the time integration of the evolution scheme. Evaluating the quality of forecasts of the system evolution against the reference solution, we show that our scheme can improve predictions based on linear extrapolations on forecast horizons shorter than the system e-folding time. Still, in the perspective of forthcoming data assimilation activities, our study underlines the need of advanced estimation techniques able to cope with the moderate to strong nonlinearities present in the geodynamo.

Late-Quaternary biogeographic scenarios for the brown bear ( Ursus arctos), a wild mammal model species

NASA Astrophysics Data System (ADS)

Davison, John; Ho, Simon Y. W.; Bray, Sarah C.; Korsten, Marju; Tammeleht, Egle; Hindrikson, Maris; Østbye, Kjartan; Østbye, Eivind; Lauritzen, Stein-Erik; Austin, Jeremy; Cooper, Alan; Saarma, Urmas

2011-02-01

This review provides an up-to-date synthesis of the matrilineal phylogeography of a uniquely well-studied Holarctic mammal, the brown bear. We extend current knowledge by presenting a DNA sequence derived from one of the earliest known fossils of a polar bear (dated to 115 000 years before present), a species that shares a paraphyletic mitochondrial association with brown bears. A molecular clock analysis of 140 mitochondrial DNA sequences, including our new polar bear sequence, provides novel insights into the times of origin for different brown bear clades. We propose a number of regional biogeographic scenarios based on genetic data, divergence time estimates and paleontological records. The case of the brown bear provides an example for researchers working with less well-studied taxa: it shows clearly that phylogeographic models based on patterns of modern genetic variation alone can be substantially improved by including data on historical patterns of genetic diversity in the form of ancient DNA sequences derived from accurately dated samples and by using an approach to divergence-time estimation that suits the data under analysis. Using such approaches it has been possible to (i) establish that the processes shaping modern genetic diversity in brown bears acted recently, within the last three glacial cycles; (ii) distinguish among hypotheses concerning species' responses to climatic oscillations in accordance with the lack of phylogeographic structure that existed in brown bears prior to the last glacial maximum (LGM); (iii) reassess theories linking monophyletic brown bear populations to particular LGM refuge areas; and (iv) identify vicariance events and track analogous patterns of migration by brown bears out of Eurasia to North America and Japan.

Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

PubMed Central

2010-01-01

Background Classical and quantitative linkage analyses of genetic crosses have traditionally been used to map genes of interest, such as those conferring chloroquine or quinine resistance in malaria parasites. Next-generation sequencing technologies now present the possibility of determining genome-wide genetic variation at single base-pair resolution. Here, we combine in vivo experimental evolution, a rapid genetic strategy and whole genome re-sequencing to identify the precise genetic basis of artemisinin resistance in a lineage of the rodent malaria parasite, Plasmodium chabaudi. Such genetic markers will further the investigation of resistance and its control in natural infections of the human malaria, P. falciparum. Results A lineage of isogenic in vivo drug-selected mutant P. chabaudi parasites was investigated. By measuring the artemisinin responses of these clones, the appearance of an in vivo artemisinin resistance phenotype within the lineage was defined. The underlying genetic locus was mapped to a region of chromosome 2 by Linkage Group Selection in two different genetic crosses. Whole-genome deep coverage short-read re-sequencing (Illumina® Solexa) defined the point mutations, insertions, deletions and copy-number variations arising in the lineage. Eight point mutations arise within the mutant lineage, only one of which appears on chromosome 2. This missense mutation arises contemporaneously with artemisinin resistance and maps to a gene encoding a de-ubiquitinating enzyme. Conclusions This integrated approach facilitates the rapid identification of mutations conferring selectable phenotypes, without prior knowledge of biological and molecular mechanisms. For malaria, this model can identify candidate genes before resistant parasites are commonly observed in natural human malaria populations. PMID:20846421

Prior Conceptual Knowledge and Textbook Search.

ERIC Educational Resources Information Center

Byrnes, James P.; Guthrie, John T.

1992-01-01

The role of a subject's conceptual knowledge in the procedural task of searching a text for information was studied for 51 college undergraduates in 2 experiments involving knowledge of anatomy. Students with more anatomical information were able to search a text more quickly. Educational implications are discussed. (SLD)

How Knowledge Powers Reading

ERIC Educational Resources Information Center

Lemov, Doug

2017-01-01

Recent research shows that reading comprehension relies heavily on prior knowledge. Far more than generic "reading skills" like drawing inferences, making predictions, and knowing the function of subheads, how well students learn from a nonfiction text depends on their background knowledge of the text's subject matter. And in a cyclical…

Employees and Creativity: Social Ties and Access to Heterogeneous Knowledge

ERIC Educational Resources Information Center

Huang, Chiung-En; Liu, Chih-Hsing Sam

2015-01-01

This study dealt with employee social ties, knowledge heterogeneity contacts, and the generation of creativity. Although prior studies demonstrated a relationship between network position and creativity, inadequate attention has been paid to network ties and heterogeneity knowledge contacts. This study considered the social interaction processes…

Computer Experiences, Self-Efficacy and Knowledge of Students Enrolled in Introductory University Agriculture Courses.

ERIC Educational Resources Information Center

Johnson, Donald M.; Ferguson, James A.; Lester, Melissa L.

1999-01-01

Of 175 freshmen agriculture students, 74% had prior computer courses, 62% owned computers. The number of computer topics studied predicted both computer self-efficacy and computer knowledge. A substantial positive correlation was found between self-efficacy and computer knowledge. (SK)

A high-resolution cattle CNV map by population-scale genome sequencing

USDA-ARS?s Scientific Manuscript database

Copy Number Variations (CNVs) are common genomic structural variations that have been linked to human diseases and phenotypic traits. Prior studies in cattle have produced low-resolution CNV maps. We constructed a draft, high-resolution map of cattle CNVs based on whole genome sequencing data from 7...

Prospects: the tomato genome as a cornerstone for gene discovery

USDA-ARS?s Scientific Manuscript database

Those involved in the international tomato genome sequencing effort contributed to not only the development of an important genome sequence relevant to a major economic and nutritional crop, but also to the tomato experimental system as a model for plant biology. Without question, prior seminal work...

Informative priors on fetal fraction increase power of the noninvasive prenatal screen

USDA-ARS?s Scientific Manuscript database

Noninvasive prenatal screening (NIPS) sequences a mixture of the maternal and fetal cell-free DNA. Fetal trisomy can be detected by examining chromosomal dosages estimated from sequencing reads. The traditional method uses the Z-test, which compares a subject against a set of euploid controls, where...

An Improved Algorithm for Predicting Free Recalls

ERIC Educational Resources Information Center

Laming, Donald

2008-01-01

Laming [Laming, D. (2006). "Predicting free recalls." "Journal of Experimental Psychology: Learning, Memory, and Cognition," 32, 1146-1163] has shown that, in a free-recall experiment in which the participants rehearsed out loud, entire sequences of recalls could be predicted, to a useful degree of precision, from the prior sequences of stimuli…

Ten-Month-Old Infants Use Prior Information to Identify an Actor's Goal

ERIC Educational Resources Information Center

Sommerville, Jessica A.; Crane, Catharyn C.

2009-01-01

For adults, prior information about an individual's likely goals, preferences or dispositions plays a powerful role in interpreting ambiguous behavior and predicting and interpreting behavior in novel contexts. Across two studies, we investigated whether 10-month-old infants' ability to identify the goal of an ambiguous action sequence was…

Does tonality boost short-term memory in congenital amusia?

PubMed

Albouy, Philippe; Schulze, Katrin; Caclin, Anne; Tillmann, Barbara

2013-11-06

Congenital amusia is a neuro-developmental disorder of music perception and production. Recent findings have demonstrated that this deficit is linked to an impaired short-term memory for tone sequences. As it has been shown before that non-musicians' implicit knowledge of musical regularities can improve short-term memory for tone information, the present study investigated if this type of implicit knowledge could also influence amusics' short-term memory performance. Congenital amusics and their matched controls, who were non-musicians, had to indicate whether sequences of five tones, presented in pairs, were the same or different; half of the pairs respected musical regularities (tonal sequences) and the other half did not (atonal sequences). As previously reported for non-musician participants, the control participants showed better performance (as measured with d') for tonal sequences than for atonal ones. While this improvement was not observed in amusics, both control and amusic participants showed faster response times for tonal sequences than for atonal sequences. These findings suggest that some implicit processing of tonal structures is potentially preserved in congenital amusia. This observation is encouraging as it strengthens the perspective to exploit implicit knowledge to help reducing pitch perception and memory deficits in amusia. © 2013 Elsevier B.V. All rights reserved.

Semantically-based priors and nuanced knowledge core for Big Data, Social AI, and language understanding.

PubMed

Olsher, Daniel

2014-10-01

Noise-resistant and nuanced, COGBASE makes 10 million pieces of commonsense data and a host of novel reasoning algorithms available via a family of semantically-driven prior probability distributions. Machine learning, Big Data, natural language understanding/processing, and social AI can draw on COGBASE to determine lexical semantics, infer goals and interests, simulate emotion and affect, calculate document gists and topic models, and link commonsense knowledge to domain models and social, spatial, cultural, and psychological data. COGBASE is especially ideal for social Big Data, which tends to involve highly implicit contexts, cognitive artifacts, difficult-to-parse texts, and deep domain knowledge dependencies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reasoning about procedural knowledge

NASA Technical Reports Server (NTRS)

Georgeff, M. P.

1985-01-01

A crucial aspect of automated reasoning about space operations is that knowledge of the problem domain is often procedural in nature - that is, the knowledge is often in the form of sequences of actions or procedures for achieving given goals or reacting to certain situations. In this paper a system is described that explicitly represents and reasons about procedural knowledge. The knowledge representation used is sufficiently rich to describe the effects of arbitrary sequences of tests and actions, and the inference mechanism provides a means for directly using this knowledge to reach desired operational goals. Furthermore, the representation has a declarative semantics that provides for incremental changes to the system, rich explanatory capabilities, and verifiability. The approach also provides a mechanism for reasoning about the use of this knowledge, thus enabling the system to choose effectively between alternative courses of action.

Do Runner Beans Really Make You Run Fast? Young Children Learning About Science-Related Food Concepts in Informal Settings

NASA Astrophysics Data System (ADS)

Cumming, Jenny

2003-08-01

Early years practitioners acknowledge that much learning takes place in a family context. Science educators, in particular, recognise the importance of children's prior knowledge, both as a foundation on which to build and as a possible source of misconceptions. However, little work has been done to discover what young children learn outside school. This study utilised parent diaries and questionnaires to elucidate the experiences of children aged four to seven which might contribute to their knowledge about the origin of food and its destiny after being eaten. The findings indicate that children learn more scientifically correct information with friends and family than teachers might realise. Awareness of children's informal knowledge can assist teachers when planning activities. As well as this, children's prior knowledge can be utilised in classroom discourse to promote understanding.

Prediction of Slot Shape and Slot Size for Improving the Performance of Microstrip Antennas Using Knowledge-Based Neural Networks.

PubMed

Khan, Taimoor; De, Asok

2014-01-01

In the last decade, artificial neural networks have become very popular techniques for computing different performance parameters of microstrip antennas. The proposed work illustrates a knowledge-based neural networks model for predicting the appropriate shape and accurate size of the slot introduced on the radiating patch for achieving desired level of resonance, gain, directivity, antenna efficiency, and radiation efficiency for dual-frequency operation. By incorporating prior knowledge in neural model, the number of required training patterns is drastically reduced. Further, the neural model incorporated with prior knowledge can be used for predicting response in extrapolation region beyond the training patterns region. For validation, a prototype is also fabricated and its performance parameters are measured. A very good agreement is attained between measured, simulated, and predicted results.

Prediction of Slot Shape and Slot Size for Improving the Performance of Microstrip Antennas Using Knowledge-Based Neural Networks

PubMed Central

De, Asok

2014-01-01

In the last decade, artificial neural networks have become very popular techniques for computing different performance parameters of microstrip antennas. The proposed work illustrates a knowledge-based neural networks model for predicting the appropriate shape and accurate size of the slot introduced on the radiating patch for achieving desired level of resonance, gain, directivity, antenna efficiency, and radiation efficiency for dual-frequency operation. By incorporating prior knowledge in neural model, the number of required training patterns is drastically reduced. Further, the neural model incorporated with prior knowledge can be used for predicting response in extrapolation region beyond the training patterns region. For validation, a prototype is also fabricated and its performance parameters are measured. A very good agreement is attained between measured, simulated, and predicted results. PMID:27382616

Tacit knowledge.

PubMed

Walker, Alexander Muir

2017-04-01

Information that is not made explicit is nonetheless embedded in most of our standard procedures. In its simplest form, embedded information may take the form of prior knowledge held by the researcher and presumed to be agreed to by consumers of the research product. More interesting are the settings in which the prior information is held unconsciously by both researcher and reader, or when the very form of an "effective procedure" incorporates its creator's (unspoken) understanding of a problem. While it may not be productive to exhaustively detail the embedded or tacit knowledge that manifests itself in creative scientific work, at least at the beginning, we may want to routinize methods for extracting and documenting the ways of thinking that make "experts" expert. We should not back away from both expecting and respecting the tacit knowledge the pervades our work and the work of others.

Preservice Agricultural Education Teachers' Experiences in and Anticipation of Content Knowledge Preparation

ERIC Educational Resources Information Center

Rice, Amber H.; Kitchel, Tracy

2015-01-01

This study explored the experiences of preservice agriculture teachers in content knowledge preparation for pedagogical content knowledge (PCK) development. The researchers employed a phenomenological approach in which six preservice teachers were interviewed the semester prior to student teaching. The researchers found there was general…

Conditional Reasoning in Autism: Activation and Integration of Knowledge and Belief

ERIC Educational Resources Information Center

McKenzie, Rebecca; Evans, Jonathan St. B. T.; Handley, Simon J.

2010-01-01

Everyday conditional reasoning is typically influenced by prior knowledge and belief in the form of specific exceptions known as counterexamples. This study explored whether adolescents with autism spectrum disorder (ASD; N = 26) were less influenced by background knowledge than typically developing adolescents (N = 38) when engaged in conditional…

The Effects of Prior Knowledge and Instruction on Understanding Image Formation.

ERIC Educational Resources Information Center

Galili, Igal; And Others

1993-01-01

Reports a study (n=27) concerning the knowledge about image formation exhibited by students following instruction in geometrical optics in an activity-based college physics course for prospective elementary teachers. Student diagrams and verbal comments indicate their knowledge can be described as an intermediate state: a hybridization of…

Designing Knowledge Scaffolds to Support Mathematical Problem Solving

ERIC Educational Resources Information Center

Rittle-Johnson, Bethany; Koedinger, Kenneth R.

2005-01-01

We present a methodology for designing better learning environments. In Phase 1, 6th-grade students' (n = 223) prior knowledge was assessed using a difficulty factors assessment (DFA). The assessment revealed that scaffolds designed to elicit contextual, conceptual, or procedural knowledge each improved students' ability to add and subtract…

Uncovering and Informing Preservice Teachers' Prior Knowledge about Poverty

ERIC Educational Resources Information Center

Mundy, Charlotte Anne; Leko, Melinda Marie

2015-01-01

This study explored 30 preservice teachers' knowledge on issues related to poverty. In an open-ended questionnaire, preservice teachers' perceptions of poverty and how teachers should respond to students from poverty were explored. Results indicated that preservice teachers' knowledge was nonspecific and lacked focus on the relationship among…

Object detection and tracking system

DOEpatents

Ma, Tian J.

2017-05-30

Methods and apparatuses for analyzing a sequence of images for an object are disclosed herein. In a general embodiment, the method identifies a region of interest in the sequence of images. The object is likely to move within the region of interest. The method divides the region of interest in the sequence of images into sections and calculates signal-to-noise ratios for a section in the sections. A signal-to-noise ratio for the section is calculated using the section in the image, a prior section in a prior image to the image, and a subsequent section in a subsequent image to the image. The signal-to-noise ratios are for potential velocities of the object in the section. The method also selects a velocity from the potential velocities for the object in the section using a potential velocity in the potential velocities having a highest signal-to-noise ratio in the signal-to-noise ratios.

Curriculum Sequencing and the Acquisition of Clock-Reading Skills among Chinese and Flemish Children

ERIC Educational Resources Information Center

Burny, Elise; Valcke, Martin; Desoete, Annemie; Van Luit, Johannes E. Hans

2013-01-01

The present study addresses the impact of the curriculum on primary school children's acquisition of clock-reading knowledge from analog and digital clocks. Focusing on Chinese and Flemish children's clock-reading knowledge, the study is about whether the differences in sequencing of learning and instruction opportunities--as defined by the…

Multiple video sequences synchronization during minimally invasive surgery

NASA Astrophysics Data System (ADS)

Belhaoua, Abdelkrim; Moreau, Johan; Krebs, Alexandre; Waechter, Julien; Radoux, Jean-Pierre; Marescaux, Jacques

2016-03-01

Hybrid operating rooms are an important development in the medical ecosystem. They allow integrating, in the same procedure, the advantages of radiological imaging and surgical tools. However, one of the challenges faced by clinical engineers is to support the connectivity and interoperability of medical-electrical point-of-care devices. A system that could enable plug-and-play connectivity and interoperability for medical devices would improve patient safety, save hospitals time and money, and provide data for electronic medical records. In this paper, we propose a hardware platform dedicated to collect and synchronize multiple videos captured from medical equipment in real-time. The final objective is to integrate augmented reality technology into an operation room (OR) in order to assist the surgeon during a minimally invasive operation. To the best of our knowledge, there is no prior work dealing with hardware based video synchronization for augmented reality applications on OR. Whilst hardware synchronization methods can embed temporal value, so called timestamp, into each sequence on-the-y and require no post-processing, they require specialized hardware. However the design of our hardware is simple and generic. This approach was adopted and implemented in this work and its performance is evaluated by comparison to the start-of-the-art methods.

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.

PubMed

Murray, Kevin D; Webers, Christfried; Ong, Cheng Soon; Borevitz, Justin; Warthmann, Norman

2017-09-01

Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

Incremental Implicit Learning of Bundles of Statistical Patterns

PubMed Central

Qian, Ting; Jaeger, T. Florian; Aslin, Richard N.

2016-01-01

Forming an accurate representation of a task environment often takes place incrementally as the information relevant to learning the representation only unfolds over time. This incremental nature of learning poses an important problem: it is usually unclear whether a sequence of stimuli consists of only a single pattern, or multiple patterns that are spliced together. In the former case, the learner can directly use each observed stimulus to continuously revise its representation of the task environment. In the latter case, however, the learner must first parse the sequence of stimuli into different bundles, so as to not conflate the multiple patterns. We created a video-game statistical learning paradigm and investigated 1) whether learners without prior knowledge of the existence of multiple “stimulus bundles” — subsequences of stimuli that define locally coherent statistical patterns — could detect their presence in the input, and 2) whether learners are capable of constructing a rich representation that encodes the various statistical patterns associated with bundles. By comparing human learning behavior to the predictions of three computational models, we find evidence that learners can handle both tasks successfully. In addition, we discuss the underlying reasons for why the learning of stimulus bundles occurs even when such behavior may seem irrational. PMID:27639552

Differentiation of Glioblastoma and Lymphoma Using Feature Extraction and Support Vector Machine.

PubMed

Yang, Zhangjing; Feng, Piaopiao; Wen, Tian; Wan, Minghua; Hong, Xunning

2017-01-01

Differentiation of glioblastoma multiformes (GBMs) and lymphomas using multi-sequence magnetic resonance imaging (MRI) is an important task that is valuable for treatment planning. However, this task is a challenge because GBMs and lymphomas may have a similar appearance in MRI images. This similarity may lead to misclassification and could affect the treatment results. In this paper, we propose a semi-automatic method based on multi-sequence MRI to differentiate these two types of brain tumors. Our method consists of three steps: 1) the key slice is selected from 3D MRIs and region of interests (ROIs) are drawn around the tumor region; 2) different features are extracted based on prior clinical knowledge and validated using a t-test; and 3) features that are helpful for classification are used to build an original feature vector and a support vector machine is applied to perform classification. In total, 58 GBM cases and 37 lymphoma cases are used to validate our method. A leave-one-out crossvalidation strategy is adopted in our experiments. The global accuracy of our method was determined as 96.84%, which indicates that our method is effective for the differentiation of GBM and lymphoma and can be applied in clinical diagnosis. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Effector-independent motor sequence representations exist in extrinsic and intrinsic reference frames.

PubMed

Wiestler, Tobias; Waters-Metenier, Sheena; Diedrichsen, Jörn

2014-04-02

Many daily activities rely on the ability to produce meaningful sequences of movements. Motor sequences can be learned in an effector-specific fashion (such that benefits of training are restricted to the trained hand) or an effector-independent manner (meaning that learning also facilitates performance with the untrained hand). Effector-independent knowledge can be represented in extrinsic/world-centered or in intrinsic/body-centered coordinates. Here, we used functional magnetic resonance imaging (fMRI) and multivoxel pattern analysis to determine the distribution of intrinsic and extrinsic finger sequence representations across the human neocortex. Participants practiced four sequences with one hand for 4 d, and then performed these sequences during fMRI with both left and right hand. Between hands, these sequences were equivalent in extrinsic or intrinsic space, or were unrelated. In dorsal premotor cortex (PMd), we found that sequence-specific activity patterns correlated higher for extrinsic than for unrelated pairs, providing evidence for an extrinsic sequence representation. In contrast, primary sensory and motor cortices showed effector-independent representations in intrinsic space, with considerable overlap of the two reference frames in caudal PMd. These results suggest that effector-independent representations exist not only in world-centered, but also in body-centered coordinates, and that PMd may be involved in transforming sequential knowledge between the two. Moreover, although effector-independent sequence representations were found bilaterally, they were stronger in the hemisphere contralateral to the trained hand. This indicates that intermanual transfer relies on motor memories that are laid down during training in both hemispheres, but preferentially draws upon sequential knowledge represented in the trained hemisphere.

Effector-Independent Motor Sequence Representations Exist in Extrinsic and Intrinsic Reference Frames

PubMed Central

Wiestler, Tobias; Waters-Metenier, Sheena

2014-01-01

Many daily activities rely on the ability to produce meaningful sequences of movements. Motor sequences can be learned in an effector-specific fashion (such that benefits of training are restricted to the trained hand) or an effector-independent manner (meaning that learning also facilitates performance with the untrained hand). Effector-independent knowledge can be represented in extrinsic/world-centered or in intrinsic/body-centered coordinates. Here, we used functional magnetic resonance imaging (fMRI) and multivoxel pattern analysis to determine the distribution of intrinsic and extrinsic finger sequence representations across the human neocortex. Participants practiced four sequences with one hand for 4 d, and then performed these sequences during fMRI with both left and right hand. Between hands, these sequences were equivalent in extrinsic or intrinsic space, or were unrelated. In dorsal premotor cortex (PMd), we found that sequence-specific activity patterns correlated higher for extrinsic than for unrelated pairs, providing evidence for an extrinsic sequence representation. In contrast, primary sensory and motor cortices showed effector-independent representations in intrinsic space, with considerable overlap of the two reference frames in caudal PMd. These results suggest that effector-independent representations exist not only in world-centered, but also in body-centered coordinates, and that PMd may be involved in transforming sequential knowledge between the two. Moreover, although effector-independent sequence representations were found bilaterally, they were stronger in the hemisphere contralateral to the trained hand. This indicates that intermanual transfer relies on motor memories that are laid down during training in both hemispheres, but preferentially draws upon sequential knowledge represented in the trained hemisphere. PMID:24695723

Integrating clinicians, knowledge and data: expert-based cooperative analysis in healthcare decision support

PubMed Central

2010-01-01

Background Decision support in health systems is a highly difficult task, due to the inherent complexity of the process and structures involved. Method This paper introduces a new hybrid methodology Expert-based Cooperative Analysis (EbCA), which incorporates explicit prior expert knowledge in data analysis methods, and elicits implicit or tacit expert knowledge (IK) to improve decision support in healthcare systems. EbCA has been applied to two different case studies, showing its usability and versatility: 1) Bench-marking of small mental health areas based on technical efficiency estimated by EbCA-Data Envelopment Analysis (EbCA-DEA), and 2) Case-mix of schizophrenia based on functional dependency using Clustering Based on Rules (ClBR). In both cases comparisons towards classical procedures using qualitative explicit prior knowledge were made. Bayesian predictive validity measures were used for comparison with expert panels results. Overall agreement was tested by Intraclass Correlation Coefficient in case "1" and kappa in both cases. Results EbCA is a new methodology composed by 6 steps:. 1) Data collection and data preparation; 2) acquisition of "Prior Expert Knowledge" (PEK) and design of the "Prior Knowledge Base" (PKB); 3) PKB-guided analysis; 4) support-interpretation tools to evaluate results and detect inconsistencies (here Implicit Knowledg -IK- might be elicited); 5) incorporation of elicited IK in PKB and repeat till a satisfactory solution; 6) post-processing results for decision support. EbCA has been useful for incorporating PEK in two different analysis methods (DEA and Clustering), applied respectively to assess technical efficiency of small mental health areas and for case-mix of schizophrenia based on functional dependency. Differences in results obtained with classical approaches were mainly related to the IK which could be elicited by using EbCA and had major implications for the decision making in both cases. Discussion This paper presents EbCA and shows the convenience of completing classical data analysis with PEK as a mean to extract relevant knowledge in complex health domains. One of the major benefits of EbCA is iterative elicitation of IK.. Both explicit and tacit or implicit expert knowledge are critical to guide the scientific analysis of very complex decisional problems as those found in health system research. PMID:20920289

Integrating clinicians, knowledge and data: expert-based cooperative analysis in healthcare decision support.

PubMed

Gibert, Karina; García-Alonso, Carlos; Salvador-Carulla, Luis

2010-09-30

Decision support in health systems is a highly difficult task, due to the inherent complexity of the process and structures involved. This paper introduces a new hybrid methodology Expert-based Cooperative Analysis (EbCA), which incorporates explicit prior expert knowledge in data analysis methods, and elicits implicit or tacit expert knowledge (IK) to improve decision support in healthcare systems. EbCA has been applied to two different case studies, showing its usability and versatility: 1) Bench-marking of small mental health areas based on technical efficiency estimated by EbCA-Data Envelopment Analysis (EbCA-DEA), and 2) Case-mix of schizophrenia based on functional dependency using Clustering Based on Rules (ClBR). In both cases comparisons towards classical procedures using qualitative explicit prior knowledge were made. Bayesian predictive validity measures were used for comparison with expert panels results. Overall agreement was tested by Intraclass Correlation Coefficient in case "1" and kappa in both cases. EbCA is a new methodology composed by 6 steps:. 1) Data collection and data preparation; 2) acquisition of "Prior Expert Knowledge" (PEK) and design of the "Prior Knowledge Base" (PKB); 3) PKB-guided analysis; 4) support-interpretation tools to evaluate results and detect inconsistencies (here Implicit Knowledg -IK- might be elicited); 5) incorporation of elicited IK in PKB and repeat till a satisfactory solution; 6) post-processing results for decision support. EbCA has been useful for incorporating PEK in two different analysis methods (DEA and Clustering), applied respectively to assess technical efficiency of small mental health areas and for case-mix of schizophrenia based on functional dependency. Differences in results obtained with classical approaches were mainly related to the IK which could be elicited by using EbCA and had major implications for the decision making in both cases. This paper presents EbCA and shows the convenience of completing classical data analysis with PEK as a mean to extract relevant knowledge in complex health domains. One of the major benefits of EbCA is iterative elicitation of IK.. Both explicit and tacit or implicit expert knowledge are critical to guide the scientific analysis of very complex decisional problems as those found in health system research.

Using expert knowledge for test linking.

PubMed

Bolsinova, Maria; Hoijtink, Herbert; Vermeulen, Jorine Adinda; Béguin, Anton

2017-12-01

Linking and equating procedures are used to make the results of different test forms comparable. In the cases where no assumption of random equivalent groups can be made some form of linking design is used. In practice the amount of data available to link the two tests is often very limited due to logistic and security reasons, which affects the precision of linking procedures. This study proposes to enhance the quality of linking procedures based on sparse data by using Bayesian methods which combine the information in the linking data with background information captured in informative prior distributions. We propose two methods for the elicitation of prior knowledge about the difference in difficulty of two tests from subject-matter experts and explain how these results can be used in the specification of priors. To illustrate the proposed methods and evaluate the quality of linking with and without informative priors, an empirical example of linking primary school mathematics tests is presented. The results suggest that informative priors can increase the precision of linking without decreasing the accuracy. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

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

Zhu, Yitan; Xu, Yanxun; Helseth, Donald L.

Background: Genetic interactions play a critical role in cancer development. Existing knowledge about cancer genetic interactions is incomplete, especially lacking evidences derived from large-scale cancer genomics data. The Cancer Genome Atlas (TCGA) produces multimodal measurements across genomics and features of thousands of tumors, which provide an unprecedented opportunity to investigate the interplays of genes in cancer. Methods: We introduce Zodiac, a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood modelmore » derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.” Results: Zodiac provides molecular interactions for about 200 million pairs of genes. All the results are generated from a big-data analysis and organized into a comprehensive database allowing customized search. In addition, Zodiac provides data processing and analysis tools that allow users to customize the prior networks and update the genetic pathways of their interest. Zodiac is publicly available at www.compgenome.org/ZODIAC. Conclusions: Zodiac recapitulates and extends existing knowledge of molecular interactions in cancer. It can be used to explore novel gene-gene interactions, transcriptional regulation, and other types of molecular interplays in cancer.« less

Fostering Upper Secondary Students' Ability to Engage in Practices of Scientific Investigation: a Comparative Analysis of an Explicit and an Implicit Instructional Approach

NASA Astrophysics Data System (ADS)

Vorholzer, Andreas; von Aufschnaiter, Claudia; Boone, William J.

2018-02-01

Inquiry-based teaching is considered as contributing to content-related, procedural, and epistemic learning goals of science education. In this study, a quasi-experimental research design was utilized to investigate to what extent embedding inquiry activities in an explicit and an implicit instructional approach fosters students' ability to engage in three practices of scientific investigation (POSI): (1) formulating questions and hypotheses, (2) planning investigations, (3) analyzing and interpreting data. Both approaches were implemented in a classroom-based intervention conducted in a German upper secondary school (N = 222). Students' procedural knowledge of the three POSI was assessed with a paper-pencil test prior and post to the intervention, their content knowledge and dispositional factors (e.g., cognitive abilities) were gathered once. Results show that not only explicit but also implicit instruction fosters students' knowledge of POSI. While overall explicit instruction was found to be more effective, the findings indicate that the effectiveness depends considerably on the practice addressed. Moreover, findings suggest that both approaches were equally beneficial for all students regardless of their prior content knowledge and their prior procedural knowledge of POSI. Potential conditions for the success of explicit and implicit approaches as well as implications for instruction on POSI in science classrooms and for future research are discussed.

Discovering Prerequisite Structure of Skills through Probabilistic Association Rules Mining

ERIC Educational Resources Information Center

Chen, Yang; Wuillemin, Pierre-Henr; Labat, Jean-Marc

2015-01-01

Estimating the prerequisite structure of skills is a crucial issue in domain modeling. Students usually learn skills in sequence since the preliminary skills need to be learned prior to the complex skills. The prerequisite relations between skills underlie the design of learning sequence and adaptation strategies for tutoring systems. The…

The tomato genome sequence provides insight into fleshy fruit evolution

USDA-ARS?s Scientific Manuscript database

The genome of the inbred tomato cultivar ‘Heinz 1706’ was sequenced and assembled using a combination of Sanger and “next generation” technologies. The predicted genome size is ~900 Mb, consistent with prior estimates, of which 760 Mb were assembled in 91 scaffolds aligned to the 12 tomato chromosom...

How Should Intelligent Tutoring Systems Sequence Multiple Graphical Representations of Fractions? A Multi-Methods Study

ERIC Educational Resources Information Center

Rau, M. A.; Aleven, V.; Rummel, N.; Pardos, Z.

2014-01-01

Providing learners with multiple representations of learning content has been shown to enhance learning outcomes. When multiple representations are presented across consecutive problems, we have to decide in what sequence to present them. Prior research has demonstrated that interleaving "tasks types" (as opposed to blocking them) can…

High-throughput sequencing of natively paired antibody chains provides evidence for original antigenic sin shaping the antibody response to influenza vaccination.

PubMed

Tan, Yann-Chong; Blum, Lisa K; Kongpachith, Sarah; Ju, Chia-Hsin; Cai, Xiaoyong; Lindstrom, Tamsin M; Sokolove, Jeremy; Robinson, William H

2014-03-01

We developed a DNA barcoding method to enable high-throughput sequencing of the cognate heavy- and light-chain pairs of the antibodies expressed by individual B cells. We used this approach to elucidate the plasmablast antibody response to influenza vaccination. We show that >75% of the rationally selected plasmablast antibodies bind and neutralize influenza, and that antibodies from clonal families, defined by sharing both heavy-chain VJ and light-chain VJ sequence usage, do so most effectively. Vaccine-induced heavy-chain VJ regions contained on average >20 nucleotide mutations as compared to their predicted germline gene sequences, and some vaccine-induced antibodies exhibited higher binding affinities for hemagglutinins derived from prior years' seasonal influenza as compared to their affinities for the immunization strains. Our results show that influenza vaccination induces the recall of memory B cells that express antibodies that previously underwent affinity maturation against prior years' seasonal influenza, suggesting that 'original antigenic sin' shapes the antibody response to influenza vaccination. Published by Elsevier Inc.

Activists within the Academy: The Role of Prior Experience in Adult Learners' Acquisition of Postgraduate Literacies in a Postapartheid South African University

ERIC Educational Resources Information Center

Cooper, Linda

2011-01-01

The article takes as a case study a group of disability rights activists who were given access to a master's program via Recognition of Prior Learning. The question explored is "Can adult learners' prior experiential knowledge act as a resource for the successful acquisition of postgraduate academic literacy practices?" The analysis is…

Gradient-based reliability maps for ACM-based segmentation of hippocampus.

PubMed

Zarpalas, Dimitrios; Gkontra, Polyxeni; Daras, Petros; Maglaveras, Nicos

2014-04-01

Automatic segmentation of deep brain structures, such as the hippocampus (HC), in MR images has attracted considerable scientific attention due to the widespread use of MRI and to the principal role of some structures in various mental disorders. In this literature, there exists a substantial amount of work relying on deformable models incorporating prior knowledge about structures' anatomy and shape information. However, shape priors capture global shape characteristics and thus fail to model boundaries of varying properties; HC boundaries present rich, poor, and missing gradient regions. On top of that, shape prior knowledge is blended with image information in the evolution process, through global weighting of the two terms, again neglecting the spatially varying boundary properties, causing segmentation faults. An innovative method is hereby presented that aims to achieve highly accurate HC segmentation in MR images, based on the modeling of boundary properties at each anatomical location and the inclusion of appropriate image information for each of those, within an active contour model framework. Hence, blending of image information and prior knowledge is based on a local weighting map, which mixes gradient information, regional and whole brain statistical information with a multi-atlas-based spatial distribution map of the structure's labels. Experimental results on three different datasets demonstrate the efficacy and accuracy of the proposed method.

An Optimization-Based Framework for the Transformation of Incomplete Biological Knowledge into a Probabilistic Structure and Its Application to the Utilization of Gene/Protein Signaling Pathways in Discrete Phenotype Classification.

PubMed

Esfahani, Mohammad Shahrokh; Dougherty, Edward R

2015-01-01

Phenotype classification via genomic data is hampered by small sample sizes that negatively impact classifier design. Utilization of prior biological knowledge in conjunction with training data can improve both classifier design and error estimation via the construction of the optimal Bayesian classifier. In the genomic setting, gene/protein signaling pathways provide a key source of biological knowledge. Although these pathways are neither complete, nor regulatory, with no timing associated with them, they are capable of constraining the set of possible models representing the underlying interaction between molecules. The aim of this paper is to provide a framework and the mathematical tools to transform signaling pathways to prior probabilities governing uncertainty classes of feature-label distributions used in classifier design. Structural motifs extracted from the signaling pathways are mapped to a set of constraints on a prior probability on a Multinomial distribution. Being the conjugate prior for the Multinomial distribution, we propose optimization paradigms to estimate the parameters of a Dirichlet distribution in the Bayesian setting. The performance of the proposed methods is tested on two widely studied pathways: mammalian cell cycle and a p53 pathway model.

Artificial Intelligence Controls Tape-Recording Sequence

NASA Technical Reports Server (NTRS)

Schwuttke, Ursula M.; Otamura, Roy M.; Zottarelli, Lawrence J.

1989-01-01

Developmental expert-system computer program intended to schedule recording of large amounts of data on limited amount of magnetic tape. Schedules recording using two sets of rules. First set incorporates knowledge of locations for recording of new data. Second set incorporates knowledge about issuing commands to recorder. Designed primarily for use on Voyager Spacecraft, also applicable to planning and sequencing in industry.

A Multicultural Sequence of Humanities Electives.

ERIC Educational Resources Information Center

Anderson, Gwendolyn; Ewing, Dessa

In order to promote multi-cultural literacy among its students, Delaware County Community College (DCCC) developed a multi-cultural sequence of humanities electives. The sequence emerged as a response to the predominantly White student body's lack of knowledge or curiosity about other cultures. The first of the four courses in the sequence is…

The Sequence of Learning Cycle Activities in High School Chemistry.

ERIC Educational Resources Information Center

Abraham, Michael R.; Renner, John W.

1986-01-01

Different learning cycle sequences were investigated to determine factors accounting for success of the cycle, compared learning with conventional instruction, and examined relationships between Piaget's theory and learning cycles. Results show that the normal learning cycle sequence is the optimum sequence for achievement of content knowledge in…

Improving Learning Outcome Using Six Sigma Methodology

ERIC Educational Resources Information Center

Tetteh, Godson A.

2015-01-01

Purpose: The purpose of this research paper is to apply the Six Sigma methodology to identify the attributes of a lecturer that will help improve a student's prior knowledge of a discipline from an initial "x" per cent knowledge to a higher "y" per cent of knowledge. Design/methodology/approach: The data collection method…

Reflective Assessment in Knowledge Building by Students with Low Academic Achievement

ERIC Educational Resources Information Center

Yang, Yuqin; van Aalst, Jan; Chan, Carol K. K.; Tian, Wen

2016-01-01

This study investigated whether and how students with low prior achievement can carry out and benefit from reflective assessment supported by the Knowledge Connections Analyzer (KCA) to collaboratively improve their knowledge-building discourse. Participants were a class of 20 Grade 11 students with low achievement taking visual art from an…

Knowledge of Algebra for Teaching: A Framework of Knowledge and Practices

ERIC Educational Resources Information Center

McCrory, Raven; Floden, Robert; Ferrini-Mundy, Joan; Reckase, Mark D.; Senk, Sharon L.

2012-01-01

Defining what teachers need to know to teach algebra successfully is important for informing teacher preparation and professional development efforts. Based on prior research, analysis of video, interviews with teachers, and analysis of textbooks, we define categories of knowledge and practices of teaching for understanding and assessing teachers'…

An Investigation of Preservice Teachers' Beliefs about the Certainty of Teaching Knowledge

ERIC Educational Resources Information Center

Ferguson, Leila E.; Brownlee, Jo Lunn

2018-01-01

Beliefs about the certainty of teaching knowledge may influence how preservice teachers engage with and learn from knowledge sources in teacher education, and their subsequent practice. In light of inconsistencies in prior findings that mainly employ epistemic questionnaires, we extended research focusing on a contextual analysis. Sixty-six…

Prior Knowledge Assessment Guide

DTIC Science & Technology

2014-12-01

marksmanship, advanced rifle marksmanship, and even specialized shooting courses. A comparison of the means on the test for the two groups showed that the...hands- on evaluations of student knowledge and/or skills. Pretests however, determine how much knowledge a student currently possesses of the course...content; thus, questions on pretests assess knowledge about what is to be taught in the course. Also, most pretests will include test items

The Interaction of Knowledge and Text Structure on the Ability to Identify Main Ideas in Texts. Content Knowledge and Reading Comprehension.

ERIC Educational Resources Information Center

Day, Jeanne D.; Engelhardt, Jean

Two studies examined how the factors of content-relevant knowledge and text organization influence students' abilities to study and to remember text information. The first experiment examined the effect of prior content knowledge on students' ability to identify important information in the text. Forty 7th- and forty 11th-grade students, experts…

Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

PubMed Central

Roos, Marco; Marshall, M Scott; Gibson, Andrew P; Schuemie, Martijn; Meij, Edgar; Katrenko, Sophia; van Hage, Willem Robert; Krommydas, Konstantinos; Adriaans, Pieter W

2009-01-01

Background Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support is exemplified by the difficulty of considering all relevant facts that are contained in the millions of documents available from PubMed. Semantic Web provides tools for sharing prior knowledge, while information retrieval and information extraction techniques enable its extraction from literature. Their combination makes prior knowledge available for computational analysis and inference. While some tools provide complete solutions that limit the control over the modeling and extraction processes, we seek a methodology that supports control by the experimenter over these critical processes. Results We describe progress towards automated support for the generation of biomolecular hypotheses. Semantic Web technologies are used to structure and store knowledge, while a workflow extracts knowledge from text. We designed minimal proto-ontologies in OWL for capturing different aspects of a text mining experiment: the biological hypothesis, text and documents, text mining, and workflow provenance. The models fit a methodology that allows focus on the requirements of a single experiment while supporting reuse and posterior analysis of extracted knowledge from multiple experiments. Our workflow is composed of services from the 'Adaptive Information Disclosure Application' (AIDA) toolkit as well as a few others. The output is a semantic model with putative biological relations, with each relation linked to the corresponding evidence. Conclusion We demonstrated a 'do-it-yourself' approach for structuring and extracting knowledge in the context of experimental research on biomolecular mechanisms. The methodology can be used to bootstrap the construction of semantically rich biological models using the results of knowledge extraction processes. Models specific to particular experiments can be constructed that, in turn, link with other semantic models, creating a web of knowledge that spans experiments. Mapping mechanisms can link to other knowledge resources such as OBO ontologies or SKOS vocabularies. AIDA Web Services can be used to design personalized knowledge extraction procedures. In our example experiment, we found three proteins (NF-Kappa B, p21, and Bax) potentially playing a role in the interplay between nutrients and epigenetic gene regulation. PMID:19796406

Quantifying transfer after perceptual-motor sequence learning: how inflexible is implicit learning?

PubMed

Sanchez, Daniel J; Yarnik, Eric N; Reber, Paul J

2015-03-01

Studies of implicit perceptual-motor sequence learning have often shown learning to be inflexibly tied to the training conditions during learning. Since sequence learning is seen as a model task of skill acquisition, limits on the ability to transfer knowledge from the training context to a performance context indicates important constraints on skill learning approaches. Lack of transfer across contexts has been demonstrated by showing that when task elements are changed following training, this leads to a disruption in performance. These results have typically been taken as suggesting that the sequence knowledge relies on integrated representations across task elements (Abrahamse, Jiménez, Verwey, & Clegg, Psychon Bull Rev 17:603-623, 2010a). Using a relatively new sequence learning task, serial interception sequence learning, three experiments are reported that quantify this magnitude of performance disruption after selectively manipulating individual aspects of motor performance or perceptual information. In Experiment 1, selective disruption of the timing or order of sequential actions was examined using a novel response manipulandum that allowed for separate analysis of these two motor response components. In Experiments 2 and 3, transfer was examined after selective disruption of perceptual information that left the motor response sequence intact. All three experiments provided quantifiable estimates of partial transfer to novel contexts that suggest some level of information integration across task elements. However, the ability to identify quantifiable levels of successful transfer indicates that integration is not all-or-none and that measurement sensitivity is a key in understanding sequence knowledge representations.

Nutrition Knowledge of Teen-Agers.

ERIC Educational Resources Information Center

Skinner, Jean D.; Woodburn, Margy J.

1984-01-01

Nutrition knowledge tests were administered to 1,193 adolescents in Oregon prior to instructional units on nutrition in health and home economics classes. Mean scores on the tests were low. Guidelines for nutrition educators of adolescents are presented. (Author/CJB)

Spatial Distribution of an Uranium-Respiring Betaproteobacterium at the Rifle, CO Field Research Site

PubMed Central

Koribanics, Nicole M.; Tuorto, Steven J.; Lopez-Chiaffarelli, Nora; McGuinness, Lora R.; Häggblom, Max M.; Williams, Kenneth H.; Long, Philip E.; Kerkhof, Lee J.

2015-01-01

The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminal electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site. PMID:25874721

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

PubMed Central

Kurcinski, Mateusz; Jamroz, Michal; Blaszczyk, Maciej; Kolinski, Andrzej; Kmiecik, Sebastian

2015-01-01

Protein–peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein–peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock does not require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein–peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock. PMID:25943545

Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site

DOE PAGES

Koribanics, Nicole M.; Tuorto, Steven J.; Lopez-Chiaffarelli, Nora; ...

2015-04-13

The Department of Energy’s Integrated Field-Scale Subsurface Research Challenge Site (IFRC) at Rifle, Colorado was created to address the gaps in knowledge on the mechanisms and rates of U(VI) bioreduction in alluvial sediments. Previous studies at the Rifle IFRC have linked microbial processes to uranium immobilization during acetate amendment. Several key bacteria believed to be involved in radionuclide containment have been described; however, most of the evidence implicating uranium reduction with specific microbiota has been indirect. Here, we report on the cultivation of a microorganism from the Rifle IFRC that reduces uranium and appears to utilize it as a terminalmore » electron acceptor for respiration with acetate as electron donor. Furthermore, this bacterium constitutes a significant proportion of the subsurface sediment community prior to biostimulation based on TRFLP profiling of 16S rRNA genes. 16S rRNA gene sequence analysis indicates that the microorganism is a betaproteobacterium with a high similarity to Burkholderia fungorum. This is, to our knowledge, the first report of a betaproteobacterium capable of uranium respiration. Our results indicate that this microorganism occurs commonly in alluvial sediments located between 3-6 m below ground surface at Rifle and may play a role in the initial reduction of uranium at the site.« less

Conceptual change strategies in teaching genetics

NASA Astrophysics Data System (ADS)

Batzli, Laura Elizabeth

The purpose of this study was to evaluate the effectiveness of utilizing conceptual change strategies when teaching high school genetics. The study examined the effects of structuring instruction to provide students with cognitive situations which promote conceptual change, specifically instruction was structured to elicit students' prior knowledge. The goal of the study was that the students would not only be able to solve genetics problems and define basic terminology but they would also have constructed more scientific schemas of the actual processes involved in inheritance. This study is based on the constructivist theory of learning and conceptual change research which suggest that students are actively involved in the process of relating new information to prior knowledge as they construct new knowledge. Two sections of biology II classes received inquiry based instruction and participated in structured cooperative learning groups. However, the unique difference in the treatment group's instruction was the use of structured thought time and the resulting social interaction between the students. The treatment group students' instructional design allowed students to socially construct their cognitive knowledge after elicitation of their prior knowledge. In contrast, the instructional design for the control group students allowed them to socially construct their cognitive knowledge of genetics without the individually structured thought time. The results indicated that the conceptual change strategies with individually structured thought time improved the students' scientific mastery of genetics concepts and they maintained fewer post instructional alternative conceptions. Although all students gained the ability to correctly solve genetics problems, the treatment group students were able to explain the processes involved in terms of meiosis. The treatment group students were also able to better apply their knowledge to novel genetic situations. The implications for genetics instruction from these results were discussed.

Advances in Pediatric Cardiology Boot Camp: Boot Camp Training Promotes Fellowship Readiness and Enables Retention of Knowledge.

PubMed

Ceresnak, Scott R; Axelrod, David M; Sacks, Loren D; Motonaga, Kara S; Johnson, Emily R; Krawczeski, Catherine D

2017-03-01

We previously demonstrated that a pediatric cardiology boot camp can improve knowledge acquisition and decrease anxiety for trainees. We sought to determine if boot camp participants entered fellowship with a knowledge advantage over fellows who did not attend and if there was moderate-term retention of that knowledge. A 2-day training program was provided for incoming pediatric cardiology fellows from eight fellowship programs in April 2016. Hands-on, immersive experiences and simulations were provided in all major areas of pediatric cardiology. Knowledge-based examinations were completed by each participant prior to boot camp (PRE), immediately post-training (POST), and prior to the start of fellowship in June 2016 (F/U). A control group of fellows who did not attend boot camp also completed an examination prior to fellowship (CTRL). Comparisons of scores were made for individual participants and between participants and controls. A total of 16 participants and 16 control subjects were included. Baseline exam scores were similar between participants and controls (PRE 47 ± 11% vs. CTRL 52 ± 10%; p = 0.22). Participants' knowledge improved with boot camp training (PRE 47 ± 11% vs. POST 70 ± 8%; p < 0.001) and there was excellent moderate-term retention of the information taught at boot camp (PRE 47 ± 11% vs. F/U 71 ± 8%; p < 0.001). Testing done at the beginning of fellowship demonstrated significantly better scores in participants versus controls (F/U 71 ± 8% vs. CTRL 52 ± 10%; p < 0.001). Boot camp participants demonstrated a significant improvement in basic cardiology knowledge after the training program and had excellent moderate-term retention of that knowledge. Participants began fellowship with a larger fund of knowledge than those fellows who did not attend.

Properties of the unusually short pulse sequences occurring prior to the first strokes of negative cloud-to-ground lightning flashes

NASA Astrophysics Data System (ADS)

Kolmasova, Ivana; Santolik, Ondrej; Farges, Thomas; Rison, William; Lan, Radek; Uhlir, Ludek

2014-05-01

We analyze pulse sequences occurring prior to first return strokes of negative cloud-to-ground lightning flashes. The magnetic-field waveforms are measured close to the thunderstorm using a broad-band analyzer with a sampling interval of 12.5 ns. The electric-field waveforms are measured at the distance of ~ 400 km using an analyzer with a sampling interval of 80 ns. The sequence is usually composed of three parts. It begins with a larger pulse train which is believed to be connected with initial breakdown processes. The train of preliminary breakdown pulses ("B" part) is followed by a relatively low and irregular pulse activity ("I" part), which is sometimes missing. The sequence ends with a pulse train attributed to the stepped leader ("L" part). We recognize two different patterns ("B-I-L" and "B-L" types) in recorded waveforms. For the first time, we analyze the time evolution of the pulse amplitudes in the "B" part of "B-I-L" type sequences. The pulse amplitude is decreasing on average by 34% of the maximum value within a given train. We observe an unusually short duration of sequences. This is probably linked to a low height of the thundercloud. Another possible explanation may be based on an untypical precipitation mix resulting in faster steeped leaders.

Later learning stages in procedural memory are impaired in children with Specific Language Impairment.

PubMed

Desmottes, Lise; Meulemans, Thierry; Maillart, Christelle

2016-01-01

According to the Procedural Deficit Hypothesis (PDH), difficulties in the procedural memory system may contribute to the language difficulties encountered by children with Specific Language Impairment (SLI). Most studies investigating the PDH have used the sequence learning paradigm; however these studies have principally focused on initial sequence learning in a single practice session. The present study sought to extend these investigations by assessing the consolidation stage and longer-term retention of implicit sequence-specific knowledge in 42 children with or without SLI. Both groups of children completed a serial reaction time task and were tested 24h and one week after practice. Results showed that children with SLI succeeded as well as children with typical development (TD) in the early acquisition stage of the sequence learning task. However, as training blocks progressed, only TD children improved their sequence knowledge while children with SLI did not appear to evolve any more. Moreover, children with SLI showed a lack of the consolidation gains in sequence knowledge displayed by the TD children. Overall, these results were in line with the predictions of the PDH and suggest that later learning stages in procedural memory are impaired in SLI. Copyright © 2015 Elsevier Ltd. All rights reserved.

Elapsed decision time affects the weighting of prior probability in a perceptual decision task

PubMed Central

Hanks, Timothy D.; Mazurek, Mark E.; Kiani, Roozbeh; Hopp, Elizabeth; Shadlen, Michael N.

2012-01-01

Decisions are often based on a combination of new evidence with prior knowledge of the probable best choice. Optimal combination requires knowledge about the reliability of evidence, but in many realistic situations, this is unknown. Here we propose and test a novel theory: the brain exploits elapsed time during decision formation to combine sensory evidence with prior probability. Elapsed time is useful because (i) decisions that linger tend to arise from less reliable evidence, and (ii) the expected accuracy at a given decision time depends on the reliability of the evidence gathered up to that point. These regularities allow the brain to combine prior information with sensory evidence by weighting the latter in accordance with reliability. To test this theory, we manipulated the prior probability of the rewarded choice while subjects performed a reaction-time discrimination of motion direction using a range of stimulus reliabilities that varied from trial to trial. The theory explains the effect of prior probability on choice and reaction time over a wide range of stimulus strengths. We found that prior probability was incorporated into the decision process as a dynamic bias signal that increases as a function of decision time. This bias signal depends on the speed-accuracy setting of human subjects, and it is reflected in the firing rates of neurons in the lateral intraparietal cortex (LIP) of rhesus monkeys performing this task. PMID:21525274

Elapsed decision time affects the weighting of prior probability in a perceptual decision task.

PubMed

Hanks, Timothy D; Mazurek, Mark E; Kiani, Roozbeh; Hopp, Elisabeth; Shadlen, Michael N

2011-04-27

Decisions are often based on a combination of new evidence with prior knowledge of the probable best choice. Optimal combination requires knowledge about the reliability of evidence, but in many realistic situations, this is unknown. Here we propose and test a novel theory: the brain exploits elapsed time during decision formation to combine sensory evidence with prior probability. Elapsed time is useful because (1) decisions that linger tend to arise from less reliable evidence, and (2) the expected accuracy at a given decision time depends on the reliability of the evidence gathered up to that point. These regularities allow the brain to combine prior information with sensory evidence by weighting the latter in accordance with reliability. To test this theory, we manipulated the prior probability of the rewarded choice while subjects performed a reaction-time discrimination of motion direction using a range of stimulus reliabilities that varied from trial to trial. The theory explains the effect of prior probability on choice and reaction time over a wide range of stimulus strengths. We found that prior probability was incorporated into the decision process as a dynamic bias signal that increases as a function of decision time. This bias signal depends on the speed-accuracy setting of human subjects, and it is reflected in the firing rates of neurons in the lateral intraparietal area (LIP) of rhesus monkeys performing this task.

Using comprehension strategies with authentic text in a college chemistry course

NASA Astrophysics Data System (ADS)

Cain, Stephen Daniel

College science students learn important topics by reading textbooks, which contain dense technical prose. Comprehension strategies are known to increase learning from reading. One class of comprehension strategies, called elaboration strategies, is intended to link new information with prior knowledge. Elaboration strategies have an appeal in science courses where new information frequently depends on previously learned information. The purpose of this study was to determine the effectiveness of an elaboration strategy in an authentic college environment. General chemistry students read text about Lewis structures, figures drawn by chemists to depict molecules, while assigned to use either an elaboration strategy, namely elaborative interrogation, or another strategy, rereading, which served as a placebo control. Two texts of equal length were employed in this pretest-posttest experimental design. One was composed by the researcher. The other was an excerpt from a college textbook and contained a procedure for constructing Lewis structures. Students (N = 252) attending a large community college were randomly assigned to one of the two texts and assigned one of the two strategies. The elaborative interrogation strategy was implemented with instructions to answer why-questions posed throughout the reading. Answering why-questions has been hypothesized to activate prior knowledge of a topic, and thus to aid in cognitively connecting new material with prior knowledge. The rereading strategy was implemented with instructions to read text twice. The use of authentic text was one of only a few instances of applying elaborative interrogation with a textbook. In addition, previous studies have generally focused on the learning of facts contained in prose. The application of elaborative interrogation to procedural text has not been previously reported. Results indicated that the more effective strategy was undetermined when reading authentic text in this setting. However, prior knowledge level was identified as a statistically significant factor for learning from authentic text. That is, students with high prior knowledge learned more, regardless of assigned strategy. Another descriptive study was conducted with a separate student sample (N = 34). Previously reported Lewis structure research was replicated. The trend of difficulty for 50 structures in the earlier work was supported.

Levels of line graph question interpretation with intermediate elementary students of varying scientific and mathematical knowledge and ability: A think aloud study

NASA Astrophysics Data System (ADS)

Keller, Stacy Kathryn

This study examined how intermediate elementary students' mathematics and science background knowledge affected their interpretation of line graphs and how their interpretations were affected by graph question levels. A purposive sample of 14 6th-grade students engaged in think aloud interviews (Ericsson & Simon, 1993) while completing an excerpted Test of Graphing in Science (TOGS) (McKenzie & Padilla, 1986). Hand gestures were video recorded. Student performance on the TOGS was assessed using an assessment rubric created from previously cited factors affecting students' graphing ability. Factors were categorized using Bertin's (1983) three graph question levels. The assessment rubric was validated by Padilla and a veteran mathematics and science teacher. Observational notes were also collected. Data were analyzed using Roth and Bowen's semiotic process of reading graphs (2001). Key findings from this analysis included differences in the use of heuristics, self-generated questions, science knowledge, and self-motivation. Students with higher prior achievement used a greater number and variety of heuristics and more often chose appropriate heuristics. They also monitored their understanding of the question and the adequacy of their strategy and answer by asking themselves questions. Most used their science knowledge spontaneously to check their understanding of the question and the adequacy of their answers. Students with lower and moderate prior achievement favored one heuristic even when it was not useful for answering the question and rarely asked their own questions. In some cases, if students with lower prior achievement had thought about their answers in the context of their science knowledge, they would have been able to recognize their errors. One student with lower prior achievement motivated herself when she thought the questions were too difficult. In addition, students answered the TOGS in one of three ways: as if they were mathematics word problems, science data to be analyzed, or they were confused and had to guess. A second set of findings corroborated how science background knowledge affected graph interpretation: correct science knowledge supported students' reasoning, but it was not necessary to answer any question correctly; correct science knowledge could not compensate for incomplete mathematics knowledge; and incorrect science knowledge often distracted students when they tried to use it while answering a question. Finally, using Roth and Bowen's (2001) two-stage semiotic model of reading graphs, representative vignettes showed emerging patterns from the study. This study added to our understanding of the role of science content knowledge during line graph interpretation, highlighted the importance of heuristics and mathematics procedural knowledge, and documented the importance of perception attentions, motivation, and students' self-generated questions. Recommendations were made for future research in line graph interpretation in mathematics and science education and for improving instruction in this area.

Knowledge-based nonuniform sampling in multidimensional NMR.

PubMed

Schuyler, Adam D; Maciejewski, Mark W; Arthanari, Haribabu; Hoch, Jeffrey C

2011-07-01

The full resolution afforded by high-field magnets is rarely realized in the indirect dimensions of multidimensional NMR experiments because of the time cost of uniformly sampling to long evolution times. Emerging methods utilizing nonuniform sampling (NUS) enable high resolution along indirect dimensions by sampling long evolution times without sampling at every multiple of the Nyquist sampling interval. While the earliest NUS approaches matched the decay of sampling density to the decay of the signal envelope, recent approaches based on coupled evolution times attempt to optimize sampling by choosing projection angles that increase the likelihood of resolving closely-spaced resonances. These approaches employ knowledge about chemical shifts to predict optimal projection angles, whereas prior applications of tailored sampling employed only knowledge of the decay rate. In this work we adapt the matched filter approach as a general strategy for knowledge-based nonuniform sampling that can exploit prior knowledge about chemical shifts and is not restricted to sampling projections. Based on several measures of performance, we find that exponentially weighted random sampling (envelope matched sampling) performs better than shift-based sampling (beat matched sampling). While shift-based sampling can yield small advantages in sensitivity, the gains are generally outweighed by diminished robustness. Our observation that more robust sampling schemes are only slightly less sensitive than schemes highly optimized using prior knowledge about chemical shifts has broad implications for any multidimensional NMR study employing NUS. The results derived from simulated data are demonstrated with a sample application to PfPMT, the phosphoethanolamine methyltransferase of the human malaria parasite Plasmodium falciparum.

Pattern Specificity in the Effect of Prior [delta]f on Auditory Stream Segregation

ERIC Educational Resources Information Center

Snyder, Joel S.; Weintraub, David M.

2011-01-01

During repeating sequences of low (A) and high (B) tones, perception of two separate streams ("streaming") increases with greater frequency separation ([delta]f) between the A and B tones; in contrast, a prior context with large [delta]f results in less streaming during a subsequent test pattern. The purpose of the present study was to…

Schema-driven facilitation of new hierarchy learning in the transitive inference paradigm

PubMed Central

Kumaran, Dharshan

2013-01-01

Prior knowledge, in the form of a mental schema or framework, is viewed to facilitate the learning of new information in a range of experimental and everyday scenarios. Despite rising interest in the cognitive and neural mechanisms underlying schema-driven facilitation of new learning, few paradigms have been developed to examine this issue in humans. Here we develop a multiphase experimental scenario aimed at characterizing schema-based effects in the context of a paradigm that has been very widely used across species, the transitive inference task. We show that an associative schema, comprised of prior knowledge of the rank positions of familiar items in the hierarchy, has a marked effect on transitivity performance and the development of relational knowledge of the hierarchy that cannot be accounted for by more general changes in task strategy. Further, we show that participants are capable of deploying prior knowledge to successful effect under surprising conditions (i.e., when corrective feedback is totally absent), but only when the associative schema is robust. Finally, our results provide insights into the cognitive mechanisms underlying such schema-driven effects, and suggest that new hierarchy learning in the transitive inference task can occur through a contextual transfer mechanism that exploits the structure of associative experiences. PMID:23782509

Orthonormal filters for identification in active control systems

NASA Astrophysics Data System (ADS)

Mayer, Dirk

2015-12-01

Many active noise and vibration control systems require models of the control paths. When the controlled system changes slightly over time, adaptive digital filters for the identification of the models are useful. This paper aims at the investigation of a special class of adaptive digital filters: orthonormal filter banks possess the robust and simple adaptation of the widely applied finite impulse response (FIR) filters, but at a lower model order, which is important when considering implementation on embedded systems. However, the filter banks require prior knowledge about the resonance frequencies and damping of the structure. This knowledge can be supposed to be of limited precision, since in many practical systems, uncertainties in the structural parameters exist. In this work, a procedure using a number of training systems to find the fixed parameters for the filter banks is applied. The effect of uncertainties in the prior knowledge on the model error is examined both with a basic example and in an experiment. Furthermore, the possibilities to compensate for the imprecise prior knowledge by a higher filter order are investigated. Also comparisons with FIR filters are implemented in order to assess the possible advantages of the orthonormal filter banks. Numerical and experimental investigations show that significantly lower computational effort can be reached by the filter banks under certain conditions.

Schema-driven facilitation of new hierarchy learning in the transitive inference paradigm.

PubMed

Kumaran, Dharshan

2013-06-19

Prior knowledge, in the form of a mental schema or framework, is viewed to facilitate the learning of new information in a range of experimental and everyday scenarios. Despite rising interest in the cognitive and neural mechanisms underlying schema-driven facilitation of new learning, few paradigms have been developed to examine this issue in humans. Here we develop a multiphase experimental scenario aimed at characterizing schema-based effects in the context of a paradigm that has been very widely used across species, the transitive inference task. We show that an associative schema, comprised of prior knowledge of the rank positions of familiar items in the hierarchy, has a marked effect on transitivity performance and the development of relational knowledge of the hierarchy that cannot be accounted for by more general changes in task strategy. Further, we show that participants are capable of deploying prior knowledge to successful effect under surprising conditions (i.e., when corrective feedback is totally absent), but only when the associative schema is robust. Finally, our results provide insights into the cognitive mechanisms underlying such schema-driven effects, and suggest that new hierarchy learning in the transitive inference task can occur through a contextual transfer mechanism that exploits the structure of associative experiences.

Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model.

PubMed

Jääskinen, Väinö; Parkkinen, Ville; Cheng, Lu; Corander, Jukka

2014-02-01

In many biological applications it is necessary to cluster DNA sequences into groups that represent underlying organismal units, such as named species or genera. In metagenomics this grouping needs typically to be achieved on the basis of relatively short sequences which contain different types of errors, making the use of a statistical modeling approach desirable. Here we introduce a novel method for this purpose by developing a stochastic partition model that clusters Markov chains of a given order. The model is based on a Dirichlet process prior and we use conjugate priors for the Markov chain parameters which enables an analytical expression for comparing the marginal likelihoods of any two partitions. To find a good candidate for the posterior mode in the partition space, we use a hybrid computational approach which combines the EM-algorithm with a greedy search. This is demonstrated to be faster and yield highly accurate results compared to earlier suggested clustering methods for the metagenomics application. Our model is fairly generic and could also be used for clustering of other types of sequence data for which Markov chains provide a reasonable way to compress information, as illustrated by experiments on shotgun sequence type data from an Escherichia coli strain.

High diversity and rapid diversification in the head louse, Pediculus humanus (Pediculidae: Phthiraptera)

PubMed Central

Ashfaq, Muhammad; Prosser, Sean; Nasir, Saima; Masood, Mariyam; Ratnasingham, Sujeevan; Hebert, Paul D. N.

2015-01-01

The study analyzes sequence variation of two mitochondrial genes (COI, cytb) in Pediculus humanus from three countries (Egypt, Pakistan, South Africa) that have received little prior attention, and integrates these results with prior data. Analysis indicates a maximum K2P distance of 10.3% among 960 COI sequences and 13.8% among 479 cytb sequences. Three analytical methods (BIN, PTP, ABGD) reveal five concordant OTUs for COI and cytb. Neighbor-Joining analysis of the COI sequences confirm five clusters; three corresponding to previously recognized mitochondrial clades A, B, C and two new clades, “D” and “E”, showing 2.3% and 2.8% divergence from their nearest neighbors (NN). Cytb data corroborate five clusters showing that clades “D” and “E” are both 4.6% divergent from their respective NN clades. Phylogenetic analysis supports the monophyly of all clusters recovered by NJ analysis. Divergence time estimates suggest that the earliest split of P. humanus clades occured slightly more than one million years ago (MYa) and the latest about 0.3 MYa. Sequence divergences in COI and cytb among the five clades of P. humanus are 10X those in their human host, a difference that likely reflects both rate acceleration and the acquisition of lice clades from several archaic hominid lineages. PMID:26373806

Phase-contrast cerebrospinal fluid flow magnetic resonance imaging in qualitative evaluation of patency of CSF flow pathways prior to infusion of chemotherapeutic and other agents into the fourth ventricle.

PubMed

Patel, Rajan P; Sitton, Clark W; Ketonen, Leena M; Hou, Ping; Johnson, Jason M; Romo, Seferino; Fletcher, Stephen; Shah, Manish N; Kerr, Marcia; Zaky, Wafik; Rytting, Michael E; Khatua, Soumen; Sandberg, David I

2018-03-01

Nuclear medicine studies have previously been utilized to assess for blockage of cerebrospinal fluid (CSF) flow prior to intraventricular chemotherapy infusions. To assess CSF flow without nuclear medicine studies, we obtained cine phase-contrast MRI sequences that assess CSF flow from the fourth ventricle down to the sacrum. In three clinical trials, 18 patients with recurrent malignant posterior fossa tumors underwent implantation of a ventricular access device (VAD) into the fourth ventricle, either with or without simultaneous tumor resection. Prior to infusing therapeutic agents into the VAD, cine MRI phase-contrast CSF flow sequences of the brain and total spine were performed. Velocity encoding (VENC) of 5 and 10 cm/s was used to confirm CSF flow from the fourth ventricular outlets to the cervical, thoracic, and lumbar spine. Qualitative CSF flow was characterized by neuroradiologists as present or absent. All 18 patients demonstrated CSF flow from the outlets of the fourth ventricle down to the sacrum with no evidence of obstruction. One of these patients, after disease progression, subsequently showed obstruction of CSF flow. No patient required a nuclear medicine study to assess CSF flow prior to initiation of infusions. Fourteen patients have received infusions to date, and none has had neurological toxicity. CSF flow including the fourth ventricle and the total spine can be assessed noninvasively with phase-contrast MRI sequences. Advantages over nuclear medicine studies include avoiding both an invasive procedure and radiation exposure.

Positive relationship between odor identification and affective responses of negatively valenced odors

PubMed Central

Martinec Nováková, Lenka; Plotěná, Dagmar; Roberts, S. Craig; Havlíček, Jan

2015-01-01

Hedonic ratings of odors and olfactory preferences are influenced by a number of modulating factors, such as prior experience and knowledge about an odor’s identity. The present study addresses the relationship between knowledge about an odor’s identity due to prior experience, assessed by means of a test of cued odor identification, and odor pleasantness ratings in children who exhibit ongoing olfactory learning. Ninety-one children aged 8–11 years rated the pleasantness of odors in the Sniffin’ Sticks test and, subsequently, took the odor identification test. A positive association between odor identification and pleasantness was found for two unpleasant food odors (garlic and fish): higher pleasantness ratings were exhibited by those participants who correctly identified these odors compared to those who failed to correctly identify them. However, we did not find a similar effect for any of the more pleasant odors. The results of this study suggest that pleasantness ratings of some odors may be modulated by the knowledge of their identity due to prior experience and that this relationship might be more evident in unpleasant odors. PMID:26029143

A technology training protocol for meeting QSEN goals: Focusing on meaningful learning.

PubMed

Luo, Shuhong; Kalman, Melanie

2018-01-01

The purpose of this paper is to describe and discuss how we designed and developed a 12-step technology training protocol. The protocol is meant to improve meaningful learning in technology education so that nursing students are able to meet the informatics requirements of Quality and Safety Education in Nursing competencies. When designing and developing the training protocol, we used a simplified experiential learning model that addressed the core features of meaningful learning: to connect new knowledge with students' prior knowledge and real-world workflow. Before training, we identified students' prior knowledge and workflow tasks. During training, students learned by doing, reflected on their prior computer skills and workflow, designed individualized procedures for integration into their workflow, and practiced the self-designed procedures in real-world settings. The trainer was a facilitator who provided a meaningful learning environment, asked the right questions to guide reflective conversation, and offered scaffoldings at critical moments. This training protocol could significantly improve nurses' competencies in using technologies and increase their desire to adopt new technologies. © 2017 Wiley Periodicals, Inc.

Topics in inference and decision-making with partial knowledge

NASA Technical Reports Server (NTRS)

Safavian, S. Rasoul; Landgrebe, David

1990-01-01

Two essential elements needed in the process of inference and decision-making are prior probabilities and likelihood functions. When both of these components are known accurately and precisely, the Bayesian approach provides a consistent and coherent solution to the problems of inference and decision-making. In many situations, however, either one or both of the above components may not be known, or at least may not be known precisely. This problem of partial knowledge about prior probabilities and likelihood functions is addressed. There are at least two ways to cope with this lack of precise knowledge: robust methods, and interval-valued methods. First, ways of modeling imprecision and indeterminacies in prior probabilities and likelihood functions are examined; then how imprecision in the above components carries over to the posterior probabilities is examined. Finally, the problem of decision making with imprecise posterior probabilities and the consequences of such actions are addressed. Application areas where the above problems may occur are in statistical pattern recognition problems, for example, the problem of classification of high-dimensional multispectral remote sensing image data.

Bayesian network prior: network analysis of biological data using external knowledge

PubMed Central

Isci, Senol; Dogan, Haluk; Ozturk, Cengizhan; Otu, Hasan H.

2014-01-01

Motivation: Reverse engineering GI networks from experimental data is a challenging task due to the complex nature of the networks and the noise inherent in the data. One way to overcome these hurdles would be incorporating the vast amounts of external biological knowledge when building interaction networks. We propose a framework where GI networks are learned from experimental data using Bayesian networks (BNs) and the incorporation of external knowledge is also done via a BN that we call Bayesian Network Prior (BNP). BNP depicts the relation between various evidence types that contribute to the event ‘gene interaction’ and is used to calculate the probability of a candidate graph (G) in the structure learning process. Results: Our simulation results on synthetic, simulated and real biological data show that the proposed approach can identify the underlying interaction network with high accuracy even when the prior information is distorted and outperforms existing methods. Availability: Accompanying BNP software package is freely available for academic use at http://bioe.bilgi.edu.tr/BNP. Contact: hasan.otu@bilgi.edu.tr Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:24215027

Overview of refinement procedures within REFMAC5: utilizing data from different sources.

PubMed

Kovalevskiy, Oleg; Nicholls, Robert A; Long, Fei; Carlon, Azzurra; Murshudov, Garib N

2018-03-01

Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (B factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures using REFMAC5 and related tools distributed as part of the CCP4 suite is discussed.

The effects of prior knowledge on study-time allocation and free recall: investigating the discrepancy reduction model.

PubMed

Verkoeijen, Peter P J L; Rikers, Remy M J P; Schmidt, Henk G

2005-01-01

In this study, the authors examined the influence of prior knowledge activation on information processing by means of a prior knowledge activation procedure adopted from the read-generate paradigm. On the basis of cue-target pairs, participants in the experimental groups generated two different sets of items before studying a relevant list. Subsequently, participants were informed that they had to study the items in the list and that they should try to remember as many items as possible. The authors assessed the processing time allocated to the items in the list and free recall of those items. The results revealed that the experimental groups spent less time on items that had already been activated. In addition, the experimental groups outperformed the control group in overall free recall and in free recall of the activated items. Between-group comparisons did not demonstrate significant effects with respect to the processing time and free recall of nonactivated items. The authors interpreted these results in terms of the discrepancy reduction model of regulating the amount of processing time allocated to different parts of the list.

Fault diagnosis of sensor networked structures with multiple faults using a virtual beam based approach

NASA Astrophysics Data System (ADS)

Wang, H.; Jing, X. J.

2017-07-01

This paper presents a virtual beam based approach suitable for conducting diagnosis of multiple faults in complex structures with limited prior knowledge of the faults involved. The "virtual beam", a recently-proposed concept for fault detection in complex structures, is applied, which consists of a chain of sensors representing a vibration energy transmission path embedded in the complex structure. Statistical tests and adaptive threshold are particularly adopted for fault detection due to limited prior knowledge of normal operational conditions and fault conditions. To isolate the multiple faults within a specific structure or substructure of a more complex one, a 'biased running' strategy is developed and embedded within the bacterial-based optimization method to construct effective virtual beams and thus to improve the accuracy of localization. The proposed method is easy and efficient to implement for multiple fault localization with limited prior knowledge of normal conditions and faults. With extensive experimental results, it is validated that the proposed method can localize both single fault and multiple faults more effectively than the classical trust index subtract on negative add on positive (TI-SNAP) method.

Deep Sequencing to Identify the Causes of Viral Encephalitis

PubMed Central

Chan, Benjamin K.; Wilson, Theodore; Fischer, Kael F.; Kriesel, John D.

2014-01-01

Deep sequencing allows for a rapid, accurate characterization of microbial DNA and RNA sequences in many types of samples. Deep sequencing (also called next generation sequencing or NGS) is being developed to assist with the diagnosis of a wide variety of infectious diseases. In this study, seven frozen brain samples from deceased subjects with recent encephalitis were investigated. RNA from each sample was extracted, randomly reverse transcribed and sequenced. The sequence analysis was performed in a blinded fashion and confirmed with pathogen-specific PCR. This analysis successfully identified measles virus sequences in two brain samples and herpes simplex virus type-1 sequences in three brain samples. No pathogen was identified in the other two brain specimens. These results were concordant with pathogen-specific PCR and partially concordant with prior neuropathological examinations, demonstrating that deep sequencing can accurately identify viral infections in frozen brain tissue. PMID:24699691

The Influence of the Knowledge Base on the Development of Mnemonic Strategies.

ERIC Educational Resources Information Center

Ornstein, Peter A.; Naus, Mary J.

A dominant theme in cognitive psychology is that prior knowledge in long-term memory has a strong influence on an individual's cognitive processing. Citing numerous memory studies with children, knowledge base effects are presented as part of a broader picture of memory development. Using the sort/recall procedure (asking subjects to group sets of…

The Roles of Ability, Personality, and Interests in Acquiring Current Events Knowledge: A Longitudinal Study

ERIC Educational Resources Information Center

Hambrick, David Z.; Pink, Jeffrey E.; Meinz, Elizabeth J.; Pettibone, Jonathan C.; Oswald, Frederick L.

2008-01-01

The purpose of this study was to investigate sources of inter-individual differences in current events knowledge. The study occurred in two sessions. In the initial session, 579 participants completed tests to ability, personality, and interest factors, as well as prior knowledge of current events. Approximately 10 weeks later, participants…

Cognitive Demand Differences in Causal Inferences: Characters' Plans Are More Difficult to Comprehend than Physical Causation

ERIC Educational Resources Information Center

Shears, Connie; Miller, Vanessa; Ball, Megan; Hawkins, Amanda; Griggs, Janna; Varner, Andria

2007-01-01

Readers may draw knowledge-based inferences to connect sentences in text differently depending on the knowledge domain being accessed. Most prior research has focused on the direction of the causal explanation (predictive vs. backward) without regard to the knowledge domain drawn on to support comprehension. We suggest that less cognitive effort…

A Connective Ethnography of Peer Knowledge Sharing and Diffusion in a Tween Virtual World

ERIC Educational Resources Information Center

Fields, Deborah A.; Kafai, Yasmin B.

2009-01-01

Prior studies have shown how knowledge diffusion occurs in classrooms and structured small groups around assigned tasks yet have not begun to account for widespread knowledge sharing in more native, unstructured group settings found in online games and virtual worlds. In this paper, we describe and analyze how an insider gaming practice spread…

Examining the Acquisition of Vocabulary Knowledge Depth among Preschool Students

ERIC Educational Resources Information Center

Hadley, Elizabeth B.; Dickinson, David K.; Hirsh-Pasek, Kathy; Golinkoff, Roberta Michnick; Nesbitt, Kimberly T.

2016-01-01

Well-developed lexical representations are important for reading comprehension, but there have been no prior attempts to track growth in the depth of knowledge of particular words. This article examines increases in depth of vocabulary knowledge in 4-5-year-old preschool students (n = 240) who participated in a vocabulary intervention that taught…

High School Students' Meta-Modeling Knowledge

ERIC Educational Resources Information Center

Fortus, David; Shwartz, Yael; Rosenfeld, Sherman

2016-01-01

Modeling is a core scientific practice. This study probed the meta-modeling knowledge (MMK) of high school students who study science but had not had any explicit prior exposure to modeling as part of their formal schooling. Our goals were to (A) evaluate the degree to which MMK is dependent on content knowledge and (B) assess whether the upper…

How to Write "How-to" Books with High School Ecology & Horticulture Students

ERIC Educational Resources Information Center

Merritt, Maya; Shajira, Natasya; Daisey, Peggy

2003-01-01

It is essential for students to think clearly about fundamental biological concepts. One of the benefits of writing is that it promotes and enhances thinking. If students can write clearly, they are thinking clearly. Writing helps to connect new knowledge with prior knowledge and promotes the construction of knowledge. Writing-to-learn activities…

5 CFR 4701.102 - Prior approval for certain outside employment.

Code of Federal Regulations, 2012 CFR

2012-01-01

... STANDARDS OF ETHICAL CONDUCT FOR EMPLOYEES OF THE FEDERAL ELECTION COMMISSION § 4701.102 Prior approval for... or consultation, which requires advanced knowledge in a field of science or learning customarily... obtain written approval from the Designated Agency Ethics Official before engaging in outside employment...

5 CFR 4701.102 - Prior approval for certain outside employment.

Code of Federal Regulations, 2013 CFR

2013-01-01

... STANDARDS OF ETHICAL CONDUCT FOR EMPLOYEES OF THE FEDERAL ELECTION COMMISSION § 4701.102 Prior approval for... or consultation, which requires advanced knowledge in a field of science or learning customarily... obtain written approval from the Designated Agency Ethics Official before engaging in outside employment...

5 CFR 4701.102 - Prior approval for certain outside employment.

Code of Federal Regulations, 2014 CFR

2014-01-01

... STANDARDS OF ETHICAL CONDUCT FOR EMPLOYEES OF THE FEDERAL ELECTION COMMISSION § 4701.102 Prior approval for... or consultation, which requires advanced knowledge in a field of science or learning customarily... obtain written approval from the Designated Agency Ethics Official before engaging in outside employment...

Do Knowledge Arrangements Affect Student Reading Comprehension of Genetics?

ERIC Educational Resources Information Center

Wu, Jen-Yi; Tung, Yu-Neng; Hwang, Bi-Chi; Lin, Chen-Yung; Che-Di, Lee; Chang, Yung-Ta

2014-01-01

Various sequences for teaching genetics have been proposed. Three seventh-grade biology textbooks in Taiwan share similar key knowledge assemblages but have different knowledge arrangements. To investigate the influence of knowledge arrangements on student understanding of genetics, we compared students' reading comprehension of the three texts…

Conceptualising GP teachers' knowledge: a pedagogical content knowledge perspective.

PubMed

Cantillon, Peter; de Grave, Willem

2012-05-01

Most teacher development initiatives focus on enhancing knowledge of teaching (pedagogy), whilst largely ignoring other important features of teacher knowledge such as subject matter knowledge and awareness of the learning context. Furthermore, teachers' ability to learn from faculty development interventions is limited by their existing (often implicit) pedagogical knowledge and beliefs. Pedagogical content knowledge (PCK) represents a model of teacher knowledge incorporating what they know about subject matter, pedagogy and context. PCK can be used to explore teachers' prior knowledge and to structure faculty development programmes so that they take account of a broader range of teachers' knowledge. We set out to examine the application of a PCK model in a general practice education setting. This study is part of a larger study that employed a mixed method approach (concept mapping, phenomenological interviews and video-stimulated recall) to explore features of GP teachers' subject matter knowledge, pedagogical knowledge and knowledge of the learning environment in the context of a general practice tutorial. This paper presents data on GP teachers' pedagogical and context knowledge. There was considerable overlap between different GP teachers' knowledge and beliefs about learners and the clinical learning environment (i.e. knowledge of context). The teachers' beliefs about learners were largely based on assumptions derived from their own student experiences. There were stark differences, however, between teachers in terms of pedagogical knowledge, particularly in terms of their teaching orientations (i.e. transmission or facilitation orientation) and this was manifest in their teaching behaviours. PCK represents a useful model for conceptualising clinical teacher prior knowledge in three domains, namely subject matter, learning context and pedagogy. It can and should be used as a simple guiding framework by faculty developers to inform the design and delivery of their faculty development programmes.

Blind Bayesian restoration of adaptive optics telescope images using generalized Gaussian Markov random field models

NASA Astrophysics Data System (ADS)

Jeffs, Brian D.; Christou, Julian C.

1998-09-01

This paper addresses post processing for resolution enhancement of sequences of short exposure adaptive optics (AO) images of space objects. The unknown residual blur is removed using Bayesian maximum a posteriori blind image restoration techniques. In the problem formulation, both the true image and the unknown blur psf's are represented by the flexible generalized Gaussian Markov random field (GGMRF) model. The GGMRF probability density function provides a natural mechanism for expressing available prior information about the image and blur. Incorporating such prior knowledge in the deconvolution optimization is crucial for the success of blind restoration algorithms. For example, space objects often contain sharp edge boundaries and geometric structures, while the residual blur psf in the corresponding partially corrected AO image is spectrally band limited, and exhibits while the residual blur psf in the corresponding partially corrected AO image is spectrally band limited, and exhibits smoothed, random , texture-like features on a peaked central core. By properly choosing parameters, GGMRF models can accurately represent both the blur psf and the object, and serve to regularize the deconvolution problem. These two GGMRF models also serve as discriminator functions to separate blur and object in the solution. Algorithm performance is demonstrated with examples from synthetic AO images. Results indicate significant resolution enhancement when applied to partially corrected AO images. An efficient computational algorithm is described.

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

PubMed

Mahajan, Gaurang; Mande, Shekhar C

2017-04-04

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

Bias in the physical examination of patients with lumbar radiculopathy

PubMed Central

2010-01-01

Background No prior studies have examined systematic bias in the musculoskeletal physical examination. The objective of this study was to assess the effects of bias due to prior knowledge of lumbar spine magnetic resonance imaging findings (MRI) on perceived diagnostic accuracy of the physical examination for lumbar radiculopathy. Methods This was a cross-sectional comparison of the performance characteristics of the physical examination with blinding to MRI results (the 'independent group') with performance in the situation where the physical examination was not blinded to MRI results (the 'non-independent group'). The reference standard was the final diagnostic impression of nerve root impingement by the examining physician. Subjects were recruited from a hospital-based outpatient specialty spine clinic. All adults age 18 and older presenting with lower extremity radiating pain of duration ≤ 12 weeks were evaluated for participation. 154 consecutively recruited subjects with lumbar disk herniation confirmed by lumbar spine MRI were included in this study. Sensitivities and specificities with 95% confidence intervals were calculated in the independent and non-independent groups for the four components of the radiculopathy examination: 1) provocative testing, 2) motor strength testing, 3) pinprick sensory testing, and 4) deep tendon reflex testing. Results The perceived sensitivity of sensory testing was higher with prior knowledge of MRI results (20% vs. 36%; p = 0.05). Sensitivities and specificities for exam components otherwise showed no statistically significant differences between groups. Conclusions Prior knowledge of lumbar MRI results may introduce bias into the pinprick sensory testing component of the physical examination for lumbar radiculopathy. No statistically significant effect of bias was seen for other components of the physical examination. The effect of bias due to prior knowledge of lumbar MRI results should be considered when an isolated sensory deficit on examination is used in medical decision-making. Further studies of bias should include surgical clinic populations and other common diagnoses including shoulder, knee and hip pathology. PMID:21118558

Bias in the physical examination of patients with lumbar radiculopathy.

PubMed

Suri, Pradeep; Hunter, David J; Katz, Jeffrey N; Li, Ling; Rainville, James

2010-11-30

No prior studies have examined systematic bias in the musculoskeletal physical examination. The objective of this study was to assess the effects of bias due to prior knowledge of lumbar spine magnetic resonance imaging findings (MRI) on perceived diagnostic accuracy of the physical examination for lumbar radiculopathy. This was a cross-sectional comparison of the performance characteristics of the physical examination with blinding to MRI results (the 'independent group') with performance in the situation where the physical examination was not blinded to MRI results (the 'non-independent group'). The reference standard was the final diagnostic impression of nerve root impingement by the examining physician. Subjects were recruited from a hospital-based outpatient specialty spine clinic. All adults age 18 and older presenting with lower extremity radiating pain of duration ≤ 12 weeks were evaluated for participation. 154 consecutively recruited subjects with lumbar disk herniation confirmed by lumbar spine MRI were included in this study. Sensitivities and specificities with 95% confidence intervals were calculated in the independent and non-independent groups for the four components of the radiculopathy examination: 1) provocative testing, 2) motor strength testing, 3) pinprick sensory testing, and 4) deep tendon reflex testing. The perceived sensitivity of sensory testing was higher with prior knowledge of MRI results (20% vs. 36%; p = 0.05). Sensitivities and specificities for exam components otherwise showed no statistically significant differences between groups. Prior knowledge of lumbar MRI results may introduce bias into the pinprick sensory testing component of the physical examination for lumbar radiculopathy. No statistically significant effect of bias was seen for other components of the physical examination. The effect of bias due to prior knowledge of lumbar MRI results should be considered when an isolated sensory deficit on examination is used in medical decision-making. Further studies of bias should include surgical clinic populations and other common diagnoses including shoulder, knee and hip pathology.

Rapidly rotating polytropes in general relativity

NASA Technical Reports Server (NTRS)

Cook, Gregory B.; Shapiro, Stuart L.; Teukolsky, Saul A.

1994-01-01

We construct an extensive set of equilibrium sequences of rotating polytropes in general relativity. We determine a number of important physical parameters of such stars, including maximum mass and maximum spin rate. The stability of the configurations against quasi-radial perturbations is diagnosed. Two classes of evolutionary sequences of fixed rest mass and entropy are explored: normal sequences which behave very much like Newtonian evolutionary sequences, and supramassive sequences which exist solely because of relativistic effects. Dissipation leading to loss of angular momentum causes a star to evolve in a quasi-stationary fashion along an evolutionary sequence. Supramassive sequences evolve towards eventual catastrophic collapse to a black hole. Prior to collapse, the star must spin up as it loses angular momentum, an effect which may provide an observational precursor to gravitational collapse to a black hole.

Lack of X inactivation associated with maternal X isodisomy: evidence for a counting mechanism prior to X inactivation during human embryogenesis.

PubMed

Migeon, B R; Jeppesen, P; Torchia, B S; Fu, S; Dunn, M A; Axelman, J; Schmeckpeper, B J; Fantes, J; Zori, R T; Driscoll, D J

1996-01-01

We have previously reported functional disomy for X-linked genes in females with tiny ring X chromosomes and a phenotype significantly more abnormal than Turner syndrome. In such cases the disomy results from failure of these X chromosomes to inactivate because they lack DNA sequences essential for cis X inactivation. Here we describe a novel molecular mechanism for functional X disomy that is associated with maternal isodisomy. In this case, the severe mental retardation and multiple congenital abnormalities in a female with a mosaic 45,X/ 46,X,del(X)(q21.3-qter)/ 46X,r(X) karyotype are associated with overexpression of the genes within Xpter to Xq21.31 in many of her cells. Her normal X, ring X, and deleted linear X chromosomes originate from the same maternal X chromosome, and all are transcriptionally active. None expresses X inactive specific transcript (XIST), although the locus and region of the putative X inactivation center (XIC) are present on both normal and linear deleted X chromosomes. To our knowledge, this is the first report of a functional maternal X isodisomy, and the largest X chromosome to escape inactivation. In addition, these results (1) show that cis inactivation does not invariably occur in human females with two X chromosomes, even when the XIC region is present on both of them; (2) provide evidence for a critical time prior to the visible onset of X inactivation in the embryo when decisions about X inactivation are made; and (3) support the hypothesis that the X chromosome counting mechanism involves chromosomal imprinting, occurs prior to the onset of random inactivation, and is required for subsequent inactivation of the chromosome.

Bayesian Correlation Analysis for Sequence Count Data

PubMed Central

Lau, Nelson; Perkins, Theodore J.

2016-01-01

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. PMID:27701449