fba-simvis interactive visualization: Topics by Science.gov

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Temporal multiplexing to simulate multifocal intraocular lenses: theoretical considerations

PubMed Central

Akondi, Vyas; Dorronsoro, Carlos; Gambra, Enrique; Marcos, Susana

2017-01-01

Fast tunable lenses allow an effective design of a portable simultaneous vision simulator (SimVis) of multifocal corrections. A novel method of evaluating the temporal profile of a tunable lens in simulating different multifocal intraocular lenses (M-IOLs) is presented. The proposed method involves the characteristic fitting of the through-focus (TF) optical quality of the multifocal component of a given M-IOL to a linear combination of TF optical quality of monofocal lenses viable with a tunable lens. Three different types of M-IOL designs are tested, namely: segmented refractive, diffractive and refractive extended depth of focus. The metric used for the optical evaluation of the temporal profile is the visual Strehl (VS) ratio. It is shown that the time profiles generated with the VS ratio as a metric in SimVis resulted in TF VS ratio and TF simulated images that closely matched the TF VS ratio and TF simulated images predicted with the M-IOL. The effects of temporal sampling, varying pupil size, monochromatic aberrations, longitudinal chromatic aberrations and temporal dynamics on SimVis are discussed. PMID:28717577
Interaction Between Spatial and Feature Attention in Posterior Parietal Cortex

PubMed Central

Ibos, Guilhem; Freedman, David J.

2016-01-01

Summary Lateral intraparietal (LIP) neurons encode a vast array of sensory and cognitive variables. Recently, we proposed that the flexibility of feature representations in LIP reflect the bottom-up integration of sensory signals, modulated by feature-based attention (FBA), from upstream feature-selective cortical neurons. Moreover, LIP activity is also strongly modulated by the position of space-based attention (SBA). However, the mechanisms by which SBA and FBA interact to facilitate the representation of task-relevant spatial and non-spatial features in LIP remain unclear. We recorded from LIP neurons during performance of a task which required monkeys to detect specific conjunctions of color, motion-direction, and stimulus position. Here we show that FBA and SBA potentiate each other’s effect in a manner consistent with attention gating the flow of visual information along the cortical visual pathway. Our results suggest that linear bottom-up integrative mechanisms allow LIP neurons to emphasize task-relevant spatial and non-spatial features. PMID:27499082
Interaction between Spatial and Feature Attention in Posterior Parietal Cortex.

PubMed

Ibos, Guilhem; Freedman, David J

2016-08-17

Lateral intraparietal (LIP) neurons encode a vast array of sensory and cognitive variables. Recently, we proposed that the flexibility of feature representations in LIP reflect the bottom-up integration of sensory signals, modulated by feature-based attention (FBA), from upstream feature-selective cortical neurons. Moreover, LIP activity is also strongly modulated by the position of space-based attention (SBA). However, the mechanisms by which SBA and FBA interact to facilitate the representation of task-relevant spatial and non-spatial features in LIP remain unclear. We recorded from LIP neurons during performance of a task that required monkeys to detect specific conjunctions of color, motion direction, and stimulus position. Here we show that FBA and SBA potentiate each other's effect in a manner consistent with attention gating the flow of visual information along the cortical visual pathway. Our results suggest that linear bottom-up integrative mechanisms allow LIP neurons to emphasize task-relevant spatial and non-spatial features. Copyright © 2016 Elsevier Inc. All rights reserved.
Feature-based attention: it is all bottom-up priming.

PubMed

Theeuwes, Jan

2013-10-19

Feature-based attention (FBA) enhances the representation of image characteristics throughout the visual field, a mechanism that is particularly useful when searching for a specific stimulus feature. Even though most theories of visual search implicitly or explicitly assume that FBA is under top-down control, we argue that the role of top-down processing in FBA may be limited. Our review of the literature indicates that all behavioural and neuro-imaging studies investigating FBA suffer from the shortcoming that they cannot rule out an effect of priming. The mere attending to a feature enhances the mandatory processing of that feature across the visual field, an effect that is likely to occur in an automatic, bottom-up way. Studies that have investigated the feasibility of FBA by means of cueing paradigms suggest that the role of top-down processing in FBA is limited (e.g. prepare for red). Instead, the actual processing of the stimulus is needed to cause the mandatory tuning of responses throughout the visual field. We conclude that it is likely that all FBA effects reported previously are the result of bottom-up priming.
Feature-based attention: it is all bottom-up priming

PubMed Central

Theeuwes, Jan

2013-01-01

Feature-based attention (FBA) enhances the representation of image characteristics throughout the visual field, a mechanism that is particularly useful when searching for a specific stimulus feature. Even though most theories of visual search implicitly or explicitly assume that FBA is under top-down control, we argue that the role of top-down processing in FBA may be limited. Our review of the literature indicates that all behavioural and neuro-imaging studies investigating FBA suffer from the shortcoming that they cannot rule out an effect of priming. The mere attending to a feature enhances the mandatory processing of that feature across the visual field, an effect that is likely to occur in an automatic, bottom-up way. Studies that have investigated the feasibility of FBA by means of cueing paradigms suggest that the role of top-down processing in FBA is limited (e.g. prepare for red). Instead, the actual processing of the stimulus is needed to cause the mandatory tuning of responses throughout the visual field. We conclude that it is likely that all FBA effects reported previously are the result of bottom-up priming. PMID:24018717
Feature-based attention potentiates recovery of fine direction discrimination in cortically blind patients.

PubMed

Cavanaugh, Matthew R; Barbot, Antoine; Carrasco, Marisa; Huxlin, Krystel R

2017-12-10

Training chronic, cortically-blind (CB) patients on a coarse [left-right] direction discrimination and integration (CDDI) task recovers performance on this task at trained, blind field locations. However, fine direction difference (FDD) thresholds remain elevated at these locations, limiting the usefulness of recovered vision in daily life. Here, we asked if this FDD impairment can be overcome by training CB subjects with endogenous, feature-based attention (FBA) cues. Ten CB subjects were recruited and trained on CDDI and FDD with an FBA cue or FDD with a neutral cue. After completion of each training protocol, FDD thresholds were re-measured with both neutral and FBA cues at trained, blind-field locations and at corresponding, intact-field locations. In intact portions of the visual field, FDD thresholds were lower when tested with FBA than neutral cues. Training subjects in the blind field on the CDDI task improved FDD performance to the point that a threshold could be measured, but these locations remained impaired relative to the intact field. FDD training with neutral cues resulted in better blind field FDD thresholds than CDDI training, but thresholds remained impaired relative to intact field levels, regardless of testing cue condition. Importantly, training FDD in the blind field with FBA lowered FDD thresholds relative to CDDI training, and allowed the blind field to reach thresholds similar to the intact field, even when FBA trained subjects were tested with a neutral rather than FBA cue. Finally, FDD training appeared to also recover normal integration thresholds at trained, blind-field locations, providing an interesting double dissociation with respect to CDDI training. In summary, mechanisms governing FBA appear to function normally in both intact and impaired regions of the visual field following V1 damage. Our results mark the first time that FDD thresholds in CB fields have been seen to reach intact field levels of performance. Moreover, FBA can be leveraged during visual training to recover normal, fine direction discrimination and integration performance at trained, blind-field locations, potentiating visual recovery of more complex and precise aspects of motion perception in cortically-blinded fields. Copyright © 2017 Elsevier Ltd. All rights reserved.
Construction and completion of flux balance models from pathway databases.

PubMed

Latendresse, Mario; Krummenacker, Markus; Trupp, Miles; Karp, Peter D

2012-02-01

Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models can be time consuming and tedious because of the difficulty in assembling completely accurate descriptions of these sets, and in identifying errors in the composition of these sets. For example, the presence of a single non-producible metabolite in the biomass will make the entire model infeasible. Other difficulties in FBA modeling are that model distributions, and predicted fluxes, can be cryptic and difficult to understand. We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software. Predicted fluxes are more easily comprehended by visualizing them on diagrams of individual metabolic pathways or of metabolic maps. MetaFlux can also remove redundant high-flux loops, solve FBA models once they are generated and model the effects of gene knockouts. MetaFlux has been validated through construction of FBA models for Escherichia coli and Homo sapiens. Pathway Tools with MetaFlux is freely available to academic users, and for a fee to commercial users. Download from: biocyc.org/download.shtml. mario.latendresse@sri.com Supplementary data are available at Bioinformatics online.
Differential Development of Selectivity for Faces and Bodies in the Fusiform Gyrus

ERIC Educational Resources Information Center

Peelen, Marius V.; Glaser, Bronwyn; Vuilleumier, Patrik; Eliez, Stephan

2009-01-01

Viewing faces or bodies activates category-selective areas of visual cortex, including the fusiform face area (FFA), fusiform body area (FBA), and extrastriate body area (EBA). Here, using fMRI, we investigate the development of these areas, focusing on the right FFA and FBA. Despite the overlap of functionally defined FFA and FBA (54%-75%…
Saccadic eye movements do not disrupt the deployment of feature-based attention.

PubMed

Kalogeropoulou, Zampeta; Rolfs, Martin

2017-07-01

The tight link of saccades to covert spatial attention has been firmly established, yet their relation to other forms of visual selection remains poorly understood. Here we studied the temporal dynamics of feature-based attention (FBA) during fixation and across saccades. Participants reported the orientation (on a continuous scale) of one of two sets of spatially interspersed Gabors (black or white). We tested performance at different intervals between the onset of a colored cue (black or white, indicating which stimulus was the most probable target; red: neutral condition) and the stimulus. FBA built up after cue onset: Benefits (errors for valid vs. neutral cues), costs (invalid vs. neutral), and the overall cueing effect (valid vs. invalid) increased with the cue-stimulus interval. Critically, we also tested visual performance at different intervals after a saccade, when FBA had been fully deployed before saccade initiation. Cueing effects were evident immediately after the saccade and were predicted most accurately and most precisely by fully deployed FBA, indicating that FBA was continuous throughout saccades. Finally, a decomposition of orientation reports into target reports and random guesses confirmed continuity of report precision and guess rates across the saccade. We discuss the role of FBA in perceptual continuity across saccades.
Microcompartmentation of cytosolic aldolase by interaction with the actin cytoskeleton in Arabidopsis.

PubMed

Garagounis, Constantine; Kostaki, Kalliopi-Ioanna; Hawkins, Tim J; Cummins, Ian; Fricker, Mark D; Hussey, Patrick J; Hetherington, Alistair M; Sweetlove, Lee J

2017-02-01

Evidence is accumulating for molecular microcompartments formed when proteins interact in localized domains with the cytoskeleton, organelle surfaces, and intracellular membranes. To understand the potential functional significance of protein microcompartmentation in plants, we studied the interaction of the glycolytic enzyme fructose bisphosphate aldolase with actin in Arabidopsis thaliana. Homology modelling of a major cytosolic isozyme of aldolase, FBA8, suggested that the tetrameric holoenzyme has two actin binding sites and could therefore act as an actin-bundling protein, as was reported for animal aldolases. This was confirmed by in vitro measurements of an increase in viscosity of F-actin polymerized in the presence of recombinant FBA8. Simultaneously, interaction with F-actin caused non-competitive inhibition of aldolase activity. We did not detect co-localization of an FBA8-RFP fusion protein, expressed in an fba8-knockout background, with the actin cytoskeleton using confocal laser-scanning microscopy. However, we did find evidence for a low level of interaction using FRET-FLIM analysis of FBA8-RFP co-expressed with the actin-binding protein GFP-Lifeact. Furthermore, knockout of FBA8 caused minor alterations of guard cell actin cytoskeleton morphology and resulted in a reduced rate of stomatal closure in response to decreased humidity. We conclude that cytosolic aldolase can be microcompartmented in vivo by interaction with the actin cytoskeleton and may subtly modulate guard cell behaviour as a result. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.
Analysis of Paracoccidioides secreted proteins reveals fructose 1,6-bisphosphate aldolase as a plasminogen-binding protein.

PubMed

Chaves, Edilânia Gomes Araújo; Weber, Simone Schneider; Báo, Sonia Nair; Pereira, Luiz Augusto; Bailão, Alexandre Melo; Borges, Clayton Luiz; Soares, Célia Maria de Almeida

2015-02-27

Despite being important thermal dimorphic fungi causing Paracoccidioidomycosis, the pathogenic mechanisms that underlie the genus Paracoccidioides remain largely unknown. Microbial pathogens express molecules that can interact with human plasminogen, a protein from blood plasma, which presents fibrinolytic activity when activated into plasmin. Additionally, plasmin exhibits the ability of degrading extracellular matrix components, favoring the pathogen spread to deeper tissues. Previous work from our group demonstrated that Paracoccidioides presents enolase, as a protein able to bind and activate plasminogen, increasing the fibrinolytic activity of the pathogen, and the potential for adhesion and invasion of the fungus to host cells. By using proteomic analysis, we aimed to identify other proteins of Paracoccidioides with the ability of binding to plasminogen. In the present study, we employed proteomic analysis of the secretome, in order to identify plasminogen-binding proteins of Paracoccidioides, Pb01. Fifteen proteins were present in the fungal secretome, presenting the ability to bind to plasminogen. Those proteins are probable targets of the fungus interaction with the host; thus, they could contribute to the invasiveness of the fungus. For validation tests, we selected the protein fructose 1,6-bisphosphate aldolase (FBA), described in other pathogens as a plasminogen-binding protein. The protein FBA at the fungus surface and the recombinant FBA (rFBA) bound human plasminogen and promoted its conversion to plasmin, potentially increasing the fibrinolytic capacity of the fungus, as demonstrated in fibrin degradation assays. The addition of rFBA or anti-rFBA antibodies was capable of reducing the interaction between macrophages and Paracoccidioides, possibly by blocking the binding sites for FBA. These data reveal the possible participation of the FBA in the processes of cell adhesion and tissue invasion/dissemination of Paracoccidioides. These data indicate that Paracoccidioides is a pathogen that has several plasminogen-binding proteins that likely play important roles in pathogen-host interaction. In this context, FBA is a protein that might be involved somehow in the processes of invasion and spread of the fungus during infection.
Feature-based attentional weighting and spreading in visual working memory

PubMed Central

Niklaus, Marcel; Nobre, Anna C.; van Ede, Freek

2017-01-01

Attention can be directed at features and feature dimensions to facilitate perception. Here, we investigated whether feature-based-attention (FBA) can also dynamically weight feature-specific representations within multi-feature objects held in visual working memory (VWM). Across three experiments, participants retained coloured arrows in working memory and, during the delay, were cued to either the colour or the orientation dimension. We show that directing attention towards a feature dimension (1) improves the performance in the cued feature dimension at the expense of the uncued dimension, (2) is more efficient if directed to the same rather than to different dimensions for different objects, and (3) at least for colour, automatically spreads to the colour representation of non-attended objects in VWM. We conclude that FBA also continues to operate on VWM representations (with similar principles that govern FBA in the perceptual domain) and challenge the classical view that VWM representations are stored solely as integrated objects. PMID:28233830
Fructose-bisphosphate aldolase and enolase from Echinococcus granulosus: genes, expression patterns and protein interactions of two potential moonlighting proteins.

PubMed

Lorenzatto, Karina Rodrigues; Monteiro, Karina Mariante; Paredes, Rodolfo; Paludo, Gabriela Prado; da Fonsêca, Marbella Maria; Galanti, Norbel; Zaha, Arnaldo; Ferreira, Henrique Bunselmeyer

2012-09-10

Glycolytic enzymes, such as fructose-bisphosphate aldolase (FBA) and enolase, have been described as complex multifunctional proteins that may perform non-glycolytic moonlighting functions, but little is known about such functions, especially in parasites. We have carried out in silico genomic searches in order to identify FBA and enolase coding sequences in Echinococcus granulosus, the causative agent of cystic hydatid disease. Four FBA genes and 3 enolase genes were found, and their sequences and exon-intron structures were characterized and compared to those of their orthologs in Echinococcus multilocularis, the causative agent of alveolar hydatid disease. To gather evidence of possible non-glycolytic functions, the expression profile of FBA and enolase isoforms detected in the E. granulosus pathogenic larval form (hydatid cyst) (EgFBA1 and EgEno1) was assessed. Using specific antibodies, EgFBA1 and EgEno1 were detected in protoscolex and germinal layer cells, as expected, but they were also found in the hydatid fluid, which contains parasite's excretory-secretory (ES) products. Besides, both proteins were found in protoscolex tegument and in vitro ES products, further suggesting possible non-glycolytic functions in the host-parasite interface. EgFBA1 modeled 3D structure predicted a F-actin binding site, and the ability of EgFBA1 to bind actin was confirmed experimentally, which was taken as an additional evidence of FBA multifunctionality in E. granulosus. Overall, our results represent the first experimental evidences of alternative functions performed by glycolytic enzymes in E. granulosus and provide relevant information for the understanding of their roles in host-parasite interplay. Copyright © 2012 Elsevier B.V. All rights reserved.
Haptic perception and body representation in lateral and medial occipito-temporal cortices.

PubMed

Costantini, Marcello; Urgesi, Cosimo; Galati, Gaspare; Romani, Gian Luca; Aglioti, Salvatore M

2011-04-01

Although vision is the primary sensory modality that humans and other primates use to identify objects in the environment, we can recognize crucial object features (e.g., shape, size) using the somatic modality. Previous studies have shown that the occipito-temporal areas dedicated to the visual processing of object forms, faces and bodies also show category-selective responses when the preferred stimuli are haptically explored out of view. Visual processing of human bodies engages specific areas in lateral (extrastriate body area, EBA) and medial (fusiform body area, FBA) occipito-temporal cortex. This study aimed at exploring the relative involvement of EBA and FBA in the haptic exploration of body parts. During fMRI scanning, participants were asked to haptically explore either real-size fake body parts or objects. We found a selective activation of right and left EBA, but not of right FBA, while participants haptically explored body parts as compared to real objects. This suggests that EBA may integrate visual body representations with somatosensory information regarding body parts and form a multimodal representation of the body. Furthermore, both left and right EBA showed a comparable level of body selectivity during haptic perception and visual imagery. However, right but not left EBA was more activated during haptic exploration than visual imagery of body parts, ruling out that the response to haptic body exploration was entirely due to the use of visual imagery. Overall, the results point to the existence of different multimodal body representations in the occipito-temporal cortex which are activated during perception and imagery of human body parts. Copyright © 2011 Elsevier Ltd. All rights reserved.
Second generation engineering of transketolase for polar aromatic aldehyde substrates.

PubMed

Payongsri, Panwajee; Steadman, David; Hailes, Helen C; Dalby, Paul A

2015-04-01

Transketolase has significant industrial potential for the asymmetric synthesis of carboncarbon bonds with new chiral centres. Variants evolved on propanal were found previously with nascent activity on polar aromatic aldehydes 3-formylbenzoic acid (3-FBA), 4-formylbenzoic acid (4-FBA), and 3-hydroxybenzaldehyde (3-HBA), suggesting a potential novel route to analogues of chloramphenicol. Here we evolved improved transketolase activities towards aromatic aldehydes, by saturation mutagenesis of two active-site residues (R358 and S385), predicted to interact with the aromatic substituents. S385 variants selectively controlled the aromatic substrate preference, with up to 13-fold enhanced activities, and KM values comparable to those of natural substrates with wild-type transketolase. S385E even completely removed the substrate inhibition for 3-FBA, observed in all previous variants. The mechanisms of catalytic improvement were both mutation type and substrate dependent. S385E improved 3-FBA activity via kcat, but reduced 4-FBA activity via KM. Conversely, S385Y/T improved 3-FBA activity via KM and 4-FBA activity via kcat. This suggested that both substrate proximity and active-site orientation are very sensitive to mutation. Comparison of all variant activities on each substrate indicated different binding modes for the three aromatic substrates, supported by computational docking. This highlights a potential divergence in the evolution of different substrate specificities, with implications for enzyme engineering. Copyright © 2015 Elsevier Inc. All rights reserved.
Fructose bisphosphate aldolase is involved in the control of RNA polymerase III-directed transcription.

PubMed

Cieśla, Małgorzata; Mierzejewska, Jolanta; Adamczyk, Małgorzata; Farrants, Ann-Kristin Östlund; Boguta, Magdalena

2014-06-01

Yeast Fba1 (fructose 1,6-bisphosphate aldolase) is a glycolytic enzyme essential for viability. The overproduction of Fba1 enables overcoming of a severe growth defect caused by a missense mutation rpc128-1007 in a gene encoding the C128 protein, the second largest subunit of the RNA polymerase III complex. The suppression of the growth phenotype by Fba1 is accompanied by enhanced de novo tRNA transcription in rpc128-1007 cells. We inactivated residues critical for the catalytic activity of Fba1. Overproduction of inactive aldolase still suppressed the rpc128-1007 phenotype, indicating that the function of this glycolytic enzyme in RNA polymerase III transcription is independent of its catalytic activity. Yeast Fba1 was determined to interact with the RNA polymerase III complex by coimmunoprecipitation. Additionally, a role of aldolase in control of tRNA transcription was confirmed by ChIP experiments. The results indicate a novel direct relationship between RNA polymerase III transcription and aldolase. Copyright © 2014 Elsevier B.V. All rights reserved.
A Rational Design, Synthesis, Biological Evaluation and Structure--Activity Relationship Study of Novel Inhibitors against Cyanobacterial Fructose-1,6-bisphosphate Aldolase.

PubMed

Han, Xinya; Zhu, Xiuyun; Zhu, Shuaihua; Wei, Lin; Hong, Zongqin; Guo, Li; Chen, Haifeng; Chi, Bo; Liu, Yan; Feng, Lingling; Ren, Yanliang; Wan, Jian

2016-01-25

In the present study, a series of novel maleimide derivatives were rationally designed and optimized, and their inhibitory activities against cyanobacteria class-II fructose-1,6-bisphosphate aldolase (Cy-FBA-II) and Synechocystis sp. PCC 6803 were further evaluated. The experimental results showed that the introduction of a bigger group (Br, Cl, CH3, or C6H3-o-F) on the pyrrole-2',5'-dione ring resulted in a decrease in the Cy-FBA-II inhibitory activity of the hit compounds. Generally, most of the hit compounds with high Cy-FBA-II inhibitory activities could also exhibit high in vivo activities against Synechocystis sp. PCC 6803. Especially, compound 10 not only shows a high Cy-FBA-II activity (IC50 = 1.7 μM) but also has the highest in vivo activity against Synechocystis sp. PCC 6803 (EC50 = 0.6 ppm). Thus, compound 10 was selected as a representative molecule, and its probable interactions with the surrounding important residues in the active site of Cy-FBA-II were elucidated by the joint use of molecular docking, molecular dynamics simulations, ONIOM calculations, and enzymatic assays to provide new insight into the binding mode of the inhibitors and Cy-FBA-II. The positive results indicate that the design strategy used in the present study is very likely to be a promising way to find novel lead compounds with high inhibitory activities against Cy-FBA-II in the future. The enzymatic and algal inhibition assays suggest that Cy-FBA-II is very likely to be a promising target for the design, synthesis, and development of novel specific algicides to solve cyanobacterial harmful algal blooms.
Incremental Contributions of FbaA and Other Impetigo-Associated Surface Proteins to Fitness and Virulence of a Classical Group A Streptococcal Skin Strain.

PubMed

Rouchon, Candace N; Ly, Anhphan T; Noto, John P; Luo, Feng; Lizano, Sergio; Bessen, Debra E

2017-11-01

Group A streptococci (GAS) are highly prevalent human pathogens whose primary ecological niche is the superficial epithelial layers of the throat and/or skin. Many GAS strains with a strong tendency to cause pharyngitis are distinct from strains that tend to cause impetigo; thus, genetic differences between them may confer host tissue-specific virulence. In this study, the FbaA surface protein gene was found to be present in most skin specialist strains but largely absent from a genetically related subset of pharyngitis isolates. In an Δ fbaA mutant constructed in the impetigo strain Alab49, loss of FbaA resulted in a slight but significant decrease in GAS fitness in a humanized mouse model of impetigo; the Δ fbaA mutant also exhibited decreased survival in whole human blood due to phagocytosis. In assays with highly sensitive outcome measures, Alab49ΔfbaA was compared to other isogenic mutants lacking virulence genes known to be disproportionately associated with classical skin strains. FbaA and PAM (i.e., the M53 protein) had additive effects in promoting GAS survival in whole blood. The pilus adhesin tip protein Cpa promoted Alab49 survival in whole blood and appears to fully account for the antiphagocytic effect attributable to pili. The finding that numerous skin strain-associated virulence factors make slight but significant contributions to virulence underscores the incremental contributions to fitness of individual surface protein genes and the multifactorial nature of GAS-host interactions. Copyright © 2017 American Society for Microbiology.
Fructose-1,6-bisphosphate aldolase of Neisseria meningitidis binds human plasminogen via its C-terminal lysine residue.

PubMed

Shams, Fariza; Oldfield, Neil J; Lai, Si Kei; Tunio, Sarfraz A; Wooldridge, Karl G; Turner, David P J

2016-04-01

Neisseria meningitidis is a leading cause of fatal sepsis and meningitis worldwide. As for commensal species of human neisseriae, N. meningitidis inhabits the human nasopharynx and asymptomatic colonization is ubiquitous. Only rarely does the organism invade and survive in the bloodstream leading to disease. Moonlighting proteins perform two or more autonomous, often dissimilar, functions using a single polypeptide chain. They have been increasingly reported on the surface of both prokaryotic and eukaryotic organisms and shown to interact with a variety of host ligands. In some organisms moonlighting proteins perform virulence-related functions, and they may play a role in the pathogenesis of N. meningitidis. Fructose-1,6-bisphosphate aldolase (FBA) was previously shown to be surface-exposed in meningococci and involved in adhesion to host cells. In this study, FBA was shown to be present on the surface of both pathogenic and commensal neisseriae, and surface localization and anchoring was demonstrated to be independent of aldolase activity. Importantly, meningococcal FBA was found to bind to human glu-plasminogen in a dose-dependent manner. Site-directed mutagenesis demonstrated that the C-terminal lysine residue of FBA was required for this interaction, whereas subterminal lysine residues were not involved. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
Molecular Characterization, Gene Evolution, and Expression Analysis of the Fructose-1, 6-bisphosphate Aldolase (FBA) Gene Family in Wheat (Triticum aestivum L.)

PubMed Central

Lv, Geng-Yin; Guo, Xiao-Guang; Xie, Li-Ping; Xie, Chang-Gen; Zhang, Xiao-Hong; Yang, Yuan; Xiao, Lei; Tang, Yu-Ying; Pan, Xing-Lai; Guo, Ai-Guang; Xu, Hong

2017-01-01

Fructose-1, 6-bisphosphate aldolase (FBA) is a key plant enzyme that is involved in glycolysis, gluconeogenesis, and the Calvin cycle. It plays significant roles in biotic and abiotic stress responses, as well as in regulating growth and development processes. In the present paper, 21 genes encoding TaFBA isoenzymes were identified, characterized, and categorized into three groups: class I chloroplast/plastid FBA (CpFBA), class I cytosol FBA (cFBA), and class II chloroplast/plastid FBA. By using a prediction online database and genomic PCR analysis of Chinese Spring nulli-tetrasomic lines, we have confirmed the chromosomal location of these genes in 12 chromosomes of four homologous groups. Sequence and genomic structure analysis revealed the high identity of the allelic TaFBA genes and the origin of different TaFBA genes. Numerous putative environment stimulus-responsive cis-elements have been identified in 1,500-bp regions of TaFBA gene promoters, of which the most abundant are the light-regulated elements (LREs). Phylogenetic reconstruction using the deduced protein sequence of 245 FBA genes indicated an independent evolutionary pathway for the class I and class II groups. Although, earlier studies have indicated that class II FBA only occurs in prokaryote and fungi, our results have demonstrated that a few class II CpFBAs exist in wheat and other closely related species. Class I TaFBA was predicted to be tetramers and class II to be dimers. Gene expression analysis based on microarray and transcriptome databases suggested the distinct role of TaFBAs in different tissues and developmental stages. The TaFBA 4–9 genes were highly expressed in leaves and might play important roles in wheat development. The differential expression patterns of the TaFBA genes in light/dark and a few abiotic stress conditions were also analyzed. The results suggested that LRE cis-elements of TaFBA gene promoters were not directly related to light responses. Most TaFBA genes had higher expression levels in the roots than in the shoots when under various stresses. Class I cytosol TaFBA genes, particularly TaFBA10/12/18 and TaFBA13/16, and three class II TaFBA genes are involved in responses to various abiotic stresses. Class I CpFBA genes in wheat are apparently sensitive to different stress conditions. PMID:28659962

Does a pre-intervention functional assessment increase intervention effectiveness? A meta-analysis of within-subject interrupted time-series studies.

PubMed

Hurl, Kylee; Wightman, Jade; Haynes, Stephen N; Virues-Ortega, Javier

2016-07-01

This study examined the relative effectiveness of interventions based on a pre-intervention functional behavioral assessment (FBA), compared to interventions not based on a pre-intervention FBA. We examined 19 studies that included a direct comparison between the effects of FBA- and non-FBA-based interventions with the same participants. A random effects meta-analysis of effect sizes indicated that FBA-based interventions were associated with large reductions in problem behaviors when using non-FBA-based interventions as a reference intervention (Effect size=0.85, 95% CI [0.42, 1.27], p<0.001). In addition, non-FBA based interventions had no effect on problem behavior when compared to no intervention (0.06, 95% CI [-0.21, 0.33], p=0.664). Interestingly, both FBA-based and non-FBA-based interventions had significant effects on appropriate behavior relative to no intervention, albeit the overall effect size was much larger for FBA-based interventions (FBA-based: 1.27, 95% CI [0.89, 1.66], p<0.001 vs. non-FBA-based: 0.35, 95% CI [0.14, 0.56], p=0.001). In spite of the evidence in favor of FBA-based interventions, the limited number of comparative studies with high methodological standards underlines the need for further comparisons of FBA-based versus non-FBA-based interventions. Copyright © 2016 Elsevier Ltd. All rights reserved.
Human functional magnetic resonance imaging reveals separation and integration of shape and motion cues in biological motion processing.

PubMed

Jastorff, Jan; Orban, Guy A

2009-06-03

In a series of human functional magnetic resonance imaging experiments, we systematically manipulated point-light stimuli to identify the contributions of the various areas implicated in biological motion processing (for review, see Giese and Poggio, 2003). The first experiment consisted of a 2 x 2 factorial design with global shape and kinematics as factors. In two additional experiments, we investigated the contributions of local opponent motion, the complexity of the portrayed movement and a one-back task to the activation pattern. Experiment 1 revealed a clear separation between shape and motion processing, resulting in two branches of activation. A ventral region, extending from the lateral occipital sulcus to the posterior inferior temporal gyrus, showed a main effect of shape and its extension into the fusiform gyrus also an interaction. The dorsal region, including the posterior inferior temporal sulcus and the posterior superior temporal sulcus (pSTS), showed a main effect of kinematics together with an interaction. Region of interest analysis identified these interaction sites as the extrastriate and fusiform body areas (EBA and FBA). The local opponent motion cue yielded only little activation, limited to the ventral region (experiment 3). Our results suggest that the EBA and the FBA correspond to the initial stages in visual action analysis, in which the performed action is linked to the body of the actor. Moreover, experiment 2 indicates that the body areas are activated automatically even in the absence of a task, whereas other cortical areas like pSTS or frontal regions depend on the complexity of movements or task instructions for their activation.
Genome-wide analysis of the fructose 1,6-bisphosphate aldolase (FBA) gene family and functional characterization of FBA7 in tomato.

PubMed

Cai, Bingbing; Li, Qiang; Xu, Yongchao; Yang, Long; Bi, Huangai; Ai, Xizhen

2016-11-01

Fructose 1,6-bisphosphate aldolase (FBA) is a key enzyme in plants that is involved in glycolysis, gluconeogenesis, and the Calvin cycle. FBA genes play significant roles in biotic and abiotic stress responses and also regulate growth and development. Despite the importance of FBA genes, little is known about it in tomato. In this study, we identified 8 FBA genes in tomato and classified them into 2 subgroups based on a phylogenetic tree, gene structures, and conserved motifs. Five (SlFBA1, 2, 3, 4 and 5) and three (SlFBA6, 7, and 8) SlFBA proteins were predicted to be localized in chloroplasts and cytoplasm, respectively. The phylogenetic analysis of FBAs from tomato, Arabidopsis, rice, and other organisms suggested that SlFBA shared the highest protein homology with FBAs from other plants. Synteny analysis indicated that segmental duplication events contributed to the expansion of the tomato FBA family. The expression profiles revealed that all SlFBAs were involved in the response to low and high temperature stresses. SlFBA7 overexpression increased the expression and activities of other main enzymes in Calvin cycle, net photosynthetic rate (Pn), seed size and stem diameter. SlFBA7 overexpression enhanced tolerances in seed germination under suboptimal temperature stresses. Taken together, comprehensive analyses of SlFBAs would provide a basis for understanding of evolution and function of SlFBA family. Copyright © 2016 Elsevier Masson SAS. All rights reserved.
Neural correlates of human body perception.

PubMed

Aleong, Rosanne; Paus, Tomás

2010-03-01

The objective of this study was to investigate potential sex differences in the neural response to human bodies using fMRI carried out in healthy young adults. We presented human bodies in a block-design experiment to identify body-responsive regions of the brain, namely, extrastriate body area (EBA) and fusiform body area (FBA). In a separate event-related "adaptation" experiment, carried out in the same group of subjects, we presented sets of four human bodies of varying body size and shape. Varying levels of body morphing were introduced to assess the degree of morphing required for adaptation release. Analysis of BOLD signal in the block-design experiment revealed significant Sex x Hemisphere interactions in the EBA and the FBA responses to human bodies. Only women showed greater BOLD response to bodies in the right hemisphere compared with the left hemisphere for both EBA and FBA. The BOLD response in right EBA was higher in women compared with men. In the adaptation experiment, greater right versus left hemisphere response for EBA and FBA was also identified among women but not men. These findings are particularly novel in that they address potential sex differences in the lateralization of EBA and FBA responses to human body images. Although previous studies have found some degree of right hemisphere dominance in body perception, our results suggest that such a functional lateralization may differ between men and women.
Demographic and Clinical Findings in Children Undergoing Bronchoscopy for Foreign Body Aspiration.

PubMed

Safari, Mojgan; Manesh, Mohammad Reza Hashemi

2016-01-01

Foreign body aspiration (FBA) is a significant cause of airway distress, mortality, and morbidity in children. Diagnosis of FBA can be challenging and is sometimes delayed for weeks or even months. If not diagnosed and treated promptly, FBA can result in serious consequences. For this retrospective study, we investigated the medical records of 89 children who underwent bronchoscopy for suspected FBA and recorded relevant demographic, clinical, and treatment data. Of the 89 patients identified for this study, 51 had a definitive diagnosis of FBA. Among these patients, choking, chronic cough and wheezing, cyanosis, and dyspnea were the most frequent symptoms of FBA. The foreign bodies were located in the left bronchus (45.1%), the right bronchus (35.3%), the trachea (15.7%), and in both the right and left bronchi (3.9%). Seeds were the most prevalent foreign body, found in 39.2% of the patients. Lack of complete medical history in patients with suspected FBA is one of the main causes of delayed FBA diagnosis. Bronchoscopy is considered the definitive diagnostic method for FBA and should be conducted in all patients with suspected FBA because of the low risk of complications and reduced probability that FBA diagnosis and treatment will be delayed.
Demographic and Clinical Findings in Children Undergoing Bronchoscopy for Foreign Body Aspiration

PubMed Central

Safari, Mojgan; Manesh, Mohammad Reza Hashemi

2016-01-01

Background: Foreign body aspiration (FBA) is a significant cause of airway distress, mortality, and morbidity in children. Diagnosis of FBA can be challenging and is sometimes delayed for weeks or even months. If not diagnosed and treated promptly, FBA can result in serious consequences. Methods: For this retrospective study, we investigated the medical records of 89 children who underwent bronchoscopy for suspected FBA and recorded relevant demographic, clinical, and treatment data. Results: Of the 89 patients identified for this study, 51 had a definitive diagnosis of FBA. Among these patients, choking, chronic cough and wheezing, cyanosis, and dyspnea were the most frequent symptoms of FBA. The foreign bodies were located in the left bronchus (45.1%), the right bronchus (35.3%), the trachea (15.7%), and in both the right and left bronchi (3.9%). Seeds were the most prevalent foreign body, found in 39.2% of the patients. Conclusion: Lack of complete medical history in patients with suspected FBA is one of the main causes of delayed FBA diagnosis. Bronchoscopy is considered the definitive diagnostic method for FBA and should be conducted in all patients with suspected FBA because of the low risk of complications and reduced probability that FBA diagnosis and treatment will be delayed. PMID:27303219
The methylotrophic Bacillus methanolicus MGA3 possesses two distinct fructose 1,6-bisphosphate aldolases.

PubMed

Stolzenberger, Jessica; Lindner, Steffen N; Wendisch, Volker F

2013-08-01

The thermotolerant Gram-positive methylotroph Bacillus methanolicus is able to grow with methanol, glucose or mannitol as a sole carbon and energy source. Fructose 1,6-bisphosphate aldolase (FBA), a key enzyme of glycolysis and gluconeogenesis, is encoded in the genome of B. methanolicus by two putative fba genes, the chromosomally located fba(C) and fba(P) on the naturally occurring plasmid pBM19. Their amino acid sequences share 75 % identity and suggest a classification as class II aldolases. Both enzymes were purified from recombinant Escherichia coli and were found to be active as homotetramers. Both enzymes were activated by either manganese or cobalt ions, and inhibited by ADP, ATP and EDTA. The kinetic parameters allowed us to distinguish the chromosomally encoded FBA(C) from the plasmid encoded FBA(P), since FBA(C) showed higher affinity towards fructose 1,6-bisphosphate (Km of 0.16±0.01 mM as compared to 2±0.08 mM) as well as higher glycolytic catalytic efficiency (31.3 as compared to 0.8 s(-1) mM(-1)) than FBA(P). However, FBA(P) exhibited a higher catalytic efficiency in gluconeogenesis (50.4 as compared to 1.4 s(-1) mM(-1) with dihydroxyacetone phosphate and 4 as compared to 0.4 s(-1) mM(-1) with glyceraldehyde 3-phosphate as limiting substrate). The aldolase-negative Corynebacterium glutamicum mutant Δfda could be complemented with both FBA genes from B. methanolicus. Based on the kinetic data, we propose that FBA(C) acts as major aldolase in glycolysis, whereas FBA(P) acts as major aldolase in gluconeogenesis in B. methanolicus.
[Study on synthesis and matching degree of energy level of terbium complexes using o-fluoro-benzoic acid as ligand].

PubMed

Tao, Dong-Liang; Zhang, Kun; Zhang, Hong; Cui, Yu-Min; Xu, Yi-Zhuang; Liu, Yu-Hai

2014-04-01

Tb(2-FBA)3 x 2H2O and Tb(2-FBA)3 phen were synthesized using o-fluoro-benzoic acid (2-FBA) as the first ligand, and 1,10-phenanthroline (phen) as the second ligand. Elemental analysis and IR spectra were employed to characterize the molecular composition of the two kinds of lanthanide complexes. The UV absorption spectra with same concentration show that the second ligand phen of Tb(2-FBA)3 phen absorbs the portion of the UV light instead of the first ligand 2-FBA. Liquid fluorescence spectra with same concentration show that the fluorescence intensity of Tb(2-FBA)3 x 2H2O is higher than that of Tb (2-FBA)3 phen. The analytical results show that the energy level of 2-FBA matches the lowest excited state energy level of Tb3+ (5D4) better than that of phen. The O-H oscillation of the crystal water in Tb(2-FBA)3 x 2H2O will greatly consume the absorbed energy by ligands, and cause the fluorescence intensity of Tb(2-FBA)3 x 2H2O significantly decline. The energy level of triplet state of the first ligand 2-FBA corresponding to the absorption peak 273 nm has poor matching degree with the 5D4 energy level of Tb3+. In this case, the emission intensity of Tb(2-FBA)3 x 2H2O is still stronger than that of Tb(2-FBA)3 phen. It illustrates that the energy level of the triplet state of the first ligand 2-FBA corresponding to 252 nm has much better matching degree with the lowest excited state of 5D4 energy level of Tb3+ than that of phen. It is the only way to compensate for energy loss by thermal vibration of water molecules and low energy transfer efficiency for poor matching degree between the energy level of corresponding to 273 nm of the first ligand 2-FBA and 5D4 energy level of Tb3+. By combining UV absorption spectra with fluorescence spectra of lanthanide complexes to qualitatively analyze energy level of ligands, the contribution of different types of ligands to the fluorescence properties can be preliminarily understood.
Steady-state visually evoked potential correlates of human body perception.

PubMed

Giabbiconi, Claire-Marie; Jurilj, Verena; Gruber, Thomas; Vocks, Silja

2016-11-01

In cognitive neuroscience, interest in the neuronal basis underlying the processing of human bodies is steadily increasing. Based on functional magnetic resonance imaging studies, it is assumed that the processing of pictures of human bodies is anchored in a network of specialized brain areas comprising the extrastriate and the fusiform body area (EBA, FBA). An alternative to examine the dynamics within these networks is electroencephalography, more specifically so-called steady-state visually evoked potentials (SSVEPs). In SSVEP tasks, a visual stimulus is presented repetitively at a predefined flickering rate and typically elicits a continuous oscillatory brain response at this frequency. This brain response is characterized by an excellent signal-to-noise ratio-a major advantage for source reconstructions. The main goal of present study was to demonstrate the feasibility of this method to study human body perception. To that end, we presented pictures of bodies and contrasted the resulting SSVEPs to two control conditions, i.e., non-objects and pictures of everyday objects (chairs). We found specific SSVEPs amplitude differences between bodies and both control conditions. Source reconstructions localized the SSVEP generators to a network of temporal, occipital and parietal areas. Interestingly, only body perception resulted in activity differences in middle temporal and lateral occipitotemporal areas, most likely reflecting the EBA/FBA.
Crystallographic snapshots of active site metal shift in E. coli fructose 1,6-bisphosphate aldolase.

PubMed

Tran, Huyen-Thi; Lee, Seon-Hwa; Ho, Thien-Hoang; Hong, Seung-Hye; Huynh, Kim-Hung; Ahn, Yeh-Jin; Oh, Deok-Kun; Kang, Lin-Woo

2016-12-01

Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between 1.8 Å and 2.0 Å. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for Zn2＋ ion. Citrate and TRIS bound EcFBA structures showed Zn2＋ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor Zn2＋ within EcFBA without losing it. [BMB Reports 2016; 49(12): 681-686].
Fully automated synthesis of 4-[18F]fluorobenzylamine based on borohydride/NiCl2 reduction.

PubMed

Way, Jenilee; Wuest, Frank

2013-04-01

4-[(18)F]Fluorobenzylamine ([(18)F]FBA) is an important building block for the synthesis of (18)F-labeled compounds. Synthesis of [(18)F]FBA usually involves application of strong reducing agents like LiAlH4 which is challenging to handle in automated synthesis units (ASUs). Therefore, alternative methods for the preparation of [(18)F]FBA compatible with remotely-controlled syntheses in ASUs are needed. (18)F]FBA was prepared in a remotely-controlled synthesis unit (GE TRACERlab™ FX) based on Ni(II)-mediated borohydride exchange resin (BER) reduction of 4-[(18)F]fluorobenzonitrile ([(18)F]FBN). [(18)F]FBA was used for the synthesis of novel thiol-reactive prosthetic group 4-[(18)F]fluorobenzyl)maleimide [(18)F]FBM and Hsp90 inhibitor 17-(4-[(18)F]fluorobenzylamino)-17-demethoxy-geldanamycin [(18)F] GA. [(18)F]FBA could be prepared in high radiochemical yield greater than 80% (decay-corrected) within 60min. In a typical experiment, 7.4GBq of [(18)F]FBA could be obtained in high radiochemical purity of greater than 95% starting from 10GBq of cyclotron-produced n.c.a. [(18)F]fluoride. [(18)F]FBA was used for the preparation of 4-[(18)F]fluorobenzyl)maleimide as a novel prosthetic group for labeling of thiol groups as demonstrated with tripeptide glutathione. [(18)F]FBA was also used as building block for the syntheses of small molecules as exemplified by the preparation of Hsp90 inhibitor 17-(4-[(18)F]fluorobenzylamino)-17-demethoxy-geldanamycin. The described remotely-controlled synthesis of [(18)F]FBA will significantly improve the availability of [(18)F]FBA as an important and versatile building block for the development of novel (18)F-labeled compounds containing a fluorobenzylamine moiety. Copyright © 2013 Elsevier Inc. All rights reserved.
An orally administered butyrate-releasing derivative reduces neutrophil recruitment and inflammation in dextran sulphate sodium-induced murine colitis.

PubMed

Simeoli, Raffaele; Mattace Raso, Giuseppina; Pirozzi, Claudio; Lama, Adriano; Santoro, Anna; Russo, Roberto; Montero-Melendez, Trinidad; Berni Canani, Roberto; Calignano, Antonio; Perretti, Mauro; Meli, Rosaria

2017-06-01

Butyrate has shown benefits in inflammatory bowel diseases. However, it is not often administered orally because of its rancid smell and unpleasant taste. The efficacy of a more palatable butyrate-releasing derivative, N-(1-carbamoyl-2-phenylethyl) butyramide (FBA), was evaluated in a mouse model of colitis induced by dextran sodium sulphate (DSS). Male 10 week-old BALB/c mice received DSS (2.5%) in drinking water (for 5 days) followed by DSS-free water for 7 days (DSS group). Oral FBA administration (42.5 mg·kg -1 ) was started 7 days before DSS as preventive (P-FBA), or 2 days after DSS as therapeutic (T-FBA); both treatments lasted 19 days. One DSS-untreated group received only tap water (CON). FBA treatments reduced colitis symptoms and colon damage. P-FBA and T-FBA significantly decreased polymorphonuclear cell infiltration score compared with the DSS group. FBA reversed the imbalance between pro- and anti-inflammatory cytokines (reducing inducible NOS protein expression, CCL2 and IL-6 transcripts in colon and increasing TGFβ and IL-10). Morever, P-FBA and T-FBA limited neutrophil recruitment (by expression and localization of the neutrophil granule protease Ly-6G), restored deficiency of the butyrate transporter and improved intestinal epithelial integrity, preventing tight-junction impairment (zonulin-1 and occludin). FBA, similar to its parental compound sodium butyrate, inhibited histone deacetylase-9 and restored H3 histone acetylation, exerting an anti-inflammatory effect through NF-κB inhibition and the up-regulation of PPARγ. FBA reduces inflammatory intestinal damage in mice indicating its potential as a postbiotic derivative without the problems associated with the oral administration of sodium butyrate. This article is part of a themed section on Principles of Pharmacological Research of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.11/issuetoc. © 2016 The British Pharmacological Society.
Principles of Positive Behaviour Supports: Using the FBA as a Problem-Solving Approach to Address Challenging Behaviours beyond Special Populations

ERIC Educational Resources Information Center

Moreno, Gerardo; Bullock, Lyndal M.

2011-01-01

The Functional Behavioural Assessment (FBA) is an investigative process that examines the context of challenging behaviours in the classroom. Information gleaned from the FBA process is used to develop a behaviour intervention plan to address the challenging behaviour and teach a socially acceptable replacement behaviour. However, the FBA has…
Engineering Yarrowia lipolytica to express secretory invertase with strong FBA1IN promoter.

PubMed

Hong, Seung-Pyo; Seip, John; Walters-Pollak, Dana; Rupert, Ross; Jackson, Raymond; Xue, Zhixiong; Zhu, Quinn

2012-02-01

Oleaginous yeast Yarrowia lipolytica is an important host for the production of lipid-derived compounds or heterologous proteins. Selection of strong promoters and effective expression systems is critical for heterologous protein secretion. To search for a strong promoter in Y. lipolytica, activities of FBA1, TDH1 and GPM1 promoters were compared to that of TEF1 promoter by constructing GUS reporter fusions. The FBA1 promoter activity was 2.2 and 5.5 times stronger than the TDH1 and GPM1 promoters, respectively. The FBA1IN promoter (FBA1 sequence of -826 to +169) containing an intron (+64 to +165) showed five-fold higher expression than the FBA1 promoter (-831 to -1). The transcriptional enhancement by the 5'-region within the FBA1 gene was confirmed by GPM1::FBA1 chimeric promoter construction. Using the strong FBA1IN promoter, four different S. cerevisiae SUC2 expression cassettes were tested for the SUC+ phenotype in Y. lipolytica. Functional invertase secretion was facilitated by the Xpr2 prepro-region with an additional 13 amino acids of mature Xpr2, or by the native Suc2 signal sequence. However, these two secretory signals in tandem, or the mature Suc2 with no secretory signal, did not direct secretion of functional invertase. Unlike previously reported Y. lipolytica SUC+ strains, our engineered stains secreted most of invertase into the medium. Copyright © 2011 John Wiley & Sons, Ltd.
Fructose-1,6-bisphosphate aldolase (class II) is the primary site of nickel toxicity in Escherichia coli.

PubMed

Macomber, Lee; Elsey, Scott P; Hausinger, Robert P

2011-12-01

Nickel is toxic to all forms of life, but the mechanisms of cell damage are unknown. Indeed, environmentally relevant nickel levels (8 µM) inhibit wild-type Escherichia coli growth on glucose minimal medium. The same concentration of nickel also inhibits growth on fructose, but not succinate, lactate or glycerol; these results suggest that fructose-1,6-bisphosphate aldolase (FbaA) is a target of nickel toxicity. Cells stressed by 8 µM Ni(II) for 20 min lost 75% of their FbaA activity, demonstrating that FbaA is inactivated during nickel stress. Furthermore, overexpression of fbaA restored growth of an rcnA mutant in glucose minimal medium supplemented with 4 µM Ni(II), thus confirming that FbaA is a primary target of nickel toxicity. This class II aldolase has an active site zinc and a non-catalytic zinc nearby. Purified FbaA lost 80 % of its activity within 2 min when challenged with 8 µM Ni(II). Nickel-challenged FbaA lost 0.8 zinc and gained 0.8 nickel per inactivated monomer. FbaA mutants (D144A and E174A) affecting the non-catalytic zinc were resistant to nickel inhibition. These results define the primary site of nickel toxicity in E. coli as the class II aldolase FbaA through binding to the non-catalytic zinc site. © 2011 Blackwell Publishing Ltd.
The Mechanism of Starch Over-Accumulation in Chlamydomonas reinhardtii High-Starch Mutants Identified by Comparative Transcriptome Analysis

PubMed Central

Koo, Kwang M.; Jung, Sera; Lee, Beom S.; Kim, Jin-Baek; Jo, Yeong D.; Choi, Hong-Il; Kang, Si-Yong; Chung, Gook-H.; Jeong, Won-Joong; Ahn, Joon-Woo

2017-01-01

The focus of this study was the mechanism of starch accumulation in Chlamydomonas reinhardtii high-starch mutants. Three C. reinhardtii mutants showing high-starch content were generated using gamma irradiation. When grown under nitrogen-deficient conditions, these mutants had more than twice as much starch than a wild-type control. The mechanism of starch over-accumulation in these mutants was studied with comparative transcriptome analysis. In all mutants, induction of phosphoglucomutase 1 (PGM1) expression was detected; PGM1 catalyzes the inter-conversion of glucose 1-phosphate and glucose 6-phosphate in both starch biosynthetic and glycolytic pathway. Interestingly, transcript levels of phosphoglucose isomerase 1 (PGI1), fructose 1,6-bisphosphate aldolase 1 and 2 (FBA1 and FBA2) were down-regulated in all mutants; PGI1, FBA1, and FBA2 act on downstream of glucose 6-phosphate conversion in glycolytic pathway. Therefore, down-regulations of PGI1, FBA1, and FBA2 may lead to accumulation of upstream metabolites, notably glucose 6-phosphate, resulting in induction of PGM1 expression through feed-forward regulation and that PGM1 overexpression caused starch over-accumulation in mutants. These results suggest that PGI1, FBA1, FBA2, and PGM1 correlate with each other in terms of coordinated transcriptional regulation and play central roles for starch over-accumulation in C. reinhardtii. PMID:28588557
Fructose-Bisphophate Aldolase Exhibits Functional Roles between Carbon Metabolism and the hrp System in Rice Pathogen Xanthomonas oryzae pv. oryzicola

PubMed Central

Li, Yu-rong; Cui, Yi-ping; Ji, Zhi-yuan; Cai, Lu-lu; Zou, Hua-song; Hutchins, William C.; Yang, Ching-hong; Chen, Gong-you

2012-01-01

Fructose-bisphophate aldolase (FbaB), is an enzyme in glycolysis and gluconeogenesis in living organisms. The mutagenesis in a unique fbaB gene of Xanthomonas oryzae pv. oryzicola, the causal agent of rice bacterial leaf streak, led the pathogen not only unable to use pyruvate and malate for growth and delayed its growth when fructose was used as the sole carbon source, but also reduced extracellular polysaccharide (EPS) production and impaired bacterial virulence and growth in rice. Intriguingly, the fbaB promoter contains an imperfect PIP-box (plant-inducible promoter) (TTCGT-N9-TTCGT). The expression of fbaB was negatively regulated by a key hrp regulatory HrpG and HrpX cascade. Base substitution in the PIP-box altered the regulation of fbaB with the cascade. Furthermore, the expression of fbaB in X. oryzae pv. oryzicola RS105 strain was inducible in planta rather than in a nutrient-rich medium. Except other hrp-hrc-hpa genes, the expression of hrpG and hrpX was repressed and the transcripts of hrcC, hrpE and hpa3 were enhanced when fbaB was deleted. The mutation in hrcC, hrpE or hpa3 reduced the ability of the pathogen to acquire pyruvate and malate. In addition, bacterial virulence and growth in planta and EPS production in RΔfbaB mutant were completely restored to the wild-type level by the presence of fbaB in trans. This is the first report to demonstrate that carbohydrates, assimilated by X. oryzae pv. oryzicola, play critical roles in coordinating hrp gene expression through a yet unknown regulator. PMID:22384086
Identification and expression of fructose-1,6-bisphosphate aldolase genes and their relations to oil content in developing seeds of tea oil tree (Camellia oleifera).

PubMed

Zeng, Yanling; Tan, Xiaofeng; Zhang, Lin; Jiang, Nan; Cao, Heping

2014-01-01

Tea oil tree (Camellia oleifera, Co) provides a fine edible oil source in China. Tea oil from the seeds is very beneficial to human health. Fructose-1,6-bisphosphate aldolase (FBA) hydrolyzes fructose-1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, two critical metabolites for oil biosynthesis. The objectives of this study were to identify FBA genes and investigate the relationship between FBA gene expression and oil content in developing seeds of tea oil tree. In this paper, four developmentally up-regulated CoFBA genes were identified in Camellia oleifera seeds based on the transcriptome from two seed developmental stages corresponding to the initiation and peak stages of lipid biosynthesis. The expression of CoFBA genes, along with three key oil biosynthesis genes CoACP, CoFAD2 and CoSAD were analyzed in seeds from eight developmental stages by real-time quantitative PCR. The oil content and fatty acid composition were also analyzed. The results showed that CoFBA and CoSAD mRNA levels were well-correlated with oil content whereas CoFAD2 gene expression levels were correlated with fatty acid composition in Camellia seeds. We propose that CoFBA and CoSAD are two important factors for determining tea oil yield because CoFBA gene controls the flux of key intermediates for oil biosynthesis and CoSAD gene controls the synthesis of oleic acid, which accounts for 80% of fatty acids in tea oil. These findings suggest that tea oil yield could be improved by enhanced expression of CoFBA and CoSAD genes in transgenic plants.
Streptococcus pneumoniae fructose-1,6-bisphosphate aldolase, a protein vaccine candidate, elicits Th1/Th2/Th17-type cytokine responses in mice.

PubMed

Elhaik Goldman, Shirin; Dotan, Shahar; Talias, Amir; Lilo, Amit; Azriel, Shalhevet; Malka, Itay; Portnoi, Maxim; Ohayon, Ariel; Kafka, Daniel; Ellis, Ronald; Elkabets, Moshe; Porgador, Angel; Levin, Ditza; Azhari, Rosa; Swiatlo, Edwin; Ling, Eduard; Feldman, Galia; Tal, Michael; Dagan, Ron; Mizrachi Nebenzahl, Yaffa

2016-04-01

Streptococcus pneumoniae (S. pneumoniae) is a major pathogen worldwide. The currently available polysaccharide-based vaccines significantly reduce morbidity and mortality. However, the inherent disadvantages of the currently available polysaccharide-based vaccines have motivated the search for other bacterial immunogens capable of eliciting a protective immune response against S. pneumoniae. Fructose-1,6-bisphosphate aldolase (FBA) is a glycolytic enzyme, which was found to localize to the bacterial surface, where it functions as an adhesin. Previously, immunizing mice with recombinant FBA (rFBA) in the presence of alum elicited a protective immune response against a lethal challenge with S. pneumoniae. Thus, the aim of the present study was to determine the cytokine responses that are indicative of protective immunity following immunization with rFBA. The protective effects against pneumococcal challenge in mice immunized with rFBA with complete Freund's adjuvant (CFA) in the initial immunization and with incomplete Freund's adjuvant (IFA) in booster immunizations surpassed the protective effects observed following immunization with either rFBA + alum or pVACfba. CD4+ T-cells obtained from the rFBA/CFA/IFA/IFA-immunized mice co-cultured with rFBA-pulsed antigen-presenting cells (APCs), exhibited a significantly greater proliferative ability than CD4+ T-cells obtained from the adjuvant-immunized mice co-cultured with rFBA‑pulsed APCs. The levels of the Th1-type cytokines, interferon (IFN)-γ, interleukin (IL)-2, tumor necrosis factor (TNF)-α and IL-12, the Th2-type cytokines, IL-4, IL-5 and IL-10, and the Th17-type cytokine, IL-17A, significantly increased within 72 h of the initiation of co-culture with CD4+ T-cells obtained from the rFBA‑immunized mice, in comparison with the co-cultures with CD4+ T-cells obtained from the adjuvant-immunized mice. Immunizing mice with rFBA resulted in an IgG1/IgG2 ratio of 41, indicating a Th2 response with substantial Th1 involvement. In addition, rabbit and mouse anti-rFBA antisera significantly protected the mice against a lethal S. pneumoniae challenge in comparison with preimmune sera. Our results emphasize the mixed involvement of the Th1, Th2 and Th17 arms of the immune system in response to immunization with pneumococcal rFBA, a potential vaccine candidate.
Facile synthesis of magnetic Fe3O4@BiOI@AgI for water decontamination with visible light irradiation: Different mechanisms for different organic pollutants degradation and bacterial disinfection.

PubMed

Liang, Jialiang; Liu, Fuyang; Li, Mian; Liu, Wen; Tong, Meiping

2018-06-15

Magnetic Fe 3 O 4 @BiOI@AgI (FBA) spheres were synthesized through a multi-step process. The fabricated photocatalysts were characterized by different techniques. To testify the visible light driven photocatalytic activity of FBA, Rhodamine B and Bisphenol A were chosen as model common and emerging organic contaminants, respectively. While, gram-negative strain Escherichia coli was selected as model waterborne bacteria. The results showed that under visible light irradiation, FBA contained strong photocatalytic degradation capacity towards both RhB and BPA. Moreover, FBA was also found to exhibit excellent disinfection activity towards E. coli. The photocatalytic mechanisms for different pollutants by FBA were determined and found to vary for different pollutants. Specifically, scavenger experiments, degradation intermediates determination, as well as theoretical density functional theory (DFT) analysis showed that RhB and BPA were degraded via photosensitization (dominated by e - and ·O 2 - ) and direct photocatalytic oxidation (contributed by h + , e - and ·O 2 - ), respectively. Whereas, E. coli cells yet were found to be inactivated by the generation of e - and ·O 2 - rather than by the released Ag + . Since it contained superparamagnetic property, FBA could be easily separated from the reaction suspension after use. Due to the excellent photo stability, FBA exhibited strong photocatalytic activity in the fourth reused recycle. Therefore, FBA could serve as a promising alternative for water purification. Copyright © 2018 Elsevier Ltd. All rights reserved.

East Tennessee State University's "Make a Difference" Project: Using a Team-Based Consultative Model To Conduct Functional Behavioral Assessments.

ERIC Educational Resources Information Center

Vaughn, Kelley; Hales, Cindy; Bush, Marta; Fox, James

1998-01-01

Describes implementation of functional behavioral assessment (FBA) through collaboration between a university (East Tennessee State University) and the local school system. Discusses related issues such as factors in team training, team size, FBA adaptations, and replicability of the FBA team model. (Author/DB)
Fructose-1,6-bisphosphate aldolase (FBA)-a conserved glycolytic enzyme with virulence functions in bacteria: 'ill met by moonlight'.

PubMed

Shams, Fariza; Oldfield, Neil J; Wooldridge, Karl G; Turner, David P J

2014-12-01

Moonlighting proteins constitute an intriguing class of multifunctional proteins. Metabolic enzymes and chaperones, which are often highly conserved proteins in bacteria, archaea and eukaryotic organisms, are among the most commonly recognized examples of moonlighting proteins. Fructose-1,6-bisphosphate aldolase (FBA) is an enzyme involved in the Embden-Meyerhof-Parnas (EMP) glycolytic pathway and in gluconeogenesis. Increasingly, it is also recognized that FBA has additional functions beyond its housekeeping role in central metabolism. In the present review, we summarize the current knowledge of the moonlighting functions of FBA in bacteria.
Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis

PubMed Central

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2014-01-01

Class II fructose 1,6-bisphosphate aldolases (FBA; E.C. 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff-base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs has been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies on class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation/deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI/DHAP bound form of the enzyme and determined the X-ray structure of MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information plus site-directed mutagenesis and kinetic studies conducted on a series of residues within the active-site loop revealed that E169 facilitates a water mediated deprotonation/protonation step of the MtFBA reaction mechanism. Also, secondary isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form. PMID:23298222
The involvement of wheat F-box protein gene TaFBA1 in the oxidative stress tolerance of plants.

PubMed

Zhou, Shu-Mei; Kong, Xiang-Zhu; Kang, Han-Han; Sun, Xiu-Dong; Wang, Wei

2015-01-01

As one of the largest gene families, F-box domain proteins have been found to play important roles in abiotic stress responses via the ubiquitin pathway. TaFBA1 encodes a homologous F-box protein contained in E3 ubiquitin ligases. In our previous study, we found that the overexpression of TaFBA1 enhanced drought tolerance in transgenic plants. To investigate the mechanisms involved, in this study, we investigated the tolerance of the transgenic plants to oxidative stress. Methyl viologen was used to induce oxidative stress conditions. Real-time PCR and western blot analysis revealed that TaFBA1 expression was up-regulated by oxidative stress treatments. Under oxidative stress conditions, the transgenic tobacco plants showed a higher germination rate, higher root length and less growth inhibition than wild type (WT). The enhanced oxidative stress tolerance of the transgenic plants was also indicated by lower reactive oxygen species (ROS) accumulation, malondialdehyde (MDA) content and cell membrane damage under oxidative stress compared with WT. Higher activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and peroxidase (POD), were observed in the transgenic plants than those in WT, which may be related to the upregulated expression of some antioxidant genes via the overexpression of TaFBA1. In others, some stress responsive elements were found in the promoter region of TaFBA1, and TaFBA1 was located in the nucleus, cytoplasm and plasma membrane. These results suggest that TaFBA1 plays an important role in the oxidative stress tolerance of plants. This is important for understanding the functions of F-box proteins in plants' tolerance to multiple stress conditions.
Fructose Degradation in the Haloarchaeon Haloferax volcanii Involves a Bacterial Type Phosphoenolpyruvate-Dependent Phosphotransferase System, Fructose-1-Phosphate Kinase, and Class II Fructose-1,6-Bisphosphate Aldolase

PubMed Central

Pickl, Andreas; Johnsen, Ulrike

2012-01-01

The halophilic archaeon Haloferax volcanii utilizes fructose as a sole carbon and energy source. Genes and enzymes involved in fructose uptake and degradation were identified by transcriptional analyses, deletion mutant experiments, and enzyme characterization. During growth on fructose, the gene cluster HVO_1495 to HVO_1499, encoding homologs of the five bacterial phosphotransferase system (PTS) components enzyme IIB (EIIB), enzyme I (EI), histidine protein (HPr), EIIA, and EIIC, was highly upregulated as a cotranscript. The in-frame deletion of HVO_1499, designated ptfC (ptf stands for phosphotransferase system for fructose) and encoding the putative fructose-specific membrane component EIIC, resulted in a loss of growth on fructose, which could be recovered by complementation in trans. Transcripts of HVO_1500 (pfkB) and HVO_1494 (fba), encoding putative fructose-1-phosphate kinase (1-PFK) and fructose-1,6-bisphosphate aldolase (FBA), respectively, as well as 1-PFK and FBA activities were specifically upregulated in fructose-grown cells. pfkB and fba knockout mutants did not grow on fructose, whereas growth on glucose was not inhibited, indicating the functional involvement of both enzymes in fructose catabolism. Recombinant 1-PFK and FBA obtained after homologous overexpression were characterized as having kinetic properties indicative of functional 1-PFK and a class II type FBA. From these data, we conclude that fructose uptake in H. volcanii involves a fructose-specific PTS generating fructose-1-phosphate, which is further converted via fructose-1,6-bisphosphate to triose phosphates by 1-PFK and FBA. This is the first report of the functional involvement of a bacterial-like PTS and of class II FBA in the sugar metabolism of archaea. PMID:22493022
The Involvement of Wheat F-Box Protein Gene TaFBA1 in the Oxidative Stress Tolerance of Plants

PubMed Central

Zhou, Shu-Mei; Kong, Xiang-Zhu; Kang, Han-Han; Sun, Xiu-Dong; Wang, Wei

2015-01-01

As one of the largest gene families, F-box domain proteins have been found to play important roles in abiotic stress responses via the ubiquitin pathway. TaFBA1 encodes a homologous F-box protein contained in E3 ubiquitin ligases. In our previous study, we found that the overexpression of TaFBA1 enhanced drought tolerance in transgenic plants. To investigate the mechanisms involved, in this study, we investigated the tolerance of the transgenic plants to oxidative stress. Methyl viologen was used to induce oxidative stress conditions. Real-time PCR and western blot analysis revealed that TaFBA1 expression was up-regulated by oxidative stress treatments. Under oxidative stress conditions, the transgenic tobacco plants showed a higher germination rate, higher root length and less growth inhibition than wild type (WT). The enhanced oxidative stress tolerance of the transgenic plants was also indicated by lower reactive oxygen species (ROS) accumulation, malondialdehyde (MDA) content and cell membrane damage under oxidative stress compared with WT. Higher activities of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and peroxidase (POD), were observed in the transgenic plants than those in WT, which may be related to the upregulated expression of some antioxidant genes via the overexpression of TaFBA1. In others, some stress responsive elements were found in the promoter region of TaFBA1, and TaFBA1 was located in the nucleus, cytoplasm and plasma membrane. These results suggest that TaFBA1 plays an important role in the oxidative stress tolerance of plants. This is important for understanding the functions of F-box proteins in plants’ tolerance to multiple stress conditions. PMID:25906259
Structural and functional characterization of methicillin-resistant Staphylococcus aureus's class IIb fructose 1,6-bisphosphate aldolase.

PubMed

Capodagli, Glenn C; Lee, Stephen A; Boehm, Kyle J; Brady, Kristin M; Pegan, Scott D

2014-12-09

Staphylococcus aureus is one of the most common nosocomial sources of soft-tissue and skin infections and has more recently become prevalent in the community setting as well. Since the use of penicillins to combat S. aureus infections in the 1940s, the bacterium has been notorious for developing resistances to antibiotics, such as methicillin-resistant Staphylococcus aureus (MRSA). With the persistence of MRSA as well as many other drug resistant bacteria and parasites, there is a growing need to focus on new pharmacological targets. Recently, class II fructose 1,6-bisphosphate aldolases (FBAs) have garnered attention to fill this role. Regrettably, scarce biochemical data and no structural data are currently available for the class II FBA found in MRSA (SaFBA). With the recent finding of a flexible active site zinc-binding loop (Z-Loop) in class IIa FBAs and its potential for broad spectrum class II FBA inhibition, the lack of information regarding this feature of class IIb FBAs, such as SaFBA, has been limiting for further Z-loop inhibitor development. Therefore, we elucidated the crystal structure of SaFBA to 2.1 Å allowing for a more direct structural analysis of SaFBA. Furthermore, we determined the KM for one of SaFBA's substrates, fructose 1,6-bisphosphate, as well as performed mode of inhibition studies for an inhibitor that takes advantage of the Z-loop's flexibility. Together the data offers insight into a class IIb FBA from a pervasively drug resistant bacterium and a comparison of Z-loops and other features between the different subtypes of class II FBAs.
Structure-Based Rational Design of Novel Inhibitors Against Fructose-1,6-Bisphosphate Aldolase from Candida albicans.

PubMed

Han, Xinya; Zhu, Xiuyun; Hong, Zongqin; Wei, Lin; Ren, Yanliang; Wan, Fen; Zhu, Shuaihua; Peng, Hao; Guo, Li; Rao, Li; Feng, Lingling; Wan, Jian

2017-06-26

Class II fructose-1,6-bisphosphate aldolases (FBA-II) are attractive new targets for the discovery of drugs to combat invasive fungal infection, because they are absent in animals and higher plants. Although several FBA-II inhibitors have been reported, none of these inhibitors exhibit antifungal effect so far. In this study, several novel inhibitors of FBA-II from C. albicans (Ca-FBA-II) with potent antifungal effects were rationally designed by jointly using a specific protocols of molecular docking-based virtual screening, accurate binding-conformation evaluation strategy, synthesis and enzymatic assays. The enzymatic assays reveal that the compounds 3c, 3e-g, 3j and 3k exhibit high inhibitory activity against Ca-FBA-II (IC 50 < 10 μM), and the most potential inhibitor is 3g, with IC 50 value of 2.7 μM. Importantly, the compounds 3f, 3g, and 3l possess not only high inhibitions against Ca-FBA-II, but also moderate antifungal activities against C. glabrata (MIC 80 = 4-64 μg/mL). The compounds 3g, 3l, and 3k in combination with fluconazole (8 μg/mL) displayed significantly synergistic antifungal activities (MIC 80 < 0.0625 μg/mL) against resistant Candida strains, which are resistant to azoles drugs. The probable binding modes between 3g and the active site of Ca-FBA-II have been proposed by using the DOX (docking, ONIOM, and XO) strategy. To our knowledge, no FBA-II inhibitors with antifungal activities against wild type and resistant strains from Candida were reported previously. The positive results suggest that the strategy adopted in this study are a promising method for the discovery of novel drugs against azole-resistant fungal pathogens in the future.
A survey of functional behavior assessment methods used by behavior analysts in practice.

PubMed

Oliver, Anthony C; Pratt, Leigh A; Normand, Matthew P

2015-12-01

To gather information about the functional behavior assessment (FBA) methods behavior analysts use in practice, we sent a web-based survey to 12,431 behavior analysts certified by the Behavior Analyst Certification Board. Ultimately, 724 surveys were returned, with the results suggesting that most respondents regularly use FBA methods, especially descriptive assessments. Moreover, the data suggest that the majority of students are being formally taught about the various FBA methods and that educators are emphasizing the range of FBA methods in their teaching. However, less than half of the respondents reported using functional analyses in practice, although many considered descriptive assessments and functional analyses to be the most useful FBA methods. Most respondents reported using informant and descriptive assessments more frequently than functional analyses, and a majority of respondents indicated that they "never" or "almost never" used functional analyses to identify the function of behavior. © Society for the Experimental Analysis of Behavior.
The role of the F-box gene TaFBA1 from wheat (Triticum aestivum L.) in drought tolerance.

PubMed

Zhou, Shumei; Sun, Xiudong; Yin, Suhong; Kong, Xiangzhu; Zhou, Shan; Xu, Ying; Luo, Yin; Wang, Wei

2014-11-01

Drought is one of the most important factors limiting plant growth and development. We identified a gene in wheat (Triticum aestivum L.) under drought stress named TaFBA1. TaFBA1 encodes a putative 325-amino-acid F-box protein with a conserved N-terminal F-box domain and a C-terminal AMN1 domain. Real-time RT-PCR analysis revealed that TaFBA1 transcript accumulation was upregulated by high-salinity, water stress, and abscisic acid (ABA) treatment. To evaluate the functions of TaFBA1 in the regulation of drought stress responses, we produced transgenic tobacco lines overexpressing TaFBA1. Under water stress conditions, the transgenic tobacco plants had a higher germination rate, higher relative water content, net photosynthesis rate (Pn), less chlorophyll loss, and less growth inhibition than WT. These results demonstrate the high tolerance of the transgenic plants to drought stress compared to the WT. The enhanced oxidative stress tolerance of these plants, which may be involved in their drought tolerance, was indicated by their lower levels of reactive oxygen species (ROS) accumulation, MDA content, and cell membrane damage under drought stress compared to WT. The antioxidant enzyme activities were higher in the transgenic plants than in WT, which may be related to the upregulated expression of some antioxidant genes via overexpression of TaFBA1. Copyright © 2014 Elsevier Masson SAS. All rights reserved.
Microscopic quantification of bacterial invasion by a novel antibody-independent staining method.

PubMed

Agerer, Franziska; Waeckerle, Stephanie; Hauck, Christof R

2004-10-01

Microscopic discrimination between extracellular and invasive, intracellular bacteria is a valuable technique in microbiology and immunology. We describe a novel fluorescence staining protocol, called FITC-biotin-avidin (FBA) staining, which allows the differentiation between extracellular and intracellular bacteria and is independent of specific antibodies directed against the microorganisms. FBA staining of eukaryotic cells infected with Gram-negative bacteria of the genus Neisseria or the Gram-positive pathogen Staphylococcus aureus are employed to validate the novel technique. The quantitative evaluation of intracellular pathogens by the FBA staining protocol yields identical results compared to parallel samples stained with conventional, antibody-dependent methods. FBA staining eliminates the need for cell permeabilization resulting in robust and rapid detection of invasive microbes. Taken together, FBA staining provides a reliable and convenient alternative for the differential detection of intracellular and extracellular bacteria and should be a valuable technical tool for the quantitative analysis of the invasive properties of pathogenic bacteria and other microorganisms.
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

PubMed Central

2017-01-01

Genome-scale metabolic network reconstructions (GENREs) are repositories of knowledge about the metabolic processes that occur in an organism. GENREs have been used to discover and interpret metabolic functions, and to engineer novel network structures. A major barrier preventing more widespread use of GENREs, particularly to study non-model organisms, is the extensive time required to produce a high-quality GENRE. Many automated approaches have been developed which reduce this time requirement, but automatically-reconstructed draft GENREs still require curation before useful predictions can be made. We present a novel approach to the analysis of GENREs which improves the predictive capabilities of draft GENREs by representing many alternative network structures, all equally consistent with available data, and generating predictions from this ensemble. This ensemble approach is compatible with many reconstruction methods. We refer to this new approach as Ensemble Flux Balance Analysis (EnsembleFBA). We validate EnsembleFBA by predicting growth and gene essentiality in the model organism Pseudomonas aeruginosa UCBPP-PA14. We demonstrate how EnsembleFBA can be included in a systems biology workflow by predicting essential genes in six Streptococcus species and mapping the essential genes to small molecule ligands from DrugBank. We found that some metabolic subsystems contributed disproportionately to the set of predicted essential reactions in a way that was unique to each Streptococcus species, leading to species-specific outcomes from small molecule interactions. Through our analyses of P. aeruginosa and six Streptococci, we show that ensembles increase the quality of predictions without drastically increasing reconstruction time, thus making GENRE approaches more practical for applications which require predictions for many non-model organisms. All of our functions and accompanying example code are available in an open online repository. PMID:28263984
Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA.

PubMed

Biggs, Matthew B; Papin, Jason A

2017-03-01

Genome-scale metabolic network reconstructions (GENREs) are repositories of knowledge about the metabolic processes that occur in an organism. GENREs have been used to discover and interpret metabolic functions, and to engineer novel network structures. A major barrier preventing more widespread use of GENREs, particularly to study non-model organisms, is the extensive time required to produce a high-quality GENRE. Many automated approaches have been developed which reduce this time requirement, but automatically-reconstructed draft GENREs still require curation before useful predictions can be made. We present a novel approach to the analysis of GENREs which improves the predictive capabilities of draft GENREs by representing many alternative network structures, all equally consistent with available data, and generating predictions from this ensemble. This ensemble approach is compatible with many reconstruction methods. We refer to this new approach as Ensemble Flux Balance Analysis (EnsembleFBA). We validate EnsembleFBA by predicting growth and gene essentiality in the model organism Pseudomonas aeruginosa UCBPP-PA14. We demonstrate how EnsembleFBA can be included in a systems biology workflow by predicting essential genes in six Streptococcus species and mapping the essential genes to small molecule ligands from DrugBank. We found that some metabolic subsystems contributed disproportionately to the set of predicted essential reactions in a way that was unique to each Streptococcus species, leading to species-specific outcomes from small molecule interactions. Through our analyses of P. aeruginosa and six Streptococci, we show that ensembles increase the quality of predictions without drastically increasing reconstruction time, thus making GENRE approaches more practical for applications which require predictions for many non-model organisms. All of our functions and accompanying example code are available in an open online repository.
Software applications for flux balance analysis.

PubMed

Lakshmanan, Meiyappan; Koh, Geoffrey; Chung, Bevan K S; Lee, Dong-Yup

2014-01-01

Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the availability of specific software tools for FBA. Each tool has its unique features and limitations with respect to operational environment, user-interface and supported analysis algorithms. Presented herein is an in-depth evaluation of currently available FBA applications, focusing mainly on usability, functionality, graphical representation and inter-operability. Overall, most of the applications are able to perform basic features of model creation and FBA simulation. COBRA toolbox, OptFlux and FASIMU are versatile to support advanced in silico algorithms to identify environmental and genetic targets for strain design. SurreyFBA, WEbcoli, Acorn, FAME, GEMSiRV and MetaFluxNet are the distinct tools which provide the user friendly interfaces in model handling. In terms of software architecture, FBA-SimVis and OptFlux have the flexible environments as they enable the plug-in/add-on feature to aid prospective functional extensions. Notably, an increasing trend towards the implementation of more tailored e-services such as central model repository and assistance to collaborative efforts was observed among the web-based applications with the help of advanced web-technologies. Furthermore, most recent applications such as the Model SEED, FAME, MetaFlux and MicrobesFlux have even included several routines to facilitate the reconstruction of genome-scale metabolic models. Finally, a brief discussion on the future directions of FBA applications was made for the benefit of potential tool developers.
fMRI-adaptation studies of viewpoint tuning in the extrastriate and fusiform body areas.

PubMed

Taylor, John C; Wiggett, Alison J; Downing, Paul E

2010-03-01

People are easily able to perceive the human body across different viewpoints, but the neural mechanisms underpinning this ability are currently unclear. In three experiments, we used functional MRI (fMRI) adaptation to study the view-invariance of representations in two cortical regions that have previously been shown to be sensitive to visual depictions of the human body--the extrastriate and fusiform body areas (EBA and FBA). The BOLD response to sequentially presented pairs of bodies was treated as an index of view invariance. Specifically, we compared trials in which the bodies in each image held identical poses (seen from different views) to trials containing different poses. EBA and FBA adapted to identical views of the same pose, and both showed a progressive rebound from adaptation as a function of the angular difference between views, up to approximately 30 degrees. However, these adaptation effects were eliminated when the body stimuli were followed by a pattern mask. Delaying the mask onset increased the response (but not the adaptation effect) in EBA, leaving FBA unaffected. We interpret these masking effects as evidence that view-dependent fMRI adaptation is driven by later waves of neuronal responses in the regions of interest. Finally, in a whole brain analysis, we identified an anterior region of the left inferior temporal sulcus (l-aITS) that responded linearly to stimulus rotation, but showed no selectivity for bodies. Our results show that body-selective cortical areas exhibit a similar degree of view-invariance as other object selective areas--such as the lateral occipitotemporal area (LO) and posterior fusiform gyrus (pFs).
Structural and functional characterization of methicillin-resistant Staphylococcus aureus’s class IIb fructose 1,6-bisphosphate aldolase

DOE PAGES

Capodagli, Glenn C.; Lee, Stephen A.; Boehm, Kyle J.; ...

2014-11-12

Staphylococcus aureus is one of the most common nosocomial sources of soft-tissue and skin infections and has more recently become prevalent in the community setting as well. Since the use of penicillins to combat S. aureus infections in the 1940s, the bacterium has been notorious for developing resistances to antibiotics, such as methicillin-resistant Staphylococcus aureus (MRSA). With the persistence of MRSA as well as many other drug resistant bacteria and parasites, there is a growing need to focus on new pharmacological targets. Recently, class II fructose 1,6-bisphosphate aldolases (FBAs) have garnered attention to fill this role. Regrettably, scarce biochemical datamore » and no structural data are currently available for the class II FBA found in MRSA (SaFBA). With the recent finding of a flexible active site zinc-binding loop (Z-Loop) in class IIa FBAs and its potential for broad spectrum class II FBA inhibition, the lack of information regarding this feature of class IIb FBAs, such as SaFBA, has been limiting for further Z-loop inhibitor development. Therefore, we elucidated the crystal structure of SaFBA to 2.1 Å allowing for a more direct structural analysis of SaFBA. Furthermore, we determined the KM for one of SaFBA’s substrates, fructose 1,6-bisphosphate, as well as performed mode of inhibition studies for an inhibitor that takes advantage of the Z-loop’s flexibility. Altogether the data offers insight into a class IIb FBA from a pervasively drug resistant bacterium and a comparison of Z-loops and other features between the different subtypes of class II FBAs.« less
Structural and functional characterization of methicillin-resistant Staphylococcus aureus’s class IIb fructose 1,6-bisphosphate aldolase

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

Capodagli, Glenn C.; Lee, Stephen A.; Boehm, Kyle J.

Staphylococcus aureus is one of the most common nosocomial sources of soft-tissue and skin infections and has more recently become prevalent in the community setting as well. Since the use of penicillins to combat S. aureus infections in the 1940s, the bacterium has been notorious for developing resistances to antibiotics, such as methicillin-resistant Staphylococcus aureus (MRSA). With the persistence of MRSA as well as many other drug resistant bacteria and parasites, there is a growing need to focus on new pharmacological targets. Recently, class II fructose 1,6-bisphosphate aldolases (FBAs) have garnered attention to fill this role. Regrettably, scarce biochemical datamore » and no structural data are currently available for the class II FBA found in MRSA (SaFBA). With the recent finding of a flexible active site zinc-binding loop (Z-Loop) in class IIa FBAs and its potential for broad spectrum class II FBA inhibition, the lack of information regarding this feature of class IIb FBAs, such as SaFBA, has been limiting for further Z-loop inhibitor development. Therefore, we elucidated the crystal structure of SaFBA to 2.1 Å allowing for a more direct structural analysis of SaFBA. Furthermore, we determined the KM for one of SaFBA’s substrates, fructose 1,6-bisphosphate, as well as performed mode of inhibition studies for an inhibitor that takes advantage of the Z-loop’s flexibility. Altogether the data offers insight into a class IIb FBA from a pervasively drug resistant bacterium and a comparison of Z-loops and other features between the different subtypes of class II FBAs.« less
Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis.

PubMed

Pegan, Scott D; Rukseree, Kamolchanok; Capodagli, Glenn C; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2013-02-05

Class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation-deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation-protonation step of the MtFBA reaction mechanism. Also, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.
A Thermodynamically-consistent FBA-based Approach to Biogeochemical Reaction Modeling

NASA Astrophysics Data System (ADS)

Shapiro, B.; Jin, Q.

2015-12-01

Microbial rates are critical to understanding biogeochemical processes in natural environments. Recently, flux balance analysis (FBA) has been applied to predict microbial rates in aquifers and other settings. FBA is a genome-scale constraint-based modeling approach that computes metabolic rates and other phenotypes of microorganisms. This approach requires a prior knowledge of substrate uptake rates, which is not available for most natural microbes. Here we propose to constrain substrate uptake rates on the basis of microbial kinetics. Specifically, we calculate rates of respiration (and fermentation) using a revised Monod equation; this equation accounts for both the kinetics and thermodynamics of microbial catabolism. Substrate uptake rates are then computed from the rates of respiration, and applied to FBA to predict rates of microbial growth. We implemented this method by linking two software tools, PHREEQC and COBRA Toolbox. We applied this method to acetotrophic methanogenesis by Methanosarcina barkeri, and compared the simulation results to previous laboratory observations. The new method constrains acetate uptake by accounting for the kinetics and thermodynamics of methanogenesis, and predicted well the observations of previous experiments. In comparison, traditional methods of dynamic-FBA constrain acetate uptake on the basis of enzyme kinetics, and failed to reproduce the experimental results. These results show that microbial rate laws may provide a better constraint than enzyme kinetics for applying FBA to biogeochemical reaction modeling.
Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

DOE PAGES

Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe; ...

2017-04-07

In this study, the increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course absolute quantitative metabolomics. This approach, termed “unsteady-state flux balance analysis” (uFBA), is applied to four cellular systems: three dynamic and one steady-state as a negative control. uFBA and FBA predictions are contrasted, and uFBA is found to be more accurate in predicting dynamic metabolic flux states for red blood cells, platelets, and Saccharomyces cerevisiae. Notably, only uFBAmore » predicts that stored red blood cells metabolize TCA intermediates to regenerate important cofactors, such as ATP, NADH, and NADPH. These pathway usage predictions were subsequently validated through 13C isotopic labeling and metabolic flux analysis in stored red blood cells. Utilizing time-course metabolomics data, uFBA provides an accurate method to predict metabolic physiology at the cellular scale for dynamic systems.« less

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

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

Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe

In this study, the increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course absolute quantitative metabolomics. This approach, termed “unsteady-state flux balance analysis” (uFBA), is applied to four cellular systems: three dynamic and one steady-state as a negative control. uFBA and FBA predictions are contrasted, and uFBA is found to be more accurate in predicting dynamic metabolic flux states for red blood cells, platelets, and Saccharomyces cerevisiae. Notably, only uFBAmore » predicts that stored red blood cells metabolize TCA intermediates to regenerate important cofactors, such as ATP, NADH, and NADPH. These pathway usage predictions were subsequently validated through 13C isotopic labeling and metabolic flux analysis in stored red blood cells. Utilizing time-course metabolomics data, uFBA provides an accurate method to predict metabolic physiology at the cellular scale for dynamic systems.« less
Visualization and Analysis of Climate Simulation Performance Data

NASA Astrophysics Data System (ADS)

Röber, Niklas; Adamidis, Panagiotis; Behrens, Jörg

2015-04-01

Visualization is the key process of transforming abstract (scientific) data into a graphical representation, to aid in the understanding of the information hidden within the data. Climate simulation data sets are typically quite large, time varying, and consist of many different variables sampled on an underlying grid. A large variety of climate models - and sub models - exist to simulate various aspects of the climate system. Generally, one is mainly interested in the physical variables produced by the simulation runs, but model developers are also interested in performance data measured along with these simulations. Climate simulation models are carefully developed complex software systems, designed to run in parallel on large HPC systems. An important goal thereby is to utilize the entire hardware as efficiently as possible, that is, to distribute the workload as even as possible among the individual components. This is a very challenging task, and detailed performance data, such as timings, cache misses etc. have to be used to locate and understand performance problems in order to optimize the model implementation. Furthermore, the correlation of performance data to the processes of the application and the sub-domains of the decomposed underlying grid is vital when addressing communication and load imbalance issues. High resolution climate simulations are carried out on tens to hundreds of thousands of cores, thus yielding a vast amount of profiling data, which cannot be analyzed without appropriate visualization techniques. This PICO presentation displays and discusses the ICON simulation model, which is jointly developed by the Max Planck Institute for Meteorology and the German Weather Service and in partnership with DKRZ. The visualization and analysis of the models performance data allows us to optimize and fine tune the model, as well as to understand its execution on the HPC system. We show and discuss our workflow, as well as present new ideas and solutions that greatly aided our understanding. The software employed is based on Avizo Green, ParaView and SimVis, as well as own developed software extensions.
Structure-based prediction and identification of 4-epimerization activity of phosphate sugars in class II aldolases.

PubMed

Lee, Seon-Hwa; Hong, Seung-Hye; An, Jung-Ung; Kim, Kyoung-Rok; Kim, Dong-Eun; Kang, Lin-Woo; Oh, Deok-Kun

2017-05-16

Sugar 4-epimerization reactions are important for the production of rare sugars and their derivatives, which have various potential industrial applications. For example, the production of tagatose, a functional sweetener, from fructose by sugar 4-epimerization is currently constrained because a fructose 4-epimerase does not exist in nature. We found that class II D-fructose-1,6-bisphosphate aldolase (FbaA) catalyzed the 4-epimerization of D-fructose-6-phosphate (F6P) to D-tagatose-6-phosphate (T6P) based on the prediction via structural comparisons with epimerase and molecular docking and the identification of the condensed products of C3 sugars. In vivo, the 4-epimerization activity of FbaA is normally repressed. This can be explained by our results showing the catalytic efficiency of D-fructose-6-phosphate kinase for F6P phosphorylation was significantly higher than that of FbaA for F6P epimerization. Here, we identified the epimerization reactions and the responsible catalytic residues through observation of the reactions of FbaA and L-rhamnulose-1-phosphate aldolases (RhaD) variants with substituted catalytic residues using different substrates. Moreover, we obtained detailed potential epimerization reaction mechanism of FbaA and a general epimerization mechanism of the class II aldolases L-fuculose-1-phosphate aldolase, RhaD, and FbaA. Thus, class II aldolases can be used as 4-epimerases for the stereo-selective synthesis of valuable carbohydrates.
Capturing the essence of a metabolic network: a flux balance analysis approach.

PubMed

Murabito, Ettore; Simeonidis, Evangelos; Smallbone, Kieran; Swinton, Jonathan

2009-10-07

As genome-scale metabolic reconstructions emerge, tools to manage their size and complexity will be increasingly important. Flux balance analysis (FBA) is a constraint-based approach widely used to study the metabolic capabilities of cellular or subcellular systems. FBA problems are highly underdetermined and many different phenotypes can satisfy any set of constraints through which the metabolic system is represented. Two of the main concerns in FBA are exploring the space of solutions for a given metabolic network and finding a specific phenotype which is representative for a given task such as maximal growth rate. Here, we introduce a recursive algorithm suitable for overcoming both of these concerns. The method proposed is able to find the alternate optimal patterns of active reactions of an FBA problem and identify the minimal subnetwork able to perform a specific task as optimally as the whole. Our method represents an alternative to and an extension of other approaches conceived for exploring the space of solutions of an FBA problem. It may also be particularly helpful in defining a scaffold of reactions upon which to build up a dynamic model, when the important pathways of the system have not yet been well-defined.
Fructose-bisphosphate aldolase and pyruvate kinase, two novel immunogens in Madurella mycetomatis.

PubMed

de Klerk, Nele; de Vogel, Corné; Fahal, Ahmed; van Belkum, Alex; van de Sande, Wendy W J

2012-02-01

Eumycetoma, a chronic granulomatous disease characterized by a subcutaneous mass, multiple sinuses and purulent discharge containing grains, remains difficult to diagnose and treat. Madurella mycetomatis is the most common causative agent of eumycetoma. Using a serum pool from patients with active mycetoma, we screened a M. mycetomatis-specific λgt11 cDNA library which was shown to contain 8% of cDNA inserts encoding proteins involved in glycolysis. Two of these enzymes, fructose-bisphosphate aldolase (FBA) and pyruvate kinase (PK), were produced in vitro and their antigenicity was studied with bead-based flow cytometry. It appeared that both FBA and PK IgG antibodies were present in eumycetoma patient sera. However, only FBA antibody levels were found to be significantly higher in eumycetoma patient sera when compared to healthy Sudanese controls. Furthermore, FBA and PK were also found to be expressed on the hyphae present in the mycetoma grain. In conclusion, this study presents two new antigenic proteins of M. mycetomatis next to the translationally controlled tumour protein (TCTP): the glycolytic enzymes FBA and PK. These antigens might be useful as vaccine-candidates in the prevention of mycetoma.
Fast flux module detection using matroid theory.

PubMed

Reimers, Arne C; Bruggeman, Frank J; Olivier, Brett G; Stougie, Leen

2015-05-01

Flux balance analysis (FBA) is one of the most often applied methods on genome-scale metabolic networks. Although FBA uniquely determines the optimal yield, the pathway that achieves this is usually not unique. The analysis of the optimal-yield flux space has been an open challenge. Flux variability analysis is only capturing some properties of the flux space, while elementary mode analysis is intractable due to the enormous number of elementary modes. However, it has been found by Kelk et al. (2012) that the space of optimal-yield fluxes decomposes into flux modules. These decompositions allow a much easier but still comprehensive analysis of the optimal-yield flux space. Using the mathematical definition of module introduced by Müller and Bockmayr (2013b), we discovered useful connections to matroid theory, through which efficient algorithms enable us to compute the decomposition into modules in a few seconds for genome-scale networks. Using that every module can be represented by one reaction that represents its function, in this article, we also present a method that uses this decomposition to visualize the interplay of modules. We expect the new method to replace flux variability analysis in the pipelines for metabolic networks.
Structural Basis for Catalysis of a Tetrameric Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

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

Pegan, Scott D.; Ruskseree, Kamolchanok; Franzblau, Scott G.

2009-03-04

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), currently infects one-third of the world's population in its latent form. The emergence of multidrug-resistant and extensive drug-resistant strains has highlighted the need for new pharmacological targets within M. tuberculosis. The class IIa fructose 1,6-bisphosphate aldolase (FBA) enzyme from M. tuberculosis (MtFBA) has been proposed as one such target since it is upregulated in latent TB. Since the structure of MtFBA has not been determined and there is little information available on its reaction mechanism, we sought to determine the X-ray structure of MtFBA in complex with its substrates. By lowering themore » pH of the enzyme in the crystalline state, we were able to determine a series of high-resolution X-ray structures of MtFBA bound to dihydroxyacetone phosphate, glyceraldehyde 3-phosphate, and fructose 1,6-bisphosphate at 1.5, 2.1, and 1.3 {angstrom}, respectively. Through these structures, it was discovered that MtFBA belongs to a novel tetrameric class of type IIa FBAs. The molecular details at the interface of the tetramer revealed important information for better predictability of the quaternary structures among the FBAs based on their primary sequences. These X-ray structures also provide interesting and new details on the reaction mechanism of class II FBAs. Substrates and products were observed in geometries poised for catalysis; in addition, unexpectedly, the hydroxyl-enolate intermediate of dihydroxyacetone phosphate was also captured and resolved structurally. These concise new details offer a better understanding of the reaction mechanisms for FBAs in general and provide a structural basis for inhibitor design efforts aimed at this class of enzymes.« less
Structural basis for catalysis of a tetrameric, class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis

PubMed Central

Pegan, Scott D.; Rukseree, Kamolchanok; Franzblau, Scott G.; Mesecar, Andrew D.

2009-01-01

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), currently infects one third of the world’s population in its latent form. The emergence of multidrug resistant strains, MDR-TB and XDR-TB has highlighted the need for new pharmacological targets within M. tuberculosis. The Class IIa fructose 1,6-bisphosphate aldolase (FBA) enzyme from M. tuberculosis (MtFBA) has been proposed as one such target since its upregulated in latent TB. Since the structure of MtFBA had not been determined and since there was little information available on its reaction mechanism, we sought to determine the X-ray structure of MtFBA in complex with its substrates. By lowering the pH of the enzyme in the crystalline state, we were able to determine a series of high-resolution X-ray structures of MtFBA bound to dihydroxyacetonephosphate (DHAP), glyceraldehyde-3-phosphate (G3P), and fructose 1,6-bisphosphate (FBP) at 1.5 Å, 2.1 Å, and 1.3 Å respectively. Through these structures it was discovered that MtFBA belongs to a novel tetrameric class of the type IIa FBAs. The molecular details at the interface of the tetramer revealed important information for being able to better predict the quaternary structures among the FBAs based on their primary sequences. These X-ray structures also provide interesting and new details on the reaction mechanism of class II FBAs. Not only were the substrates and products observed in geometries poised for catalysis, but unexpectedly the hydroxyl enolate intermediate of DHAP was also captured and resolved structurally. These concise new details provide a better understanding of the reaction mechanisms for FBAs in general and provide a structural basis for inhibitor design efforts aimed at this class of enzymes. PMID:19167403
Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

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

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.

The class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprises one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported,more » the structure of the active site loop responsible for catalyzing the protonation–deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA–PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation–protonation step of the MtFBA reaction mechanism. Furthermore, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.« less
Impact of human activity and natural processes on groundwater arsenic in an urbanized area (South China) using multivariate statistical techniques.

PubMed

Huang, Guanxing; Chen, Zongyu; Liu, Fan; Sun, Jichao; Wang, Jincui

2014-11-01

Anthropogenic factors resulted from the urbanization may affect the groundwater As in urbanized areas. Groundwater samples from the Guangzhou city (South China) were collected for As and other parameter analysis, in order to assess the impact of urbanization and natural processes on As distribution in aquifers. Nearly 25.5 % of groundwater samples were above the WHO drinking water standard for As, and the As concentrations in the granular aquifer (GA) were generally far higher than that in the fractured bedrock aquifer (FBA). Samples were classified into four clusters by using hierarchical cluster analysis. Cluster 1 is mainly located in the FBA and controlled by natural processes. Anthropogenic pollution resulted from the urbanization is responsible for high As concentrations identified in cluster 2. Clusters 3 and 4 are mainly located in the GA and controlled by both natural processes and anthropogenic factors. Three main mechanisms control the source and mobilization of groundwater As in the study area. Firstly, the interaction of water and calcareous rocks appears to be responsible for As release in the FBA. Secondly, reduction of Fe/Mn oxyhydroxides and decomposition of organic matter are probably responsible for high As concentrations in the GA. Thirdly, during the process of urbanization, the infiltration of wastewater/leachate with a high As content is likely to be the main source for groundwater As, while NO3 (-) contamination diminishes groundwater As.
Turbidimetric and photometric determination of total tannins in tea using a micro-flow-batch analyzer.

PubMed

Lima, Marcelo B; Andrade, Stéfani I E; Harding, David P; Pistonesi, Marcelo F; Band, Beatriz S F; Araújo, Mário C U

2012-01-15

Both turbidimetric and photometric determinations of total tannins in samples of green and black tea, using a micro-flow-batch analyzer (μFBA) were studied. The miniaturized system was formed using photocurable urethane-acrylate resin and ultraviolet lithography technique. The turbidimetric method was based on the precipitation reaction of Cu (II) with tannins in acetate medium at a pH of 4.5. The photometric method was based on the complexation reaction of tannins with ferrous tartrate. The turbidimetric μFBA was able to test 200 samples per hour. The photometric μFBA allowed 300 analyses per hour, generating 136μL of residue per analysis. The paired t test, at a 95% confidence level, showed no statistically significant differences between results obtained by both methods and the reference method. The urethane-acrylate μFBA maintained satisfactory physical and chemical properties, and represents an improvement over conventional flow-batch analyzer. Copyright © 2011 Elsevier B.V. All rights reserved.
Foreign body aspiration in children: A study of children who lived or died following aspiration.

PubMed

Mohammad, Maha; Saleem, Mohammad; Mahseeri, Mohamad; Alabdallat, Imad; Alomari, Ali; Za'atreh, Ala'; Qudaisat, Ibraheem; Shudifat, Abdulrahman; Nasri Alzoubi, Mohammad

2017-07-01

Foreign body aspiration (FBA) is a preventable cause of mortality and morbidity in children. We conducted a chart review of children who presented to a university hospital due to FBA in the period 1999-2014. Children were either managed with bronchoscopy for removal of the foreign body or died due to FBA. A total of 103 children were seen due to FBA including 27 deaths. The majority of children were boys and were less than 3 years old. Most aspirated foreign bodies were food-related, mainly peanuts. The majority of children presented with acute choking incidents, a smaller number presented with recurrent chest infections, and few children's choking incidents were unwitnessed. X-ray had a high rate of false negatives and bronchoscopy was the gold standard technique for assessment and management. Aspiration of foreign bodies is a preventable, life-threatening condition that calls for increased parent education and awareness. Copyright © 2017 Elsevier B.V. All rights reserved.
Neural adaptation to thin and fat bodies in the fusiform body area and middle occipital gyrus: an fMRI adaptation study.

PubMed

Hummel, Dennis; Rudolf, Anne K; Brandi, Marie-Luise; Untch, Karl-Heinz; Grabhorn, Ralph; Hampel, Harald; Mohr, Harald M

2013-12-01

Visual perception can be strongly biased due to exposure to specific stimuli in the environment, often causing neural adaptation and visual aftereffects. In this study, we investigated whether adaptation to certain body shapes biases the perception of the own body shape. Furthermore, we aimed to evoke neural adaptation to certain body shapes. Participants completed a behavioral experiment (n = 14) to rate manipulated pictures of their own bodies after adaptation to demonstratively thin or fat pictures of their own bodies. The same stimuli were used in a second experiment (n = 16) using functional magnetic resonance imaging (fMRI) adaptation. In the behavioral experiment, after adapting to a thin picture of the own body participants also judged a thinner than actual body picture to be the most realistic and vice versa, resembling a typical aftereffect. The fusiform body area (FBA) and the right middle occipital gyrus (rMOG) show neural adaptation to specific body shapes while the extrastriate body area (EBA) bilaterally does not. The rMOG cluster is highly selective for bodies and perhaps body parts. The findings of the behavioral experiment support the existence of a perceptual body shape aftereffect, resulting from a specific adaptation to thin and fat pictures of one's own body. The fMRI results imply that body shape adaptation occurs in the FBA and the rMOG. The role of the EBA in body shape processing remains unclear. The results are also discussed in the light of clinical body image disturbances. Copyright © 2012 Wiley Periodicals, Inc.
Constraint-based stoichiometric modelling from single organisms to microbial communities

PubMed Central

Olivier, Brett G.; Bruggeman, Frank J.; Teusink, Bas

2016-01-01

Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge. In view of the complexity, computational models of microbial communities are essential to obtain systems-level understanding of ecosystem functioning. This review discusses the applications and limitations of constraint-based stoichiometric modelling tools, and in particular flux balance analysis (FBA). We explain this approach from first principles and identify the challenges one faces when extending it to communities, and discuss the approaches used in the field in view of these challenges. We distinguish between steady-state and dynamic FBA approaches extended to communities. We conclude that much progress has been made, but many of the challenges are still open. PMID:28334697
Removing lead in drinking water with activated carbon

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

Taylor, R.M.; Kuennen, R.W.

A point-of-use (POU) granular activated carbon (GAC) fixed bed adsorber (FBA) was evaluated for reduction of soluble and insoluble lead from drinking water. Some of the factors which affect lead removal by GAC were evaluated, such as carbon type, solution pH, and a limited amount of work on competitive interactions. The design criteria for lead reduction by a POU device are also addressed. Minicolumns were used to evaluate the capacity of carbon for lead under a variety of conditions. The importance of surface chemistry of the carbon and the relationship with the pH of the water for lead reduction wasmore » demonstrated. Results indicate that a properly designed POU-GAC-FBA can reduce lead in drinking water to below the EPA action level of 15 ppb while being tested under a variety of conditions as specified under the National Sanitation Foundation (NSF) International Standard 53 test protocol. 37 refs., 9 figs., 1 tab.« less
Improving Preservice Teachers' Knowledge and Application of Functional Behavioral Assessments Using Multimedia

ERIC Educational Resources Information Center

Hirsch, Shanna Eisner; Kennedy, Michael J.; Haines, Shana J.; Thomas, Cathy Newman; Alves, Kat D.

2015-01-01

Functional behavioral assessment (FBA) is an empirically supported intervention associated with decreasing problem behavior and increasing appropriate behavior. To date, few studies have examined multimedia approaches to FBA training. This paper provides the outcomes of a randomized controlled trial across three university sites and evaluates…
A triple-bridged azido-Cu(II) chain compound fine-tuned by mixed carboxylate/ethanol linkers displays slow-relaxation and ferromagnetic order: synthesis, crystal structure, magnetic properties and DFT calculations.

PubMed

Liu, Xiangyu; Chen, Sanping; Grancha, Thais; Pardo, Emilio; Ke, Hongshan; Yin, Bing; Wei, Qing; Xie, Gang; Gao, Shengli

2014-11-07

A new azido-Cu(II) compound, [Cu(4-fba)(N3)(C2H5OH)] (4-fba = 4-fluorobenzoic acid) (1), has been synthesized and characterized. The X-ray crystal structure analysis demonstrates that only one crystallographically independent Cu(II) ion in the asymmetric unit of 1 exhibits a stretched octahedral geometry in which two azido N atoms and two carboxylic O atoms locate in the equatorial square, while two ethanol O atoms occupy the apical positions, forming a 1D Cu(II) chain with an alternating triple-bridge of EO-azido, syn,syn-carboxylate, and μ2-ethanol. The title compound consists of ferromagnetically interacting ferromagnetic chains, which exhibit ferromagnetic order (T(c) = 7.0 K). The strong ferromagnetic coupling between adjacent Cu(II) ions within each chain is due to the countercomplementarity of the super-exchange pathways, whereas the ferromagnetic interchain interactions--responsible for the long-range magnetic ordering--are most likely due to the presence of coordinated ethanol molecules establishing hydrogen bonds with neighboring chains. DFT calculations have been performed on compound 1 to offer a qualitative theoretical explanation of the magnetic behavior.
A Survey of Functional Behavior Assessment Methods Used by Behavior Analysts in Practice

ERIC Educational Resources Information Center

Oliver, Anthony C.; Pratt, Leigh A.; Normand, Matthew P.

2015-01-01

To gather information about the functional behavior assessment (FBA) methods behavior analysts use in practice, we sent a web-based survey to 12,431 behavior analysts certified by the Behavior Analyst Certification Board. Ultimately, 724 surveys were returned, with the results suggesting that most respondents regularly use FBA methods, especially…
Functional Behavioral Assessment State Policies and Procedures. Quick Turn Around (QTA).

ERIC Educational Resources Information Center

National Association of State Directors of Special Education, Alexandria, VA.

This brief report provides an analysis of survey data collected from 45 states and territories about policies, procedures, and guidelines related to Functional Behavioral Assessment (FBA), plans to develop or revise policy in this area, and technical assistance needs related to FBA, especially for students who exhibit behavior that interferes with…
Examining the Efficacy of a Basic Functional Behavioral Assessment Training Package for School Personnel

ERIC Educational Resources Information Center

Loman, Sheldon L.; Horner, Robert H.

2014-01-01

This study evaluated the effects of manualized training in "Basic" functional behavioral assessment (FBA) for typical school professionals on the ability of these professionals to complete technically adequate FBAs. Twelve school professionals participated in four 1-hr training sessions using the Basic FBA training handbook. After…

Early Childhood Practitioner Involvement in Functional Behavioral Assessment and Function-Based Interventions: A Literature Review

ERIC Educational Resources Information Center

Wood, Brenna K.; Drogan, Robin R.; Janney, Donna M.

2014-01-01

Reviewers analyzed studies published from 1990 to 2012 to determine early childhood practitioner involvement in functional behavioral assessment (FBA) and function-based behavioral intervention plans (BIP) for children with challenging behavior, age 6 and younger. Coding of 30 studies included practitioner involvement in FBA and BIP processes,…
Improving Outcomes of Behavioral Intervention Plans

ERIC Educational Resources Information Center

Walker, Jennifer D.; Barry, Colleen

2017-01-01

According to federal mandates, if a student's behavior impedes their learning or the learning of others, the individualized education program team is required to address this with a functional behavioral assessment (FBA). The intent of the FBA is to determine the function, or reason, of the impeding behavior for the development of a behavioral…
FBA and BIP: Increasing the Behavior Adjustment of African American Boys in Schools

ERIC Educational Resources Information Center

Lo, Ya-yu; Cartledge, Gwendolyn

2006-01-01

Overrepresentation of African American boys in disciplinary and special education referrals has been a national concern. This study used functional behavioral assessments (FBAs) and behavioral intervention plans (BIPs) as a means to prevent disproportionality of African American boys. Based on FBA results, interventions were developed for four…
Electron-ion collision rates in noble gas clusters irradiated by femtosecond laser pulse

NASA Astrophysics Data System (ADS)

Dey, R.; Roy, A. C.

2012-05-01

We report a theoretical analysis of electron-ion collision rates in xenon gas clusters irradiated by femtosecond laser pulses. The present analysis is based on the eikonal approximation (EA), the first Born approximation (FBA) and the classical (CL) methods. The calculations are performed using the plasma-screened Rogers potential introduced by Moll et al. [J. Phys. B. 43, 135103 (2010)] as well as the Debye potential for a wide range of experimental parameters. We find that the magnitudes of electron-ion collision frequency obtained in the EA do not fall as rapidly with the kinetic energy of electrons as in the FBA and CL methods for higher charge states of xenon ion (Xe8+ and Xe14+). Furthermore, EA shows that the effect of the inner structure of ion is most dominant for the lowest charge state of xenon ion (Xe1+). In the case of the present effective potential, FBA overestimates the CL results for all three different charge states of xenon, whereas for the Debye potential, both the FBA and CL methods predict collision frequencies which are nearly close to each other.
Self-Adjuvanting Glycopeptide Conjugate Vaccine against Disseminated Candidiasis

PubMed Central

Xin, Hong; Cartmell, Jonathan; Bailey, Justin J.; Dziadek, Sebastian; Bundle, David R.; Cutler, Jim E.

2012-01-01

Our research on pathogenesis of disseminated candidiasis led to the discovery that antibodies specific for Candida albicans cell surface β-1, 2–mannotriose [β-(Man)3] protect mice. A 14 mer peptide Fba, which derived from the N-terminal portion of the C. albicans cytosolic/cell surface protein fructose-bisphosphate aldolase, was used as the glycan carrier and resulted in a novel synthetic glycopeptide vaccine β-(Man)3-Fba. By a dendritic cell-based immunization approach, this conjugate induced protective antibody responses against both the glycan and peptide parts of the vaccine. In this report, we modified the β-(Man)3-Fba conjugate by coupling it to tetanus toxoid (TT) in order to improve immunogenicity and allow for use of an adjuvant suitable for human use. By new immunization procedures entirely compatible with human use, the modified β-(Man)3-Fba-TT was administered either alone or as a mixture made with alum or monophosphoryl lipid A (MPL) adjuvants and given to mice by a subcutaneous (s.c.) route. Mice vaccinated with or, surprisingly, without adjuvant responded well by making robust antibody responses. The immunized groups showed a high degree of protection against a lethal challenge with C. albicans as evidenced by increased survival times and reduced kidney fungal burden as compared to control groups that received only adjuvant or DPBS buffer prior to challenge. To confirm that induced antibodies were protective, sera from mice immunized against the β-(Man)3-Fba-TT conjugate transferred protection against disseminated candidiasis to naïve mice, whereas C. albicans-absorbed immune sera did not. Similar antibody responses and protection induced by the β-(Man)3-Fba-TT vaccine was observed in inbred BALB/c and outbred Swiss Webster mice. We conclude that addition of TT to the glycopeptide conjugate results in a self-adjuvanting vaccine that promotes robust antibody responses without the need for additional adjuvant, which is novel and represents a major step forward in vaccine design against disseminated candidiasis. PMID:22563378
Using Multimodal Functional Behavioral Assessment to Inform Treatment Selection for Children with Either Emotional Disturbance or Social Maladjustment

ERIC Educational Resources Information Center

Miller, Jeffrey A.; Williams, Shelagh J.; McCoy, Erika L. B.

2004-01-01

Functional behavioral assessment (FBA) is an assessment procedure used to identify the reasons for children's misbehavior. In this article we provide an overview of one approach to FBA known as "multimodal functional behavioral assessment" (MFBA) that provides a comprehensive examination of the causes of children's disruptive behavior. The…
Professional Development and Learning by General Teachers Implementing Functional Behavioural Assessment in Thai Inclusive Classrooms

ERIC Educational Resources Information Center

Opartkiattikul, Watinee; Arthur-Kelly, Michael; Dempsey, Ian

2016-01-01

Functional Behavioural Assessment (FBA) is identified as a research-based approach used in many Western schools to support student behaviour. This study aimed to assist Thai classroom teachers by providing a professional development and learning programme in FBA to develop an effective and efficient process to address behaviour problems and allow…
Investigation on the Practice of the Functional Behavioral Assessment: Survey of Educators and Their Experiences in the Field

ERIC Educational Resources Information Center

Moreno, Gerardo; Wong-Lo, Mickie; Bullock, Lyndal M.

2017-01-01

The functional behavioral assessment (FBA) has been a hallmark practice amongst educators working with students demonstrating challenging behaviors. Although the process has been mandated in special education since the Individuals with Disabilities Education Act of 1997, the FBA varies in form and implementation across the United States of America…
From FBA to Implementation: A Look at What Is Actually Being Delivered

ERIC Educational Resources Information Center

Blood, Erika; Neel, Richard S.

2007-01-01

This study looks at the utilization of assessments on developing behavior intervention plans (BIPs) and their use in designing actual implementation for the children (elementary through high school) labeled EBD in a mid-sized district in eastern Washington. Files were reviewed to determine the types of assessments used, FBA components addressed,…
Special Considerations for Using Functional Behavior Assessment and Functionally-Indicated Interventions with Students in Alternative Educational Settings

ERIC Educational Resources Information Center

Ennis, Robin Parks; Jolivette, Kristine; Swoszowski, Nicole Cain

2017-01-01

Functional behavior assessment (FBA) is the process of collecting data to determine the function of an individual's behavior to develop a functionally-indicated behavioral intervention (BIP). Special adaptations may be needed to conduct FBA and implement BIPs in alternative educational settings. In this article, we highlight suggestions for…
FBAs and BIPs: Avoiding and Addressing Four Common Challenges Related to Fidelity

ERIC Educational Resources Information Center

Hirsch, Shanna E.; Bruhn, Allison L.; Lloyd, John Wills; Katsiyannis, Antonis

2017-01-01

There is substantial empirical evidence that the Functional Behavioral Assessment (FBA) process is an effective means to reduce student problem behavior and increase desirable behaviors (e.g., What Works Clearinghouse, 2016). The use of an FBA as the basis for a behavior intervention plan (BIP) has been a requirement for certain disciplinary…
Training School Personnel to Identify Interventions Based on Functional Behavioral Assessment

ERIC Educational Resources Information Center

Borgmeier, Chris; Loman, Sheldon L.; Hara, Motoaki; Rodriguez, Billie Jo

2015-01-01

Over 15 years after passage of legislation requiring the use of functional behavioral assessment (FBA) to inform the development of positive behavior support plans (BSPs) in special education, schools are still struggling to implement BSPs based on FBA and the function of behavior. A primary concern is that school teams regularly fail to use…
Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria

PubMed Central

Rogers, Matthew B; Patron, Nicola J; Keeling, Patrick J

2007-01-01

Background Horizontal or lateral transfer of genetic material between distantly related prokaryotes has been shown to play a major role in the evolution of bacterial and archaeal genomes, but exchange of genes between prokaryotes and eukaryotes is not as well understood. In particular, gene flow from eukaryotes to prokaryotes is rarely documented with strong support, which is unusual since prokaryotic genomes appear to readily accept foreign genes. Results Here, we show that abundant marine cyanobacteria in the related genera Synechococcus and Prochlorococcus acquired a key Calvin cycle/glycolytic enzyme from a eukaryote. Two non-homologous forms of fructose bisphosphate aldolase (FBA) are characteristic of eukaryotes and prokaryotes respectively. However, a eukaryotic gene has been inserted immediately upstream of the ancestral prokaryotic gene in several strains (ecotypes) of Synechococcus and Prochlorococcus. In one lineage this new gene has replaced the ancestral gene altogether. The eukaryotic gene is most closely related to the plastid-targeted FBA from red algae. This eukaryotic-type FBA once replaced the plastid/cyanobacterial type in photosynthetic eukaryotes, hinting at a possible functional advantage in Calvin cycle reactions. The strains that now possess this eukaryotic FBA are scattered across the tree of Synechococcus and Prochlorococcus, perhaps because the gene has been transferred multiple times among cyanobacteria, or more likely because it has been selectively retained only in certain lineages. Conclusion A gene for plastid-targeted FBA has been transferred from red algae to cyanobacteria, where it has inserted itself beside its non-homologous, functional analogue. Its current distribution in Prochlorococcus and Synechococcus is punctate, suggesting a complex history since its introduction to this group. PMID:17584924
Functional Behavior Assessment and Function-Based Intervention Planning: Considering the Simple Logic of the Process

ERIC Educational Resources Information Center

Scott, Terrance M.; Cooper, Justin T.

2017-01-01

While functional behavior assessment (FBA) has been a part of special education law and embedded in Individuals With Disabilities Education Act (IDEA) since 1997, a precise definition of what actions or processes constitute a legal FBA has never been adequately addressed in the law. This article provides an overview of the underlying logic of FBA…
Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli.

PubMed

Chen, Xuewen; Alonso, Ana P; Allen, Doug K; Reed, Jennifer L; Shachar-Hill, Yair

2011-01-01

Genome-based Flux Balance Analysis (FBA) and steady-state isotopic-labeling-based Metabolic Flux Analysis (MFA) are complimentary approaches to predicting and measuring the operation and regulation of metabolic networks. Here, genome-derived models of Escherichia coli (E. coli) metabolism were used for FBA and ¹³C-MFA analyses of aerobic and anaerobic growths of wild-type E. coli (K-12 MG1655) cells. Validated MFA flux maps reveal that the fraction of maintenance ATP consumption in total ATP production is about 14% higher under anaerobic (51.1%) than aerobic conditions (37.2%). FBA revealed that an increased ATP utilization is consumed by ATP synthase to secrete protons from fermentation. The TCA cycle is shown to be incomplete in aerobically growing cells and submaximal growth is due to limited oxidative phosphorylation. An FBA was successful in predicting product secretion rates in aerobic culture if both glucose and oxygen uptake measurement were constrained, but the most-frequently predicted values of internal fluxes yielded from sampling the feasible space differ substantially from MFA-derived fluxes. © 2010 Elsevier Inc. All rights reserved.
A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves.

PubMed

Cheung, C Y Maurice; Poolman, Mark G; Fell, David A; Ratcliffe, R George; Sweetlove, Lee J

2014-06-01

Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux-balance analysis (FBA) have so far been confined to consideration of the network under continuous light. An FBA framework is presented that solves the two phases of the diel cycle as a single optimization problem and, thus, provides a more representative model of leaf metabolism. The requirement to support continued export of sugar and amino acids from the leaf during the night and to meet overnight cellular maintenance costs forces the model to set aside stores of both carbon and nitrogen during the day. With only minimal constraints, the model successfully captures many of the known features of C 3 leaf metabolism, including the recently discovered role of citrate synthesis and accumulation in the night as a precursor for the provision of carbon skeletons for amino acid synthesis during the day. The diel FBA model can be applied to other temporal separations, such as that which occurs in Crassulacean acid metabolism (CAM) photosynthesis, allowing a system-level analysis of the energetics of CAM. The diel model predicts that there is no overall energetic advantage to CAM, despite the potential for suppression of photorespiration through CO 2 concentration. Moreover, any savings in enzyme machinery costs through suppression of photorespiration are likely to be offset by the higher flux demand of the CAM cycle. It is concluded that energetic or nitrogen use considerations are unlikely to be evolutionary drivers for CAM photosynthesis. © 2014 American Society of Plant Biologists. All Rights Reserved.
A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves1[C][W][OPEN

PubMed Central

Cheung, C.Y. Maurice; Poolman, Mark G.; Fell, David. A.; Ratcliffe, R. George; Sweetlove, Lee J.

2014-01-01

Although leaves have to accommodate markedly different metabolic flux patterns in the light and the dark, models of leaf metabolism based on flux-balance analysis (FBA) have so far been confined to consideration of the network under continuous light. An FBA framework is presented that solves the two phases of the diel cycle as a single optimization problem and, thus, provides a more representative model of leaf metabolism. The requirement to support continued export of sugar and amino acids from the leaf during the night and to meet overnight cellular maintenance costs forces the model to set aside stores of both carbon and nitrogen during the day. With only minimal constraints, the model successfully captures many of the known features of C3 leaf metabolism, including the recently discovered role of citrate synthesis and accumulation in the night as a precursor for the provision of carbon skeletons for amino acid synthesis during the day. The diel FBA model can be applied to other temporal separations, such as that which occurs in Crassulacean acid metabolism (CAM) photosynthesis, allowing a system-level analysis of the energetics of CAM. The diel model predicts that there is no overall energetic advantage to CAM, despite the potential for suppression of photorespiration through CO2 concentration. Moreover, any savings in enzyme machinery costs through suppression of photorespiration are likely to be offset by the higher flux demand of the CAM cycle. It is concluded that energetic or nitrogen use considerations are unlikely to be evolutionary drivers for CAM photosynthesis. PMID:24596328
Vaccine and Monoclonal Antibody That Enhance Mouse Resistance to Candidiasis ▿

PubMed Central

Xin, Hong; Cutler, Jim E.

2011-01-01

Previously we showed that antibodies specific for the glycan β-1,2-mannotriose [β-(Man)3] on the cell surface of Candida albicans protect mice against disseminated candidiasis (H. Xin, S. Dziadek, D. R. Bundle, and J. E. Cutler, Proc. Natl. Acad. Sci. U. S. A. 105:13526–13531, 2008). Furthermore, six 14-mer peptides that are within the N-terminal portion of C. albicans wall proteins were conjugated to the glycan in an attempt to create immunogenic glycopeptide conjugates. By a dendritic cell (DC)-based immunization approach, all were immunogenic and three of the six conjugates induced a high degree of protection in mice. Interestingly, whereas all six peptides induced antibody responses when used alone to pulse DCs for subsequent immunizations, three peptides induced protection, and one in particular, peptide Fba (derived from fructose-bisphosphate aldolase), induced robust protective responses and is the focus of the current work. Fba peptide is not restricted by the major histocompatibility complex class II (MHC-II), as it induced anti-Fba antibodies in mice of different H-2 haplotypes and in rabbits. Furthermore, the peptide induced protection against disease caused by different C. albicans strains. Partial protection was achieved when alum was used in place of DCs for Fba immunizations. The passive transfer of immune sera from Fba-vaccinated mice, but not immune serum preabsorbed with fungal cells, conferred protection in naïve mice. This result, along with our finding that a monoclonal antibody specific for the peptide, E2-9 (IgM), protected mice against candidiasis, provide strong evidence that antibodies contribute to protection. Our work demonstrates the utility of cell wall peptides alone or as glycopeptides in vaccines designed for the induction of immunity against candidiasis and monoclonal antibodies as a rapid immunoprotective approach against the disease. PMID:21832099
Diagnostic value of immunoglobulin G antibodies against Candida enolase and fructose-bisphosphate aldolase for candidemia

PubMed Central

2013-01-01

Background The yeast Candida is one of the most frequent pathogens isolated from bloodstream infections and is associated with significant morbidity and mortality. Problems with clinical and microbiological diagnosis of invasive candidiasis (IC) have prompted the development of non-culture-based laboratory methods. Previous reports suggest that serological detection of antibodies might be useful for diagnosing systemic candidiasis. Methods Diagnosis of IC using antibodies against recombinant Candida albicans enolase (Eno) and fructose-bisphosphate aldolase (Fba1) was evaluated. Using recombinant Eno and Fba1 as coating antigens, enzyme-linked immunosorbent assays (ELISAs) were used to analyze sera from patients with candidemia (n = 101), Candida colonization (n = 50), bacteremia (n = 84), invasive aspergillosis (n = 40); and from healthy controls (n = 200). Results The results demonstrated that ELISA detection of anti-Eno and anti-Fba1 IgG distinguished IC from other pathogenic infections in patients and healthy individuals. The sensitivity, specificity, and positive and negative predictive values were 72.3%, 94.7%, 78.5% and 93% for anti-Eno, and 87.1%, 92.8%, 76.5% and 96.4% for anti-Fba1 antibodies, respectively. Combining these two tests improved sensitivity up to 90.1% and negative predictive value up to 97.1%, with specificity and positive predictive values of 90.6% and 72.2%. The tests were specific to the Candida genus and antibody titers were higher for candidemia patients than for controls. Positive antibody tests were obtained before blood culture results for 42.2% of patients for anti-Eno and 51.1% for anti-Fba1. Conclusion These data suggest that tests that detect IgG antibodies against Candida enolase and fructose-bisphosphate aldolase, especially when used in combination, could be a powerful tool for diagnosing IC. PMID:23725337
Diagnostic value of immunoglobulin G antibodies against Candida enolase and fructose-bisphosphate aldolase for candidemia.

PubMed

Li, Fang-Qiu; Ma, Chun-Fang; Shi, Li-Ning; Lu, Jing-Fen; Wang, Ying; Huang, Mei; Kong, Qian-Qian

2013-05-31

The yeast Candida is one of the most frequent pathogens isolated from bloodstream infections and is associated with significant morbidity and mortality. Problems with clinical and microbiological diagnosis of invasive candidiasis (IC) have prompted the development of non-culture-based laboratory methods. Previous reports suggest that serological detection of antibodies might be useful for diagnosing systemic candidiasis. Diagnosis of IC using antibodies against recombinant Candida albicans enolase (Eno) and fructose-bisphosphate aldolase (Fba1) was evaluated. Using recombinant Eno and Fba1 as coating antigens, enzyme-linked immunosorbent assays (ELISAs) were used to analyze sera from patients with candidemia (n = 101), Candida colonization (n = 50), bacteremia (n = 84), invasive aspergillosis (n = 40); and from healthy controls (n = 200). The results demonstrated that ELISA detection of anti-Eno and anti-Fba1 IgG distinguished IC from other pathogenic infections in patients and healthy individuals. The sensitivity, specificity, and positive and negative predictive values were 72.3%, 94.7%, 78.5% and 93% for anti-Eno, and 87.1%, 92.8%, 76.5% and 96.4% for anti-Fba1 antibodies, respectively. Combining these two tests improved sensitivity up to 90.1% and negative predictive value up to 97.1%, with specificity and positive predictive values of 90.6% and 72.2%. The tests were specific to the Candida genus and antibody titers were higher for candidemia patients than for controls. Positive antibody tests were obtained before blood culture results for 42.2% of patients for anti-Eno and 51.1% for anti-Fba1. These data suggest that tests that detect IgG antibodies against Candida enolase and fructose-bisphosphate aldolase, especially when used in combination, could be a powerful tool for diagnosing IC.

DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

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

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less
DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

DOE PAGES

Heirendt, Laurent; Thiele, Ines; Fleming, Ronan M. T.

2017-01-16

Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on amore » subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.« less
Tracheobronchial foreign body aspiration in children.

PubMed

Burton, E M; Brick, W G; Hall, J D; Riggs, W; Houston, C S

1996-02-01

In this retrospective study, we reviewed the demographic and radiographic findings of 155 children with bronchoscopy-proven tracheobronchial foreign body aspiration (FBA). Two thirds of the patients were male, and most were children between 1 and 2 years of age. An aspirated peanut accounted for one third of all cases. Foreign body location was distributed nearly evenly to the right and left primary bronchi; tracheal foreign body was noted in 16 patients. The most frequent symptoms of FBA were cough (85 patients) and wheezing (60 patients). Although most patients were seen within 1 day of aspiration, 30 patients had symptoms that lasted at least 1 week before diagnosis. The most common radiographic findings were unilateral or segmental hyperlucency (59) or atelectasis (38). The trachea was the site of the foreign body in one half of children with a normal chest radiograph and FBA.
Functional Behavioral Assessment-Based Interventions for Students with or at Risk for Emotional and/or Behavioral Disorders in School: A Hierarchical Linear Modeling Meta-Analysis

ERIC Educational Resources Information Center

Gage, Nicholas A.; Lewis, Timothy J.; Stichter, Janine P.

2012-01-01

Of the myriad practices currently utilized for students with disabilities, particularly students with or at risk for emotional and/or behavioral disorder (EBD), functional behavior assessment (FBA) is a practice with an emerging solid research base. However, the FBA research base relies on single-subject design (SSD) and synthesis has relied on…
Transport characteristics of three fluorescent conjugated bile acid analogs in isolated rat hepatocytes and couplets.

PubMed

Maglova, L M; Jackson, A M; Meng, X J; Carruth, M W; Schteingart, C D; Ton-Nu, H T; Hofmann, A F; Weinman, S A

1995-08-01

The transport properties of three different synthetically prepared fluorescent conjugated bile acid analogs (FBA), all with the fluorophore on the side chain, were determined using isolated rat hepatocytes and hepatocyte couplets. The compounds studied were cholylglycylamidofluorescein (CGamF), cholyl(N epsilon-nitrobenzoxadiazolyl [NBD])-lysine (C-NBD-L), and chenodeoxycholyl-(N epsilon-NBD)-lysine (CDC-NBD-L). When hepatocytes were incubated at 37 degrees C with 0.3 mumol/L of FBA and 0.15 mol/L of Na+, cell fluorescence increased linearly with time at a rate (U/min) of 7.8 +/- 0.5 for CGamF, 7.2 +/- 0.3 for C-NBD-L, and 13.7 +/- 1.0 for CDC-NBD-L (mean, +/- SE; n = 40 to 90). Uptake was concentration dependent for concentrations less than 20 mumol/L and was saturable. The Michaelis constant (Km) value (mumol/L) for CGamF was 10.8, for C-NBD-L was 3.8, and for CDC-NBD-L was 3.0. In the absence of Na+, the uptake rate was decreased by 50% for CGamF and by 38% for C-NBD-L; but uptake of CDC-NBD-L was unchanged and thus Na+ independent. Cellular uptake of all three derivatives was specific to hepatocytes and was absent in several nonhepatocyte cell lines. For CGamF and C-NBD-L, both Na(+)-dependent and Na(+)-independent uptake was inhibited by 200-fold excess concentrations of cholyltaurine, dehydrocholyltaurine, and cholate, but for CDC-NBD-L, these nonfluorescent bile acids did not inhibit initial uptake. The intracellular fluorescence of CGamF was strongly pH dependent at an excitation wavelength of 495 nm, but pH independent at 440 nm excitation. In contrast, intracellular fluorescence of C-NBD-L and CDC-NBD-L was pH independent. All three FBA were secreted into the canalicular space of approximately 50% to 60% of couplets. Cellular adenosine triphosphate (ATP) depletion with either CN- or atractyloside inhibited secretion of all three FBA. The multispecific organic anion transporter (MOAT) inhibitor, chlorodinitrobenzene, blocked secretion of fluorescent MOAT substrates at a concentration of 1 mumol/L. At this concentration it did not affect secretion of the three FBA. At higher concentrations, chlorodinitrobenzene partially inhibited the canalicular secretion of CGamF but not the other two FBA. In conclusion, all three FBA are secreted by canalicular membrane bile acid transporters, but the sinusoidal uptake characteristics of CGamF and C-NBD-L are more similar than those of CDC-NBD-L to the transport properties of cholyltaurine. Therefore, C-NBD-L appears to be the best of the three for studies of conjugated trihydroxy-bile acid transport in hepatocytes.
Prediction of Metabolic Flux Distribution from Gene Expression Data Based on the Flux Minimization Principle

DTIC Science & Technology

2014-11-14

problem. Modification of the PLOS ONE | www.plosone.org 1 November 2014 | Volume 9 | Issue 11 | e112524 Report Documentation Page Form ApprovedOMB No. 0704... Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 FBA algorithm to incorporate additional biological information from gene expression profiles is...We set the maximization of biomass production as the objective of FBA and implemented it in two different forms : without flux minimization (or
Human attention filters for single colors.

PubMed

Sun, Peng; Chubb, Charles; Wright, Charles E; Sperling, George

2016-10-25

The visual images in the eyes contain much more information than the brain can process. An important selection mechanism is feature-based attention (FBA). FBA is best described by attention filters that specify precisely the extent to which items containing attended features are selectively processed and the extent to which items that do not contain the attended features are attenuated. The centroid-judgment paradigm enables quick, precise measurements of such human perceptual attention filters, analogous to transmission measurements of photographic color filters. Subjects use a mouse to locate the centroid-the center of gravity-of a briefly displayed cloud of dots and receive precise feedback. A subset of dots is distinguished by some characteristic, such as a different color, and subjects judge the centroid of only the distinguished subset (e.g., dots of a particular color). The analysis efficiently determines the precise weight in the judged centroid of dots of every color in the display (i.e., the attention filter for the particular attended color in that context). We report 32 attention filters for single colors. Attention filters that discriminate one saturated hue from among seven other equiluminant distractor hues are extraordinarily selective, achieving attended/unattended weight ratios >20:1. Attention filters for selecting a color that differs in saturation or lightness from distractors are much less selective than attention filters for hue (given equal discriminability of the colors), and their filter selectivities are proportional to the discriminability distance of neighboring colors, whereas in the same range hue attention-filter selectivity is virtually independent of discriminabilty.
Genome-scale modelling of microbial metabolism with temporal and spatial resolution.

PubMed

Henson, Michael A

2015-12-01

Most natural microbial systems have evolved to function in environments with temporal and spatial variations. A major limitation to understanding such complex systems is the lack of mathematical modelling frameworks that connect the genomes of individual species and temporal and spatial variations in the environment to system behaviour. The goal of this review is to introduce the emerging field of spatiotemporal metabolic modelling based on genome-scale reconstructions of microbial metabolism. The extension of flux balance analysis (FBA) to account for both temporal and spatial variations in the environment is termed spatiotemporal FBA (SFBA). Following a brief overview of FBA and its established dynamic extension, the SFBA problem is introduced and recent progress is described. Three case studies are reviewed to illustrate the current state-of-the-art and possible future research directions are outlined. The author posits that SFBA is the next frontier for microbial metabolic modelling and a rapid increase in methods development and system applications is anticipated. © 2015 Authors; published by Portland Press Limited.
My Body Looks Like That Girl’s: Body Mass Index Modulates Brain Activity during Body Image Self-Reflection among Young Women

PubMed Central

Wen, Xin; She, Ying; Vinke, Petra Corianne; Chen, Hong

2016-01-01

Body image distress or body dissatisfaction is one of the most common consequences of obesity and overweight. We investigated the neural bases of body image processing in overweight and average weight young women to understand whether brain regions that were previously found to be involved in processing self-reflective, perspective and affective components of body image would show different activation between two groups. Thirteen overweight (O-W group, age = 20.31±1.70 years) and thirteen average weight (A-W group, age = 20.15±1.62 years) young women underwent functional magnetic resonance imaging while performing a body image self-reflection task. Among both groups, whole-brain analysis revealed activations of a brain network related to perceptive and affective components of body image processing. ROI analysis showed a main effect of group in ACC as well as a group by condition interaction within bilateral EBA, bilateral FBA, right IPL, bilateral DLPFC, left amygdala and left MPFC. For the A-W group, simple effect analysis revealed stronger activations in Thin-Control compared to Fat-Control condition within regions related to perceptive (including bilateral EBA, bilateral FBA, right IPL) and affective components of body image processing (including bilateral DLPFC, left amygdala), as well as self-reference (left MPFC). The O-W group only showed stronger activations in Fat-Control than in Thin-Control condition within regions related to the perceptive component of body image processing (including left EBA and left FBA). Path analysis showed that in the Fat-Thin contrast, body dissatisfaction completely mediated the group difference in brain response in left amygdala across the whole sample. Our data are the first to demonstrate differences in brain response to body pictures between average weight and overweight young females involved in a body image self-reflection task. These results provide insights for understanding the vulnerability to body image distress among overweight or obese young females. PMID:27764116
My Body Looks Like That Girl's: Body Mass Index Modulates Brain Activity during Body Image Self-Reflection among Young Women.

PubMed

Gao, Xiao; Deng, Xiao; Wen, Xin; She, Ying; Vinke, Petra Corianne; Chen, Hong

2016-01-01

Body image distress or body dissatisfaction is one of the most common consequences of obesity and overweight. We investigated the neural bases of body image processing in overweight and average weight young women to understand whether brain regions that were previously found to be involved in processing self-reflective, perspective and affective components of body image would show different activation between two groups. Thirteen overweight (O-W group, age = 20.31±1.70 years) and thirteen average weight (A-W group, age = 20.15±1.62 years) young women underwent functional magnetic resonance imaging while performing a body image self-reflection task. Among both groups, whole-brain analysis revealed activations of a brain network related to perceptive and affective components of body image processing. ROI analysis showed a main effect of group in ACC as well as a group by condition interaction within bilateral EBA, bilateral FBA, right IPL, bilateral DLPFC, left amygdala and left MPFC. For the A-W group, simple effect analysis revealed stronger activations in Thin-Control compared to Fat-Control condition within regions related to perceptive (including bilateral EBA, bilateral FBA, right IPL) and affective components of body image processing (including bilateral DLPFC, left amygdala), as well as self-reference (left MPFC). The O-W group only showed stronger activations in Fat-Control than in Thin-Control condition within regions related to the perceptive component of body image processing (including left EBA and left FBA). Path analysis showed that in the Fat-Thin contrast, body dissatisfaction completely mediated the group difference in brain response in left amygdala across the whole sample. Our data are the first to demonstrate differences in brain response to body pictures between average weight and overweight young females involved in a body image self-reflection task. These results provide insights for understanding the vulnerability to body image distress among overweight or obese young females.
Analysis of optimality in natural and perturbed metabolic networks

PubMed Central

Segrè, Daniel; Vitkup, Dennis; Church, George M.

2002-01-01

An important goal of whole-cell computational modeling is to integrate detailed biochemical information with biological intuition to produce testable predictions. Based on the premise that prokaryotes such as Escherichia coli have maximized their growth performance along evolution, flux balance analysis (FBA) predicts metabolic flux distributions at steady state by using linear programming. Corroborating earlier results, we show that recent intracellular flux data for wild-type E. coli JM101 display excellent agreement with FBA predictions. Although the assumption of optimality for a wild-type bacterium is justifiable, the same argument may not be valid for genetically engineered knockouts or other bacterial strains that were not exposed to long-term evolutionary pressure. We address this point by introducing the method of minimization of metabolic adjustment (MOMA), whereby we test the hypothesis that knockout metabolic fluxes undergo a minimal redistribution with respect to the flux configuration of the wild type. MOMA employs quadratic programming to identify a point in flux space, which is closest to the wild-type point, compatibly with the gene deletion constraint. Comparing MOMA and FBA predictions to experimental flux data for E. coli pyruvate kinase mutant PB25, we find that MOMA displays a significantly higher correlation than FBA. Our method is further supported by experimental data for E. coli knockout growth rates. It can therefore be used for predicting the behavior of perturbed metabolic networks, whose growth performance is in general suboptimal. MOMA and its possible future extensions may be useful in understanding the evolutionary optimization of metabolism. PMID:12415116
Key glycolytic branch influences mesocarp oil content in oil palm.

PubMed

Ruzlan, Nurliyana; Low, Yoke Sum Jaime; Win, Wilonita; Azizah Musa, Noor; Ong, Ai-Ling; Chew, Fook-Tim; Appleton, David; Mohd Yusof, Hirzun; Kulaveerasingam, Harikrishna

2017-08-29

The fructose-1,6-bisphosphate aldolase catalyzed glycolysis branch that forms dihydroxyacetone phosphate and glyceraldehyde-3-phosphate was identified as a key driver of increased oil synthesis in oil palm and was validated in Saccharomyces cerevisiae. Reduction in triose phosphate isomerase (TPI) activity in a yeast knockdown mutant resulted in 19% increase in lipid content, while yeast strains overexpressing oil palm fructose-1,6-bisphosphate aldolase (EgFBA) and glycerol-3-phosphate dehydrogenase (EgG3PDH) showed increased lipid content by 16% and 21%, respectively. Genetic association analysis on oil palm SNPs of EgTPI SD_SNP_000035801 and EgGAPDH SD_SNP_000041011 showed that palms harboring homozygous GG in EgTPI and heterozygous AG in EgGAPDH exhibited higher mesocarp oil content based on dry weight. In addition, AG genotype of the SNP of EgG3PDH SD_SNP_000008411 was associated with higher mean mesocarp oil content, whereas GG genotype of the EgFBA SNP SD_SNP_000007765 was favourable. Additive effects were observed with a combination of favourable alleles in TPI and FBA in Nigerian x AVROS population (family F7) with highest allele frequency GG.GG being associated with a mean increase of 3.77% (p value = 2.3E -16 ) oil content over the Family 1. An analogous effect was observed in yeast, where overexpressed EgFBA in TPI - resulted in a 30% oil increment. These results provide insights into flux balances in glycolysis leading to higher yield in mesocarp oil-producing fruit.
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

PubMed Central

Hoppe, Andreas; Hoffmann, Sabrina; Holzhütter, Hermann-Georg

2007-01-01

Background In recent years, constrained optimization – usually referred to as flux balance analysis (FBA) – has become a widely applied method for the computation of stationary fluxes in large-scale metabolic networks. The striking advantage of FBA as compared to kinetic modeling is that it basically requires only knowledge of the stoichiometry of the network. On the other hand, results of FBA are to a large degree hypothetical because the method relies on plausible but hardly provable optimality principles that are thought to govern metabolic flux distributions. Results To augment the reliability of FBA-based flux calculations we propose an additional side constraint which assures thermodynamic realizability, i.e. that the flux directions are consistent with the corresponding changes of Gibb's free energies. The latter depend on metabolite levels for which plausible ranges can be inferred from experimental data. Computationally, our method results in the solution of a mixed integer linear optimization problem with quadratic scoring function. An optimal flux distribution together with a metabolite profile is determined which assures thermodynamic realizability with minimal deviations of metabolite levels from their expected values. We applied our novel approach to two exemplary metabolic networks of different complexity, the metabolic core network of erythrocytes (30 reactions) and the metabolic network iJR904 of Escherichia coli (931 reactions). Our calculations show that increasing network complexity entails increasing sensitivity of predicted flux distributions to variations of standard Gibb's free energy changes and metabolite concentration ranges. We demonstrate the usefulness of our method for assessing critical concentrations of external metabolites preventing attainment of a metabolic steady state. Conclusion Our method incorporates the thermodynamic link between flux directions and metabolite concentrations into a practical computational algorithm. The weakness of conventional FBA to rely on intuitive assumptions about the reversibility of biochemical reactions is overcome. This enables the computation of reliable flux distributions even under extreme conditions of the network (e.g. enzyme inhibition, depletion of substrates or accumulation of end products) where metabolite concentrations may be drastically altered. PMID:17543097
Evolution and functional diversification of fructose bisphosphate aldolase genes in photosynthetic marine diatoms.

PubMed

Allen, Andrew E; Moustafa, Ahmed; Montsant, Anton; Eckert, Angelika; Kroth, Peter G; Bowler, Chris

2012-01-01

Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively.
Evolution and Functional Diversification of Fructose Bisphosphate Aldolase Genes in Photosynthetic Marine Diatoms

PubMed Central

Allen, Andrew E.; Moustafa, Ahmed; Montsant, Anton; Eckert, Angelika; Kroth, Peter G.; Bowler, Chris

2012-01-01

Diatoms and other chlorophyll-c containing, or chromalveolate, algae are among the most productive and diverse phytoplankton in the ocean. Evolutionarily, chlorophyll-c algae are linked through common, although not necessarily monophyletic, acquisition of plastid endosymbionts of red as well as most likely green algal origin. There is also strong evidence for a relatively high level of lineage-specific bacterial gene acquisition within chromalveolates. Therefore, analyses of gene content and derivation in chromalveolate taxa have indicated particularly diverse origins of their overall gene repertoire. As a single group of functionally related enzymes spanning two distinct gene families, fructose 1,6-bisphosphate aldolases (FBAs) illustrate the influence on core biochemical pathways of specific evolutionary associations among diatoms and other chromalveolates with various plastid-bearing and bacterial endosymbionts. Protein localization and activity, gene expression, and phylogenetic analyses indicate that the pennate diatom Phaeodactylum tricornutum contains five FBA genes with very little overall functional overlap. Three P. tricornutum FBAs, one class I and two class II, are plastid localized, and each appears to have a distinct evolutionary origin as well as function. Class I plastid FBA appears to have been acquired by chromalveolates from a red algal endosymbiont, whereas one copy of class II plastid FBA is likely to have originated from an ancient green algal endosymbiont. The other copy appears to be the result of a chromalveolate-specific gene duplication. Plastid FBA I and chromalveolate-specific class II plastid FBA are localized in the pyrenoid region of the chloroplast where they are associated with β-carbonic anhydrase, which is known to play a significant role in regulation of the diatom carbon concentrating mechanism. The two pyrenoid-associated FBAs are distinguished by contrasting gene expression profiles under nutrient limiting compared with optimal CO2 fixation conditions, suggestive of a distinct specialized function for each. Cytosolically localized FBAs in P. tricornutum likely play a role in glycolysis and cytoskeleton function and seem to have originated from the stramenopile host cell and from diatom-specific bacterial gene transfer, respectively. PMID:21903677
A flow-batch analyzer with piston propulsion applied to automatic preparation of calibration solutions for Mn determination in mineral waters by ET AAS.

PubMed

Almeida, Luciano F; Vale, Maria G R; Dessuy, Morgana B; Silva, Márcia M; Lima, Renato S; Santos, Vagner B; Diniz, Paulo H D; Araújo, Mário C U

2007-10-31

The increasing development of miniaturized flow systems and the continuous monitoring of chemical processes require dramatically simplified and cheap flow schemes and instrumentation with large potential for miniaturization and consequent portability. For these purposes, the development of systems based on flow and batch technologies may be a good alternative. Flow-batch analyzers (FBA) have been successfully applied to implement analytical procedures, such as: titrations, sample pre-treatment, analyte addition and screening analysis. In spite of its favourable characteristics, the previously proposed FBA uses peristaltic pumps to propel the fluids and this kind of propulsion presents high cost and large dimension, making unfeasible its miniaturization and portability. To overcome these drawbacks, a low cost, robust, compact and non-propelled by peristaltic pump FBA is proposed. It makes use of a lab-made piston coupled to a mixing chamber and a step motor controlled by a microcomputer. The piston-propelled FBA (PFBA) was applied for automatic preparation of calibration solutions for manganese determination in mineral waters by electrothermal atomic-absorption spectrometry (ET AAS). Comparing the results obtained with two sets of calibration curves (five by manual and five by PFBA preparations), no significant statistical differences at a 95% confidence level were observed by applying the paired t-test. The standard deviation of manual and PFBA procedures were always smaller than 0.2 and 0.1mugL(-1), respectively. By using PFBA it was possible to prepare about 80 calibration solutions per hour.
Stress-Inducible Expression of an F-box Gene TaFBA1 from Wheat Enhanced the Drought Tolerance in Transgenic Tobacco Plants without Impacting Growth and Development.

PubMed

Kong, Xiangzhu; Zhou, Shumei; Yin, Suhong; Zhao, Zhongxian; Han, Yangyang; Wang, Wei

2016-01-01

E3 ligase plays an important role in the response to many environment stresses in plants. In our previous study, constitutive overexpression of an F-box protein gene TaFBA1 driven by 35S promoter improved the drought tolerance in transgenic tobacco plants, but the growth and development in transgenic plants was altered in normal conditions. In this study, we used stress-inducible promoter RD29A instead of 35S promoter, as a results, the stress-inducible transgenic tobacco plants exhibit a similar phenotype with wild type (WT) plants. However, the drought tolerance of the transgenic plants with stress-inducible expressed TaFBA1 was enhanced. The improved drought tolerance of transgenic plants was indicated by their higher seed germination rate and survival rate, greater biomass and photosynthesis than those of WT under water stress, which may be related to their greater water retention capability and osmotic adjustment. Moreover, the transgenic plants accumulated less reactive oxygen species, kept lower MDA content and membrane leakage under water stress, which may be related to their higher levels of antioxidant enzyme activity and upregulated gene expression of some antioxidant enzymes. These results suggest that stress induced expression of TaFBA1 confers drought tolerance via the improved water retention and antioxidative compete ability. Meanwhile, this stress-inducible expression strategy by RD29A promoter can minimize the unexpectable effects by 35S constitutive promoter on phenotypes of the transgenic plants.
Fructose 1,6-Bisphosphate Aldolase, a Novel Immunogenic Surface Protein on Listeria Species

PubMed Central

Conceição, Fabricio Rochedo; Hust, Michael; Mendonça, Karla Sequeira; Moreira, Ângela Nunes; França, Rodrigo Correa; da Silva, Wladimir Padilha; Aleixo, José Antonio G.

2016-01-01

Listeria monocytogenes is a ubiquitous food-borne pathogen, and its presence in food or production facilities highlights the importance of surveillance. Increased understanding of the surface exposed antigens on Listeria would provide potential diagnostic and therapeutic targets. In the present work, using mass spectrometry and genetic cloning, we show that fructose-1,6-bisphosphate aldolase (FBA) class II in Listeria species is the antigen target of the previously described mAb-3F8. Western and dot blot assays confirmed that the mAb-3F8 could distinguish all tested Listeria species from close-related bacteria. Localization studies indicated that FBA is present in every fraction of Listeria cells, including supernatant and the cell wall, setting Listeria spp. as one of the few bacteria described to have this protein on their cell surface. Epitope mapping using ORFeome display and a peptide membrane revealed a 14-amino acid peptide as the potential mAb-3F8 epitope. The target epitope in FBA allowed distinguishing Listeria spp. from closely-related bacteria, and was identified as part of the active site in the dimeric enzyme. However, its function in cell surface seems not to be host cell adhesion-related. Western and dot blot assays further demonstrated that mAb-3F8 together with anti-InlA mAb-2D12 could differentiate pathogenic from non-pathogenic Listeria isolated from artificially contaminated cheese. In summary, we report FBA as a novel immunogenic surface target useful for the detection of Listeria genus. PMID:27489951
Fructose 1,6-Bisphosphate Aldolase, a Novel Immunogenic Surface Protein on Listeria Species.

PubMed

Mendonça, Marcelo; Moreira, Gustavo Marçal Schmidt Garcia; Conceição, Fabricio Rochedo; Hust, Michael; Mendonça, Karla Sequeira; Moreira, Ângela Nunes; França, Rodrigo Correa; da Silva, Wladimir Padilha; Bhunia, Arun K; Aleixo, José Antonio G

2016-01-01

Listeria monocytogenes is a ubiquitous food-borne pathogen, and its presence in food or production facilities highlights the importance of surveillance. Increased understanding of the surface exposed antigens on Listeria would provide potential diagnostic and therapeutic targets. In the present work, using mass spectrometry and genetic cloning, we show that fructose-1,6-bisphosphate aldolase (FBA) class II in Listeria species is the antigen target of the previously described mAb-3F8. Western and dot blot assays confirmed that the mAb-3F8 could distinguish all tested Listeria species from close-related bacteria. Localization studies indicated that FBA is present in every fraction of Listeria cells, including supernatant and the cell wall, setting Listeria spp. as one of the few bacteria described to have this protein on their cell surface. Epitope mapping using ORFeome display and a peptide membrane revealed a 14-amino acid peptide as the potential mAb-3F8 epitope. The target epitope in FBA allowed distinguishing Listeria spp. from closely-related bacteria, and was identified as part of the active site in the dimeric enzyme. However, its function in cell surface seems not to be host cell adhesion-related. Western and dot blot assays further demonstrated that mAb-3F8 together with anti-InlA mAb-2D12 could differentiate pathogenic from non-pathogenic Listeria isolated from artificially contaminated cheese. In summary, we report FBA as a novel immunogenic surface target useful for the detection of Listeria genus.
Construction of robust dynamic genome-scale metabolic model structures of Saccharomyces cerevisiae through iterative re-parameterization.

PubMed

Sánchez, Benjamín J; Pérez-Correa, José R; Agosin, Eduardo

2014-09-01

Dynamic flux balance analysis (dFBA) has been widely employed in metabolic engineering to predict the effect of genetic modifications and environmental conditions in the cell׳s metabolism during dynamic cultures. However, the importance of the model parameters used in these methodologies has not been properly addressed. Here, we present a novel and simple procedure to identify dFBA parameters that are relevant for model calibration. The procedure uses metaheuristic optimization and pre/post-regression diagnostics, fixing iteratively the model parameters that do not have a significant role. We evaluated this protocol in a Saccharomyces cerevisiae dFBA framework calibrated for aerobic fed-batch and anaerobic batch cultivations. The model structures achieved have only significant, sensitive and uncorrelated parameters and are able to calibrate different experimental data. We show that consumption, suboptimal growth and production rates are more useful for calibrating dynamic S. cerevisiae metabolic models than Boolean gene expression rules, biomass requirements and ATP maintenance. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Efficient and robust model-to-image alignment using 3D scale-invariant features.

PubMed

Toews, Matthew; Wells, William M

2013-04-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. Copyright © 2012 Elsevier B.V. All rights reserved.
Coping with challenging behaviours of children with autism: effectiveness of brief training workshop for frontline staff in special education settings.

PubMed

Ling, C Y M; Mak, W W S

2012-03-01

The present study examined the effectiveness of three staff training elements: psychoeducation (PE) on autism, introduction of functional behavioural analysis (FBA) and emotional management (EM), on the reaction of challenging behaviours for frontline staff towards children with autism in Hong Kong special education settings. A sample of 311 frontline staff in educational settings was recruited to one of the three conditions: control, PE-FBA and PE-FBA-EM groups. A total of 175 participants completed all three sets of questionnaires during pre-training, immediate post-training and 1-month follow-up. Findings showed that the one-session staff training workshop increased staff knowledge of autism and perceived efficacy but decrease helping behavioural intention. In spite of the limited effectiveness of a one-session staff training workshop, continued staff training is still necessary for the improvement of service quality. Further exploration on how to change emotion response of staff is important. © 2011 The Authors. Journal of Intellectual Disability Research © 2011 Blackwell Publishing Ltd.
Efficient and Robust Model-to-Image Alignment using 3D Scale-Invariant Features

PubMed Central

Toews, Matthew; Wells, William M.

2013-01-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a-posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. PMID:23265799
Human attention filters for single colors

PubMed Central

Sun, Peng; Chubb, Charles; Wright, Charles E.; Sperling, George

2016-01-01

The visual images in the eyes contain much more information than the brain can process. An important selection mechanism is feature-based attention (FBA). FBA is best described by attention filters that specify precisely the extent to which items containing attended features are selectively processed and the extent to which items that do not contain the attended features are attenuated. The centroid-judgment paradigm enables quick, precise measurements of such human perceptual attention filters, analogous to transmission measurements of photographic color filters. Subjects use a mouse to locate the centroid—the center of gravity—of a briefly displayed cloud of dots and receive precise feedback. A subset of dots is distinguished by some characteristic, such as a different color, and subjects judge the centroid of only the distinguished subset (e.g., dots of a particular color). The analysis efficiently determines the precise weight in the judged centroid of dots of every color in the display (i.e., the attention filter for the particular attended color in that context). We report 32 attention filters for single colors. Attention filters that discriminate one saturated hue from among seven other equiluminant distractor hues are extraordinarily selective, achieving attended/unattended weight ratios >20:1. Attention filters for selecting a color that differs in saturation or lightness from distractors are much less selective than attention filters for hue (given equal discriminability of the colors), and their filter selectivities are proportional to the discriminability distance of neighboring colors, whereas in the same range hue attention-filter selectivity is virtually independent of discriminabilty. PMID:27791040
Impaired activity of adherens junctions contributes to endothelial dilator dysfunction in ageing rat arteries.

PubMed

Chang, Fumin; Flavahan, Sheila; Flavahan, Nicholas A

2017-08-01

Ageing-induced endothelial dysfunction contributes to organ dysfunction and progression of cardiovascular disease. VE-cadherin clustering at adherens junctions promotes protective endothelial functions, including endothelium-dependent dilatation. Ageing increased internalization and degradation of VE-cadherin, resulting in impaired activity of adherens junctions. Inhibition of VE-cadherin clustering at adherens junctions (function-blocking antibody; FBA) reduced endothelial dilatation in young arteries but did not affect the already impaired dilatation in old arteries. After junctional disruption with the FBA, dilatation was similar in young and old arteries. Src tyrosine kinase activity and tyrosine phosphorylation of VE-cadherin were increased in old arteries. Src inhibition increased VE-cadherin at adherens junctions and increased endothelial dilatation in old, but not young, arteries. Src inhibition did not increase dilatation in old arteries treated with the VE-cadherin FBA. Ageing impairs the activity of adherens junctions, which contributes to endothelial dilator dysfunction. Restoring the activity of adherens junctions could be of therapeutic benefit in vascular ageing. Endothelial dilator dysfunction contributes to pathological vascular ageing. Experiments assessed whether altered activity of endothelial adherens junctions (AJs) might contribute to this dysfunction. Aortas and tail arteries were isolated from young (3-4 months) and old (22-24 months) F344 rats. VE-cadherin immunofluorescent staining at endothelial AJs and AJ width were reduced in old compared to young arteries. A 140 kDa VE-cadherin species was present on the cell surface and in TTX-insoluble fractions, consistent with junctional localization. Levels of the 140 kDa VE-cadherin were decreased, whereas levels of a TTX-soluble 115 kDa VE-cadherin species were increased in old compared to young arteries. Acetylcholine caused endothelium-dependent dilatation that was decreased in old compared to young arteries. Disruption of VE-cadherin clustering at AJs (function-blocking antibody, FBA) inhibited dilatation to acetylcholine in young, but not old, arteries. After the FBA, there was no longer any difference in dilatation between old and young arteries. Src activity and tyrosine phosphorylation of VE-cadherin were increased in old compared to young arteries. In old arteries, Src inhibition (saracatinib) increased: (i) 140 kDa VE-cadherin in the TTX-insoluble fraction, (ii) VE-cadherin intensity at AJs, (iii) AJ width, and (iv) acetylcholine dilatation. In old arteries treated with the FBA, saracatinib no longer increased acetylcholine dilatation. Saracatinib did not affect dilatation in young arteries. Therefore, ageing impairs AJ activity, which appears to reflect Src-induced phosphorylation, internalization and degradation of VE-cadherin. Moreover, impaired AJ activity can account for the endothelial dilator dysfunction in old arteries. Restoring endothelial AJ activity may be a novel therapeutic approach to vascular ageing. © 2017 The Authors. The Journal of Physiology © 2017 The Physiological Society.
Passive treatment of acid mine drainage using coal combustion by-products and spent mushroom substrate: Results of column study

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

Crisp, T.E.; Nairn, R.W.; Strevett, K.A.

1998-12-31

A column study was conducted to evaluate the feasibility of using of coal combustion by-products (CCB) as alkaline materials in a field scale downflow constructed wetlands for acid mine drainage treatment. Five columns (15.24 cm in diameter and 91.44 cm high) were constructed and filled with a combination of spent mushroom substrate (SMS) and one of three alkaline materials (limestone, hydrated fly ash, or fluidized bed ash). The five mixtures utilized were 10% fluidized bed ash/40% limestone (FBA/LS), 10% fluidized bed ash (FBA), 50% limestone (LS), 50% hydrated fly ash (HFA),m and 50% sieved (>1.5 cm) hydrated fly ash (S.more » HFA) with the remainder as SMS on a w/w basis. Column received synthetic acid mine drainage containing: 400 mg/L iron, 59 mg/L aluminum, 11 mg/L manganese, 50% mg/L magnesium, 40 mg/L calcium, and 1200 mg/L sulfate for 5 months. Anoxic conditions in the influent reservoirs were maintained by a positive nitrogen pressure head. Flow rates of 2.0 mL/minute to each column were maintained by a multichannel peristaltic pump. For all columns, effluent acidity concentrations were less than influent acidity concentration (877{sup {minus}}30, n = 75f). Mean effluent acidity concentrations were 241 mg/L (FBA/LS), 186 mg/L (FBA), 419 mg/L (LS), {minus}28.5 mg/L (HFA), and 351 mg/L (S. HFA), respectively. While all column produced measurable alkalinity, only the HFA column produced a net alkaline discharge. The results of these column studies are applicable to the design and sizing of innovative field scale systems using alkaline-rich CCB`s.« less
Rational synthetic combination genetic devices boosting high temperature ethanol fermentation.

PubMed

Sun, Huan; Jia, Haiyang; Li, Jun; Feng, Xudong; Liu, Yueqin; Zhou, Xiaohong; Li, Chun

2017-06-01

The growth and production of yeast in the industrial fermentation are seriously restrained by heat stress and exacerbated by heat induced oxidative stress. In this study, a novel synthetic biology approach was developed to globally boost the viability and production ability of S. cerevisiae at high temperature through rationally designing and combing heat shock protein (HSP) and superoxide dismutase (SOD) genetic devices to ultimately synergistically alleviate both heat stress and oxidative stress. HSP and SOD from extremophiles were constructed to be different genetic devices and they were preliminary screened by heat resistant experiments and anti-oxidative experiments, respectively. Then in order to customize and further improve thermotolerance of S. cerevisiae , the HSP genetic device and SOD genetic device were rationally combined. The results show the simply assemble of the same function genetic devices to solve heat stress or oxidative stress could not enhance the thermotolerance considerably. Only S. cerevisiae with the combination genetic device (FBA1p- sod-MB4 -FBA1p- shsp-HB8 ) solving both stress showed 250% better thermotolerance than the control and displayed further 55% enhanced cell density compared with the strains with single FBA1p- sod-MB4 or FBA1p- shsp-HB8 at 42 °C. Then the most excellent combination genetic device was introduced into lab S. cerevisiae and industrial S. cerevisiae for ethanol fermentation. The ethanol yields of the two strains were increased by 20.6% and 26.3% compared with the control under high temperature, respectively. These results indicate synergistically defensing both heat stress and oxidative stress is absolutely necessary to enhance the thermotolerance and production of S. cerevisiae .
Bronchial Leech Infestation in a 15-Year-Old Female.

PubMed

Moslehi, Mohammad Ashkan; Imanieh, Mohammad Hadi; Adib, Ali

2016-01-01

Foreign body aspiration (FBA) is a common incidence in young children. Leeches are rarely reported as FBA at any age. This study describes a 15-year-old female who presented with hemoptysis, hematemesis, coughs, melena, and anemia seven months prior to admission. Chest X-ray showed a round hyperdensity in the right lower lobe. A chest computed tomography (CT) demonstrated an area of consolidation and surrounding ground glass opacities in the right lower lobe. Hematological investigations revealed anemia. Finally, bronchoscopy was performed and a 5 cm leech was found within the right B 7-8 bronchus and removed by forceps and a Dormia basket.
Bronchial Leech Infestation in a 15-Year-Old Female

PubMed Central

Moslehi, Mohammad Ashkan; Imanieh, Mohammad Hadi

2016-01-01

Foreign body aspiration (FBA) is a common incidence in young children. Leeches are rarely reported as FBA at any age. This study describes a 15-year-old female who presented with hemoptysis, hematemesis, coughs, melena, and anemia seven months prior to admission. Chest X-ray showed a round hyperdensity in the right lower lobe. A chest computed tomography (CT) demonstrated an area of consolidation and surrounding ground glass opacities in the right lower lobe. Hematological investigations revealed anemia. Finally, bronchoscopy was performed and a 5 cm leech was found within the right B7-8 bronchus and removed by forceps and a Dormia basket. PMID:27752380
Molecular and biochemical characterizations of three fructose-1,6-bisphosphate aldolases from Clonorchis sinensis.

PubMed

Li, Shan; Bian, Meng; Wang, Xiaoyun; Chen, Xueqing; Xie, Zhizhi; Sun, Hengchang; Jia, Feifei; Liang, Pei; Zhou, Chenhui; He, Lei; Mao, Qiang; Huang, Bo; Liang, Chi; Wu, Zhongdao; Li, Xuerong; Xu, Jin; Huang, Yan; Yu, Xinbing

2014-01-01

Fructose-1,6-bisphosphate aldolase (FbA) is a ubiquitous enzyme in glycolysis. In the present study, we screened out three distinct genes encoding FbA isozymes (CsFbAs, CsFbA-1/2/3) from Clonorchis sinensis (C. sinensis) and characterized their sequences and structures profiles as well as biochemical properties. The amino acid sequences of CsFbAs shared homology with those of Class I FbAs from other species. The putative quaternary structures revealed that CsFbA-2 and CsFbA-3 were tetramers, while CsFbA-1 was dimer. Recombinant CsFbA-2 and CsFbA-3 (rCsFbA-2/3) were confirmed to be Class I FbAs for their stable enzymatic activities in the presence of EDTA or metal ions. However, recombinant CsFbA-1 (rCsFbA-1) did not show the catalytic activity, which might be due to the inappropriate fold and interaction between its subunits. Both rCsFbA-2 and rCsFbA-3 showed similar enzymatic properties such as optimal temperatures and broad pH ranges that similar to human FbA isozymes. They showed relatively higher affinities for fructose-1,6-bisphosphate (FBP) than fructose-1-phosphate (F-1-P). Their kcat ratios of FBP to F-1-P were in accordance with those of human FbA-A or C. In addition, CsFbAs were differentially transcribed in the developmental stages of C. sinensis, suggesting their essential roles throughout the life stages. Extensive distribution of CsFbAs in adult worms indicated that ubiquitous activities of CsFbAs took place in these organs. Collectively, these results suggested that long-term parasitic environment might adapt these isozymes similar to host FbAs for metabolic requirement. Our study will provide new insight into CsFbAs in the glycometabolism of C. sinensis and relationship between the host and the parasite. Copyright © 2014 Elsevier B.V. All rights reserved.
Effects of overexpressing photosynthetic carbon flux control enzymes in the cyanobacterium Synechocystis PCC 6803.

PubMed

Liang, Feiyan; Lindblad, Peter

2016-11-01

Synechocystis PCC 6803 is a model unicellular cyanobacterium used in e.g. photosynthesis and CO 2 assimilation research. In the present study we examined the effects of overexpressing Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), sedoheptulose 1,7-biphosphatase (SBPase), fructose-bisphosphate aldolase (FBA) and transketolase (TK), confirmed carbon flux control enzymes of the Calvin-Bassham-Benson (CBB) cycle in higher plants, in Synechocystis PCC 6803. Overexpressing RuBisCO, SBPase and FBA resulted in increased in vivo oxygen evolution (maximal 115%), growth rate and biomass accumulation (maximal 52%) under 100μmolphotonsm -2 s -1 light condition. Cells overexpressing TK showed a chlorotic phenotype but increased biomass by approximately 42% under 100μmolphotonsm -2 s -1 light condition. Under 15μmolphotonsm -2 s -1 light condition, cells overexpressing TK showed enhanced in vivo oxygen evolution. This study demonstrates increased growth and biomass accumulation when overexpressing selected enzymes of the CBB cycle. RuBisCO, SBPase, FBA and TK are identified as four potential targets to improve growth and subsequently also yield of valuable products from Synechocystis PCC 6803. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.
Photometric determination of phosphorus in mineralized biodiesel using a micro-flow-batch analyzer with solenoid micro-pumps.

PubMed

Lima, Marcelo B; Barreto, Inakã S; Andrade, Stéfani Iury E; Neta, Maria S S; Almeida, Luciano F; Araújo, Mário C U

2012-08-30

A method for the determination of phosphorus in mineralized biodiesel using a micro-flow-batch analyzer (μFBA) with solenoid micro-pumps was proposed. The samples were mineralized using an ashing procedure at 550 °C followed by dissolution of the residue. The determination of phosphorus was performed by employing the well-known molybdenum blue method. The measures of the absorbance were performed at 850 nm using an InfraRed LED integrated into the μFBA. Comparing with the reference method, no statistically significant differences were observed when applying the paired t-test at a 95% confidence level. Recovery study shows results between 97.9% and 105.8%. The proposed microsystem using solenoid micro-pumps presented satisfactory robustness and high sampling rate (190 h(-1)), with satisfactory reproducibility (relative standard deviation <4.5%, n=3), low reagents consumption (32 μL per analysis) and cost to build the device. Moreover, μFBA presents limit of detection (0.014 mg Kg(-1)), precision and accuracy compatible with the biodiesel regulations that establish a maximum concentration of 10 mg Kg(-1) (Brazil, USA, EU), suggesting that it is a good alternative for the determination of phosphorus in biodiesel. Copyright © 2012 Elsevier B.V. All rights reserved.
Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data.

PubMed

Kawasaki, Regiane; Baraúna, Rafael A; Silva, Artur; Carepo, Marta S P; Oliveira, Rui; Marques, Rodolfo; Ramos, Rommel T J; Schneider, Maria P C

2016-01-01

Exiguobacterium antarcticum B7 is extremophile Gram-positive bacteria able to survive in cold environments. A key factor to understanding cold adaptation processes is related to the modification of fatty acids composing the cell membranes of psychrotrophic bacteria. In our study we show the in silico reconstruction of the fatty acid biosynthesis pathway of E. antarcticum B7. To build the stoichiometric model, a semiautomatic procedure was applied, which integrates genome information using KEGG and RAST/SEED. Constraint-based methods, namely, Flux Balance Analysis (FBA) and elementary modes (EM), were applied. FBA was implemented in the sense of hexadecenoic acid production maximization. To evaluate the influence of the gene expression in the fluxome analysis, FBA was also calculated using the log2⁡FC values obtained in the transcriptome analysis at 0°C and 37°C. The fatty acid biosynthesis pathway showed a total of 13 elementary flux modes, four of which showed routes for the production of hexadecenoic acid. The reconstructed pathway demonstrated the capacity of E. antarcticum B7 to de novo produce fatty acid molecules. Under the influence of the transcriptome, the fluxome was altered, promoting the production of short-chain fatty acids. The calculated models contribute to better understanding of the bacterial adaptation at cold environments.
Structural Control of Metabolic Flux

PubMed Central

Sajitz-Hermstein, Max; Nikoloski, Zoran

2013-01-01

Organisms have to continuously adapt to changing environmental conditions or undergo developmental transitions. To meet the accompanying change in metabolic demands, the molecular mechanisms of adaptation involve concerted interactions which ultimately induce a modification of the metabolic state, which is characterized by reaction fluxes and metabolite concentrations. These state transitions are the effect of simultaneously manipulating fluxes through several reactions. While metabolic control analysis has provided a powerful framework for elucidating the principles governing this orchestrated action to understand metabolic control, its applications are restricted by the limited availability of kinetic information. Here, we introduce structural metabolic control as a framework to examine individual reactions' potential to control metabolic functions, such as biomass production, based on structural modeling. The capability to carry out a metabolic function is determined using flux balance analysis (FBA). We examine structural metabolic control on the example of the central carbon metabolism of Escherichia coli by the recently introduced framework of functional centrality (FC). This framework is based on the Shapley value from cooperative game theory and FBA, and we demonstrate its superior ability to assign “share of control” to individual reactions with respect to metabolic functions and environmental conditions. A comparative analysis of various scenarios illustrates the usefulness of FC and its relations to other structural approaches pertaining to metabolic control. We propose a Monte Carlo algorithm to estimate FCs for large networks, based on the enumeration of elementary flux modes. We further give detailed biological interpretation of FCs for production of lactate and ATP under various respiratory conditions. PMID:24367246
Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

NASA Technical Reports Server (NTRS)

Beard, Daniel A.; Liang, Shou-Dan; Qian, Hong; Biegel, Bryan (Technical Monitor)

2001-01-01

Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.
Stainless steel crown aspiration during sedation in pediatric dentistry.

PubMed

Adewumi, A; Kays, David W

2008-01-01

Foreign body aspiration (FBA) causes death in more than 300 children every year in the United States. Morbidity and mortality are increased in children due to narrow airways and immature protective mechanisms. Factors to consider in pediatric dentistry are: (1) the patient's age and behavior; (2) presence and extent of disability; (3) local anesthesia; (4) body positioning; and (5) loose teeth. FBA requires prompt recognition and early treatment to minimize potentially serious and sometimes fatal consequences. The purpose of this case report was to describe the aspiration of a stainless steel crown in a 5-year-old boy during conscious sedation. It also discusses how a prompt and accurate diagnosis, early referral, and immediate treatment helped prevent serious complications.
Natural products as sources of new fungicides (IV): Synthesis and biological evaluation of isobutyrophenone analogs as potential inhibitors of class-II fructose-1,6-bisphosphate aldolase.

PubMed

Li, Ding; Luong, Tuong Thi Mai; Dan, Wen-Jia; Ren, Yanliang; Nien, Hoang Xuan; Zhang, An-Ling; Gao, Jin-Ming

2018-01-15

Several recently identified antifungal compounds share the backbone structure of acetophenones. The aim of the present study was to develop new isobutyrophenone analogs as new antifungal agents. A series of new 2,4-dihydroxy-5-methyl isobutyrophenone derivatives were prepared and characterized by 1 H, 13 C NMR and MS spectroscopic data. These products were evaluated for in vitro antifungal activities against seven plant fungal pathogens by the mycelial growth inhibitory rate assay. Compounds 3, 4a, 5a, 5b, 5e, 5f and 5g showed a broad-spectrum high antifungal activity. On the other hand, for the first time, these compounds were also assayed as potential inhibitors against Class II fructose-1,6-bisphosphate aldolase (Fba) from the rice blast fungus, Magnaporthe grisea. Compounds 5e and 5g were found to exhibit the inhibition constants (Ki) for 15.12 and 14.27 μM, respectively, as the strongest competitive inhibitors against Fba activity. The possible binding-modes of compounds 5e and 5g were further analyzed by molecular docking algorithms. The results strongly suggested that compound 5g could be a promising lead for the discovery of new fungicides via targeting Class II Fba. Copyright © 2017 Elsevier Ltd. All rights reserved.
Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data

PubMed Central

Kawasaki, Regiane; Carepo, Marta S. P.; Oliveira, Rui; Marques, Rodolfo; Ramos, Rommel T. J.; Schneider, Maria P. C.

2016-01-01

Exiguobacterium antarcticum B7 is extremophile Gram-positive bacteria able to survive in cold environments. A key factor to understanding cold adaptation processes is related to the modification of fatty acids composing the cell membranes of psychrotrophic bacteria. In our study we show the in silico reconstruction of the fatty acid biosynthesis pathway of E. antarcticum B7. To build the stoichiometric model, a semiautomatic procedure was applied, which integrates genome information using KEGG and RAST/SEED. Constraint-based methods, namely, Flux Balance Analysis (FBA) and elementary modes (EM), were applied. FBA was implemented in the sense of hexadecenoic acid production maximization. To evaluate the influence of the gene expression in the fluxome analysis, FBA was also calculated using the log2⁡FC values obtained in the transcriptome analysis at 0°C and 37°C. The fatty acid biosynthesis pathway showed a total of 13 elementary flux modes, four of which showed routes for the production of hexadecenoic acid. The reconstructed pathway demonstrated the capacity of E. antarcticum B7 to de novo produce fatty acid molecules. Under the influence of the transcriptome, the fluxome was altered, promoting the production of short-chain fatty acids. The calculated models contribute to better understanding of the bacterial adaptation at cold environments. PMID:27595107
Rational Design Synthesis and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases

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

R Daher; M Coincon; M Fonvielle

2011-12-31

We report the synthesis and biochemical evaluation of several selective inhibitors of class II (zinc dependent) fructose bis-phosphate aldolases (Fba). The products were designed as transition-state analogues of the catalyzed reaction, structurally related to the substrate fructose bis-phosphate (or sedoheptulose bis-phosphate) and based on an N-substituted hydroxamic acid, as a chelator of the zinc ion present in active site. The compounds synthesized were tested on class II Fbas from various pathogenic microorganisms and, by comparison, on a mammalian class I Fba. The best inhibitor shows Ki against class II Fbas from various pathogens in the nM range, with very highmore » selectivity (up to 105). Structural analyses of inhibitors in complex with aldolases rationalize and corroborate the enzymatic kinetics results. These inhibitors represent lead compounds for the preparation of new synthetic antibiotics, notably for tuberculosis prophylaxis.« less
Total Born approximation cross sections for single electron loss by atoms and ions colliding with atoms

NASA Technical Reports Server (NTRS)

Rule, D. W.

1977-01-01

The first born approximation (FBA) is applied to the calculation of single electron loss cross sections for various ions and atoms containing from one to seven electrons. Screened hydrogenic wave functions were used for the states of the electron ejected from the projectile, and Hartree-Fock elastic and incoherent scattering factors were used to describe the target. The effect of the target atom on the scaling of projectile ionization cross sections with respect to the projectile nuclear charge was explored in the case of hydrogen-like ions. Scaling of the cross section with respect to the target nuclear charge for electron loss by Fe (+25) in collision with neutral atoms ranging from H to Fe is also examined. These results were compared to those of the binary encounter approximation and to the FBA for the case of ionization by completely stripped target ions.

Pediatric airway foreign bodies.

PubMed

Fitzpatrick, P C; Guarisco, J L

1998-04-01

Foreign body aspiration (FBA) is a leading cause of accidental death in children less than one year old and is the cause of death in 7% of children less than four. Food items, especially peanuts, are the most common items aspirated in infants and toddlers, whereas older children are more likely to aspirate non-food items such as pen caps, pins, and paper clips. A high degree of suspicion is required to diagnose FBA. A history of a witnessed choking episode is most important in early diagnosis. An asymptomatic period is common after aspiration and contributes to a delay in diagnosis of greater than one week in 12% to 26% of patients. This delay in diagnosis causes increased morbidity from bronchial inflammation, obstruction, and pneumonia which is resistant to treatment. Prompt endoscopic removal of the foreign body with an open rigid bronchoscope under general anesthesia is the mainstay of therapy.
Fluxomics - connecting 'omics analysis and phenotypes.

PubMed

Winter, Gal; Krömer, Jens O

2013-07-01

In our modern 'omics era, metabolic flux analysis (fluxomics) represents the physiological counterpart of its siblings transcriptomics, proteomics and metabolomics. Fluxomics integrates in vivo measurements of metabolic fluxes with stoichiometric network models to allow the determination of absolute flux through large networks of the central carbon metabolism. There are many approaches to implement fluxomics including flux balance analysis (FBA), (13) C fluxomics and (13) C-constrained FBA as well as many experimental settings for flux measurement including dynamic, stationary and semi-stationary. Here we outline the principles of the different approaches and their relative advantages. We demonstrate the unique contribution of flux analysis for phenotype elucidation using a thoroughly studied metabolic reaction as a case study, the microbial aerobic/anaerobic shift, highlighting the importance of flux analysis as a single layer of data as well as interlaced in multi-omics studies. © 2012 John Wiley & Sons Ltd and Society for Applied Microbiology.
MOST: a software environment for constraint-based metabolic modeling and strain design.

PubMed

Kelley, James J; Lane, Anatoliy; Li, Xiaowei; Mutthoju, Brahmaji; Maor, Shay; Egen, Dennis; Lun, Desmond S

2015-02-15

MOST (metabolic optimization and simulation tool) is a software package that implements GDBB (genetic design through branch and bound) in an intuitive user-friendly interface with excel-like editing functionality, as well as implementing FBA (flux balance analysis), and supporting systems biology markup language and comma-separated values files. GDBB is currently the fastest algorithm for finding gene knockouts predicted by FBA to increase production of desired products, but GDBB has only been available on a command line interface, which is difficult to use for those without programming knowledge, until the release of MOST. MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
An individually tailored behavioral medicine treatment in physical therapy for tension-type headache - two experimental case studies.

PubMed

Söderlund, Anne; Lagerlöf, Helena

2016-01-01

The aim of this study was to describe and evaluate the effect of an individually tailored behavioral medicine treatment in physical therapy, based on a functional behavioral analysis (FBA), for tension-type headache (TTH). Two case studies with A1-A2-B-A3 design of two patients with TTH was conducted. Outcome variables were headache frequency, headache index (mean intensity), consumption of analgesics, self-efficacy in headache management (Headache Management Self-efficacy Scale [HMSE]), disability, and perceived loss of happiness for activities with family and friends. The results showed that headache frequency and headache index decreased for one of the patients. Self-efficacy in headache management increased markedly for both patients. A behavioral medicine treatment in physical therapy based on an FBA can be a way for physical therapists to handle patients with TTH. Future investigations should focus on large group studies with longer observation periods.
Exploration and comparison of inborn capacity of aerobic and anaerobic metabolisms of Saccharomyces cerevisiae for microbial electrical current production.

PubMed

Mao, Longfei; Verwoerd, Wynand S

2013-01-01

Saccharomyces cerevisiae possesses numerous advantageous biological features, such as being robust, easily handled, mostly non-pathogenic and having high catabolic rates, etc., which can be considered as merits for being used as a promising biocatalyst in microbial fuel cells (MFCs) for electricity generation. Previous studies have developed efficient MFC configurations to convert metabolic electron shuttles, such as cytoplasmic NADH, into usable electric current. However, no studies have elucidated the maximum potential of S. cerevisiae for current output and the underlying metabolic pathways, resulting from the interaction of thousands of reactions inside the cell during MFC operation. To address these two key issues, this study used in silico metabolic engineering techniques, flux balance analysis (FBA), and flux variability analysis with target flux minimization (FATMIN), to model the metabolic perturbation of S. cerevisiae under the MFC-energy extraction. The FBA results showed that, in the cytoplasmic NADH-dependent mediated electron transfer (MET) mode, S. cerevisiae had a potential to produce currents at up to 5.781 A/gDW for the anaerobic and 6.193 A/gDW for the aerobic environments. The FATMIN results showed that the aerobic and anaerobic metabolisms are resilient, relying on six and five contributing reactions respectively for high current production. Two reactions, catalyzed by glutamate dehydrogenase (NAD) (EC 1.4.1.3) and methylene tetrahydrofolate dehydrogenase (NAD) (EC 1.5.1.5), were shared in both current-production modes and contributed to over 80% of the identified maximum current outputs. It is also shown that the NADH regeneration was much less energy costly than biomass production rate. Taken together, our finding suggests that S. cerevisiae should receive more research effort for MFC electricity production.
Exploration and comparison of inborn capacity of aerobic and anaerobic metabolisms of Saccharomyces cerevisiae for microbial electrical current production

PubMed Central

Mao, Longfei; Verwoerd, Wynand S

2013-01-01

Saccharomyces cerevisiae possesses numerous advantageous biological features, such as being robust, easily handled, mostly non-pathogenic and having high catabolic rates, etc., which can be considered as merits for being used as a promising biocatalyst in microbial fuel cells (MFCs) for electricity generation. Previous studies have developed efficient MFC configurations to convert metabolic electron shuttles, such as cytoplasmic NADH, into usable electric current. However, no studies have elucidated the maximum potential of S. cerevisiae for current output and the underlying metabolic pathways, resulting from the interaction of thousands of reactions inside the cell during MFC operation. To address these two key issues, this study used in silico metabolic engineering techniques, flux balance analysis (FBA), and flux variability analysis with target flux minimization (FATMIN), to model the metabolic perturbation of S. cerevisiae under the MFC-energy extraction. The FBA results showed that, in the cytoplasmic NADH-dependent mediated electron transfer (MET) mode, S. cerevisiae had a potential to produce currents at up to 5.781 A/gDW for the anaerobic and 6.193 A/gDW for the aerobic environments. The FATMIN results showed that the aerobic and anaerobic metabolisms are resilient, relying on six and five contributing reactions respectively for high current production. Two reactions, catalyzed by glutamate dehydrogenase (NAD) (EC 1.4.1.3) and methylene tetrahydrofolate dehydrogenase (NAD) (EC 1.5.1.5), were shared in both current-production modes and contributed to over 80% of the identified maximum current outputs. It is also shown that the NADH regeneration was much less energy costly than biomass production rate. Taken together, our finding suggests that S. cerevisiae should receive more research effort for MFC electricity production. PMID:23969939
Effects of soya oligosaccharides and soya oligopeptides on lipid metabolism in hyperlipidaemic rats.

PubMed

Xie, Shali; Zhu, Jundong; Zhang, Yanqi; Shi, Kai; Shi, Yuangang; Ma, Xiao

2012-08-01

In the present study, we aimed to examine the effects of soya oligosaccharides (SOS) and soya oligopeptides (SOP) on blood lipid levels, release of vasoactive substances, antioxidant activity and faecal bile acid (FBA) excretion in rats fed a high-fat diet (HFD). Male Sprague-Dawley rats were evenly divided into five groups according to diets as follows: regular diet (control), HFD, HFD enriched with 2 % of SOS (SOS), HFD enriched with 3 % of SOP (SOP) and HFD enriched with 2 % SOS and 3 % SOP (SOSP). The results showed that SOS and SOP significantly reduced plasma total cholesterol, LDL-cholesterol and TAG, whereas HDL-cholesterol concentration was significantly increased. Furthermore, SOS and SOP reduced plasma apoB, apoE and the apoB:apoAI ratio, whereas apoAI was significantly increased. Moreover, SOS and SOP also reduced plasma thromboxane A₂ (TXA₂) and the TXA₂:prostacyclin (PGI₂) ratio, whereas plasma PGI₂ and nitric oxide were significantly increased. In addition, SOS and SOP significantly reduced serum and liver malondialdehyde concentrations and increased FBA excretion. However, we did not observe obvious influences of SOS and SOP on superoxide dismutase activities in the liver of HFD-fed rats. The combination of 2 % SOS and 3 % SOP showed a more marked effect than SOS or SOP alone in improving the lipid profile, release of vasoactive substances and increasing FBA excretion (P < 0.05). In summary, SOS and SOP might help prevent atherosclerosis through improving abnormal blood lipid levels, regulating vasoactive substances and protecting against oxidative stress.
Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks.

PubMed

Samal, Areejit

2008-12-01

Constraint-based flux balance analysis (FBA) has proven successful in predicting the flux distribution of metabolic networks in diverse environmental conditions. FBA finds one of the alternate optimal solutions that maximizes the biomass production rate. Almaas et al. have shown that the flux distribution follows a power law, and it is possible to associate with most metabolites two reactions which maximally produce and consume a given metabolite, respectively. This observation led to the concept of high-flux backbone (HFB) in metabolic networks. In previous work, the HFB has been computed using a particular optima obtained using FBA. In this paper, we investigate the conservation of HFB of a particular solution for a given medium across different alternate optima and near-optima in metabolic networks of E. coli and S. cerevisiae. Using flux variability analysis (FVA), we propose a method to determine reactions that are guaranteed to be in HFB regardless of alternate solutions. We find that the HFB of a particular optima is largely conserved across alternate optima in E. coli, while it is only moderately conserved in S. cerevisiae. However, the HFB of a particular near-optima shows a large variation across alternate near-optima in both organisms. We show that the conserved set of reactions in HFB across alternate near-optima has a large overlap with essential reactions and reactions which are both uniquely consuming (UC) and uniquely producing (UP). Our findings suggest that the structure of the metabolic network admits a high degree of redundancy and plasticity in near-optimal flow patterns enhancing system robustness for a given environmental condition.
Brain activity correlates with emotional perception induced by dynamic avatars.

PubMed

Goldberg, Hagar; Christensen, Andrea; Flash, Tamar; Giese, Martin A; Malach, Rafael

2015-11-15

An accurate judgment of the emotional state of others is a prerequisite for successful social interaction and hence survival. Thus, it is not surprising that we are highly skilled at recognizing the emotions of others. Here we aimed to examine the neuronal correlates of emotion recognition from gait. To this end we created highly controlled dynamic body-movement stimuli based on real human motion-capture data (Roether et al., 2009). These animated avatars displayed gait in four emotional (happy, angry, fearful, and sad) and speed-matched neutral styles. For each emotional gait and its equivalent neutral gait, avatars were displayed at five morphing levels between the two. Subjects underwent fMRI scanning while classifying the emotions and the emotional intensity levels expressed by the avatars. Our results revealed robust brain selectivity to emotional compared to neutral gait stimuli in brain regions which are involved in emotion and biological motion processing, such as the extrastriate body area (EBA), fusiform body area (FBA), superior temporal sulcus (STS), and the amygdala (AMG). Brain activity in the amygdala reflected emotional awareness: for visually identical stimuli it showed amplified stronger response when the stimulus was perceived as emotional. Notably, in avatars gradually morphed along an emotional expression axis there was a parametric correlation between amygdala activity and emotional intensity. This study extends the mapping of emotional decoding in the human brain to the domain of highly controlled dynamic biological motion. Our results highlight an extensive level of brain processing of emotional information related to body language, which relies mostly on body kinematics. Copyright © 2015. Published by Elsevier Inc.
The Road to Prison is Paved with Bad Evaluations: The Case for Functional Behavioral Assessments and Behavior Intervention Plans.

PubMed

Poucher, Stephanie M

In 1997, Congress amended the Individuals with Disabilities Education Act ("IDEA") to include provisions meant to assist school districts in educating students with behavioral needs. These amendments required schools to use functional behavioral assessments ("FBA") and behavior intervention plans ("BIP") under certain circumstances. Congress did not, however, include a definition of or substantive requirements for either system of behavior management. As a result, although BIPs and FBAs are now federally mandated requirements, and it is clear that disregarding behavioral issues is a denial of a free appropriate public education ("FAPE"), the IDEA’s adjudicative standard, there is no clear consensus as to whether a student with behavioral needs must have an FBA or a BIP or what either must include. The IDEA’s lack of guidance has resulted in inconsistent and often contradictory court rulings, and the lack of specific definitions and procedures has allowed schools to develop purportedly legal but substantively deficient behavior evaluations and intervention plans for special needs students. Despite this confusion, some courts have properly looked to the administrative record for guidance on the substantive elements of FBAs and BIPs. Deference to hearing officers, along with other provisions within the IDEA, such as Child Find and inclusion obligations, may assist courts in determining whether a school’s failure to use an FBA and a BIP for a student with behavioral needs falls short of Board of Education v. Rowley’s requirements for FAPE. FBAs and BIPs aim to prevent and correct student misconduct before it escalates and results in drastic disciplinary action. Given the impact punitive school discipline policies have had on students with special needs, the added procedural safeguards these proactive behavior management schemes could provide are imperative to dismantling the school-to-prison pipeline.
Glycolytic enzymes associated with the cell surface of Streptococcus pneumoniae are antigenic in humans and elicit protective immune responses in the mouse

PubMed Central

LING, E; FELDMAN, G; PORTNOI, M; DAGAN, R; OVERWEG, K; MULHOLLAND, F; CHALIFA-CASPI, V; WELLS, J; MIZRACHI-NEBENZAHL, Y

2004-01-01

Streptococcus pneumoniae is a leading cause of otitis media, sinusitis, pneumonia, bacteraemia and meningitis worldwide. The drawbacks associated with the limited number of various capsular polysaccharides that can be included in the polysaccharide-based vaccines focuses much attention on pneumococcal proteins as vaccine candidates. We extracted an enriched cell wall fraction from S. pneumoniae WU2. Approximately 150 soluble proteins could be identified by 2D gel electrophoresis. The proteins were screened by 2D-Western blotting using sera that were obtained longitudinally from children attending day-care centres at 18, 30 and 42 months of age and sera from healthy adult volunteers. The proteins were further identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Seventeen proteins were antigenic in children and adults, of which 13 showed an increasing antibody response with age in all eight children analysed. Two immunogenic proteins, fructose–bisphosphate aldolase (FBA) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and a control protein with known low immunogenicity, heat shock protein 70 (DnaK), were expressed in Escherichia coli, purified and used to immunize mice. Mouse antibodies elicited to the recombinant (r) FBA and rGAPDH were cross-reactive with several genetically unrelated strains of different serotypes and conferred protection to respiratory challenge with virulent pneumococci. In addition, the FBA used in this study (NP_345117) does not have a human ortholog and warrants further investigation as a candidate for a pneumococcal vaccine. In conclusion, the immunoproteomics based approach utilized in the present study appears to be a suitable tool for identification of novel S. pneumoniae vaccine candidates. PMID:15498039
Tracheobronchial Foreign Bodies in Children: The Role of Emergency Rigid Bronchoscopy

PubMed Central

Baram, Aram; Sherzad, Hewa; Saeed, Sara; Kakamad, Fahmi H.; Hamawandi, Adnan M. H.

2017-01-01

Foreign body aspiration (FBA) is a common and lethal accident in the pediatric age group. It requires early recognition and treatment by rigid bronchoscopy to avoid fatal outcomes. Objective. The aim of this study was to study the pattern of FBA in the tracheobronchial tree as well as the success rate of rigid bronchoscopy in children admitted to a single center and to analyze the relationship of the type of foreign body (FB) with patients’ age, presentation, and complications. Methods. A retrospective cross-sectional study of FBA was conducted in children in the Sulaimani/Kurdistan region, Iraq, admitted to the emergency teaching hospital of the University of Sulaimani from January 2014 to March 2016. Result. Data of 83 patients between 6 months and 15 years old were studied. The most affected was the 1- to 5-year-old group. There was a slight female predominance (male to female ratio 0.93:1). The most common FB was sunflower seed (49.4%). History of choking was present in 92.8% of patients; 55.4% had normal air entry, and 37.3% had no added sound on chest auscultation. Normal chest X-ray (CXR) was found in 40% of patients. The most common site was the right bronchial tree (39.8%). Two patients needed mechanical ventilation; both of them died. There was a significant relationship between the type of FB (P = .013, .000, respectively). Conclusion. Medical history is the most important factor for reaching the diagnosis; bronchoscopy is mandatory if choking was witnessed, even if examination and CXR are normal. Organic material causes more local reaction than nonorganic material. PMID:29226187
The secreted fructose 1,6-bisphosphate aldolase as a broad spectrum vaccine candidate against pathogenic bacteria in aquaculture.

PubMed

Sun, Zhongyang; Shen, Binbing; Wu, Haizhen; Zhou, Xiangyu; Wang, Qiyao; Xiao, Jingfan; Zhang, Yuanxing

2015-10-01

The development of aquaculture has been hampered by different aquatic pathogens that can cause edwardsiellosis, vibriosis, or other diseases. Therefore, developing a broad spectrum vaccine against different fish diseases is necessary. In this study, fructose 1,6-bisphosphate aldolase (FBA), a conserved enzyme in the glycolytic pathway, was demonstrated to be located in the non-cytoplasmic components of five aquatic pathogenic bacteria and exhibited remarkable protection and cross-protection against these pathogens in turbot and zebrafish. Further analysis revealed that sera sampled from vaccinated turbot had a high level of specific antibody and bactericidal activity against these pathogens. Meanwhile, the increased expressions of immune response-related genes associated with antigen recognition and presentation indicated that the adaptive immune response was effectively aroused. Taken together, our results suggest that FBA can be utilized as a broad-spectrum vaccine against various pathogenic bacteria of aquaculture in the future. Copyright © 2015 Elsevier Ltd. All rights reserved.
An objective function exploiting suboptimal solutions in metabolic networks

PubMed Central

2013-01-01

Background Flux Balance Analysis is a theoretically elegant, computationally efficient, genome-scale approach to predicting biochemical reaction fluxes. Yet FBA models exhibit persistent mathematical degeneracy that generally limits their predictive power. Results We propose a novel objective function for cellular metabolism that accounts for and exploits degeneracy in the metabolic network to improve flux predictions. In our model, regulation drives metabolism toward a region of flux space that allows nearly optimal growth. Metabolic mutants deviate minimally from this region, a function represented mathematically as a convex cone. Near-optimal flux configurations within this region are considered equally plausible and not subject to further optimizing regulation. Consistent with relaxed regulation near optimality, we find that the size of the near-optimal region predicts flux variability under experimental perturbation. Conclusion Accounting for suboptimal solutions can improve the predictive power of metabolic FBA models. Because fluctuations of enzyme and metabolite levels are inevitable, tolerance for suboptimality may support a functionally robust metabolic network. PMID:24088221
The metabolic enzyme fructose-1,6-bisphosphate aldolase acts as a transcriptional regulator in pathogenic Francisella.

PubMed

Ziveri, Jason; Tros, Fabiola; Guerrera, Ida Chiara; Chhuon, Cerina; Audry, Mathilde; Dupuis, Marion; Barel, Monique; Korniotis, Sarantis; Fillatreau, Simon; Gales, Lara; Cahoreau, Edern; Charbit, Alain

2017-10-11

The enzyme fructose-bisphosphate aldolase occupies a central position in glycolysis and gluconeogenesis pathways. Beyond its housekeeping role in metabolism, fructose-bisphosphate aldolase has been involved in additional functions and is considered as a potential target for drug development against pathogenic bacteria. Here, we address the role of fructose-bisphosphate aldolase in the bacterial pathogen Francisella novicida. We demonstrate that fructose-bisphosphate aldolase is important for bacterial multiplication in macrophages in the presence of gluconeogenic substrates. In addition, we unravel a direct role of this metabolic enzyme in transcription regulation of genes katG and rpoA, encoding catalase and an RNA polymerase subunit, respectively. We propose a model in which fructose-bisphosphate aldolase participates in the control of host redox homeostasis and the inflammatory immune response.The enzyme fructose-bisphosphate aldolase (FBA) plays central roles in glycolysis and gluconeogenesis. Here, Ziveri et al. show that FBA of the pathogen Francisella novicida acts, in addition, as a transcriptional regulator and is important for bacterial multiplication in macrophages.
Effects of Training in Functional Behavior Assessment

ERIC Educational Resources Information Center

Dukes, Charles; Rosenberg, Howard; Brady, Michael

2008-01-01

The purpose of this study was to investigate the effectiveness of training special education teachers in the process of functional behavioral assessment (FBA) and subsequent development of recommendations to promote behavior change. An original evaluation instrument was developed that included measures of special education teachers' knowledge of…
Individualized Positive Behavior Support in School Settings: A Meta-Analysis

ERIC Educational Resources Information Center

Goh, Ailsa E.; Bambara, Linda M.

2012-01-01

This meta-analysis examined school-based intervention research based on functional behavioral assessment (FBA) to determine the effectiveness of key individualized positive behavior support (IPBS) practices in school settings. In all, 83 studies representing 145 participants were included in the meta-analysis. Intervention, maintenance, and…
The Effects of Function-Based Self-Management Interventions on Student Behavior

ERIC Educational Resources Information Center

Hansen, Blake D.; Wills, Howard P.; Kamps, Debra M.; Greenwood, Charles R.

2014-01-01

Children with emotional and behavioral disorders (E/BD) struggle to achieve social and academic outcomes. Many studies have demonstrated self-management interventions to be effective at reducing problem behavior and increasing positive social and academic behaviors. Functional behavior assessment (FBA) information may be used in designing…
Acceptability of Functional Behavioral Assessment Procedures to Special Educators and School Psychologists

ERIC Educational Resources Information Center

O'Neill, Robert E.; Bundock, Kaitlin; Kladis, Kristin; Hawken, Leanne S.

2015-01-01

This survey study assessed the acceptability of a variety of functional behavioral assessment (FBA) procedures (i.e., functional assessment interviews, rating scales/questionnaires, systematic direct observations, functional analysis manipulations) to a national sample of 123 special educators and a state sample of 140 school psychologists.…
Recent Case Law Regarding Functional Behavioral Assessments: Implications for Practice

ERIC Educational Resources Information Center

Losinski, Mickey L.; Katsiyannis, Antonis; Ryan, Joseph B.

2014-01-01

While functional behavioral assessments (FBAs) are currently federally mandated requirements, public schools have not been provided clear federal guidance concerning what constitutes an acceptable FBA through Individuals With Disabilities Education Act or related regulations. The purpose of this article is to examine recent rulings regarding FBAs…

Functional Behavioral Assessment-Based Interventions. What Works Clearinghouse Intervention Report

ERIC Educational Resources Information Center

What Works Clearinghouse, 2016

2016-01-01

This intervention report presents findings from a systematic review of "functional behavioral assessment-based interventions" conducted using the WWC Procedures and Standards Handbook, version 3.0, and the Children Identified With or At Risk for an Emotional Disturbance review protocol, version 3.0. Functional behavioral assessment (FBA)…
Promoting Self-Determination throughout the FBA/BIP Process

ERIC Educational Resources Information Center

Korinek, Lori

2015-01-01

Student behavior that interferes with teaching and learning remains a major concern for educators. In-school and postschool outcomes for students with challenging behaviors are among the poorest. Many of these students require a functional behavioral assessment and intervention plan to become more successful. Externally-driven behavior change…
Functional Behavioral Assessments and Intervention Plans in Early Intervention Settings.

ERIC Educational Resources Information Center

LaRocque, Michelle; Brown, Sharan E.; Johnson, Kurt L.

2001-01-01

This article advocates the use of functional behavioral assessments (FBAs) and behavior intervention plans (BIPs) in the development of Individualized Family Service Plans for children with or at risk of developing behavioral disorders. It describes the FBA and BIP processes and proposes a parent collaborative model for assessment and…
State Special Education Laws for Functional Behavioral Assessment and Behavior Intervention Plans

ERIC Educational Resources Information Center

Zirkel, Perry A.

2011-01-01

A comprehensive search identified 31 state statutes and regulations specific to functional behavioral assessments (FBA) and behavior intervention plans (BIP) in the special education context. A systematic tabulation of the state law provisions that exceed the rather narrow foundation requirements of the Individuals with Disabilities Education Act…
Factors in Teacher Adherence to Treatment.

ERIC Educational Resources Information Center

Gum, Louann

Treatment integrity, a measure of how accurately a treatment is carried out, is integral to the concept of effective behavioral analysis and intervention. This study sought to correlate teachers' perceptions of the functional behavior assessment and behavior intervention process (FBA/BIP) with their confidence that the process is an effective and…
An integrated pathway system modeling of Saccharomyces cerevisiae HOG pathway: a Petri net based approach.

PubMed

Tomar, Namrata; Choudhury, Olivia; Chakrabarty, Ankush; De, Rajat K

2013-02-01

Biochemical networks comprise many diverse components and interactions between them. It has intracellular signaling, metabolic and gene regulatory pathways which are highly integrated and whose responses are elicited by extracellular actions. Previous modeling techniques mostly consider each pathway independently without focusing on the interrelation of these which actually functions as a single system. In this paper, we propose an approach of modeling an integrated pathway using an event-driven modeling tool, i.e., Petri nets (PNs). PNs have the ability to simulate the dynamics of the system with high levels of accuracy. The integrated set of signaling, regulatory and metabolic reactions involved in Saccharomyces cerevisiae's HOG pathway has been collected from the literature. The kinetic parameter values have been used for transition firings. The dynamics of the system has been simulated and the concentrations of major biological species over time have been observed. The phenotypic characteristics of the integrated system have been investigated under two conditions, viz., under the absence and presence of osmotic pressure. The results have been validated favorably with the existing experimental results. We have also compared our study with the study of idFBA (Lee et al., PLoS Comput Biol 4:e1000-e1086, 2008) and pointed out the differences between both studies. We have simulated and monitored concentrations of multiple biological entities over time and also incorporated feedback inhibition by Ptp2 which has not been included in the idFBA study. We have concluded that our study is the first to the best of our knowledge to model signaling, metabolic and regulatory events in an integrated form through PN model framework. This study is useful in computational simulation of system dynamics for integrated pathways as there are growing evidences that the malfunctioning of the interplay among these pathways is associated with disease.
The Use of Structural Behavioral Assessment to Develop Interventions for Secondary Students Exhibiting Challenging Behaviors

ERIC Educational Resources Information Center

Losinski, Mickey; Maag, John W.; Katsiyannis, Antonis; Ryan, Joseph B.

2015-01-01

Structural behavioral assessment (SBA) involves a series of heuristic approaches similar to those used with functional behavioral assessment (FBA). It involves assessing contextual variables that precede the occurrence of a behavior. These variables have also been termed antecedents, setting events, or establishing operations. Once these variables…
Positive Behavior Support for a Child with Inattentive Behavior in a Japanese Regular Classroom

ERIC Educational Resources Information Center

Baba, Chiharu; Tanaka-Matsumi, Junko

2011-01-01

Nondisruptive problem behaviors exist to a large extent in group-oriented Japanese regular classrooms. However, many children remain untreated. We implemented an antecedent-based functional behavioral assessment (FBA) and developed a behavioral support program for a first-grade boy who exhibited inattentive behavior in a Japanese regular…
Questions about Behavioral Function (QABF): Adaptation and Validation of the Spanish Version

ERIC Educational Resources Information Center

Simo-Pinatella, David; Alomar-Kurz, Elisabeth; Font-Roura, Josep; Gine, Climent; Matson, Johnny L.; Cifre, Ignacio

2013-01-01

People with intellectual disabilities (ID) often engage in problem behaviors, such as verbal or physical aggression, property destruction, or self-injury. These behaviors become a challenge for the families and for professionals. Functional behavioral assessment (FBA) is a method used to identify variables that influence or maintain challenging…
Multidimensional Functional Behaviour Assessment within a Problem Analysis Framework.

ERIC Educational Resources Information Center

Ryba, Ken; Annan, Jean

This paper presents a new approach to contextualized problem analysis developed for use with multimodal Functional Behaviour Assessment (FBA) at Massey University in Auckland, New Zealand. The aim of problem analysis is to simplify complex problems that are difficult to understand. It accomplishes this by providing a high order framework that can…
Transitioning Non-Traditional Students to an Undergraduate Business Program

ERIC Educational Resources Information Center

Bailey, April E.; Marsh, Michael T.

2010-01-01

This paper reports experiences of non-traditional students in a specially designed section of seminar course which was primarily designed for first-year traditional business students. The College of Business's BSN101, Foundations of Business Administration (FBA), is designed to serves as a course to assist the students with transitioning into the…
Implementing and Evaluating Effective Professional Development in Functional Behavioral Assessment in Rural Schools.

ERIC Educational Resources Information Center

Mitchem, Katherine; Richards, Ann; Wells, Deborah

The use of positive behavior supports (PBS) based on functional behavioral assessment (FBA) has produced dramatic improvements in problem behaviors of challenging students. This approach is a long-term strategy to reduce inappropriate behavior, teach more appropriate behavior, and provide contextual supports necessary for successful outcomes. Yet…
An Evidence-Driven, Solution-Focused Approach to Functional Behavior Assessment Report Writing

ERIC Educational Resources Information Center

Farmer, Ryan L.; Floyd, Randy G.

2016-01-01

School-based practitioners are to implement and report functional behavior assessments (FBAs) that are consistent with both the research literature and the law, both federal and state. However, the literature regarding how best to document the FBA process is underdeveloped. A review of applied behavior analytic and school psychology literature as…
Facilitating Effective Team-Based Functional Behavioral Assessments in Typical School Settings

ERIC Educational Resources Information Center

Park, Kristy Lee

2007-01-01

School systems face the challenge of effectively and efficiently addressing the disciplinary needs of their students and providing a safe environment conducive to learning. The 1997 and 2004 reauthorization of the Individuals With Disabilities Education Act (IDEA) mandates the use of functional behavioral assessment (FBA) for students who, because…
An Evaluation of the Relative Effectiveness of Function-Based Consequent and Antecedent Interventions in a Preschool Setting

ERIC Educational Resources Information Center

von Schulz, Jonna H.; Dufrene, Brad A.; LaBrot, Zachary C.; Tingstrom, Daniel H.; Olmi, D. Joe; Radley, Keith; Mitchell, Rachel; Maldonado, Aimee

2018-01-01

Although there is substantial functional behavioral assessment (FBA) literature suggesting that function-based interventions are effective for improving problem behavior, only a limited number of studies have examined the effectiveness of function-based antecedent versus consequent interventions. Additionally, although there has been a recent…
Respiratory-aspirated 35-mm hairpin successfully retrieved with a Teflon® snare system under fluoroscopic guidance via a split endotracheal tube: a useful technique in cases of failed extraction by bronchoscopy and avoiding the need for a thoracotomy.

PubMed

Gill, S S; Pease, R A; Ashwin, C J; Gill, S S; Tait, N P

2012-09-01

Respiratory foreign body aspiration (FBA) is a common global health problem requiring prompt recognition and early treatment to prevent potentially fatal complications. The majority of FBAs are due to organic objects and treatment is usually via either endoscopic or surgical extraction. FBA of a straight hairpin has been described as a unique entity in the literature, occurring most commonly in females, particularly during adolescence. In the process of inserting hairpins, the pins will typically be between the teeth with the head tilted backwards, while tying their hair with both hands. This position increases the risk of aspiration, particularly if there is any sudden coughing or laughing. To our knowledge, this is the first case report of a 35-mm straight metallic hairpin foreign body that has been successfully retrieved by a radiological snare system under fluoroscopic guidance. This was achieved with the use of a split endotracheal tube, and therefore avoided the need for a thoracotomy in an adolescent female patient.
Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.

PubMed

Toya, Yoshihiro; Shimizu, Hiroshi

2013-11-01

Rational engineering of metabolism is important for bio-production using microorganisms. Metabolic design based on in silico simulations and experimental validation of the metabolic state in the engineered strain helps in accomplishing systematic metabolic engineering. Flux balance analysis (FBA) is a method for the prediction of metabolic phenotype, and many applications have been developed using FBA to design metabolic networks. Elementary mode analysis (EMA) and ensemble modeling techniques are also useful tools for in silico strain design. The metabolome and flux distribution of the metabolic pathways enable us to evaluate the metabolic state and provide useful clues to improve target productivity. Here, we reviewed several computational applications for metabolic engineering by using genome-scale metabolic models of microorganisms. We also discussed the recent progress made in the field of metabolomics and (13)C-metabolic flux analysis techniques, and reviewed these applications pertaining to bio-production development. Because these in silico or experimental approaches have their respective advantages and disadvantages, the combined usage of these methods is complementary and effective for metabolic engineering. Copyright © 2013 Elsevier Inc. All rights reserved.
Systematic development and optimization of chemically defined medium supporting high cell density growth of Bacillus coagulans.

PubMed

Chen, Yu; Dong, Fengqing; Wang, Yonghong

2016-09-01

With determined components and experimental reducibility, the chemically defined medium (CDM) and the minimal chemically defined medium (MCDM) are used in many metabolism and regulation studies. This research aimed to develop the chemically defined medium supporting high cell density growth of Bacillus coagulans, which is a promising producer of lactic acid and other bio-chemicals. In this study, a systematic methodology combining the experimental technique with flux balance analysis (FBA) was proposed to design and simplify a CDM. The single omission technique and single addition technique were employed to determine the essential and stimulatory compounds, before the optimization of their concentrations by the statistical method. In addition, to improve the growth rationally, in silico omission and addition were performed by FBA based on the construction of a medium-size metabolic model of B. coagulans 36D1. Thus, CDMs were developed to obtain considerable biomass production of at least five B. coagulans strains, in which two model strains B. coagulans 36D1 and ATCC 7050 were involved.
Microalgal bioengineering for sustainable energy development: Recent transgenesis and metabolic engineering strategies.

PubMed

Banerjee, Chiranjib; Singh, Puneet Kumar; Shukla, Pratyoosh

2016-03-01

Exploring the efficiency of algae to produce remarkable products can be directly benefitted by studying its mechanism at systems level. Recent advents in biotechnology like flux balance analysis (FBA), genomics and in silico proteomics minimize the wet lab exertion. It is understood that FBA predicts the metabolic products, metabolic pathways and alternative pathway to maximize the desired product, and these are key components for microalgae bio-engineering. This review encompasses recent transgenesis techniques and metabolic engineering strategies applied to different microalgae for improving different traits. Further it also throws light on RNAi and riboswitch engineering based methods which may be advantageous for high throughput microalgal research. A valid and optimally designed microalga can be developed where every engineering strategies meet each other successfully and will definitely fulfill the market needs. It is also to be noted that Omics (viz. genetic and metabolic manipulation with bioinformatics) should be integrated to develop a strain which could prove to be a futuristic solution for sustainable development for energy. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Using foreground/background analysis to determine leaf and canopy chemistry

NASA Technical Reports Server (NTRS)

Pinzon, J. E.; Ustin, S. L.; Hart, Q. J.; Jacquemoud, S.; Smith, M. O.

1995-01-01

Spectral Mixture Analysis (SMA) has become a well established procedure for analyzing imaging spectrometry data, however, the technique is relatively insensitive to minor sources of spectral variation (e.g., discriminating stressed from unstressed vegetation and variations in canopy chemistry). Other statistical approaches have been tried e.g., stepwise multiple linear regression analysis to predict canopy chemistry. Grossman et al. reported that SMLR is sensitive to measurement error and that the prediction of minor chemical components are not independent of patterns observed in more dominant spectral components like water. Further, they observed that the relationships were strongly dependent on the mode of expressing reflectance (R, -log R) and whether chemistry was expressed on a weight (g/g) or are basis (g/sq m). Thus, alternative multivariate techniques need to be examined. Smith et al. reported a revised SMA that they termed Foreground/Background Analysis (FBA) that permits directing the analysis along any axis of variance by identifying vectors through the n-dimensional spectral volume orthonormal to each other. Here, we report an application of the FBA technique for the detection of canopy chemistry using a modified form of the analysis.

Advanced Stoichiometric Analysis of Metabolic Networks of Mammalian Systems

PubMed Central

Orman, Mehmet A.; Berthiaume, Francois; Androulakis, Ioannis P.; Ierapetritou, Marianthi G.

2013-01-01

Metabolic engineering tools have been widely applied to living organisms to gain a comprehensive understanding about cellular networks and to improve cellular properties. Metabolic flux analysis (MFA), flux balance analysis (FBA), and metabolic pathway analysis (MPA) are among the most popular tools in stoichiometric network analysis. Although application of these tools into well-known microbial systems is extensive in the literature, various barriers prevent them from being utilized in mammalian cells. Limited experimental data, complex regulatory mechanisms, and the requirement of more complex nutrient media are some major obstacles in mammalian cell systems. However, mammalian cells have been used to produce therapeutic proteins, to characterize disease states or related abnormal metabolic conditions, and to analyze the toxicological effects of some medicinally important drugs. Therefore, there is a growing need for extending metabolic engineering principles to mammalian cells in order to understand their underlying metabolic functions. In this review article, advanced metabolic engineering tools developed for stoichiometric analysis including MFA, FBA, and MPA are described. Applications of these tools in mammalian cells are discussed in detail, and the challenges and opportunities are highlighted. PMID:22196224
Vehicle tracking using fuzzy-based vehicle detection window with adaptive parameters

NASA Astrophysics Data System (ADS)

Chitsobhuk, Orachat; Kasemsiri, Watjanapong; Glomglome, Sorayut; Lapamonpinyo, Pipatphon

2018-04-01

In this paper, fuzzy-based vehicle tracking system is proposed. The proposed system consists of two main processes: vehicle detection and vehicle tracking. In the first process, the Gradient-based Adaptive Threshold Estimation (GATE) algorithm is adopted to provide the suitable threshold value for the sobel edge detection. The estimated threshold can be adapted to the changes of diverse illumination conditions throughout the day. This leads to greater vehicle detection performance compared to a fixed user's defined threshold. In the second process, this paper proposes the novel vehicle tracking algorithms namely Fuzzy-based Vehicle Analysis (FBA) in order to reduce the false estimation of the vehicle tracking caused by uneven edges of the large vehicles and vehicle changing lanes. The proposed FBA algorithm employs the average edge density and the Horizontal Moving Edge Detection (HMED) algorithm to alleviate those problems by adopting fuzzy rule-based algorithms to rectify the vehicle tracking. The experimental results demonstrate that the proposed system provides the high accuracy of vehicle detection about 98.22%. In addition, it also offers the low false detection rates about 3.92%.
A Novel Strategy for Selection and Validation of Reference Genes in Dynamic Multidimensional Experimental Design in Yeast

PubMed Central

Cankorur-Cetinkaya, Ayca; Dereli, Elif; Eraslan, Serpil; Karabekmez, Erkan; Dikicioglu, Duygu; Kirdar, Betul

2012-01-01

Background Understanding the dynamic mechanism behind the transcriptional organization of genes in response to varying environmental conditions requires time-dependent data. The dynamic transcriptional response obtained by real-time RT-qPCR experiments could only be correctly interpreted if suitable reference genes are used in the analysis. The lack of available studies on the identification of candidate reference genes in dynamic gene expression studies necessitates the identification and the verification of a suitable gene set for the analysis of transient gene expression response. Principal Findings In this study, a candidate reference gene set for RT-qPCR analysis of dynamic transcriptional changes in Saccharomyces cerevisiae was determined using 31 different publicly available time series transcriptome datasets. Ten of the twelve candidates (TPI1, FBA1, CCW12, CDC19, ADH1, PGK1, GCN4, PDC1, RPS26A and ARF1) we identified were not previously reported as potential reference genes. Our method also identified the commonly used reference genes ACT1 and TDH3. The most stable reference genes from this pool were determined as TPI1, FBA1, CDC19 and ACT1 in response to a perturbation in the amount of available glucose and as FBA1, TDH3, CCW12 and ACT1 in response to a perturbation in the amount of available ammonium. The use of these newly proposed gene sets outperformed the use of common reference genes in the determination of dynamic transcriptional response of the target genes, HAP4 and MEP2, in response to relaxation from glucose and ammonium limitations, respectively. Conclusions A candidate reference gene set to be used in dynamic real-time RT-qPCR expression profiling in yeast was proposed for the first time in the present study. Suitable pools of stable reference genes to be used under different experimental conditions could be selected from this candidate set in order to successfully determine the expression profiles for the genes of interest. PMID:22675547
Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools

PubMed Central

Reznik, Ed; Mehta, Pankaj; Segrè, Daniel

2013-01-01

Stoichiometric models of metabolism, such as flux balance analysis (FBA), are classically applied to predicting steady state rates - or fluxes - of metabolic reactions in genome-scale metabolic networks. Here we revisit the central assumption of FBA, i.e. that intracellular metabolites are at steady state, and show that deviations from flux balance (i.e. flux imbalances) are informative of some features of in vivo metabolite concentrations. Mathematically, the sensitivity of FBA to these flux imbalances is captured by a native feature of linear optimization, the dual problem, and its corresponding variables, known as shadow prices. First, using recently published data on chemostat growth of Saccharomyces cerevisae under different nutrient limitations, we show that shadow prices anticorrelate with experimentally measured degrees of growth limitation of intracellular metabolites. We next hypothesize that metabolites which are limiting for growth (and thus have very negative shadow price) cannot vary dramatically in an uncontrolled way, and must respond rapidly to perturbations. Using a collection of published datasets monitoring the time-dependent metabolomic response of Escherichia coli to carbon and nitrogen perturbations, we test this hypothesis and find that metabolites with negative shadow price indeed show lower temporal variation following a perturbation than metabolites with zero shadow price. Finally, we illustrate the broader applicability of flux imbalance analysis to other constraint-based methods. In particular, we explore the biological significance of shadow prices in a constraint-based method for integrating gene expression data with a stoichiometric model. In this case, shadow prices point to metabolites that should rise or drop in concentration in order to increase consistency between flux predictions and gene expression data. In general, these results suggest that the sensitivity of metabolic optima to violations of the steady state constraints carries biologically significant information on the processes that control intracellular metabolites in the cell. PMID:24009492
Effect of amino acid supplementation on titer and glycosylation distribution in hybridoma cell cultures-Systems biology-based interpretation using genome-scale metabolic flux balance model and multivariate data analysis.

PubMed

Reimonn, Thomas M; Park, Seo-Young; Agarabi, Cyrus D; Brorson, Kurt A; Yoon, Seongkyu

2016-09-01

Genome-scale flux balance analysis (FBA) is a powerful systems biology tool to characterize intracellular reaction fluxes during cell cultures. FBA estimates intracellular reaction rates by optimizing an objective function, subject to the constraints of a metabolic model and media uptake/excretion rates. A dynamic extension to FBA, dynamic flux balance analysis (DFBA), can calculate intracellular reaction fluxes as they change during cell cultures. In a previous study by Read et al. (2013), a series of informed amino acid supplementation experiments were performed on twelve parallel murine hybridoma cell cultures, and this data was leveraged for further analysis (Read et al., Biotechnol Prog. 2013;29:745-753). In order to understand the effects of media changes on the model murine hybridoma cell line, a systems biology approach is applied in the current study. Dynamic flux balance analysis was performed using a genome-scale mouse metabolic model, and multivariate data analysis was used for interpretation. The calculated reaction fluxes were examined using partial least squares and partial least squares discriminant analysis. The results indicate media supplementation increases product yield because it raises nutrient levels extending the growth phase, and the increased cell density allows for greater culture performance. At the same time, the directed supplementation does not change the overall metabolism of the cells. This supports the conclusion that product quality, as measured by glycoform assays, remains unchanged because the metabolism remains in a similar state. Additionally, the DFBA shows that metabolic state varies more at the beginning of the culture but less by the middle of the growth phase, possibly due to stress on the cells during inoculation. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1163-1173, 2016. © 2016 American Institute of Chemical Engineers.
Characterizing the optimal flux space of genome-scale metabolic reconstructions through modified latin-hypercube sampling.

PubMed

Chaudhary, Neha; Tøndel, Kristin; Bhatnagar, Rakesh; dos Santos, Vítor A P Martins; Puchałka, Jacek

2016-03-01

Genome-Scale Metabolic Reconstructions (GSMRs), along with optimization-based methods, predominantly Flux Balance Analysis (FBA) and its derivatives, are widely applied for assessing and predicting the behavior of metabolic networks upon perturbation, thereby enabling identification of potential novel drug targets and biotechnologically relevant pathways. The abundance of alternate flux profiles has led to the evolution of methods to explore the complete solution space aiming to increase the accuracy of predictions. Herein we present a novel, generic algorithm to characterize the entire flux space of GSMR upon application of FBA, leading to the optimal value of the objective (the optimal flux space). Our method employs Modified Latin-Hypercube Sampling (LHS) to effectively border the optimal space, followed by Principal Component Analysis (PCA) to identify and explain the major sources of variability within it. The approach was validated with the elementary mode analysis of a smaller network of Saccharomyces cerevisiae and applied to the GSMR of Pseudomonas aeruginosa PAO1 (iMO1086). It is shown to surpass the commonly used Monte Carlo Sampling (MCS) in providing a more uniform coverage for a much larger network in less number of samples. Results show that although many fluxes are identified as variable upon fixing the objective value, majority of the variability can be reduced to several main patterns arising from a few alternative pathways. In iMO1086, initial variability of 211 reactions could almost entirely be explained by 7 alternative pathway groups. These findings imply that the possibilities to reroute greater portions of flux may be limited within metabolic networks of bacteria. Furthermore, the optimal flux space is subject to change with environmental conditions. Our method may be a useful device to validate the predictions made by FBA-based tools, by describing the optimal flux space associated with these predictions, thus to improve them.
Functional Behavioral Assessment for a Boy with Duchenne Muscular Dystrophy and Problem Behavior: A Case Study from Greece

ERIC Educational Resources Information Center

Theodoridou, Zoe; Koutsoklenis, Athanasios

2013-01-01

This article focuses on the application of functional behavioral assessment (FBA) to design a positive behavior intervention (PBI) for a boy with Duchenne muscular dystrophy (DMD) who encounters serious difficulties at the mainstream school because of behavioral problems and physical limitations. After the definition of problem behavior and its…
Coping with Challenging Behaviours of Children with Autism: Effectiveness of Brief Training Workshop for Frontline Staff in Special Education Settings

ERIC Educational Resources Information Center

Ling, C. Y. M.; Mak, W. W. S.

2012-01-01

Background: The present study examined the effectiveness of three staff training elements: psychoeducation (PE) on autism, introduction of functional behavioural analysis (FBA) and emotional management (EM), on the reaction of challenging behaviours for frontline staff towards children with autism in Hong Kong special education settings. Methods:…
A Comparison of Functional Behavioral Assessment and Functional Analysis Methodology among Students with Mild Disabilities

ERIC Educational Resources Information Center

Lewis, Timothy J.; Mitchell, Barbara S.; Harvey, Kristin; Green, Ambra; McKenzie, Jennifer

2015-01-01

Functional behavioral assessment (FBA) and functional analyses (FA) are grounded in the applied behavior analysis principle that posits problem behavior is functionally related to the environment in which it occurs and is maintained by either providing access to reinforcing outcomes or allowing the individual to avoid or escape that which they…
The Role of the Replacement Behavior in Function-Based Intervention

ERIC Educational Resources Information Center

Reeves, Linda M.; Ferro, Jolenea B.; Umbreit, John; Liaupsin, Carl J.

2017-01-01

Three students with autism spectrum disorder (ASD) who displayed off-task behavior participated in a two-phase study. In Phase 1, a functional behavioral assessment (FBA) was conducted for each student. In addition, an assessment of each student's ability to perform the replacement behavior identified that none of the participants was able to do…
Exploring the Link among Behavior Intervention Plans, Treatment Integrity, and Student Outcomes under Natural Educational Conditions

ERIC Educational Resources Information Center

Cook, Clayton R.; Mayer, G. Roy; Wright, Diana Browning; Kraemer, Bonnie; Wallace, Michele D.; Dart, Evan; Collins, Tai; Restori, Alberto

2012-01-01

Several researchers have argued that the functional behavior assessment (FBA) and behavior intervention plan (BIP) mandates in the Individuals With Disabilities Education Act of 2004 have gone beyond the current research base. For instance, although BIPs have been shown to improve student outcomes when implemented with strict control and oversight…
When to Use Functional Behavioral Assessment? Best Practice vs. Legal Guidance

ERIC Educational Resources Information Center

von Ravensberg, Heidi; Blakely, Allison

2014-01-01

When to conduct a functional behavioral assessment (FBA) is a question answered by both best practice and the law. The special education field continues to improve the effectiveness and efficiency of the functional behavioral assessment, an evidence-based technology that is the basis of a behavior intervention plan (BIP) and a cornerstone of the…
Teacher Involvement in the Development of Function-Based Behaviour Intervention Plans for Students with Challenging Behaviour

ERIC Educational Resources Information Center

O'Neill, Sue; Stephenson, Jennifer

2009-01-01

This article examines literature published since 1997 on functional behaviour assessment (FBA) and behaviour intervention plans (BIPs), involving school-based personnel, for children identified as having or being at risk of emotional/behavioural disorder (E/BD) in school settings. Of interest was the level of involvement of school-based personnel…
The Use of a Functional Behavioral Assessment-Based Self Management Intervention for Students with Emotional/Behavioral Disorders

ERIC Educational Resources Information Center

Rasheed, Saleem A.; Fore, Cecil, III; Jones, Arthur; Smith, Latisha

2012-01-01

The research literature on the use of Functional Behavioral Assessments (FBA) to develop Behavior Intervention Plans (BIP) for students with emotional/behavioral disorders, who present problem classroom behaviors for use in the schools, is well documented. There are school-wide, district-wide, and state-wide plans that are currently being…
Are We on the Right Course? Lessons Learned about Current FBA/BIP Practices in Schools

ERIC Educational Resources Information Center

Van Acker, Richard; Boreson, Lynn; Gable, Robert A.; Potterton, Thomas

2005-01-01

Schools across the nation have been charged with the task of conducting functional behavioral assessments (FBAs) to aid in the development of behavior intervention plans (BIPs) to address the challenging behavior of students with special education needs. In response, schools have initiated efforts to provide the various members of their student…
Investigating host-pathogen behavior and their interaction using genome-scale metabolic network models.

PubMed

Sadhukhan, Priyanka P; Raghunathan, Anu

2014-01-01

Genome Scale Metabolic Modeling methods represent one way to compute whole cell function starting from the genome sequence of an organism and contribute towards understanding and predicting the genotype-phenotype relationship. About 80 models spanning all the kingdoms of life from archaea to eukaryotes have been built till date and used to interrogate cell phenotype under varying conditions. These models have been used to not only understand the flux distribution in evolutionary conserved pathways like glycolysis and the Krebs cycle but also in applications ranging from value added product formation in Escherichia coli to predicting inborn errors of Homo sapiens metabolism. This chapter describes a protocol that delineates the process of genome scale metabolic modeling for analysing host-pathogen behavior and interaction using flux balance analysis (FBA). The steps discussed in the process include (1) reconstruction of a metabolic network from the genome sequence, (2) its representation in a precise mathematical framework, (3) its translation to a model, and (4) the analysis using linear algebra and optimization. The methods for biological interpretations of computed cell phenotypes in the context of individual host and pathogen models and their integration are also discussed.
Comparing University Academic Performances of HSC Students at the Three Art-Based Faculties

ERIC Educational Resources Information Center

Ismail, Noor Azina; Othman, Azmah

2006-01-01

University Malaya enrolls students from all states in Malaysia as well as a small number of students from overseas. The objective of this paper is to investigate the effect of past performance on students at three faculties, namely, Faculty of Economics and Administration(FEA), Faculty of Business and Accounting(FBA) and Faculty of Arts and Social…
Identification and expression of fructose-1,6-bisphosphate aldolase genes and their relations to oil content in developing seeds of tea oil tree (Camellia oleifera)

USDA-ARS?s Scientific Manuscript database

Tea oil tree (Camellia oleifera, Co) provides a fine edible oil source in China. Tea oil from the seeds is very beneficial to human health. Fructose-1,6-bisphosphate aldolase (FBA) hydrolyzes fructose-1,6-bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, two critical metab...
Addressing Challenging Behaviours in the General Education Setting: Conducting a Teacher-Based Functional Behavioural Assessment (FBA)

ERIC Educational Resources Information Center

Moreno, Gerardo

2011-01-01

When a student demonstrates a challenging or problematic behaviour in the classroom, the climate and the instructional experience can change dramatically for both the students and the classroom teacher. Before resorting to sanctions and punitive consequences, there is a series of steps a classroom teacher can conduct to reduce and replace the…
Functional Behavioral Assessment and Students at Risk for or with Emotional Disabilities: Current Issues and Considerations

ERIC Educational Resources Information Center

Gable, Robert A.; Park, Kristy Lee; Scott, Terrance M.

2014-01-01

The use of functional behavioral assessment (FBA) is an effective tool to address a wide range of severe behavior problems of students at risk for or with emotional disabilities (ED). However, the transformation of a procedure proven effective under highly-controlled clinical conditions to a practical and effective strategy for use in applied…

You Can Help Every Provider Have a Better Understanding of Functional Behavior Assessment! A Review of the Website: Basic FBA to BSP

ERIC Educational Resources Information Center

Shultz, Gwendolyn Joy; Havens, Nathan; Gurney, Beth Newberry; Burt, Jon

2017-01-01

Managing problematic classroom behavior is a challenge for many teachers, regardless of population. The website, www.basicfba.com, designed by researchers at Portland State University, offers teachers and practitioners a wealth of materials to assist them in conducting and maintaining a functional behavior assessment and behavior support plan.…
The Shock and Vibration Digest. Volume 16, Number 5

DTIC Science & Technology

1984-05-01

Lu, Y.P. and Everstine, G.C., "More on Finite Element Modelling of Damped Composite 45. Narayanan, S., Verma, J.P., and Mallik , A.K., Systems," J...78-78-FBA, p 461 (1978). 46. Narayanan, S. and Mallik , A.K., "Free Vibrations of Thin Walled Open Section Beams with Con- 34. Lunden, R., "Damping of
Implementation of a Single Comprehensive Function-Based Intervention across Multiple Classrooms for a High School Student

ERIC Educational Resources Information Center

Whitford, Denise K.; Liaupsin, Carl J.; Umbreit, John; Ferro, Jolenea B.

2013-01-01

A comprehensive function-based intervention was developed to address the chronic, high levels of off-task behavior by a 15-year-old ninth grade Caucasian male with learning disabilities and ADHD. A descriptive FBA identified that the student's off-task behavior was reinforced by peer attention and task avoidance. Intervention involved the…
Commentary on Zirkel: Judicial Rulings Specific to FBAs or BIPs under the IDEA and Corollary State Laws--An Update

ERIC Educational Resources Information Center

Horner, Robert H.; Yell, Mitchell L.

2017-01-01

The authors discuss the journal article by Perry Zirkel on legal action in regard to functional behavioral assessment (FBA) and behavior intervention plans (BIPs). They contend that the Zirkel article opens larger questions that will be central to ongoing discussions at the national, state, district, school, and family levels. Such issues include…
A Comparison of Functional Behavior Assessment Methodologies with Young Children: Descriptive Methods and Functional Analysis

ERIC Educational Resources Information Center

Alter, Peter J.; Conroy, Maureen A.; Mancil, G. Rich; Haydon, Todd

2008-01-01

The use of functional behavior assessment (FBA) to guide the development of behavior intervention plans continues to increase since they were first mandated in IDEA (Individuals with Disabilities Education Act Amendments of 1997, 20 U.S.C. Section 1400 et seq, 1997). A variety of indirect and direct instruments have been developed to facilitate…
An enhanced genome-scale metabolic reconstruction of Streptomyces clavuligerus identifies novel strain improvement strategies.

PubMed

Toro, León; Pinilla, Laura; Avignone-Rossa, Claudio; Ríos-Estepa, Rigoberto

2018-05-01

In this work, we expanded and updated a genome-scale metabolic model of Streptomyces clavuligerus. The model includes 1021 genes and 1494 biochemical reactions; genome-reaction information was curated and new features related to clavam metabolism and to the biomass synthesis equation were incorporated. The model was validated using experimental data from the literature and simulations were performed to predict cellular growth and clavulanic acid biosynthesis. Flux balance analysis (FBA) showed that limiting concentrations of phosphate and an excess of ammonia accumulation are unfavorable for growth and clavulanic acid biosynthesis. The evaluation of different objective functions for FBA showed that maximization of ATP yields the best predictions for cellular behavior in continuous cultures, while the maximization of growth rate provides better predictions for batch cultures. Through gene essentiality analysis, 130 essential genes were found using a limited in silico media, while 100 essential genes were identified in amino acid-supplemented media. Finally, a strain design was carried out to identify candidate genes to be overexpressed or knocked out so as to maximize antibiotic biosynthesis. Interestingly, potential metabolic engineering targets, identified in this study, have not been tested experimentally.
Categorical discrimination of human body parts by magnetoencephalography

PubMed Central

Nakamura, Misaki; Yanagisawa, Takufumi; Okamura, Yumiko; Fukuma, Ryohei; Hirata, Masayuki; Araki, Toshihiko; Kamitani, Yukiyasu; Yorifuji, Shiro

2015-01-01

Humans recognize body parts in categories. Previous studies have shown that responses in the fusiform body area (FBA) and extrastriate body area (EBA) are evoked by the perception of the human body, when presented either as whole or as isolated parts. These responses occur approximately 190 ms after body images are visualized. The extent to which body-sensitive responses show specificity for different body part categories remains to be largely clarified. We used a decoding method to quantify neural responses associated with the perception of different categories of body parts. Nine subjects underwent measurements of their brain activities by magnetoencephalography (MEG) while viewing 14 images of feet, hands, mouths, and objects. We decoded categories of the presented images from the MEG signals using a support vector machine (SVM) and calculated their accuracy by 10-fold cross-validation. For each subject, a response that appeared to be a body-sensitive response was observed and the MEG signals corresponding to the three types of body categories were classified based on the signals in the occipitotemporal cortex. The accuracy in decoding body-part categories (with a peak at approximately 48%) was above chance (33.3%) and significantly higher than that for random categories. According to the time course and location, the responses are suggested to be body-sensitive and to include information regarding the body-part category. Finally, this non-invasive method can decode category information of a visual object with high temporal and spatial resolution and this result may have a significant impact in the field of brain–machine interface research. PMID:26582986
Categorical discrimination of human body parts by magnetoencephalography.

PubMed

Nakamura, Misaki; Yanagisawa, Takufumi; Okamura, Yumiko; Fukuma, Ryohei; Hirata, Masayuki; Araki, Toshihiko; Kamitani, Yukiyasu; Yorifuji, Shiro

2015-01-01

Humans recognize body parts in categories. Previous studies have shown that responses in the fusiform body area (FBA) and extrastriate body area (EBA) are evoked by the perception of the human body, when presented either as whole or as isolated parts. These responses occur approximately 190 ms after body images are visualized. The extent to which body-sensitive responses show specificity for different body part categories remains to be largely clarified. We used a decoding method to quantify neural responses associated with the perception of different categories of body parts. Nine subjects underwent measurements of their brain activities by magnetoencephalography (MEG) while viewing 14 images of feet, hands, mouths, and objects. We decoded categories of the presented images from the MEG signals using a support vector machine (SVM) and calculated their accuracy by 10-fold cross-validation. For each subject, a response that appeared to be a body-sensitive response was observed and the MEG signals corresponding to the three types of body categories were classified based on the signals in the occipitotemporal cortex. The accuracy in decoding body-part categories (with a peak at approximately 48%) was above chance (33.3%) and significantly higher than that for random categories. According to the time course and location, the responses are suggested to be body-sensitive and to include information regarding the body-part category. Finally, this non-invasive method can decode category information of a visual object with high temporal and spatial resolution and this result may have a significant impact in the field of brain-machine interface research.
The Use of Functional Behavioural Assessment for Students with Challenging Behaviours: Current Patterns and Experience of Australian Practitioners.

ERIC Educational Resources Information Center

O'Neill, Sue; Stephenson, Jennifer

2010-01-01

With the growing adoption of the Positive Behaviour Support (PBS) system state-wide in New South Wales, Australia, it was of interest to determine the readiness of behaviour specialists to conduct Functional Behaviour Assessments (FBA) as part of the third tier of School-wide PBS provision. This article presents the findings from a survey…
Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii.

PubMed

Boyle, Nanette R; Morgan, John A

2009-01-07

Photosynthetic organisms convert atmospheric carbon dioxide into numerous metabolites along the pathways to make new biomass. Aquatic photosynthetic organisms, which fix almost half of global inorganic carbon, have great potential: as a carbon dioxide fixation method, for the economical production of chemicals, or as a source for lipids and starch which can then be converted to biofuels. To harness this potential through metabolic engineering and to maximize production, a more thorough understanding of photosynthetic metabolism must first be achieved. A model algal species, C. reinhardtii, was chosen and the metabolic network reconstructed. Intracellular fluxes were then calculated using flux balance analysis (FBA). The metabolic network of primary metabolism for a green alga, C. reinhardtii, was reconstructed using genomic and biochemical information. The reconstructed network accounts for the intracellular localization of enzymes to three compartments and includes 484 metabolic reactions and 458 intracellular metabolites. Based on BLAST searches, one newly annotated enzyme (fructose-1,6-bisphosphatase) was added to the Chlamydomonas reinhardtii database. FBA was used to predict metabolic fluxes under three growth conditions, autotrophic, heterotrophic and mixotrophic growth. Biomass yields ranged from 28.9 g per mole C for autotrophic growth to 15 g per mole C for heterotrophic growth. The flux balance analysis model of central and intermediary metabolism in C. reinhardtii is the first such model for algae and the first model to include three metabolically active compartments. In addition to providing estimates of intracellular fluxes, metabolic reconstruction and modelling efforts also provide a comprehensive method for annotation of genome databases. As a result of our reconstruction, one new enzyme was annotated in the database and several others were found to be missing; implying new pathways or non-conserved enzymes. The use of FBA to estimate intracellular fluxes also provides flux values that can be used as a starting point for rational engineering of C. reinhardtii. From these initial estimates, it is clear that aerobic heterotrophic growth on acetate has a low yield on carbon, while mixotrophically and autotrophically grown cells are significantly more carbon efficient.
Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia

PubMed Central

Çakιr, Tunahan; Alsan, Selma; Saybaşιlι, Hale; Akιn, Ata; Ülgen, Kutlu Ö

2007-01-01

Background It is a daunting task to identify all the metabolic pathways of brain energy metabolism and develop a dynamic simulation environment that will cover a time scale ranging from seconds to hours. To simplify this task and make it more practicable, we undertook stoichiometric modeling of brain energy metabolism with the major aim of including the main interacting pathways in and between astrocytes and neurons. Model The constructed model includes central metabolism (glycolysis, pentose phosphate pathway, TCA cycle), lipid metabolism, reactive oxygen species (ROS) detoxification, amino acid metabolism (synthesis and catabolism), the well-known glutamate-glutamine cycle, other coupling reactions between astrocytes and neurons, and neurotransmitter metabolism. This is, to our knowledge, the most comprehensive attempt at stoichiometric modeling of brain metabolism to date in terms of its coverage of a wide range of metabolic pathways. We then attempted to model the basal physiological behaviour and hypoxic behaviour of the brain cells where astrocytes and neurons are tightly coupled. Results The reconstructed stoichiometric reaction model included 217 reactions (184 internal, 33 exchange) and 216 metabolites (183 internal, 33 external) distributed in and between astrocytes and neurons. Flux balance analysis (FBA) techniques were applied to the reconstructed model to elucidate the underlying cellular principles of neuron-astrocyte coupling. Simulation of resting conditions under the constraints of maximization of glutamate/glutamine/GABA cycle fluxes between the two cell types with subsequent minimization of Euclidean norm of fluxes resulted in a flux distribution in accordance with literature-based findings. As a further validation of our model, the effect of oxygen deprivation (hypoxia) on fluxes was simulated using an FBA-derivative approach, known as minimization of metabolic adjustment (MOMA). The results show the power of the constructed model to simulate disease behaviour on the flux level, and its potential to analyze cellular metabolic behaviour in silico. Conclusion The predictive power of the constructed model for the key flux distributions, especially central carbon metabolism and glutamate-glutamine cycle fluxes, and its application to hypoxia is promising. The resultant acceptable predictions strengthen the power of such stoichiometric models in the analysis of mammalian cell metabolism. PMID:18070347
In vivo and in silico determination of essential genes of Campylobacter jejuni.

PubMed

Metris, Aline; Reuter, Mark; Gaskin, Duncan J H; Baranyi, Jozsef; van Vliet, Arnoud H M

2011-11-01

In the United Kingdom, the thermophilic Campylobacter species C. jejuni and C. coli are the most frequent causes of food-borne gastroenteritis in humans. While campylobacteriosis is usually a relatively mild infection, it has a significant public health and economic impact, and possible complications include reactive arthritis and the autoimmune diseases Guillain-Barré syndrome. The rapid developments in "omics" technologies have resulted in the availability of diverse datasets allowing predictions of metabolism and physiology of pathogenic micro-organisms. When combined, these datasets may allow for the identification of potential weaknesses that can be used for development of new antimicrobials to reduce or eliminate C. jejuni and C. coli from the food chain. A metabolic model of C. jejuni was constructed using the annotation of the NCTC 11168 genome sequence, a published model of the related bacterium Helicobacter pylori, and extensive literature mining. Using this model, we have used in silico Flux Balance Analysis (FBA) to determine key metabolic routes that are essential for generating energy and biomass, thus creating a list of genes potentially essential for growth under laboratory conditions. To complement this in silico approach, candidate essential genes have been determined using a whole genome transposon mutagenesis method. FBA and transposon mutagenesis (both this study and a published study) predict a similar number of essential genes (around 200). The analysis of the intersection between the three approaches highlights the shikimate pathway where genes are predicted to be essential by one or more method, and tend to be network hubs, based on a previously published Campylobacter protein-protein interaction network, and could therefore be targets for novel antimicrobial therapy. We have constructed the first curated metabolic model for the food-borne pathogen Campylobacter jejuni and have presented the resulting metabolic insights. We have shown that the combination of in silico and in vivo approaches could point to non-redundant, indispensable genes associated with the well characterised shikimate pathway, and also genes of unknown function specific to C. jejuni, which are all potential novel Campylobacter intervention targets.
Human body perception and higher-level person perception are dissociated in early development.

PubMed

Slaughter, Virginia

2011-01-01

Abstract Developmental data support the proposal that human body perceptual processing is distinct from other aspects of person perception. Infants are sensitive to human bodily motion and attribute goals to human arm movements before they demonstrate recognition of human body structure. The developmental data suggest the possibility of bidirectional linkages between EBA- and FBA-mediated representations and these higher-level elements of person perception.
Acquisition: Direct Care Medical Services Contracts

DTIC Science & Technology

2004-06-24

System FAR Federal Acquisition Regulation FBA Franchise Business Activity FICA Federal Insurance Contributions Act FISC Fleet Industrial Supply Center...regarding the use of Franchise Business Activity contracts to forward fund appropriations from one fiscal year for work performed in the next fiscal year...2002 to 63 in FY 2003. 3 As discussed in Inspector General of the Department of Defense Report No. D-2003-113, “ Franchise Business Activity Contracts
Dynamic leaching behavior of geogenic As in soils after cement-based stabilization/solidification.

PubMed

Li, Jiang-Shan; Wang, Lei; Tsang, Daniel C W; Beiyuan, Jingzi; Poon, Chi Sun

2017-12-01

Cement-based stabilization/solidification (S/S) is a practical treatment approach for hazardous waste with anthropogenic As sources; however, its applicability for geogenic As-containing soil and the long-term leaching potential remain uncertain. In this study, semi-dynamic leaching test was performed to investigate the influence of S/S binders (cement blended with fuel ash (FA), furnace bottom ash (FBA), or ground granulated blast furnace slag (GGBS)) on the long-term leaching characteristics of geogenic As. The results showed that mineral admixtures with higher Ca content and pozzolanic activity were more effective in reducing the leached As concentrations. Thus, cement blended with FBA was inferior to other binders in suppressing the As leaching, while 20% replacement of ordinary Portland cement by GGBS was considered most feasible for the S/S treatment of As-containing soils. The leachability of geogenic As was suppressed by the encapsulation effect of solidified matrix and interlocking network of hydration products that were supported by scanning electron microscopy (SEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) results. The long-term leaching of geogenic As from the monolithic samples was diffusion-controlled. Increasing the Ca content in the samples led to a decrease in diffusion coefficient and an increase in feasibility for "controlled utilization" of the S/S-treated soils.
Bridging the gap between fluxomics and industrial biotechnology.

PubMed

Feng, Xueyang; Page, Lawrence; Rubens, Jacob; Chircus, Lauren; Colletti, Peter; Pakrasi, Himadri B; Tang, Yinjie J

2010-01-01

Metabolic flux analysis is a vital tool used to determine the ultimate output of cellular metabolism and thus detect biotechnologically relevant bottlenecks in productivity. ¹³C-based metabolic flux analysis (¹³C-MFA) and flux balance analysis (FBA) have many potential applications in biotechnology. However, noteworthy hurdles in fluxomics study are still present. First, several technical difficulties in both ¹³C-MFA and FBA severely limit the scope of fluxomics findings and the applicability of obtained metabolic information. Second, the complexity of metabolic regulation poses a great challenge for precise prediction and analysis of metabolic networks, as there are gaps between fluxomics results and other omics studies. Third, despite identified metabolic bottlenecks or sources of host stress from product synthesis, it remains difficult to overcome inherent metabolic robustness or to efficiently import and express nonnative pathways. Fourth, product yields often decrease as the number of enzymatic steps increases. Such decrease in yield may not be caused by rate-limiting enzymes, but rather is accumulated through each enzymatic reaction. Fifth, a high-throughput fluxomics tool hasnot been developed for characterizing nonmodel microorganisms and maximizing their application in industrial biotechnology. Refining fluxomics tools and understanding these obstacles will improve our ability to engineer highly efficient metabolic pathways in microbial hosts.
Metabolism and evolution: A comparative study of reconstructed genome-level metabolic networks

NASA Astrophysics Data System (ADS)

Almaas, Eivind

2008-03-01

The availability of high-quality annotations of sequenced genomes has made it possible to generate organism-specific comprehensive maps of cellular metabolism. Currently, more than twenty such metabolic reconstructions are publicly available, with the majority focused on bacteria. A typical metabolic reconstruction for a bacterium results in a complex network containing hundreds of metabolites (nodes) and reactions (links), while some even contain more than a thousand. The constrain-based optimization approach of flux-balance analysis (FBA) is used to investigate the functional characteristics of such large-scale metabolic networks, making it possible to estimate an organism's growth behavior in a wide variety of nutrient environments, as well as its robustness to gene loss. We have recently completed the genome-level metabolic reconstruction of Yersinia pseudotuberculosis, as well as the three Yersinia pestis biovars Antiqua, Mediaevalis, and Orientalis. While Y. pseudotuberculosis typically only causes fever and abdominal pain that can mimic appendicitis, the evolutionary closely related Y. pestis strains are the aetiological agents of the bubonic plague. In this presentation, I will discuss our results and conclusions from a comparative study on the evolution of metabolic function in the four Yersiniae networks using FBA and related techniques, and I will give particular focus to the interplay between metabolic network topology and evolutionary flexibility.
Dynamic flux balancing elucidates NAD(P)H production as limiting response to furfural inhibition in Saccharomyces cerevisiae.

PubMed

Pornkamol, Unrean; Franzen, Carl J

2015-08-01

Achieving efficient and economical lignocellulose-based bioprocess requires a robust organism tolerant to furfural, a major inhibitory compound present in lignocellulosic hydrolysate. The aim of this study was to develop a model that could generate quantitative descriptions of cell metabolism for elucidating the cell's adaptive response to furfural. Such a modelling tool could provide strategies for the design of more robust cells. A dynamic flux balance (dFBA) model of Saccharomyces cerevisiae was created by coupling a kinetic fermentation model with a previously published genome-scale stoichiometric model. The dFBA model was used for studying intracellular and extracellular flux responses to furfural perturbations under steady state and dynamic conditions. The predicted effects of furfural on dynamic flux profiles agreed well with previously published experimental results. The model showed that the yeast cell adjusts its metabolism in response to furfural challenge by increasing fluxes through the pentose phosphate pathway, TCA cycle, and proline and serine biosynthesis in order to meet the high demand of NAD(P)H cofactors. The model described here can be used to aid in systematic optimization of the yeast, as well as of the fermentation process, for efficient lignocellulosic ethanol production. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Modeling and Simulation of Optimal Resource Management during the Diurnal Cycle in Emiliania huxleyi by Genome-Scale Reconstruction and an Extended Flux Balance Analysis Approach.

PubMed

Knies, David; Wittmüß, Philipp; Appel, Sebastian; Sawodny, Oliver; Ederer, Michael; Feuer, Ronny

2015-10-28

The coccolithophorid unicellular alga Emiliania huxleyi is known to form large blooms, which have a strong effect on the marine carbon cycle. As a photosynthetic organism, it is subjected to a circadian rhythm due to the changing light conditions throughout the day. For a better understanding of the metabolic processes under these periodically-changing environmental conditions, a genome-scale model based on a genome reconstruction of the E. huxleyi strain CCMP 1516 was created. It comprises 410 reactions and 363 metabolites. Biomass composition is variable based on the differentiation into functional biomass components and storage metabolites. The model is analyzed with a flux balance analysis approach called diurnal flux balance analysis (diuFBA) that was designed for organisms with a circadian rhythm. It allows storage metabolites to accumulate or be consumed over the diurnal cycle, while keeping the structure of a classical FBA problem. A feature of this approach is that the production and consumption of storage metabolites is not defined externally via the biomass composition, but the result of optimal resource management adapted to the diurnally-changing environmental conditions. The model in combination with this approach is able to simulate the variable biomass composition during the diurnal cycle in proximity to literature data.
Developing Positive Behavioral Support for Students with Challenging Behaviors. From the Third CCBD Mini-Library Series, What Works for Children and Youth with E/BD: Linking Yesterday and Today with Tomorrow.

ERIC Educational Resources Information Center

Sugai, George, Ed.; Lewis, Timothy J., Ed.

This monograph is a guide to positive behavioral intervention and support (PBIS) and functional behavioral assessment (FBA) in the special education of students with behavior disorders as emphasized in the 1997 amendments to the Individuals with Disabilities Act (IDEA 97). An introduction explains that positive behavioral support represents the…

Testability Design Rating System: Testability Handbook. Volume 1

DTIC Science & Technology

1992-02-01

4-10 4.7.5 Summary of False BIT Alarms (FBA) ............................. 4-10 4.7.6 Smart BIT Technique...Circuit Board PGA Pin Grid Array PLA Programmable Logic Array PLD Programmable Logic Device PN Pseudo-Random Number PREDICT Probabilistic Estimation of...11 4.7.6 Smart BIT ( reference: RADC-TR-85-198). " Smart " BIT is a term given to BIT circuitry in a system LRU which includes dedicated processor/memory
An evaluation-guided approach for effective data visualization on tablets

NASA Astrophysics Data System (ADS)

Games, Peter S.; Joshi, Alark

2015-01-01

There is a rising trend of data analysis and visualization tasks being performed on a tablet device. Apps with interactive data visualization capabilities are available for a wide variety of domains. We investigate whether users grasp how to effectively interpret and interact with visualizations. We conducted a detailed user evaluation to study the abilities of individuals with respect to analyzing data on a tablet through an interactive visualization app. Based upon the results of the user evaluation, we find that most subjects performed well at understanding and interacting with simple visualizations, specifically tables and line charts. A majority of the subjects struggled with identifying interactive widgets, recognizing interactive widgets with overloaded functionality, and understanding visualizations which do not display data for sorted attributes. Based on our study, we identify guidelines for designers and developers of mobile data visualization apps that include recommendations for effective data representation and interaction.
Integrating visualization and interaction research to improve scientific workflows.

PubMed

Keefe, Daniel F

2010-01-01

Scientific-visualization research is, nearly by necessity, interdisciplinary. In addition to their collaborators in application domains (for example, cell biology), researchers regularly build on close ties with disciplines related to visualization, such as graphics, human-computer interaction, and cognitive science. One of these ties is the connection between visualization and interaction research. This isn't a new direction for scientific visualization (see the "Early Connections" sidebar). However, momentum recently seems to be increasing toward integrating visualization research (for example, effective visual presentation of data) with interaction research (for example, innovative interactive techniques that facilitate manipulating and exploring data). We see evidence of this trend in several places, including the visualization literature and conferences.
Active Immunizations with Peptide-DC Vaccines and Passive Transfer with Antibodies Protect Neutropenic Mice against Disseminated Candidiasis

PubMed Central

Xin, Hong

2015-01-01

We previously report that peptide-pulsed dendritic cell (DC) vaccination, which targeting two peptides (Fba and Met6) expressed on the cell surface of Candida albicans, can induce high degree of protection against disseminated candidiasis in immunocompetent mice. Passive transfer of immune sera from the peptide immunized mice or peptide-related monoclonal antibodies demonstrated that protection was medicated by peptide-specific antibodies. In this study the efficacy of active and passive immunization against disseminated candidiasis was tested in mice with cyclophosphamide-induced neutropenia. Peptide-DC vaccines were given to mice prior to induction of neutropenia. We show active immunization with either Fba or Met6 peptide-DC vaccine significantly improved the survival and reduced the fungal burden of disseminated candidiasis in those immunocompromised mice. Importantly, we show that administration of two protective monoclonal antibodies also protect neutropenic mice against the disease, implying possibility of developing a successful passive immunotherapy strategy to treat the disease and protect against disseminated candidiasis. The results of this study are crucial as they address the fundamental questions as to whether the synthetic peptide vaccine induced immunity protects the host during a neutropenic episode. We anticipate that this peptide-vaccine study will serve as the foundation of future investigations into new peptide vaccines comprised of cell surface peptides from other medically important Candida species, as well as other fungi. PMID:26620842
A Proteomic Approach to Investigate the Drought Response in the Orphan Crop Eragrostis tef.

PubMed

Kamies, Rizqah; Farrant, Jill M; Tadele, Zerihun; Cannarozzi, Gina; Rafudeen, Mohammed Suhail

2017-11-15

The orphan crop, Eragrostis tef , was subjected to controlled drought conditions to observe the physiological parameters and proteins changing in response to dehydration stress. Physiological measurements involving electrolyte leakage, chlorophyll fluorescence and ultra-structural analysis showed tef plants tolerated water loss to 50% relative water content (RWC) before adverse effects in leaf tissues were observed. Proteomic analysis using isobaric tag for relative and absolute quantification (iTRAQ) mass spectrometry and appropriate database searching enabled the detection of 5727 proteins, of which 211 proteins, including a number of spliced variants, were found to be differentially regulated with the imposed stress conditions. Validation of the iTRAQ dataset was done with selected stress-related proteins, fructose-bisphosphate aldolase (FBA) and the protective antioxidant proteins, monodehydroascorbate reductase (MDHAR) and peroxidase (POX). Western blot analyses confirmed protein presence and showed increased protein abundance levels during water deficit while enzymatic activity for FBA, MDHAR and POX increased at selected RWC points. Gene ontology (GO)-term enrichment and analysis revealed terms involved in biotic and abiotic stress response, signaling, transport, cellular homeostasis and pentose metabolic processes, to be enriched in tef upregulated proteins, while terms linked to reactive oxygen species (ROS)-producing processes under water-deficit, such as photosynthesis and associated light harvesting reactions, manganese transport and homeostasis, the synthesis of sugars and cell wall catabolism and modification, to be enriched in tef downregulated proteins.
A micro-flow-batch analyzer with solenoid micro-pumps for the photometric determination of iodate in table salt.

PubMed

Lima, Marcelo B; Barreto, Inakã S; Andrade, Stéfani Iury E; Almeida, Luciano F; Araújo, Mário C U

2012-10-15

In this study, a micro-flow-batch analyzer (μFBA) with solenoid micro-pumps for the photometric determination of iodate in table salt is described. The method is based on the reaction of iodate with iodide to form molecular iodine followed by the reaction with N,N-diethyl-p-phenylenediamine (DPD). The analytical signal was measured at 520 nm using a green LED integrated into the μFBA built in the urethane-acrylate resin. The analytical curve for iodate was linear in the range of 0.01-10.0 mg L(-1) with a correlation coefficient of 0.997. The limit of detection and relative standard deviation were estimated at 0.004 mg L(-1) and<1.5% (n=3), respectively. The accuracy was assessed through recovery test (97.6-103.5%) and independent analysis by a conventional titrimetric method. Comparing this technique with the conventional method, no statistically significant differences were observed when applying the paired t-test at a 95% confidence level. The proposed microsystem using solenoid micro-pumps presented satisfactory robustness and high sampling rate (170 h(-1)), with a low reagents consumption and a low cost to build the device. The proposed microsystem is a new alternative for automatic determination of iodate in table salt, comparing satisfactory to the recently flow system. Copyright © 2012 Elsevier B.V. All rights reserved.
Visual adaptation dominates bimodal visual-motor action adaptation

PubMed Central

de la Rosa, Stephan; Ferstl, Ylva; Bülthoff, Heinrich H.

2016-01-01

A long standing debate revolves around the question whether visual action recognition primarily relies on visual or motor action information. Previous studies mainly examined the contribution of either visual or motor information to action recognition. Yet, the interaction of visual and motor action information is particularly important for understanding action recognition in social interactions, where humans often observe and execute actions at the same time. Here, we behaviourally examined the interaction of visual and motor action recognition processes when participants simultaneously observe and execute actions. We took advantage of behavioural action adaptation effects to investigate behavioural correlates of neural action recognition mechanisms. In line with previous results, we find that prolonged visual exposure (visual adaptation) and prolonged execution of the same action with closed eyes (non-visual motor adaptation) influence action recognition. However, when participants simultaneously adapted visually and motorically – akin to simultaneous execution and observation of actions in social interactions - adaptation effects were only modulated by visual but not motor adaptation. Action recognition, therefore, relies primarily on vision-based action recognition mechanisms in situations that require simultaneous action observation and execution, such as social interactions. The results suggest caution when associating social behaviour in social interactions with motor based information. PMID:27029781
The effect of bi-terminal PEGylation of an integrin α vβ 6-targeted 18F peptide on pharmacokinetics and tumor uptake

DOE PAGES

Hausner, Sven H.; Bauer, Nadine; Hu, Lina Y.; ...

2015-03-26

Radiotracers based on the peptide A20FMDV2 selectively target the cell surface receptor integrin α vβ 6. This integrin has been identified as a prognostic indicator correlating with the severity of disease for several challenging malignancies. In previous studies of A20FMDV2 peptides labeled with 4- 18F-fluorobenzoic acid ( 18F-FBA), we have shown that the introduction of poly(ethylene glycol) (PEG) improves pharmacokinetics, including increased uptake in α vβ 6-expressing tumors. The present study evaluated the effect of site-specific C-terminal or dual (N- and C-terminal) PEGylation, yielding 18F-FBA-A20FMDV2-PEG 28 (4) and 18F-FBA-PEG 28-A20FMDV2-PEG 28 (5), on α vβ 6-targeted tumor uptake and pharmacokinetics.more » The results are compared with 18F-FBA–labeled A20FMDV2 radiotracers (1–3) bearing either no PEG or different PEG units at the N terminus. The radiotracers were prepared and radiolabeled on solid phase. Using 3 cell lines, DX3puroβ6 (α vβ 6+), DX3puro (α vβ 6–), and BxPC-3 (α vβ 6+), we evaluated the radiotracers in vitro (serum stability; cell binding and internalization) and in vivo in mouse models bearing paired DX3puroβ6–DX3puro and, for 5, BxPC-3 xenografts. Here, the size and location of the PEG units significantly affected α vβ 6 targeting and pharmacokinetics. Although the C-terminally PEGylated 4 showed some improvements over the un-PEGylated 18F-FBA-A20FMDV2 (1), it was the bi-terminally PEGylated 5 that displayed the more favorable combination of high α vβ 6 affinity, selectivity, and pharmacokinetic profile. In vitro, 5 bound to α vβ 6-expressing DX3puroβ6 and BxPC-3 cells with 60.5% ± 3.3% and 48.8% ± 8.3%, respectively, with a significant fraction of internalization (37.2% ± 4.0% and 37.6% ± 4.1% of total radioactivity, respectively). By comparison, in the DX3puro control 5 showed only 3.0% ± 0.5% binding and 0.9% ± 0.2% internalization. In vivo, 5 maintained high, α vβ 6-directed binding in the paired DX3puroβ6–DX3puro model (1 h: DX3puroβ6, 2.3 ± 0.2 percentage injected dose per gram [%ID/g]; DX3puroβ6/DX3puro ratio, 6.5:1; 4 h: 10.7:1). In the pancreatic BxPC-3 model, uptake was 4.7 ± 0.9 %ID/g (1 h) despite small tumor sizes (20–80 mg). In conclusion, the bi-PEGylated radiotracer 5 showed a greatly improved pharmacokinetic profile, beyond what was predicted from individual N- or C-terminal PEGylation. It appears that the 2 PEG units acted synergistically to result in an improved metabolic profile including high α vβ 6+ tumor uptake and retention.« less
The effect of bi-terminal PEGylation of an integrin α vβ 6-targeted 18F peptide on pharmacokinetics and tumor uptake

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

Hausner, Sven H.; Bauer, Nadine; Hu, Lina Y.

Radiotracers based on the peptide A20FMDV2 selectively target the cell surface receptor integrin α vβ 6. This integrin has been identified as a prognostic indicator correlating with the severity of disease for several challenging malignancies. In previous studies of A20FMDV2 peptides labeled with 4- 18F-fluorobenzoic acid ( 18F-FBA), we have shown that the introduction of poly(ethylene glycol) (PEG) improves pharmacokinetics, including increased uptake in α vβ 6-expressing tumors. The present study evaluated the effect of site-specific C-terminal or dual (N- and C-terminal) PEGylation, yielding 18F-FBA-A20FMDV2-PEG 28 (4) and 18F-FBA-PEG 28-A20FMDV2-PEG 28 (5), on α vβ 6-targeted tumor uptake and pharmacokinetics.more » The results are compared with 18F-FBA–labeled A20FMDV2 radiotracers (1–3) bearing either no PEG or different PEG units at the N terminus. The radiotracers were prepared and radiolabeled on solid phase. Using 3 cell lines, DX3puroβ6 (α vβ 6+), DX3puro (α vβ 6–), and BxPC-3 (α vβ 6+), we evaluated the radiotracers in vitro (serum stability; cell binding and internalization) and in vivo in mouse models bearing paired DX3puroβ6–DX3puro and, for 5, BxPC-3 xenografts. Here, the size and location of the PEG units significantly affected α vβ 6 targeting and pharmacokinetics. Although the C-terminally PEGylated 4 showed some improvements over the un-PEGylated 18F-FBA-A20FMDV2 (1), it was the bi-terminally PEGylated 5 that displayed the more favorable combination of high α vβ 6 affinity, selectivity, and pharmacokinetic profile. In vitro, 5 bound to α vβ 6-expressing DX3puroβ6 and BxPC-3 cells with 60.5% ± 3.3% and 48.8% ± 8.3%, respectively, with a significant fraction of internalization (37.2% ± 4.0% and 37.6% ± 4.1% of total radioactivity, respectively). By comparison, in the DX3puro control 5 showed only 3.0% ± 0.5% binding and 0.9% ± 0.2% internalization. In vivo, 5 maintained high, α vβ 6-directed binding in the paired DX3puroβ6–DX3puro model (1 h: DX3puroβ6, 2.3 ± 0.2 percentage injected dose per gram [%ID/g]; DX3puroβ6/DX3puro ratio, 6.5:1; 4 h: 10.7:1). In the pancreatic BxPC-3 model, uptake was 4.7 ± 0.9 %ID/g (1 h) despite small tumor sizes (20–80 mg). In conclusion, the bi-PEGylated radiotracer 5 showed a greatly improved pharmacokinetic profile, beyond what was predicted from individual N- or C-terminal PEGylation. It appears that the 2 PEG units acted synergistically to result in an improved metabolic profile including high α vβ 6+ tumor uptake and retention.« less
Beyond Control Panels: Direct Manipulation for Visual Analytics

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

Endert, Alexander; Bradel, Lauren; North, Chris

2013-07-19

Information Visualization strives to provide visual representations through which users can think about and gain insight into information. By leveraging the visual and cognitive systems of humans, complex relationships and phenomena occurring within datasets can be uncovered by exploring information visually. Interaction metaphors for such visualizations are designed to enable users direct control over the filters, queries, and other parameters controlling how the data is visually represented. Through the evolution of information visualization, more complex mathematical and data analytic models are being used to visualize relationships and patterns in data – creating the field of Visual Analytics. However, the expectationsmore » for how users interact with these visualizations has remained largely unchanged – focused primarily on the direct manipulation of parameters of the underlying mathematical models. In this article we present an opportunity to evolve the methodology for user interaction from the direct manipulation of parameters through visual control panels, to interactions designed specifically for visual analytic systems. Instead of focusing on traditional direct manipulation of mathematical parameters, the evolution of the field can be realized through direct manipulation within the visual representation – where users can not only gain insight, but also interact. This article describes future directions and research challenges that fundamentally change the meaning of direct manipulation with regards to visual analytics, advancing the Science of Interaction.« less
Low-energy Scattering of Positronium by Atoms

NASA Technical Reports Server (NTRS)

Ray, Hasi

2007-01-01

The survey reports theoretical studies involving positronium (Ps) - atom scattering. Investigations carried out in last few decades have been briefly reviewed in this article. A brief description of close-coupling approximation (CCA), the first-Born approximation (FBA) and the Born-Oppenheimer approximation (BOA) for Ps-Atom systems are made. The CCA codes of Ray et a1 [1-6] are reinvestigated using very fine mesh-points to search for resonances. The article advocates the need for an extended basis set & a systematic study using CCAs.
Interaction Junk: User Interaction-Based Evaluation of Visual Analytic Systems

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

Endert, Alexander; North, Chris

2012-10-14

With the growing need for visualization to aid users in understanding large, complex datasets, the ability for users to interact and explore these datasets is critical. As visual analytic systems have advanced to leverage powerful computational models and data analytics capabilities, the modes by which users engage and interact with the information are limited. Often, users are taxed with directly manipulating parameters of these models through traditional GUIs (e.g., using sliders to directly manipulate the value of a parameter). However, the purpose of user interaction in visual analytic systems is to enable visual data exploration – where users can focusmore » on their task, as opposed to the tool or system. As a result, users can engage freely in data exploration and decision-making, for the purpose of gaining insight. In this position paper, we discuss how evaluating visual analytic systems can be approached through user interaction analysis, where the goal is to minimize the cognitive translation between the visual metaphor and the mode of interaction (i.e., reducing the “Interactionjunk”). We motivate this concept through a discussion of traditional GUIs used in visual analytics for direct manipulation of model parameters, and the importance of designing interactions the support visual data exploration.« less
An Exploratory Study of Interactivity in Visualization Tools: "Flow" of Interaction

ERIC Educational Resources Information Center

Liang, Hai-Ning; Parsons, Paul C.; Wu, Hsien-Chi; Sedig, Kamran

2010-01-01

This paper deals with the design of interactivity in visualization tools. There are several factors that can be used to guide the analysis and design of the interactivity of these tools. One such factor is flow, which is concerned with the duration of interaction with visual representations of information--interaction being the actions performed…
Novel Interactome of Saccharomyces cerevisiae Myosin Type II Identified by a Modified Integrated Membrane Yeast Two-Hybrid (iMYTH) Screen.

PubMed

Santiago, Ednalise; Akamine, Pearl; Snider, Jamie; Wong, Victoria; Jessulat, Matthew; Deineko, Viktor; Gagarinova, Alla; Aoki, Hiroyuki; Minic, Zoran; Phanse, Sadhna; San Antonio, Andrea; Cubano, Luis A; Rymond, Brian C; Babu, Mohan; Stagljar, Igor; Rodriguez-Medina, Jose R

2016-05-03

Nonmuscle myosin type II (Myo1p) is required for cytokinesis in the budding yeast Saccharomyces cerevisiae Loss of Myo1p activity has been associated with growth abnormalities and enhanced sensitivity to osmotic stress, making it an appealing antifungal therapeutic target. The Myo1p tail-only domain was previously reported to have functional activity equivalent to the full-length Myo1p whereas the head-only domain did not. Since Myo1p tail-only constructs are biologically active, the tail domain must have additional functions beyond its previously described role in myosin dimerization or trimerization. The identification of new Myo1p-interacting proteins may shed light on the other functions of the Myo1p tail domain. To identify novel Myo1p-interacting proteins, and determine if Myo1p can serve as a scaffold to recruit proteins to the bud neck during cytokinesis, we used the integrated split-ubiquitin membrane yeast two-hybrid (iMYTH) system. Myo1p was iMYTH-tagged at its C-terminus, and screened against both cDNA and genomic prey libraries to identify interacting proteins. Control experiments showed that the Myo1p-bait construct was appropriately expressed, and that the protein colocalized to the yeast bud neck. Thirty novel Myo1p-interacting proteins were identified by iMYTH. Eight proteins were confirmed by coprecipitation (Ape2, Bzz1, Fba1, Pdi1, Rpl5, Tah11, and Trx2) or mass spectrometry (AP-MS) (Abp1). The novel Myo1p-interacting proteins identified come from a range of different processes, including cellular organization and protein synthesis. Actin assembly/disassembly factors such as the SH3 domain protein Bzz1 and the actin-binding protein Abp1 represent likely Myo1p interactions during cytokinesis. Copyright © 2016 Santiago et al.
Effects of visual and verbal interaction on unintentional interpersonal coordination.

PubMed

Richardson, Michael J; Marsh, Kerry L; Schmidt, R C

2005-02-01

Previous research has demonstrated that people's movements can become unintentionally coordinated during interpersonal interaction. The current study sought to uncover the degree to which visual and verbal (conversation) interaction constrains and organizes the rhythmic limb movements of coactors. Two experiments were conducted in which pairs of participants completed an interpersonal puzzle task while swinging handheld pendulums with instructions that minimized intentional coordination but facilitated either visual or verbal interaction. Cross-spectral analysis revealed a higher degree of coordination for conditions in which the pairs were visually coupled. In contrast, verbal interaction alone was not found to provide a sufficient medium for unintentional coordination to occur, nor did it enhance the unintentional coordination that emerged during visual interaction. The results raise questions concerning differences between visual and verbal informational linkages during interaction and how these differences may affect interpersonal movement production and its coordination.
Interactive Learning System "VisMis" for Scientific Visualization Course

ERIC Educational Resources Information Center

Zhu, Xiaoming; Sun, Bo; Luo, Yanlin

2018-01-01

Now visualization courses have been taught at universities around the world. Keeping students motivated and actively engaged in this course can be a challenging task. In this paper we introduce our developed interactive learning system called VisMis (Visualization and Multi-modal Interaction System) for postgraduate scientific visualization course…
Active immunizations with peptide-DC vaccines and passive transfer with antibodies protect neutropenic mice against disseminated candidiasis.

PubMed

Xin, Hong

2016-01-04

We previously report that peptide-pulsed dendritic cell (DC) vaccination, which targeting two peptides (Fba and Met6) expressed on the cell surface of Candida albicans, can induce high degree of protection against disseminated candidiasis in immunocompetent mice. Passive transfer of immune sera from the peptide immunized mice or peptide-related monoclonal antibodies demonstrated that protection was medicated by peptide-specific antibodies. In this study the efficacy of active and passive immunization against disseminated candidiasis was tested in mice with cyclophosphamide-induced neutropenia. Peptide-DC vaccines were given to mice prior to induction of neutropenia. We show active immunization with either Fba or Met6 peptide-DC vaccine significantly improved the survival and reduced the fungal burden of disseminated candidiasis in those immunocompromised mice. Importantly, we show that administration of two protective monoclonal antibodies also protect neutropenic mice against the disease, implying possibility of developing a successful passive immunotherapy strategy to treat the disease and protect against disseminated candidiasis. The results of this study are crucial as they address the fundamental questions as to whether the synthetic peptide vaccine induced immunity protects the host during a neutropenic episode. We anticipate that this peptide-vaccine study will serve as the foundation of future investigations into new peptide vaccines comprised of cell surface peptides from other medically important Candida species, as well as other fungi. Copyright © 2015 Elsevier Ltd. All rights reserved.
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm.

PubMed

Xie, Zhengwei; Zhang, Tianyu; Ouyang, Qi

2018-02-01

One of the long-expected goals of genome-scale metabolic modelling is to evaluate the influence of the perturbed enzymes on flux distribution. Both ordinary differential equation (ODE) models and constraint-based models, like Flux balance analysis (FBA), lack the capacity to perform metabolic control analysis (MCA) for large-scale networks. In this study, we developed a hyper-cube shrink algorithm (HCSA) to incorporate the enzymatic properties into the FBA model by introducing a pseudo reaction V constrained by enzymatic parameters. Our algorithm uses the enzymatic information quantitatively rather than qualitatively. We first demonstrate the concept by applying HCSA to a simple three-node network, whereby we obtained a good correlation between flux and enzyme abundance. We then validate its prediction by comparison with ODE and with a synthetic network producing voilacein and analogues in Saccharomyces cerevisiae. We show that HCSA can mimic the state-state results of ODE. Finally, we show its capability of predicting the flux distribution in genome-scale networks by applying it to sporulation in yeast. We show the ability of HCSA to operate without biomass flux and perform MCA to determine rate-limiting reactions. Algorithm was implemented by Matlab and C ++. The code is available at https://github.com/kekegg/HCSA. xiezhengwei@hsc.pku.edu.cn or qi@pku.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
Is chloroplastic class IIA aldolase a marine enzyme?

PubMed

Miyasaka, Hitoshi; Ogata, Takeru; Tanaka, Satoshi; Ohama, Takeshi; Kano, Sanae; Kazuhiro, Fujiwara; Hayashi, Shuhei; Yamamoto, Shinjiro; Takahashi, Hiro; Matsuura, Hideyuki; Hirata, Kazumasa

2016-11-01

Expressed sequence tag analyses revealed that two marine Chlorophyceae green algae, Chlamydomonas sp. W80 and Chlamydomonas sp. HS5, contain genes coding for chloroplastic class IIA aldolase (fructose-1, 6-bisphosphate aldolase: FBA). These genes show robust monophyly with those of the marine Prasinophyceae algae genera Micromonas, Ostreococcus and Bathycoccus, indicating that the acquisition of this gene through horizontal gene transfer by an ancestor of the green algal lineage occurred prior to the divergence of the core chlorophytes (Chlorophyceae and Trebouxiophyceae) and the prasinophytes. The absence of this gene in some freshwater chlorophytes, such as Chlamydomonas reinhardtii, Volvox carteri, Chlorella vulgaris, Chlorella variabilis and Coccomyxa subellipsoidea, can therefore be explained by the loss of this gene somewhere in the evolutionary process. Our survey on the distribution of this gene in genomic and transcriptome databases suggests that this gene occurs almost exclusively in marine algae, with a few exceptions, and as such, we propose that chloroplastic class IIA FBA is a marine environment-adapted enzyme. This hypothesis was also experimentally tested using Chlamydomonas W80, for which we found that the transcript levels of this gene to be significantly lower under low-salt (that is, simulated terrestrial) conditions. Expression analyses of transcriptome data for two algae, Prymnesium parvum and Emiliania huxleyi, taken from the Sequence Read Archive database also indicated that the expression of this gene under terrestrial conditions (low NaCl and low sulfate) is significantly downregulated. Thus, these experimental and transcriptome data provide support for our hypothesis.
A Method to Constrain Genome-Scale Models with 13C Labeling Data

PubMed Central

García Martín, Héctor; Kumar, Vinay Satish; Weaver, Daniel; Ghosh, Amit; Chubukov, Victor; Mukhopadhyay, Aindrila; Arkin, Adam; Keasling, Jay D.

2015-01-01

Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from 13C labeling experiments and genome-scale models. The data from 13C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA). This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by 13C labeling data. A comparison shows that the results of this new method are similar to those found through 13C Metabolic Flux Analysis (13C MFA) for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA) flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems. PMID:26379153

Fluxes through plant metabolic networks: measurements, predictions, insights and challenges.

PubMed

Kruger, Nicholas J; Ratcliffe, R George

2015-01-01

Although the flows of material through metabolic networks are central to cell function, they are not easy to measure other than at the level of inputs and outputs. This is particularly true in plant cells, where the network spans multiple subcellular compartments and where the network may function either heterotrophically or photoautotrophically. For many years, kinetic modelling of pathways provided the only method for describing the operation of fragments of the network. However, more recently, it has become possible to map the fluxes in central carbon metabolism using the stable isotope labelling techniques of metabolic flux analysis (MFA), and to predict intracellular fluxes using constraints-based modelling procedures such as flux balance analysis (FBA). These approaches were originally developed for the analysis of microbial metabolism, but over the last decade, they have been adapted for the more demanding analysis of plant metabolic networks. Here, the principal features of MFA and FBA as applied to plants are outlined, followed by a discussion of the insights that have been gained into plant metabolic networks through the application of these time-consuming and non-trivial methods. The discussion focuses on how a system-wide view of plant metabolism has increased our understanding of network structure, metabolic perturbations and the provision of reducing power and energy for cell function. Current methodological challenges that limit the scope of plant MFA are discussed and particular emphasis is placed on the importance of developing methods for cell-specific MFA.
Is chloroplastic class IIA aldolase a marine enzyme?

PubMed Central

Miyasaka, Hitoshi; Ogata, Takeru; Tanaka, Satoshi; Ohama, Takeshi; Kano, Sanae; Kazuhiro, Fujiwara; Hayashi, Shuhei; Yamamoto, Shinjiro; Takahashi, Hiro; Matsuura, Hideyuki; Hirata, Kazumasa

2016-01-01

Expressed sequence tag analyses revealed that two marine Chlorophyceae green algae, Chlamydomonas sp. W80 and Chlamydomonas sp. HS5, contain genes coding for chloroplastic class IIA aldolase (fructose-1, 6-bisphosphate aldolase: FBA). These genes show robust monophyly with those of the marine Prasinophyceae algae genera Micromonas, Ostreococcus and Bathycoccus, indicating that the acquisition of this gene through horizontal gene transfer by an ancestor of the green algal lineage occurred prior to the divergence of the core chlorophytes (Chlorophyceae and Trebouxiophyceae) and the prasinophytes. The absence of this gene in some freshwater chlorophytes, such as Chlamydomonas reinhardtii, Volvox carteri, Chlorella vulgaris, Chlorella variabilis and Coccomyxa subellipsoidea, can therefore be explained by the loss of this gene somewhere in the evolutionary process. Our survey on the distribution of this gene in genomic and transcriptome databases suggests that this gene occurs almost exclusively in marine algae, with a few exceptions, and as such, we propose that chloroplastic class IIA FBA is a marine environment-adapted enzyme. This hypothesis was also experimentally tested using Chlamydomonas W80, for which we found that the transcript levels of this gene to be significantly lower under low-salt (that is, simulated terrestrial) conditions. Expression analyses of transcriptome data for two algae, Prymnesium parvum and Emiliania huxleyi, taken from the Sequence Read Archive database also indicated that the expression of this gene under terrestrial conditions (low NaCl and low sulfate) is significantly downregulated. Thus, these experimental and transcriptome data provide support for our hypothesis. PMID:27058504
Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

PubMed Central

Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

2016-01-01

We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can be used to analyze complex “omics” data and to infer and optimize metabolic processes. Thereby, SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, microalgae blooms methanogenic fermentation, and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations. PMID:27242701
EINVis: a visualization tool for analyzing and exploring genetic interactions in large-scale association studies.

PubMed

Wu, Yubao; Zhu, Xiaofeng; Chen, Jian; Zhang, Xiang

2013-11-01

Epistasis (gene-gene interaction) detection in large-scale genetic association studies has recently drawn extensive research interests as many complex traits are likely caused by the joint effect of multiple genetic factors. The large number of possible interactions poses both statistical and computational challenges. A variety of approaches have been developed to address the analytical challenges in epistatic interaction detection. These methods usually output the identified genetic interactions and store them in flat file formats. It is highly desirable to develop an effective visualization tool to further investigate the detected interactions and unravel hidden interaction patterns. We have developed EINVis, a novel visualization tool that is specifically designed to analyze and explore genetic interactions. EINVis displays interactions among genetic markers as a network. It utilizes a circular layout (specially, a tree ring view) to simultaneously visualize the hierarchical interactions between single nucleotide polymorphisms (SNPs), genes, and chromosomes, and the network structure formed by these interactions. Using EINVis, the user can distinguish marginal effects from interactions, track interactions involving more than two markers, visualize interactions at different levels, and detect proxy SNPs based on linkage disequilibrium. EINVis is an effective and user-friendly free visualization tool for analyzing and exploring genetic interactions. It is publicly available with detailed documentation and online tutorial on the web at http://filer.case.edu/yxw407/einvis/. © 2013 WILEY PERIODICALS, INC.
Application of Frameworks in the Analysis and (Re)design of Interactive Visual Learning Tools

ERIC Educational Resources Information Center

Liang, Hai-Ning; Sedig, Kamran

2009-01-01

Interactive visual learning tools (IVLTs) are software environments that encode and display information visually and allow learners to interact with the visual information. This article examines the application and utility of frameworks in the analysis and design of IVLTs at the micro level. Frameworks play an important role in any design. They…
Advanced Visualization and Interactive Display Rapid Innovation and Discovery Evaluation Research (VISRIDER) Program Task 6: Point Cloud Visualization Techniques for Desktop and Web Platforms

DTIC Science & Technology

2017-04-01

ADVANCED VISUALIZATION AND INTERACTIVE DISPLAY RAPID INNOVATION AND DISCOVERY EVALUATION RESEARCH (VISRIDER) PROGRAM TASK 6: POINT CLOUD...To) OCT 2013 – SEP 2014 4. TITLE AND SUBTITLE ADVANCED VISUALIZATION AND INTERACTIVE DISPLAY RAPID INNOVATION AND DISCOVERY EVALUATION RESEARCH...various point cloud visualization techniques for viewing large scale LiDAR datasets. Evaluate their potential use for thick client desktop platforms
Integrated web visualizations for protein-protein interaction databases.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Holzinger, Andreas

2015-06-16

Understanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions. Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery. They provide predictions and correlations, indicate possibilities for future experimental research and fill the gaps to complete the picture of biochemical processes. There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. Many computational resources integrate interaction data with additional information on molecular background. However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks. We selected M=10 out of N=53 resources supporting visualization, and we tested against the following set of criteria: interoperability, data integration, quantity of possible interactions, data visualization quality and data coverage. The study reveals differences in usability, visualization features and quality as well as the quantity of interactions. StringDB is the recommended first choice. CPDB presents a comprehensive dataset and IntAct lets the user change the network layout. A comprehensive comparison table is available via web. The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015. Only some web resources featuring graph visualization can be successfully applied to interactive visual analysis of protein-protein interaction. Study results underline the necessity for further enhancements of visualization integration in biochemical analysis tools. Identified challenges are data comprehensiveness, confidence, interactive feature and visualization maturing.
Suggested Interactivity: Seeking Perceived Affordances for Information Visualization.

PubMed

Boy, Jeremy; Eveillard, Louis; Detienne, Françoise; Fekete, Jean-Daniel

2016-01-01

In this article, we investigate methods for suggesting the interactivity of online visualizations embedded with text. We first assess the need for such methods by conducting three initial experiments on Amazon's Mechanical Turk. We then present a design space for Suggested Interactivity (i. e., visual cues used as perceived affordances-SI), based on a survey of 382 HTML5 and visualization websites. Finally, we assess the effectiveness of three SI cues we designed for suggesting the interactivity of bar charts embedded with text. Our results show that only one cue (SI3) was successful in inciting participants to interact with the visualizations, and we hypothesize this is because this particular cue provided feedforward.
Physical and Visual Accessibilities in Intensive Care Units: A Comparative Study of Open-Plan and Racetrack Units.

PubMed

Rashid, Mahbub; Khan, Nayma; Jones, Belinda

2016-01-01

This study compared physical and visual accessibilities and their associations with staff perception and interaction behaviors in 2 intensive care units (ICUs) with open-plan and racetrack layouts. For the study, physical and visual accessibilities were measured using the spatial analysis techniques of Space Syntax. Data on staff perception were collected from 81 clinicians using a questionnaire survey. The locations of 2233 interactions, and the location and length of another 339 interactions in these units were collected using systematic field observation techniques. According to the study, physical and visual accessibilities were different in the 2 ICUs, and clinicians' primary workspaces were physically and visually more accessible in the open-plan ICU. Physical and visual accessibilities affected how well clinicians' knew their peers and where their peers were located in these units. Physical and visual accessibilities also affected clinicians' perception of interaction and communication and of teamwork and collaboration in these units. Additionally, physical and visual accessibilities showed significant positive associations with interaction behaviors in these units, with the open-plan ICU showing stronger associations. However, physical accessibilities were less important than visual accessibilities in relation to interaction behaviors in these ICUs. The implications of these findings for ICU design are discussed.
Motor-visual neurons and action recognition in social interactions.

PubMed

de la Rosa, Stephan; Bülthoff, Heinrich H

2014-04-01

Cook et al. suggest that motor-visual neurons originate from associative learning. This suggestion has interesting implications for the processing of socially relevant visual information in social interactions. Here, we discuss two aspects of the associative learning account that seem to have particular relevance for visual recognition of social information in social interactions - namely, context-specific and contingency based learning.
Experimenter's Laboratory for Visualized Interactive Science

NASA Technical Reports Server (NTRS)

Hansen, Elaine R.; Rodier, Daniel R.; Klemp, Marjorie K.

1994-01-01

ELVIS (Experimenter's Laboratory for Visualized Interactive Science) is an interactive visualization environment that enables scientists, students, and educators to visualize and analyze large, complex, and diverse sets of scientific data. It accomplishes this by presenting the data sets as 2-D, 3-D, color, stereo, and graphic images with movable and multiple light sources combined with displays of solid-surface, contours, wire-frame, and transparency. By simultaneously rendering diverse data sets acquired from multiple sources, formats, and resolutions and by interacting with the data through an intuitive, direct-manipulation interface, ELVIS provides an interactive and responsive environment for exploratory data analysis.
A hierarchy of timescales explains distinct effects of local inhibition of primary visual cortex and frontal eye fields

PubMed Central

Cocchi, Luca; Sale, Martin V; L Gollo, Leonardo; Bell, Peter T; Nguyen, Vinh T; Zalesky, Andrew; Breakspear, Michael; Mattingley, Jason B

2016-01-01

Within the primate visual system, areas at lower levels of the cortical hierarchy process basic visual features, whereas those at higher levels, such as the frontal eye fields (FEF), are thought to modulate sensory processes via feedback connections. Despite these functional exchanges during perception, there is little shared activity between early and late visual regions at rest. How interactions emerge between regions encompassing distinct levels of the visual hierarchy remains unknown. Here we combined neuroimaging, non-invasive cortical stimulation and computational modelling to characterize changes in functional interactions across widespread neural networks before and after local inhibition of primary visual cortex or FEF. We found that stimulation of early visual cortex selectively increased feedforward interactions with FEF and extrastriate visual areas, whereas identical stimulation of the FEF decreased feedback interactions with early visual areas. Computational modelling suggests that these opposing effects reflect a fast-slow timescale hierarchy from sensory to association areas. DOI: http://dx.doi.org/10.7554/eLife.15252.001 PMID:27596931
A hierarchy of timescales explains distinct effects of local inhibition of primary visual cortex and frontal eye fields.

PubMed

Cocchi, Luca; Sale, Martin V; L Gollo, Leonardo; Bell, Peter T; Nguyen, Vinh T; Zalesky, Andrew; Breakspear, Michael; Mattingley, Jason B

2016-09-06

Within the primate visual system, areas at lower levels of the cortical hierarchy process basic visual features, whereas those at higher levels, such as the frontal eye fields (FEF), are thought to modulate sensory processes via feedback connections. Despite these functional exchanges during perception, there is little shared activity between early and late visual regions at rest. How interactions emerge between regions encompassing distinct levels of the visual hierarchy remains unknown. Here we combined neuroimaging, non-invasive cortical stimulation and computational modelling to characterize changes in functional interactions across widespread neural networks before and after local inhibition of primary visual cortex or FEF. We found that stimulation of early visual cortex selectively increased feedforward interactions with FEF and extrastriate visual areas, whereas identical stimulation of the FEF decreased feedback interactions with early visual areas. Computational modelling suggests that these opposing effects reflect a fast-slow timescale hierarchy from sensory to association areas.
Interactive Visualization of Dependencies

ERIC Educational Resources Information Center

Moreno, Camilo Arango; Bischof, Walter F.; Hoover, H. James

2012-01-01

We present an interactive tool for browsing course requisites as a case study of dependency visualization. This tool uses multiple interactive visualizations to allow the user to explore the dependencies between courses. A usability study revealed that the proposed browser provides significant advantages over traditional methods, in terms of…
Query2Question: Translating Visualization Interaction into Natural Language.

PubMed

Nafari, Maryam; Weaver, Chris

2015-06-01

Richly interactive visualization tools are increasingly popular for data exploration and analysis in a wide variety of domains. Existing systems and techniques for recording provenance of interaction focus either on comprehensive automated recording of low-level interaction events or on idiosyncratic manual transcription of high-level analysis activities. In this paper, we present the architecture and translation design of a query-to-question (Q2Q) system that automatically records user interactions and presents them semantically using natural language (written English). Q2Q takes advantage of domain knowledge and uses natural language generation (NLG) techniques to translate and transcribe a progression of interactive visualization states into a visual log of styled text that complements and effectively extends the functionality of visualization tools. We present Q2Q as a means to support a cross-examination process in which questions rather than interactions are the focus of analytic reasoning and action. We describe the architecture and implementation of the Q2Q system, discuss key design factors and variations that effect question generation, and present several visualizations that incorporate Q2Q for analysis in a variety of knowledge domains.
SPV: a JavaScript Signaling Pathway Visualizer.

PubMed

Calderone, Alberto; Cesareni, Gianni

2018-03-24

The visualization of molecular interactions annotated in web resources is useful to offer to users such information in a clear intuitive layout. These interactions are frequently represented as binary interactions that are laid out in free space where, different entities, cellular compartments and interaction types are hardly distinguishable. SPV (Signaling Pathway Visualizer) is a free open source JavaScript library which offers a series of pre-defined elements, compartments and interaction types meant to facilitate the representation of signaling pathways consisting of causal interactions without neglecting simple protein-protein interaction networks. freely available under Apache version 2 license; Source code: https://github.com/Sinnefa/SPV_Signaling_Pathway_Visualizer_v1.0. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. sinnefa@gmail.com.
Communicative interactions between visually impaired mothers and their sighted children: analysis of gaze, facial expressions, voice and physical contacts.

PubMed

Chiesa, S; Galati, D; Schmidt, S

2015-11-01

Social and emotional development of infants and young children is largely based on the communicative interaction with their mother, or principal caretaker (Trevarthen ). The main modalities implied in this early communication are voice, facial expressions and gaze (Stern ). This study aims at analysing early mother-child interactions in the case of visually impaired mothers who do not have access to their children's gaze and facial expressions. Spontaneous play interactions between seven visually impaired mothers and their sighted children aged between 6 months and 3 years were filmed. These dyads were compared with a control group of sighted mothers and children analysing four modalities of communication and interaction regulation: gaze, physical contacts, verbal productions and facial expressions. The visually impaired mothers' facial expressions differed from the ones of sighted mothers mainly with respect to forehead movements, leading to an impoverishment of conveyed meaning. Regarding the other communicative modalities, results suggest that visually impaired mothers and their children use compensatory strategies to guaranty harmonic interaction despite the mother's impairment: whereas gaze results the main factor of interaction regulation in sighted dyads, physical contacts and verbal productions assume a prevalent role in dyads with visually impaired mothers. Moreover, visually impaired mother's children seem to be able to differentiate between their mother and sighted interaction partners, adapting differential modes of communication. The results of this study show that, in spite of the obvious differences in the modes of communication, visual impairment does not prevent a harmonious interaction with the child. © 2015 John Wiley & Sons Ltd.
The Perceptual Root of Object-Based Storage: An Interactive Model of Perception and Visual Working Memory

ERIC Educational Resources Information Center

Gao, Tao; Gao, Zaifeng; Li, Jie; Sun, Zhongqiang; Shen, Mowei

2011-01-01

Mainstream theories of visual perception assume that visual working memory (VWM) is critical for integrating online perceptual information and constructing coherent visual experiences in changing environments. Given the dynamic interaction between online perception and VWM, we propose that how visual information is processed during visual…
Visual exploration and analysis of human-robot interaction rules

NASA Astrophysics Data System (ADS)

Zhang, Hui; Boyles, Michael J.

2013-01-01

We present a novel interaction paradigm for the visual exploration, manipulation and analysis of human-robot interaction (HRI) rules; our development is implemented using a visual programming interface and exploits key techniques drawn from both information visualization and visual data mining to facilitate the interaction design and knowledge discovery process. HRI is often concerned with manipulations of multi-modal signals, events, and commands that form various kinds of interaction rules. Depicting, manipulating and sharing such design-level information is a compelling challenge. Furthermore, the closed loop between HRI programming and knowledge discovery from empirical data is a relatively long cycle. This, in turn, makes design-level verification nearly impossible to perform in an earlier phase. In our work, we exploit a drag-and-drop user interface and visual languages to support depicting responsive behaviors from social participants when they interact with their partners. For our principal test case of gaze-contingent HRI interfaces, this permits us to program and debug the robots' responsive behaviors through a graphical data-flow chart editor. We exploit additional program manipulation interfaces to provide still further improvement to our programming experience: by simulating the interaction dynamics between a human and a robot behavior model, we allow the researchers to generate, trace and study the perception-action dynamics with a social interaction simulation to verify and refine their designs. Finally, we extend our visual manipulation environment with a visual data-mining tool that allows the user to investigate interesting phenomena such as joint attention and sequential behavioral patterns from multiple multi-modal data streams. We have created instances of HRI interfaces to evaluate and refine our development paradigm. As far as we are aware, this paper reports the first program manipulation paradigm that integrates visual programming interfaces, information visualization, and visual data mining methods to facilitate designing, comprehending, and evaluating HRI interfaces.
Interactive Visualization of Assessment Data: The Software Package Mondrian

ERIC Educational Resources Information Center

Unlu, Ali; Sargin, Anatol

2009-01-01

Mondrian is state-of-the-art statistical data visualization software featuring modern interactive visualization techniques for a wide range of data types. This article reviews the capabilities, functionality, and interactive properties of this software package. Key features of Mondrian are illustrated with data from the Programme for International…

Crossmodal interactions during non-linguistic auditory processing in cochlear-implanted deaf patients.

PubMed

Barone, Pascal; Chambaudie, Laure; Strelnikov, Kuzma; Fraysse, Bernard; Marx, Mathieu; Belin, Pascal; Deguine, Olivier

2016-10-01

Due to signal distortion, speech comprehension in cochlear-implanted (CI) patients relies strongly on visual information, a compensatory strategy supported by important cortical crossmodal reorganisations. Though crossmodal interactions are evident for speech processing, it is unclear whether a visual influence is observed in CI patients during non-linguistic visual-auditory processing, such as face-voice interactions, which are important in social communication. We analyse and compare visual-auditory interactions in CI patients and normal-hearing subjects (NHS) at equivalent auditory performance levels. Proficient CI patients and NHS performed a voice-gender categorisation in the visual-auditory modality from a morphing-generated voice continuum between male and female speakers, while ignoring the presentation of a male or female visual face. Our data show that during the face-voice interaction, CI deaf patients are strongly influenced by visual information when performing an auditory gender categorisation task, in spite of maximum recovery of auditory speech. No such effect is observed in NHS, even in situations of CI simulation. Our hypothesis is that the functional crossmodal reorganisation that occurs in deafness could influence nonverbal processing, such as face-voice interaction; this is important for patient internal supramodal representation. Copyright © 2016 Elsevier Ltd. All rights reserved.
Testing the Usability of Interactive Visualizations for Complex Problem-Solving: Findings Related to Improving Interfaces and Help.

ERIC Educational Resources Information Center

Mirel, Barbara

2001-01-01

Conducts a scenario-based usability test with 10 data analysts using visual querying (visually analyzing data with interactive graphics). Details a range of difficulties found in visual selection that, at times, gave rise to inaccurate selections, invalid conclusions, and misguided decisions. Argues that support for visual selection must be built…
Numerical simulation of the generation of reactive oxygen and nitrogen species (RONS) in water by atmospheric-pressure plasmas and their effects on Escherichia coli (E. coli)

NASA Astrophysics Data System (ADS)

Ikuse, Kazumasa; Hamaguchi, Satoshi

2016-09-01

We have used two types of numerical simulations to examine biological effects of reactive oxygen and nitrogen species (RONS) generated in water by an atmospheric-pressure plasma (APP) that irradiates the water surface. One is numerical simulation for the generation and transport of RONS in water based on the reaction-diffusion-advection equations coupled with Poisson equation. The rate constants, mobilities, and diffusion coefficients used in the equations are obtained from the literature. The gaseous species are given as boundary conditions and time evolution of the concentrations of chemical species in pure water is solved numerically as functions of the depth in one dimension. Although it is not clear how living organisms respond to such exogenous RONS, we also use numerical simulation for metabolic reactions of Escherichia coli (E. coli) and examine possible effects of such RONS on an in-silico model organism. The computation model is based on the flux balance analysis (FBA), where the fluxes of the metabolites in a biological system are evaluated in steady state, i.e., under the assumption that the fluxes do not change in time. The fluxes are determined with liner programming to maximize the growth rate of the bacteria under the given conditions. Although FBA cannot be directly applied to dynamical responses of metabolic reactions, the simulation still gives insight into the biological reactions to exogenous chemical species generated by an APP. Partially supported by JSPS Grants-in-Aid for Scientific Research.
Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory.

PubMed

Heuett, William J; Beard, Daniel A; Qian, Hong

2008-05-15

Several approaches, including metabolic control analysis (MCA), flux balance analysis (FBA), correlation metric construction (CMC), and biochemical circuit theory (BCT), have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS) biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RTBS and STBS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA).
Applying Pragmatics Principles for Interaction with Visual Analytics.

PubMed

Hoque, Enamul; Setlur, Vidya; Tory, Melanie; Dykeman, Isaac

2018-01-01

Interactive visual data analysis is most productive when users can focus on answering the questions they have about their data, rather than focusing on how to operate the interface to the analysis tool. One viable approach to engaging users in interactive conversations with their data is a natural language interface to visualizations. These interfaces have the potential to be both more expressive and more accessible than other interaction paradigms. We explore how principles from language pragmatics can be applied to the flow of visual analytical conversations, using natural language as an input modality. We evaluate the effectiveness of pragmatics support in our system Evizeon, and present design considerations for conversation interfaces to visual analytics tools.
Does Seeing Ice Really Feel Cold? Visual-Thermal Interaction under an Illusory Body-Ownership

PubMed Central

Kanaya, Shoko; Matsushima, Yuka; Yokosawa, Kazuhiko

2012-01-01

Although visual information seems to affect thermal perception (e.g. red color is associated with heat), previous studies have failed to demonstrate the interaction between visual and thermal senses. However, it has been reported that humans feel an illusory thermal sensation in conjunction with an apparently-thermal visual stimulus placed on a prosthetic hand in the rubber hand illusion (RHI) wherein an individual feels that a prosthetic (rubber) hand belongs to him/her. This study tests the possibility that the ownership of the body surface on which a visual stimulus is placed enhances the likelihood of a visual-thermal interaction. We orthogonally manipulated three variables: induced hand-ownership, visually-presented thermal information, and tactically-presented physical thermal information. Results indicated that the sight of an apparently-thermal object on a rubber hand that is illusorily perceived as one's own hand affects thermal judgments about the object physically touching this hand. This effect was not observed without the RHI. The importance of ownership of a body part that is touched by the visual object on the visual-thermal interaction is discussed. PMID:23144814
Does seeing ice really feel cold? Visual-thermal interaction under an illusory body-ownership.

PubMed

Kanaya, Shoko; Matsushima, Yuka; Yokosawa, Kazuhiko

2012-01-01

Although visual information seems to affect thermal perception (e.g. red color is associated with heat), previous studies have failed to demonstrate the interaction between visual and thermal senses. However, it has been reported that humans feel an illusory thermal sensation in conjunction with an apparently-thermal visual stimulus placed on a prosthetic hand in the rubber hand illusion (RHI) wherein an individual feels that a prosthetic (rubber) hand belongs to him/her. This study tests the possibility that the ownership of the body surface on which a visual stimulus is placed enhances the likelihood of a visual-thermal interaction. We orthogonally manipulated three variables: induced hand-ownership, visually-presented thermal information, and tactically-presented physical thermal information. Results indicated that the sight of an apparently-thermal object on a rubber hand that is illusorily perceived as one's own hand affects thermal judgments about the object physically touching this hand. This effect was not observed without the RHI. The importance of ownership of a body part that is touched by the visual object on the visual-thermal interaction is discussed.
Headphone and Head-Mounted Visual Displays for Virtual Environments

NASA Technical Reports Server (NTRS)

Begault, Duran R.; Ellis, Stephen R.; Wenzel, Elizabeth M.; Trejo, Leonard J. (Technical Monitor)

1998-01-01

A realistic auditory environment can contribute to both the overall subjective sense of presence in a virtual display, and to a quantitative metric predicting human performance. Here, the role of audio in a virtual display and the importance of auditory-visual interaction are examined. Conjectures are proposed regarding the effectiveness of audio compared to visual information for creating a sensation of immersion, the frame of reference within a virtual display, and the compensation of visual fidelity by supplying auditory information. Future areas of research are outlined for improving simulations of virtual visual and acoustic spaces. This paper will describe some of the intersensory phenomena that arise during operator interaction within combined visual and auditory virtual environments. Conjectures regarding audio-visual interaction will be proposed.
Modeling and evaluating user behavior in exploratory visual analysis

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

Reda, Khairi; Johnson, Andrew E.; Papka, Michael E.

Empirical evaluation methods for visualizations have traditionally focused on assessing the outcome of the visual analytic process as opposed to characterizing how that process unfolds. There are only a handful of methods that can be used to systematically study how people use visualizations, making it difficult for researchers to capture and characterize the subtlety of cognitive and interaction behaviors users exhibit during visual analysis. To validate and improve visualization design, however, it is important for researchers to be able to assess and understand how users interact with visualization systems under realistic scenarios. This paper presents a methodology for modeling andmore » evaluating the behavior of users in exploratory visual analysis. We model visual exploration using a Markov chain process comprising transitions between mental, interaction, and computational states. These states and the transitions between them can be deduced from a variety of sources, including verbal transcripts, videos and audio recordings, and log files. This model enables the evaluator to characterize the cognitive and computational processes that are essential to insight acquisition in exploratory visual analysis, and reconstruct the dynamics of interaction between the user and the visualization system. We illustrate this model with two exemplar user studies, and demonstrate the qualitative and quantitative analytical tools it affords.« less
Visual Design Guidelines for Improving Learning from Dynamic and Interactive Digital Text

ERIC Educational Resources Information Center

Jin, Sung-Hee

2013-01-01

Despite the dynamic and interactive features of digital text, the visual design guidelines for digital text are similar to those for printed text. The purpose of this study was to develop visual design guidelines for improving learning from dynamic and interactive digital text and to validate them by controlled testing. Two structure design…
Spatial Reasoning with External Visualizations: What Matters Is What You See, Not whether You Interact

ERIC Educational Resources Information Center

Keehner, Madeleine; Hegarty, Mary; Cohen, Cheryl; Khooshabeh, Peter; Montello, Daniel R.

2008-01-01

Three experiments examined the effects of interactive visualizations and spatial abilities on a task requiring participants to infer and draw cross sections of a three-dimensional (3D) object. The experiments manipulated whether participants could interactively control a virtual 3D visualization of the object while performing the task, and…
Scientific Visualization of Radio Astronomy Data using Gesture Interaction

NASA Astrophysics Data System (ADS)

Mulumba, P.; Gain, J.; Marais, P.; Woudt, P.

2015-09-01

MeerKAT in South Africa (Meer = More Karoo Array Telescope) will require software to help visualize, interpret and interact with multidimensional data. While visualization of multi-dimensional data is a well explored topic, little work has been published on the design of intuitive interfaces to such systems. More specifically, the use of non-traditional interfaces (such as motion tracking and multi-touch) has not been widely investigated within the context of visualizing astronomy data. We hypothesize that a natural user interface would allow for easier data exploration which would in turn lead to certain kinds of visualizations (volumetric, multidimensional). To this end, we have developed a multi-platform scientific visualization system for FITS spectral data cubes using VTK (Visualization Toolkit) and a natural user interface to explore the interaction between a gesture input device and multidimensional data space. Our system supports visual transformations (translation, rotation and scaling) as well as sub-volume extraction and arbitrary slicing of 3D volumetric data. These tasks were implemented across three prototypes aimed at exploring different interaction strategies: standard (mouse/keyboard) interaction, volumetric gesture tracking (Leap Motion controller) and multi-touch interaction (multi-touch monitor). A Heuristic Evaluation revealed that the volumetric gesture tracking prototype shows great promise for interfacing with the depth component (z-axis) of 3D volumetric space across multiple transformations. However, this is limited by users needing to remember the required gestures. In comparison, the touch-based gesture navigation is typically more familiar to users as these gestures were engineered from standard multi-touch actions. Future work will address a complete usability test to evaluate and compare the different interaction modalities against the different visualization tasks.
Design of an 8-40 GHz Antenna for the Wideband Instrument for Snow Measurements (WISM)

NASA Technical Reports Server (NTRS)

Durham, Timothy E.; Vanhille, Kenneth J.; Trent, Christopher R.; Lambert, Kevin M.; Miranda, Felix A.

2015-01-01

This poster describes the implementation of a 6x6 element, dual linear polarized array with beamformer that operates from about 8-40 GHz. It is implemented using a relatively new multi-layer microfabrication process. The beamformer includes baluns that feed dual-polarized differential antenna elements and reactive splitters that cover the full frequency range of operation. This fixed beam array (FBA) serves as the feed for a multi-band instrument designed to measure snow water equivalent (SWE) from an airborne platform known as the Wideband Instrument for Snow Measurements (WISM).
A randomised, double-blind, placebo-controlled phase 1 study of the safety, tolerability and pharmacodynamics of volixibat in overweight and obese but otherwise healthy adults: implications for treatment of non-alcoholic steatohepatitis.

PubMed

Palmer, Melissa; Jennings, Lee; Silberg, Debra G; Bliss, Caleb; Martin, Patrick

2018-03-16

Accumulation of toxic free cholesterol in hepatocytes may cause hepatic inflammation and fibrosis. Volixibat inhibits bile acid reuptake via the apical sodium bile acid transporter located on the luminal surface of the ileum. The resulting increase in bile acid synthesis from cholesterol could be beneficial in patients with non-alcoholic steatohepatitis. This adaptive dose-finding study investigated the safety, tolerability, pharmacodynamics, and pharmacokinetics of volixibat. Overweight and obese adults were randomised 3:1 to double-blind volixibat or placebo, respectively, for 12 days. Volixibat was initiated at a once-daily dose of 20 mg, 40 mg or 80 mg. Based on the assessment of predefined safety events, volixibat dosing was either escalated or reduced. Other dose regimens (titrations and twice-daily dosing) were also evaluated. Assessments included safety, tolerability, stool hardness, faecal bile acid (FBA) excretion, and serum levels of 7α-hydroxy-4-cholesten-3-one (C4) and lipids. All 84 randomised participants (volixibat, 63; placebo, 21) completed the study, with no serious adverse events at doses of up to 80 mg per day (maximum assessed dose). The median number of daily bowel evacuations increased from 1 (range 0-4) to 2 (0-8) during volixibat treatment, and stool was looser with volixibat than placebo. Volixibat was minimally absorbed; serum levels were rarely quantifiable at any dose or sampling time point, thereby precluding pharmacokinetic analyses. Mean daily FBA excretion was 930.61 μmol (standard deviation [SD] 468.965) with volixibat and 224.75 μmol (195.403) with placebo; effects were maximal at volixibat doses ≥20 mg/day. Mean serum C4 concentrations at day 12 were 98.767 ng/mL (standard deviation, 61.5841) with volixibat and 16.497 ng/mL (12.9150) with placebo. Total and low-density lipoprotein cholesterol levels decreased in the volixibat group, with median changes of - 0.70 mmol/L (range - 2.8 to 0.4) and - 0.6990 mmol/L (- 3.341 to 0.570), respectively. This study indicates that maximal inhibition of bile acid reabsorption, as assessed by FBA excretion, occurs at volixibat doses of ≥20 mg/day in obese and overweight adults, without appreciable change in gastrointestinal tolerability. These findings guided dose selection for an ongoing phase 2 study in patients with non-alcoholic steatohepatitis. ClinicalTrials.gov identifier: NCT02287779 (registration first received 6 November 2014).
A Model of an Integrated Immune System Pathway in Homo sapiens and Its Interaction with Superantigen Producing Expression Regulatory Pathway in Staphylococcus aureus: Comparing Behavior of Pathogen Perturbed and Unperturbed Pathway

PubMed Central

Tomar, Namrata; De, Rajat K.

2013-01-01

Response of an immune system to a pathogen attack depends on the balance between the host immune defense and the virulence of the pathogen. Investigation of molecular interactions between the proteins of a host and a pathogen helps in identifying the pathogenic proteins. It is necessary to understand the dynamics of a normally behaved host system to evaluate the capacity of its immune system upon pathogen attack. In this study, we have compared the behavior of an unperturbed and pathogen perturbed host system. Moreover, we have developed a formalism under Flux Balance Analysis (FBA) for the optimization of conflicting objective functions. We have constructed an integrated pathway system, which includes Staphylococcal Superantigen (SAg) expression regulatory pathway and TCR signaling pathway of Homo sapiens. We have implemented the method on this pathway system and observed the behavior of host signaling molecules upon pathogen attack. The entire study has been divided into six different cases, based on the perturbed/unperturbed conditions. In other words, we have investigated unperturbed and pathogen perturbed human TCR signaling pathway, with different combinations of optimization of concentrations of regulatory and signaling molecules. One of these cases has aimed at finding out whether minimization of the toxin production in a pathogen leads to the change in the concentration levels of the proteins coded by TCR signaling pathway genes in the infected host. Based on the computed results, we have hypothesized that the balance between TCR signaling inhibitory and stimulatory molecules can keep TCR signaling system into resting/stimulating state, depending upon the perturbation. The proposed integrated host-pathogen interaction pathway model has accurately reflected the experimental evidences, which we have used for validation purpose. The significance of this kind of investigation lies in revealing the susceptible interaction points that can take back the Staphylococcal Enterotoxin (SE)-challenged system within the range of normal behavior. PMID:24324645
Bimolecular fluorescence complementation: visualization of molecular interactions in living cells.

PubMed

Kerppola, Tom K

2008-01-01

A variety of experimental methods have been developed for the analysis of protein interactions. The majority of these methods either require disruption of the cells to detect molecular interactions or rely on indirect detection of the protein interaction. The bimolecular fluorescence complementation (BiFC) assay provides a direct approach for the visualization of molecular interactions in living cells and organisms. The BiFC approach is based on the facilitated association between two fragments of a fluorescent protein when the fragments are brought together by an interaction between proteins fused to the fragments. The BiFC approach has been used for visualization of interactions among a variety of structurally diverse interaction partners in many different cell types. It enables detection of transient complexes as well as complexes formed by a subpopulation of the interaction partners. It is essential to include negative controls in each experiment in which the interface between the interaction partners has been mutated or deleted. The BiFC assay has been adapted for simultaneous visualization of multiple protein complexes in the same cell and the competition for shared interaction partners. A ubiquitin-mediated fluorescence complementation assay has also been developed for visualization of the covalent modification of proteins by ubiquitin family peptides. These fluorescence complementation assays have a great potential to illuminate a variety of biological interactions in the future.
Web-based interactive visualization in a Grid-enabled neuroimaging application using HTML5.

PubMed

Siewert, René; Specovius, Svenja; Wu, Jie; Krefting, Dagmar

2012-01-01

Interactive visualization and correction of intermediate results are required in many medical image analysis pipelines. To allow certain interaction in the remote execution of compute- and data-intensive applications, new features of HTML5 are used. They allow for transparent integration of user interaction into Grid- or Cloud-enabled scientific workflows. Both 2D and 3D visualization and data manipulation can be performed through a scientific gateway without the need to install specific software or web browser plugins. The possibilities of web-based visualization are presented along the FreeSurfer-pipeline, a popular compute- and data-intensive software tool for quantitative neuroimaging.
Hybrid 2-D and 3-D Immersive and Interactive User Interface for Scientific Data Visualization

DTIC Science & Technology

2017-08-01

visualization, 3-D interactive visualization, scientific visualization, virtual reality, real -time ray tracing 16. SECURITY CLASSIFICATION OF: 17...scientists to employ in the real world. Other than user-friendly software and hardware setup, scientists also need to be able to perform their usual...and scientific visualization communities mostly have different research priorities. For the VR community, the ability to support real -time user
Web-based visual analysis for high-throughput genomics

PubMed Central

2013-01-01

Background Visualization plays an essential role in genomics research by making it possible to observe correlations and trends in large datasets as well as communicate findings to others. Visual analysis, which combines visualization with analysis tools to enable seamless use of both approaches for scientific investigation, offers a powerful method for performing complex genomic analyses. However, there are numerous challenges that arise when creating rich, interactive Web-based visualizations/visual analysis applications for high-throughput genomics. These challenges include managing data flow from Web server to Web browser, integrating analysis tools and visualizations, and sharing visualizations with colleagues. Results We have created a platform simplifies the creation of Web-based visualization/visual analysis applications for high-throughput genomics. This platform provides components that make it simple to efficiently query very large datasets, draw common representations of genomic data, integrate with analysis tools, and share or publish fully interactive visualizations. Using this platform, we have created a Circos-style genome-wide viewer, a generic scatter plot for correlation analysis, an interactive phylogenetic tree, a scalable genome browser for next-generation sequencing data, and an application for systematically exploring tool parameter spaces to find good parameter values. All visualizations are interactive and fully customizable. The platform is integrated with the Galaxy (http://galaxyproject.org) genomics workbench, making it easy to integrate new visual applications into Galaxy. Conclusions Visualization and visual analysis play an important role in high-throughput genomics experiments, and approaches are needed to make it easier to create applications for these activities. Our framework provides a foundation for creating Web-based visualizations and integrating them into Galaxy. Finally, the visualizations we have created using the framework are useful tools for high-throughput genomics experiments. PMID:23758618
Narrating the Visual: Accounting for and Projecting Actions in Webinar Q&As

ERIC Educational Resources Information Center

Yu, Di; Tadic, Nadja

2018-01-01

Visual conduct, including the use of gaze to attend to bodily-visual cues and other semiotic resources in interaction, has long been a topic of interest in ethnomethodology and conversation analysis (EMCA). Past EMCA work has examined visual conduct in face-to-face interaction, shedding light on the use of gaze to secure recipiency, facilitate…

An Interactive Approach to Learning and Teaching in Visual Arts Education

ERIC Educational Resources Information Center

Tomljenovic, Zlata

2015-01-01

The present research focuses on modernising the approach to learning and teaching the visual arts in teaching practice, as well as examining the performance of an interactive approach to learning and teaching in visual arts classes with the use of a combination of general and specific (visual arts) teaching methods. The study uses quantitative…
A Grammar-based Approach for Modeling User Interactions and Generating Suggestions During the Data Exploration Process.

PubMed

Dabek, Filip; Caban, Jesus J

2017-01-01

Despite the recent popularity of visual analytics focusing on big data, little is known about how to support users that use visualization techniques to explore multi-dimensional datasets and accomplish specific tasks. Our lack of models that can assist end-users during the data exploration process has made it challenging to learn from the user's interactive and analytical process. The ability to model how a user interacts with a specific visualization technique and what difficulties they face are paramount in supporting individuals with discovering new patterns within their complex datasets. This paper introduces the notion of visualization systems understanding and modeling user interactions with the intent of guiding a user through a task thereby enhancing visual data exploration. The challenges faced and the necessary future steps to take are discussed; and to provide a working example, a grammar-based model is presented that can learn from user interactions, determine the common patterns among a number of subjects using a K-Reversible algorithm, build a set of rules, and apply those rules in the form of suggestions to new users with the goal of guiding them along their visual analytic process. A formal evaluation study with 300 subjects was performed showing that our grammar-based model is effective at capturing the interactive process followed by users and that further research in this area has the potential to positively impact how users interact with a visualization system.
SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications

PubMed Central

Kalinin, Alexandr A.; Palanimalai, Selvam; Dinov, Ivo D.

2018-01-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis. PMID:29630069
SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications.

PubMed

Kalinin, Alexandr A; Palanimalai, Selvam; Dinov, Ivo D

2017-04-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis.
Visualization and Tracking of Parallel CFD Simulations

NASA Technical Reports Server (NTRS)

Vaziri, Arsi; Kremenetsky, Mark

1995-01-01

We describe a system for interactive visualization and tracking of a 3-D unsteady computational fluid dynamics (CFD) simulation on a parallel computer. CM/AVS, a distributed, parallel implementation of a visualization environment (AVS) runs on the CM-5 parallel supercomputer. A CFD solver is run as a CM/AVS module on the CM-5. Data communication between the solver, other parallel visualization modules, and a graphics workstation, which is running AVS, are handled by CM/AVS. Partitioning of the visualization task, between CM-5 and the workstation, can be done interactively in the visual programming environment provided by AVS. Flow solver parameters can also be altered by programmable interactive widgets. This system partially removes the requirement of storing large solution files at frequent time steps, a characteristic of the traditional 'simulate (yields) store (yields) visualize' post-processing approach.
Characterizing Interaction with Visual Mathematical Representations

ERIC Educational Resources Information Center

Sedig, Kamran; Sumner, Mark

2006-01-01

This paper presents a characterization of computer-based interactions by which learners can explore and investigate visual mathematical representations (VMRs). VMRs (e.g., geometric structures, graphs, and diagrams) refer to graphical representations that visually encode properties and relationships of mathematical structures and concepts.…
Verbal-spatial and visuospatial coding of power-space interactions.

PubMed

Dai, Qiang; Zhu, Lei

2018-05-10

A power-space interaction, which denotes the phenomenon that people responded faster to powerful words when they are placed higher in a visual field and faster to powerless words when they are placed lower in a visual field, has been repeatedly found. The dominant explanation of this power-space interaction is that it results from a tight correspondence between the representation of power and visual space (i.e., a visuospatial coding account). In the present study, we demonstrated that the interaction between power and space could be also based on a verbal-spatial coding in absence of any vertical spatial information. Additionally, the verbal-spatial coding was dominant in driving the power-space interaction when verbal space was contrasted with the visual space. Copyright © 2018 Elsevier Inc. All rights reserved.
Digestive Symptoms in Healthy People and Subjects With Irritable Bowel Syndrome

PubMed Central

Guyonnet, Denis; Donazzolo, Yves; Gendre, David; Tanguy, Jérôme; Guarner, Francisco

2015-01-01

Goals: The aim of this study was to validate the ability of symptom frequency questionnaire to differentiate between irritable bowel syndrome (IBS) patients and healthy subjects. Background: A digestive symptom frequency questionnaire (DSFQ) was previously used in a food efficacy trial in a non-IBS population with mild gastrointestinal symptoms. Study: We compared 2 well-defined populations: 100 IBS patients fulfilling Rome III criteria (mean age 32 y; range, 18 to 59 y), and 100 sex-matched and age-matched healthy subjects. Frequency of individual digestive symptoms (abdominal pain/discomfort, bloating, flatulence, borborygmi) was assessed using a 5-point Likert scale (from none to everyday of the week) and the IBS severity with the IBS-SSS questionnaire. Health-Related Quality of life (HRQoL) was assessed with the Food and Benefits Assessment (FBA) and Functional Digestive Disorders Quality of Life (FDDQL) questionnaires. The digestive (dis)comfort dimension of these questionnaires was considered as the main dimension for HRQoL. Results: The DSFQ discriminated IBS from healthy subjects with a significant difference (P<0.001) between groups (estimated mean difference=5.58; 95% CI, 4.91-6.28). On the basis of the ROC curve (AUC=0.9479), a cutoff value of 5 gives a sensitivity of 92% and a specificity of 84%, with a positive likelihood ratio of 5.75. Composite score of symptoms correlated strongly (P<0.0001) with digestive discomfort measured by FDDQL (−0.816), digestive comfort measured by FBA (−0.789), and the IBS-SSS score (0.762). Conclusions: Measurement of digestive symptom frequency by means of the DSFQ can differentiate IBS from healthy subjects, and shows a good correlation with other validated questionnaires (clinical trial #NCT01457378). PMID:25014236
Simultaneous Analyses and Applications of Multiple Fluorobenzoate and Halide Tracers in Hydrologic Studies

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

Hu, Q; Moran, J E

2004-01-22

An analytical method that employs ion chromatography has been developed to more fully exploit the use of fluorobenzoic acids (FBAs) and halides as hydrologic tracers. In a single run, this reliable, sensitive, and robust method can simultaneously separate and quantify halides (fluoride, chloride, bromide, and iodide) and up to seven FBAs from other common groundwater constituents (e.g., nitrate and sulfate). The usefulness of this ion chromatographic (IC) analytical method is demonstrated in both field and laboratory tracer experiments. Field experiments in unsaturated tuff featuring fractures or a fault show that this efficient and cost-effective method helps achieve the objectives ofmore » tracer studies that use multiple FBAs and/or diffusivity tracers (simultaneous use of one or more FBA and halide). The field study examines the hydrologic response of fractures and the matrix to different flow rates and the contribution of matrix diffusion in chemical transport. Laboratory tracer experiments with eight geologic media from across the United States--mostly from Department of Energy facilities where groundwater contamination is prevalent and where subsurface characterization employing tracers has been ongoing or is in need--reveal several insights about tracer transport behavior: (1) Bromide and FBAs are not always transported conservatively. (2) The delayed transport of these anionic tracers is likely related to geologic media characteristics, such as organic matter, pH, iron oxide content, and clay mineralogy. (3) Any use of iodine as a hydrologic tracer should take into account the different sorption behaviors of iodide and iodate and the possible conversion of iodine's initial chemical form. (4) The transport behavior of potential FBA and halide tracers under relevant geochemical conditions should be evaluated before beginning ambitious, large-scale field tracer experiments.« less
DOE Office of Scientific and Technical Information (OSTI.GOV)

Pin, F.G.

Sensor-based operation of autonomous robots in unstructured and/or outdoor environments has revealed to be an extremely challenging problem, mainly because of the difficulties encountered when attempting to represent the many uncertainties which are always present in the real world. These uncertainties are primarily due to sensor imprecisions and unpredictability of the environment, i.e., lack of full knowledge of the environment characteristics and dynamics. An approach. which we have named the {open_quotes}Fuzzy Behaviorist Approach{close_quotes} (FBA) is proposed in an attempt to remedy some of these difficulties. This approach is based on the representation of the system`s uncertainties using Fuzzy Set Theory-basedmore » approximations and on the representation of the reasoning and control schemes as sets of elemental behaviors. Using the FBA, a formalism for rule base development and an automated generator of fuzzy rules have been developed. This automated system can automatically construct the set of membership functions corresponding to fuzzy behaviors. Once these have been expressed in qualitative terms by the user. The system also checks for completeness of the rule base and for non-redundancy of the rules (which has traditionally been a major hurdle in rule base development). Two major conceptual features, the suppression and inhibition mechanisms which allow to express a dominance between behaviors are discussed in detail. Some experimental results obtained with the automated fuzzy, rule generator applied to the domain of sensor-based navigation in aprion unknown environments. using one of our autonomous test-bed robots as well as a real car in outdoor environments, are then reviewed and discussed to illustrate the feasibility of large-scale automatic fuzzy rule generation using the {open_quotes}Fuzzy Behaviorist{close_quotes} concepts.« less
Linear analysis near a steady-state of biochemical networks: Control analysis, correlation metrics and circuit theory

PubMed Central

Heuett, William J; Beard, Daniel A; Qian, Hong

2008-01-01

Background Several approaches, including metabolic control analysis (MCA), flux balance analysis (FBA), correlation metric construction (CMC), and biochemical circuit theory (BCT), have been developed for the quantitative analysis of complex biochemical networks. Here, we present a comprehensive theory of linear analysis for nonequilibrium steady-state (NESS) biochemical reaction networks that unites these disparate approaches in a common mathematical framework and thermodynamic basis. Results In this theory a number of relationships between key matrices are introduced: the matrix A obtained in the standard, linear-dynamic-stability analysis of the steady-state can be decomposed as A = SRT where R and S are directly related to the elasticity-coefficient matrix for the fluxes and chemical potentials in MCA, respectively; the control-coefficients for the fluxes and chemical potentials can be written in terms of RTBS and STBS respectively where matrix B is the inverse of A; the matrix S is precisely the stoichiometric matrix in FBA; and the matrix eAt plays a central role in CMC. Conclusion One key finding that emerges from this analysis is that the well-known summation theorems in MCA take different forms depending on whether metabolic steady-state is maintained by flux injection or concentration clamping. We demonstrate that if rate-limiting steps exist in a biochemical pathway, they are the steps with smallest biochemical conductances and largest flux control-coefficients. We hypothesize that biochemical networks for cellular signaling have a different strategy for minimizing energy waste and being efficient than do biochemical networks for biosynthesis. We also discuss the intimate relationship between MCA and biochemical systems analysis (BSA). PMID:18482450
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.

PubMed

Klamt, Steffen; Regensburger, Georg; Gerstl, Matthias P; Jungreuthmayer, Christian; Schuster, Stefan; Mahadevan, Radhakrishnan; Zanghellini, Jürgen; Müller, Stefan

2017-04-01

Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising from reaction irreversibilities and the assumption of steady state; however, other (inhomogeneous) linear constraints, such as minimal and maximal reaction rates frequently used by other constraint-based techniques (such as flux balance analysis [FBA]), cannot be directly integrated. These additional constraints further restrict the space of feasible flux vectors and turn the flux cone into a general flux polyhedron in which the concept of EFMs is not directly applicable anymore. For this reason, there has been a conceptual gap between EFM-based (pathway) analysis methods and linear optimization (FBA) techniques, as they operate on different geometric objects. One approach to overcome these limitations was proposed ten years ago and is based on the concept of elementary flux vectors (EFVs). Only recently has the community started to recognize the potential of EFVs for metabolic network analysis. In fact, EFVs exactly represent the conceptual development required to generalize the idea of EFMs from flux cones to flux polyhedra. This work aims to present a concise theoretical and practical introduction to EFVs that is accessible to a broad audience. We highlight the close relationship between EFMs and EFVs and demonstrate that almost all applications of EFMs (in flux cones) are possible for EFVs (in flux polyhedra) as well. In fact, certain properties can only be studied with EFVs. Thus, we conclude that EFVs provide a powerful and unifying framework for constraint-based modeling of metabolic networks.
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

PubMed Central

Klamt, Steffen; Gerstl, Matthias P.; Jungreuthmayer, Christian; Mahadevan, Radhakrishnan; Müller, Stefan

2017-01-01

Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic pathways and have become an established tool for constraint-based modeling and metabolic network analysis. EFMs are characteristic (support-minimal) vectors of the flux cone that contains all feasible steady-state flux vectors of a given metabolic network. EFMs account for (homogeneous) linear constraints arising from reaction irreversibilities and the assumption of steady state; however, other (inhomogeneous) linear constraints, such as minimal and maximal reaction rates frequently used by other constraint-based techniques (such as flux balance analysis [FBA]), cannot be directly integrated. These additional constraints further restrict the space of feasible flux vectors and turn the flux cone into a general flux polyhedron in which the concept of EFMs is not directly applicable anymore. For this reason, there has been a conceptual gap between EFM-based (pathway) analysis methods and linear optimization (FBA) techniques, as they operate on different geometric objects. One approach to overcome these limitations was proposed ten years ago and is based on the concept of elementary flux vectors (EFVs). Only recently has the community started to recognize the potential of EFVs for metabolic network analysis. In fact, EFVs exactly represent the conceptual development required to generalize the idea of EFMs from flux cones to flux polyhedra. This work aims to present a concise theoretical and practical introduction to EFVs that is accessible to a broad audience. We highlight the close relationship between EFMs and EFVs and demonstrate that almost all applications of EFMs (in flux cones) are possible for EFVs (in flux polyhedra) as well. In fact, certain properties can only be studied with EFVs. Thus, we conclude that EFVs provide a powerful and unifying framework for constraint-based modeling of metabolic networks. PMID:28406903
Status of serum-calcium and -albumin measurement in Argentina assessed in 300 representative laboratories with 20 fresh frozen single donation sera.

PubMed

Stepman, Hedwig C M; Stöckl, Dietmar; Acheme, Rosana; Sesini, Sandra; Mazziotta, Daniel; Thienpont, Linda M

2011-11-01

The Fundación Bioquímica Argentina (FBA) performs external quality assessment (EQA) of >3200 laboratories. However, FBA realizes that sample non-commutability and predominant use of heterogeneous systems may bias the estimated performance and standardization status. To eliminate these confounding factors, a study using frozen single donation sera was undertaken with the focus on serum-calcium and -albumin measurement. Target values were established from the results produced with homogeneous systems. In groups of n=7, system effects were investigated. Laboratory performance was evaluated from the correlation coefficient r between the measurement results for all sera and the target values. This allowed ranking of the laboratories and judgment of the deviation for individual samples (total error) against a 10% limit. The total error specification was a deviation for ≥ 5 samples exceeding 10% and/or causing a result outside the laboratory's reference interval. For calcium (n=303) (range: 2.06-2.42 mmol/L), 81 laboratories had an r-value <0.6, 43 even <0.4; the total error was relevant for 97 (10% limit) and 111 (reference interval) laboratories. For albumin (n=311) (range: 34.7-45.7 g/L) r was <0.7 (<0.4) in 44 (16) laboratories; 83 and 36 laboratories exceeded the total error criteria. Laboratories using homogeneous systems were generally ranked higher by correlation. System effects were moderate for calcium, but significant for albumin. The study demonstrated the need to improve the quality and harmonization of calcium and albumin testing in the investigated laboratories. To achieve this objective, we promote co-operation between laboratories, EQA provider and manufacturers.
Using the clustered circular layout as an informative method for visualizing protein-protein interaction networks.

PubMed

Fung, David C Y; Wilkins, Marc R; Hart, David; Hong, Seok-Hee

2010-07-01

The force-directed layout is commonly used in computer-generated visualizations of protein-protein interaction networks. While it is good for providing a visual outline of the protein complexes and their interactions, it has two limitations when used as a visual analysis method. The first is poor reproducibility. Repeated running of the algorithm does not necessarily generate the same layout, therefore, demanding cognitive readaptation on the investigator's part. The second limitation is that it does not explicitly display complementary biological information, e.g. Gene Ontology, other than the protein names or gene symbols. Here, we present an alternative layout called the clustered circular layout. Using the human DNA replication protein-protein interaction network as a case study, we compared the two network layouts for their merits and limitations in supporting visual analysis.
The role of 3-D interactive visualization in blind surveys of H I in galaxies

NASA Astrophysics Data System (ADS)

Punzo, D.; van der Hulst, J. M.; Roerdink, J. B. T. M.; Oosterloo, T. A.; Ramatsoku, M.; Verheijen, M. A. W.

2015-09-01

Upcoming H I surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize H I objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. We discuss how Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain. The requirements for a fully interactive visualization tool are: coupled 1-D/2-D/3-D visualization, quantitative and comparative capabilities, combined with supervised semi-automated analysis. Moreover, the source code must have the following characteristics for enabling collaborative work: open, modular, well documented, and well maintained. We review four state of-the-art, 3-D visualization packages assessing their capabilities and feasibility for use in the case of 3-D astronomical data.
iview: an interactive WebGL visualizer for protein-ligand complex.

PubMed

Li, Hongjian; Leung, Kwong-Sak; Nakane, Takanori; Wong, Man-Hon

2014-02-25

Visualization of protein-ligand complex plays an important role in elaborating protein-ligand interactions and aiding novel drug design. Most existing web visualizers either rely on slow software rendering, or lack virtual reality support. The vital feature of macromolecular surface construction is also unavailable. We have developed iview, an easy-to-use interactive WebGL visualizer of protein-ligand complex. It exploits hardware acceleration rather than software rendering. It features three special effects in virtual reality settings, namely anaglyph, parallax barrier and oculus rift, resulting in visually appealing identification of intermolecular interactions. It supports four surface representations including Van der Waals surface, solvent excluded surface, solvent accessible surface and molecular surface. Moreover, based on the feature-rich version of iview, we have also developed a neat and tailor-made version specifically for our istar web platform for protein-ligand docking purpose. This demonstrates the excellent portability of iview. Using innovative 3D techniques, we provide a user friendly visualizer that is not intended to compete with professional visualizers, but to enable easy accessibility and platform independence.
NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.

PubMed

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

2016-07-01

The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization. Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/ mohamed@kuicr.kyoto-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Interactive visual exploration and analysis of origin-destination data

NASA Astrophysics Data System (ADS)

Ding, Linfang; Meng, Liqiu; Yang, Jian; Krisp, Jukka M.

2018-05-01

In this paper, we propose a visual analytics approach for the exploration of spatiotemporal interaction patterns of massive origin-destination data. Firstly, we visually query the movement database for data at certain time windows. Secondly, we conduct interactive clustering to allow the users to select input variables/features (e.g., origins, destinations, distance, and duration) and to adjust clustering parameters (e.g. distance threshold). The agglomerative hierarchical clustering method is applied for the multivariate clustering of the origin-destination data. Thirdly, we design a parallel coordinates plot for visualizing the precomputed clusters and for further exploration of interesting clusters. Finally, we propose a gradient line rendering technique to show the spatial and directional distribution of origin-destination clusters on a map view. We implement the visual analytics approach in a web-based interactive environment and apply it to real-world floating car data from Shanghai. The experiment results show the origin/destination hotspots and their spatial interaction patterns. They also demonstrate the effectiveness of our proposed approach.
Visual Sensitivity of Deepwater Fishes in Lake Superior

PubMed Central

Harrington, Kelly A.; Hrabik, Thomas R.; Mensinger, Allen F.

2015-01-01

The predator-prey interactions in the offshore food web of Lake Superior have been well documented, but the sensory systems mediating these interactions remain unknown. The deepwater sculpin, (Myoxocephalus thompsoni), siscowet (Salvelinus namaycush siscowet), and kiyi (Coregonus kiyi) inhabit low light level environments. To investigate the potential role of vision in predator-prey interactions, electroretinography was used to determine visual sensitivity for each species. Spectral sensitivity curves revealed peak sensitivity at 525 nm for each species which closely corresponds to the prevalent downwelling light spectrum at depth. To determine if sufficient light was available to mediate predator-prey interactions, visual sensitivity was correlated with the intensity of downwelling light in Lake Superior to construct visual depth profiles for each species. Sufficient daytime irradiance exists for visual interactions to approximately 325 m for siscowet and kiyi and 355 m for the deepwater sculpin during summer months. Under full moon conditions, sufficient irradiance exists to elicit ERG response to light available at approximately 30 m for the siscowet and kiyi and 45 m for the deepwater sculpin. Visual interactions are therefore possible at the depths and times when these organisms overlap in the water column indicating that vision may play a far greater role at depth in deep freshwater lakes than had been previously documented. PMID:25646781

View-Dependent Streamline Deformation and Exploration

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

Tong, Xin; Edwards, John; Chen, Chun-Ming

Occlusion presents a major challenge in visualizing 3D flow and tensor fields using streamlines. Displaying too many streamlines creates a dense visualization filled with occluded structures, but displaying too few streams risks losing important features. We propose a new streamline exploration approach by visually manipulating the cluttered streamlines by pulling visible layers apart and revealing the hidden structures underneath. This paper presents a customized view-dependent deformation algorithm and an interactive visualization tool to minimize visual cluttering for visualizing 3D vector and tensor fields. The algorithm is able to maintain the overall integrity of the fields and expose previously hidden structures.more » Our system supports both mouse and direct-touch interactions to manipulate the viewing perspectives and visualize the streamlines in depth. By using a lens metaphor of different shapes to select the transition zone of the targeted area interactively, the users can move their focus and examine the vector or tensor field freely.« less
Living Liquid: Design and Evaluation of an Exploratory Visualization Tool for Museum Visitors.

PubMed

Ma, J; Liao, I; Ma, Kwan-Liu; Frazier, J

2012-12-01

Interactive visualizations can allow science museum visitors to explore new worlds by seeing and interacting with scientific data. However, designing interactive visualizations for informal learning environments, such as museums, presents several challenges. First, visualizations must engage visitors on a personal level. Second, visitors often lack the background to interpret visualizations of scientific data. Third, visitors have very limited time at individual exhibits in museums. This paper examines these design considerations through the iterative development and evaluation of an interactive exhibit as a visualization tool that gives museumgoers access to scientific data generated and used by researchers. The exhibit prototype, Living Liquid, encourages visitors to ask and answer their own questions while exploring the time-varying global distribution of simulated marine microbes using a touchscreen interface. Iterative development proceeded through three rounds of formative evaluations using think-aloud protocols and interviews, each round informing a key visualization design decision: (1) what to visualize to initiate inquiry, (2) how to link data at the microscopic scale to global patterns, and (3) how to include additional data that allows visitors to pursue their own questions. Data from visitor evaluations suggests that, when designing visualizations for public audiences, one should (1) avoid distracting visitors from data that they should explore, (2) incorporate background information into the visualization, (3) favor understandability over scientific accuracy, and (4) layer data accessibility to structure inquiry. Lessons learned from this case study add to our growing understanding of how to use visualizations to actively engage learners with scientific data.
Chronodes: Interactive Multifocus Exploration of Event Sequences

PubMed Central

POLACK, PETER J.; CHEN, SHANG-TSE; KAHNG, MINSUK; DE BARBARO, KAYA; BASOLE, RAHUL; SHARMIN, MOUSHUMI; CHAU, DUEN HORNG

2018-01-01

The advent of mobile health (mHealth) technologies challenges the capabilities of current visualizations, interactive tools, and algorithms. We present Chronodes, an interactive system that unifies data mining and human-centric visualization techniques to support explorative analysis of longitudinal mHealth data. Chronodes extracts and visualizes frequent event sequences that reveal chronological patterns across multiple participant timelines of mHealth data. It then combines novel interaction and visualization techniques to enable multifocus event sequence analysis, which allows health researchers to interactively define, explore, and compare groups of participant behaviors using event sequence combinations. Through summarizing insights gained from a pilot study with 20 behavioral and biomedical health experts, we discuss Chronodes’s efficacy and potential impact in the mHealth domain. Ultimately, we outline important open challenges in mHealth, and offer recommendations and design guidelines for future research. PMID:29515937
Not Just a Game … When We Play Together, We Learn Together: Interactive Virtual Environments and Gaming Engines for Geospatial Visualization

NASA Astrophysics Data System (ADS)

Shipman, J. S.; Anderson, J. W.

2017-12-01

An ideal tool for ecologists and land managers to investigate the impacts of both projected environmental changes and policy alternatives is the creation of immersive, interactive, virtual landscapes. As a new frontier in visualizing and understanding geospatial data, virtual landscapes require a new toolbox for data visualization that includes traditional GIS tools and uncommon tools such as the Unity3d game engine. Game engines provide capabilities to not only explore data but to build and interact with dynamic models collaboratively. These virtual worlds can be used to display and illustrate data that is often more understandable and plausible to both stakeholders and policy makers than is achieved using traditional maps.Within this context we will present funded research that has been developed utilizing virtual landscapes for geographic visualization and decision support among varied stakeholders. We will highlight the challenges and lessons learned when developing interactive virtual environments that require large multidisciplinary team efforts with varied competences. The results will emphasize the importance of visualization and interactive virtual environments and the link with emerging research disciplines within Visual Analytics.
Instant Gratification: Striking a Balance Between Rich Interactive Visualization and Ease of Use for Casual Web Surfers

NASA Astrophysics Data System (ADS)

Russell, R. M.; Johnson, R. M.; Gardiner, E. S.; Bergman, J. J.; Genyuk, J.; Henderson, S.

2004-12-01

Interactive visualizations can be powerful tools for helping students, teachers, and the general public comprehend significant features in rich datasets and complex systems. Successful use of such visualizations requires viewers to have, or to acquire, adequate expertise in use of the relevant visualization tools. In many cases, the learning curve associated with competent use of such tools is too steep for casual users, such as members of the lay public browsing science outreach web sites or K-12 students and teachers trying to integrate such tools into their learning about geosciences. "Windows to the Universe" (http://www.windows.ucar.edu) is a large (roughly 6,000 web pages), well-established (first posted online in 1995), and popular (over 5 million visitor sessions and 40 million pages viewed per year) science education web site that covers a very broad range of Earth science and space science topics. The primary audience of the site consists of K-12 students and teachers and the general public. We have developed several interactive visualizations for use on the site in conjunction with text and still image reference materials. One major emphasis in the design of these interactives has been to ensure that casual users can quickly learn how to use the interactive features without becoming frustrated and departing before they were able to appreciate the visualizations displayed. We will demonstrate several of these "user-friendly" interactive visualizations and comment on the design philosophy we have employed in developing them.
Cross-modal interactions during perception of audiovisual speech and nonspeech signals: an fMRI study.

PubMed

Hertrich, Ingo; Dietrich, Susanne; Ackermann, Hermann

2011-01-01

During speech communication, visual information may interact with the auditory system at various processing stages. Most noteworthy, recent magnetoencephalography (MEG) data provided first evidence for early and preattentive phonetic/phonological encoding of the visual data stream--prior to its fusion with auditory phonological features [Hertrich, I., Mathiak, K., Lutzenberger, W., & Ackermann, H. Time course of early audiovisual interactions during speech and non-speech central-auditory processing: An MEG study. Journal of Cognitive Neuroscience, 21, 259-274, 2009]. Using functional magnetic resonance imaging, the present follow-up study aims to further elucidate the topographic distribution of visual-phonological operations and audiovisual (AV) interactions during speech perception. Ambiguous acoustic syllables--disambiguated to /pa/ or /ta/ by the visual channel (speaking face)--served as test materials, concomitant with various control conditions (nonspeech AV signals, visual-only and acoustic-only speech, and nonspeech stimuli). (i) Visual speech yielded an AV-subadditive activation of primary auditory cortex and the anterior superior temporal gyrus (STG), whereas the posterior STG responded both to speech and nonspeech motion. (ii) The inferior frontal and the fusiform gyrus of the right hemisphere showed a strong phonetic/phonological impact (differential effects of visual /pa/ vs. /ta/) upon hemodynamic activation during presentation of speaking faces. Taken together with the previous MEG data, these results point at a dual-pathway model of visual speech information processing: On the one hand, access to the auditory system via the anterior supratemporal “what" path may give rise to direct activation of "auditory objects." On the other hand, visual speech information seems to be represented in a right-hemisphere visual working memory, providing a potential basis for later interactions with auditory information such as the McGurk effect.
What Makes a Message Stick? The Role of Content and Context in Social Media Epidemics

DTIC Science & Technology

2013-09-23

First, we propose visual memes , or frequently re-posted short video segments, for detecting and monitoring latent video interactions at scale. Content...interactions (such as quoting, or remixing, parts of a video). Visual memes are extracted by scalable detection algorithms that we develop, with...high accuracy. We further augment visual memes with text, via a statistical model of latent topics. We model content interactions on YouTube with
One year study on the integrative intervention of acupressure and interactive multimedia for visual health in school children.

PubMed

Yeh, Mei-Ling; Chen, Hsing-Hsia; Chung, Yu-Chu

2012-12-01

This study used a larger sample size, added a long-term observation of the effect of intervention, and provided an integrated intervention of acupressure and interactive multimedia of visual health instruction for school children. The short- and long-term effects of the interventions were then evaluated by visual health knowledge, visual acuity, and refractive error. A repeated pretest-posttest controlled trial was used with two experimental groups and one control group. Four elementary schools in northern Taiwan. 287 School children with visual impairment in fourth grade were recruited. One experimental group received the integrative intervention of acupressure and interactive multimedia of visual health instruction (ACIMU), and another received auricular acupressure (AC) alone; whereas a control group received no intervention. Two 10-week interventions were separately given in the fall and spring semesters. The short- and long-term effects of the interventions were then evaluated by visual health knowledge, visual acuity, and refractive error. During the school year the visual health knowledge was significantly higher in the ACIMU group than the control group (p<0.001). A significant difference in the changing visual acuity was in the three groups (p<0.001), with the improvement in the ACIMU group. No difference in the refractive error was found between any two groups (p>0.05). This study demonstrated that a long-term period of acupressure is required to improve school children's visual health. School children receiving the intervention of acupressure combined with interactive multimedia had better improvement of visual health and related knowledge than others. Further study is suggested in which visual health and preventative needs can be established for early childhood. Copyright © 2012 Elsevier Ltd. All rights reserved.
Mapping the landscape of metabolic goals of a cell

DOE PAGES

Zhao, Qi; Stettner, Arion I.; Reznik, Ed; ...

2016-05-23

Here, genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function. We introduce an efficient inverse flux balance analysis (invFBA) approach, based on linear programming duality, to characterize the space of possible objective functions compatible with measured fluxes. After testing our algorithm on simulated E. coli data and time-dependent S. oneidensis fluxes inferred from gene expression, we apply our inverse approach to flux measurements in long-term evolved E. coli strains, revealing objective functions that provide insight into metabolic adaptationmore » trajectories.« less
Metabolic network modeling with model organisms.

PubMed

Yilmaz, L Safak; Walhout, Albertha Jm

2017-02-01

Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases. Here, we discuss GSMNMs of most highly used model organisms with the emphasis on recent reconstructions. Published by Elsevier Ltd.
Metabolic network modeling with model organisms

PubMed Central

Yilmaz, L. Safak; Walhout, Albertha J.M.

2017-01-01

Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases. Here, we discuss GSMNMs of most highly used model organisms with the emphasis on recent reconstructions. PMID:28088694
On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

PubMed

Gomez-Ramirez, Jaime; Sanz, Ricardo

2013-09-01

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.
Interactive visualization of numerical simulation results: A tool for mission planning and data analysis

NASA Technical Reports Server (NTRS)

Berchem, J.; Raeder, J.; Walker, R. J.; Ashour-Abdalla, M.

1995-01-01

We report on the development of an interactive system for visualizing and analyzing numerical simulation results. This system is based on visualization modules which use the Application Visualization System (AVS) and the NCAR graphics packages. Examples from recent simulations are presented to illustrate how these modules can be used for displaying and manipulating simulation results to facilitate their comparison with phenomenological model results and observations.
Interactive Visualization of Healthcare Data Using Tableau.

PubMed

Ko, Inseok; Chang, Hyejung

2017-10-01

Big data analysis is receiving increasing attention in many industries, including healthcare. Visualization plays an important role not only in intuitively showing the results of data analysis but also in the whole process of collecting, cleaning, analyzing, and sharing data. This paper presents a procedure for the interactive visualization and analysis of healthcare data using Tableau as a business intelligence tool. Starting with installation of the Tableau Desktop Personal version 10.3, this paper describes the process of understanding and visualizing healthcare data using an example. The example data of colon cancer patients were obtained from health insurance claims in years 2012 and 2013, provided by the Health Insurance Review and Assessment Service. To explore the visualization of healthcare data using Tableau for beginners, this paper describes the creation of a simple view for the average length of stay of colon cancer patients. Since Tableau provides various visualizations and customizations, the level of analysis can be increased with small multiples, view filtering, mark cards, and Tableau charts. Tableau is a software that can help users explore and understand their data by creating interactive visualizations. The software has the advantages that it can be used in conjunction with almost any database, and it is easy to use by dragging and dropping to create an interactive visualization expressing the desired format.
Frontal–Occipital Connectivity During Visual Search

PubMed Central

Pantazatos, Spiro P.; Yanagihara, Ted K.; Zhang, Xian; Meitzler, Thomas

2012-01-01

Abstract Although expectation- and attention-related interactions between ventral and medial prefrontal cortex and stimulus category-selective visual regions have been identified during visual detection and discrimination, it is not known if similar neural mechanisms apply to other tasks such as visual search. The current work tested the hypothesis that high-level frontal regions, previously implicated in expectation and visual imagery of object categories, interact with visual regions associated with object recognition during visual search. Using functional magnetic resonance imaging, subjects searched for a specific object that varied in size and location within a complex natural scene. A model-free, spatial-independent component analysis isolated multiple task-related components, one of which included visual cortex, as well as a cluster within ventromedial prefrontal cortex (vmPFC), consistent with the engagement of both top-down and bottom-up processes. Analyses of psychophysiological interactions showed increased functional connectivity between vmPFC and object-sensitive lateral occipital cortex (LOC), and results from dynamic causal modeling and Bayesian Model Selection suggested bidirectional connections between vmPFC and LOC that were positively modulated by the task. Using image-guided diffusion-tensor imaging, functionally seeded, probabilistic white-matter tracts between vmPFC and LOC, which presumably underlie this effective interconnectivity, were also observed. These connectivity findings extend previous models of visual search processes to include specific frontal–occipital neuronal interactions during a natural and complex search task. PMID:22708993
Smelling directions: Olfaction modulates ambiguous visual motion perception

PubMed Central

Kuang, Shenbing; Zhang, Tao

2014-01-01

Senses of smells are often accompanied by simultaneous visual sensations. Previous studies have documented enhanced olfactory performance with concurrent presence of congruent color- or shape- related visual cues, and facilitated visual object perception when congruent smells are simultaneously present. These visual object-olfaction interactions suggest the existences of couplings between the olfactory pathway and the visual ventral processing stream. However, it is not known if olfaction can modulate visual motion perception, a function that is related to the visual dorsal stream. We tested this possibility by examining the influence of olfactory cues on the perceptions of ambiguous visual motion signals. We showed that, after introducing an association between motion directions and olfactory cues, olfaction could indeed bias ambiguous visual motion perceptions. Our result that olfaction modulates visual motion processing adds to the current knowledge of cross-modal interactions and implies a possible functional linkage between the olfactory system and the visual dorsal pathway. PMID:25052162
Visualization of protein interaction networks: problems and solutions

PubMed Central

2013-01-01

Background Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. The set of all interactions of an organism forms a protein-protein interaction network (PIN) and is an important tool for studying the behaviour of the cell machinery. Since graphic representation of PINs may highlight important substructures, e.g. protein complexes, visualization is more and more used to study the underlying graph structure of PINs. Although graphs are well known data structures, there are different open problems regarding PINs visualization: the high number of nodes and connections, the heterogeneity of nodes (proteins) and edges (interactions), the possibility to annotate proteins and interactions with biological information extracted by ontologies (e.g. Gene Ontology) that enriches the PINs with semantic information, but complicates their visualization. Methods In these last years many software tools for the visualization of PINs have been developed. Initially thought for visualization only, some of them have been successively enriched with new functions for PPI data management and PIN analysis. The paper analyzes the main software tools for PINs visualization considering four main criteria: (i) technology, i.e. availability/license of the software and supported OS (Operating System) platforms; (ii) interoperability, i.e. ability to import/export networks in various formats, ability to export data in a graphic format, extensibility of the system, e.g. through plug-ins; (iii) visualization, i.e. supported layout and rendering algorithms and availability of parallel implementation; (iv) analysis, i.e. availability of network analysis functions, such as clustering or mining of the graph, and the possibility to interact with external databases. Results Currently, many tools are available and it is not easy for the users choosing one of them. Some tools offer sophisticated 2D and 3D network visualization making available many layout algorithms, others tools are more data-oriented and support integration of interaction data coming from different sources and data annotation. Finally, some specialistic tools are dedicated to the analysis of pathways and cellular processes and are oriented toward systems biology studies, where the dynamic aspects of the processes being studied are central. Conclusion A current trend is the deployment of open, extensible visualization tools (e.g. Cytoscape), that may be incrementally enriched by the interactomics community with novel and more powerful functions for PIN analysis, through the development of plug-ins. On the other hand, another emerging trend regards the efficient and parallel implementation of the visualization engine that may provide high interactivity and near real-time response time, as in NAViGaTOR. From a technological point of view, open-source, free and extensible tools, like Cytoscape, guarantee a long term sustainability due to the largeness of the developers and users communities, and provide a great flexibility since new functions are continuously added by the developer community through new plug-ins, but the emerging parallel, often closed-source tools like NAViGaTOR, can offer near real-time response time also in the analysis of very huge PINs. PMID:23368786
Vestibular-visual interactions in flight simulators

NASA Technical Reports Server (NTRS)

Clark, B.

1977-01-01

The following research work is reported: (1) vestibular-visual interactions; (2) flight management and crew system interactions; (3) peripheral cue utilization in simulation technology; (4) control of signs and symptoms of motion sickness; (5) auditory cue utilization in flight simulators, and (6) vestibular function: Animal experiments.
SOCR "Motion Charts": An Efficient, Open-Source, Interactive and Dynamic Applet for Visualizing Longitudinal Multivariate Data

ERIC Educational Resources Information Center

Al-Aziz, Jameel; Christou, Nicolas; Dinov, Ivo D.

2010-01-01

The amount, complexity and provenance of data have dramatically increased in the past five years. Visualization of observed and simulated data is a critical component of any social, environmental, biomedical or scientific quest. Dynamic, exploratory and interactive visualization of multivariate data, without preprocessing by dimensionality…
Bioluminescence resonance energy transfer (BRET) to detect the interactions between kappa opioid receptor and non visual arrestins.

PubMed

Bedini, Andrea

2015-01-01

Bioluminescence resonance energy transfer (BRET) is a very sensitive technique employed to study protein-protein interactions, including G-protein-coupled receptors (GPCRs) hetero- and homo-dimerization. Recently, BRET has also been used to investigate the interaction between GPCRs (e.g., β2 adrenergic receptor, muscarinic M2 receptor, dopaminergic D2 receptor) and non-visual arrestins. Here a BRET protocol is described to investigate interactions between the kappa opioid receptor (KOR) and non visual arrestins (arrestin-2 and arrestin-3) in HEK-293 cells, both under basal conditions and after exposure to KOR ligands.

Visual and proprioceptive interaction in patients with bilateral vestibular loss☆

PubMed Central

Cutfield, Nicholas J.; Scott, Gregory; Waldman, Adam D.; Sharp, David J.; Bronstein, Adolfo M.

2014-01-01

Following bilateral vestibular loss (BVL) patients gradually adapt to the loss of vestibular input and rely more on other sensory inputs. Here we examine changes in the way proprioceptive and visual inputs interact. We used functional magnetic resonance imaging (fMRI) to investigate visual responses in the context of varying levels of proprioceptive input in 12 BVL subjects and 15 normal controls. A novel metal-free vibrator was developed to allow vibrotactile neck proprioceptive input to be delivered in the MRI system. A high level (100 Hz) and low level (30 Hz) control stimulus was applied over the left splenius capitis; only the high frequency stimulus generates a significant proprioceptive stimulus. The neck stimulus was applied in combination with static and moving (optokinetic) visual stimuli, in a factorial fMRI experimental design. We found that high level neck proprioceptive input had more cortical effect on brain activity in the BVL patients. This included a reduction in visual motion responses during high levels of proprioceptive input and differential activation in the midline cerebellum. In early visual cortical areas, the effect of high proprioceptive input was present for both visual conditions but in lateral visual areas, including V5/MT, the effect was only seen in the context of visual motion stimulation. The finding of a cortical visuo-proprioceptive interaction in BVL patients is consistent with behavioural data indicating that, in BVL patients, neck afferents partly replace vestibular input during the CNS-mediated compensatory process. An fMRI cervico-visual interaction may thus substitute the known visuo-vestibular interaction reported in normal subject fMRI studies. The results provide evidence for a cortical mechanism of adaptation to vestibular failure, in the form of an enhanced proprioceptive influence on visual processing. The results may provide the basis for a cortical mechanism involved in proprioceptive substitution of vestibular function in BVL patients. PMID:25061564
Visual and proprioceptive interaction in patients with bilateral vestibular loss.

PubMed

Cutfield, Nicholas J; Scott, Gregory; Waldman, Adam D; Sharp, David J; Bronstein, Adolfo M

2014-01-01

Following bilateral vestibular loss (BVL) patients gradually adapt to the loss of vestibular input and rely more on other sensory inputs. Here we examine changes in the way proprioceptive and visual inputs interact. We used functional magnetic resonance imaging (fMRI) to investigate visual responses in the context of varying levels of proprioceptive input in 12 BVL subjects and 15 normal controls. A novel metal-free vibrator was developed to allow vibrotactile neck proprioceptive input to be delivered in the MRI system. A high level (100 Hz) and low level (30 Hz) control stimulus was applied over the left splenius capitis; only the high frequency stimulus generates a significant proprioceptive stimulus. The neck stimulus was applied in combination with static and moving (optokinetic) visual stimuli, in a factorial fMRI experimental design. We found that high level neck proprioceptive input had more cortical effect on brain activity in the BVL patients. This included a reduction in visual motion responses during high levels of proprioceptive input and differential activation in the midline cerebellum. In early visual cortical areas, the effect of high proprioceptive input was present for both visual conditions but in lateral visual areas, including V5/MT, the effect was only seen in the context of visual motion stimulation. The finding of a cortical visuo-proprioceptive interaction in BVL patients is consistent with behavioural data indicating that, in BVL patients, neck afferents partly replace vestibular input during the CNS-mediated compensatory process. An fMRI cervico-visual interaction may thus substitute the known visuo-vestibular interaction reported in normal subject fMRI studies. The results provide evidence for a cortical mechanism of adaptation to vestibular failure, in the form of an enhanced proprioceptive influence on visual processing. The results may provide the basis for a cortical mechanism involved in proprioceptive substitution of vestibular function in BVL patients.
View-Dependent Streamline Deformation and Exploration

PubMed Central

Tong, Xin; Edwards, John; Chen, Chun-Ming; Shen, Han-Wei; Johnson, Chris R.; Wong, Pak Chung

2016-01-01

Occlusion presents a major challenge in visualizing 3D flow and tensor fields using streamlines. Displaying too many streamlines creates a dense visualization filled with occluded structures, but displaying too few streams risks losing important features. We propose a new streamline exploration approach by visually manipulating the cluttered streamlines by pulling visible layers apart and revealing the hidden structures underneath. This paper presents a customized view-dependent deformation algorithm and an interactive visualization tool to minimize visual clutter in 3D vector and tensor fields. The algorithm is able to maintain the overall integrity of the fields and expose previously hidden structures. Our system supports both mouse and direct-touch interactions to manipulate the viewing perspectives and visualize the streamlines in depth. By using a lens metaphor of different shapes to select the transition zone of the targeted area interactively, the users can move their focus and examine the vector or tensor field freely. PMID:26600061
Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data

PubMed Central

Fernandez, Nicolas F.; Gundersen, Gregory W.; Rahman, Adeeb; Grimes, Mark L.; Rikova, Klarisa; Hornbeck, Peter; Ma’ayan, Avi

2017-01-01

Most tools developed to visualize hierarchically clustered heatmaps generate static images. Clustergrammer is a web-based visualization tool with interactive features such as: zooming, panning, filtering, reordering, sharing, performing enrichment analysis, and providing dynamic gene annotations. Clustergrammer can be used to generate shareable interactive visualizations by uploading a data table to a web-site, or by embedding Clustergrammer in Jupyter Notebooks. The Clustergrammer core libraries can also be used as a toolkit by developers to generate visualizations within their own applications. Clustergrammer is demonstrated using gene expression data from the cancer cell line encyclopedia (CCLE), original post-translational modification data collected from lung cancer cells lines by a mass spectrometry approach, and original cytometry by time of flight (CyTOF) single-cell proteomics data from blood. Clustergrammer enables producing interactive web based visualizations for the analysis of diverse biological data. PMID:28994825
View-Dependent Streamline Deformation and Exploration.

PubMed

Tong, Xin; Edwards, John; Chen, Chun-Ming; Shen, Han-Wei; Johnson, Chris R; Wong, Pak Chung

2016-07-01

Occlusion presents a major challenge in visualizing 3D flow and tensor fields using streamlines. Displaying too many streamlines creates a dense visualization filled with occluded structures, but displaying too few streams risks losing important features. We propose a new streamline exploration approach by visually manipulating the cluttered streamlines by pulling visible layers apart and revealing the hidden structures underneath. This paper presents a customized view-dependent deformation algorithm and an interactive visualization tool to minimize visual clutter in 3D vector and tensor fields. The algorithm is able to maintain the overall integrity of the fields and expose previously hidden structures. Our system supports both mouse and direct-touch interactions to manipulate the viewing perspectives and visualize the streamlines in depth. By using a lens metaphor of different shapes to select the transition zone of the targeted area interactively, the users can move their focus and examine the vector or tensor field freely.
Interactions between Visual Attention and Episodic Retrieval: Dissociable Contributions of Parietal Regions during Gist-Based False Recognition

PubMed Central

Guerin, Scott A.; Robbins, Clifford A.; Gilmore, Adrian W.; Schacter, Daniel L.

2012-01-01

SUMMARY The interaction between episodic retrieval and visual attention is relatively unexplored. Given that systems mediating attention and episodic memory appear to be segregated, and perhaps even in competition, it is unclear how visual attention is recruited during episodic retrieval. We investigated the recruitment of visual attention during the suppression of gist-based false recognition, the tendency to falsely recognize items that are similar to previously encountered items. Recruitment of visual attention was associated with activity in the dorsal attention network. The inferior parietal lobule, often implicated in episodic retrieval, tracked veridical retrieval of perceptual detail and showed reduced activity during the engagement of visual attention, consistent with a competitive relationship with the dorsal attention network. These findings suggest that the contribution of the parietal cortex to interactions between visual attention and episodic retrieval entails distinct systems that contribute to different components of the task while also suppressing each other. PMID:22998879
Real-time scalable visual analysis on mobile devices

NASA Astrophysics Data System (ADS)

Pattath, Avin; Ebert, David S.; May, Richard A.; Collins, Timothy F.; Pike, William

2008-02-01

Interactive visual presentation of information can help an analyst gain faster and better insight from data. When combined with situational or context information, visualization on mobile devices is invaluable to in-field responders and investigators. However, several challenges are posed by the form-factor of mobile devices in developing such systems. In this paper, we classify these challenges into two broad categories - issues in general mobile computing and issues specific to visual analysis on mobile devices. Using NetworkVis and Infostar as example systems, we illustrate some of the techniques that we employed to overcome many of the identified challenges. NetworkVis is an OpenVG-based real-time network monitoring and visualization system developed for Windows Mobile devices. Infostar is a flash-based interactive, real-time visualization application intended to provide attendees access to conference information. Linked time-synchronous visualization, stylus/button-based interactivity, vector graphics, overview-context techniques, details-on-demand and statistical information display are some of the highlights of these applications.
Auditory enhancement of visual perception at threshold depends on visual abilities.

PubMed

Caclin, Anne; Bouchet, Patrick; Djoulah, Farida; Pirat, Elodie; Pernier, Jacques; Giard, Marie-Hélène

2011-06-17

Whether or not multisensory interactions can improve detection thresholds, and thus widen the range of perceptible events is a long-standing debate. Here we revisit this question, by testing the influence of auditory stimuli on visual detection threshold, in subjects exhibiting a wide range of visual-only performance. Above the perceptual threshold, crossmodal interactions have indeed been reported to depend on the subject's performance when the modalities are presented in isolation. We thus tested normal-seeing subjects and short-sighted subjects wearing their usual glasses. We used a paradigm limiting potential shortcomings of previous studies: we chose a criterion-free threshold measurement procedure and precluded exogenous cueing effects by systematically presenting a visual cue whenever a visual target (a faint Gabor patch) might occur. Using this carefully controlled procedure, we found that concurrent sounds only improved visual detection thresholds in the sub-group of subjects exhibiting the poorest performance in the visual-only conditions. In these subjects, for oblique orientations of the visual stimuli (but not for vertical or horizontal targets), the auditory improvement was still present when visual detection was already helped with flanking visual stimuli generating a collinear facilitation effect. These findings highlight that crossmodal interactions are most efficient to improve perceptual performance when an isolated modality is deficient. Copyright © 2011 Elsevier B.V. All rights reserved.
The Human is the Loop: New Directions for Visual Analytics

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

Endert, Alexander; Hossain, Shahriar H.; Ramakrishnan, Naren

2014-01-28

Visual analytics is the science of marrying interactive visualizations and analytic algorithms to support exploratory knowledge discovery in large datasets. We argue for a shift from a ‘human in the loop’ philosophy for visual analytics to a ‘human is the loop’ viewpoint, where the focus is on recognizing analysts’ work processes, and seamlessly fitting analytics into that existing interactive process. We survey a range of projects that provide visual analytic support contextually in the sensemaking loop, and outline a research agenda along with future challenges.
An interactive, stereoscopic virtual environment for medical imaging visualization, simulation and training

NASA Astrophysics Data System (ADS)

Krueger, Evan; Messier, Erik; Linte, Cristian A.; Diaz, Gabriel

2017-03-01

Recent advances in medical image acquisition allow for the reconstruction of anatomies with 3D, 4D, and 5D renderings. Nevertheless, standard anatomical and medical data visualization still relies heavily on the use of traditional 2D didactic tools (i.e., textbooks and slides), which restrict the presentation of image data to a 2D slice format. While these approaches have their merits beyond being cost effective and easy to disseminate, anatomy is inherently three-dimensional. By using 2D visualizations to illustrate more complex morphologies, important interactions between structures can be missed. In practice, such as in the planning and execution of surgical interventions, professionals require intricate knowledge of anatomical complexities, which can be more clearly communicated and understood through intuitive interaction with 3D volumetric datasets, such as those extracted from high-resolution CT or MRI scans. Open source, high quality, 3D medical imaging datasets are freely available, and with the emerging popularity of 3D display technologies, affordable and consistent 3D anatomical visualizations can be created. In this study we describe the design, implementation, and evaluation of one such interactive, stereoscopic visualization paradigm for human anatomy extracted from 3D medical images. A stereoscopic display was created by projecting the scene onto the lab floor using sequential frame stereo projection and viewed through active shutter glasses. By incorporating a PhaseSpace motion tracking system, a single viewer can navigate an augmented reality environment and directly manipulate virtual objects in 3D. While this paradigm is sufficiently versatile to enable a wide variety of applications in need of 3D visualization, we designed our study to work as an interactive game, which allows users to explore the anatomy of various organs and systems. In this study we describe the design, implementation, and evaluation of an interactive and stereoscopic visualization platform for exploring and understanding human anatomy. This system can present medical imaging data in three dimensions and allows for direct physical interaction and manipulation by the viewer. This should provide numerous benefits over traditional, 2D display and interaction modalities, and in our analysis, we aim to quantify and qualify users' visual and motor interactions with the virtual environment when employing this interactive display as a 3D didactic tool.
Rethinking Visual Analytics for Streaming Data Applications

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

Crouser, R. Jordan; Franklin, Lyndsey; Cook, Kris

In the age of data science, the use of interactive information visualization techniques has become increasingly ubiquitous. From online scientific journals to the New York Times graphics desk, the utility of interactive visualization for both storytelling and analysis has become ever more apparent. As these techniques have become more readily accessible, the appeal of combining interactive visualization with computational analysis continues to grow. Arising out of a need for scalable, human-driven analysis, primary objective of visual analytics systems is to capitalize on the complementary strengths of human and machine analysis, using interactive visualization as a medium for communication between themore » two. These systems leverage developments from the fields of information visualization, computer graphics, machine learning, and human-computer interaction to support insight generation in areas where purely computational analyses fall short. Over the past decade, visual analytics systems have generated remarkable advances in many historically challenging analytical contexts. These include areas such as modeling political systems [Crouser et al. 2012], detecting financial fraud [Chang et al. 2008], and cybersecurity [Harrison et al. 2012]. In each of these contexts, domain expertise and human intuition is a necessary component of the analysis. This intuition is essential to building trust in the analytical products, as well as supporting the translation of evidence into actionable insight. In addition, each of these examples also highlights the need for scalable analysis. In each case, it is infeasible for a human analyst to manually assess the raw information unaided, and the communication overhead to divide the task between a large number of analysts makes simple parallelism intractable. Regardless of the domain, visual analytics tools strive to optimize the allocation of human analytical resources, and to streamline the sensemaking process on data that is massive, complex, incomplete, and uncertain in scenarios requiring human judgment.« less
3D Exploration of Meteorological Data: Facing the challenges of operational forecasters

NASA Astrophysics Data System (ADS)

Koutek, Michal; Debie, Frans; van der Neut, Ian

2016-04-01

In the past years the Royal Netherlands Meteorological Institute (KNMI) has been working on innovation in the field of meteorological data visualization. We are dealing with Numerical Weather Prediction (NWP) model data and observational data, i.e. satellite images, precipitation radar, ground and air-borne measurements. These multidimensional multivariate data are geo-referenced and can be combined in 3D space to provide more intuitive views on the atmospheric phenomena. We developed the Weather3DeXplorer (W3DX), a visualization framework for processing and interactive exploration and visualization using Virtual Reality (VR) technology. We managed to have great successes with research studies on extreme weather situations. In this paper we will elaborate what we have learned from application of interactive 3D visualization in the operational weather room. We will explain how important it is to control the degrees-of-freedom during interaction that are given to the users: forecasters/scientists; (3D camera and 3D slicing-plane navigation appear to be rather difficult for the users, when not implemented properly). We will present a novel approach of operational 3D visualization user interfaces (UI) that for a great deal eliminates the obstacle and the time it usually takes to set up the visualization parameters and an appropriate camera view on a certain atmospheric phenomenon. We have found our inspiration in the way our operational forecasters work in the weather room. We decided to form a bridge between 2D visualization images and interactive 3D exploration. Our method combines WEB-based 2D UI's, pre-rendered 3D visualization catalog for the latest NWP model runs, with immediate entry into interactive 3D session for selected visualization setting. Finally, we would like to present the first user experiences with this approach.
Visualizing Dispersion Interactions

ERIC Educational Resources Information Center

Gottschalk, Elinor; Venkataraman, Bhawani

2014-01-01

An animation and accompanying activity has been developed to help students visualize how dispersion interactions arise. The animation uses the gecko's ability to walk on vertical surfaces to illustrate how dispersion interactions play a role in macroscale outcomes. Assessment of student learning reveals that students were able to develop…
A Multidimensional Analysis Tool for Visualizing Online Interactions

ERIC Educational Resources Information Center

Kim, Minjeong; Lee, Eunchul

2012-01-01

This study proposes and verifies the performance of an analysis tool for visualizing online interactions. A review of the most widely used methods for analyzing online interactions, including quantitative analysis, content analysis, and social network analysis methods, indicates these analysis methods have some limitations resulting from their…
CollaborationViz: Interactive Visual Exploration of Biomedical Research Collaboration Networks

PubMed Central

Bian, Jiang; Xie, Mengjun; Hudson, Teresa J.; Eswaran, Hari; Brochhausen, Mathias; Hanna, Josh; Hogan, William R.

2014-01-01

Social network analysis (SNA) helps us understand patterns of interaction between social entities. A number of SNA studies have shed light on the characteristics of research collaboration networks (RCNs). Especially, in the Clinical Translational Science Award (CTSA) community, SNA provides us a set of effective tools to quantitatively assess research collaborations and the impact of CTSA. However, descriptive network statistics are difficult for non-experts to understand. In this article, we present our experiences of building meaningful network visualizations to facilitate a series of visual analysis tasks. The basis of our design is multidimensional, visual aggregation of network dynamics. The resulting visualizations can help uncover hidden structures in the networks, elicit new observations of the network dynamics, compare different investigators and investigator groups, determine critical factors to the network evolution, and help direct further analyses. We applied our visualization techniques to explore the biomedical RCNs at the University of Arkansas for Medical Sciences – a CTSA institution. And, we created CollaborationViz, an open-source visual analytical tool to help network researchers and administration apprehend the network dynamics of research collaborations through interactive visualization. PMID:25405477
Using Interactive Data Visualizations for Exploratory Analysis in Undergraduate Genomics Coursework: Field Study Findings and Guidelines

NASA Astrophysics Data System (ADS)

Mirel, Barbara; Kumar, Anuj; Nong, Paige; Su, Gang; Meng, Fan

2016-02-01

Life scientists increasingly use visual analytics to explore large data sets and generate hypotheses. Undergraduate biology majors should be learning these same methods. Yet visual analytics is one of the most underdeveloped areas of undergraduate biology education. This study sought to determine the feasibility of undergraduate biology majors conducting exploratory analysis using the same interactive data visualizations as practicing scientists. We examined 22 upper level undergraduates in a genomics course as they engaged in a case-based inquiry with an interactive heat map. We qualitatively and quantitatively analyzed students' visual analytic behaviors, reasoning and outcomes to identify student performance patterns, commonly shared efficiencies and task completion. We analyzed students' successes and difficulties in applying knowledge and skills relevant to the visual analytics case and related gaps in knowledge and skill to associated tool designs. Findings show that undergraduate engagement in visual analytics is feasible and could be further strengthened through tool usability improvements. We identify these improvements. We speculate, as well, on instructional considerations that our findings suggested may also enhance visual analytics in case-based modules.
Using Interactive Data Visualizations for Exploratory Analysis in Undergraduate Genomics Coursework: Field Study Findings and Guidelines

PubMed Central

Kumar, Anuj; Nong, Paige; Su, Gang; Meng, Fan

2016-01-01

Life scientists increasingly use visual analytics to explore large data sets and generate hypotheses. Undergraduate biology majors should be learning these same methods. Yet visual analytics is one of the most underdeveloped areas of undergraduate biology education. This study sought to determine the feasibility of undergraduate biology majors conducting exploratory analysis using the same interactive data visualizations as practicing scientists. We examined 22 upper level undergraduates in a genomics course as they engaged in a case-based inquiry with an interactive heat map. We qualitatively and quantitatively analyzed students’ visual analytic behaviors, reasoning and outcomes to identify student performance patterns, commonly shared efficiencies and task completion. We analyzed students’ successes and difficulties in applying knowledge and skills relevant to the visual analytics case and related gaps in knowledge and skill to associated tool designs. Findings show that undergraduate engagement in visual analytics is feasible and could be further strengthened through tool usability improvements. We identify these improvements. We speculate, as well, on instructional considerations that our findings suggested may also enhance visual analytics in case-based modules. PMID:26877625
Color surface-flow visualization of fin-generated shock wave boundary-layer interactions

NASA Technical Reports Server (NTRS)

Lu, F. K.; Settles, G. S.

1990-01-01

Kerosene-lampblack mixtures with addition of a ground colored chalk were used in an experiment on visualizing surface flows of swept shock boundary-layer interactions. The results show that contrasting colors intensify the visualization of different regions of the interaction surface, and help the eye in following the fine streaks to locate the upstream influence. The study confirms observations of the separation occurring at shock strength below accepted values. The superiority of the reported technique over the previous monochrome technique is demonstrated.
Color surface-flow visualization of fin-generated shock wave boundary-layer interactions

NASA Astrophysics Data System (ADS)

Lu, F. K.; Settles, G. S.

1990-03-01

Kerosene-lampblack mixtures with addition of a ground colored chalk were used in an experiment on visualizing surface flows of swept shock boundary-layer interactions. The results show that contrasting colors intensify the visualization of different regions of the interaction surface, and help the eye in following the fine streaks to locate the upstream influence. The study confirms observations of the separation occurring at shock strength below accepted values. The superiority of the reported technique over the previous monochrome technique is demonstrated.
Effects of interactive visual feedback training on post-stroke pusher syndrome: a pilot randomized controlled study.

PubMed

Yang, Yea-Ru; Chen, Yi-Hua; Chang, Heng-Chih; Chan, Rai-Chi; Wei, Shun-Hwa; Wang, Ray-Yau

2015-10-01

We investigated the effects of a computer-generated interactive visual feedback training program on the recovery from pusher syndrome in stroke patients. Assessor-blinded, pilot randomized controlled study. A total of 12 stroke patients with pusher syndrome were randomly assigned to either the experimental group (N = 7, computer-generated interactive visual feedback training) or control group (N = 5, mirror visual feedback training). The scale for contraversive pushing for severity of pusher syndrome, the Berg Balance Scale for balance performance, and the Fugl-Meyer assessment scale for motor control were the outcome measures. Patients were assessed pre- and posttraining. A comparison of pre- and posttraining assessment results revealed that both training programs led to the following significant changes: decreased severity of pusher syndrome scores (decreases of 4.0 ± 1.1 and 1.4 ± 1.0 in the experimental and control groups, respectively); improved balance scores (increases of 14.7 ± 4.3 and 7.2 ± 1.6 in the experimental and control groups, respectively); and higher scores for lower extremity motor control (increases of 8.4 ± 2.2 and 5.6 ± 3.3 in the experimental and control groups, respectively). Furthermore, the computer-generated interactive visual feedback training program produced significantly better outcomes in the improvement of pusher syndrome (p < 0.01) and balance (p < 0.05) compared with the mirror visual feedback training program. Although both training programs were beneficial, the computer-generated interactive visual feedback training program more effectively aided recovery from pusher syndrome compared with mirror visual feedback training. © The Author(s) 2014.

The interplay of bottom-up and top-down mechanisms in visual guidance during object naming.

PubMed

Coco, Moreno I; Malcolm, George L; Keller, Frank

2014-01-01

An ongoing issue in visual cognition concerns the roles played by low- and high-level information in guiding visual attention, with current research remaining inconclusive about the interaction between the two. In this study, we bring fresh evidence into this long-standing debate by investigating visual saliency and contextual congruency during object naming (Experiment 1), a task in which visual processing interacts with language processing. We then compare the results of this experiment to data of a memorization task using the same stimuli (Experiment 2). In Experiment 1, we find that both saliency and congruency influence visual and naming responses and interact with linguistic factors. In particular, incongruent objects are fixated later and less often than congruent ones. However, saliency is a significant predictor of object naming, with salient objects being named earlier in a trial. Furthermore, the saliency and congruency of a named object interact with the lexical frequency of the associated word and mediate the time-course of fixations at naming. In Experiment 2, we find a similar overall pattern in the eye-movement responses, but only the congruency of the target is a significant predictor, with incongruent targets fixated less often than congruent targets. Crucially, this finding contrasts with claims in the literature that incongruent objects are more informative than congruent objects by deviating from scene context and hence need a longer processing. Overall, this study suggests that different sources of information are interactively used to guide visual attention on the targets to be named and raises new questions for existing theories of visual attention.
Effects of Visual and Verbal Interaction on Unintentional Interpersonal Coordination

ERIC Educational Resources Information Center

Richardson, Michael J.; Marsh, Kerry L.; Schmidt, R. C.

2005-01-01

Previous research has demonstrated that people's movements can become unintentionally coordinated during interpersonal interaction. The current study sought to uncover the degree to which visual and verbal (conversation) interaction constrains and organizes the rhythmic limb movements of coactors. Two experiments were conducted in which pairs of…
LSSGalPy: Interactive Visualization of the Large-scale Environment Around Galaxies

NASA Astrophysics Data System (ADS)

Argudo-Fernández, M.; Duarte Puertas, S.; Ruiz, J. E.; Sabater, J.; Verley, S.; Bergond, G.

2017-05-01

New tools are needed to handle the growth of data in astrophysics delivered by recent and upcoming surveys. We aim to build open-source, light, flexible, and interactive software designed to visualize extensive three-dimensional (3D) tabular data. Entirely written in the Python language, we have developed interactive tools to browse and visualize the positions of galaxies in the universe and their positions with respect to its large-scale structures (LSS). Motivated by a previous study, we created two codes using Mollweide projection and wedge diagram visualizations, where survey galaxies can be overplotted on the LSS of the universe. These are interactive representations where the visualizations can be controlled by widgets. We have released these open-source codes that have been designed to be easily re-used and customized by the scientific community to fulfill their needs. The codes are adaptable to other kinds of 3D tabular data and are robust enough to handle several millions of objects. .
Desktop Cloud Visualization: the new technology to remote access 3D interactive applications in the Cloud.

PubMed

Torterolo, Livia; Ruffino, Francesco

2012-01-01

In the proposed demonstration we will present DCV (Desktop Cloud Visualization): a unique technology that allows users to remote access 2D and 3D interactive applications over a standard network. This allows geographically dispersed doctors work collaboratively and to acquire anatomical or pathological images and visualize them for further investigations.
Visuals for Interactive Video: Old Fashioned Images for a New Fangled Technology.

ERIC Educational Resources Information Center

Braden, Roberts A.

Pointing out that interactive video (IAV) represents a synthesis of four primary technologies--computers, television, visual design, and instructional design--this paper discusses the what, why, and how of IAV visuals. The features and relevant aspects of each technology are briefly discussed, as well as the impact of each of these technologies…
Visual Analytics in Public Safety: Example Capabilities for Example Government Agencies

DTIC Science & Technology

2011-10-01

is not limited to: the Police Records Information Management Environment for British Columbia (PRIME-BC), the Police Reporting and Occurrence System...and filtering for rapid identification of relevant documents - Graphical environment for visual evidence marshaling - Interactive linking and...analytical reasoning facilitated by interactive visual interfaces and integration with computational analytics. Indeed, a wide variety of technologies
A graph-theoretical analysis algorithm for quantifying the transition from sensory input to motor output by an emotional stimulus.

PubMed

Karmonik, Christof; Fung, Steve H; Dulay, M; Verma, A; Grossman, Robert G

2013-01-01

Graph-theoretical analysis algorithms have been used for identifying subnetworks in the human brain during the Default Mode State. Here, these methods are expanded to determine the interaction of the sensory and the motor subnetworks during the performance of an approach-avoidance paradigm utilizing the correlation strength between the signal intensity time courses as measure of synchrony. From functional magnetic resonance imaging (fMRI) data of 9 healthy volunteers, two signal time courses, one from the primary visual cortex (sensory input) and one from the motor cortex (motor output) were identified and a correlation difference map was calculated. Graph networks were created from this map and visualized with spring-embedded layouts and 3D layouts in the original anatomical space. Functional clusters in these networks were identified with the MCODE clustering algorithm. Interactions between the sensory sub-network and the motor sub-network were quantified through the interaction strengths of these clusters. The percentages of interactions involving the visual cortex ranged from 85 % to 18 % and the motor cortex ranged from 40 % to 9 %. Other regions with high interactions were: frontal cortex (19 ± 18 %), insula (17 ± 22 %), cuneus (16 ± 15 %), supplementary motor area (SMA, 11 ± 18 %) and subcortical regions (11 ± 10 %). Interactions between motor cortex, SMA and visual cortex accounted for 12 %, between visual cortex and cuneus for 8 % and between motor cortex, SMA and cuneus for 6 % of all interactions. These quantitative findings are supported by the visual impressions from the 2D and 3D network layouts.
Visualizer: 3D Gridded Data Visualization Software for Geoscience Education and Research

NASA Astrophysics Data System (ADS)

Harwood, C.; Billen, M. I.; Kreylos, O.; Jadamec, M.; Sumner, D. Y.; Kellogg, L. H.; Hamann, B.

2008-12-01

In both research and education learning is an interactive and iterative process of exploring and analyzing data or model results. However, visualization software often presents challenges on the path to learning because it assumes the user already knows the locations and types of features of interest, instead of enabling flexible and intuitive examination of results. We present examples of research and teaching using the software, Visualizer, specifically designed to create an effective and intuitive environment for interactive, scientific analysis of 3D gridded data. Visualizer runs in a range of 3D virtual reality environments (e.g., GeoWall, ImmersaDesk, or CAVE), but also provides a similar level of real-time interactivity on a desktop computer. When using Visualizer in a 3D-enabled environment, the software allows the user to interact with the data images as real objects, grabbing, rotating or walking around the data to gain insight and perspective. On the desktop, simple features, such as a set of cross-bars marking the plane of the screen, provide extra 3D spatial cues that allow the user to more quickly understand geometric relationships within the data. This platform portability allows the user to more easily integrate research results into classroom demonstrations and exercises, while the interactivity provides an engaging environment for self-directed and inquiry-based learning by students. Visualizer software is freely available for download (www.keckcaves.org) and runs on Mac OSX and Linux platforms.
Non-visual spatial tasks reveal increased interactions with stance postural control.

PubMed

Woollacott, Marjorie; Vander Velde, Timothy

2008-05-07

The current investigation aimed to contrast the level and quality of dual-task interactions resulting from the combined performance of a challenging primary postural task and three specific, yet categorically dissociated, secondary central executive tasks. Experiments determined the extent to which modality (visual vs. auditory) and code (non-spatial vs. spatial) specific cognitive resources contributed to postural interference in young adults (n=9) in a dual-task setting. We hypothesized that the different forms of executive n-back task processing employed (visual-object, auditory-object and auditory-spatial) would display contrasting levels of interactions with tandem Romberg stance postural control, and that interactions within the spatial domain would be revealed as most vulnerable to dual-task interactions. Across all cognitive tasks employed, including auditory-object (aOBJ), auditory-spatial (aSPA), and visual-object (vOBJ) tasks, increasing n-back task complexity produced correlated increases in verbal reaction time measures. Increasing cognitive task complexity also resulted in consistent decreases in judgment accuracy. Postural performance was significantly influenced by the type of cognitive loading delivered. At comparable levels of cognitive task difficulty (n-back demands and accuracy judgments) the performance of challenging auditory-spatial tasks produced significantly greater levels of postural sway than either the auditory-object or visual-object based tasks. These results suggest that it is the employment of limited non-visual spatially based coding resources that may underlie previously observed visual dual-task interference effects with stance postural control in healthy young adults.
Elevated audiovisual temporal interaction in patients with migraine without aura

PubMed Central

2014-01-01

Background Photophobia and phonophobia are the most prominent symptoms in patients with migraine without aura. Hypersensitivity to visual stimuli can lead to greater hypersensitivity to auditory stimuli, which suggests that the interaction between visual and auditory stimuli may play an important role in the pathogenesis of migraine. However, audiovisual temporal interactions in migraine have not been well studied. Therefore, our aim was to examine auditory and visual interactions in migraine. Methods In this study, visual, auditory, and audiovisual stimuli with different temporal intervals between the visual and auditory stimuli were randomly presented to the left or right hemispace. During this time, the participants were asked to respond promptly to target stimuli. We used cumulative distribution functions to analyze the response times as a measure of audiovisual integration. Results Our results showed that audiovisual integration was significantly elevated in the migraineurs compared with the normal controls (p < 0.05); however, audiovisual suppression was weaker in the migraineurs compared with the normal controls (p < 0.05). Conclusions Our findings further objectively support the notion that migraineurs without aura are hypersensitive to external visual and auditory stimuli. Our study offers a new quantitative and objective method to evaluate hypersensitivity to audio-visual stimuli in patients with migraine. PMID:24961903
Gestalten of today: early processing of visual contours and surfaces.

PubMed

Kovács, I

1996-12-01

While much is known about the specialized, parallel processing streams of low-level vision that extract primary visual cues, there is only limited knowledge about the dynamic interactions between them. How are the fragments, caught by local analyzers, assembled together to provide us with a unified percept? How are local discontinuities in texture, motion or depth evaluated with respect to object boundaries and surface properties? These questions are presented within the framework of orientation-specific spatial interactions of early vision. Key observations of psychophysics, anatomy and neurophysiology on interactions of various spatial and temporal ranges are reviewed. Aspects of the functional architecture and possible neural substrates of local orientation-specific interactions are discussed, underlining their role in the integration of information across the visual field, and particularly in contour integration. Examples are provided demonstrating that global context, such as contour closure and figure-ground assignment, affects these local interactions. It is illustrated that figure-ground assignment is realized early in visual processing, and that the pattern of early interactions also brings about an effective and sparse coding of visual shape. Finally, it is concluded that the underlying functional architecture is not only dynamic and context dependent, but the pattern of connectivity depends as much on past experience as on actual stimulation.
Exploring Gigabyte Datasets in Real Time: Architectures, Interfaces and Time-Critical Design

NASA Technical Reports Server (NTRS)

Bryson, Steve; Gerald-Yamasaki, Michael (Technical Monitor)

1998-01-01

Architectures and Interfaces: The implications of real-time interaction on software architecture design: decoupling of interaction/graphics and computation into asynchronous processes. The performance requirements of graphics and computation for interaction. Time management in such an architecture. Examples of how visualization algorithms must be modified for high performance. Brief survey of interaction techniques and design, including direct manipulation and manipulation via widgets. talk discusses how human factors considerations drove the design and implementation of the virtual wind tunnel. Time-Critical Design: A survey of time-critical techniques for both computation and rendering. Emphasis on the assignment of a time budget to both the overall visualization environment and to each individual visualization technique in the environment. The estimation of the benefit and cost of an individual technique. Examples of the modification of visualization algorithms to allow time-critical control.
The Hologram in My Hand: How Effective is Interactive Exploration of 3D Visualizations in Immersive Tangible Augmented Reality?

PubMed

Bach, Benjamin; Sicat, Ronell; Beyer, Johanna; Cordeil, Maxime; Pfister, Hanspeter

2018-01-01

We report on a controlled user study comparing three visualization environments for common 3D exploration. Our environments differ in how they exploit natural human perception and interaction capabilities. We compare an augmented-reality head-mounted display (Microsoft HoloLens), a handheld tablet, and a desktop setup. The novel head-mounted HoloLens display projects stereoscopic images of virtual content into a user's real world and allows for interaction in-situ at the spatial position of the 3D hologram. The tablet is able to interact with 3D content through touch, spatial positioning, and tangible markers, however, 3D content is still presented on a 2D surface. Our hypothesis is that visualization environments that match human perceptual and interaction capabilities better to the task at hand improve understanding of 3D visualizations. To better understand the space of display and interaction modalities in visualization environments, we first propose a classification based on three dimensions: perception, interaction, and the spatial and cognitive proximity of the two. Each technique in our study is located at a different position along these three dimensions. We asked 15 participants to perform four tasks, each task having different levels of difficulty for both spatial perception and degrees of freedom for interaction. Our results show that each of the tested environments is more effective for certain tasks, but that generally the desktop environment is still fastest and most precise in almost all cases.
Innovative Visualization Techniques applied to a Flood Scenario

NASA Astrophysics Data System (ADS)

Falcão, António; Ho, Quan; Lopes, Pedro; Malamud, Bruce D.; Ribeiro, Rita; Jern, Mikael

2013-04-01

The large and ever-increasing amounts of multi-dimensional, time-varying and geospatial digital information from multiple sources represent a major challenge for today's analysts. We present a set of visualization techniques that can be used for the interactive analysis of geo-referenced and time sampled data sets, providing an integrated mechanism and that aids the user to collaboratively explore, present and communicate visually complex and dynamic data. Here we present these concepts in the context of a 4 hour flood scenario from Lisbon in 2010, with data that includes measures of water column (flood height) every 10 minutes at a 4.5 m x 4.5 m resolution, topography, building damage, building information, and online base maps. Techniques we use include web-based linked views, multiple charts, map layers and storytelling. We explain two of these in more detail that are not currently in common use for visualization of data: storytelling and web-based linked views. Visual storytelling is a method for providing a guided but interactive process of visualizing data, allowing more engaging data exploration through interactive web-enabled visualizations. Within storytelling, a snapshot mechanism helps the author of a story to highlight data views of particular interest and subsequently share or guide others within the data analysis process. This allows a particular person to select relevant attributes for a snapshot, such as highlighted regions for comparisons, time step, class values for colour legend, etc. and provide a snapshot of the current application state, which can then be provided as a hyperlink and recreated by someone else. Since data can be embedded within this snapshot, it is possible to interactively visualize and manipulate it. The second technique, web-based linked views, includes multiple windows which interactively respond to the user selections, so that when selecting an object and changing it one window, it will automatically update in all the other windows. These concepts can be part of a collaborative platform, where multiple people share and work together on the data, via online access, which also allows its remote usage from a mobile platform. Storytelling augments analysis and decision-making capabilities allowing to assimilate complex situations and reach informed decisions, in addition to helping the public visualize information. In our visualization scenario, developed in the context of the VA-4D project for the European Space Agency (see http://www.ca3-uninova.org/project_va4d), we make use of the GAV (GeoAnalytics Visualization) framework, a web-oriented visual analytics application based on multiple interactive views. The final visualization that we produce includes multiple interactive views, including a dynamic multi-layer map surrounded by other visualizations such as bar charts, time graphs and scatter plots. The map provides flood and building information, on top of a base city map (street maps and/or satellite imagery provided by online map services such as Google Maps, Bing Maps etc.). Damage over time for selected buildings, damage for all buildings at a chosen time period, correlation between damage and water depth can be analysed in the other views. This interactive web-based visualization that incorporates the ideas of storytelling, web-based linked views, and other visualization techniques, for a 4 hour flood event in Lisbon in 2010, can be found online at http://www.ncomva.se/flash/projects/esa/flooding/.
Interactive displays in medical art

NASA Technical Reports Server (NTRS)

Mcconathy, Deirdre Alla; Doyle, Michael

1989-01-01

Medical illustration is a field of visual communication with a long history. Traditional medical illustrations are static, 2-D, printed images; highly realistic depictions of the gross morphology of anatomical structures. Today medicine requires the visualization of structures and processes that have never before been seen. Complex 3-D spatial relationships require interpretation from 2-D diagnostic imagery. Pictures that move in real time have become clinical and research tools for physicians. Medical illustrators are involved with the development of interactive visual displays for three different, but not discrete, functions: as educational materials, as clinical and research tools, and as data bases of standard imagery used to produce visuals. The production of interactive displays in the medical arts is examined.
BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.

PubMed

Cui, Ya; Chen, Xiaowei; Luo, Huaxia; Fan, Zhen; Luo, Jianjun; He, Shunmin; Yue, Haiyan; Zhang, Peng; Chen, Runsheng

2016-06-01

We here present BioCircos.js, an interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js facilitates the development of web-based applications for circular visualization of various biological data, such as genomic features, genetic variations, gene expression and biomolecular interactions. BioCircos.js and its manual are freely available online at http://bioinfo.ibp.ac.cn/biocircos/ rschen@ibp.ac.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Scalable Visual Analytics of Massive Textual Datasets

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

Krishnan, Manoj Kumar; Bohn, Shawn J.; Cowley, Wendy E.

2007-04-01

This paper describes the first scalable implementation of text processing engine used in Visual Analytics tools. These tools aid information analysts in interacting with and understanding large textual information content through visual interfaces. By developing parallel implementation of the text processing engine, we enabled visual analytics tools to exploit cluster architectures and handle massive dataset. The paper describes key elements of our parallelization approach and demonstrates virtually linear scaling when processing multi-gigabyte data sets such as Pubmed. This approach enables interactive analysis of large datasets beyond capabilities of existing state-of-the art visual analytics tools.
Design and outcomes of an acoustic data visualization seminar.

PubMed

Robinson, Philip W; Pätynen, Jukka; Haapaniemi, Aki; Kuusinen, Antti; Leskinen, Petri; Zan-Bi, Morley; Lokki, Tapio

2014-01-01

Recently, the Department of Media Technology at Aalto University offered a seminar entitled Applied Data Analysis and Visualization. The course used spatial impulse response measurements from concert halls as the context to explore high-dimensional data visualization methods. Students were encouraged to represent source and receiver positions, spatial aspects, and temporal development of sound fields, frequency characteristics, and comparisons between halls, using animations and interactive graphics. The primary learning objectives were for the students to translate their skills across disciplines and gain a working understanding of high-dimensional data visualization techniques. Accompanying files present examples of student-generated, animated and interactive visualizations.
Information visualization: Beyond traditional engineering

NASA Technical Reports Server (NTRS)

Thomas, James J.

1995-01-01

This presentation addresses a different aspect of the human-computer interface; specifically the human-information interface. This interface will be dominated by an emerging technology called Information Visualization (IV). IV goes beyond the traditional views of computer graphics, CADS, and enables new approaches for engineering. IV specifically must visualize text, documents, sound, images, and video in such a way that the human can rapidly interact with and understand the content structure of information entities. IV is the interactive visual interface between humans and their information resources.
Time Series Data Visualization in World Wide Telescope

NASA Astrophysics Data System (ADS)

Fay, J.

WorldWide Telescope provides a rich set of timer series visualization for both archival and real time data. WWT consists of both interactive desktop tools for interactive immersive visualization and HTML5 web based controls that can be utilized in customized web pages. WWT supports a range of display options including full dome, power walls, stereo and virtual reality headsets.

Interactive Visual Least Absolutes Method: Comparison with the Least Squares and the Median Methods

ERIC Educational Resources Information Center

Kim, Myung-Hoon; Kim, Michelle S.

2016-01-01

A visual regression analysis using the least absolutes method (LAB) was developed, utilizing an interactive approach of visually minimizing the sum of the absolute deviations (SAB) using a bar graph in Excel; the results agree very well with those obtained from nonvisual LAB using a numerical Solver in Excel. These LAB results were compared with…
Interactive Exploration of Cosmological Dark-Matter Simulation Data.

PubMed

Scherzinger, Aaron; Brix, Tobias; Drees, Dominik; Volker, Andreas; Radkov, Kiril; Santalidis, Niko; Fieguth, Alexander; Hinrichs, Klaus H

2017-01-01

The winning entry of the 2015 IEEE Scientific Visualization Contest, this article describes a visualization tool for cosmological data resulting from dark-matter simulations. The proposed system helps users explore all aspects of the data at once and receive more detailed information about structures of interest at any time. Moreover, novel methods for visualizing and interactively exploring dark-matter halo substructures are proposed.
Maternal play behaviors, child negativity, and preterm or low birthweight toddlers' visual-spatial outcomes: testing a differential susceptibility hypothesis.

PubMed

Dilworth-Bart, Janean E; Miller, Kyle E; Hane, Amanda

2012-04-01

We examined the joint roles of child negative emotionality and parenting in the visual-spatial development of toddlers born preterm or with low birthweights (PTLBW). Neonatal risk data were collected at hospital discharge, observer- and parent-rated child negative emotionality was assessed at 9-months postterm, and mother-initiated task changes and flexibility during play were observed during a dyadic play interaction at 16-months postterm. Abbreviated IQ scores, and verbal/nonverbal and visual-spatial processing data were collected at 24-months postterm. Hierarchical regression analyses did not support our hypothesis that the visual-spatial processing of PTLBW toddlers with higher negative emotionality would be differentially susceptible to parenting behaviors during play. Instead, observer-rated distress and a negativity composite score were associated with less optimal visual-spatial processing when mothers were more flexible during the 16-month play interaction. Mother-initiated task changes did not interact with any of the negative emotionality variables to predict any of the 24-month neurocognitive outcomes, nor did maternal flexibility interact with mother-rated difficult temperament to predict the visual-spatial processing outcomes. Copyright Â© 2011 Elsevier Inc. All rights reserved.
Vocal and visual stimulation, congruence and lateralization affect brain oscillations in interspecies emotional positive and negative interactions.

PubMed

Balconi, Michela; Vanutelli, Maria Elide

2016-01-01

The present research explored the effect of cross-modal integration of emotional cues (auditory and visual (AV)) compared with only visual (V) emotional cues in observing interspecies interactions. The brain activity was monitored when subjects processed AV and V situations, which represented an emotional (positive or negative), interspecies (human-animal) interaction. Congruence (emotionally congruous or incongruous visual and auditory patterns) was also modulated. electroencephalography brain oscillations (from delta to beta) were analyzed and the cortical source localization (by standardized Low Resolution Brain Electromagnetic Tomography) was applied to the data. Frequency band (mainly low-frequency delta and theta) showed a significant brain activity increasing in response to negative compared to positive interactions within the right hemisphere. Moreover, differences were found based on stimulation type, with an increased effect for AV compared with V. Finally, delta band supported a lateralized right dorsolateral prefrontal cortex (DLPFC) activity in response to negative and incongruous interspecies interactions, mainly for AV. The contribution of cross-modality, congruence (incongruous patterns), and lateralization (right DLPFC) in response to interspecies emotional interactions was discussed at light of a "negative lateralized effect."
HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways.

PubMed

Subramani, Suresh; Kalpana, Raja; Monickaraj, Pankaj Moses; Natarajan, Jeyakumar

2015-04-01

The knowledge on protein-protein interactions (PPI) and their related pathways are equally important to understand the biological functions of the living cell. Such information on human proteins is highly desirable to understand the mechanism of several diseases such as cancer, diabetes, and Alzheimer's disease. Because much of that information is buried in biomedical literature, an automated text mining system for visualizing human PPI and pathways is highly desirable. In this paper, we present HPIminer, a text mining system for visualizing human protein interactions and pathways from biomedical literature. HPIminer extracts human PPI information and PPI pairs from biomedical literature, and visualize their associated interactions, networks and pathways using two curated databases HPRD and KEGG. To our knowledge, HPIminer is the first system to build interaction networks from literature as well as curated databases. Further, the new interactions mined only from literature and not reported earlier in databases are highlighted as new. A comparative study with other similar tools shows that the resultant network is more informative and provides additional information on interacting proteins and their associated networks. Copyright © 2015 Elsevier Inc. All rights reserved.
IViPP: A Tool for Visualization in Particle Physics

NASA Astrophysics Data System (ADS)

Tran, Hieu; Skiba, Elizabeth; Baldwin, Doug

2011-10-01

Experiments and simulations in physics generate a lot of data; visualization is helpful to prepare that data for analysis. IViPP (Interactive Visualizations in Particle Physics) is an interactive computer program that visualizes results of particle physics simulations or experiments. IViPP can handle data from different simulators, such as SRIM or MCNP. It can display relevant geometry and measured scalar data; it can do simple selection from the visualized data. In order to be an effective visualization tool, IViPP must have a software architecture that can flexibly adapt to new data sources and display styles. It must be able to display complicated geometry and measured data with a high dynamic range. We therefore organize it in a highly modular structure, we develop libraries to describe geometry algorithmically, use rendering algorithms running on the powerful GPU to display 3-D geometry at interactive rates, and we represent scalar values in a visual form of scientific notation that shows both mantissa and exponent. This work was supported in part by the US Department of Energy through the Laboratory for Laser Energetics (LLE), with special thanks to Craig Sangster at LLE.
Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.

PubMed

Wiebrands, Michael; Malajczuk, Chris J; Woods, Andrew J; Rohl, Andrew L; Mancera, Ricardo L

2018-06-21

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets.
Three visualization approaches for communicating and exploring PIT tag data

USGS Publications Warehouse

Letcher, Benjamin; Walker, Jeffrey D.; O'Donnell, Matthew; Whiteley, Andrew R.; Nislow, Keith; Coombs, Jason

2018-01-01

As the number, size and complexity of ecological datasets has increased, narrative and interactive raw data visualizations have emerged as important tools for exploring and understanding these large datasets. As a demonstration, we developed three visualizations to communicate and explore passive integrated transponder tag data from two long-term field studies. We created three independent visualizations for the same dataset, allowing separate entry points for users with different goals and experience levels. The first visualization uses a narrative approach to introduce users to the study. The second visualization provides interactive cross-filters that allow users to explore multi-variate relationships in the dataset. The last visualization allows users to visualize the movement histories of individual fish within the stream network. This suite of visualization tools allows a progressive discovery of more detailed information and should make the data accessible to users with a wide variety of backgrounds and interests.
SYMBMAT: Symbolic computation of quantum transition matrix elements

NASA Astrophysics Data System (ADS)

Ciappina, M. F.; Kirchner, T.

2012-08-01

We have developed a set of Mathematica notebooks to compute symbolically quantum transition matrices relevant for atomic ionization processes. The utilization of a symbolic language allows us to obtain analytical expressions for the transition matrix elements required in charged-particle and laser induced ionization of atoms. Additionally, by using a few simple commands, it is possible to export these symbolic expressions to standard programming languages, such as Fortran or C, for the subsequent computation of differential cross sections or other observables. One of the main drawbacks in the calculation of transition matrices is the tedious algebraic work required when initial states other than the simple hydrogenic 1s state need to be considered. Using these notebooks the work is dramatically reduced and it is possible to generate exact expressions for a large set of bound states. We present explicit examples of atomic collisions (in First Born Approximation and Distorted Wave Theory) and laser-matter interactions (within the Dipole and Strong Field Approximations and different gauges) using both hydrogenic wavefunctions and Slater-Type Orbitals with arbitrary nlm quantum numbers as initial states. Catalogue identifier: AEMI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 71 628 No. of bytes in distributed program, including test data, etc.: 444 195 Distribution format: tar.gz Programming language: Mathematica Computer: Single machines using Linux or Windows (with cores with any clock speed, cache memory and bits in a word) Operating system: Any OS that supports Mathematica. The notebooks have been tested under Windows and Linux and with versions 6.x, 7.x and 8.x Classification: 2.6 Nature of problem: The notebooks generate analytical expressions for quantum transition matrix elements required in diverse atomic processes: ionization by ion, electron, or photon impact and ionization within the framework of strong field physics. In charged-particle collisions approaches based on perturbation theory enjoy widespread utilization. Accordingly, we have chosen the First Born Approximation and Distorted Wave theories as examples. In light-matter interactions, the main ingredient for many types of calculations is the dipole transition matrix in its different formulations, i.e. length, velocity, and acceleration gauges. In all these cases the transitions of interest occur between a bound state and a continuum state which can be described in different ways. With the notebooks developed in the present work it is possible to calculate transition matrix elements analytically for any set of quantum numbers nlm of initial hydrogenic states or Slater-Type Orbitals and for plane waves or Coulomb waves as final continuum states. Solution method: The notebooks employ symbolic computation to generate analytical expressions for transition matrix elements used in both collision and light-matter interaction physics. fba_hyd.nb - This notebook computes analytical expressions for the transition matrix of collision-induced ionization in the First Born Approximation (FBA). The transitions considered are from a bound hydrogenic state with arbitrary quantum numbers nlm to a continuum state represented by a plane wave (PW) or a Coulomb wave (CW). distorted_hyd.nb - This notebook computes analytical expressions for the transition matrix of collision-induced ionization in Distorted Wave (DW) theories. The transitions considered are from a (distorted) bound hydrogenic state with arbitrary quantum numbers nlm to a distorted-wave continuum state. The computations are based on scalar and vectorial integrals (see the text for details). dipoleLength_hyd.nb - This notebook computes analytical expressions for the dipole transition matrix in length gauge. The transitions considered are from a bound hydrogenic state with arbitrary quantum numbers nlm to a continuum state represented by a PW (the Strong Field Approximation (SFA)) or a CW (the Coulomb-Volkov Approximation (CVA)). dipoleVelocity_hyd.nb - This notebook computes analytical expressions for the dipole transition matrix in velocity gauge. The transitions considered are from a bound hydrogenic state with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA) or a CW (the CVA). dipoleAcceleration_hyd.nb - This notebook computes analytical expressions for the dipole transition matrix in acceleration gauge. The transitions considered are from a bound hydrogenic state with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA). For the case of the CVA we only include the transition from the 1s state to a continuum state represented by a CW. fba_STO.nb - This notebook computes analytical expressions for the transition matrix of collision-induced ionization in the FBA. The transitions considered are from a Slater-Type Orbital (STO) with arbitrary quantum numbers nlm to a continuum state represented by a PW or a CW. distorted_STO.nb - This notebook computes analytical expressions for the transition matrix of collision-induced ionization in DW theories. The transitions considered are from a (distorted) STO with arbitrary quantum numbers nlm to a distorted-wave continuum state. The computations are based on scalar and vectorial integrals (see the text for details). dipoleLength_STO.nb - This notebook computes analytical expressions for the dipole transition matrix in length gauge. The transitions considered are from an STO with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA) or a CW (the CVA). dipoleVelocity_STO.nb - This notebook computes analytical expressions for the dipole transition matrix in velocity gauge. The transitions considered are from an STO with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA) or a CW (the CVA). dipoleAcceleration_STO.nb - This notebook computes analytical expressions for the dipole transition matrix in acceleration gauge. The transitions considered are from an STO with arbitrary quantum numbers nlm to a continuum state represented by a PW (the SFA). The symbolic expressions obtained within each notebook can be exported to standard programming languages such as Fortran or C using the Format.m package (see the text and Ref. Sofroniou (1993) [16] for details). Running time: Computational times vary according to the transition matrix selected and quantum numbers nlm of the initial state used. The typical running time is several minutes, but it will take longer for large values of nlm.
Metabolic Plasticity and Inter-Compartmental Interactions in Rice Metabolism: An Analysis from Reaction Deletion Study.

PubMed

Shaw, Rahul; Kundu, Sudip

2015-01-01

More than 20% of the total caloric intake of human population comes from rice. The expression of rice genes and hence, the concentration of enzymatic proteins might vary due to several biotic and abiotic stresses. It in turn, can influence the overall metabolism and survivability of rice plant. Thus, understanding the rice cellular metabolism, its plasticity and potential readjustments under different perturbations can help rice biotechnologists to design efficient rice cultivars. Here, using the flux balance analysis (FBA) method, with the help of in-silico reaction deletion strategy, we study the metabolic plasticity of genome-scale metabolic model of rice leaf. A set of 131 reactions, essential for the production of primary biomass precursors is identified; deletion of any of them can inhibit the overall biomass production. Usability Index (IU) for the rest of the reactions are estimated and based on this parameter, they are classified into three categories-maximally-favourable, quasi-favourable and unfavourable for the primary biomass production. The lower value of 1 - IU of a reaction suggests that the cell cannot easily bypass it for biomass production. While some of the alternative paths are energetically equally efficient, others demand for higher photon. The variations in (i) ATP/NADPH ratio, (ii) exchange of metabolites through chloroplastic transporters and (iii) total biomass production are also presented here. Mutual metabolic dependencies of different cellular compartments are also demonstrated.
Protein-Protein Interaction Network and Gene Ontology

NASA Astrophysics Data System (ADS)

Choi, Yunkyu; Kim, Seok; Yi, Gwan-Su; Park, Jinah

Evolution of computer technologies makes it possible to access a large amount and various kinds of biological data via internet such as DNA sequences, proteomics data and information discovered about them. It is expected that the combination of various data could help researchers find further knowledge about them. Roles of a visualization system are to invoke human abilities to integrate information and to recognize certain patterns in the data. Thus, when the various kinds of data are examined and analyzed manually, an effective visualization system is an essential part. One instance of these integrated visualizations can be combination of protein-protein interaction (PPI) data and Gene Ontology (GO) which could help enhance the analysis of PPI network. We introduce a simple but comprehensive visualization system that integrates GO and PPI data where GO and PPI graphs are visualized side-by-side and supports quick reference functions between them. Furthermore, the proposed system provides several interactive visualization methods for efficiently analyzing the PPI network and GO directedacyclic- graph such as context-based browsing and common ancestors finding.
VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability.

PubMed

Rathi, Prakash Chandra; Mulnaes, Daniel; Gohlke, Holger

2015-07-15

Constraint network analysis (CNA) is a graph theory-based rigidity analysis approach for linking a biomolecule's structure, flexibility, (thermo)stability and function. Results from CNA are highly information-rich and require intuitive, synchronized and interactive visualization for a comprehensive analysis. We developed VisualCNA, an easy-to-use PyMOL plug-in that allows setup of CNA runs and analysis of CNA results linking plots with molecular graphics representations. From a practical viewpoint, the most striking feature of VisualCNA is that it facilitates interactive protein engineering aimed at improving thermostability. VisualCNA and its dependencies (CNA and FIRST software) are available free of charge under GPL and academic licenses, respectively. VisualCNA and CNA are available at http://cpclab.uni-duesseldorf.de/software; FIRST is available at http://flexweb.asu.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
High resolution renderings and interactive visualization of the 2006 Huntington Beach experiment

NASA Astrophysics Data System (ADS)

Im, T.; Nayak, A.; Keen, C.; Samilo, D.; Matthews, J.

2006-12-01

The Visualization Center at the Scripps Institution of Oceanography investigates innovative ways to represent graphically interactive 3D virtual landscapes and to produce high resolution, high quality renderings of Earth sciences data and the sensors and instruments used to collect the data . Among the Visualization Center's most recent work is the visualization of the Huntington Beach experiment, a study launched in July 2006 by the Southern California Ocean Observing System (http://www.sccoos.org/) to record and synthesize data of the Huntington Beach coastal region. Researchers and students at the Visualization Center created visual presentations that combine bathymetric data provided by SCCOOS with USGS aerial photography and with 3D polygonal models of sensors created in Maya into an interactive 3D scene using the Fledermaus suite of visualization tools (http://www.ivs3d.com). In addition, the Visualization Center has produced high definition (HD) animations of SCCOOS sensor instruments (e.g. REMUS, drifters, spray glider, nearshore mooring, OCSD/USGS mooring and CDIP mooring) using the Maya modeling and animation software and rendered over multiple nodes of the OptIPuter Visualization Cluster at Scripps. These visualizations are aimed at providing researchers with a broader context of sensor locations relative to geologic characteristics, to promote their use as an educational resource for informal education settings and increasing public awareness, and also as an aid for researchers' proposals and presentations. These visualizations are available for download on the Visualization Center website at http://siovizcenter.ucsd.edu/sccoos/hb2006.php.
Auditory and visual interactions between the superior and inferior colliculi in the ferret.

PubMed

Stitt, Iain; Galindo-Leon, Edgar; Pieper, Florian; Hollensteiner, Karl J; Engler, Gerhard; Engel, Andreas K

2015-05-01

The integration of visual and auditory spatial information is important for building an accurate perception of the external world, but the fundamental mechanisms governing such audiovisual interaction have only partially been resolved. The earliest interface between auditory and visual processing pathways is in the midbrain, where the superior (SC) and inferior colliculi (IC) are reciprocally connected in an audiovisual loop. Here, we investigate the mechanisms of audiovisual interaction in the midbrain by recording neural signals from the SC and IC simultaneously in anesthetized ferrets. Visual stimuli reliably produced band-limited phase locking of IC local field potentials (LFPs) in two distinct frequency bands: 6-10 and 15-30 Hz. These visual LFP responses co-localized with robust auditory responses that were characteristic of the IC. Imaginary coherence analysis confirmed that visual responses in the IC were not volume-conducted signals from the neighboring SC. Visual responses in the IC occurred later than retinally driven superficial SC layers and earlier than deep SC layers that receive indirect visual inputs, suggesting that retinal inputs do not drive visually evoked responses in the IC. In addition, SC and IC recording sites with overlapping visual spatial receptive fields displayed stronger functional connectivity than sites with separate receptive fields, indicating that visual spatial maps are aligned across both midbrain structures. Reciprocal coupling between the IC and SC therefore probably serves the dynamic integration of visual and auditory representations of space. © 2015 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.
Visualization of volumetric seismic data

NASA Astrophysics Data System (ADS)

Spickermann, Dela; Böttinger, Michael; Ashfaq Ahmed, Khawar; Gajewski, Dirk

2015-04-01

Mostly driven by demands of high quality subsurface imaging, highly specialized tools and methods have been developed to support the processing, visualization and interpretation of seismic data. 3D seismic data acquisition and 4D time-lapse seismic monitoring are well-established techniques in academia and industry, producing large amounts of data to be processed, visualized and interpreted. In this context, interactive 3D visualization methods proved to be valuable for the analysis of 3D seismic data cubes - especially for sedimentary environments with continuous horizons. In crystalline and hard rock environments, where hydraulic stimulation techniques may be applied to produce geothermal energy, interpretation of the seismic data is a more challenging problem. Instead of continuous reflection horizons, the imaging targets are often steep dipping faults, causing a lot of diffractions. Without further preprocessing these geological structures are often hidden behind the noise in the data. In this PICO presentation we will present a workflow consisting of data processing steps, which enhance the signal-to-noise ratio, followed by a visualization step based on the use the commercially available general purpose 3D visualization system Avizo. Specifically, we have used Avizo Earth, an extension to Avizo, which supports the import of seismic data in SEG-Y format and offers easy access to state-of-the-art 3D visualization methods at interactive frame rates, even for large seismic data cubes. In seismic interpretation using visualization, interactivity is a key requirement for understanding complex 3D structures. In order to enable an easy communication of the insights gained during the interactive visualization process, animations of the visualized data were created which support the spatial understanding of the data.
The Visual Geophysical Exploration Environment: A Multi-dimensional Scientific Visualization

NASA Astrophysics Data System (ADS)

Pandya, R. E.; Domenico, B.; Murray, D.; Marlino, M. R.

2003-12-01

The Visual Geophysical Exploration Environment (VGEE) is an online learning environment designed to help undergraduate students understand fundamental Earth system science concepts. The guiding principle of the VGEE is the importance of hands-on interaction with scientific visualization and data. The VGEE consists of four elements: 1) an online, inquiry-based curriculum for guiding student exploration; 2) a suite of El Nino-related data sets adapted for student use; 3) a learner-centered interface to a scientific visualization tool; and 4) a set of concept models (interactive tools that help students understand fundamental scientific concepts). There are two key innovations featured in this interactive poster session. One is the integration of concept models and the visualization tool. Concept models are simple, interactive, Java-based illustrations of fundamental physical principles. We developed eight concept models and integrated them into the visualization tool to enable students to probe data. The ability to probe data using a concept model addresses the common problem of transfer: the difficulty students have in applying theoretical knowledge to everyday phenomenon. The other innovation is a visualization environment and data that are discoverable in digital libraries, and installed, configured, and used for investigations over the web. By collaborating with the Integrated Data Viewer developers, we were able to embed a web-launchable visualization tool and access to distributed data sets into the online curricula. The Thematic Real-time Environmental Data Distributed Services (THREDDS) project is working to provide catalogs of datasets that can be used in new VGEE curricula under development. By cataloging this curricula in the Digital Library for Earth System Education (DLESE), learners and educators can discover the data and visualization tool within a framework that guides their use.
An optimized web-based approach for collaborative stereoscopic medical visualization

PubMed Central

Kaspar, Mathias; Parsad, Nigel M; Silverstein, Jonathan C

2013-01-01

Objective Medical visualization tools have traditionally been constrained to tethered imaging workstations or proprietary client viewers, typically part of hospital radiology systems. To improve accessibility to real-time, remote, interactive, stereoscopic visualization and to enable collaboration among multiple viewing locations, we developed an open source approach requiring only a standard web browser with no added client-side software. Materials and Methods Our collaborative, web-based, stereoscopic, visualization system, CoWebViz, has been used successfully for the past 2 years at the University of Chicago to teach immersive virtual anatomy classes. It is a server application that streams server-side visualization applications to client front-ends, comprised solely of a standard web browser with no added software. Results We describe optimization considerations, usability, and performance results, which make CoWebViz practical for broad clinical use. We clarify technical advances including: enhanced threaded architecture, optimized visualization distribution algorithms, a wide range of supported stereoscopic presentation technologies, and the salient theoretical and empirical network parameters that affect our web-based visualization approach. Discussion The implementations demonstrate usability and performance benefits of a simple web-based approach for complex clinical visualization scenarios. Using this approach overcomes technical challenges that require third-party web browser plug-ins, resulting in the most lightweight client. Conclusions Compared to special software and hardware deployments, unmodified web browsers enhance remote user accessibility to interactive medical visualization. Whereas local hardware and software deployments may provide better interactivity than remote applications, our implementation demonstrates that a simplified, stable, client approach using standard web browsers is sufficient for high quality three-dimensional, stereoscopic, collaborative and interactive visualization. PMID:23048008
MEVA--An Interactive Visualization Application for Validation of Multifaceted Meteorological Data with Multiple 3D Devices.

PubMed

Helbig, Carolin; Bilke, Lars; Bauer, Hans-Stefan; Böttinger, Michael; Kolditz, Olaf

2015-01-01

To achieve more realistic simulations, meteorologists develop and use models with increasing spatial and temporal resolution. The analyzing, comparing, and visualizing of resulting simulations becomes more and more challenging due to the growing amounts and multifaceted character of the data. Various data sources, numerous variables and multiple simulations lead to a complex database. Although a variety of software exists suited for the visualization of meteorological data, none of them fulfills all of the typical domain-specific requirements: support for quasi-standard data formats and different grid types, standard visualization techniques for scalar and vector data, visualization of the context (e.g., topography) and other static data, support for multiple presentation devices used in modern sciences (e.g., virtual reality), a user-friendly interface, and suitability for cooperative work. Instead of attempting to develop yet another new visualization system to fulfill all possible needs in this application domain, our approach is to provide a flexible workflow that combines different existing state-of-the-art visualization software components in order to hide the complexity of 3D data visualization tools from the end user. To complete the workflow and to enable the domain scientists to interactively visualize their data without advanced skills in 3D visualization systems, we developed a lightweight custom visualization application (MEVA - multifaceted environmental data visualization application) that supports the most relevant visualization and interaction techniques and can be easily deployed. Specifically, our workflow combines a variety of different data abstraction methods provided by a state-of-the-art 3D visualization application with the interaction and presentation features of a computer-games engine. Our customized application includes solutions for the analysis of multirun data, specifically with respect to data uncertainty and differences between simulation runs. In an iterative development process, our easy-to-use application was developed in close cooperation with meteorologists and visualization experts. The usability of the application has been validated with user tests. We report on how this application supports the users to prove and disprove existing hypotheses and discover new insights. In addition, the application has been used at public events to communicate research results.
MEVA - An Interactive Visualization Application for Validation of Multifaceted Meteorological Data with Multiple 3D Devices

PubMed Central

Helbig, Carolin; Bilke, Lars; Bauer, Hans-Stefan; Böttinger, Michael; Kolditz, Olaf

2015-01-01

Background To achieve more realistic simulations, meteorologists develop and use models with increasing spatial and temporal resolution. The analyzing, comparing, and visualizing of resulting simulations becomes more and more challenging due to the growing amounts and multifaceted character of the data. Various data sources, numerous variables and multiple simulations lead to a complex database. Although a variety of software exists suited for the visualization of meteorological data, none of them fulfills all of the typical domain-specific requirements: support for quasi-standard data formats and different grid types, standard visualization techniques for scalar and vector data, visualization of the context (e.g., topography) and other static data, support for multiple presentation devices used in modern sciences (e.g., virtual reality), a user-friendly interface, and suitability for cooperative work. Methods and Results Instead of attempting to develop yet another new visualization system to fulfill all possible needs in this application domain, our approach is to provide a flexible workflow that combines different existing state-of-the-art visualization software components in order to hide the complexity of 3D data visualization tools from the end user. To complete the workflow and to enable the domain scientists to interactively visualize their data without advanced skills in 3D visualization systems, we developed a lightweight custom visualization application (MEVA - multifaceted environmental data visualization application) that supports the most relevant visualization and interaction techniques and can be easily deployed. Specifically, our workflow combines a variety of different data abstraction methods provided by a state-of-the-art 3D visualization application with the interaction and presentation features of a computer-games engine. Our customized application includes solutions for the analysis of multirun data, specifically with respect to data uncertainty and differences between simulation runs. In an iterative development process, our easy-to-use application was developed in close cooperation with meteorologists and visualization experts. The usability of the application has been validated with user tests. We report on how this application supports the users to prove and disprove existing hypotheses and discover new insights. In addition, the application has been used at public events to communicate research results. PMID:25915061
Multivariate spatiotemporal visualizations for mobile devices in Flyover Country

NASA Astrophysics Data System (ADS)

Loeffler, S.; Thorn, R.; Myrbo, A.; Roth, R.; Goring, S. J.; Williams, J.

2017-12-01

Visualizing and interacting with complex multivariate and spatiotemporal datasets on mobile devices is challenging due to their smaller screens, reduced processing power, and limited data connectivity. Pollen data require visualizing pollen assemblages spatially, temporally, and across multiple taxa to understand plant community dynamics through time. Drawing from cartography, information visualization, and paleoecology, we have created new mobile-first visualization techniques that represent multiple taxa across many sites and enable user interaction. Using pollen datasets from the Neotoma Paleoecology Database as a case study, the visualization techniques allow ecological patterns and trends to be quickly understood on a mobile device compared to traditional pollen diagrams and maps. This flexible visualization system can be used for datasets beyond pollen, with the only requirements being point-based localities and multiple variables changing through time or depth.

Fundamental Visual Representations of Social Cognition in ASD

DTIC Science & Technology

2016-12-01

visual adaptation functions in Autism , again pointing to basic sensory processing anomalies in this population. Our research team is developing...challenging-to-test ASD pediatric population. 15. SUBJECT TERMS Autism , Visual Adaptation, Retinotopy, Social Communication, Eye-movements, fMRI, EEG, ERP...social interaction are a hallmark symptom of Autism , and the lack of appropriate eye- contact during interpersonal interactions is an oft-noted feature
Re-Examining Format Distortion and Orthographic Neighbourhood Size Effects in the Left, Central and Right Visual Fields

ERIC Educational Resources Information Center

Mano, Quintino R.; Patrick, Cory J.; Andresen, Elizabeth N.; Capizzi, Kyle; Biagioli, Raschel; Osmon, David C.

2010-01-01

Research has shown orthographic neighbourhood size effects (ONS) in the left visual field (LVF) but not in the right visual field (RVF). An earlier study examined the combined effects of ONS and font distortion in the LVF and RVF, but did not find an interaction. The current lexical decision experiment re-examined the interaction between ONS and…
Classroom Environments: An Experiential Analysis of the Pupil-Teacher Visual Interaction in Uruguay

ERIC Educational Resources Information Center

Cardellino, Paula; Araneda, Claudio; García Alvarado, Rodrigo

2017-01-01

We argue that the traditional physical environment is commonly taken for granted and that little consideration has been given to how this affects pupil-teacher interactions. This article presents evidence that certain physical environments do not allow equal visual interaction and, as a result, we derive a set of basic guiding principles that…
E-Books Plus: Role of Interactive Visuals in Exploration of Mathematical Information and E-Learning

ERIC Educational Resources Information Center

Rowhani, Sonja; Sedig, Kamran

2005-01-01

E-books promise to become a widespread delivery mechanism for educational resources. However, current e-books do not take full advantage of the power of computing tools. In particular, interaction with the content is often reduced to navigation through the information. This article investigates how adding interactive visuals to an e-book…
Effects of Video-Feedback Interaction Training for Professional Caregivers of Children and Adults with Visual and Intellectual Disabilities

ERIC Educational Resources Information Center

Damen, S.; Kef, S.; Worm, M.; Janssen, M. J.; Schuengel, C.

2011-01-01

Background: Individuals in group homes may experience poor quality of social interaction with their professional caregivers, limiting their quality of life. The video-based Contact programme may help caregivers to improve their interaction with clients. Method: Seventy-two caregivers of 12 individuals with visual and intellectual disabilities…
Combining computational analyses and interactive visualization for document exploration and sensemaking in jigsaw.

PubMed

Görg, Carsten; Liu, Zhicheng; Kihm, Jaeyeon; Choo, Jaegul; Park, Haesun; Stasko, John

2013-10-01

Investigators across many disciplines and organizations must sift through large collections of text documents to understand and piece together information. Whether they are fighting crime, curing diseases, deciding what car to buy, or researching a new field, inevitably investigators will encounter text documents. Taking a visual analytics approach, we integrate multiple text analysis algorithms with a suite of interactive visualizations to provide a flexible and powerful environment that allows analysts to explore collections of documents while sensemaking. Our particular focus is on the process of integrating automated analyses with interactive visualizations in a smooth and fluid manner. We illustrate this integration through two example scenarios: an academic researcher examining InfoVis and VAST conference papers and a consumer exploring car reviews while pondering a purchase decision. Finally, we provide lessons learned toward the design and implementation of visual analytics systems for document exploration and understanding.
Interactive visualization of public health indicators to support policymaking: An exploratory study

PubMed Central

Zakkar, Moutasem; Sedig, Kamran

2017-01-01

Purpose The purpose of this study is to examine the use of interactive visualizations to represent data/information related to social determinants of health and public health indicators, and to investigate the benefits of such visualizations for health policymaking. Methods: The study developed a prototype for an online interactive visualization tool that represents the social determinants of health. The study participants explored and used the tool. The tool was evaluated using the informal user experience evaluation method. This method involves the prospective users of a tool to use and play with it and their feedback to be collected through interviews. Results: Using visualizations to represent and interact with health indicators has advantages over traditional representation techniques that do not allow users to interact with the information. Communicating healthcare indicators to policymakers is a complex task because of the complexity of the indicators, diversity of audiences, and different audience needs. This complexity can lead to information misinterpretation, which occurs when users of the health data ignore or do not know why, where, and how the data has been produced, or where and how it can be used. Conclusions: Public health policymaking is a complex process, and data is only one element among others needed in this complex process. Researchers and healthcare organizations should conduct a strategic evaluation to assess the usability of interactive visualizations and decision support tools before investing in these tools. Such evaluation should take into consideration the cost, ease of use, learnability, and efficiency of those tools, and the factors that influence policymaking. PMID:29026455
Vision in two cyprinid fish: implications for collective behavior

PubMed Central

Moore, Bret A.; Tyrrell, Luke P.; Fernández-Juricic, Esteban

2015-01-01

Many species of fish rely on their visual systems to interact with conspecifics and these interactions can lead to collective behavior. Individual-based models have been used to predict collective interactions; however, these models generally make simplistic assumptions about the sensory systems that are applied without proper empirical testing to different species. This could limit our ability to predict (and test empirically) collective behavior in species with very different sensory requirements. In this study, we characterized components of the visual system in two species of cyprinid fish known to engage in visually dependent collective interactions (zebrafish Danio rerio and golden shiner Notemigonus crysoleucas) and derived quantitative predictions about the positioning of individuals within schools. We found that both species had relatively narrow binocular and blind fields and wide visual coverage. However, golden shiners had more visual coverage in the vertical plane (binocular field extending behind the head) and higher visual acuity than zebrafish. The centers of acute vision (areae) of both species projected in the fronto-dorsal region of the visual field, but those of the zebrafish projected more dorsally than those of the golden shiner. Based on this visual sensory information, we predicted that: (a) predator detection time could be increased by >1,000% in zebrafish and >100% in golden shiners with an increase in nearest neighbor distance, (b) zebrafish schools would have a higher roughness value (surface area/volume ratio) than those of golden shiners, (c) and that nearest neighbor distance would vary from 8 to 20 cm to visually resolve conspecific striping patterns in both species. Overall, considering between-species differences in the sensory system of species exhibiting collective behavior could change the predictions about the positioning of individuals in the group as well as the shape of the school, which can have implications for group cohesion. We suggest that more effort should be invested in assessing the role of the sensory system in shaping local interactions driving collective behavior. PMID:26290783
Map Learning with a 3D Printed Interactive Small-Scale Model: Improvement of Space and Text Memorization in Visually Impaired Students.

PubMed

Giraud, Stéphanie; Brock, Anke M; Macé, Marc J-M; Jouffrais, Christophe

2017-01-01

Special education teachers for visually impaired students rely on tools such as raised-line maps (RLMs) to teach spatial knowledge. These tools do not fully and adequately meet the needs of the teachers because they are long to produce, expensive, and not versatile enough to provide rapid updating of the content. For instance, the same RLM can barely be used during different lessons. In addition, those maps do not provide any interactivity, which reduces students' autonomy. With the emergence of 3D printing and low-cost microcontrollers, it is now easy to design affordable interactive small-scale models (SSMs) which are adapted to the needs of special education teachers. However, no study has previously been conducted to evaluate non-visual learning using interactive SSMs. In collaboration with a specialized teacher, we designed a SSM and a RLM representing the evolution of the geography and history of a fictitious kingdom. The two conditions were compared in a study with 24 visually impaired students regarding the memorization of the spatial layout and historical contents. The study showed that the interactive SSM improved both space and text memorization as compared to the RLM with braille legend. In conclusion, we argue that affordable home-made interactive small scale models can improve learning for visually impaired students. Interestingly, they are adaptable to any teaching situation including students with specific needs.
STRAD Wheel: Web-Based Library for Visualizing Temporal Data.

PubMed

Fernondez-Prieto, Diana; Naranjo-Valero, Carol; Hernandez, Jose Tiberio; Hagen, Hans

2017-01-01

Recent advances in web development, including the introduction of HTML5, have opened a door for visualization researchers and developers to quickly access larger audiences worldwide. Open source libraries for the creation of interactive visualizations are becoming more specialized but also modular, which makes them easy to incorporate in domain-specific applications. In this context, the authors developed STRAD (Spatio-Temporal-Radar) Wheel, a web-based library that focuses on the visualization and interactive query of temporal data in a compact view with multiple temporal granularities. This article includes two application examples in urban planning to help illustrate the proposed visualization's use in practice.
Reviewing and visualizing the interactions of natural hazards

NASA Astrophysics Data System (ADS)

Gill, Joel C.; Malamud, Bruce D.

2014-12-01

This paper presents a broad overview, characterization, and visualization of the interaction relationships between 21 natural hazards, drawn from six hazard groups (geophysical, hydrological, shallow Earth, atmospheric, biophysical, and space hazards). A synthesis is presented of the identified interaction relationships between these hazards, using an accessible visual format particularly suited to end users. Interactions considered are primarily those where a primary hazard triggers or increases the probability of secondary hazards occurring. In this paper we do the following: (i) identify, through a wide-ranging review of grey- and peer-review literature, 90 interactions; (ii) subdivide the interactions into three levels, based on how well we can characterize secondary hazards, given information about the primary hazard; (iii) determine the spatial overlap and temporal likelihood of the triggering relationships occurring; and (iv) examine the relationship between primary and secondary hazard intensities for each identified hazard interaction and group these into five possible categories. In this study we have synthesized, using accessible visualization techniques, large amounts of information drawn from many scientific disciplines. We outline the importance of constraining hazard interactions and reinforce the importance of a holistic (or multihazard) approach to natural hazard assessment. This approach allows those undertaking research into single hazards to place their work within the context of other hazards. It also communicates important aspects of hazard interactions, facilitating an effective analysis by those working on reducing and managing disaster risk within both the policy and practitioner communities.
Exclusively visual analysis of classroom group interactions

NASA Astrophysics Data System (ADS)

Tucker, Laura; Scherr, Rachel E.; Zickler, Todd; Mazur, Eric

2016-12-01

Large-scale audiovisual data that measure group learning are time consuming to collect and analyze. As an initial step towards scaling qualitative classroom observation, we qualitatively coded classroom video using an established coding scheme with and without its audio cues. We find that interrater reliability is as high when using visual data only—without audio—as when using both visual and audio data to code. Also, interrater reliability is high when comparing use of visual and audio data to visual-only data. We see a small bias to code interactions as group discussion when visual and audio data are used compared with video-only data. This work establishes that meaningful educational observation can be made through visual information alone. Further, it suggests that after initial work to create a coding scheme and validate it in each environment, computer-automated visual coding could drastically increase the breadth of qualitative studies and allow for meaningful educational analysis on a far greater scale.
Three-dimensional visualization of nanostructured surfaces and bacterial attachment using Autodesk® Maya®.

PubMed

Boshkovikj, Veselin; Fluke, Christopher J; Crawford, Russell J; Ivanova, Elena P

2014-02-28

There has been a growing interest in understanding the ways in which bacteria interact with nano-structured surfaces. As a result, there is a need for innovative approaches to enable researchers to visualize the biological processes taking place, despite the fact that it is not possible to directly observe these processes. We present a novel approach for the three-dimensional visualization of bacterial interactions with nano-structured surfaces using the software package Autodesk Maya. Our approach comprises a semi-automated stage, where actual surface topographic parameters, obtained using an atomic force microscope, are imported into Maya via a custom Python script, followed by a 'creative stage', where the bacterial cells and their interactions with the surfaces are visualized using available experimental data. The 'Dynamics' and 'nDynamics' capabilities of the Maya software allowed the construction and visualization of plausible interaction scenarios. This capability provides a practical aid to knowledge discovery, assists in the dissemination of research results, and provides an opportunity for an improved public understanding. We validated our approach by graphically depicting the interactions between the two bacteria being used for modeling purposes, Staphylococcus aureus and Pseudomonas aeruginosa, with different titanium substrate surfaces that are routinely used in the production of biomedical devices.
Three-dimensional visualization of nanostructured surfaces and bacterial attachment using Autodesk® Maya®

NASA Astrophysics Data System (ADS)

Boshkovikj, Veselin; Fluke, Christopher J.; Crawford, Russell J.; Ivanova, Elena P.

2014-02-01

There has been a growing interest in understanding the ways in which bacteria interact with nano-structured surfaces. As a result, there is a need for innovative approaches to enable researchers to visualize the biological processes taking place, despite the fact that it is not possible to directly observe these processes. We present a novel approach for the three-dimensional visualization of bacterial interactions with nano-structured surfaces using the software package Autodesk Maya. Our approach comprises a semi-automated stage, where actual surface topographic parameters, obtained using an atomic force microscope, are imported into Maya via a custom Python script, followed by a `creative stage', where the bacterial cells and their interactions with the surfaces are visualized using available experimental data. The `Dynamics' and `nDynamics' capabilities of the Maya software allowed the construction and visualization of plausible interaction scenarios. This capability provides a practical aid to knowledge discovery, assists in the dissemination of research results, and provides an opportunity for an improved public understanding. We validated our approach by graphically depicting the interactions between the two bacteria being used for modeling purposes, Staphylococcus aureus and Pseudomonas aeruginosa, with different titanium substrate surfaces that are routinely used in the production of biomedical devices.
Interactive Learning Environment: Web-based Virtual Hydrological Simulation System using Augmented and Immersive Reality

NASA Astrophysics Data System (ADS)

Demir, I.

2014-12-01

Recent developments in internet technologies make it possible to manage and visualize large data on the web. Novel visualization techniques and interactive user interfaces allow users to create realistic environments, and interact with data to gain insight from simulations and environmental observations. The hydrological simulation system is a web-based 3D interactive learning environment for teaching hydrological processes and concepts. The simulation systems provides a visually striking platform with realistic terrain information, and water simulation. Students can create or load predefined scenarios, control environmental parameters, and evaluate environmental mitigation alternatives. The web-based simulation system provides an environment for students to learn about the hydrological processes (e.g. flooding and flood damage), and effects of development and human activity in the floodplain. The system utilizes latest web technologies and graphics processing unit (GPU) for water simulation and object collisions on the terrain. Users can access the system in three visualization modes including virtual reality, augmented reality, and immersive reality using heads-up display. The system provides various scenarios customized to fit the age and education level of various users. This presentation provides an overview of the web-based flood simulation system, and demonstrates the capabilities of the system for various visualization and interaction modes.
Three-dimensional visualization of nanostructured surfaces and bacterial attachment using Autodesk® Maya®

PubMed Central

Boshkovikj, Veselin; Fluke, Christopher J.; Crawford, Russell J.; Ivanova, Elena P.

2014-01-01

There has been a growing interest in understanding the ways in which bacteria interact with nano-structured surfaces. As a result, there is a need for innovative approaches to enable researchers to visualize the biological processes taking place, despite the fact that it is not possible to directly observe these processes. We present a novel approach for the three-dimensional visualization of bacterial interactions with nano-structured surfaces using the software package Autodesk Maya. Our approach comprises a semi-automated stage, where actual surface topographic parameters, obtained using an atomic force microscope, are imported into Maya via a custom Python script, followed by a ‘creative stage', where the bacterial cells and their interactions with the surfaces are visualized using available experimental data. The ‘Dynamics' and ‘nDynamics' capabilities of the Maya software allowed the construction and visualization of plausible interaction scenarios. This capability provides a practical aid to knowledge discovery, assists in the dissemination of research results, and provides an opportunity for an improved public understanding. We validated our approach by graphically depicting the interactions between the two bacteria being used for modeling purposes, Staphylococcus aureus and Pseudomonas aeruginosa, with different titanium substrate surfaces that are routinely used in the production of biomedical devices. PMID:24577105
The Impact of Visual Communication on the Intersubjective Development of Early Parent?Child Interaction with 18- to 24-Month-Old Deaf Toddlers

ERIC Educational Resources Information Center

Loots, Gerrit; Devise, Isabel; Jacquet, Wolfgang

2005-01-01

This article presents a study that examined the impact of visual communication on the quality of the early interaction between deaf and hearing mothers and fathers and their deaf children aged between 18 and 24 months. Three communication mode groups of parent?deaf child dyads that differed by the use of signing and visual?tactile communication…
A Scalable Cyberinfrastructure for Interactive Visualization of Terascale Microscopy Data

PubMed Central

Venkat, A.; Christensen, C.; Gyulassy, A.; Summa, B.; Federer, F.; Angelucci, A.; Pascucci, V.

2017-01-01

The goal of the recently emerged field of connectomics is to generate a wiring diagram of the brain at different scales. To identify brain circuitry, neuroscientists use specialized microscopes to perform multichannel imaging of labeled neurons at a very high resolution. CLARITY tissue clearing allows imaging labeled circuits through entire tissue blocks, without the need for tissue sectioning and section-to-section alignment. Imaging the large and complex non-human primate brain with sufficient resolution to identify and disambiguate between axons, in particular, produces massive data, creating great computational challenges to the study of neural circuits. Researchers require novel software capabilities for compiling, stitching, and visualizing large imagery. In this work, we detail the image acquisition process and a hierarchical streaming platform, ViSUS, that enables interactive visualization of these massive multi-volume datasets using a standard desktop computer. The ViSUS visualization framework has previously been shown to be suitable for 3D combustion simulation, climate simulation and visualization of large scale panoramic images. The platform is organized around a hierarchical cache oblivious data layout, called the IDX file format, which enables interactive visualization and exploration in ViSUS, scaling to the largest 3D images. In this paper we showcase the VISUS framework used in an interactive setting with the microscopy data. PMID:28638896
A Scalable Cyberinfrastructure for Interactive Visualization of Terascale Microscopy Data.

PubMed

Venkat, A; Christensen, C; Gyulassy, A; Summa, B; Federer, F; Angelucci, A; Pascucci, V

2016-08-01

The goal of the recently emerged field of connectomics is to generate a wiring diagram of the brain at different scales. To identify brain circuitry, neuroscientists use specialized microscopes to perform multichannel imaging of labeled neurons at a very high resolution. CLARITY tissue clearing allows imaging labeled circuits through entire tissue blocks, without the need for tissue sectioning and section-to-section alignment. Imaging the large and complex non-human primate brain with sufficient resolution to identify and disambiguate between axons, in particular, produces massive data, creating great computational challenges to the study of neural circuits. Researchers require novel software capabilities for compiling, stitching, and visualizing large imagery. In this work, we detail the image acquisition process and a hierarchical streaming platform, ViSUS, that enables interactive visualization of these massive multi-volume datasets using a standard desktop computer. The ViSUS visualization framework has previously been shown to be suitable for 3D combustion simulation, climate simulation and visualization of large scale panoramic images. The platform is organized around a hierarchical cache oblivious data layout, called the IDX file format, which enables interactive visualization and exploration in ViSUS, scaling to the largest 3D images. In this paper we showcase the VISUS framework used in an interactive setting with the microscopy data.
Maximizing Impact: Pairing interactive web visualizations with traditional print media

NASA Astrophysics Data System (ADS)

Read, E. K.; Appling, A.; Carr, L.; De Cicco, L.; Read, J. S.; Walker, J. I.; Winslow, L. A.

2016-12-01

Our Nation's rapidly growing store of environmental data makes new demands on researchers: to take on increasingly broad-scale, societally relevant analyses and to rapidly communicate findings to the public. Interactive web-based data visualizations now commonly supplement or comprise journalism, and science journalism has followed suit. To maximize the impact of US Geological Survey (USGS) science, the USGS Office of Water Information Data Science team builds tools and products that combine traditional static research products (e.g., print journal articles) with web-based, interactive data visualizations that target non-scientific audiences. We developed a lightweight, open-source framework for web visualizations to reduce time to production. The framework provides templates for a data visualization workflow and the packaging of text, interactive figures, and images into an appealing web interface with standardized look and feel, usage tracking, and responsiveness. By partnering with subject matter experts to focus on timely, societally relevant issues, we use these tools to produce appealing visual stories targeting specific audiences, including managers, the general public, and scientists, on diverse topics including drought, microplastic pollution, and fisheries response to climate change. We will describe the collaborative and technical methodologies used; describe some examples of how it's worked; and challenges and opportunities for the future.

Lateral interactions and speed of information processing in highly functioning multiple sclerosis patients.

PubMed

Nagy, Helga; Bencsik, Krisztina; Rajda, Cecília; Benedek, Krisztina; Janáky, Márta; Beniczky, Sándor; Kéri, Szabolcs; Vécsei, László

2007-06-01

Visual impairment is a common feature of multiple sclerosis. The aim of this study was to investigate lateral interactions in the visual cortex of highly functioning patients with multiple sclerosis and to compare that with basic visual and neuropsychologic functions. Twenty-two young, visually unimpaired multiple sclerosis patients with minimal symptoms (Expanded Disability Status Scale <2) and 30 healthy controls subjects participated in the study. Lateral interactions were investigated with the flanker task, during which participants were asked to detect the orientation of a low-contrast Gabor patch (vertical or horizontal), flanked with 2 collinear or orthogonal Gabor patches. Stimulus exposure time was 40, 60, 80, and 100 ms. Digit span forward/backward, digit symbol, verbal fluency, and California Verbal Learning Test procedures were used for background neuropsychologic assessment. Results revealed that patients with multiple sclerosis showed intact visual contrast sensitivity and neuropsychologic functions, whereas orientation detection in the orthogonal condition was significantly impaired. At 40-ms exposure time, collinear flankers facilitated the orientation detection performance of the patients resulting in normal performance. In conclusion, the detection of briefly presented, low-contrast visual stimuli was selectively impaired in multiple sclerosis. Lateral interactions between target and flankers robustly facilitated target detection in the patient group.
Personal factors influencing the visual reaction time of pedestrians to detect turn indicators in the presence of Daytime Running Lamps.

PubMed

Peña-García, Antonio; de Oña, Rocío; García, Pedro Antonio; de Oña, Juan

2016-12-01

Daytime running lamps (DRL) on vehicles have proven to be an effective measure to prevent accidents during the daytime, particularly when pedestrians and cyclists are involved. However, there are negative interactions of DRL with other functions in automotive lighting, such as delays in pedestrians' visual reaction time (VRT) when turn indicators are activated in the presence of DRL. These negative interactions need to be reduced. This work analyses the influence of variables inherent to pedestrians, such as height, gender and visual defects, on the VRT using a classification and regression tree as an exploratory analysis and a generalized linear model to validate the results. Some pedestrian characteristics, such as gender, alone or combined with the DRL colour, and visual defects, were found to have a statistically significant influence on VRT and, hence, on traffic safety. These results and conclusions concerning the interaction between pedestrians and vehicles are presented and discussed. Practitioner Summary: Visual interactions of vehicle daytime running lamps (DRL) with other functions in automotive lighting, such as turn indicators, have an important impact on a vehicle's conspicuity for pedestrians. Depending on several factors inherent to pedestrians, the visual reaction time (VRT) can be remarkably delayed, which has implications in traffic safety.
Imagery and Visual Literacy: Selected Readings from the Annual Conference of the International Visual Literacy Association (26th, Tempe, Arizona, October 12-16, 1994).

ERIC Educational Resources Information Center

Beauchamp, Darrell G.; And Others

This document contains selected conference papers all relating to visual literacy. The topics include: process issues in visual literacy; interpreting visual statements; what teachers need to know; multimedia presentations; distance education materials for correctional use; visual culture; audio-visual interaction in desktop multimedia; the…
Perceptual learning improves contrast sensitivity, visual acuity, and foveal crowding in amblyopia.

PubMed

Barollo, Michele; Contemori, Giulio; Battaglini, Luca; Pavan, Andrea; Casco, Clara

2017-01-01

Amblyopic observers present abnormal spatial interactions between a low-contrast sinusoidal target and high-contrast collinear flankers. It has been demonstrated that perceptual learning (PL) can modulate these low-level lateral interactions, resulting in improved visual acuity and contrast sensitivity. We measured the extent and duration of generalization effects to various spatial tasks (i.e., visual acuity, Vernier acuity, and foveal crowding) through PL on the target's contrast detection. Amblyopic observers were trained on a contrast-detection task for a central target (i.e., a Gabor patch) flanked above and below by two high-contrast Gabor patches. The pre- and post-learning tasks included lateral interactions at different target-to-flankers separations (i.e., 2, 3, 4, 8λ) and included a range of spatial frequencies and stimulus durations as well as visual acuity, Vernier acuity, contrast-sensitivity function, and foveal crowding. The results showed that perceptual training reduced the target's contrast-detection thresholds more for the longest target-to-flanker separation (i.e., 8λ). We also found generalization of PL to different stimuli and tasks: contrast sensitivity for both trained and untrained spatial frequencies, visual acuity for Sloan letters, and foveal crowding, and partially for Vernier acuity. Follow-ups after 5-7 months showed not only complete maintenance of PL effects on visual acuity and contrast sensitivity function but also further improvement in these tasks. These results suggest that PL improves facilitatory lateral interactions in amblyopic observers, which usually extend over larger separations than in typical foveal vision. The improvement in these basic visual spatial operations leads to a more efficient capability of performing spatial tasks involving high levels of visual processing, possibly due to the refinement of bottom-up and top-down networks of visual areas.
The national cost burden of bronchial foreign body aspiration in children.

PubMed

Kim, Irene A; Shapiro, Nina; Bhattacharyya, Neil

2015-05-01

Foreign body aspiration (FBA) continues to be a concerning pediatric problem, accounting for thousands of emergency room visits and more than 100 deaths each year in the United States. The costs incurred with hospitalizations and procedures following these events are the focus of this study. Retrospective review. The Nationwide Inpatient Sample from 2009 to 2011 was analyzed, and all cases with pediatric bronchial foreign body aspirations (International Classification of Diseases-9 codes: 934.0, 934.1, 934.8, and 934.9) were reviewed. Cases were analyzed to determine type of foreign body aspiration, procedural interventions performed, duration of inpatient stay, mortality rate, complications, and posthospitalization disposition. The median length of hospital stay and total costs associated with aspiration events were determined. An estimated 1,908 ± 273 pediatric bronchial FBA patients were admitted annually over the 3-year period (mean age, 3.6 ± 0.3 years; 61.3% ± 1.9% male). The ratio of foreign object aspiration to food aspiration was 5:3. Overall, 56%.0 ± 3.6% of the patients underwent a bronchoscopic procedure for foreign body removal; of those, 41.5% ± 2.5% had a foreign body removed at the time of the endoscopy. The hospital mortality rate associated with bronchial aspiration was 1.8% ± 0.4%; and 2.2% ± 0.5% of patients were diagnosed with anoxic brain injury. The median length of stay was 3 days (25th-75th interquartile range, 1-7 days).The median charges and actual costs per case were $20,820 ($10,800-$53,453) and $6,720 ($3,628-$16,723), respectively. The annual overall inpatient cost associated with pediatric bronchial foreign-body aspiration is approximately $12.8 million. Combined, the rate of death or anoxic brain injury associated with pediatric foreign body is approximately 4%. 2C. © 2014 The American Laryngological, Rhinological and Otological Society, Inc.
Food choking hazards in children.

PubMed

Sidell, Douglas R; Kim, Irene A; Coker, Tumaini R; Moreno, Candice; Shapiro, Nina L

2013-12-01

To review the literature on pediatric food choking risks, with the long-term goal of supporting legislation regulating the production, labeling, and distribution of high-risk foods. A PubMed search (Keywords: choking, obstruction, asphyxiation, foreign body, food) was conducted in July-September 2010 with publication dates ranging from 1966 to 2010. Articles related to pediatric foreign body aspiration (FBA) were selected by three independent reviewers. 1145 articles were initially identified. Abstracts were then screened utilizing a tool designed to isolate relevant pediatric choking events; this tool helped to only select abstracts which presented data on patients younger than 18 years of age who had choked on food items. Through this, a total of 72 pertinent articles were isolated (55 observational studies, 17 case reports/series). For each study, patient age, sex, foreign body location, presenting signs and symptoms, utility of radiographic studies, and type of foreign body detected in the majority of study participants were determined. A "majority" of patients for each study was predetermined arbitrarily to be 2/3 of the studied population. The majority of patients in each observational study was determined to be: male (87% of all studies) and age <5 years (95% of all studies). Aspirated foreign bodies were mostly detected in the right main bronchus foreign body (72% of all studies), and there were abnormal radiographic signs (81% of all studies) at the time of evaluation. Food-object foreign bodies were the most frequent factors associated with choking (94% of all studies). Childhood aspiration of food-objects is a significant public health issue. Although there is substantial legislation regulating non-food items that pose a choking hazard, equivalent guidelines do not exist for high-risk foods. Our study identifies and confirms several risk factors for pediatric FBA events. In doing so, it echoes the concerns and suggestions of various groups in supporting the development of legislation which may reduce the incidence of food-object aspiration. Copyright © 2013. Published by Elsevier Ireland Ltd.
Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints

PubMed Central

2013-01-01

Background Optimization procedures to identify gene knockouts for targeted biochemical overproduction have been widely in use in modern metabolic engineering. Flux balance analysis (FBA) framework has provided conceptual simplifications for genome-scale dynamic analysis at steady states. Based on FBA, many current optimization methods for targeted bio-productions have been developed under the maximum cell growth assumption. The optimization problem to derive gene knockout strategies recently has been formulated as a bi-level programming problem in OptKnock for maximum targeted bio-productions with maximum growth rates. However, it has been shown that knockout mutants in fact reach the steady states with the minimization of metabolic adjustment (MOMA) from the corresponding wild-type strains instead of having maximal growth rates after genetic or metabolic intervention. In this work, we propose a new bi-level computational framework--MOMAKnock--which can derive robust knockout strategies under the MOMA flux distribution approximation. Methods In this new bi-level optimization framework, we aim to maximize the production of targeted chemicals by identifying candidate knockout genes or reactions under phenotypic constraints approximated by the MOMA assumption. Hence, the targeted chemical production is the primary objective of MOMAKnock while the MOMA assumption is formulated as the inner problem of constraining the knockout metabolic flux to be as close as possible to the steady-state phenotypes of wide-type strains. As this new inner problem becomes a quadratic programming problem, a novel adaptive piecewise linearization algorithm is developed in this paper to obtain the exact optimal solution to this new bi-level integer quadratic programming problem for MOMAKnock. Results Our new MOMAKnock model and the adaptive piecewise linearization solution algorithm are tested with a small E. coli core metabolic network and a large-scale iAF1260 E. coli metabolic network. The derived knockout strategies are compared with those from OptKnock. Our preliminary experimental results show that MOMAKnock can provide improved targeted productions with more robust knockout strategies. PMID:23368729
Reflection and Transmission of Plane Electromagnetic Waves by a Geologic Layer.

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

Aldridge, David F.

Electric field and magnetic field reflection and transmission responses generated by a plane wave normally incident onto a finite - thickness geologic layer are mathematically derived and numerically evaluated. A thin layer with enhanced electric current conductivity and/or magnetic permeability is a reasonable geophysical representation of a hydraulic fracture inject ed with a high - contrast proppant pack. Both theory and numerics indicate that backward - and forward - scattered electromagnetic wavefields are potentially observable in a field experiment, despite the extreme thinness of a fracture compared to a typical low - frequency electromagnetic wavelength. The First Born Approximation (FBA)more » representation of layer scattering, significant for inversion studies, is shown to be accurate for a thin layer with mild medium parameter (i.e., conductivity, permeability, and per mittivity) contrasts with the surrounding homogeneous wholespace. However, FBA scattering theory breaks down for thick layers and strong parameter contrasts. ACKNOWLEDGEMENTS Sandia National Laboratories is a multi - mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under contract DE - AC04 - 94AL85000. This research is conducted under the auspices of CRADA (Cooperative Research and Development Agreement) SC11/01780.00 between Carbo Ceramics Inc. and Sandia National Laboratories. The author acknowledges former Carbo R&D Vic e - President Mr. Chad Cannan and former SNL Geophysics Department manage r Ms. Amy Halloran for their interest i n and support of this work. Technical discussions with Project Manager and Principal Investigator Dr. Chester J. Weiss of the SNL Geophysics Department greatly benefited this work. Dr. Lewis C. Bartel, formerly with S NL and presently a consultant to Carbo Ceramics, provided many useful and intuitive insights, and is acknowledged as the originator of the concept underpinning a recent patent grant (Aldridge and Bartel, 2016) involving electromagnetic wave scattering.« less
Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints.

PubMed

Ren, Shaogang; Zeng, Bo; Qian, Xiaoning

2013-01-01

Optimization procedures to identify gene knockouts for targeted biochemical overproduction have been widely in use in modern metabolic engineering. Flux balance analysis (FBA) framework has provided conceptual simplifications for genome-scale dynamic analysis at steady states. Based on FBA, many current optimization methods for targeted bio-productions have been developed under the maximum cell growth assumption. The optimization problem to derive gene knockout strategies recently has been formulated as a bi-level programming problem in OptKnock for maximum targeted bio-productions with maximum growth rates. However, it has been shown that knockout mutants in fact reach the steady states with the minimization of metabolic adjustment (MOMA) from the corresponding wild-type strains instead of having maximal growth rates after genetic or metabolic intervention. In this work, we propose a new bi-level computational framework--MOMAKnock--which can derive robust knockout strategies under the MOMA flux distribution approximation. In this new bi-level optimization framework, we aim to maximize the production of targeted chemicals by identifying candidate knockout genes or reactions under phenotypic constraints approximated by the MOMA assumption. Hence, the targeted chemical production is the primary objective of MOMAKnock while the MOMA assumption is formulated as the inner problem of constraining the knockout metabolic flux to be as close as possible to the steady-state phenotypes of wide-type strains. As this new inner problem becomes a quadratic programming problem, a novel adaptive piecewise linearization algorithm is developed in this paper to obtain the exact optimal solution to this new bi-level integer quadratic programming problem for MOMAKnock. Our new MOMAKnock model and the adaptive piecewise linearization solution algorithm are tested with a small E. coli core metabolic network and a large-scale iAF1260 E. coli metabolic network. The derived knockout strategies are compared with those from OptKnock. Our preliminary experimental results show that MOMAKnock can provide improved targeted productions with more robust knockout strategies.
Using perceptual rules in interactive visualization

NASA Astrophysics Data System (ADS)

Rogowitz, Bernice E.; Treinish, Lloyd A.

1994-05-01

In visualization, data are represented as variations in grayscale, hue, shape, and texture. They can be mapped to lines, surfaces, and glyphs, and can be represented statically or in animation. In modem visualization systems, the choices for representing data seem unlimited. This is both a blessing and a curse, however, since the visual impression created by the visualization depends critically on which dimensions are selected for representing the data (Bertin, 1967; Tufte, 1983; Cleveland, 1991). In modem visualization systems, the user can interactively select many different mapping and representation operations, and can interactively select processing operations (e.g., applying a color map), realization operations (e.g., generating geometric structures such as contours or streamlines), and rendering operations (e.g., shading or ray-tracing). The user can, for example, map data to a color map, then apply contour lines, then shift the viewing angle, then change the color map again, etc. In many systems, the user can vary the choices for each operation, selecting, for example, particular color maps, contour characteristics, and shading techniques. The hope is that this process will eventually converge on a visual representation which expresses the structure of the data and effectively communicates its message in a way that meets the user's goals. Sometimes, however, it results in visual representations which are confusing, misleading, and garish.
BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa–Function Relationships in Microbiome Data

PubMed Central

McNally, Colin P.; Eng, Alexander; Noecker, Cecilia; Gagne-Maynard, William C.; Borenstein, Elhanan

2018-01-01

The abundance of both taxonomic groups and gene categories in microbiome samples can now be easily assayed via various sequencing technologies, and visualized using a variety of software tools. However, the assemblage of taxa in the microbiome and its gene content are clearly linked, and tools for visualizing the relationship between these two facets of microbiome composition and for facilitating exploratory analysis of their co-variation are lacking. Here we introduce BURRITO, a web tool for interactive visualization of microbiome multi-omic data with paired taxonomic and functional information. BURRITO simultaneously visualizes the taxonomic and functional compositions of multiple samples and dynamically highlights relationships between taxa and functions to capture the underlying structure of these data. Users can browse for taxa and functions of interest and interactively explore the share of each function attributed to each taxon across samples. BURRITO supports multiple input formats for taxonomic and metagenomic data, allows adjustment of data granularity, and can export generated visualizations as static publication-ready formatted figures. In this paper, we describe the functionality of BURRITO, and provide illustrative examples of its utility for visualizing various trends in the relationship between the composition of taxa and functions in complex microbiomes. PMID:29545787
Celeris: A GPU-accelerated open source software with a Boussinesq-type wave solver for real-time interactive simulation and visualization

NASA Astrophysics Data System (ADS)

Tavakkol, Sasan; Lynett, Patrick

2017-08-01

In this paper, we introduce an interactive coastal wave simulation and visualization software, called Celeris. Celeris is an open source software which needs minimum preparation to run on a Windows machine. The software solves the extended Boussinesq equations using a hybrid finite volume-finite difference method and supports moving shoreline boundaries. The simulation and visualization are performed on the GPU using Direct3D libraries, which enables the software to run faster than real-time. Celeris provides a first-of-its-kind interactive modeling platform for coastal wave applications and it supports simultaneous visualization with both photorealistic and colormapped rendering capabilities. We validate our software through comparison with three standard benchmarks for non-breaking and breaking waves.
ViSEN: methodology and software for visualization of statistical epistasis networks

PubMed Central

Hu, Ting; Chen, Yuanzhu; Kiralis, Jeff W.; Moore, Jason H.

2013-01-01

The non-linear interaction effect among multiple genetic factors, i.e. epistasis, has been recognized as a key component in understanding the underlying genetic basis of complex human diseases and phenotypic traits. Due to the statistical and computational complexity, most epistasis studies are limited to interactions with an order of two. We developed ViSEN to analyze and visualize epistatic interactions of both two-way and three-way. ViSEN not only identifies strong interactions among pairs or trios of genetic attributes, but also provides a global interaction map that shows neighborhood and clustering structures. This visualized information could be very helpful to infer the underlying genetic architecture of complex diseases and to generate plausible hypotheses for further biological validations. ViSEN is implemented in Java and freely available at https://sourceforge.net/projects/visen/. PMID:23468157
Visualizing Chemical Interaction Dynamics of Confined DNA Molecules

NASA Astrophysics Data System (ADS)

Henkin, Gilead; Berard, Daniel; Stabile, Frank; Leslie, Sabrina

We present a novel nanofluidic approach to controllably introducing reagent molecules to interact with confined biopolymers and visualizing the reaction dynamics in real time. By dynamically deforming a flow cell using CLiC (Convex Lens-induced Confinement) microscopy, we are able to tune reaction chamber dimensions from micrometer to nanometer scales. We apply this gentle deformation to load and extend DNA polymers within embedded nanotopographies and visualize their interactions with other molecules in solution. Quantifying the change in configuration of polymers within embedded nanotopographies in response to binding/unbinding of reagent molecules provides new insights into their consequent change in physical properties. CLiC technology enables an ultra sensitive, massively parallel biochemical analysis platform which can acces a broader range of interaction parameters than existing devices.
Design and implementation of bimolecular fluorescence complementation (BiFC) assays for the visualization of protein interactions in living cells.

PubMed

Kerppola, Tom K

2006-01-01

Bimolecular fluorescence complementation (BiFC) analysis enables direct visualization of protein interactions in living cells. The BiFC assay is based on the discoveries that two non-fluorescent fragments of a fluorescent protein can form a fluorescent complex and that the association of the fragments can be facilitated when they are fused to two proteins that interact with each other. BiFC must be confirmed by parallel analysis of proteins in which the interaction interface has been mutated. It is not necessary for the interaction partners to juxtapose the fragments within a specific distance of each other because they can associate when they are tethered to a complex with flexible linkers. It is also not necessary for the interaction partners to form a complex with a long half-life or a high occupancy since the fragments can associate in a transient complex and un-associated fusion proteins do not interfere with detection of the complex. Many interactions can be visualized when the fusion proteins are expressed at levels comparable to their endogenous counterparts. The BiFC assay has been used for the visualization of interactions between many types of proteins in different subcellular locations and in different cell types and organisms. It is technically straightforward and can be performed using a regular fluorescence microscope and standard molecular biology and cell culture reagents.
A visualization system for CT based pulmonary fissure analysis

NASA Astrophysics Data System (ADS)

Pu, Jiantao; Zheng, Bin; Park, Sang Cheol

2009-02-01

In this study we describe a visualization system of pulmonary fissures depicted on CT images. The purpose is to provide clinicians with an intuitive perception of a patient's lung anatomy through an interactive examination of fissures, enhancing their understanding and accurate diagnosis of lung diseases. This system consists of four key components: (1) region-of-interest segmentation; (2) three-dimensional surface modeling; (3) fissure type classification; and (4) an interactive user interface, by which the extracted fissures are displayed flexibly in different space domains including image space, geometric space, and mixed space using simple toggling "on" and "off" operations. In this system, the different visualization modes allow users not only to examine the fissures themselves but also to analyze the relationship between fissures and their surrounding structures. In addition, the users can adjust thresholds interactively to visualize the fissure surface under different scanning and processing conditions. Such a visualization tool is expected to facilitate investigation of structures near the fissures and provide an efficient "visual aid" for other applications such as treatment planning and assessment of therapeutic efficacy as well as education of medical professionals.
The efficacy of VIPP-V parenting training for parents of young children with a visual or visual-and-intellectual disability: a randomized controlled trial.

PubMed

Platje, Evelien; Sterkenburg, Paula; Overbeek, Mathile; Kef, Sabina; Schuengel, Carlo

2018-01-23

Video-feedback Intervention to promote positive parenting-visual (VIPP-V) or visual-and-intellectual disability is an attachment-based intervention aimed at enhancing sensitive parenting and promoting positive parent-child relationships. A randomized controlled trial was conducted to assess the efficacy of VIPP-V for parents of children aged 1-5 with visual or visual-and-intellectual disabilities. A total of 37 dyads received only care-as-usual (CAU) and 40 received VIPP-V besides CAU. The parents receiving VIPP-V did not show increased parental sensitivity or parent-child interaction quality, however, their parenting self-efficacy increased. Moreover, the increase in parental self-efficacy predicted the increase in parent-child interaction. In conclusion, VIPP-V does not appear to directly improve the quality of contact between parent and child, but does contribute to the self-efficacy of parents to support and to comfort their child. Moreover, as parents experience their parenting as more positive, this may eventually lead to higher sensitive responsiveness and more positive parent-child interactions.
A Dual-Route Perspective on Brain Activation in Response to Visual Words: Evidence for a Length by Lexicality Interaction in the Visual Word Form Area (VWFA)

PubMed Central

Schurz, Matthias; Sturm, Denise; Richlan, Fabio; Kronbichler, Martin; Ladurner, Gunther; Wimmer, Heinz

2010-01-01

Based on our previous work, we expected the Visual Word Form Area (VWFA) in the left ventral visual pathway to be engaged by both whole-word recognition and by serial sublexical coding of letter strings. To examine this double function, a phonological lexical decision task (i.e., “Does xxx sound like an existing word?”) presented short and long letter strings of words, pseudohomophones, and pseudowords (e.g., Taxi, Taksi and Tazi). Main findings were that the length effect for words was limited to occipital regions and absent in the VWFA. In contrast, a marked length effect for pseudowords was found throughout the ventral visual pathway including the VWFA, as well as in regions presumably engaged by visual attention and silent-articulatory processes. The length by lexicality interaction on brain activation corresponds to well-established behavioral findings of a length by lexicality interaction on naming latencies and speaks for the engagement of the VWFA by both lexical and sublexical processes. PMID:19896538
A dual-route perspective on brain activation in response to visual words: evidence for a length by lexicality interaction in the visual word form area (VWFA).

PubMed

Schurz, Matthias; Sturm, Denise; Richlan, Fabio; Kronbichler, Martin; Ladurner, Gunther; Wimmer, Heinz

2010-02-01

Based on our previous work, we expected the Visual Word Form Area (VWFA) in the left ventral visual pathway to be engaged by both whole-word recognition and by serial sublexical coding of letter strings. To examine this double function, a phonological lexical decision task (i.e., "Does xxx sound like an existing word?") presented short and long letter strings of words, pseudohomophones, and pseudowords (e.g., Taxi, Taksi and Tazi). Main findings were that the length effect for words was limited to occipital regions and absent in the VWFA. In contrast, a marked length effect for pseudowords was found throughout the ventral visual pathway including the VWFA, as well as in regions presumably engaged by visual attention and silent-articulatory processes. The length by lexicality interaction on brain activation corresponds to well-established behavioral findings of a length by lexicality interaction on naming latencies and speaks for the engagement of the VWFA by both lexical and sublexical processes. Copyright (c) 2009 Elsevier Inc. All rights reserved.
A Nonlinear Model for Interactive Data Analysis and Visualization and an Implementation Using Progressive Computation for Massive Remote Climate Data Ensembles

NASA Astrophysics Data System (ADS)

Christensen, C.; Liu, S.; Scorzelli, G.; Lee, J. W.; Bremer, P. T.; Summa, B.; Pascucci, V.

2017-12-01

The creation, distribution, analysis, and visualization of large spatiotemporal datasets is a growing challenge for the study of climate and weather phenomena in which increasingly massive domains are utilized to resolve finer features, resulting in datasets that are simply too large to be effectively shared. Existing workflows typically consist of pipelines of independent processes that preclude many possible optimizations. As data sizes increase, these pipelines are difficult or impossible to execute interactively and instead simply run as large offline batch processes. Rather than limiting our conceptualization of such systems to pipelines (or dataflows), we propose a new model for interactive data analysis and visualization systems in which we comprehensively consider the processes involved from data inception through analysis and visualization in order to describe systems composed of these processes in a manner that facilitates interactive implementations of the entire system rather than of only a particular component. We demonstrate the application of this new model with the implementation of an interactive system that supports progressive execution of arbitrary user scripts for the analysis and visualization of massive, disparately located climate data ensembles. It is currently in operation as part of the Earth System Grid Federation server running at Lawrence Livermore National Lab, and accessible through both web-based and desktop clients. Our system facilitates interactive analysis and visualization of massive remote datasets up to petabytes in size, such as the 3.5 PB 7km NASA GEOS-5 Nature Run simulation, previously only possible offline or at reduced resolution. To support the community, we have enabled general distribution of our application using public frameworks including Docker and Anaconda.

Spatiotemporal Processing in Crossmodal Interactions for Perception of the External World: A Review

PubMed Central

Hidaka, Souta; Teramoto, Wataru; Sugita, Yoichi

2015-01-01

Research regarding crossmodal interactions has garnered much interest in the last few decades. A variety of studies have demonstrated that multisensory information (vision, audition, tactile sensation, and so on) can perceptually interact with each other in the spatial and temporal domains. Findings regarding crossmodal interactions in the spatiotemporal domain (i.e., motion processing) have also been reported, with updates in the last few years. In this review, we summarize past and recent findings on spatiotemporal processing in crossmodal interactions regarding perception of the external world. A traditional view regarding crossmodal interactions holds that vision is superior to audition in spatial processing, but audition is dominant over vision in temporal processing. Similarly, vision is considered to have dominant effects over the other sensory modalities (i.e., visual capture) in spatiotemporal processing. However, recent findings demonstrate that sound could have a driving effect on visual motion perception. Moreover, studies regarding perceptual associative learning reported that, after association is established between a sound sequence without spatial information and visual motion information, the sound sequence could trigger visual motion perception. Other sensory information, such as motor action or smell, has also exhibited similar driving effects on visual motion perception. Additionally, recent brain imaging studies demonstrate that similar activation patterns could be observed in several brain areas, including the motion processing areas, between spatiotemporal information from different sensory modalities. Based on these findings, we suggest that multimodal information could mutually interact in spatiotemporal processing in the percept of the external world and that common perceptual and neural underlying mechanisms would exist for spatiotemporal processing. PMID:26733827
Visual functions and interocular interactions in anisometropic children with and without amblyopia.

PubMed

Lai, Xin Jie; Alexander, Jack; He, Mingguang; Yang, Zhikuan; Suttle, Catherine

2011-08-29

In uncorrected anisometropia, protracted dichoptic stimulation may result in interocular inhibition, which may be a contributing factor in amblyopia development. This study investigates the relationship between interocular interactions and anisometropic amblyopia. Three visual functions (low-contrast acuity, contrast sensitivity, and alignment sensitivity) were measured in the nondominant eye of 44 children aged 5 to 11 years: 10 with normal vision, 17 with anisometropia without amblyopia, and 17 with anisometropic amblyopia. The dominant eye was either fully or partially occluded. The difference in nondominant eye visual function between the full-and partial-occlusion conditions was termed the interaction index. The index of each visual function was compared between subject groups. A higher index indicates stronger inhibition of nondominant eye function with partial occlusion of the dominant eye. Amblyopic children had 6 months of therapy (refractive correction and occlusion), and the reduction in interocular difference in high-contrast acuity was regarded as the treatment outcome. The relationships of the interaction index with the degree of anisometropia, the severity of amblyopia, and the treatment outcomes were examined. The acuity interaction index was significantly higher in anisometropic children with amblyopia than in those without (P = 0.003). It was positively correlated with the degree of anisometropia (r(s) = 0.35, P = 0.042) and the amblyopic treatment outcomes (r(s) = 0.54, P = 0.038). No such difference or association was found between the contrast sensitivity or alignment sensitivity interaction index and anisometropic amblyopia. Interocular interactions are associated with amblyopia, the degree of anisometropia, and amblyopia treatment outcomes, but these associations are visual function dependent.
Visuo-Vestibular Interactions

NASA Technical Reports Server (NTRS)

1997-01-01

Session TA3 includes short reports covering: (1) Vestibulo-Oculomotor Interaction in Long-Term Microgravity; (2) Effects of Weightlessness on the Spatial Orientation of Visually Induced Eye Movements; (3) Adaptive Modification of the Three-Dimensional Vestibulo-Ocular Reflex during Prolonged Microgravity; (4) The Dynamic Change of Brain Potential Related to Selective Attention to Visual Signals from Left and Right Visual Fields; (5) Locomotor Errors Caused by Vestibular Suppression; and (6) A Novel, Image-Based Technique for Three-Dimensional Eye Measurement.
Selective visual attention to emotional words: Early parallel frontal and visual activations followed by interactive effects in visual cortex.

PubMed

Schindler, Sebastian; Kissler, Johanna

2016-10-01

Human brains spontaneously differentiate between various emotional and neutral stimuli, including written words whose emotional quality is symbolic. In the electroencephalogram (EEG), emotional-neutral processing differences are typically reflected in the early posterior negativity (EPN, 200-300 ms) and the late positive potential (LPP, 400-700 ms). These components are also enlarged by task-driven visual attention, supporting the assumption that emotional content naturally drives attention. Still, the spatio-temporal dynamics of interactions between emotional stimulus content and task-driven attention remain to be specified. Here, we examine this issue in visual word processing. Participants attended to negative, neutral, or positive nouns while high-density EEG was recorded. Emotional content and top-down attention both amplified the EPN component in parallel. On the LPP, by contrast, emotion and attention interacted: Explicit attention to emotional words led to a substantially larger amplitude increase than did explicit attention to neutral words. Source analysis revealed early parallel effects of emotion and attention in bilateral visual cortex and a later interaction of both in right visual cortex. Distinct effects of attention were found in inferior, middle and superior frontal, paracentral, and parietal areas, as well as in the anterior cingulate cortex (ACC). Results specify separate and shared mechanisms of emotion and attention at distinct processing stages. Hum Brain Mapp 37:3575-3587, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
VisFlow - Web-based Visualization Framework for Tabular Data with a Subset Flow Model.

PubMed

Yu, Bowen; Silva, Claudio T

2017-01-01

Data flow systems allow the user to design a flow diagram that specifies the relations between system components which process, filter or visually present the data. Visualization systems may benefit from user-defined data flows as an analysis typically consists of rendering multiple plots on demand and performing different types of interactive queries across coordinated views. In this paper, we propose VisFlow, a web-based visualization framework for tabular data that employs a specific type of data flow model called the subset flow model. VisFlow focuses on interactive queries within the data flow, overcoming the limitation of interactivity from past computational data flow systems. In particular, VisFlow applies embedded visualizations and supports interactive selections, brushing and linking within a visualization-oriented data flow. The model requires all data transmitted by the flow to be a data item subset (i.e. groups of table rows) of some original input table, so that rendering properties can be assigned to the subset unambiguously for tracking and comparison. VisFlow features the analysis flexibility of a flow diagram, and at the same time reduces the diagram complexity and improves usability. We demonstrate the capability of VisFlow on two case studies with domain experts on real-world datasets showing that VisFlow is capable of accomplishing a considerable set of visualization and analysis tasks. The VisFlow system is available as open source on GitHub.
Top-down alpha oscillatory network interactions during visuospatial attention orienting.

PubMed

Doesburg, Sam M; Bedo, Nicolas; Ward, Lawrence M

2016-05-15

Neuroimaging and lesion studies indicate that visual attention is controlled by a distributed network of brain areas. The covert control of visuospatial attention has also been associated with retinotopic modulation of alpha-band oscillations within early visual cortex, which are thought to underlie inhibition of ignored areas of visual space. The relation between distributed networks mediating attention control and more focal oscillatory mechanisms, however, remains unclear. The present study evaluated the hypothesis that alpha-band, directed, network interactions within the attention control network are systematically modulated by the locus of visuospatial attention. We localized brain areas involved in visuospatial attention orienting using magnetoencephalographic (MEG) imaging and investigated alpha-band Granger-causal interactions among activated regions using narrow-band transfer entropy. The deployment of attention to one side of visual space was indexed by lateralization of alpha power changes between about 400ms and 700ms post-cue onset. The changes in alpha power were associated, in the same time period, with lateralization of anterior-to-posterior information flow in the alpha-band from various brain areas involved in attention control, including the anterior cingulate cortex, left middle and inferior frontal gyri, left superior temporal gyrus, and right insula, and inferior parietal lobule, to early visual areas. We interpreted these results to indicate that distributed network interactions mediated by alpha oscillations exert top-down influences on early visual cortex to modulate inhibition of processing for ignored areas of visual space. Copyright © 2016. Published by Elsevier Inc.
Map Learning with a 3D Printed Interactive Small-Scale Model: Improvement of Space and Text Memorization in Visually Impaired Students

PubMed Central

Giraud, Stéphanie; Brock, Anke M.; Macé, Marc J.-M.; Jouffrais, Christophe

2017-01-01

Special education teachers for visually impaired students rely on tools such as raised-line maps (RLMs) to teach spatial knowledge. These tools do not fully and adequately meet the needs of the teachers because they are long to produce, expensive, and not versatile enough to provide rapid updating of the content. For instance, the same RLM can barely be used during different lessons. In addition, those maps do not provide any interactivity, which reduces students’ autonomy. With the emergence of 3D printing and low-cost microcontrollers, it is now easy to design affordable interactive small-scale models (SSMs) which are adapted to the needs of special education teachers. However, no study has previously been conducted to evaluate non-visual learning using interactive SSMs. In collaboration with a specialized teacher, we designed a SSM and a RLM representing the evolution of the geography and history of a fictitious kingdom. The two conditions were compared in a study with 24 visually impaired students regarding the memorization of the spatial layout and historical contents. The study showed that the interactive SSM improved both space and text memorization as compared to the RLM with braille legend. In conclusion, we argue that affordable home-made interactive small scale models can improve learning for visually impaired students. Interestingly, they are adaptable to any teaching situation including students with specific needs. PMID:28649209
Vestibular-visual interactions in flight simulators

NASA Technical Reports Server (NTRS)

Clark, B.

1977-01-01

All 139 research papers published under this ten-year program are listed. Experimental work was carried out at the Ames Research Center involving man's sensitivity to rotational acceleration, and psychophysical functioning of the semicircular canals; vestibular-visual interactions and effects of other sensory systems were studied in flight simulator environments. Experiments also dealt with the neurophysiological vestibular functions of animals, and flight management investigations of man-vehicle interactions.
Dynamic Interactions for Network Visualization and Simulation

DTIC Science & Technology

2009-03-01

projects.htm, Site accessed January 5, 2009. 12. John S. Weir, Major, USAF, Mediated User-Simulator Interactive Command with Visualization ( MUSIC -V). Master’s...Computing Sciences in Colleges, December 2005). 14. Enrique Campos -Nanez, “nscript user manual,” Department of System Engineer- ing University of
Designing Online Mathematical Investigation

ERIC Educational Resources Information Center

Gadanidis, George; Sedig, Kamran; Liang, Hai-Ning

2004-01-01

In this paper we focus on interactive visualizations that support mathematical investigation. In the context of analyzing and redesigning an interactive visualization from the National Council of Teachers of Mathematics's (NCTM's) Illuminations Web site, we consider two interrelated issues: (1) how the pedagogy of mathematical investigation may be…
Modeling the Perception of Audiovisual Distance: Bayesian Causal Inference and Other Models

PubMed Central

2016-01-01

Studies of audiovisual perception of distance are rare. Here, visual and auditory cue interactions in distance are tested against several multisensory models, including a modified causal inference model. In this causal inference model predictions of estimate distributions are included. In our study, the audiovisual perception of distance was overall better explained by Bayesian causal inference than by other traditional models, such as sensory dominance and mandatory integration, and no interaction. Causal inference resolved with probability matching yielded the best fit to the data. Finally, we propose that sensory weights can also be estimated from causal inference. The analysis of the sensory weights allows us to obtain windows within which there is an interaction between the audiovisual stimuli. We find that the visual stimulus always contributes by more than 80% to the perception of visual distance. The visual stimulus also contributes by more than 50% to the perception of auditory distance, but only within a mobile window of interaction, which ranges from 1 to 4 m. PMID:27959919
Inferring Interaction Force from Visual Information without Using Physical Force Sensors.

PubMed

Hwang, Wonjun; Lim, Soo-Chul

2017-10-26

In this paper, we present an interaction force estimation method that uses visual information rather than that of a force sensor. Specifically, we propose a novel deep learning-based method utilizing only sequential images for estimating the interaction force against a target object, where the shape of the object is changed by an external force. The force applied to the target can be estimated by means of the visual shape changes. However, the shape differences in the images are not very clear. To address this problem, we formulate a recurrent neural network-based deep model with fully-connected layers, which models complex temporal dynamics from the visual representations. Extensive evaluations show that the proposed learning models successfully estimate the interaction forces using only the corresponding sequential images, in particular in the case of three objects made of different materials, a sponge, a PET bottle, a human arm, and a tube. The forces predicted by the proposed method are very similar to those measured by force sensors.
New techniques for experimental generation of two-dimensional blade-vortex interaction at low Reynolds numbers

NASA Technical Reports Server (NTRS)

Booth, E., Jr.; Yu, J. C.

1986-01-01

An experimental investigation of two dimensional blade vortex interaction was held at NASA Langley Research Center. The first phase was a flow visualization study to document the approach process of a two dimensional vortex as it encountered a loaded blade model. To accomplish the flow visualization study, a method for generating two dimensional vortex filaments was required. The numerical study used to define a new vortex generation process and the use of this process in the flow visualization study were documented. Additionally, photographic techniques and data analysis methods used in the flow visualization study are examined.
High Performance Real-Time Visualization of Voluminous Scientific Data Through the NOAA Earth Information System (NEIS).

NASA Astrophysics Data System (ADS)

Stewart, J.; Hackathorn, E. J.; Joyce, J.; Smith, J. S.

2014-12-01

Within our community data volume is rapidly expanding. These data have limited value if one cannot interact or visualize the data in a timely manner. The scientific community needs the ability to dynamically visualize, analyze, and interact with these data along with other environmental data in real-time regardless of the physical location or data format. Within the National Oceanic Atmospheric Administration's (NOAA's), the Earth System Research Laboratory (ESRL) is actively developing the NOAA Earth Information System (NEIS). Previously, the NEIS team investigated methods of data discovery and interoperability. The recent focus shifted to high performance real-time visualization allowing NEIS to bring massive amounts of 4-D data, including output from weather forecast models as well as data from different observations (surface obs, upper air, etc...) in one place. Our server side architecture provides a real-time stream processing system which utilizes server based NVIDIA Graphical Processing Units (GPU's) for data processing, wavelet based compression, and other preparation techniques for visualization, allows NEIS to minimize the bandwidth and latency for data delivery to end-users. Client side, users interact with NEIS services through the visualization application developed at ESRL called TerraViz. Terraviz is developed using the Unity game engine and takes advantage of the GPU's allowing a user to interact with large data sets in real time that might not have been possible before. Through these technologies, the NEIS team has improved accessibility to 'Big Data' along with providing tools allowing novel visualization and seamless integration of data across time and space regardless of data size, physical location, or data format. These capabilities provide the ability to see the global interactions and their importance for weather prediction. Additionally, they allow greater access than currently exists helping to foster scientific collaboration and new ideas. This presentation will provide an update of the recent enhancements of the NEIS architecture and visualization capabilities, challenges faced, as well as ongoing research activities related to this project.
VisIO: enabling interactive visualization of ultra-scale, time-series data via high-bandwidth distributed I/O systems

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

Mitchell, Christopher J; Ahrens, James P; Wang, Jun

2010-10-15

Petascale simulations compute at resolutions ranging into billions of cells and write terabytes of data for visualization and analysis. Interactive visuaUzation of this time series is a desired step before starting a new run. The I/O subsystem and associated network often are a significant impediment to interactive visualization of time-varying data; as they are not configured or provisioned to provide necessary I/O read rates. In this paper, we propose a new I/O library for visualization applications: VisIO. Visualization applications commonly use N-to-N reads within their parallel enabled readers which provides an incentive for a shared-nothing approach to I/O, similar tomore » other data-intensive approaches such as Hadoop. However, unlike other data-intensive applications, visualization requires: (1) interactive performance for large data volumes, (2) compatibility with MPI and POSIX file system semantics for compatibility with existing infrastructure, and (3) use of existing file formats and their stipulated data partitioning rules. VisIO, provides a mechanism for using a non-POSIX distributed file system to provide linear scaling of 110 bandwidth. In addition, we introduce a novel scheduling algorithm that helps to co-locate visualization processes on nodes with the requested data. Testing using VisIO integrated into Para View was conducted using the Hadoop Distributed File System (HDFS) on TACC's Longhorn cluster. A representative dataset, VPIC, across 128 nodes showed a 64.4% read performance improvement compared to the provided Lustre installation. Also tested, was a dataset representing a global ocean salinity simulation that showed a 51.4% improvement in read performance over Lustre when using our VisIO system. VisIO, provides powerful high-performance I/O services to visualization applications, allowing for interactive performance with ultra-scale, time-series data.« less
Knowledge is power: how conceptual knowledge transforms visual cognition.

PubMed

Collins, Jessica A; Olson, Ingrid R

2014-08-01

In this review, we synthesize the existing literature demonstrating the dynamic interplay between conceptual knowledge and visual perceptual processing. We consider two theoretical frameworks that demonstrate interactions between processes and brain areas traditionally considered perceptual or conceptual. Specifically, we discuss categorical perception, in which visual objects are represented according to category membership, and highlight studies showing that category knowledge can penetrate early stages of visual analysis. We next discuss the embodied account of conceptual knowledge, which holds that concepts are instantiated in the same neural regions required for specific types of perception and action, and discuss the limitations of this framework. We additionally consider studies showing that gaining abstract semantic knowledge about objects and faces leads to behavioral and electrophysiological changes that are indicative of more efficient stimulus processing. Finally, we consider the role that perceiver goals and motivation may play in shaping the interaction between conceptual and perceptual processing. We hope to demonstrate how pervasive such interactions between motivation, conceptual knowledge, and perceptual processing are in our understanding of the visual environment, and to demonstrate the need for future research aimed at understanding how such interactions arise in the brain.
Knowledge is Power: How Conceptual Knowledge Transforms Visual Cognition

PubMed Central

Collins, Jessica A.; Olson, Ingrid R.

2014-01-01

In this review we synthesize the existing literature demonstrating the dynamic interplay between conceptual knowledge and visual perceptual processing. We consider two theoretical frameworks demonstrating interactions between processes and brain areas traditionally considered perceptual or conceptual. Specifically, we discuss categorical perception, in which visual objects are represented according to category membership, and highlight studies showing that category knowledge can penetrate early stages of visual analysis. We next discuss the embodied account of conceptual knowledge, which holds that concepts are instantiated in the same neural regions required for specific types of perception and action, and discuss the limitations of this framework. We additionally consider studies showing that gaining abstract semantic knowledge about objects and faces leads to behavioral and electrophysiological changes that are indicative of more efficient stimulus processing. Finally, we consider the role that perceiver goals and motivation may play in shaping the interaction between conceptual and perceptual processing. We hope to demonstrate how pervasive such interactions between motivation, conceptual knowledge, and perceptual processing are to our understanding of the visual environment, and demonstrate the need for future research aimed at understanding how such interactions arise in the brain. PMID:24402731
A novel visualization model for web search results.

PubMed

Nguyen, Tien N; Zhang, Jin

2006-01-01

This paper presents an interactive visualization system, named WebSearchViz, for visualizing the Web search results and acilitating users' navigation and exploration. The metaphor in our model is the solar system with its planets and asteroids revolving around the sun. Location, color, movement, and spatial distance of objects in the visual space are used to represent the semantic relationships between a query and relevant Web pages. Especially, the movement of objects and their speeds add a new dimension to the visual space, illustrating the degree of relevance among a query and Web search results in the context of users' subjects of interest. By interacting with the visual space, users are able to observe the semantic relevance between a query and a resulting Web page with respect to their subjects of interest, context information, or concern. Users' subjects of interest can be dynamically changed, redefined, added, or deleted from the visual space.
Linked exploratory visualizations for uncertain MR spectroscopy data

NASA Astrophysics Data System (ADS)

Feng, David; Kwock, Lester; Lee, Yueh; Taylor, Russell M., II

2010-01-01

We present a system for visualizing magnetic resonance spectroscopy (MRS) data sets. Using MRS, radiologists generate multiple 3D scalar fields of metabolite concentrations within the brain and compare them to anatomical magnetic resonance imaging. By understanding the relationship between metabolic makeup and anatomical structure, radiologists hope to better diagnose and treat tumors and lesions. Our system consists of three linked visualizations: a spatial glyph-based technique we call Scaled Data-Driven Spheres, a parallel coordinates visualization augmented to incorporate uncertainty in the data, and a slice plane for accurate data value extraction. The parallel coordinates visualization uses specialized brush interactions designed to help users identify nontrivial linear relationships between scalar fields. We describe two novel contributions to parallel coordinates visualizations: linear function brushing and new axis construction. Users have discovered significant relationships among metabolites and anatomy by linking interactions between the three visualizations.
Linked Exploratory Visualizations for Uncertain MR Spectroscopy Data

PubMed Central

Feng, David; Kwock, Lester; Lee, Yueh; Taylor, Russell M.

2010-01-01

We present a system for visualizing magnetic resonance spectroscopy (MRS) data sets. Using MRS, radiologists generate multiple 3D scalar fields of metabolite concentrations within the brain and compare them to anatomical magnetic resonance imaging. By understanding the relationship between metabolic makeup and anatomical structure, radiologists hope to better diagnose and treat tumors and lesions. Our system consists of three linked visualizations: a spatial glyph-based technique we call Scaled Data-Driven Spheres, a parallel coordinates visualization augmented to incorporate uncertainty in the data, and a slice plane for accurate data value extraction. The parallel coordinates visualization uses specialized brush interactions designed to help users identify nontrivial linear relationships between scalar fields. We describe two novel contributions to parallel coordinates visualizations: linear function brushing and new axis construction. Users have discovered significant relationships among metabolites and anatomy by linking interactions between the three visualizations. PMID:21152337

GLO-STIX: Graph-Level Operations for Specifying Techniques and Interactive eXploration

PubMed Central

Stolper, Charles D.; Kahng, Minsuk; Lin, Zhiyuan; Foerster, Florian; Goel, Aakash; Stasko, John; Chau, Duen Horng

2015-01-01

The field of graph visualization has produced a wealth of visualization techniques for accomplishing a variety of analysis tasks. Therefore analysts often rely on a suite of different techniques, and visual graph analysis application builders strive to provide this breadth of techniques. To provide a holistic model for specifying network visualization techniques (as opposed to considering each technique in isolation) we present the Graph-Level Operations (GLO) model. We describe a method for identifying GLOs and apply it to identify five classes of GLOs, which can be flexibly combined to re-create six canonical graph visualization techniques. We discuss advantages of the GLO model, including potentially discovering new, effective network visualization techniques and easing the engineering challenges of building multi-technique graph visualization applications. Finally, we implement the GLOs that we identified into the GLO-STIX prototype system that enables an analyst to interactively explore a graph by applying GLOs. PMID:26005315
Visual Complexity and Pictorial Memory: A Fifteen Year Research Perspective.

ERIC Educational Resources Information Center

Berry, Louis H.

For 15 years an ongoing research project at the University of Pittsburgh has focused on the effects of variations in visual complexity and color on the storage and retrieval of visual information by learners. Research has shown that visual materials facilitate instruction, but has not fully delineated the interactions of visual complexity and…
Visual acuity in adults with Asperger's syndrome: no evidence for "eagle-eyed" vision.

PubMed

Falkmer, Marita; Stuart, Geoffrey W; Danielsson, Henrik; Bram, Staffan; Lönebrink, Mikael; Falkmer, Torbjörn

2011-11-01

Autism spectrum conditions (ASC) are defined by criteria comprising impairments in social interaction and communication. Altered visual perception is one possible and often discussed cause of difficulties in social interaction and social communication. Recently, Ashwin et al. suggested that enhanced ability in local visual processing in ASC was due to superior visual acuity, but that study has been the subject of methodological criticism, placing the findings in doubt. The present study investigated visual acuity thresholds in 24 adults with Asperger's syndrome and compared their results with 25 control subjects with the 2 Meter 2000 Series Revised ETDRS Chart. The distribution of visual acuities within the two groups was highly similar, and none of the participants had superior visual acuity. Superior visual acuity in individuals with Asperger's syndrome could not be established, suggesting that differences in visual perception in ASC are not explained by this factor. A continued search for explanations of superior ability in local visual processing in persons with ASC is therefore warranted. Copyright © 2011 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.
Pycortex: an interactive surface visualizer for fMRI

PubMed Central

Gao, James S.; Huth, Alexander G.; Lescroart, Mark D.; Gallant, Jack L.

2015-01-01

Surface visualizations of fMRI provide a comprehensive view of cortical activity. However, surface visualizations are difficult to generate and most common visualization techniques rely on unnecessary interpolation which limits the fidelity of the resulting maps. Furthermore, it is difficult to understand the relationship between flattened cortical surfaces and the underlying 3D anatomy using tools available currently. To address these problems we have developed pycortex, a Python toolbox for interactive surface mapping and visualization. Pycortex exploits the power of modern graphics cards to sample volumetric data on a per-pixel basis, allowing dense and accurate mapping of the voxel grid across the surface. Anatomical and functional information can be projected onto the cortical surface. The surface can be inflated and flattened interactively, aiding interpretation of the correspondence between the anatomical surface and the flattened cortical sheet. The output of pycortex can be viewed using WebGL, a technology compatible with modern web browsers. This allows complex fMRI surface maps to be distributed broadly online without requiring installation of complex software. PMID:26483666
Molecules to maps: tools for visualization and interaction in support of computational biology.

PubMed

Kraemer, E T; Ferrin, T E

1998-01-01

The volume of data produced by genome projects, X-ray crystallography, NMR spectroscopy, and electron and confocal microscopy present the bioinformatics community with new challenges for analyzing, understanding, and exchanging this data. At the 1998 Pacific Symposium on Biocomputing, a track entitled 'Molecules to Maps: Tools for Visualization and Interaction in Computational Biology' provided tool developers and users with the opportunity to discuss advances in tools and techniques to assist scientists in evaluating, absorbing, navigating, and correlating this sea of information, through visualization and user interaction. In this paper we present these advances and discuss some of the challenges that remain to be solved.
Data Visualization Using Immersive Virtual Reality Tools

NASA Astrophysics Data System (ADS)

Cioc, Alexandru; Djorgovski, S. G.; Donalek, C.; Lawler, E.; Sauer, F.; Longo, G.

2013-01-01

The growing complexity of scientific data poses serious challenges for an effective visualization. Data sets, e.g., catalogs of objects detected in sky surveys, can have a very high dimensionality, ~ 100 - 1000. Visualizing such hyper-dimensional data parameter spaces is essentially impossible, but there are ways of visualizing up to ~ 10 dimensions in a pseudo-3D display. We have been experimenting with the emerging technologies of immersive virtual reality (VR) as a platform for a scientific, interactive, collaborative data visualization. Our initial experiments used the virtual world of Second Life, and more recently VR worlds based on its open source code, OpenSimulator. There we can visualize up to ~ 100,000 data points in ~ 7 - 8 dimensions (3 spatial and others encoded as shapes, colors, sizes, etc.), in an immersive virtual space where scientists can interact with their data and with each other. We are now developing a more scalable visualization environment using the popular (practically an emerging standard) Unity 3D Game Engine, coded using C#, JavaScript, and the Unity Scripting Language. This visualization tool can be used through a standard web browser, or a standalone browser of its own. Rather than merely plotting data points, the application creates interactive three-dimensional objects of various shapes, colors, and sizes, and of course the XYZ positions, encoding various dimensions of the parameter space, that can be associated interactively. Multiple users can navigate through this data space simultaneously, either with their own, independent vantage points, or with a shared view. At this stage ~ 100,000 data points can be easily visualized within seconds on a simple laptop. The displayed data points can contain linked information; e.g., upon a clicking on a data point, a webpage with additional information can be rendered within the 3D world. A range of functionalities has been already deployed, and more are being added. We expect to make this visualization tool freely available to the academic community within a few months, on an experimental (beta testing) basis.
Using Photography to Foster Intergenerational Understanding

ERIC Educational Resources Information Center

Fearnside, Lee; Bereza, Matthew; McConn, Gabriel

2015-01-01

This study examines how a visual art academic experience might help to reduce anxiety about interactions with the elderly, mitigate fears over aging, encourage more interactions with older people and improve visual literacy skills. University students in an introductory digital photography course interpreted conversations with residents of a local…
Implementation of an oblique-sectioning visualization tool for line-of-sight stereotactic neurosurgical navigation using the AVW toolkit

NASA Astrophysics Data System (ADS)

Bates, Lisa M.; Hanson, Dennis P.; Kall, Bruce A.; Meyer, Frederic B.; Robb, Richard A.

1998-06-01

An important clinical application of biomedical imaging and visualization techniques is provision of image guided neurosurgical planning and navigation techniques using interactive computer display systems in the operating room. Current systems provide interactive display of orthogonal images and 3D surface or volume renderings integrated with and guided by the location of a surgical probe. However, structures in the 'line-of-sight' path which lead to the surgical target cannot be directly visualized, presenting difficulty in obtaining full understanding of the 3D volumetric anatomic relationships necessary for effective neurosurgical navigation below the cortical surface. Complex vascular relationships and histologic boundaries like those found in artereovenous malformations (AVM's) also contribute to the difficulty in determining optimal approaches prior to actual surgical intervention. These difficulties demonstrate the need for interactive oblique imaging methods to provide 'line-of-sight' visualization. Capabilities for 'line-of- sight' interactive oblique sectioning are present in several current neurosurgical navigation systems. However, our implementation is novel, in that it utilizes a completely independent software toolkit, AVW (A Visualization Workshop) developed at the Mayo Biomedical Imaging Resource, integrated with a current neurosurgical navigation system, the COMPASS stereotactic system at Mayo Foundation. The toolkit is a comprehensive, C-callable imaging toolkit containing over 500 optimized imaging functions and structures. The powerful functionality and versatility of the AVW imaging toolkit provided facile integration and implementation of desired interactive oblique sectioning using a finite set of functions. The implementation of the AVW-based code resulted in higher-level functions for complete 'line-of-sight' visualization.
Mixed Initiative Visual Analytics Using Task-Driven Recommendations

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

Cook, Kristin A.; Cramer, Nicholas O.; Israel, David

2015-12-07

Visual data analysis is composed of a collection of cognitive actions and tasks to decompose, internalize, and recombine data to produce knowledge and insight. Visual analytic tools provide interactive visual interfaces to data to support tasks involved in discovery and sensemaking, including forming hypotheses, asking questions, and evaluating and organizing evidence. Myriad analytic models can be incorporated into visual analytic systems, at the cost of increasing complexity in the analytic discourse between user and system. Techniques exist to increase the usability of interacting with such analytic models, such as inferring data models from user interactions to steer the underlying modelsmore » of the system via semantic interaction, shielding users from having to do so explicitly. Such approaches are often also referred to as mixed-initiative systems. Researchers studying the sensemaking process have called for development of tools that facilitate analytic sensemaking through a combination of human and automated activities. However, design guidelines do not exist for mixed-initiative visual analytic systems to support iterative sensemaking. In this paper, we present a candidate set of design guidelines and introduce the Active Data Environment (ADE) prototype, a spatial workspace supporting the analytic process via task recommendations invoked by inferences on user interactions within the workspace. ADE recommends data and relationships based on a task model, enabling users to co-reason with the system about their data in a single, spatial workspace. This paper provides an illustrative use case, a technical description of ADE, and a discussion of the strengths and limitations of the approach.« less
Multimodal Virtual Environments: MAGIC Toolkit and Visual-Haptic Interaction Paradigms

DTIC Science & Technology

1998-01-01

2.7.3 Load/Save Options ..... 2.7.4 Information Display .... 2.8 Library Files. 2.9 Evaluation .............. 3 Visual-Haptic Interactions 3.1...Northwestern University[ Colgate , 1994]. It is possible for a user to touch one side of a thin object and be propelled out the opposite side, because...when there is a high correlation in motion and force between the visual and haptic realms. * Chapter 7 concludes with an evaluation of the application
Interactive Particle Visualization

NASA Astrophysics Data System (ADS)

Gribble, Christiaan P.

Particle-based simulation methods are used to model a wide range of complex phenomena and to solve time-dependent problems of various scales. Effective visualizations of the resulting state will communicate subtle changes in the three-dimensional structure, spatial organization, and qualitative trends within a simulation as it evolves. This chapter discusses two approaches to interactive particle visualization that satisfy these goals: one targeting desktop systems equipped with programmable graphics hardware, and the other targeting moderately sized multicore systems using packet-based ray tracing.
Multiscale neural connectivity during human sensory processing in the brain

NASA Astrophysics Data System (ADS)

Maksimenko, Vladimir A.; Runnova, Anastasia E.; Frolov, Nikita S.; Makarov, Vladimir V.; Nedaivozov, Vladimir; Koronovskii, Alexey A.; Pisarchik, Alexander; Hramov, Alexander E.

2018-05-01

Stimulus-related brain activity is considered using wavelet-based analysis of neural interactions between occipital and parietal brain areas in alpha (8-12 Hz) and beta (15-30 Hz) frequency bands. We show that human sensory processing related to the visual stimuli perception induces brain response resulted in different ways of parieto-occipital interactions in these bands. In the alpha frequency band the parieto-occipital neuronal network is characterized by homogeneous increase of the interaction between all interconnected areas both within occipital and parietal lobes and between them. In the beta frequency band the occipital lobe starts to play a leading role in the dynamics of the occipital-parietal network: The perception of visual stimuli excites the visual center in the occipital area and then, due to the increase of parieto-occipital interactions, such excitation is transferred to the parietal area, where the attentional center takes place. In the case when stimuli are characterized by a high degree of ambiguity, we find greater increase of the interaction between interconnected areas in the parietal lobe due to the increase of human attention. Based on revealed mechanisms, we describe the complex response of the parieto-occipital brain neuronal network during the perception and primary processing of the visual stimuli. The results can serve as an essential complement to the existing theory of neural aspects of visual stimuli processing.
Interactions of Top-Down and Bottom-Up Mechanisms in Human Visual Cortex

PubMed Central

McMains, Stephanie; Kastner, Sabine

2011-01-01

Multiple stimuli present in the visual field at the same time compete for neural representation by mutually suppressing their evoked activity throughout visual cortex, providing a neural correlate for the limited processing capacity of the visual system. Competitive interactions among stimuli can be counteracted by top-down, goal-directed mechanisms such as attention, and by bottom-up, stimulus-driven mechanisms. Because these two processes cooperate in everyday life to bias processing toward behaviorally relevant or particularly salient stimuli, it has proven difficult to study interactions between top-down and bottom-up mechanisms. Here, we used an experimental paradigm in which we first isolated the effects of a bottom-up influence on neural competition by parametrically varying the degree of perceptual grouping in displays that were not attended. Second, we probed the effects of directed attention on the competitive interactions induced with the parametric design. We found that the amount of attentional modulation varied linearly with the degree of competition left unresolved by bottom-up processes, such that attentional modulation was greatest when neural competition was little influenced by bottom-up mechanisms and smallest when competition was strongly influenced by bottom-up mechanisms. These findings suggest that the strength of attentional modulation in the visual system is constrained by the degree to which competitive interactions have been resolved by bottom-up processes related to the segmentation of scenes into candidate objects. PMID:21228167
XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data

PubMed Central

2015-01-01

Background Though cluster analysis has become a routine analytic task for bioinformatics research, it is still arduous for researchers to assess the quality of a clustering result. To select the best clustering method and its parameters for a dataset, researchers have to run multiple clustering algorithms and compare them. However, such a comparison task with multiple clustering results is cognitively demanding and laborious. Results In this paper, we present XCluSim, a visual analytics tool that enables users to interactively compare multiple clustering results based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms. The efficacy of XCluSim is shown through case studies with a bioinformatician. Conclusions Compared to other relevant tools, XCluSim enables users to compare multiple clustering results in a more scalable manner. Moreover, XCluSim supports diverse clustering algorithms and dedicated visualizations and interactions for different types of clustering results, allowing more effective exploration of details on demand. Through case studies with a bioinformatics researcher, we received positive feedback on the functionalities of XCluSim, including its ability to help identify stably clustered items across multiple clustering results. PMID:26328893
SOCR Motion Charts: An Efficient, Open-Source, Interactive and Dynamic Applet for Visualizing Longitudinal Multivariate Data

PubMed Central

Al-Aziz, Jameel; Christou, Nicolas; Dinov, Ivo D.

2011-01-01

The amount, complexity and provenance of data have dramatically increased in the past five years. Visualization of observed and simulated data is a critical component of any social, environmental, biomedical or scientific quest. Dynamic, exploratory and interactive visualization of multivariate data, without preprocessing by dimensionality reduction, remains a nearly insurmountable challenge. The Statistics Online Computational Resource (www.SOCR.ucla.edu) provides portable online aids for probability and statistics education, technology-based instruction and statistical computing. We have developed a new Java-based infrastructure, SOCR Motion Charts, for discovery-based exploratory analysis of multivariate data. This interactive data visualization tool enables the visualization of high-dimensional longitudinal data. SOCR Motion Charts allows mapping of ordinal, nominal and quantitative variables onto time, 2D axes, size, colors, glyphs and appearance characteristics, which facilitates the interactive display of multidimensional data. We validated this new visualization paradigm using several publicly available multivariate datasets including Ice-Thickness, Housing Prices, Consumer Price Index, and California Ozone Data. SOCR Motion Charts is designed using object-oriented programming, implemented as a Java Web-applet and is available to the entire community on the web at www.socr.ucla.edu/SOCR_MotionCharts. It can be used as an instructional tool for rendering and interrogating high-dimensional data in the classroom, as well as a research tool for exploratory data analysis. PMID:21479108
Front-Presented Looming Sound Selectively Alters the Perceived Size of a Visual Looming Object.

PubMed

Yamasaki, Daiki; Miyoshi, Kiyofumi; Altmann, Christian F; Ashida, Hiroshi

2018-07-01

In spite of accumulating evidence for the spatial rule governing cross-modal interaction according to the spatial consistency of stimuli, it is still unclear whether 3D spatial consistency (i.e., front/rear of the body) of stimuli also regulates audiovisual interaction. We investigated how sounds with increasing/decreasing intensity (looming/receding sound) presented from the front and rear space of the body impact the size perception of a dynamic visual object. Participants performed a size-matching task (Experiments 1 and 2) and a size adjustment task (Experiment 3) of visual stimuli with increasing/decreasing diameter, while being exposed to a front- or rear-presented sound with increasing/decreasing intensity. Throughout these experiments, we demonstrated that only the front-presented looming sound caused overestimation of the spatially consistent looming visual stimulus in size, but not of the spatially inconsistent and the receding visual stimulus. The receding sound had no significant effect on vision. Our results revealed that looming sound alters dynamic visual size perception depending on the consistency in the approaching quality and the front-rear spatial location of audiovisual stimuli, suggesting that the human brain differently processes audiovisual inputs based on their 3D spatial consistency. This selective interaction between looming signals should contribute to faster detection of approaching threats. Our findings extend the spatial rule governing audiovisual interaction into 3D space.
A prototype system based on visual interactive SDM called VGC

NASA Astrophysics Data System (ADS)

Jia, Zelu; Liu, Yaolin; Liu, Yanfang

2009-10-01

In many application domains, data is collected and referenced by its geo-spatial location. Spatial data mining, or the discovery of interesting patterns in such databases, is an important capability in the development of database systems. Spatial data mining recently emerges from a number of real applications, such as real-estate marketing, urban planning, weather forecasting, medical image analysis, road traffic accident analysis, etc. It demands for efficient solutions for many new, expensive, and complicated problems. For spatial data mining of large data sets to be effective, it is also important to include humans in the data exploration process and combine their flexibility, creativity, and general knowledge with the enormous storage capacity and computational power of today's computers. Visual spatial data mining applies human visual perception to the exploration of large data sets. Presenting data in an interactive, graphical form often fosters new insights, encouraging the information and validation of new hypotheses to the end of better problem-solving and gaining deeper domain knowledge. In this paper a visual interactive spatial data mining prototype system (visual geo-classify) based on VC++6.0 and MapObject2.0 are designed and developed, the basic algorithms of the spatial data mining is used decision tree and Bayesian networks, and data classify are used training and learning and the integration of the two to realize. The result indicates it's a practical and extensible visual interactive spatial data mining tool.
Joseph Needham, CH, FRS, FBA., b. 9 December 1900; d. 24 April 1995. A Sailor's Tribute and a Memoir

NASA Astrophysics Data System (ADS)

Waters, D. W.

Sailors, indeed anyone interested in the development of sailing craft, will be for ever indebted to Joseph Needham. Today they will find with ease literature that describes the origins, characteristics, and development of sailing craft in the various regions of the world; the inter-relationships between natural products, and native hull stuctures and forms, sails' fabrics, shapes, and performance. They can learn, too, that the closestowing anchor, the water-tight bulkhead, the balanced rudder (and other features of the modern efficiency-conscious ship constructor) have all been adapted from the millenniaold, so-long-despised by Westerners, Chinese junk, just as has, late in this twentieth century, the stiffened sail of the modern high-performance yacht.
OpinionSeer: interactive visualization of hotel customer feedback.

PubMed

Wu, Yingcai; Wei, Furu; Liu, Shixia; Au, Norman; Cui, Weiwei; Zhou, Hong; Qu, Huamin

2010-01-01

The rapid development of Web technology has resulted in an increasing number of hotel customers sharing their opinions on the hotel services. Effective visual analysis of online customer opinions is needed, as it has a significant impact on building a successful business. In this paper, we present OpinionSeer, an interactive visualization system that could visually analyze a large collection of online hotel customer reviews. The system is built on a new visualization-centric opinion mining technique that considers uncertainty for faithfully modeling and analyzing customer opinions. A new visual representation is developed to convey customer opinions by augmenting well-established scatterplots and radial visualization. To provide multiple-level exploration, we introduce subjective logic to handle and organize subjective opinions with degrees of uncertainty. Several case studies illustrate the effectiveness and usefulness of OpinionSeer on analyzing relationships among multiple data dimensions and comparing opinions of different groups. Aside from data on hotel customer feedback, OpinionSeer could also be applied to visually analyze customer opinions on other products or services.
Compression and reflection of visually evoked cortical waves

PubMed Central

Xu, Weifeng; Huang, Xiaoying; Takagaki, Kentaroh; Wu, Jian-young

2007-01-01

Summary Neuronal interactions between primary and secondary visual cortical areas are important for visual processing, but the spatiotemporal patterns of the interaction are not well understood. We used voltage-sensitive dye imaging to visualize neuronal activity in rat visual cortex and found novel visually evoked waves propagating from V1 to other visual areas. A primary wave originated in the monocular area of V1 and was “compressed” when propagating to V2. A reflected wave initiated after compression and propagated backward into V1. The compression occurred at the V1/V2 border, and local GABAA inhibition is important for the compression. The compression/reflection pattern provides a two-phase modulation: V1 is first depolarized by the primary wave and then V1 and V2 are simultaneously depolarized by the reflected and primary waves, respectively. The compression/reflection pattern only occurred for evoked but not for spontaneous waves, suggesting that it is organized by an internal mechanism associated with visual processing. PMID:17610821

Visual Analytics of Surveillance Data on Foodborne Vibriosis, United States, 1973–2010

PubMed Central

Sims, Jennifer N.; Isokpehi, Raphael D.; Cooper, Gabrielle A.; Bass, Michael P.; Brown, Shyretha D.; St John, Alison L.; Gulig, Paul A.; Cohly, Hari H.P.

2011-01-01

Foodborne illnesses caused by microbial and chemical contaminants in food are a substantial health burden worldwide. In 2007, human vibriosis (non-cholera Vibrio infections) became a notifiable disease in the United States. In addition, Vibrio species are among the 31 major known pathogens transmitted through food in the United States. Diverse surveillance systems for foodborne pathogens also track outbreaks, illnesses, hospitalization and deaths due to non-cholera vibrios. Considering the recognition of vibriosis as a notifiable disease in the United States and the availability of diverse surveillance systems, there is a need for the development of easily deployed visualization and analysis approaches that can combine diverse data sources in an interactive manner. Current efforts to address this need are still limited. Visual analytics is an iterative process conducted via visual interfaces that involves collecting information, data preprocessing, knowledge representation, interaction, and decision making. We have utilized public domain outbreak and surveillance data sources covering 1973 to 2010, as well as visual analytics software to demonstrate integrated and interactive visualizations of data on foodborne outbreaks and surveillance of Vibrio species. Through the data visualization, we were able to identify unique patterns and/or novel relationships within and across datasets regarding (i) causative agent; (ii) foodborne outbreaks and illness per state; (iii) location of infection; (iv) vehicle (food) of infection; (v) anatomical site of isolation of Vibrio species; (vi) patients and complications of vibriosis; (vii) incidence of laboratory-confirmed vibriosis and V. parahaemolyticus outbreaks. The additional use of emerging visual analytics approaches for interaction with data on vibriosis, including non-foodborne related disease, can guide disease control and prevention as well as ongoing outbreak investigations. PMID:22174586
Evidence for the Activation of Sensorimotor Information during Visual Word Recognition: The Body-Object Interaction Effect

ERIC Educational Resources Information Center

Siakaluk, Paul D.; Pexman, Penny M.; Aguilera, Laura; Owen, William J.; Sears, Christopher R.

2008-01-01

We examined the effects of sensorimotor experience in two visual word recognition tasks. Body-object interaction (BOI) ratings were collected for a large set of words. These ratings assess perceptions of the ease with which a human body can physically interact with a word's referent. A set of high BOI words (e.g., "mask") and a set of low BOI…
Semantic Interaction for Sensemaking: Inferring Analytical Reasoning for Model Steering.

PubMed

Endert, A; Fiaux, P; North, C

2012-12-01

Visual analytic tools aim to support the cognitively demanding task of sensemaking. Their success often depends on the ability to leverage capabilities of mathematical models, visualization, and human intuition through flexible, usable, and expressive interactions. Spatially clustering data is one effective metaphor for users to explore similarity and relationships between information, adjusting the weighting of dimensions or characteristics of the dataset to observe the change in the spatial layout. Semantic interaction is an approach to user interaction in such spatializations that couples these parametric modifications of the clustering model with users' analytic operations on the data (e.g., direct document movement in the spatialization, highlighting text, search, etc.). In this paper, we present results of a user study exploring the ability of semantic interaction in a visual analytic prototype, ForceSPIRE, to support sensemaking. We found that semantic interaction captures the analytical reasoning of the user through keyword weighting, and aids the user in co-creating a spatialization based on the user's reasoning and intuition.
A Novel Interhemispheric Interaction: Modulation of Neuronal Cooperativity in the Visual Areas

PubMed Central

Carmeli, Cristian; Lopez-Aguado, Laura; Schmidt, Kerstin E.; De Feo, Oscar; Innocenti, Giorgio M.

2007-01-01

Background The cortical representation of the visual field is split along the vertical midline, with the left and the right hemi-fields projecting to separate hemispheres. Connections between the visual areas of the two hemispheres are abundant near the representation of the visual midline. It was suggested that they re-establish the functional continuity of the visual field by controlling the dynamics of the responses in the two hemispheres. Methods/Principal Findings To understand if and how the interactions between the two hemispheres participate in processing visual stimuli, the synchronization of responses to identical or different moving gratings in the two hemi-fields were studied in anesthetized ferrets. The responses were recorded by multiple electrodes in the primary visual areas and the synchronization of local field potentials across the electrodes were analyzed with a recent method derived from dynamical system theory. Inactivating the visual areas of one hemisphere modulated the synchronization of the stimulus-driven activity in the other hemisphere. The modulation was stimulus-specific and was consistent with the fine morphology of callosal axons in particular with the spatio-temporal pattern of activity that axonal geometry can generate. Conclusions/Significance These findings describe a new kind of interaction between the cerebral hemispheres and highlight the role of axonal geometry in modulating aspects of cortical dynamics responsible for stimulus detection and/or categorization. PMID:18074012
Ergonomic Guidelines for Designing Effective and Healthy Learning Environments for Interactive Technologies.

ERIC Educational Resources Information Center

Weisberg, Michael

Many of the findings from ergonomics research on visual display workstations are relevant to the design of interactive learning stations. This 1993 paper briefly reviews ergonomics research on visual display workstations; specifically, (1) potential health hazards from electromagnetic radiation; (2) musculoskeletal disorders; (3)vision complaints;…
Enhanced Visual Short-Term Memory for Angry Faces

ERIC Educational Resources Information Center

Jackson, Margaret C.; Wu, Chia-Yun; Linden, David E. J.; Raymond, Jane E.

2009-01-01

Although some views of face perception posit independent processing of face identity and expression, recent studies suggest interactive processing of these 2 domains. The authors examined expression-identity interactions in visual short-term memory (VSTM) by assessing recognition performance in a VSTM task in which face identity was relevant and…
Visualizing Interaction Patterns in Online Discussions and Indices of Cognitive Presence

ERIC Educational Resources Information Center

Gibbs, William J.

2006-01-01

This paper discusses Mapping Temporal Relations of Discussions Software (MTRDS), a Web-based application that visually represents the temporal relations of online discussions. MTRDS was used to observe interaction characteristics of three online discussions. In addition, the research employed the Practical Inquiry Model to identify indices of…
An Evaluation of Multimodal Interactions with Technology while Learning Science Concepts

ERIC Educational Resources Information Center

Anastopoulou, Stamatina; Sharples, Mike; Baber, Chris

2011-01-01

This paper explores the value of employing multiple modalities to facilitate science learning with technology. In particular, it is argued that when multiple modalities are employed, learners construct strong relations between physical movement and visual representations of motion. Body interactions with visual representations, enabled by…
How Information Visualization Systems Change Users' Understandings of Complex Data

ERIC Educational Resources Information Center

Allendoerfer, Kenneth Robert

2009-01-01

User-centered evaluations of information systems often focus on the usability of the system rather its usefulness. This study examined how a using an interactive knowledge-domain visualization (KDV) system affected users' understanding of a domain. Interactive KDVs allow users to create graphical representations of domains that depict important…
Interactivity of Visual Mathematical Representations: Factors Affecting Learning and Cognitive Processes

ERIC Educational Resources Information Center

Sedig, Kamran; Liang, Hai-Ning

2006-01-01

Computer-based mathematical cognitive tools (MCTs) are a category of external aids intended to support and enhance learning and cognitive processes of learners. MCTs often contain interactive visual mathematical representations (VMRs), where VMRs are graphical representations that encode properties and relationships of mathematical concepts. In…
Role of Interaction in Enhancing the Epistemic Utility of 3D Mathematical Visualizations

ERIC Educational Resources Information Center

Liang, Hai-Ning; Sedig, Kamran

2010-01-01

Many epistemic activities, such as spatial reasoning, sense-making, problem solving, and learning, are information-based. In the context of epistemic activities involving mathematical information, learners often use interactive 3D mathematical visualizations (MVs). However, performing such activities is not always easy. Although it is generally…
Monitoring of Students' Interaction in Online Learning Settings by Structural Network Analysis and Indicators.

PubMed

Ammenwerth, Elske; Hackl, Werner O

2017-01-01

Learning as a constructive process works best in interaction with other learners. Support of social interaction processes is a particular challenge within online learning settings due to the spatial and temporal distribution of participants. It should thus be carefully monitored. We present structural network analysis and related indicators to analyse and visualize interaction patterns of participants in online learning settings. We validate this approach in two online courses and show how the visualization helps to monitor interaction and to identify activity profiles of learners. Structural network analysis is a feasible approach for an analysis of the intensity and direction of interaction in online learning settings.
FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.

PubMed

Mader, Malte; Simon, Ronald; Kurtz, Stefan

2014-03-31

A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events. We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. A powerful search interface and a fast visualization engine provide a highly interactive visualization for such data. High quality image export enables the life scientist to easily communicate their results. A comprehensive data administration allows to keep track of the available data sets. We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before. The interactive nature of FISH Oracle 2 and the possibility to store, select and visualize large amounts of downstream processed data support life scientists in generating hypotheses. The export of high quality images supports explanatory data visualization, simplifying the communication of new biological findings. A FISH Oracle 2 demo server and the software is available at http://www.zbh.uni-hamburg.de/fishoracle.
GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.

PubMed

Laird, Matthew R; Langille, Morgan G I; Brinkman, Fiona S L

2015-10-15

A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations. GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general. GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/. brinkman@sfu.ca. © The Author 2015. Published by Oxford University Press.
Visual Testing: An Experimental Assessment of the Encoding Specificity Hypothesis.

ERIC Educational Resources Information Center

DeMelo, Hermes T.; And Others

This study of 96 high school biology students investigates the effectiveness of visual instruction composed of simple line drawings and printed words as compared to printed-words-only instruction, visual tests, and the interaction between visual or non-visual mode of instruction and mode of testing. The subjects were randomly assigned to be given…
[Preliminary construction of three-dimensional visual educational system for clinical dentistry based on world wide web webpage].

PubMed

Hu, Jian; Xu, Xiang-yang; Song, En-min; Tan, Hong-bao; Wang, Yi-ning

2009-09-01

To establish a new visual educational system of virtual reality for clinical dentistry based on world wide web (WWW) webpage in order to provide more three-dimensional multimedia resources to dental students and an online three-dimensional consulting system for patients. Based on computer graphics and three-dimensional webpage technologies, the software of 3Dsmax and Webmax were adopted in the system development. In the Windows environment, the architecture of whole system was established step by step, including three-dimensional model construction, three-dimensional scene setup, transplanting three-dimensional scene into webpage, reediting the virtual scene, realization of interactions within the webpage, initial test, and necessary adjustment. Five cases of three-dimensional interactive webpage for clinical dentistry were completed. The three-dimensional interactive webpage could be accessible through web browser on personal computer, and users could interact with the webpage through rotating, panning and zooming the virtual scene. It is technically feasible to implement the visual educational system of virtual reality for clinical dentistry based on WWW webpage. Information related to clinical dentistry can be transmitted properly, visually and interactively through three-dimensional webpage.
Dynamic interactions between visual working memory and saccade target selection

PubMed Central

Schneegans, Sebastian; Spencer, John P.; Schöner, Gregor; Hwang, Seongmin; Hollingworth, Andrew

2014-01-01

Recent psychophysical experiments have shown that working memory for visual surface features interacts with saccadic motor planning, even in tasks where the saccade target is unambiguously specified by spatial cues. Specifically, a match between a memorized color and the color of either the designated target or a distractor stimulus influences saccade target selection, saccade amplitudes, and latencies in a systematic fashion. To elucidate these effects, we present a dynamic neural field model in combination with new experimental data. The model captures the neural processes underlying visual perception, working memory, and saccade planning relevant to the psychophysical experiment. It consists of a low-level visual sensory representation that interacts with two separate pathways: a spatial pathway implementing spatial attention and saccade generation, and a surface feature pathway implementing color working memory and feature attention. Due to bidirectional coupling between visual working memory and feature attention in the model, the working memory content can indirectly exert an effect on perceptual processing in the low-level sensory representation. This in turn biases saccadic movement planning in the spatial pathway, allowing the model to quantitatively reproduce the observed interaction effects. The continuous coupling between representations in the model also implies that modulation should be bidirectional, and model simulations provide specific predictions for complementary effects of saccade target selection on visual working memory. These predictions were empirically confirmed in a new experiment: Memory for a sample color was biased toward the color of a task-irrelevant saccade target object, demonstrating the bidirectional coupling between visual working memory and perceptual processing. PMID:25228628
Visualizing the intercity correlation of PM2.5 time series in the Beijing-Tianjin-Hebei region using ground-based air quality monitoring data.

PubMed

Liu, Jianzheng; Li, Weifeng; Wu, Jiansheng; Liu, Yonghong

2018-01-01

The Beijing-Tianjin-Hebei area faces a severe fine particulate matter (PM2.5) problem. To date, considerable progress has been made toward understanding the PM2.5 problem, including spatial-temporal characterization, driving factors, and health effects. However, little research has been done on the dynamic interactions and relationships between PM2.5 concentrations in different cities in this area. To address the research gap, this study discovered a phenomenon of time-lagged intercity correlations of PM2.5 time series and proposed a visualization framework based on this phenomenon to visualize the interaction in PM2.5 concentrations between cities. The visualizations produced using the framework show that there are significant time-lagged correlations between the PM2.5 time series in different cities in this area. The visualizations also show that the correlations are more significant in colder months and between cities that are closer, and that there are seasonal changes in the temporal order of the correlated PM2.5 time series. Further analysis suggests that the time-lagged intercity correlations of PM2.5 time series are most likely due to synoptic meteorological variations. We argue that the visualizations demonstrate the interactions of air pollution between cities in the Beijing-Tianjin-Hebei area and the significant effect of synoptic meteorological conditions on PM2.5 pollution. The visualization framework could help determine the pathway of regional transportation of air pollution and may also be useful in delineating the area of interaction of PM2.5 pollution for impact analysis.
Visualizing the intercity correlation of PM2.5 time series in the Beijing-Tianjin-Hebei region using ground-based air quality monitoring data

PubMed Central

Li, Weifeng; Wu, Jiansheng; Liu, Yonghong

2018-01-01

The Beijing-Tianjin-Hebei area faces a severe fine particulate matter (PM2.5) problem. To date, considerable progress has been made toward understanding the PM2.5 problem, including spatial-temporal characterization, driving factors, and health effects. However, little research has been done on the dynamic interactions and relationships between PM2.5 concentrations in different cities in this area. To address the research gap, this study discovered a phenomenon of time-lagged intercity correlations of PM2.5 time series and proposed a visualization framework based on this phenomenon to visualize the interaction in PM2.5 concentrations between cities. The visualizations produced using the framework show that there are significant time-lagged correlations between the PM2.5 time series in different cities in this area. The visualizations also show that the correlations are more significant in colder months and between cities that are closer, and that there are seasonal changes in the temporal order of the correlated PM2.5 time series. Further analysis suggests that the time-lagged intercity correlations of PM2.5 time series are most likely due to synoptic meteorological variations. We argue that the visualizations demonstrate the interactions of air pollution between cities in the Beijing-Tianjin-Hebei area and the significant effect of synoptic meteorological conditions on PM2.5 pollution. The visualization framework could help determine the pathway of regional transportation of air pollution and may also be useful in delineating the area of interaction of PM2.5 pollution for impact analysis. PMID:29438417
FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web.

PubMed

Probst, Daniel; Reymond, Jean-Louis

2018-04-15

During the past decade, big data have become a major tool in scientific endeavors. Although statistical methods and algorithms are well-suited for analyzing and summarizing enormous amounts of data, the results do not allow for a visual inspection of the entire data. Current scientific software, including R packages and Python libraries such as ggplot2, matplotlib and plot.ly, do not support interactive visualizations of datasets exceeding 100 000 data points on the web. Other solutions enable the web-based visualization of big data only through data reduction or statistical representations. However, recent hardware developments, especially advancements in graphical processing units, allow for the rendering of millions of data points on a wide range of consumer hardware such as laptops, tablets and mobile phones. Similar to the challenges and opportunities brought to virtually every scientific field by big data, both the visualization of and interaction with copious amounts of data are both demanding and hold great promise. Here we present FUn, a framework consisting of a client (Faerun) and server (Underdark) module, facilitating the creation of web-based, interactive 3D visualizations of large datasets, enabling record level visual inspection. We also introduce a reference implementation providing access to SureChEMBL, a database containing patent information on more than 17 million chemical compounds. The source code and the most recent builds of Faerun and Underdark, Lore.js and the data preprocessing toolchain used in the reference implementation, are available on the project website (http://doc.gdb.tools/fun/). daniel.probst@dcb.unibe.ch or jean-louis.reymond@dcb.unibe.ch.

Accessibility of Mobile Devices for Visually Impaired Users: An Evaluation of the Screen-Reader VoiceOver.

PubMed

Smaradottir, Berglind; Håland, Jarle; Martinez, Santiago

2017-01-01

A mobile device's touchscreen allows users to use a choreography of hand gestures to interact with the user interface. A screen reader on a mobile device is designed to support the interaction of visually disabled users while using gestures. This paper presents an evaluation of VoiceOver, a screen reader in Apple Inc. products. The evaluation was a part of the research project "Visually impaired users touching the screen - a user evaluation of assistive technology".
MRIVIEW: An interactive computational tool for investigation of brain structure and function

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

Ranken, D.; George, J.

MRIVIEW is a software system which uses image processing and visualization to provide neuroscience researchers with an integrated environment for combining functional and anatomical information. Key features of the software include semi-automated segmentation of volumetric head data and an interactive coordinate reconciliation method which utilizes surface visualization. The current system is a precursor to a computational brain atlas. We describe features this atlas will incorporate, including methods under development for visualizing brain functional data obtained from several different research modalities.
Interactions between attention, context and learning in primary visual cortex.

PubMed

Gilbert, C; Ito, M; Kapadia, M; Westheimer, G

2000-01-01

Attention in early visual processing engages the higher order, context dependent properties of neurons. Even at the earliest stages of visual cortical processing neurons play a role in intermediate level vision - contour integration and surface segmentation. The contextual influences mediating this process may be derived from long range connections within primary visual cortex (V1). These influences are subject to perceptual learning, and are strongly modulated by visuospatial attention, which is itself a learning dependent process. The attentional influences may involve interactions between feedback and horizontal connections in V1. V1 is therefore a dynamic and active processor, subject to top-down influences.
Visualization of the tire-soil interaction area by means of ObjectARX programming interface

NASA Astrophysics Data System (ADS)

Mueller, W.; Gruszczyński, M.; Raba, B.; Lewicki, A.; Przybył, K.; Zaborowicz, M.; Koszela, K.; Boniecki, P.

2014-04-01

The process of data visualization, important for their analysis, becomes problematic when large data sets generated via computer simulations are available. This problem concerns, among others, the models that describe the geometry of tire-soil interaction. For the purpose of a graphical representation of this area and implementation of various geometric calculations the authors have developed a plug-in application for AutoCAD, based on the latest technologies, including ObjectARX, LINQ and the use of Visual Studio platform. Selected programming tools offer a wide variety of IT structures that enable data visualization and data analysis and are important e.g. in model verification.
CellMap visualizes protein-protein interactions and subcellular localization

PubMed Central

Dallago, Christian; Goldberg, Tatyana; Andrade-Navarro, Miguel Angel; Alanis-Lobato, Gregorio; Rost, Burkhard

2018-01-01

Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers. PMID:29497493
A taxonomy of visualization tasks for the analysis of biological pathway data.

PubMed

Murray, Paul; McGee, Fintan; Forbes, Angus G

2017-02-15

Understanding complicated networks of interactions and chemical components is essential to solving contemporary problems in modern biology, especially in domains such as cancer and systems research. In these domains, biological pathway data is used to represent chains of interactions that occur within a given biological process. Visual representations can help researchers understand, interact with, and reason about these complex pathways in a number of ways. At the same time, these datasets offer unique challenges for visualization, due to their complexity and heterogeneity. Here, we present taxonomy of tasks that are regularly performed by researchers who work with biological pathway data. The generation of these tasks was done in conjunction with interviews with several domain experts in biology. These tasks require further classification than is provided by existing taxonomies. We also examine existing visualization techniques that support each task, and we discuss gaps in the existing visualization space revealed by our taxonomy. Our taxonomy is designed to support the development and design of future biological pathway visualization applications. We conclude by suggesting future research directions based on our taxonomy and motivated by the comments received by our domain experts.
Applying a visual language for image processing as a graphical teaching tool in medical imaging

NASA Astrophysics Data System (ADS)

Birchman, James J.; Tanimoto, Steven L.; Rowberg, Alan H.; Choi, Hyung-Sik; Kim, Yongmin

1992-05-01

Typical user interaction in image processing is with command line entries, pull-down menus, or text menu selections from a list, and as such is not generally graphical in nature. Although applying these interactive methods to construct more sophisticated algorithms from a series of simple image processing steps may be clear to engineers and programmers, it may not be clear to clinicians. A solution to this problem is to implement a visual programming language using visual representations to express image processing algorithms. Visual representations promote a more natural and rapid understanding of image processing algorithms by providing more visual insight into what the algorithms do than the interactive methods mentioned above can provide. Individuals accustomed to dealing with images will be more likely to understand an algorithm that is represented visually. This is especially true of referring physicians, such as surgeons in an intensive care unit. With the increasing acceptance of picture archiving and communications system (PACS) workstations and the trend toward increasing clinical use of image processing, referring physicians will need to learn more sophisticated concepts than simply image access and display. If the procedures that they perform commonly, such as window width and window level adjustment and image enhancement using unsharp masking, are depicted visually in an interactive environment, it will be easier for them to learn and apply these concepts. The software described in this paper is a visual programming language for imaging processing which has been implemented on the NeXT computer using NeXTstep user interface development tools and other tools in an object-oriented environment. The concept is based upon the description of a visual language titled `Visualization of Vision Algorithms' (VIVA). Iconic representations of simple image processing steps are placed into a workbench screen and connected together into a dataflow path by the user. As the user creates and edits a dataflow path, more complex algorithms can be built on the screen. Once the algorithm is built, it can be executed, its results can be reviewed, and operator parameters can be interactively adjusted until an optimized output is produced. The optimized algorithm can then be saved and added to the system as a new operator. This system has been evaluated as a graphical teaching tool for window width and window level adjustment, image enhancement using unsharp masking, and other techniques.
Building Stories about Sea Level Rise through Interactive Visualizations

NASA Astrophysics Data System (ADS)

Stephens, S. H.; DeLorme, D. E.; Hagen, S. C.

2013-12-01

Digital media provide storytellers with dynamic new tools for communicating about scientific issues via interactive narrative visualizations. While traditional storytelling uses plot, characterization, and point of view to engage audiences with underlying themes and messages, interactive visualizations can be described as 'narrative builders' that promote insight through the process of discovery (Dove, G. & Jones, S. 2012, Proc. IHCI 2012). Narrative visualizations are used in online journalism to tell complex stories that allow readers to select aspects of datasets to explore and construct alternative interpretations of information (Segel, E. & Heer, J. 2010, IEEE Trans. Vis. Comp. Graph.16, 1139), thus enabling them to participate in the story-building process. Nevertheless, narrative visualizations also incorporate author-selected narrative elements that help guide and constrain the overall themes and messaging of the visualization (Hullman, J. & Diakopoulos, N. 2011, IEEE Trans. Vis. Comp. Graph. 17, 2231). One specific type of interactive narrative visualization that is used for science communication is the sea level rise (SLR) viewer. SLR viewers generally consist of a base map, upon which projections of sea level rise scenarios can be layered, and various controls for changing the viewpoint and scenario parameters. They are used to communicate the results of scientific modeling and help readers visualize the potential impacts of SLR on the coastal zone. Readers can use SLR viewers to construct personal narratives of the effects of SLR under different scenarios in locations that are important to them, thus extending the potential reach and impact of scientific research. With careful selection of narrative elements that guide reader interpretation, the communicative aspects of these visualizations may be made more effective. This presentation reports the results of a content analysis of a subset of existing SLR viewers selected in order to comprehensively identify and characterize the narrative elements that contribute to this storytelling medium. The results describe four layers of narrative elements in these viewers: data, visual representations, annotations, and interactivity; and explain the ways in which these elements are used to communicate about SLR. Most existing SLR viewers have been designed with attention to technical usability; however, careful design of narrative elements could increase their overall effectiveness as story-building tools. The analysis concludes with recommendations for narrative elements that should be considered when designing new SLR viewers, and offers suggestions for integrating these components to balance author-driven and reader-driven design features for more effective messaging.
Spatial interactions reveal inhibitory cortical networks in human amblyopia.

PubMed

Wong, Erwin H; Levi, Dennis M; McGraw, Paul V

2005-10-01

Humans with amblyopia have a well-documented loss of sensitivity for first-order, or luminance defined, visual information. Recent studies show that they also display a specific loss of sensitivity for second-order, or contrast defined, visual information; a type of image structure encoded by neurons found predominantly in visual area A18/V2. In the present study, we investigate whether amblyopia disrupts the normal architecture of spatial interactions in V2 by determining the contrast detection threshold of a second-order target in the presence of second-order flanking stimuli. Adjacent flanks facilitated second-order detectability in normal observers. However, in marked contrast, they suppressed detection in each eye of the majority of amblyopic observers. Furthermore, strabismic observers with no loss of visual acuity show a similar pattern of detection suppression. We speculate that amblyopia results in predominantly inhibitory cortical interactions between second-order neurons.
A collaborative interaction and visualization multi-modal environment for surgical planning.

PubMed

Foo, Jung Leng; Martinez-Escobar, Marisol; Peloquin, Catherine; Lobe, Thom; Winer, Eliot

2009-01-01

The proliferation of virtual reality visualization and interaction technologies has changed the way medical image data is analyzed and processed. This paper presents a multi-modal environment that combines a virtual reality application with a desktop application for collaborative surgical planning. Both visualization applications can function independently but can also be synced over a network connection for collaborative work. Any changes to either application is immediately synced and updated to the other. This is an efficient collaboration tool that allows multiple teams of doctors with only an internet connection to visualize and interact with the same patient data simultaneously. With this multi-modal environment framework, one team working in the VR environment and another team from a remote location working on a desktop machine can both collaborate in the examination and discussion for procedures such as diagnosis, surgical planning, teaching and tele-mentoring.
Interactive Visualization of Infrared Spectral Data: Synergy of Computation, Visualization, and Experiment for Learning Spectroscopy

NASA Astrophysics Data System (ADS)

Lahti, Paul M.; Motyka, Eric J.; Lancashire, Robert J.

2000-05-01

A straightforward procedure is described to combine computation of molecular vibrational modes using commonly available molecular modeling programs with visualization of the modes using advanced features of the MDL Information Systems Inc. Chime World Wide Web browser plug-in. Minor editing of experimental spectra that are stored in the JCAMP-DX format allows linkage of IR spectral frequency ranges to Chime molecular display windows. The spectra and animation files can be combined by Hypertext Markup Language programming to allow interactive linkage between experimental spectra and computationally generated vibrational displays. Both the spectra and the molecular displays can be interactively manipulated to allow the user maximum control of the objects being viewed. This procedure should be very valuable not only for aiding students through visual linkage of spectra and various vibrational animations, but also by assisting them in learning the advantages and limitations of computational chemistry by comparison to experiment.
Integrating natural language processing and web GIS for interactive knowledge domain visualization

NASA Astrophysics Data System (ADS)

Du, Fangming

Recent years have seen a powerful shift towards data-rich environments throughout society. This has extended to a change in how the artifacts and products of scientific knowledge production can be analyzed and understood. Bottom-up approaches are on the rise that combine access to huge amounts of academic publications with advanced computer graphics and data processing tools, including natural language processing. Knowledge domain visualization is one of those multi-technology approaches, with its aim of turning domain-specific human knowledge into highly visual representations in order to better understand the structure and evolution of domain knowledge. For example, network visualizations built from co-author relations contained in academic publications can provide insight on how scholars collaborate with each other in one or multiple domains, and visualizations built from the text content of articles can help us understand the topical structure of knowledge domains. These knowledge domain visualizations need to support interactive viewing and exploration by users. Such spatialization efforts are increasingly looking to geography and GIS as a source of metaphors and practical technology solutions, even when non-georeferenced information is managed, analyzed, and visualized. When it comes to deploying spatialized representations online, web mapping and web GIS can provide practical technology solutions for interactive viewing of knowledge domain visualizations, from panning and zooming to the overlay of additional information. This thesis presents a novel combination of advanced natural language processing - in the form of topic modeling - with dimensionality reduction through self-organizing maps and the deployment of web mapping/GIS technology towards intuitive, GIS-like, exploration of a knowledge domain visualization. A complete workflow is proposed and implemented that processes any corpus of input text documents into a map form and leverages a web application framework to let users explore knowledge domain maps interactively. This workflow is implemented and demonstrated for a data set of more than 66,000 conference abstracts.
Visual interaction: models, systems, prototypes. The Pictorial Computing Laboratory at the University of Rome La Sapienza.

PubMed

Bottoni, Paolo; Cinque, Luigi; De Marsico, Maria; Levialdi, Stefano; Panizzi, Emanuele

2006-06-01

This paper reports on the research activities performed by the Pictorial Computing Laboratory at the University of Rome, La Sapienza, during the last 5 years. Such work, essentially is based on the study of humancomputer interaction, spans from metamodels of interaction down to prototypes of interactive systems for both synchronous multimedia communication and groupwork, annotation systems for web pages, also encompassing theoretical and practical issues of visual languages and environments also including pattern recognition algorithms. Some applications are also considered like e-learning and collaborative work.
Audio-visual integration through the parallel visual pathways.

PubMed

Kaposvári, Péter; Csete, Gergő; Bognár, Anna; Csibri, Péter; Tóth, Eszter; Szabó, Nikoletta; Vécsei, László; Sáry, Gyula; Tamás Kincses, Zsigmond

2015-10-22

Audio-visual integration has been shown to be present in a wide range of different conditions, some of which are processed through the dorsal, and others through the ventral visual pathway. Whereas neuroimaging studies have revealed integration-related activity in the brain, there has been no imaging study of the possible role of segregated visual streams in audio-visual integration. We set out to determine how the different visual pathways participate in this communication. We investigated how audio-visual integration can be supported through the dorsal and ventral visual pathways during the double flash illusion. Low-contrast and chromatic isoluminant stimuli were used to drive preferably the dorsal and ventral pathways, respectively. In order to identify the anatomical substrates of the audio-visual interaction in the two conditions, the psychophysical results were correlated with the white matter integrity as measured by diffusion tensor imaging.The psychophysiological data revealed a robust double flash illusion in both conditions. A correlation between the psychophysical results and local fractional anisotropy was found in the occipito-parietal white matter in the low-contrast condition, while a similar correlation was found in the infero-temporal white matter in the chromatic isoluminant condition. Our results indicate that both of the parallel visual pathways may play a role in the audio-visual interaction. Copyright © 2015. Published by Elsevier B.V.
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.

PubMed

Wei, Qing; Khan, Ishita K; Ding, Ziyun; Yerneni, Satwica; Kihara, Daisuke

2017-03-20

The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion. NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes. Similarity of GO terms and gene functions is quantified with six different scores including protein-protein interaction and context based association scores we have developed in our previous works. Interactive navigation of the GO function space provides intuitive and effective real-time visualization of functional groupings of GO terms and genes as well as statistical analysis of enriched functions. We developed NaviGO, which visualizes and analyses functional similarity and associations of GO terms and genes. The NaviGO webserver is freely available at: http://kiharalab.org/web/navigo .
Audio-Visual Perception System for a Humanoid Robotic Head

PubMed Central

Viciana-Abad, Raquel; Marfil, Rebeca; Perez-Lorenzo, Jose M.; Bandera, Juan P.; Romero-Garces, Adrian; Reche-Lopez, Pedro

2014-01-01

One of the main issues within the field of social robotics is to endow robots with the ability to direct attention to people with whom they are interacting. Different approaches follow bio-inspired mechanisms, merging audio and visual cues to localize a person using multiple sensors. However, most of these fusion mechanisms have been used in fixed systems, such as those used in video-conference rooms, and thus, they may incur difficulties when constrained to the sensors with which a robot can be equipped. Besides, within the scope of interactive autonomous robots, there is a lack in terms of evaluating the benefits of audio-visual attention mechanisms, compared to only audio or visual approaches, in real scenarios. Most of the tests conducted have been within controlled environments, at short distances and/or with off-line performance measurements. With the goal of demonstrating the benefit of fusing sensory information with a Bayes inference for interactive robotics, this paper presents a system for localizing a person by processing visual and audio data. Moreover, the performance of this system is evaluated and compared via considering the technical limitations of unimodal systems. The experiments show the promise of the proposed approach for the proactive detection and tracking of speakers in a human-robot interactive framework. PMID:24878593
Comparison of User Performance with Interactive and Static 3d Visualization - Pilot Study

NASA Astrophysics Data System (ADS)

Herman, L.; Stachoň, Z.

2016-06-01

Interactive 3D visualizations of spatial data are currently available and popular through various applications such as Google Earth, ArcScene, etc. Several scientific studies have focused on user performance with 3D visualization, but static perspective views are used as stimuli in most of the studies. The main objective of this paper is to try to identify potential differences in user performance with static perspective views and interactive visualizations. This research is an exploratory study. An experiment was designed as a between-subject study and a customized testing tool based on open web technologies was used for the experiment. The testing set consists of an initial questionnaire, a training task and four experimental tasks. Selection of the highest point and determination of visibility from the top of a mountain were used as the experimental tasks. Speed and accuracy of each task performance of participants were recorded. The movement and actions in the virtual environment were also recorded within the interactive variant. The results show that participants deal with the tasks faster when using static visualization. The average error rate was also higher in the static variant. The findings from this pilot study will be used for further testing, especially for formulating of hypotheses and designing of subsequent experiments.
Progressive Visual Analytics: User-Driven Visual Exploration of In-Progress Analytics.

PubMed

Stolper, Charles D; Perer, Adam; Gotz, David

2014-12-01

As datasets grow and analytic algorithms become more complex, the typical workflow of analysts launching an analytic, waiting for it to complete, inspecting the results, and then re-Iaunching the computation with adjusted parameters is not realistic for many real-world tasks. This paper presents an alternative workflow, progressive visual analytics, which enables an analyst to inspect partial results of an algorithm as they become available and interact with the algorithm to prioritize subspaces of interest. Progressive visual analytics depends on adapting analytical algorithms to produce meaningful partial results and enable analyst intervention without sacrificing computational speed. The paradigm also depends on adapting information visualization techniques to incorporate the constantly refining results without overwhelming analysts and provide interactions to support an analyst directing the analytic. The contributions of this paper include: a description of the progressive visual analytics paradigm; design goals for both the algorithms and visualizations in progressive visual analytics systems; an example progressive visual analytics system (Progressive Insights) for analyzing common patterns in a collection of event sequences; and an evaluation of Progressive Insights and the progressive visual analytics paradigm by clinical researchers analyzing electronic medical records.
Dynamic Assessment of Microbial Ecology (DAME): A web app for interactive analysis and visualization of microbial sequencing data

USDA-ARS?s Scientific Manuscript database

Dynamic Assessment of Microbial Ecology (DAME) is a shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequenci...
Enhancing Interactive Tutorial Effectiveness through Visual Cueing

ERIC Educational Resources Information Center

Jamet, Eric; Fernandez, Jonathan

2016-01-01

The present study investigated whether learning how to use a web service with an interactive tutorial can be enhanced by cueing. We expected the attentional guidance provided by visual cues to facilitate the selection of information in static screen displays that corresponded to spoken explanations. Unlike most previous studies in this area, we…

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