Environmental versatility promotes modularity in large scale metabolic networks

OpenAIRE

Samal A.; Wagner Andreas; Martin O.C.

2011-01-01

Abstract Background The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new arrangements that may benefit their carrier. Conversely, modularity may emerge as a by-product of some trait. We here ask whether this last scenario may play a role in genome-scale metabolic networks that need to sustain life in one or more chem...

Why allometric variation in mammalian metabolism is curvilinear on the logarithmic scale.

Science.gov (United States)

Packard, Gary C

2017-11-01

Studies performed over the last 20 years have repeatedly documented a slight convex curvature (relative to the x-axis) in double-logarithmic plots of basal metabolic rate (BMR) versus body mass in mammals. This curvilinear pattern has usually been interpreted in the context of a simple, two-parameter power function on the arithmetic scale, y  =  a  ×  x b , with the exponent in the equation supposedly increasing systematically with body size. An equation of this form has caused concern among ecologists because a variable exponent is inconsistent with an assumption underlying the metabolic theory of ecology (MTE). However, the appearance of an exponent that varies with body size is an artifact resulting from the widespread use of logarithmic transformations in allometric analyses. Curvature in the distribution on the logarithmic scale actually is caused by a requirement for an explicit, non-zero intercept-and not a variable exponent-in the model describing the distribution on the arithmetic scale. Thus, the MTE need not be revised to accommodate an exponent that varies with body size in the scaling of mammalian BMR, but the theory may need to be tweaked to accommodate an intercept in the allometric equation. In general, any bivariate dataset that is well described by a three-parameter power equation on the arithmetic scale will follow a curvilinear path when displayed on the logarithmic scale. Consequently, reports of curvilinearity in log domain (i.e., "complex allometry") need to be revisited because conclusions from those investigations are likely to be flawed. © 2018 Wiley Periodicals, Inc.

Basal metabolic rate scaled to body mass within species by the ...

African Journals Online (AJOL)

Basal metabolic rate scaled to body mass within species by the fractal dimension of the vascular system and body composition. ... The postulate bd = c is shown to hold for both these species within the limits of experimental error, with the crucian carp evidence being especially convincing, since b, c and d are estimated from ...

Scaled nonuniform Fourier transform for image reconstruction in swept source optical coherence tomography

Science.gov (United States)

Mezgebo, Biniyam; Nagib, Karim; Fernando, Namal; Kordi, Behzad; Sherif, Sherif

2018-02-01

Swept Source optical coherence tomography (SS-OCT) is an important imaging modality for both medical and industrial diagnostic applications. A cross-sectional SS-OCT image is obtained by applying an inverse discrete Fourier transform (DFT) to axial interferograms measured in the frequency domain (k-space). This inverse DFT is typically implemented as a fast Fourier transform (FFT) that requires the data samples to be equidistant in k-space. As the frequency of light produced by a typical wavelength-swept laser is nonlinear in time, the recorded interferogram samples will not be uniformly spaced in k-space. Many image reconstruction methods have been proposed to overcome this problem. Most such methods rely on oversampling the measured interferogram then use either hardware, e.g., Mach-Zhender interferometer as a frequency clock module, or software, e.g., interpolation in k-space, to obtain equally spaced samples that are suitable for the FFT. To overcome the problem of nonuniform sampling in k-space without any need for interferogram oversampling, an earlier method demonstrated the use of the nonuniform discrete Fourier transform (NDFT) for image reconstruction in SS-OCT. In this paper, we present a more accurate method for SS-OCT image reconstruction from nonuniform samples in k-space using a scaled nonuniform Fourier transform. The result is demonstrated using SS-OCT images of Axolotl salamander eggs.

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

Science.gov (United States)

Preciat Gonzalez, German A; El Assal, Lemmer R P; Noronha, Alberto; Thiele, Ines; Haraldsdóttir, Hulda S; Fleming, Ronan M T

2017-06-14

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, many algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom mappings? For more than four thousand metabolic reactions in the latest human metabolic reconstruction, Recon 3D, we compared the atom mappings predicted by six atom mapping algorithms. We also compared these predictions to those obtained by manual curation of atom mappings for over five hundred reactions distributed among all top level Enzyme Commission number classes. Five of the evaluated algorithms had similarly high prediction accuracy of over 91% when compared to manually curated atom mapped reactions. On average, the accuracy of the prediction was highest for reactions catalysed by oxidoreductases and lowest for reactions catalysed by ligases. In addition to prediction accuracy, the algorithms were evaluated on their accessibility, their advanced features, such as the ability to identify equivalent atoms, and their ability to map hydrogen atoms. In addition to prediction accuracy, we found that software accessibility and advanced features were fundamental to the selection of an atom mapping algorithm in practice.

Basal metabolic rate scaled to body mass between species by the ...

African Journals Online (AJOL)

The principal reason that basal metabolic rate (BMR) and MMR scale with different power exponents to whole body mass is that MMR is due mainly to respiration in skeletal muscle during exercise and BMR to respiration in the viscera during rest. It follows, therefore, from the self-similarity of the vascular system that BMR is ...

Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production

Directory of Open Access Journals (Sweden)

Brooks J Paul

2010-03-01

Full Text Available Abstract Background Microorganisms possess diverse metabolic capabilities that can potentially be leveraged for efficient production of biofuels. Clostridium thermocellum (ATCC 27405 is a thermophilic anaerobe that is both cellulolytic and ethanologenic, meaning that it can directly use the plant sugar, cellulose, and biochemically convert it to ethanol. A major challenge in using microorganisms for chemical production is the need to modify the organism to increase production efficiency. The process of properly engineering an organism is typically arduous. Results Here we present a genome-scale model of C. thermocellum metabolism, iSR432, for the purpose of establishing a computational tool to study the metabolic network of C. thermocellum and facilitate efforts to engineer C. thermocellum for biofuel production. The model consists of 577 reactions involving 525 intracellular metabolites, 432 genes, and a proteomic-based representation of a cellulosome. The process of constructing this metabolic model led to suggested annotation refinements for 27 genes and identification of areas of metabolism requiring further study. The accuracy of the iSR432 model was tested using experimental growth and by-product secretion data for growth on cellobiose and fructose. Analysis using this model captures the relationship between the reduction-oxidation state of the cell and ethanol secretion and allowed for prediction of gene deletions and environmental conditions that would increase ethanol production. Conclusions By incorporating genomic sequence data, network topology, and experimental measurements of enzyme activities and metabolite fluxes, we have generated a model that is reasonably accurate at predicting the cellular phenotype of C. thermocellum and establish a strong foundation for rational strain design. In addition, we are able to draw some important conclusions regarding the underlying metabolic mechanisms for observed behaviors of C. thermocellum

Reconstruction of a large-scale reconnection exhaust structure in the solar wind

Directory of Open Access Journals (Sweden)

W.-L. Teh

2009-02-01

Full Text Available We recover two-dimensional (2-D magnetic field and flow field configurations from three spacecraft encounters with a single large-scale reconnection exhaust structure in the solar wind, using a new reconstruction method (Sonnerup and Teh, 2008 based on the ideal single-fluid MHD equations in a steady-state, 2-D geometry. The reconstruction is performed in the rest frame of the X-line, where the flow into, and the plasma jetting within, the exhaust region are clearly visible. The event was first identified by Phan et al. (2006 in the ACE, Cluster, and Wind data sets; they argued that quasi-steady reconnection persisted for over 2 h at a long (390 R_E X-line. The reconnection exhaust is sandwiched between two discontinuities, both of which contain elements of intermediate- and slow-mode behavior; these elements are co-located rather than being spatially separated. These composite discontinuities do not satisfy the coplanarity condition or the standard MHD jump conditions. For all three spacecraft, the Walén regression line slope was positive (negative for the leading (trailing discontinuity. Our MHD reconstruction shows that: (1 the X-line orientation was close to the bisector of the overall magnetic shear angle and exhibited a slow rotating motion toward the Sun-Earth line; (2 the X-line moved earthward, dawnward, and southward; (3 the reconnection electric field was small (~0.02 mV/m on average and gradually decreased from the first crossing (ACE to the last (Wind. The magnetic field and flow field configurations recovered from ACE and Cluster are similar while those recovered from Wind also include a magnetic island and an associated vortex. Reconnection persisted for at least 2.4 h involving inflow into the exhaust region from its two sides. Time-dependence in the reconnection electric fields seen by ACE and Wind indicates local temporal variations in the field configuration. In addition to the reconstruction results, we

Reconstruction of a large-scale reconnection exhaust structure in the solar wind

International Nuclear Information System (INIS)

Teh, W.L.; Sonnerup, B.U.Oe.; Hu, Q.; Farrugia, C.J.

2009-01-01

We recover two-dimensional (2-D) magnetic field and flow field configurations from three spacecraft encounters with a single large-scale reconnection exhaust structure in the solar wind, using a new reconstruction method (Sonnerup and Teh, 2008) based on the ideal single-fluid MHD equations in a steady-state, 2-D geometry. The reconstruction is performed in the rest frame of the X-line, where the flow into, and the plasma jetting within, the exhaust region are clearly visible. The event was first identified by Phan et al. (2006) in the ACE, Cluster, and Wind data sets; they argued that quasi-steady reconnection persisted for over 2 h at a long (390 R E ) X-line. The reconnection exhaust is sandwiched between two discontinuities, both of which contain elements of intermediate- and slow-mode behavior; these elements are co-located rather than being spatially separated. These composite discontinuities do not satisfy the coplanarity condition or the standard MHD jump conditions. For all three spacecraft, the Walen regression line slope was positive (negative) for the leading (trailing) discontinuity. Our MHD reconstruction shows that: (1) the X-line orientation was close to the bisector of the overall magnetic shear angle and exhibited a slow rotating motion toward the Sun-Earth line; (2) the X-line moved earthward, dawnward, and southward; (3) the reconnection electric field was small (∝0.02 mV/m on average) and gradually decreased from the first crossing (ACE) to the last (Wind). The magnetic field and flow field configurations recovered from ACE and Cluster are similar while those recovered from Wind also include a magnetic island and an associated vortex. Reconnection persisted for at least 2.4 h involving inflow into the exhaust region from its two sides. Time-dependence in the reconnection electric fields seen by ACE and Wind indicates local temporal variations in the field configuration. In addition to the reconstruction results, we provide a description and

Reconstruction of a large-scale reconnection exhaust structure in the solar wind

Directory of Open Access Journals (Sweden)

W.-L. Teh

2009-02-01

Full Text Available We recover two-dimensional (2-D magnetic field and flow field configurations from three spacecraft encounters with a single large-scale reconnection exhaust structure in the solar wind, using a new reconstruction method (Sonnerup and Teh, 2008 based on the ideal single-fluid MHD equations in a steady-state, 2-D geometry. The reconstruction is performed in the rest frame of the X-line, where the flow into, and the plasma jetting within, the exhaust region are clearly visible. The event was first identified by Phan et al. (2006 in the ACE, Cluster, and Wind data sets; they argued that quasi-steady reconnection persisted for over 2 h at a long (390 RE X-line. The reconnection exhaust is sandwiched between two discontinuities, both of which contain elements of intermediate- and slow-mode behavior; these elements are co-located rather than being spatially separated. These composite discontinuities do not satisfy the coplanarity condition or the standard MHD jump conditions. For all three spacecraft, the Walén regression line slope was positive (negative for the leading (trailing discontinuity. Our MHD reconstruction shows that: (1 the X-line orientation was close to the bisector of the overall magnetic shear angle and exhibited a slow rotating motion toward the Sun-Earth line; (2 the X-line moved earthward, dawnward, and southward; (3 the reconnection electric field was small (~0.02 mV/m on average and gradually decreased from the first crossing (ACE to the last (Wind. The magnetic field and flow field configurations recovered from ACE and Cluster are similar while those recovered from Wind also include a magnetic island and an associated vortex. Reconnection persisted for at least 2.4 h involving inflow into the exhaust region from its two sides. Time-dependence in the reconnection electric fields seen by ACE and Wind indicates local temporal variations in the field configuration. In addition to the reconstruction results, we provide a description

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

Directory of Open Access Journals (Sweden)

Alyaa M Abdel-Haleem

2018-01-01

Full Text Available Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale metabolic models (GeMMs of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1, choline, and pantothenate (vitamin B5 metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.

Studies of Sensitivity in the Dictionary Learning Approach to Computed Tomography: Simplifying the Reconstruction Problem, Rotation, and Scale

DEFF Research Database (Denmark)

Soltani, Sara

investigate the sensitivity and robustness of the reconstruction to variations of the scale and orientation in the training images and we suggest algorithms to estimate the correct relative scale and orientation of the unknown image to the training images from the data....... formulation in [22] enforces that the solution is an exact representation by the dictionary; in this report, we investigate this requirement. Furthermore, the underlying assumption that the scale and orientation of the training images are consistent with the unknown image of interest may not be realistic. We...

Deriving metabolic engineering strategies from genome-scale modeling with flux ratio constraints.

Science.gov (United States)

Yen, Jiun Y; Nazem-Bokaee, Hadi; Freedman, Benjamin G; Athamneh, Ahmad I M; Senger, Ryan S

2013-05-01

Optimized production of bio-based fuels and chemicals from microbial cell factories is a central goal of systems metabolic engineering. To achieve this goal, a new computational method of using flux balance analysis with flux ratios (FBrAtio) was further developed in this research and applied to five case studies to evaluate and design metabolic engineering strategies. The approach was implemented using publicly available genome-scale metabolic flux models. Synthetic pathways were added to these models along with flux ratio constraints by FBrAtio to achieve increased (i) cellulose production from Arabidopsis thaliana; (ii) isobutanol production from Saccharomyces cerevisiae; (iii) acetone production from Synechocystis sp. PCC6803; (iv) H2 production from Escherichia coli MG1655; and (v) isopropanol, butanol, and ethanol (IBE) production from engineered Clostridium acetobutylicum. The FBrAtio approach was applied to each case to simulate a metabolic engineering strategy already implemented experimentally, and flux ratios were continually adjusted to find (i) the end-limit of increased production using the existing strategy, (ii) new potential strategies to increase production, and (iii) the impact of these metabolic engineering strategies on product yield and culture growth. The FBrAtio approach has the potential to design "fine-tuned" metabolic engineering strategies in silico that can be implemented directly with available genomic tools. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT

OpenAIRE

Choudhary, Kumari Sonal; Rohatgi, Neha; Halldorsson, Skarphedinn; Briem, Eirikur; Gudjonsson, Thorarinn; Gudmundsson, Steinn; Rolfsson, Ottar

2016-01-01

Epithelial to mesenchymal transition (EMT) is an important event during development and cancer metastasis. There is limited understanding of the metabolic alterations that give rise to and take place during EMT. Dysregulation of signalling pathways that impact metabolism, including epidermal growth factor receptor (EGFR), are however a hallmark of EMT and metastasis. In this study, we report the investigation into EGFR signalling and metabolic crosstalk of EMT through constraint-based modelli...

EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT.

Directory of Open Access Journals (Sweden)

Kumari Sonal Choudhary

2016-06-01

Full Text Available Epithelial to mesenchymal transition (EMT is an important event during development and cancer metastasis. There is limited understanding of the metabolic alterations that give rise to and take place during EMT. Dysregulation of signalling pathways that impact metabolism, including epidermal growth factor receptor (EGFR, are however a hallmark of EMT and metastasis. In this study, we report the investigation into EGFR signalling and metabolic crosstalk of EMT through constraint-based modelling and analysis of the breast epithelial EMT cell model D492 and its mesenchymal counterpart D492M. We built an EGFR signalling network for EMT based on stoichiometric coefficients and constrained the network with gene expression data to build epithelial (EGFR_E and mesenchymal (EGFR_M networks. Metabolic alterations arising from differential expression of EGFR genes was derived from a literature review of AKT regulated metabolic genes. Signaling flux differences between EGFR_E and EGFR_M models subsequently allowed metabolism in D492 and D492M cells to be assessed. Higher flux within AKT pathway in the D492 cells compared to D492M suggested higher glycolytic activity in D492 that we confirmed experimentally through measurements of glucose uptake and lactate secretion rates. The signaling genes from the AKT, RAS/MAPK and CaM pathways were predicted to revert D492M to D492 phenotype. Follow-up analysis of EGFR signaling metabolic crosstalk in three additional breast epithelial cell lines highlighted variability in in vitro cell models of EMT. This study shows that the metabolic phenotype may be predicted by in silico analyses of gene expression data of EGFR signaling genes, but this phenomenon is cell-specific and does not follow a simple trend.

EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT.

Science.gov (United States)

Choudhary, Kumari Sonal; Rohatgi, Neha; Halldorsson, Skarphedinn; Briem, Eirikur; Gudjonsson, Thorarinn; Gudmundsson, Steinn; Rolfsson, Ottar

2016-06-01

Epithelial to mesenchymal transition (EMT) is an important event during development and cancer metastasis. There is limited understanding of the metabolic alterations that give rise to and take place during EMT. Dysregulation of signalling pathways that impact metabolism, including epidermal growth factor receptor (EGFR), are however a hallmark of EMT and metastasis. In this study, we report the investigation into EGFR signalling and metabolic crosstalk of EMT through constraint-based modelling and analysis of the breast epithelial EMT cell model D492 and its mesenchymal counterpart D492M. We built an EGFR signalling network for EMT based on stoichiometric coefficients and constrained the network with gene expression data to build epithelial (EGFR_E) and mesenchymal (EGFR_M) networks. Metabolic alterations arising from differential expression of EGFR genes was derived from a literature review of AKT regulated metabolic genes. Signaling flux differences between EGFR_E and EGFR_M models subsequently allowed metabolism in D492 and D492M cells to be assessed. Higher flux within AKT pathway in the D492 cells compared to D492M suggested higher glycolytic activity in D492 that we confirmed experimentally through measurements of glucose uptake and lactate secretion rates. The signaling genes from the AKT, RAS/MAPK and CaM pathways were predicted to revert D492M to D492 phenotype. Follow-up analysis of EGFR signaling metabolic crosstalk in three additional breast epithelial cell lines highlighted variability in in vitro cell models of EMT. This study shows that the metabolic phenotype may be predicted by in silico analyses of gene expression data of EGFR signaling genes, but this phenomenon is cell-specific and does not follow a simple trend.

Metabolic Trade-offs between Biomass Synthesis and Photosynthate Export at Different Light Intensities in a Genome–Scale Metabolic Model of Rice

Directory of Open Access Journals (Sweden)

Mark Graham Poolman

2014-11-01

Full Text Available Previously we have used a genome scale model of rice metabolism to describe how metabolism reconfigures at different light intensities in an expanding leaf of rice. Although this established that the metabolism of the leaf was adequatelyrepresented, in the model, the scenario was not that of the typical function of the leaf --- to provide material for the rest of the plant. Here we extend our analysis to explore the transition to a source leaf as export of photosynthate increases at the expense of making leaf biomass precursors, again as a function of light intensity. In particular we investigate whether, when the leaf is making a smaller range of compounds for export to the phloem, the same changes occur in the interactions between mitochondrial and chloroplast metabolism as seen in biomass synthesis for growth when light intensity increases. Our results show that the same changes occur qualitatively, though there are slight quantitative differences reflecting differences in the energy and redox requirements for the different metabolic outputs.

Mapping the Diffusion Potential of a Reconstructed Au(111) Surface at Nanometer Scale with 2D Molecular Gas

International Nuclear Information System (INIS)

Yan Shi-Chao; Xie Nan; Gong Hui-Qi; Guo Yang; Shan Xin-Yan; Lu Xing-Hua; Sun Qian

2012-01-01

The adsorption and diffusion behaviors of benzene molecules on an Au(111) surface are investigated by low-temperature scanning tunneling microscopy. A herringbone surface reconstruction of the Au(111) surface is imaged with atomic resolution, and significantly different behaviors are observed for benzene molecules adsorbed on step edges and terraces. The electric field induced modification in the molecular diffusion potential is revealed with a 2D molecular gas model, and a new method is developed to map the diffusion potential over the reconstructed Au(111) surface at the nanometer scale. (condensed matter: structure, mechanical and thermal properties)

Metabolic Profile and Inflammatory Responses in Dairy Cows with Left Displaced Abomasum Kept under Small-Scaled Farm Conditions

Directory of Open Access Journals (Sweden)

Fenja Klevenhusen

2015-10-01

Full Text Available Left displaced abomasum (LDA is a severe metabolic disease of cattle with a strong negative impact on production efficiency of dairy farms. Metabolic and inflammatory alterations associated with this disease have been reported in earlier studies, conducted mostly in large dairy farms. This research aimed to: (1 evaluate metabolic and inflammatory responses in dairy cows affected by LDA in small-scaled dairy farms; and (2 establish an Animals 2015, 5 1022 association between lactation number and milk production with the outcome of metabolic variables. The cows with LDA had lower serum calcium (Ca, but greater concentrations of non-esterified fatty acids (NEFA and beta-hydroxy-butyrate (BHBA, in particular when lactation number was >2. Cows with LDA showed elevated levels of aspartate aminotransferase, glutamate dehydrogenase, and serum amyloid A (SAA, regardless of lactation number. In addition, this study revealed strong associations between milk yield and the alteration of metabolic profile but not with inflammation in the sick cows. Results indicate metabolic alterations, liver damage, and inflammation in LDA cows kept under small-scale farm conditions. Furthermore, the data suggest exacerbation of metabolic profile and Ca metabolism but not of inflammation and liver health with increasing lactation number and milk yield in cows affected by LDA.

Metabolic Profile and Inflammatory Responses in Dairy Cows with Left Displaced Abomasum Kept under Small-Scaled Farm Conditions.

Science.gov (United States)

Klevenhusen, Fenja; Humer, Elke; Metzler-Zebeli, Barbara; Podstatzky-Lichtenstein, Leopold; Wittek, Thomas; Zebeli, Qendrim

2015-10-13

Left displaced abomasum (LDA) is a severe metabolic disease of cattle with a strong negative impact on production efficiency of dairy farms. Metabolic and inflammatory alterations associated with this disease have been reported in earlier studies, conducted mostly in large dairy farms. This research aimed to: (1) evaluate metabolic and inflammatory responses in dairy cows affected by LDA in small-scaled dairy farms; and (2) establish an Animals 2015, 5 1022 association between lactation number and milk production with the outcome of metabolic variables. The cows with LDA had lower serum calcium (Ca), but greater concentrations of non-esterified fatty acids (NEFA) and beta-hydroxy-butyrate (BHBA), in particular when lactation number was >2. Cows with LDA showed elevated levels of aspartate aminotransferase, glutamate dehydrogenase, and serum amyloid A (SAA), regardless of lactation number. In addition, this study revealed strong associations between milk yield and the alteration of metabolic profile but not with inflammation in the sick cows. Results indicate metabolic alterations, liver damage, and inflammation in LDA cows kept under small-scale farm conditions. Furthermore, the data suggest exacerbation of metabolic profile and Ca metabolism but not of inflammation and liver health with increasing lactation number and milk yield in cows affected by LDA.

Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations.

Science.gov (United States)

Bragg, Elise M; Briggs, Farran

2017-02-15

This protocol outlines large-scale reconstructions of neurons combined with the use of independent and unbiased clustering analyses to create a comprehensive survey of the morphological characteristics observed among a selective neuronal population. Combination of these techniques constitutes a novel approach for the collection and analysis of neuroanatomical data. Together, these techniques enable large-scale, and therefore more comprehensive, sampling of selective neuronal populations and establish unbiased quantitative methods for describing morphologically unique neuronal classes within a population. The protocol outlines the use of modified rabies virus to selectively label neurons. G-deleted rabies virus acts like a retrograde tracer following stereotaxic injection into a target brain structure of interest and serves as a vehicle for the delivery and expression of EGFP in neurons. Large numbers of neurons are infected using this technique and express GFP throughout their dendrites, producing "Golgi-like" complete fills of individual neurons. Accordingly, the virus-mediated retrograde tracing method improves upon traditional dye-based retrograde tracing techniques by producing complete intracellular fills. Individual well-isolated neurons spanning all regions of the brain area under study are selected for reconstruction in order to obtain a representative sample of neurons. The protocol outlines procedures to reconstruct cell bodies and complete dendritic arborization patterns of labeled neurons spanning multiple tissue sections. Morphological data, including positions of each neuron within the brain structure, are extracted for further analysis. Standard programming functions were utilized to perform independent cluster analyses and cluster evaluations based on morphological metrics. To verify the utility of these analyses, statistical evaluation of a cluster analysis performed on 160 neurons reconstructed in the thalamic reticular nucleus of the thalamus

Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02.

Science.gov (United States)

Guo, Jing; Zhang, Hong; Wang, Cheng; Chang, Ji-Wei; Chen, Ling-Ling

2016-05-01

We constructed the genome-scale metabolic network of Bacillus licheniformis (B. licheniformis) WX-02 by combining genomic annotation, high-throughput phenotype microarray (PM) experiments and literature-based metabolic information. The accuracy of the metabolic network was assessed by an OmniLog PM experiment. The final metabolic model iWX1009 contains 1009 genes, 1141 metabolites and 1762 reactions, and the predicted metabolic phenotypes showed an agreement rate of 76.8% with experimental PM data. In addition, key metabolic features such as growth yield, utilization of different substrates and essential genes were identified by flux balance analysis. A total of 195 essential genes were predicted from LB medium, among which 149 were verified with the experimental essential gene set of B. subtilis 168. With the removal of 5 reactions from the network, pathways for poly-γ-glutamic acid (γ-PGA) synthesis were optimized and the γ-PGA yield reached 83.8 mmol/h. Furthermore, the important metabolites and pathways related to γ-PGA synthesis and bacterium growth were comprehensively analyzed. The present study provides valuable clues for exploring the metabolisms and metabolic regulation of γ-PGA synthesis in B. licheniformis WX-02. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Systematic construction of kinetic models from genome-scale metabolic networks.

Directory of Open Access Journals (Sweden)

Natalie J Stanford

Full Text Available The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments.

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

Science.gov (United States)

Smallbone, Kieran; Klipp, Edda; Mendes, Pedro; Liebermeister, Wolfram

2013-01-01

The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments. PMID:24324546

Reconstructions of spring/summer precipitation for the Eastern Mediterranean from tree-ring widths and its connection to large-scale atmospheric circulation

Energy Technology Data Exchange (ETDEWEB)

Touchan, Ramzi; Funkhouser, Gary; Hughes, Malcolm K. [The University of Arizona, Laboratory of Tree-Ring Research, Tucson, AZ (United States); Xoplaki, Elena; Luterbacher, Juerg [University of Bern, Institute of Geography and NCCR Climate, Bern (Switzerland); Erkan, Nesat [Southwest Anatolia Forest Research Institute (SAFRI), Antalya (Turkey); Akkemik, Uenal [University of Istanbul, Faculty of Forestry, Department of Forest Botany, Bahcekoey-Istanbul (Turkey); Stephan, Jean [Ministry of Agriculture, Forestry Department, Beirut (Lebanon)

2005-07-01

This study represents the first large-scale systematic dendroclimatic sampling focused on developing chronologies from different species in the eastern Mediterranean region. Six reconstructions were developed from chronologies ranging in length from 115 years to 600 years. The first reconstruction (1885-2000) was derived from principal components (PCs) of 36 combined chronologies. The remaining five, 1800-2000, 1700-2000, 1600-2000, 1500-2000 and 1400-2000 were developed from PCs of 32, 18, 14, 9, and 7 chronologies, respectively. Calibration and verification statistics for the period 1931-2000 show good levels of skill for all reconstructions. The longest period of consecutive dry years, defined as those with less than 90% of the mean of the observed May-August precipitation, was 5 years (1591-1595) and occurred only once during the last 600 years. The longest reconstructed wet period was 5 years (1601-1605 and 1751-1755). No long term trends were found in May-August precipitation during the last few centuries. Regression maps are used to identify the influence of large-scale atmospheric circulation on regional precipitation. In general, tree-ring indices are influenced by May-August precipitation, which is driven by anomalous below (above) normal pressure at all atmospheric levels and by convection (subsidence) and small pressure gradients at sea level. These atmospheric conditions also control the anomaly surface air temperature distribution which indicates below (above) normal values in the southern regions and warmer (cooler) conditions north of around 40 N. A compositing technique is used to extract information on large-scale climate signals from extreme wet and dry summers for the second half of the twentieth century and an independent reconstruction over the last 237 years. Similar main modes of atmospheric patterns and surface air temperature distribution related to extreme dry and wet summers were identified both for the most recent 50 years and the last

The fractal geometry of nutrient exchange surfaces does not provide an explanation for 3/4-power metabolic scaling

Directory of Open Access Journals (Sweden)

Painter Page R

2005-08-01

Full Text Available Abstract Background A prominent theoretical explanation for 3/4-power allometric scaling of metabolism proposes that the nutrient exchange surface of capillaries has properties of a space-filling fractal. The theory assumes that nutrient exchange surface area has a fractal dimension equal to or greater than 2 and less than or equal to 3 and that the volume filled by the exchange surface area has a fractal dimension equal to or greater than 3 and less than or equal to 4. Results It is shown that contradicting predictions can be derived from the assumptions of the model. When errors in the model are corrected, it is shown to predict that metabolic rate is proportional to body mass (proportional scaling. Conclusion The presence of space-filling fractal nutrient exchange surfaces does not provide a satisfactory explanation for 3/4-power metabolic rate scaling.

Association of metabolic syndrome and change in Unified Parkinson's Disease Rating Scale scores.

Science.gov (United States)

Leehey, Maureen; Luo, Sheng; Sharma, Saloni; Wills, Anne-Marie A; Bainbridge, Jacquelyn L; Wong, Pei Shieen; Simon, David K; Schneider, Jay; Zhang, Yunxi; Pérez, Adriana; Dhall, Rohit; Christine, Chadwick W; Singer, Carlos; Cambi, Franca; Boyd, James T

2017-10-24

To explore the association between metabolic syndrome and the Unified Parkinson's Disease Rating Scale (UPDRS) scores and, secondarily, the Symbol Digit Modalities Test (SDMT). This is a secondary analysis of data from 1,022 of 1,741 participants of the National Institute of Neurological Disorders and Stroke Exploratory Clinical Trials in Parkinson Disease Long-Term Study 1, a randomized, placebo-controlled trial of creatine. Participants were categorized as having or not having metabolic syndrome on the basis of modified criteria from the National Cholesterol Education Program Adult Treatment Panel III. Those who had the same metabolic syndrome status at consecutive annual visits were included. The change in UPDRS and SDMT scores from randomization to 3 years was compared in participants with and without metabolic syndrome. Participants with metabolic syndrome (n = 396) compared to those without (n = 626) were older (mean [SD] 63.9 [8.1] vs 59.9 [9.4] years; p metabolic syndrome experienced an additional 0.6- (0.2) unit annual increase in total UPDRS ( p = 0.02) and 0.5- (0.2) unit increase in motor UPDRS ( p = 0.01) scores compared with participants without metabolic syndrome. There was no difference in the change in SDMT scores. Persons with Parkinson disease meeting modified criteria for metabolic syndrome experienced a greater increase in total UPDRS scores over time, mainly as a result of increases in motor scores, compared to those who did not. Further studies are needed to confirm this finding. NCT00449865. © 2017 American Academy of Neurology.

Phylogenomic reconstruction of archaeal fatty acid metabolism

Science.gov (United States)

Dibrova, Daria V.; Galperin, Michael Y.; Mulkidjanian, Armen Y.

2014-01-01

While certain archaea appear to synthesize and/or metabolize fatty acids, the respective pathways still remain obscure. By analyzing the genomic distribution of the key lipid-related enzymes, we were able to identify the likely components of the archaeal pathway of fatty acid metabolism, namely, a combination of the enzymes of bacterial-type β-oxidation of fatty acids (acyl-CoA-dehydrogenase, enoyl-CoA hydratase, and 3-hydroxyacyl-CoA dehydrogenase) with paralogs of the archaeal acetyl-CoA C-acetyltransferase, an enzyme of the mevalonate biosynthesis pathway. These three β-oxidation enzymes working in the reverse direction could potentially catalyze biosynthesis of fatty acids, with paralogs of acetyl-CoA C-acetyltransferase performing addition of C2 fragments. The presence in archaea of the genes for energy-transducing membrane enzyme complexes, such as cytochrome bc complex, cytochrome c oxidase, and diverse rhodopsins, was found to correlate with the presence of the proposed system of fatty acid biosynthesis. We speculate that because these membrane complexes functionally depend on fatty acid chains, their genes could have been acquired via lateral gene transfer from bacteria only by those archaea that already possessed a system of fatty acid biosynthesis. The proposed pathway of archaeal fatty acid metabolism operates in extreme conditions and therefore might be of interest in the context of biofuel production and other industrial applications. PMID:24818264

Improved reconstruction for IDEAL spiral CSI

DEFF Research Database (Denmark)

Hansen, Rie Beck; Mariager, Christian; Laustsen, Christoffer

2017-01-01

In this study we demonstrate how reconstruction for IDEAL spiral CSI (spectroscopic imaging scheme developed for hyperpolarized dynamic metabolic MR imaging) can be improved by using regularization with a sparsity constraint. By exploiting sparsity of the spectral domain, IDEAL spiral CSI can...

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

KAUST Repository

Abdel-Haleem, Alyaa M.

2018-01-04

Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale models (GEMs) of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1), choline, and pantothenate (vitamin B5) metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.

Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic networks.

Science.gov (United States)

Xu, Zixiang; Sun, Jibin; Wu, Qiaqing; Zhu, Dunming

2017-12-11

Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry. In addition, the shortest pathways may not be the pathways with high yield. At the same time, a pathway, which exists in stoichiometry, may not be feasible in thermodynamics. By using mixed integer programming strategy, we put forward an algorithm to identify all the smallest balanced pathways which convert the source compound to the target compound in large-scale metabolic networks. The resulting pathways by our method can finely satisfy the stoichiometric constraints and non-decomposability condition. Especially, the functions of high yield and thermodynamics feasibility have been considered in our approach. This tool is tailored to direct the metabolic engineering practice to enlarge the metabolic potentials of industrial strains by integrating the extensive metabolic network information built from systems biology dataset.

A Picea crassifolia Tree-Ring Width-Based Temperature Reconstruction for the Mt. Dongda Region, Northwest China, and Its Relationship to Large-Scale Climate Forcing.

Directory of Open Access Journals (Sweden)

Yu Liu

Full Text Available The historical May-October mean temperature since 1831 was reconstructed based on tree-ring width of Qinghai spruce (Picea crassifolia Kom. collected on Mt. Dongda, North of the Hexi Corridor in Northwest China. The regression model explained 46.6% of the variance of the instrumentally observed temperature. The cold periods in the reconstruction were 1831-1889, 1894-1901, 1908-1934 and 1950-1952, and the warm periods were 1890-1893, 1902-1907, 1935-1949 and 1953-2011. During the instrumental period (1951-2011, an obvious warming trend appeared in the last twenty years. The reconstruction displayed similar patterns to a temperature reconstruction from the east-central Tibetan Plateau at the inter-decadal timescale, indicating that the temperature reconstruction in this study was a reliable proxy for Northwest China. It was also found that the reconstruction series had good consistency with the Northern Hemisphere temperature at a decadal timescale. Multi-taper method spectral analysis detected some low- and high-frequency cycles (2.3-2.4-year, 2.8-year, 3.4-3.6-year, 5.0-year, 9.9-year and 27.0-year. Combining these cycles, the relationship of the low-frequency change with the Pacific Decadal Oscillation (PDO, North Atlantic Oscillation (NAO and Southern Oscillation (SO suggested that the reconstructed temperature variations may be related to large-scale atmospheric-oceanic variations. Major volcanic eruptions were partly reflected in the reconstructed temperatures after high-pass filtering; these events promoted anomalous cooling in this region. The results of this study not only provide new information for assessing the long-term temperature changes in the Hexi Corridor of Northwest China, but also further demonstrate the effects of large-scale atmospheric-oceanic circulation on climate change in Northwest China.

Ontogenetic scaling of fish metabolism in the mouse-to-elephant mass magnitude range

DEFF Research Database (Denmark)

Moran, Damian; Wells, R.M.G.

2007-01-01

, and are therefore not statistically comparable. In this study the metabolic rate of yellowtail kingfish was measured from 0.6 mg-2.2 kg, a mass range comparable to that between a mouse and an elephant. Linear regression of the log transformed data resulted in a scaling exponent of 0.90 and high correlation...

Reducing computational costs in large scale 3D EIT by using a sparse Jacobian matrix with block-wise CGLS reconstruction

International Nuclear Information System (INIS)

Yang, C L; Wei, H Y; Soleimani, M; Adler, A

2013-01-01

Electrical impedance tomography (EIT) is a fast and cost-effective technique to provide a tomographic conductivity image of a subject from boundary current–voltage data. This paper proposes a time and memory efficient method for solving a large scale 3D EIT inverse problem using a parallel conjugate gradient (CG) algorithm. The 3D EIT system with a large number of measurement data can produce a large size of Jacobian matrix; this could cause difficulties in computer storage and the inversion process. One of challenges in 3D EIT is to decrease the reconstruction time and memory usage, at the same time retaining the image quality. Firstly, a sparse matrix reduction technique is proposed using thresholding to set very small values of the Jacobian matrix to zero. By adjusting the Jacobian matrix into a sparse format, the element with zeros would be eliminated, which results in a saving of memory requirement. Secondly, a block-wise CG method for parallel reconstruction has been developed. The proposed method has been tested using simulated data as well as experimental test samples. Sparse Jacobian with a block-wise CG enables the large scale EIT problem to be solved efficiently. Image quality measures are presented to quantify the effect of sparse matrix reduction in reconstruction results. (paper)

Reducing computational costs in large scale 3D EIT by using a sparse Jacobian matrix with block-wise CGLS reconstruction.

Science.gov (United States)

Yang, C L; Wei, H Y; Adler, A; Soleimani, M

2013-06-01

Electrical impedance tomography (EIT) is a fast and cost-effective technique to provide a tomographic conductivity image of a subject from boundary current-voltage data. This paper proposes a time and memory efficient method for solving a large scale 3D EIT inverse problem using a parallel conjugate gradient (CG) algorithm. The 3D EIT system with a large number of measurement data can produce a large size of Jacobian matrix; this could cause difficulties in computer storage and the inversion process. One of challenges in 3D EIT is to decrease the reconstruction time and memory usage, at the same time retaining the image quality. Firstly, a sparse matrix reduction technique is proposed using thresholding to set very small values of the Jacobian matrix to zero. By adjusting the Jacobian matrix into a sparse format, the element with zeros would be eliminated, which results in a saving of memory requirement. Secondly, a block-wise CG method for parallel reconstruction has been developed. The proposed method has been tested using simulated data as well as experimental test samples. Sparse Jacobian with a block-wise CG enables the large scale EIT problem to be solved efficiently. Image quality measures are presented to quantify the effect of sparse matrix reduction in reconstruction results.

Bio-crude transcriptomics: Gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa*

Directory of Open Access Journals (Sweden)

Molnár István

2012-10-01

Full Text Available Abstract Background Microalgae hold promise for yielding a biofuel feedstock that is sustainable, carbon-neutral, distributed, and only minimally disruptive for the production of food and feed by traditional agriculture. Amongst oleaginous eukaryotic algae, the B race of Botryococcus braunii is unique in that it produces large amounts of liquid hydrocarbons of terpenoid origin. These are comparable to fossil crude oil, and are sequestered outside the cells in a communal extracellular polymeric matrix material. Biosynthetic engineering of terpenoid bio-crude production requires identification of genes and reconstruction of metabolic pathways responsible for production of both hydrocarbons and other metabolites of the alga that compete for photosynthetic carbon and energy. Results A de novo assembly of 1,334,609 next-generation pyrosequencing reads form the Showa strain of the B race of B. braunii yielded a transcriptomic database of 46,422 contigs with an average length of 756 bp. Contigs were annotated with pathway, ontology, and protein domain identifiers. Manual curation allowed the reconstruction of pathways that produce terpenoid liquid hydrocarbons from primary metabolites, and pathways that divert photosynthetic carbon into tetraterpenoid carotenoids, diterpenoids, and the prenyl chains of meroterpenoid quinones and chlorophyll. Inventories of machine-assembled contigs are also presented for reconstructed pathways for the biosynthesis of competing storage compounds including triacylglycerol and starch. Regeneration of S-adenosylmethionine, and the extracellular localization of the hydrocarbon oils by active transport and possibly autophagy are also investigated. Conclusions The construction of an annotated transcriptomic database, publicly available in a web-based data depository and annotation tool, provides a foundation for metabolic pathway and network reconstruction, and facilitates further omics studies in the absence of a genome

MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks.

Science.gov (United States)

Kelley, James J; Maor, Shay; Kim, Min Kyung; Lane, Anatoliy; Lun, Desmond S

2017-08-15

Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii). 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. 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

GPU-accelerated brain connectivity reconstruction and visualization in large-scale electron micrographs

KAUST Repository

Jeong, Wonki

2011-01-01

This chapter introduces a GPU-accelerated interactive, semiautomatic axon segmentation and visualization system. Two challenging problems have been addressed: the interactive 3D axon segmentation and the interactive 3D image filtering and rendering of implicit surfaces. The reconstruction of neural connections to understand the function of the brain is an emerging and active research area in neuroscience. With the advent of high-resolution scanning technologies, such as 3D light microscopy and electron microscopy (EM), reconstruction of complex 3D neural circuits from large volumes of neural tissues has become feasible. Among them, only EM data can provide sufficient resolution to identify synapses and to resolve extremely narrow neural processes. These high-resolution, large-scale datasets pose challenging problems, for example, how to process and manipulate large datasets to extract scientifically meaningful information using a compact representation in a reasonable processing time. The running time of the multiphase level set segmentation method has been measured on the CPU and GPU. The CPU version is implemented using the ITK image class and the ITK distance transform filter. The numerical part of the CPU implementation is similar to the GPU implementation for fair comparison. The main focus of this chapter is introducing the GPU algorithms and their implementation details, which are the core components of the interactive segmentation and visualization system. © 2011 Copyright © 2011 NVIDIA Corporation and Wen-mei W. Hwu Published by Elsevier Inc. All rights reserved..

Trajectory Reconstruction and Uncertainty Analysis Using Mars Science Laboratory Pre-Flight Scale Model Aeroballistic Testing

Science.gov (United States)

Lugo, Rafael A.; Tolson, Robert H.; Schoenenberger, Mark

2013-01-01

As part of the Mars Science Laboratory (MSL) trajectory reconstruction effort at NASA Langley Research Center, free-flight aeroballistic experiments of instrumented MSL scale models was conducted at Aberdeen Proving Ground in Maryland. The models carried an inertial measurement unit (IMU) and a flush air data system (FADS) similar to the MSL Entry Atmospheric Data System (MEADS) that provided data types similar to those from the MSL entry. Multiple sources of redundant data were available, including tracking radar and on-board magnetometers. These experimental data enabled the testing and validation of the various tools and methodologies that will be used for MSL trajectory reconstruction. The aerodynamic parameters Mach number, angle of attack, and sideslip angle were estimated using minimum variance with a priori to combine the pressure data and pre-flight computational fluid dynamics (CFD) data. Both linear and non-linear pressure model terms were also estimated for each pressure transducer as a measure of the errors introduced by CFD and transducer calibration. Parameter uncertainties were estimated using a "consider parameters" approach.

Factors associated with metabolic syndrome and related medical costs by the scale of enterprise in Korea.

Science.gov (United States)

Kong, Hyung-Sik; Lee, Kang-Sook; Yim, Eun-Shil; Lee, Seon-Young; Cho, Hyun-Young; Lee, Bin Na; Park, Jee Young

2013-10-21

The purpose of this study was to identify the risk factors of metabolic syndrome (MS) and to analyze the relationship between the risk factors of MS and medical cost of major diseases related to MS in Korean workers, according to the scale of the enterprise. Data was obtained from annual physical examinations, health insurance qualification and premiums, and health insurance benefits of 4,094,217 male and female workers who underwent medical examinations provided by the National Health Insurance Corporation in 2009. Logistic regression analyses were used to the identify risk factors of MS and multiple regression was used to find factors associated with medical expenditures due to major diseases related to MS. The study found that low-income workers were more likely to work in small-scale enterprises. The prevalence rate of MS in males and females, respectively, was 17.2% and 9.4% in small-scale enterprises, 15.9% and 8.9% in medium-scale enterprises, and 15.9% and 5.5% in large-scale enterprises. The risks of MS increased with age, lower income status, and smoking in small-scale enterprise workers. The medical costs increased in workers with old age and past smoking history. There was also a gender difference in the pattern of medical expenditures related to MS. Health promotion programs to manage metabolic syndrome should be developed to focus on workers who smoke, drink, and do little exercise in small scale enterprises.

A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.

Science.gov (United States)

Mih, Nathan; Brunk, Elizabeth; Bordbar, Aarash; Palsson, Bernhard O

2016-07-01

Progress in systems medicine brings promise to addressing patient heterogeneity and individualized therapies. Recently, genome-scale models of metabolism have been shown to provide insight into the mechanistic link between drug therapies and systems-level off-target effects while being expanded to explicitly include the three-dimensional structure of proteins. The integration of these molecular-level details, such as the physical, structural, and dynamical properties of proteins, notably expands the computational description of biochemical network-level properties and the possibility of understanding and predicting whole cell phenotypes. In this study, we present a multi-scale modeling framework that describes biological processes which range in scale from atomistic details to an entire metabolic network. Using this approach, we can understand how genetic variation, which impacts the structure and reactivity of a protein, influences both native and drug-induced metabolic states. As a proof-of-concept, we study three enzymes (catechol-O-methyltransferase, glucose-6-phosphate dehydrogenase, and glyceraldehyde-3-phosphate dehydrogenase) and their respective genetic variants which have clinically relevant associations. Using all-atom molecular dynamic simulations enables the sampling of long timescale conformational dynamics of the proteins (and their mutant variants) in complex with their respective native metabolites or drug molecules. We find that changes in a protein's structure due to a mutation influences protein binding affinity to metabolites and/or drug molecules, and inflicts large-scale changes in metabolism.

Systematic Review: Aesthetic Assessment of Breast Reconstruction Outcomes by Healthcare Professionals.

Science.gov (United States)

Maass, Saskia W M C; Bagher, Shaghayegh; Hofer, Stefan O P; Baxter, Nancy N; Zhong, Toni

2015-12-01

Achieving an aesthetic outcome following postmastectomy breast reconstruction is both an important goal for the patient and plastic surgeon. However, there is currently an absence of a widely accepted, standardized, and validated professional aesthetic assessment scale following postmastectomy breast reconstruction. A systematic review was performed to identify all articles that provided professional assessment of the aesthetic outcome following postmastectomy, implant- or autologous tissue-based breast reconstruction. A modified version of the Scientific Advisory Committee's Medical Outcomes Trust (MOT) criteria was used to evaluate all professional aesthetic assessment scales identified by our systematic review. The criteria included conceptual framework formation, reliability, validity, responsiveness, interpretability, burden, and correlation with patient-reported outcomes. A total of 120 articles were identified: 52 described autologous breast reconstruction, 37 implant-based reconstruction, and 29 both. Of the 12 different professional aesthetic assessment scales that exist in the literature, the most commonly used scale was the four-point professional aesthetic assessment scale. The highest score on the modified MOT criteria was assigned to the ten-point professional aesthetic assessment scale. However, this scale has limited clinical usefulness due to its poor responsiveness to change, lack of interpretability, and wide range of intra- and inter-rater agreements (Veiga et al. in Ann Plast Surg 48(5):515-520, 2002). A "gold standard" professional aesthetic assessment scale needs to be developed to enhance the comparability of breast reconstruction results across techniques, surgeons, and studies to aid with the selection of procedures that produce the best aesthetic results from both the perspectives of the surgeon and patients.

Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins.

Science.gov (United States)

Irani, Zahra Azimzadeh; Kerkhoven, Eduard J; Shojaosadati, Seyed Abbas; Nielsen, Jens

2016-05-01

Pichia pastoris is used for commercial production of human therapeutic proteins, and genome-scale models of P. pastoris metabolism have been generated in the past to study the metabolism and associated protein production by this yeast. A major challenge with clinical usage of recombinant proteins produced by P. pastoris is the difference in N-glycosylation of proteins produced by humans and this yeast. However, through metabolic engineering, a P. pastoris strain capable of producing humanized N-glycosylated proteins was constructed. The current genome-scale models of P. pastoris do not address native nor humanized N-glycosylation, and we therefore developed ihGlycopastoris, an extension to the iLC915 model with both native and humanized N-glycosylation for recombinant protein production, but also an estimation of N-glycosylation of P. pastoris native proteins. This new model gives a better prediction of protein yield, demonstrates the effect of the different types of N-glycosylation of protein yield, and can be used to predict potential targets for strain improvement. The model represents a step towards a more complete description of protein production in P. pastoris, which is required for using these models to understand and optimize protein production processes. © 2015 Wiley Periodicals, Inc.

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

Directory of Open Access Journals (Sweden)

Feng Xueyang

2012-08-01

Full Text Available Abstract Background Concurrent with the efforts currently underway in mapping microbial genomes using high-throughput sequencing methods, systems biologists are building metabolic models to characterize and predict cell metabolisms. One of the key steps in building a metabolic model is using multiple databases to collect and assemble essential information about genome-annotations and the architecture of the metabolic network for a specific organism. To speed up metabolic model development for a large number of microorganisms, we need a user-friendly platform to construct metabolic networks and to perform constraint-based flux balance analysis based on genome databases and experimental results. Results We have developed a semi-automatic, web-based platform (MicrobesFlux for generating and reconstructing metabolic models for annotated microorganisms. MicrobesFlux is able to automatically download the metabolic network (including enzymatic reactions and metabolites of ~1,200 species from the KEGG database (Kyoto Encyclopedia of Genes and Genomes and then convert it to a metabolic model draft. The platform also provides diverse customized tools, such as gene knockouts and the introduction of heterologous pathways, for users to reconstruct the model network. The reconstructed metabolic network can be formulated to a constraint-based flux model to predict and analyze the carbon fluxes in microbial metabolisms. The simulation results can be exported in the SBML format (The Systems Biology Markup Language. Furthermore, we also demonstrated the platform functionalities by developing an FBA model (including 229 reactions for a recent annotated bioethanol producer, Thermoanaerobacter sp. strain X514, to predict its biomass growth and ethanol production. Conclusion MicrobesFlux is an installation-free and open-source platform that enables biologists without prior programming knowledge to develop metabolic models for annotated microorganisms in the KEGG

Reconstructing the δ(18) O of atmospheric water vapour via the CAM epiphyte Tillandsia usneoides: seasonal controls on δ(18) O in the field and large-scale reconstruction of δ(18) Oa.

Science.gov (United States)

Helliker, Brent R

2014-03-01

Using both oxygen isotope ratios of leaf water (δ(18) OL ) and cellulose (δ(18) OC ) of Tillandsia usneoides in situ, this paper examined how short- and long-term responses to environmental variation and model parameterization affected the reconstruction of the atmospheric water vapour (δ(18) Oa ). During sample-intensive field campaigns, predictions of δ(18) OL matched observations well using a non-steady-state model, but the model required data-rich parameterization. Predictions from the more easily parameterized maximum enrichment model (δ(18) OL-M ) matched observed δ(18) OL and observed δ(18) Oa when leaf water turnover was less than 3.5 d. Using the δ(18) OL-M model and weekly samples of δ(18) OL across two growing seasons in Florida, USA, reconstructed δ(18) Oa was -12.6 ± 0.3‰. This is compared with δ(18) Oa of -12.4 ± 0.2‰ resolved from the growing-season-weighted δ(18) OC . Both of these values were similar to δ(18) Oa in equilibrium with precipitation, -12.9‰. δ(18) Oa was also reconstructed through a large-scale transect with δ(18) OL and the growing-season-integrated δ(18) OC across the southeastern United States. There was considerable large-scale variation, but there was regional, weather-induced coherence in δ(18) Oa when using δ(18) OL . The reconstruction of δ(18) Oa with δ(18) OC generally supported the assumption of δ(18) Oa being in equilibrium with precipitation δ(18) O (δ(18) Oppt ), but the pool of δ(18) Oppt with which δ(18) Oa was in equilibrium - growing season versus annual δ(18) Oppt - changed with latitude. © 2013 John Wiley & Sons Ltd.

A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.

Directory of Open Access Journals (Sweden)

Nathan Mih

2016-07-01

Full Text Available Progress in systems medicine brings promise to addressing patient heterogeneity and individualized therapies. Recently, genome-scale models of metabolism have been shown to provide insight into the mechanistic link between drug therapies and systems-level off-target effects while being expanded to explicitly include the three-dimensional structure of proteins. The integration of these molecular-level details, such as the physical, structural, and dynamical properties of proteins, notably expands the computational description of biochemical network-level properties and the possibility of understanding and predicting whole cell phenotypes. In this study, we present a multi-scale modeling framework that describes biological processes which range in scale from atomistic details to an entire metabolic network. Using this approach, we can understand how genetic variation, which impacts the structure and reactivity of a protein, influences both native and drug-induced metabolic states. As a proof-of-concept, we study three enzymes (catechol-O-methyltransferase, glucose-6-phosphate dehydrogenase, and glyceraldehyde-3-phosphate dehydrogenase and their respective genetic variants which have clinically relevant associations. Using all-atom molecular dynamic simulations enables the sampling of long timescale conformational dynamics of the proteins (and their mutant variants in complex with their respective native metabolites or drug molecules. We find that changes in a protein's structure due to a mutation influences protein binding affinity to metabolites and/or drug molecules, and inflicts large-scale changes in metabolism.

An iterative reconstruction of cosmological initial density fields

Science.gov (United States)

Hada, Ryuichiro; Eisenstein, Daniel J.

2018-05-01

We present an iterative method to reconstruct the linear-theory initial conditions from the late-time cosmological matter density field, with the intent of improving the recovery of the cosmic distance scale from the baryon acoustic oscillations (BAOs). We present tests using the dark matter density field in both real and redshift space generated from an N-body simulation. In redshift space at z = 0.5, we find that the reconstructed displacement field using our iterative method are more than 80% correlated with the true displacement field of the dark matter particles on scales k < 0.10h Mpc-1. Furthermore, we show that the two-point correlation function of our reconstructed density field matches that of the initial density field substantially better, especially on small scales (<40h-1 Mpc). Our redshift-space results are improved if we use an anisotropic smoothing so as to account for the reduced small-scale information along the line of sight in redshift space.

Computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks

Directory of Open Access Journals (Sweden)

Benjamin eMerlet

2016-02-01

Full Text Available This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc and flat file formats (SBML and Matlab files. We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics and Glasgow Polyomics on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks.In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks.In order to achieve this goal we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

Capturing the essence of a metabolic network: a flux balance analysis approach.

Science.gov (United States)

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.

NR-code: Nonlinear reconstruction code

Science.gov (United States)

Yu, Yu; Pen, Ue-Li; Zhu, Hong-Ming

2018-04-01

NR-code applies nonlinear reconstruction to the dark matter density field in redshift space and solves for the nonlinear mapping from the initial Lagrangian positions to the final redshift space positions; this reverses the large-scale bulk flows and improves the precision measurement of the baryon acoustic oscillations (BAO) scale.

Reconstructing Information in Large-Scale Structure via Logarithmic Mapping

Science.gov (United States)

Szapudi, Istvan

We propose to develop a new method to extract information from large-scale structure data combining two-point statistics and non-linear transformations; before, this information was available only with substantially more complex higher-order statistical methods. Initially, most of the cosmological information in large-scale structure lies in two-point statistics. With non- linear evolution, some of that useful information leaks into higher-order statistics. The PI and group has shown in a series of theoretical investigations how that leakage occurs, and explained the Fisher information plateau at smaller scales. This plateau means that even as more modes are added to the measurement of the power spectrum, the total cumulative information (loosely speaking the inverse errorbar) is not increasing. Recently we have shown in Neyrinck et al. (2009, 2010) that a logarithmic (and a related Gaussianization or Box-Cox) transformation on the non-linear Dark Matter or galaxy field reconstructs a surprisingly large fraction of this missing Fisher information of the initial conditions. This was predicted by the earlier wave mechanical formulation of gravitational dynamics by Szapudi & Kaiser (2003). The present proposal is focused on working out the theoretical underpinning of the method to a point that it can be used in practice to analyze data. In particular, one needs to deal with the usual real-life issues of galaxy surveys, such as complex geometry, discrete sam- pling (Poisson or sub-Poisson noise), bias (linear, or non-linear, deterministic, or stochastic), redshift distortions, pro jection effects for 2D samples, and the effects of photometric redshift errors. We will develop methods for weak lensing and Sunyaev-Zeldovich power spectra as well, the latter specifically targetting Planck. In addition, we plan to investigate the question of residual higher- order information after the non-linear mapping, and possible applications for cosmology. Our aim will be to work out

Recon 2.2

DEFF Research Database (Denmark)

Swainston, Neil; Smallbone, Kieran; Hefzi, Hooman

2016-01-01

The human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort...

Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803.

Directory of Open Access Journals (Sweden)

Rajib Saha

Full Text Available Cyanobacteria are an important group of photoautotrophic organisms that can synthesize valuable bio-products by harnessing solar energy. They are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuels and their precursors. However, less well studied are the similarities and differences in metabolism of different species of cyanobacteria as they pertain to their suitability as microbial production chassis. Here we assemble, update and compare genome-scale models (iCyt773 and iSyn731 for two phylogenetically related cyanobacterial species, namely Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. All reactions are elementally and charge balanced and localized into four different intracellular compartments (i.e., periplasm, cytosol, carboxysome and thylakoid lumen and biomass descriptions are derived based on experimental measurements. Newly added reactions absent in earlier models (266 and 322, respectively span most metabolic pathways with an emphasis on lipid biosynthesis. All thermodynamically infeasible loops are identified and eliminated from both models. Comparisons of model predictions against gene essentiality data reveal a specificity of 0.94 (94/100 and a sensitivity of 1 (19/19 for the Synechocystis iSyn731 model. The diurnal rhythm of Cyanothece 51142 metabolism is modeled by constructing separate (light/dark biomass equations and introducing regulatory restrictions over light and dark phases. Specific metabolic pathway differences between the two cyanobacteria alluding to different bio-production potentials are reflected in both models.

Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production.

Science.gov (United States)

Agren, Rasmus; Otero, José Manuel; Nielsen, Jens

2013-07-01

In this work, we describe the application of a genome-scale metabolic model and flux balance analysis for the prediction of succinic acid overproduction strategies in Saccharomyces cerevisiae. The top three single gene deletion strategies, Δmdh1, Δoac1, and Δdic1, were tested using knock-out strains cultivated anaerobically on glucose, coupled with physiological and DNA microarray characterization. While Δmdh1 and Δoac1 strains failed to produce succinate, Δdic1 produced 0.02 C-mol/C-mol glucose, in close agreement with model predictions (0.03 C-mol/C-mol glucose). Transcriptional profiling suggests that succinate formation is coupled to mitochondrial redox balancing, and more specifically, reductive TCA cycle activity. While far from industrial titers, this proof-of-concept suggests that in silico predictions coupled with experimental validation can be used to identify novel and non-intuitive metabolic engineering strategies.

A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks.

Science.gov (United States)

Merlet, Benjamin; Paulhe, Nils; Vinson, Florence; Frainay, Clément; Chazalviel, Maxime; Poupin, Nathalie; Gloaguen, Yoann; Giacomoni, Franck; Jourdan, Fabien

2016-01-01

This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

Model simulations and proxy-based reconstructions for the European region in the past millennium (Invited)

Science.gov (United States)

Zorita, E.

2009-12-01

One of the objectives when comparing simulations of past climates to proxy-based climate reconstructions is to asses the skill of climate models to simulate climate change. This comparison may accomplished at large spatial scales, for instance the evolution of simulated and reconstructed Northern Hemisphere annual temperature, or at regional or point scales. In both approaches a 'fair' comparison has to take into account different aspects that affect the inevitable uncertainties and biases in the simulations and in the reconstructions. These efforts face a trade-off: climate models are believed to be more skillful at large hemispheric scales, but climate reconstructions are these scales are burdened by the spatial distribution of available proxies and by methodological issues surrounding the statistical method used to translate the proxy information into large-spatial averages. Furthermore, the internal climatic noise at large hemispheric scales is low, so that the sampling uncertainty tends to be also low. On the other hand, the skill of climate models at regional scales is limited by the coarse spatial resolution, which hinders a faithful representation of aspects important for the regional climate. At small spatial scales, the reconstruction of past climate probably faces less methodological problems if information from different proxies is available. The internal climatic variability at regional scales is, however, high. In this contribution some examples of the different issues faced when comparing simulation and reconstructions at small spatial scales in the past millennium are discussed. These examples comprise reconstructions from dendrochronological data and from historical documentary data in Europe and climate simulations with global and regional models. These examples indicate that the centennial climate variations can offer a reasonable target to assess the skill of global climate models and of proxy-based reconstructions, even at small spatial scales

Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens by Using Proteomic Data from a Field Biostimulation Experiment

Science.gov (United States)

Fang, Yilin; Yabusaki, Steven B.; Lipton, Mary S.; Long, Philip E.

2012-01-01

Accurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within an in silico model using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model of Geobacter metallireducens—specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment. PMID:23042184

Muon reconstruction performance in ATLAS at Run 2

CERN Document Server

Lesage, Arthur; The ATLAS collaboration

2016-01-01

This article documents the performance of the ATLAS muon identification and reconstruction using the first LHC dataset recorded at $\\sqrt{s} = 13$ TeV in 2015. Using a large sample of $J/\\psi\\rightarrow\\mu\\mu$ and $Z\\rightarrow\\mu\\mu$ decays, measurements of the reconstruction efficiency, as well as of the momentum scale and resolution, are presented and compared to Monte Carlo simulations. The reconstruction efficiency is measured to be close to $99\\%$ over most of the covered phase space ($|\\eta| 2.2$, the $p_{\\text{T}}$ resolution for a typical muon from $Z\\rightarrow\\mu\\mu$ decays is $2.9\\%$ while the precision on the momentum scale for low-$p_{\\text{T}}$ muons from $J/\\psi\\rightarrow\\mu\\mu$ decays is about $0.2\\%$.

Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism

Science.gov (United States)

2016-03-15

RESEARCH ARTICLE Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism Francisco G...jaques.reifman.civ@mail.mil Abstract A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm -based infections that are difficult to...eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic

Metabolism and disease

National Research Council Canada - National Science Library

Grodzicker, Terri; Stewart, David J; Stillman, Bruce

2011-01-01

...), cellular, organ system (cardiovascular, bone), and organismal (timing and life span) scales. Diseases impacted by metabolic imbalance or dysregulation that were covered in detail included diabetes, obesity, metabolic syndrome, and cancer...

RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

Science.gov (United States)

Novichkov, Pavel S; Kazakov, Alexey E; Ravcheev, Dmitry A; Leyn, Semen A; Kovaleva, Galina Y; Sutormin, Roman A; Kazanov, Marat D; Riehl, William; Arkin, Adam P; Dubchak, Inna; Rodionov, Dmitry A

2013-11-01

Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches). RegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes. RegPrecise 3.0 gives access to the transcriptional regulons reconstructed in

Weak lensing galaxy cluster field reconstruction

Science.gov (United States)

Jullo, E.; Pires, S.; Jauzac, M.; Kneib, J.-P.

2014-02-01

In this paper, we compare three methods to reconstruct galaxy cluster density fields with weak lensing data. The first method called FLens integrates an inpainting concept to invert the shear field with possible gaps, and a multi-scale entropy denoising procedure to remove the noise contained in the final reconstruction, that arises mostly from the random intrinsic shape of the galaxies. The second and third methods are based on a model of the density field made of a multi-scale grid of radial basis functions. In one case, the model parameters are computed with a linear inversion involving a singular value decomposition (SVD). In the other case, the model parameters are estimated using a Bayesian Monte Carlo Markov Chain optimization implemented in the lensing software LENSTOOL. Methods are compared on simulated data with varying galaxy density fields. We pay particular attention to the errors estimated with resampling. We find the multi-scale grid model optimized with Monte Carlo Markov Chain to provide the best results, but at high computational cost, especially when considering resampling. The SVD method is much faster but yields noisy maps, although this can be mitigated with resampling. The FLens method is a good compromise with fast computation, high signal-to-noise ratio reconstruction, but lower resolution maps. All three methods are applied to the MACS J0717+3745 galaxy cluster field, and reveal the filamentary structure discovered in Jauzac et al. We conclude that sensitive priors can help to get high signal-to-noise ratio, and unbiased reconstructions.

Computing the functional proteome

DEFF Research Database (Denmark)

O'Brien, Edward J.; Palsson, Bernhard

2015-01-01

Constraint-based models enable the computation of feasible, optimal, and realized biological phenotypes from reaction network reconstructions and constraints on their operation. To date, stoichiometric reconstructions have largely focused on metabolism, resulting in genome-scale metabolic models (M...

Catalonia's energy metabolism: Using the MuSIASEM approach at different scales

International Nuclear Information System (INIS)

Ramos-Martin, Jesus; Canellas-Bolta, Silvia; Giampietro, Mario; Gamboa, Gonzalo

2009-01-01

This paper applies the so-called Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism (MuSIASEM), based on Georgescu-Roegen's fund-flow model, to the Spanish region of Catalonia. It arrives to the conclusion that within the context of the end of cheap oil, the current development model of the Catalan economy, based on the growth of low-productivity sectors such as services and construction, must be changed. The change is needed not only because of the increasing scarcity of affordable energy and the increasing environmental impact of present development, but also because of the aging population. Moreover, the situation experienced by Catalonia is similar to that of other European countries and many other developed countries. This implies that we can expect a wave of major structural changes in the economy of developed countries worldwide. To make things more challenging, according to current trends, the energy intensity and exosomatic energy metabolism of Catalonia will keep increasing in the near future. To avoid a reduction in the standard of living of Catalans due to a reduction in the available energy it is important that the Government of Catalonia implement major adjustments and conservation efforts in both the household and paid-work sectors.

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model

NARCIS (Netherlands)

Teusink, B.; Wiersma, A.; Molenaar, D.; Francke, C.; Vos, de W.M.; Siezen, R.J.; Smid, E.J.

2006-01-01

A genome-scale metabolic model of the lactic acid bacterium Lactobacillus plantarum WCFS1 was constructed based on genomic content and experimental data. The complete model includes 721 genes, 643 reactions, and 531 metabolites. Different stoichiometric modeling techniques were used for

Flux Balance Analysis of Cyanobacterial Metabolism.The Metabolic Network of Synechocystis sp. PCC 6803

Czech Academy of Sciences Publication Activity Database

Knoop, H.; Gründel, M.; Zilliges, Y.; Lehmann, R.; Hoffmann, S.; Lockau, W.; Steuer, Ralf

2013-01-01

Roč. 9, č. 6 (2013), e1003081-e1003081 ISSN 1553-7358 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : SP STRAIN PCC-6803 * SP ATCC 51142 * photoautotrophic metabolism * anacystis-nidulans * reconstructions * pathway * plants * models * growth Subject RIV: EI - Biotechnology ; Bionics Impact factor: 4.829, year: 2013

Microbial community assembly and metabolic function during mammalian corpse decomposition

Energy Technology Data Exchange (ETDEWEB)

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.; Lax, S.; Van Treuren, W.; Hyde, E. R.; Song, S. J.; Amir, A.; Larsen, P.; Sangwan, N.; Haarmann, D.; Humphrey, G. C.; Ackermann, G.; Thompson, L. R.; Lauber, C.; Bibat, A.; Nicholas, C.; Gebert, M. J.; Petrosino, J. F.; Reed, S. C.; Gilbert, J. A.; Lynne, A. M.; Bucheli, S. R.; Carter, D. O.; Knight, R.

2015-12-10

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Microbial community assembly and metabolic function during mammalian corpse decomposition

Science.gov (United States)

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-01

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Metabolic modeling of synthesis gas fermentation in bubble column reactors.

Science.gov (United States)

Chen, Jin; Gomez, Jose A; Höffner, Kai; Barton, Paul I; Henson, Michael A

2015-01-01

A promising route to renewable liquid fuels and chemicals is the fermentation of synthesis gas (syngas) streams to synthesize desired products such as ethanol and 2,3-butanediol. While commercial development of syngas fermentation technology is underway, an unmet need is the development of integrated metabolic and transport models for industrially relevant syngas bubble column reactors. We developed and evaluated a spatiotemporal metabolic model for bubble column reactors with the syngas fermenting bacterium Clostridium ljungdahlii as the microbial catalyst. Our modeling approach involved combining a genome-scale reconstruction of C. ljungdahlii metabolism with multiphase transport equations that govern convective and dispersive processes within the spatially varying column. The reactor model was spatially discretized to yield a large set of ordinary differential equations (ODEs) in time with embedded linear programs (LPs) and solved using the MATLAB based code DFBAlab. Simulations were performed to analyze the effects of important process and cellular parameters on key measures of reactor performance including ethanol titer, ethanol-to-acetate ratio, and CO and H2 conversions. Our computational study demonstrated that mathematical modeling provides a complementary tool to experimentation for understanding, predicting, and optimizing syngas fermentation reactors. These model predictions could guide future cellular and process engineering efforts aimed at alleviating bottlenecks to biochemical production in syngas bubble column reactors.

Pediatric 320-row cardiac computed tomography using electrocardiogram-gated model-based full iterative reconstruction

Energy Technology Data Exchange (ETDEWEB)

Shirota, Go; Maeda, Eriko; Namiki, Yoko; Bari, Razibul; Abe, Osamu [The University of Tokyo, Department of Radiology, Graduate School of Medicine, Tokyo (Japan); Ino, Kenji [The University of Tokyo Hospital, Imaging Center, Tokyo (Japan); Torigoe, Rumiko [Toshiba Medical Systems, Tokyo (Japan)

2017-10-15

Full iterative reconstruction algorithm is available, but its diagnostic quality in pediatric cardiac CT is unknown. To compare the imaging quality of two algorithms, full and hybrid iterative reconstruction, in pediatric cardiac CT. We included 49 children with congenital cardiac anomalies who underwent cardiac CT. We compared quality of images reconstructed using the two algorithms (full and hybrid iterative reconstruction) based on a 3-point scale for the delineation of the following anatomical structures: atrial septum, ventricular septum, right atrium, right ventricle, left atrium, left ventricle, main pulmonary artery, ascending aorta, aortic arch including the patent ductus arteriosus, descending aorta, right coronary artery and left main trunk. We evaluated beam-hardening artifacts from contrast-enhancement material using a 3-point scale, and we evaluated the overall image quality using a 5-point scale. We also compared image noise, signal-to-noise ratio and contrast-to-noise ratio between the algorithms. The overall image quality was significantly higher with full iterative reconstruction than with hybrid iterative reconstruction (3.67±0.79 vs. 3.31±0.89, P=0.0072). The evaluation scores for most of the gross structures were higher with full iterative reconstruction than with hybrid iterative reconstruction. There was no significant difference between full and hybrid iterative reconstruction for the presence of beam-hardening artifacts. Image noise was significantly lower in full iterative reconstruction, while signal-to-noise ratio and contrast-to-noise ratio were significantly higher in full iterative reconstruction. The diagnostic quality was superior in images with cardiac CT reconstructed with electrocardiogram-gated full iterative reconstruction. (orig.)

Pediatric 320-row cardiac computed tomography using electrocardiogram-gated model-based full iterative reconstruction

International Nuclear Information System (INIS)

Shirota, Go; Maeda, Eriko; Namiki, Yoko; Bari, Razibul; Abe, Osamu; Ino, Kenji; Torigoe, Rumiko

2017-01-01

Full iterative reconstruction algorithm is available, but its diagnostic quality in pediatric cardiac CT is unknown. To compare the imaging quality of two algorithms, full and hybrid iterative reconstruction, in pediatric cardiac CT. We included 49 children with congenital cardiac anomalies who underwent cardiac CT. We compared quality of images reconstructed using the two algorithms (full and hybrid iterative reconstruction) based on a 3-point scale for the delineation of the following anatomical structures: atrial septum, ventricular septum, right atrium, right ventricle, left atrium, left ventricle, main pulmonary artery, ascending aorta, aortic arch including the patent ductus arteriosus, descending aorta, right coronary artery and left main trunk. We evaluated beam-hardening artifacts from contrast-enhancement material using a 3-point scale, and we evaluated the overall image quality using a 5-point scale. We also compared image noise, signal-to-noise ratio and contrast-to-noise ratio between the algorithms. The overall image quality was significantly higher with full iterative reconstruction than with hybrid iterative reconstruction (3.67±0.79 vs. 3.31±0.89, P=0.0072). The evaluation scores for most of the gross structures were higher with full iterative reconstruction than with hybrid iterative reconstruction. There was no significant difference between full and hybrid iterative reconstruction for the presence of beam-hardening artifacts. Image noise was significantly lower in full iterative reconstruction, while signal-to-noise ratio and contrast-to-noise ratio were significantly higher in full iterative reconstruction. The diagnostic quality was superior in images with cardiac CT reconstructed with electrocardiogram-gated full iterative reconstruction. (orig.)

Evaluation of proxy-based millennial reconstruction methods

Energy Technology Data Exchange (ETDEWEB)

Lee, Terry C.K.; Tsao, Min [University of Victoria, Department of Mathematics and Statistics, Victoria, BC (Canada); Zwiers, Francis W. [Environment Canada, Climate Research Division, Toronto, ON (Canada)

2008-08-15

A range of existing statistical approaches for reconstructing historical temperature variations from proxy data are compared using both climate model data and real-world paleoclimate proxy data. We also propose a new method for reconstruction that is based on a state-space time series model and Kalman filter algorithm. The state-space modelling approach and the recently developed RegEM method generally perform better than their competitors when reconstructing interannual variations in Northern Hemispheric mean surface air temperature. On the other hand, a variety of methods are seen to perform well when reconstructing surface air temperature variability on decadal time scales. An advantage of the new method is that it can incorporate additional, non-temperature, information into the reconstruction, such as the estimated response to external forcing, thereby permitting a simultaneous reconstruction and detection analysis as well as future projection. An application of these extensions is also demonstrated in the paper. (orig.)

Industrial dynamic tomographic reconstruction

International Nuclear Information System (INIS)

Oliveira, Eric Ferreira de

2016-01-01

The state of the art methods applied to industrial processes is currently based on the principles of classical tomographic reconstructions developed for tomographic patterns of static distributions, or is limited to cases of low variability of the density distribution function of the tomographed object. Noise and motion artifacts are the main problems caused by a mismatch in the data from views acquired in different instants. All of these add to the known fact that using a limited amount of data can result in the presence of noise, artifacts and some inconsistencies with the distribution under study. One of the objectives of the present work is to discuss the difficulties that arise from implementing reconstruction algorithms in dynamic tomography that were originally developed for static distributions. Another objective is to propose solutions that aim at reducing a temporal type of information loss caused by employing regular acquisition systems to dynamic processes. With respect to dynamic image reconstruction it was conducted a comparison between different static reconstruction methods, like MART and FBP, when used for dynamic scenarios. This comparison was based on a MCNPx simulation as well as an analytical setup of an aluminum cylinder that moves along the section of a riser during the process of acquisition, and also based on cross section images from CFD techniques. As for the adaptation of current tomographic acquisition systems for dynamic processes, this work established a sequence of tomographic views in a just-in-time fashion for visualization purposes, a form of visually disposing density information as soon as it becomes amenable to image reconstruction. A third contribution was to take advantage of the triple color channel necessary to display colored images in most displays, so that, by appropriately scaling the acquired values of each view in the linear system of the reconstruction, it was possible to imprint a temporal trace into the regularly

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions

DEFF Research Database (Denmark)

Kavvas, Erol S.; Seif, Yara; Yurkovich, James T.

2018-01-01

previous M. tuberculosis H37Rv genome-scale reconstructions. We functionally assess iEK1011 against previous models and show that the model increases correct gene essentiality predictions on two different experimental datasets by 6% (53% to 60%) and 18% (60% to 71%), respectively. We compared simulations...

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.

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

David Knies

2015-10-01

Full Text Available 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.

Image quality of iterative reconstruction in cranial CT imaging: comparison of model-based iterative reconstruction (MBIR) and adaptive statistical iterative reconstruction (ASiR).

Science.gov (United States)

Notohamiprodjo, S; Deak, Z; Meurer, F; Maertz, F; Mueck, F G; Geyer, L L; Wirth, S

2015-01-01

The purpose of this study was to compare cranial CT (CCT) image quality (IQ) of the MBIR algorithm with standard iterative reconstruction (ASiR). In this institutional review board (IRB)-approved study, raw data sets of 100 unenhanced CCT examinations (120 kV, 50-260 mAs, 20 mm collimation, 0.984 pitch) were reconstructed with both ASiR and MBIR. Signal-to-noise (SNR) and contrast-to-noise (CNR) were calculated from attenuation values measured in caudate nucleus, frontal white matter, anterior ventricle horn, fourth ventricle, and pons. Two radiologists, who were blinded to the reconstruction algorithms, evaluated anonymized multiplanar reformations of 2.5 mm with respect to depiction of different parenchymal structures and impact of artefacts on IQ with a five-point scale (0: unacceptable, 1: less than average, 2: average, 3: above average, 4: excellent). MBIR decreased artefacts more effectively than ASiR (p ASiR was 2 (p ASiR (p ASiR. As CCT is an examination that is frequently required, the use of MBIR may allow for substantial reduction of radiation exposure caused by medical diagnostics. • Model-Based iterative reconstruction (MBIR) effectively decreased artefacts in cranial CT. • MBIR reconstructed images were rated with significantly higher scores for image quality. • Model-Based iterative reconstruction may allow reduced-dose diagnostic examination protocols.

Voxel-based statistical analysis of cerebral glucose metabolism in the rat cortical deafness model by 3D reconstruction of brain from autoradiographic images

Energy Technology Data Exchange (ETDEWEB)

Lee, Jae Sung; Park, Kwang Suk [Seoul National University College of Medicine, Department of Nuclear Medicine, 28 Yungun-Dong, Chongno-Ku, Seoul (Korea); Seoul National University College of Medicine, Department of Biomedical Engineering, Seoul (Korea); Ahn, Soon-Hyun; Oh, Seung Ha; Kim, Chong Sun; Chung, June-Key; Lee, Myung Chul [Seoul National University College of Medicine, Department of Otolaryngology, Head and Neck Surgery, Seoul (Korea); Lee, Dong Soo; Jeong, Jae Min [Seoul National University College of Medicine, Department of Nuclear Medicine, 28 Yungun-Dong, Chongno-Ku, Seoul (Korea)

2005-06-01

any other area, and no area showed a significant increase in metabolism in the deaf rats with the same threshold, demonstrating the high localization accuracy and specificity of the method developed in this study. This study established new procedures for the 3D reconstruction and voxel-based analysis of autoradiographic data which will be useful for examining the cerebral glucose metabolism in a rat cortical deafness model. (orig.)

Voxel-based statistical analysis of cerebral glucose metabolism in the rat cortical deafness model by 3D reconstruction of brain from autoradiographic images

International Nuclear Information System (INIS)

Lee, Jae Sung; Park, Kwang Suk; Ahn, Soon-Hyun; Oh, Seung Ha; Kim, Chong Sun; Chung, June-Key; Lee, Myung Chul; Lee, Dong Soo; Jeong, Jae Min

2005-01-01

other area, and no area showed a significant increase in metabolism in the deaf rats with the same threshold, demonstrating the high localization accuracy and specificity of the method developed in this study. This study established new procedures for the 3D reconstruction and voxel-based analysis of autoradiographic data which will be useful for examining the cerebral glucose metabolism in a rat cortical deafness model. (orig.)

Integrated Approach to Reconstruction of Microbial Regulatory Networks

Energy Technology Data Exchange (ETDEWEB)

Rodionov, Dmitry A [Sanford-Burnham Medical Research Institute; Novichkov, Pavel S [Lawrence Berkeley National Laboratory

2013-11-04

This project had the goal(s) of development of integrated bioinformatics platform for genome-scale inference and visualization of transcriptional regulatory networks (TRNs) in bacterial genomes. The work was done in Sanford-Burnham Medical Research Institute (SBMRI, P.I. D.A. Rodionov) and Lawrence Berkeley National Laboratory (LBNL, co-P.I. P.S. Novichkov). The developed computational resources include: (1) RegPredict web-platform for TRN inference and regulon reconstruction in microbial genomes, and (2) RegPrecise database for collection, visualization and comparative analysis of transcriptional regulons reconstructed by comparative genomics. These analytical resources were selected as key components in the DOE Systems Biology KnowledgeBase (SBKB). The high-quality data accumulated in RegPrecise will provide essential datasets of reference regulons in diverse microbes to enable automatic reconstruction of draft TRNs in newly sequenced genomes. We outline our progress toward the three aims of this grant proposal, which were: Develop integrated platform for genome-scale regulon reconstruction; Infer regulatory annotations in several groups of bacteria and building of reference collections of microbial regulons; and Develop KnowledgeBase on microbial transcriptional regulation.

Scaling dynamic response and destructive metabolism in an immunosurveillant anti-tumor system modulated by different external periodic interventions.

Directory of Open Access Journals (Sweden)

Yuanzhi Shao

Full Text Available On the basis of two universal power-law scaling laws, i.e. the scaling dynamic hysteresis in physics and the allometric scaling metabolism in biosystem, we studied the dynamic response and the evolution of an immunosurveillant anti-tumor system subjected to a periodic external intervention, which is equivalent to the scheme of a radiotherapy or chemotherapy, within the framework of the growth dynamics of tumor. Under the modulation of either an abrupt or a gradual change external intervention, the population density of tumors exhibits a dynamic hysteresis to the intervention. The area of dynamic hysteresis loop characterizes a sort of dissipative-therapeutic relationship of the dynamic responding of treated tumors with the dose consumption of accumulated external intervention per cycle of therapy. Scaling the area of dynamic hysteresis loops against the intensity of an external intervention, we deduced a characteristic quantity which was defined as the theoretical therapeutic effectiveness of treated tumor and related with the destructive metabolism of tumor under treatment. The calculated dose-effectiveness profiles, namely the dose cumulant per cycle of intervention versus the therapeutic effectiveness, could be well scaled into a universal quadratic formula regardless of either an abrupt or a gradual change intervention involved. We present a new concept, i.e., the therapy-effect matrix and the dose cumulant matrix, to expound the new finding observed in the growth and regression dynamics of a modulated anti-tumor system.

Engineering Cellular Metabolism

DEFF Research Database (Denmark)

Nielsen, Jens; Keasling, Jay

2016-01-01

Metabolic engineering is the science of rewiring the metabolism of cells to enhance production of native metabolites or to endow cells with the ability to produce new products. The potential applications of such efforts are wide ranging, including the generation of fuels, chemicals, foods, feeds...... of metabolic engineering and will discuss how new technologies can enable metabolic engineering to be scaled up to the industrial level, either by cutting off the lines of control for endogenous metabolism or by infiltrating the system with disruptive, heterologous pathways that overcome cellular regulation....

Reconstruction of Single-Grain Orientation Distribution Functions for Crystalline Materials

DEFF Research Database (Denmark)

Hansen, Per Christian; Sørensen, Henning Osholm; Sükösd, Zsuzsanna

2009-01-01

for individual grains of the material in consideration. We study two iterative large-scale reconstruction algorithms, the algebraic reconstruction technique (ART) and conjugate gradients for least squares (CGLS), and demonstrate that right preconditioning is necessary in both algorithms to provide satisfactory...

Iterative reconstruction reduces abdominal CT dose

International Nuclear Information System (INIS)

Martinsen, Anne Catrine Trægde; Sæther, Hilde Kjernlie; Hol, Per Kristian; Olsen, Dag Rune; Skaane, Per

2012-01-01

Objective: In medical imaging, lowering radiation dose from computed tomography scanning, without reducing diagnostic performance is a desired achievement. Iterative image reconstruction may be one tool to achieve dose reduction. This study reports the diagnostic performance using a blending of 50% statistical iterative reconstruction (ASIR) and filtered back projection reconstruction (FBP) compared to standard FBP image reconstruction at different dose levels for liver phantom examinations. Methods: An anthropomorphic liver phantom was scanned at 250, 185, 155, 140, 120 and 100 mA s, on a 64-slice GE Lightspeed VCT scanner. All scans were reconstructed with ASIR and FBP. Four readers evaluated independently on a 5-point scale 21 images, each containing 32 test sectors. In total 672 areas were assessed. ROC analysis was used to evaluate the differences. Results: There was a difference in AUC between the 250 mA s FBP images and the 120 and 100 mA s FBP images. ASIR reconstruction gave a significantly higher diagnostic performance compared to standard reconstruction at 100 mA s. Conclusion: A blending of 50–90% ASIR and FBP may improve image quality of low dose CT examinations of the liver, and thus give a potential for reducing radiation dose.

Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data.

Science.gov (United States)

Gu, Deqing; Jian, Xingxing; Zhang, Cheng; Hua, Qiang

2017-01-01

Genome-scale metabolic network models (GEMs) have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, most algorithms have limited capabilities with respect to directly predicting accurate genetic design for metabolic engineering. In particular, methods that predict reaction knockout strategies leading to overproduction are often impractical in terms of gene manipulations. Recently, we proposed a method named logical transformation of model (LTM) to simplify the gene-reaction associations by introducing intermediate pseudo reactions, which makes it possible to generate genetic design. Here, we propose an alternative method to relieve researchers from deciphering complex gene-reactions by adding pseudo gene controlling reactions. In comparison to LTM, this new method introduces fewer pseudo reactions and generates a much smaller model system named as gModel. We showed that gModel allows two seldom reported applications: identification of minimal genomes and design of minimal cell factories within a modified OptKnock framework. In addition, gModel could be used to integrate expression data directly and improve the performance of the E-Fmin method for predicting fluxes. In conclusion, the model transformation procedure will facilitate genetic research based on GEMs, extending their applications.

Ranking of tree-ring based temperature reconstructions of the past millennium

Science.gov (United States)

Esper, Jan; Krusic, Paul J.; Ljungqvist, Fredrik C.; Luterbacher, Jürg; Carrer, Marco; Cook, Ed; Davi, Nicole K.; Hartl-Meier, Claudia; Kirdyanov, Alexander; Konter, Oliver; Myglan, Vladimir; Timonen, Mauri; Treydte, Kerstin; Trouet, Valerie; Villalba, Ricardo; Yang, Bao; Büntgen, Ulf

2016-08-01

Tree-ring chronologies are widely used to reconstruct high-to low-frequency variations in growing season temperatures over centuries to millennia. The relevance of these timeseries in large-scale climate reconstructions is often determined by the strength of their correlation against instrumental temperature data. However, this single criterion ignores several important quantitative and qualitative characteristics of tree-ring chronologies. Those characteristics are (i) data homogeneity, (ii) sample replication, (iii) growth coherence, (iv) chronology development, and (v) climate signal including the correlation with instrumental data. Based on these 5 characteristics, a reconstruction-scoring scheme is proposed and applied to 39 published, millennial-length temperature reconstructions from Asia, Europe, North America, and the Southern Hemisphere. Results reveal no reconstruction scores highest in every category and each has their own strengths and weaknesses. Reconstructions that perform better overall include N-Scan and Finland from Europe, E-Canada from North America, Yamal and Dzhelo from Asia. Reconstructions performing less well include W-Himalaya and Karakorum from Asia, Tatra and S-Finland from Europe, and Great Basin from North America. By providing a comprehensive set of criteria to evaluate tree-ring chronologies we hope to improve the development of large-scale temperature reconstructions spanning the past millennium. All reconstructions and their corresponding scores are provided at http://www.blogs.uni-mainz.de/fb09climatology.

ReacKnock: identifying reaction deletion strategies for microbial strain optimization based on genome-scale metabolic network.

Directory of Open Access Journals (Sweden)

Zixiang Xu

Full Text Available Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective.

Reconstructing European forest management from 1600 to 2010

Science.gov (United States)

McGrath, M. J.; Luyssaert, S.; Meyfroidt, P.; Kaplan, J. O.; Buergi, M.; Chen, Y.; Erb, K.; Gimmi, U.; McInerney, D.; Naudts, K.; Otto, J.; Pasztor, F.; Ryder, J.; Schelhaas, M.-J.; Valade, A.

2015-04-01

European forest use for fuel, timber and food dates back to pre-Roman times. Century-scale ecological processes and their legacy effects require accounting for forest management when studying today's forest carbon sink. Forest management reconstructions that are used to drive land surface models are one way to quantify the impact of both historical and today's large scale application of forest management on today's forest-related carbon sink and surface climate. In this study we reconstruct European forest management from 1600 to 2010 making use of diverse approaches, data sources and assumptions. Between 1600 and 1828, a demand-supply approach was used in which wood supply was reconstructed based on estimates of historical annual wood increment and land cover reconstructions. For the same period demand estimates accounted for the fuelwood needed in households, wood used in food processing, charcoal used in metal smelting and salt production, timber for construction and population estimates. Comparing estimated demand and supply resulted in a spatially explicit reconstruction of the share of forests under coppice, high stand management and forest left unmanaged. For the reconstruction between 1829 and 2010 a supply-driven back-casting method was used. The method used age reconstructions from the years 1950 to 2010 as its starting point. Our reconstruction reproduces the most important changes in forest management between 1600 and 2010: (1) an increase of 593 000 km2 in conifers at the expense of deciduous forest (decreasing by 538 000 km2), (2) a 612 000 km2 decrease in unmanaged forest, (3) a 152 000 km2 decrease in coppice management, (4) a 818 000 km2 increase in high stand management, and (5) the rise and fall of litter raking which at its peak in 1853 removed 50 Tg dry litter per year.

Parallel CT image reconstruction based on GPUs

International Nuclear Information System (INIS)

Flores, Liubov A.; Vidal, Vicent; Mayo, Patricia; Rodenas, Francisco; Verdú, Gumersindo

2014-01-01

In X-ray computed tomography (CT) iterative methods are more suitable for the reconstruction of images with high contrast and precision in noisy conditions from a small number of projections. However, in practice, these methods are not widely used due to the high computational cost of their implementation. Nowadays technology provides the possibility to reduce effectively this drawback. It is the goal of this work to develop a fast GPU-based algorithm to reconstruct high quality images from under sampled and noisy projection data. - Highlights: • We developed GPU-based iterative algorithm to reconstruct images. • Iterative algorithms are capable to reconstruct images from under sampled set of projections. • The computer cost of the implementation of the developed algorithm is low. • The efficiency of the algorithm increases for the large scale problems

Reconstructing baryon oscillations: A Lagrangian theory perspective

International Nuclear Information System (INIS)

Padmanabhan, Nikhil; White, Martin; Cohn, J. D.

2009-01-01

Recently Eisenstein and collaborators introduced a method to 'reconstruct' the linear power spectrum from a nonlinearly evolved galaxy distribution in order to improve precision in measurements of baryon acoustic oscillations. We reformulate this method within the Lagrangian picture of structure formation, to better understand what such a method does, and what the resulting power spectra are. We show that reconstruction does not reproduce the linear density field, at second order. We however show that it does reduce the damping of the oscillations due to nonlinear structure formation, explaining the improvements seen in simulations. Our results suggest that the reconstructed power spectrum is potentially better modeled as the sum of three different power spectra, each dominating over different wavelength ranges and with different nonlinear damping terms. Finally, we also show that reconstruction reduces the mode-coupling term in the power spectrum, explaining why miscalibrations of the acoustic scale are reduced when one considers the reconstructed power spectrum.

3D reconstruction based on light field images

Science.gov (United States)

Zhu, Dong; Wu, Chunhong; Liu, Yunluo; Fu, Dongmei

2018-04-01

This paper proposed a method of reconstructing three-dimensional (3D) scene from two light field images capture by Lytro illium. The work was carried out by first extracting the sub-aperture images from light field images and using the scale-invariant feature transform (SIFT) for feature registration on the selected sub-aperture images. Structure from motion (SFM) algorithm is further used on the registration completed sub-aperture images to reconstruct the three-dimensional scene. 3D sparse point cloud was obtained in the end. The method shows that the 3D reconstruction can be implemented by only two light field camera captures, rather than at least a dozen times captures by traditional cameras. This can effectively solve the time-consuming, laborious issues for 3D reconstruction based on traditional digital cameras, to achieve a more rapid, convenient and accurate reconstruction.

Acellular dermal matrix based nipple reconstruction: A modified technique

Directory of Open Access Journals (Sweden)

Raghavan Vidya

2017-09-01

Full Text Available Nipple areolar reconstruction (NAR has evolved with the advancement in breast reconstruction and can improve self-esteem and, consequently, patient satisfaction. Although a variety of reconstruction techniques have been described in the literature varying from nipple sharing, local flaps to alloplastic and allograft augmentation, over time, loss of nipple projection remains a major problem. Acellular dermal matrices (ADM have revolutionised breast reconstruction more recently. We discuss the use of ADM to act as a base plate and strut to give support to the base and offer nipple bulk and projection in a primary procedure of NAR with a local clover shaped dermal flap in 5 breasts (4 patients. We used 5-point Likert scales (1 = highly unsatisfied, 5 = highly satisfied to assess patient satisfaction. Median age was 46 years (range: 38–55 years. Nipple projection of 8 mm, 7 mm, and 7 mms were achieved in the unilateral cases and 6 mm in the bilateral case over a median 18 month period. All patients reported at least a 4 on the Likert scale. We had no post-operative complications. It seems that nipple areolar reconstruction [NAR] using ADM can achieve nipple projection which is considered aesthetically pleasing for patients.

Dynamic Metabolic Footprinting Reveals the Key Components of Metabolic Network in Yeast Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Chumnanpuen, Pramote; Hansen, Michael Adsetts Edberg; Smedsgaard, Jørn

2014-01-01

relies on analysis at a single time point. Using direct infusion-mass spectrometry (DI-MS), we could observe the dynamic metabolic footprinting in yeast S. cerevisiae BY4709 (wild type) cultured on 3 different C-sources (glucose, glycerol, and ethanol) and sampled along 10 time points with 5 biological...... replicates. In order to analyze the dynamic mass spectrometry data, we developed the novel analysis methods that allow us to perform correlation analysis to identify metabolites that significantly correlate over time during growth on the different carbon sources. Both positive and negative electrospray...... reconstructed an interaction map that provides information of how different metabolic pathways have correlated patterns during growth on the different carbon sources....

Joint reconstruction of activity and attenuation in Time-of-Flight PET: A Quantitative Analysis.

Science.gov (United States)

Rezaei, Ahmadreza; Deroose, Christophe M; Vahle, Thomas; Boada, Fernando; Nuyts, Johan

2018-03-01

Joint activity and attenuation reconstruction methods from time of flight (TOF) positron emission tomography (PET) data provide an effective solution to attenuation correction when no (or incomplete/inaccurate) information on the attenuation is available. One of the main barriers limiting their use in clinical practice is the lack of validation of these methods on a relatively large patient database. In this contribution, we aim at validating the activity reconstructions of the maximum likelihood activity reconstruction and attenuation registration (MLRR) algorithm on a whole-body patient data set. Furthermore, a partial validation (since the scale problem of the algorithm is avoided for now) of the maximum likelihood activity and attenuation reconstruction (MLAA) algorithm is also provided. We present a quantitative comparison of the joint reconstructions to the current clinical gold-standard maximum likelihood expectation maximization (MLEM) reconstruction with CT-based attenuation correction. Methods: The whole-body TOF-PET emission data of each patient data set is processed as a whole to reconstruct an activity volume covering all the acquired bed positions, which helps to reduce the problem of a scale per bed position in MLAA to a global scale for the entire activity volume. Three reconstruction algorithms are used: MLEM, MLRR and MLAA. A maximum likelihood (ML) scaling of the single scatter simulation (SSS) estimate to the emission data is used for scatter correction. The reconstruction results are then analyzed in different regions of interest. Results: The joint reconstructions of the whole-body patient data set provide better quantification in case of PET and CT misalignments caused by patient and organ motion. Our quantitative analysis shows a difference of -4.2% (±2.3%) and -7.5% (±4.6%) between the joint reconstructions of MLRR and MLAA compared to MLEM, averaged over all regions of interest, respectively. Conclusion: Joint activity and attenuation

Last millennium Northern Hemisphere summer temperatures from tree rings: Part II, spatially resolved reconstructions

Science.gov (United States)

Anchukaitis, Kevin J.; Wilson, Rob; Briffa, Keith R.; Büntgen, Ulf; Cook, Edward R.; D'Arrigo, Rosanne; Davi, Nicole; Esper, Jan; Frank, David; Gunnarson, Björn E.; Hegerl, Gabi; Helama, Samuli; Klesse, Stefan; Krusic, Paul J.; Linderholm, Hans W.; Myglan, Vladimir; Osborn, Timothy J.; Zhang, Peng; Rydval, Milos; Schneider, Lea; Schurer, Andrew; Wiles, Greg; Zorita, Eduardo

2017-05-01

Climate field reconstructions from networks of tree-ring proxy data can be used to characterize regional-scale climate changes, reveal spatial anomaly patterns associated with atmospheric circulation changes, radiative forcing, and large-scale modes of ocean-atmosphere variability, and provide spatiotemporal targets for climate model comparison and evaluation. Here we use a multiproxy network of tree-ring chronologies to reconstruct spatially resolved warm season (May-August) mean temperatures across the extratropical Northern Hemisphere (40-90°N) using Point-by-Point Regression (PPR). The resulting annual maps of temperature anomalies (750-1988 CE) reveal a consistent imprint of volcanism, with 96% of reconstructed grid points experiencing colder conditions following eruptions. Solar influences are detected at the bicentennial (de Vries) frequency, although at other time scales the influence of insolation variability is weak. Approximately 90% of reconstructed grid points show warmer temperatures during the Medieval Climate Anomaly when compared to the Little Ice Age, although the magnitude varies spatially across the hemisphere. Estimates of field reconstruction skill through time and over space can guide future temporal extension and spatial expansion of the proxy network.

Baryon Acoustic Oscillations reconstruction with pixels

Energy Technology Data Exchange (ETDEWEB)

Obuljen, Andrej [SISSA—International School for Advanced Studies, Via Bonomea 265, 34136 Trieste (Italy); Villaescusa-Navarro, Francisco [Center for Computational Astrophysics, 160 5th Ave, New York, NY, 10010 (United States); Castorina, Emanuele [Berkeley Center for Cosmological Physics, University of California, Berkeley, CA 94720 (United States); Viel, Matteo, E-mail: aobuljen@sissa.it, E-mail: fvillaescusa@simonsfoundation.org, E-mail: ecastorina@berkeley.edu, E-mail: viel@oats.inaf.it [INAF, Osservatorio Astronomico di Trieste, via Tiepolo 11, I-34131 Trieste (Italy)

2017-09-01

Gravitational non-linear evolution induces a shift in the position of the baryon acoustic oscillations (BAO) peak together with a damping and broadening of its shape that bias and degrades the accuracy with which the position of the peak can be determined. BAO reconstruction is a technique developed to undo part of the effect of non-linearities. We present and analyse a reconstruction method that consists of displacing pixels instead of galaxies and whose implementation is easier than the standard reconstruction method. We show that this method is equivalent to the standard reconstruction technique in the limit where the number of pixels becomes very large. This method is particularly useful in surveys where individual galaxies are not resolved, as in 21cm intensity mapping observations. We validate this method by reconstructing mock pixelated maps, that we build from the distribution of matter and halos in real- and redshift-space, from a large set of numerical simulations. We find that this method is able to decrease the uncertainty in the BAO peak position by 30-50% over the typical angular resolution scales of 21 cm intensity mapping experiments.

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Directory of Open Access Journals (Sweden)

Xing-Xing Shen

2016-12-01

Full Text Available Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence and two data matrices (amino acids or the first two codon positions yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

Science.gov (United States)

Shen, Xing-Xing; Zhou, Xiaofan; Kominek, Jacek; Kurtzman, Cletus P.; Hittinger, Chris Todd; Rokas, Antonis

2016-01-01

Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast. PMID:27672114

Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain.

NARCIS (Netherlands)

Gavai, Anand K.; Supandi, Farahaniza; Hettling, Hannes; Murell, Paul; Leunissen, Jack A.M.; van Beek, Johannes H.G.M.

2015-01-01

Predicting the distribution of metabolic fluxes in biochemical networks is of major interest in systems biology. Several databases provide metabolic reconstructions for different organisms. Software to analyze flux distributions exists, among others for the proprietary MATLAB environment. Given the

Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain

NARCIS (Netherlands)

Gavai, A.K.; Supandi, F.; Hettling, H.; Murrell, P.; Leunissen, J.A.M.; Beek, van J.H.G.M.

2015-01-01

Predicting the distribution of metabolic fluxes in biochemical networks is of major interest in systems biology. Several databases provide metabolic reconstructions for different organisms. Software to analyze flux distributions exists, among others for the proprietary MATLAB environment. Given the

The Impact of Facial Aesthetic and Reconstructive Surgeries on Patients' Quality of Life.

Science.gov (United States)

Yıldız, Tülin; Selimen, Deniz

2015-12-01

The aim of the present prospective and descriptive study was to assess the impact of facial aesthetic and reconstructive surgeries on quality of life. Ninety-one patients, of whom 43 had aesthetic surgery and 48 had reconstructive surgery, were analysed. The data were collected using the patient information form, body cathexis scale, and short form (SF)-36 quality of life scale. There were significant differences between before and after the surgery in both groups in terms of body cathexis scale and quality of life (p aesthetic and reconstructive surgery patients before the surgery. However, the problems were decreased, and the quality of life was enhanced after the surgery. Among the parameters of SF-36 quality of life scale, particularly the mean scores of social functioning, physical role functioning, emotional role functioning, mental health, and vitality/fatigue were found low before the surgery, whereas the mean scores were significantly improved after the surgery. The results revealed that facial aesthetic and reconstructive surgical interventions favourably affected the body image perception and self-esteem and that positive reflections in emotional, social, and mental aspects were effective in enhancing self-confidence and quality of life of the individual.

Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes

DEFF Research Database (Denmark)

Zelezniak, Aleksej; Pers, Tune Hannes; Pinho Soares, Simao Pedro

2010-01-01

mechanisms underlying these transcriptional changes and their impact on the cellular metabolic phenotype is a challenging task due to the complexity of transcriptional regulation and the highly interconnected nature of the metabolic network. In this study we integrate skeletal muscle gene expression datasets...... with human metabolic network reconstructions to identify key metabolic regulatory features of T2DM. These features include reporter metabolites—metabolites with significant collective transcriptional response in the associated enzyme-coding genes, and transcription factors with significant enrichment...... factor regulatory network connecting several parts of metabolism. The identified transcription factors include members of the CREB, NRF1 and PPAR family, among others, and represent regulatory targets for further experimental analysis. Overall, our results provide a holistic picture of key metabolic...

Lensing reconstruction from a patchwork of polarization maps

International Nuclear Information System (INIS)

Namikawa, Toshiya; Nagata, Ryo

2014-01-01

The lensing signals involved in CMB polarization maps have already been measured with ground-based experiments such as SPTpol and POLARBEAR, and would become important as a probe of cosmological and astrophysical issues in the near future. Sizes of polarization maps from ground-based experiments are, however, limited by contamination of long wavelength modes of observational noise. To further extract the lensing signals, we explore feasibility of measuring lensing signals from a collection of small sky maps each of which is observed separately by a ground-based large telescope, i.e., lensing reconstruction from a patchwork map of large sky coverage organized from small sky patches. We show that, although the B-mode power spectrum obtained from the patchwork map is biased due to baseline uncertainty, bias on the lensing potential would be negligible if the B-mode on scales larger than the blowup scale of 1/f noise is removed in the lensing reconstruction. As examples of cosmological applications, we also show 1) the cross-correlations between the reconstructed lensing potential and full-sky temperature/polarization maps from satellite missions such as PLANCK and LiteBIRD, and 2) the use of the reconstructed potential for delensing B-mode polarization of LiteBIRD observation

Light-flavor squark reconstruction at CLIC

CERN Document Server

AUTHOR|(SzGeCERN)548062; Weuste, Lars

2015-01-01

We present a simulation study of the prospects for the mass measurement of TeV-scale light- flavored right-handed squark at a 3 TeV e+e collider based on CLIC technology. The analysis is based on full GEANT4 simulations of the CLIC_ILD detector concept, including Standard Model physics backgrounds and beam-induced hadronic backgrounds from two- photon processes. The analysis serves as a generic benchmark for the reconstruction of highly energetic jets in events with substantial missing energy. Several jet finding algorithms were evaluated, with the longitudinally invariant kt algorithm showing a high degree of robustness towards beam-induced background while preserving the features typically found in algorithms developed for e+e- collisions. The presented study of the reconstruction of light-flavored squarks shows that for TeV-scale squark masses, sub-percent accuracy on the mass measurement can be achieved at CLIC.

LUMINOUS RED GALAXY HALO DENSITY FIELD RECONSTRUCTION AND APPLICATION TO LARGE-SCALE STRUCTURE MEASUREMENTS

International Nuclear Information System (INIS)

Reid, Beth A.; Spergel, David N.; Bode, Paul

2009-01-01

The nontrivial relationship between observations of galaxy positions in redshift space and the underlying matter field complicates our ability to determine the linear theory power spectrum and extract cosmological information from galaxy surveys. The Sloan Digital Sky Survey (SDSS) luminous red galaxy (LRG) catalog has the potential to place powerful constraints on cosmological parameters. LRGs are bright, highly biased tracers of large-scale structure. However, because they are highly biased, the nonlinear contribution of satellite galaxies to the galaxy power spectrum is large and fingers-of-God (FOGs) are significant. The combination of these effects leads to a ∼10% correction in the underlying power spectrum at k = 0.1 h Mpc -1 and ∼40% correction at k = 0.2 h Mpc -1 in the LRG P(k) analysis of Tegmark et al., thereby compromising the cosmological constraints when this potentially large correction is left as a free parameter. We propose an alternative approach to recovering the matter field from galaxy observations. Our approach is to use halos rather than galaxies to trace the underlying mass distribution. We identify FOGs and replace each FOG with a single halo object. This removes the nonlinear contribution of satellite galaxies, the one-halo term. We test our method on a large set of high-fidelity mock SDSS LRG catalogs and find that the power spectrum of the reconstructed halo density field deviates from the underlying matter power spectrum at the ≤1% level for k ≤ 0.1 h Mpc -1 and ≤4% at k = 0.2 h Mpc -1 . The reconstructed halo density field also removes the bias in the measurement of the redshift space distortion parameter β induced by the FOG smearing of the linear redshift space distortions.

Reconstruction of networks from one-step data by matching positions

Science.gov (United States)

Wu, Jianshe; Dang, Ni; Jiao, Yang

2018-05-01

It is a challenge in estimating the topology of a network from short time series data. In this paper, matching positions is developed to reconstruct the topology of a network from only one-step data. We consider a general network model of coupled agents, in which the phase transformation of each node is determined by its neighbors. From the phase transformation information from one step to the next, the connections of the tail vertices are reconstructed firstly by the matching positions. Removing the already reconstructed vertices, and repeatedly reconstructing the connections of tail vertices, the topology of the entire network is reconstructed. For sparse scale-free networks with more than ten thousands nodes, we almost obtain the actual topology using only the one-step data in simulations.

The natural selection of metabolism explains curvature in allometric scaling

OpenAIRE

Witting, Lars

2016-01-01

I simulate the evolution of metabolism and mass to explain the curvature in the metabolic allometry for placental and marsupial mammals. I assume that the release of inter-specific competition by the extinction of dinosaurs 65 million years ago made it possible for each clade to diversity into a multitude of species across a wide range of niches. The natural selection of metabolism and mass was then fitted to explain the maximum observed body masses over time, as well as the current inter-spe...

Three-dimensional digital reconstruction of skin epidermis and dermis.

Science.gov (United States)

Liu, P; Zhu, J-Y; Tang, B; Hu, Z-C

2018-05-01

This study describes how three-dimensional (3D) human skin tissue is reconstructed, and provides digital anatomical data for the physiological structure of human skin tissue based on large-scale thin serial sections. Human skin samples embedded in paraffin were cut serially into thin sections and then stained with hematoxylin-eosin. Images of serial sections obtained from lighting microscopy were scanned and aligned by the scale-invariant feature transform algorithm. 3D reconstruction of the skin tissue was generated using Mimics software. Fibre content, porosity, average pore diameter and specific surface area of dermis were analysed using the ImageJ analysis system. The root mean square error and mutual information based on the scale-invariant feature transform algorithm registration were significantly greater than those based on the manual registration. Fibre distribution gradually decreased from top to bottom; while porosity showed an opposite trend with irregular average pore diameter distribution. A specific surface area of the dermis showed a 'V' shape trend. Our data suggested that 3D reconstruction of human skin tissue based on large-scale serial sections could be a valuable tool for providing a highly accurate histological structure for analysis of skin tissue. Moreover, this technology could be utilized to produce tissue-engineered skin via a 3D bioprinter in the future. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Predicting supramolecular self-assembly on reconstructed metal surfaces

Science.gov (United States)

Roussel, Thomas J.; Barrena, Esther; Ocal, Carmen; Faraudo, Jordi

2014-06-01

The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern.The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule

Joint reconstruction via coupled Bregman iterations with applications to PET-MR imaging

Science.gov (United States)

Rasch, Julian; Brinkmann, Eva-Maria; Burger, Martin

2018-01-01

Joint reconstruction has recently attracted a lot of attention, especially in the field of medical multi-modality imaging such as PET-MRI. Most of the developed methods rely on the comparison of image gradients, or more precisely their location, direction and magnitude, to make use of structural similarities between the images. A challenge and still an open issue for most of the methods is to handle images in entirely different scales, i.e. different magnitudes of gradients that cannot be dealt with by a global scaling of the data. We propose the use of generalized Bregman distances and infimal convolutions thereof with regard to the well-known total variation functional. The use of a total variation subgradient respectively the involved vector field rather than an image gradient naturally excludes the magnitudes of gradients, which in particular solves the scaling behavior. Additionally, the presented method features a weighting that allows to control the amount of interaction between channels. We give insights into the general behavior of the method, before we further tailor it to a particular application, namely PET-MRI joint reconstruction. To do so, we compute joint reconstruction results from blurry Poisson data for PET and undersampled Fourier data from MRI and show that we can gain a mutual benefit for both modalities. In particular, the results are superior to the respective separate reconstructions and other joint reconstruction methods.

Cyanobacterial Biofuels: Strategies and Developments on Network and Modeling.

Science.gov (United States)

Klanchui, Amornpan; Raethong, Nachon; Prommeenate, Peerada; Vongsangnak, Wanwipa; Meechai, Asawin

Cyanobacteria, the phototrophic microorganisms, have attracted much attention recently as a promising source for environmentally sustainable biofuels production. However, barriers for commercial markets of cyanobacteria-based biofuels concern the economic feasibility. Miscellaneous strategies for improving the production performance of cyanobacteria have thus been developed. Among these, the simple ad hoc strategies resulting in failure to optimize fully cell growth coupled with desired product yield are explored. With the advancement of genomics and systems biology, a new paradigm toward systems metabolic engineering has been recognized. In particular, a genome-scale metabolic network reconstruction and modeling is a crucial systems-based tool for whole-cell-wide investigation and prediction. In this review, the cyanobacterial genome-scale metabolic models, which offer a system-level understanding of cyanobacterial metabolism, are described. The main process of metabolic network reconstruction and modeling of cyanobacteria are summarized. Strategies and developments on genome-scale network and modeling through the systems metabolic engineering approach are advanced and employed for efficient cyanobacterial-based biofuels production.

iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states.

Science.gov (United States)

Bordbar, Aarash; Jamshidi, Neema; Palsson, Bernhard O

2011-07-12

The development of high-throughput technologies capable of whole cell measurements of genes, proteins, and metabolites has led to the emergence of systems biology. Integrated analysis of the resulting omic data sets has proved to be hard to achieve. Metabolic network reconstructions enable complex relationships amongst molecular components to be represented formally in a biologically relevant manner while respecting physical constraints. In silico models derived from such reconstructions can then be queried or interrogated through mathematical simulations. Proteomic profiling studies of the mature human erythrocyte have shown more proteins present related to metabolic function than previously thought; however the significance and the causal consequences of these findings have not been explored. Erythrocyte proteomic data was used to reconstruct the most expansive description of erythrocyte metabolism to date, following extensive manual curation, assessment of the literature, and functional testing. The reconstruction contains 281 enzymes representing functions from glycolysis to cofactor and amino acid metabolism. Such a comprehensive view of erythrocyte metabolism implicates the erythrocyte as a potential biomarker for different diseases as well as a 'cell-based' drug-screening tool. The analysis shows that 94 erythrocyte enzymes are implicated in morbid single nucleotide polymorphisms, representing 142 pathologies. In addition, over 230 FDA-approved and experimental pharmaceuticals have enzymatic targets in the erythrocyte. The advancement of proteomic technologies and increased generation of high-throughput proteomic data have created the need for a means to analyze these data in a coherent manner. Network reconstructions provide a systematic means to integrate and analyze proteomic data in a biologically meaning manner. Analysis of the red cell proteome has revealed an unexpected level of complexity in the functional capabilities of human erythrocyte metabolism.

Using a genome-scale metabolic network model to elucidate the mechanism of chloroquine action in Plasmodium falciparum

Directory of Open Access Journals (Sweden)

Shivendra G. Tewari

2017-08-01

Full Text Available Chloroquine, long the default first-line treatment against malaria, is now abandoned in large parts of the world because of widespread drug-resistance in Plasmodium falciparum. In spite of its importance as a cost-effective and efficient drug, a coherent understanding of the cellular mechanisms affected by chloroquine and how they influence the fitness and survival of the parasite remains elusive. Here, we used a systems biology approach to integrate genome-scale transcriptomics to map out the effects of chloroquine, identify targeted metabolic pathways, and translate these findings into mechanistic insights. Specifically, we first developed a method that integrates transcriptomic and metabolomic data, which we independently validated against a recently published set of such data for Krebs-cycle mutants of P. falciparum. We then used the method to calculate the effect of chloroquine treatment on the metabolic flux profiles of P. falciparum during the intraerythrocytic developmental cycle. The model predicted dose-dependent inhibition of DNA replication, in agreement with earlier experimental results for both drug-sensitive and drug-resistant P. falciparum strains. Our simulations also corroborated experimental findings that suggest differences in chloroquine sensitivity between ring- and schizont-stage P. falciparum. Our analysis also suggests that metabolic fluxes that govern reduced thioredoxin and phosphoenolpyruvate synthesis are significantly decreased and are pivotal to chloroquine-based inhibition of P. falciparum DNA replication. The consequences of impaired phosphoenolpyruvate synthesis and redox metabolism are reduced carbon fixation and increased oxidative stress, respectively, both of which eventually facilitate killing of the parasite. Our analysis suggests that a combination of chloroquine (or an analogue and another drug, which inhibits carbon fixation and/or increases oxidative stress, should increase the clearance of P

When the world collapses: changed worldview and social reconstruction in a traumatized community

Directory of Open Access Journals (Sweden)

Dinka Corkalo Biruski

2014-09-01

Full Text Available Background: Traumatic experience can affect the individual's basic beliefs about the world as a predictable and safe place. One of the cornerstones in recovery from trauma is reestablishment of safety, connectedness, and the shattered schema of a worldview. Objective: This study explored the role of negatively changed worldview in the relationship between war-related traumatization and readiness for social reconstruction of intergroup relations in a post-conflict community measured by three processes: intergroup rapprochement, rebuilding trust, and need for apology. It was hypothesized that more traumatized people are less supportive of social reconstruction and that this relationship is mediated by the changed worldview. Method: The study included a community random sample of 333 adults in the city of Vukovar, Croatia, that was most devastated during the 1991–1995 war. Six instruments were administered: Stressful Events Scale, Impact of Event Scale-Revised, Changed Worldview Scale, and three scales measuring the post-conflict social reconstruction processes: Intergroup Rapprochement, Intergroup Trust and Need for Apology. Results: Mediation analyses showed that the worldview change fully mediated between traumatization and all three aspects of social reconstruction. Conclusions: In a population exposed to war traumatization the worldview change mediates post-conflict social recovery of community relations.

Improved Wallis Dodging Algorithm for Large-Scale Super-Resolution Reconstruction Remote Sensing Images

Directory of Open Access Journals (Sweden)

Chong Fan

2017-03-01

Full Text Available A sub-block algorithm is usually applied in the super-resolution (SR reconstruction of images because of limitations in computer memory. However, the sub-block SR images can hardly achieve a seamless image mosaicking because of the uneven distribution of brightness and contrast among these sub-blocks. An effectively improved weighted Wallis dodging algorithm is proposed, aiming at the characteristic that SR reconstructed images are gray images with the same size and overlapping region. This algorithm can achieve consistency of image brightness and contrast. Meanwhile, a weighted adjustment sequence is presented to avoid the spatial propagation and accumulation of errors and the loss of image information caused by excessive computation. A seam line elimination method can share the partial dislocation in the seam line to the entire overlapping region with a smooth transition effect. Subsequently, the improved method is employed to remove the uneven illumination for 900 SR reconstructed images of ZY-3. Then, the overlapping image mosaic method is adopted to accomplish a seamless image mosaic based on the optimal seam line.

Quick plasma equilibrium reconstruction based on GPU

International Nuclear Information System (INIS)

Xiao Bingjia; Huang, Y.; Luo, Z.P.; Yuan, Q.P.; Lao, L.

2014-01-01

A parallel code named P-EFIT which could complete an equilibrium reconstruction iteration in 250 μs is described. It is built with the CUDA TM architecture by using Graphical Processing Unit (GPU). It is described for the optimization of middle-scale matrix multiplication on GPU and an algorithm which could solve block tri-diagonal linear system efficiently in parallel. Benchmark test is conducted. Static test proves the accuracy of the P-EFIT and simulation-test proves the feasibility of using P-EFIT for real-time reconstruction on 65x65 computation grids. (author)

Reconstructing building mass models from UAV images

KAUST Repository

Li, Minglei; Nan, Liangliang; Smith, Neil; Wonka, Peter

2015-01-01

We present an automatic reconstruction pipeline for large scale urban scenes from aerial images captured by a camera mounted on an unmanned aerial vehicle. Using state-of-the-art Structure from Motion and Multi-View Stereo algorithms, we first

A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction

Energy Technology Data Exchange (ETDEWEB)

Zheng, Shawn Q.; Branlund, Eric; Kesthelyi, Bettina; Braunfeld, Michael B.; Cheng, Yifan; Sedat, John W. [The Howard Hughes Medical Institute and the W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, 600, 16th Street, Room S412D, CA 94158-2517 (United States); Agard, David A., E-mail: agard@msg.ucsf.edu [The Howard Hughes Medical Institute and the W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, 600, 16th Street, Room S412D, CA 94158-2517 (United States)

2011-07-15

Full resolution electron microscopic tomographic (EMT) reconstruction of large-scale tilt series requires significant computing power. The desire to perform multiple cycles of iterative reconstruction and realignment dramatically increases the pressing need to improve reconstruction performance. This has motivated us to develop a distributed multi-GPU (graphics processing unit) system to provide the required computing power for rapid constrained, iterative reconstructions of very large three-dimensional (3D) volumes. The participating GPUs reconstruct segments of the volume in parallel, and subsequently, the segments are assembled to form the complete 3D volume. Owing to its power and versatility, the CUDA (NVIDIA, USA) platform was selected for GPU implementation of the EMT reconstruction. For a system containing 10 GPUs provided by 5 GTX295 cards, 10 cycles of SIRT reconstruction for a tomogram of 4096{sup 2}x512 voxels from an input tilt series containing 122 projection images of 4096{sup 2} pixels (single precision float) takes a total of 1845 s of which 1032 s are for computation with the remainder being the system overhead. The same system takes only 39 s total to reconstruct 1024{sup 2}x256 voxels from 122 1024{sup 2} pixel projections. While the system overhead is non-trivial, performance analysis indicates that adding extra GPUs to the system would lead to steadily enhanced overall performance. Therefore, this system can be easily expanded to generate superior computing power for very large tomographic reconstructions and especially to empower iterative cycles of reconstruction and realignment. -- Highlights: {yields} A distributed multi-GPU system has been developed for electron microscopic tomography (EMT). {yields} This system allows for rapid constrained, iterative reconstruction of very large volumes. {yields} This system can be easily expanded to generate superior computing power for large-scale iterative EMT realignment.

A distributed multi-GPU system for high speed electron microscopic tomographic reconstruction

International Nuclear Information System (INIS)

Zheng, Shawn Q.; Branlund, Eric; Kesthelyi, Bettina; Braunfeld, Michael B.; Cheng, Yifan; Sedat, John W.; Agard, David A.

2011-01-01

Full resolution electron microscopic tomographic (EMT) reconstruction of large-scale tilt series requires significant computing power. The desire to perform multiple cycles of iterative reconstruction and realignment dramatically increases the pressing need to improve reconstruction performance. This has motivated us to develop a distributed multi-GPU (graphics processing unit) system to provide the required computing power for rapid constrained, iterative reconstructions of very large three-dimensional (3D) volumes. The participating GPUs reconstruct segments of the volume in parallel, and subsequently, the segments are assembled to form the complete 3D volume. Owing to its power and versatility, the CUDA (NVIDIA, USA) platform was selected for GPU implementation of the EMT reconstruction. For a system containing 10 GPUs provided by 5 GTX295 cards, 10 cycles of SIRT reconstruction for a tomogram of 4096 2 x512 voxels from an input tilt series containing 122 projection images of 4096 2 pixels (single precision float) takes a total of 1845 s of which 1032 s are for computation with the remainder being the system overhead. The same system takes only 39 s total to reconstruct 1024 2 x256 voxels from 122 1024 2 pixel projections. While the system overhead is non-trivial, performance analysis indicates that adding extra GPUs to the system would lead to steadily enhanced overall performance. Therefore, this system can be easily expanded to generate superior computing power for very large tomographic reconstructions and especially to empower iterative cycles of reconstruction and realignment. -- Highlights: → A distributed multi-GPU system has been developed for electron microscopic tomography (EMT). → This system allows for rapid constrained, iterative reconstruction of very large volumes. → This system can be easily expanded to generate superior computing power for large-scale iterative EMT realignment.

Shredded banknotes reconstruction using AKAZE points.

Science.gov (United States)

Nabiyev, Vasif V; Yılmaz, Seçkin; Günay, Asuman; Muzaffer, Gül; Ulutaş, Güzin

2017-09-01

Shredded banknote reconstruction is a recent topic and can be viewed as solving large-scale jigsaw puzzles. Also, problems such as reconstruction of fragmented documents, photographs and historical artefacts are closely related with this topic. The high computational complexity of these problems increases the need for the development of new methods Reconstruction of shredded banknotes consists of three main stages. (1) Matching fragments with a reference banknote. (2) Aligning the fragments by rotating at certain angles. (3) Assembling the fragments. The existing methods can successfully applied to synthetic banknote fragments which are created in computer environment. But when real banknote reconstruction problem is considered, different sub problems arise and make the existing methods inadequate. In this study, a keypoint based method, named AKAZE, was used to make the matching process effective. This is the first study that uses the AKAZE method in the reconstruction of shredded banknotes. A new method for fragment alignment has also been proposed. In this method, the convex hulls that contain all true matched AKAZE keypoints were found on reference banknote and fragments. The orientations of fragments were estimated accurately by comparing these convex polygons. Also, a new criterion was developed to reveal the success rates of reconstructed banknotes. In addition, two different data sets including real and synthetic banknote fragments of different countries were created to test the success of proposed method. Copyright © 2017 Elsevier B.V. All rights reserved.

Simultaneous maximum a posteriori longitudinal PET image reconstruction

Science.gov (United States)

Ellis, Sam; Reader, Andrew J.

2017-09-01

Positron emission tomography (PET) is frequently used to monitor functional changes that occur over extended time scales, for example in longitudinal oncology PET protocols that include routine clinical follow-up scans to assess the efficacy of a course of treatment. In these contexts PET datasets are currently reconstructed into images using single-dataset reconstruction methods. Inspired by recently proposed joint PET-MR reconstruction methods, we propose to reconstruct longitudinal datasets simultaneously by using a joint penalty term in order to exploit the high degree of similarity between longitudinal images. We achieved this by penalising voxel-wise differences between pairs of longitudinal PET images in a one-step-late maximum a posteriori (MAP) fashion, resulting in the MAP simultaneous longitudinal reconstruction (SLR) method. The proposed method reduced reconstruction errors and visually improved images relative to standard maximum likelihood expectation-maximisation (ML-EM) in simulated 2D longitudinal brain tumour scans. In reconstructions of split real 3D data with inserted simulated tumours, noise across images reconstructed with MAP-SLR was reduced to levels equivalent to doubling the number of detected counts when using ML-EM. Furthermore, quantification of tumour activities was largely preserved over a variety of longitudinal tumour changes, including changes in size and activity, with larger changes inducing larger biases relative to standard ML-EM reconstructions. Similar improvements were observed for a range of counts levels, demonstrating the robustness of the method when used with a single penalty strength. The results suggest that longitudinal regularisation is a simple but effective method of improving reconstructed PET images without using resolution degrading priors.

From genomes to in silico cells via metabolic networks

DEFF Research Database (Denmark)

Borodina, Irina; Nielsen, Jens

2005-01-01

Genome-scale metabolic models are the focal point of systems biology as they allow the collection of various data types in a form suitable for mathematical analysis. High-quality metabolic networks and metabolic networks with incorporated regulation have been successfully used for the analysis...... of phenotypes from phenotypic arrays and in gene-deletion studies. They have also been used for gene expression analysis guided by metabolic network structure, leading to the identification of commonly regulated genes. Thus, genome-scale metabolic modeling currently stands out as one of the most promising...

Computer-assisted three-dimensional reconstructions of [14C]-2-deoxy-D-glucose metabolism in cat lumbosacral spinal cord following cutaneous stimulation of the hindfoot

International Nuclear Information System (INIS)

Crockett, D.P.; Smith, W.K.; Proshansky, E.; Kauer, J.S.; Stewart, W.B.; Woodward, D.J.; Schlusselberg, D.S.; Egger, M.D.

1989-01-01

We report on computer-assisted three-dimensional reconstruction of spinal cord activity associated with stimulation of the plantar cushion (PC) as revealed by [14C]-2-deoxy-D-glucose (2-DG) serial autoradiographs. Moderate PC stimulation in cats elicits a reflex phasic plantar flexion of the toes. Four cats were chronically spinalized at about T6 under barbiturate anesthesia. Four to 11 days later, the cats were injected (i.v.) with 2-DG (100 microCi/kg) and the PC was electrically stimulated with needle electrodes at 2-5 times threshold for eliciting a reflex. Following stimulation, the spinal cord was processed for autoradiography. Subsequently, autoradiographs, representing approximately 8-18 mm from spinal segments L6-S1, were digitized for computer analysis and 3-D reconstruction. Several strategies of analysis were employed: (1) Three-dimensional volume images were color-coded to represent different levels of functional activity. (2) On the reconstructed volumes, virtual sections were made in the horizontal, sagittal, and transverse planes to view regions of 2-DG activity. (3) In addition, we were able to sample different regions within the grey and white matter semi-quantitatively (i.e., pixel intensity) from section to section to reveal differences between ipsi- and contralateral activity, as well as possible variation between sections. These analyses revealed 2-DG activity associated with moderate PC stimulation, not only in the ipsilateral dorsal horn as we had previously demonstrated, but also in both the ipsilateral and contralateral ventral horns, as well as in the intermediate grey matter. The use of novel computer analysis techniques--combined with an unanesthetized preparation--enabled us to demonstrate that the increased metabolic activity in the lumbosacral spinal cord associated with PC stimulation was much more extensive than had heretofore been observed

Blueprint for antimicrobial hit discovery targeting metabolic networks.

Science.gov (United States)

Shen, Y; Liu, J; Estiu, G; Isin, B; Ahn, Y-Y; Lee, D-S; Barabási, A-L; Kapatral, V; Wiest, O; Oltvai, Z N

2010-01-19

Advances in genome analysis, network biology, and computational chemistry have the potential to revolutionize drug discovery by combining system-level identification of drug targets with the atomistic modeling of small molecules capable of modulating their activity. To demonstrate the effectiveness of such a discovery pipeline, we deduced common antibiotic targets in Escherichia coli and Staphylococcus aureus by identifying shared tissue-specific or uniformly essential metabolic reactions in their metabolic networks. We then predicted through virtual screening dozens of potential inhibitors for several enzymes of these reactions and showed experimentally that a subset of these inhibited both enzyme activities in vitro and bacterial cell viability. This blueprint is applicable for any sequenced organism with high-quality metabolic reconstruction and suggests a general strategy for strain-specific antiinfective therapy.

An interactive display system for large-scale 3D models

Science.gov (United States)

Liu, Zijian; Sun, Kun; Tao, Wenbing; Liu, Liman

2018-04-01

With the improvement of 3D reconstruction theory and the rapid development of computer hardware technology, the reconstructed 3D models are enlarging in scale and increasing in complexity. Models with tens of thousands of 3D points or triangular meshes are common in practical applications. Due to storage and computing power limitation, it is difficult to achieve real-time display and interaction with large scale 3D models for some common 3D display software, such as MeshLab. In this paper, we propose a display system for large-scale 3D scene models. We construct the LOD (Levels of Detail) model of the reconstructed 3D scene in advance, and then use an out-of-core view-dependent multi-resolution rendering scheme to realize the real-time display of the large-scale 3D model. With the proposed method, our display system is able to render in real time while roaming in the reconstructed scene and 3D camera poses can also be displayed. Furthermore, the memory consumption can be significantly decreased via internal and external memory exchange mechanism, so that it is possible to display a large scale reconstructed scene with over millions of 3D points or triangular meshes in a regular PC with only 4GB RAM.

Quantitative ptychographic reconstruction by applying a probe constraint

Science.gov (United States)

Reinhardt, J.; Schroer, C. G.

2018-04-01

The coherent scanning technique X-ray ptychography has become a routine tool for high-resolution imaging and nanoanalysis in various fields of research such as chemistry, biology or materials science. Often the ptychographic reconstruction results are analysed in order to yield absolute quantitative values for the object transmission and illuminating probe function. In this work, we address a common ambiguity encountered in scaling the object transmission and probe intensity via the application of an additional constraint to the reconstruction algorithm. A ptychographic measurement of a model sample containing nanoparticles is used as a test data set against which to benchmark in the reconstruction results depending on the type of constraint used. Achieving quantitative absolute values for the reconstructed object transmission is essential for advanced investigation of samples that are changing over time, e.g., during in-situ experiments or in general when different data sets are compared.

Optimisation of the ATLAS Track Reconstruction Software for Run-2

CERN Document Server

Salzburger, Andreas; The ATLAS collaboration

2015-01-01

The reconstruction of particle trajectories in the tracking detectors of experiments at the Large Hadron Collider (LHC) is one of the most complex parts in analysing the collected data from beam-beam collisions. To achieve the desired integrated luminosity during Run-1 of the LHC data taking period, the number of simultaneous proton-proton interactions per beam crossing (pile-up) was steadily increased. The track reconstruction is the most time consuming reconstruction component and scales non-linear in high luminosity environments. Flat budget projections (at best) for computing resources during the upcoming Run-2 of the LHC together with the demands of reconstructing higher pile-up collision data at rates more than double compared to Run-1 have put pressure on the track reconstruction software to stay within the available computing resources. The ATLAS experiment has thus performed a two year long software campaign which led to a reduction of the reconstruction time for Run-2 conditions by a factor of four:...

Reconstruction of a Large-scale Pre-flare Coronal Current Sheet Associated with a Homologous X-shaped Flare

Science.gov (United States)

Jiang, Chaowei; Yan, Xiaoli; Feng, Xueshang; Duan, Aiying; Hu, Qiang; Zuo, Pingbing; Wang, Yi

2017-11-01

As a fundamental magnetic structure in the solar corona, electric current sheets (CSs) can form either prior to or during a solar flare, and they are essential for magnetic energy dissipation in the solar corona because they enable magnetic reconnection. However, the static reconstruction of a CS is rare, possibly due to limitations that are inherent in the available coronal field extrapolation codes. Here we present the reconstruction of a large-scale pre-flare CS in solar active region 11967 using an MHD-relaxation model constrained by the SDO/HMI vector magnetogram. The CS is associated with a set of peculiar homologous flares that exhibit unique X-shaped ribbons and loops occurring in a quadrupolar magnetic configuration.This is evidenced by an ’X’ shape, formed from the field lines traced from the CS to the photosphere. This nearly reproduces the shape of the observed flare ribbons, suggesting that the flare is a product of the dissipation of the CS via reconnection. The CS forms in a hyperbolic flux tube, which is an intersection of two quasi-separatrix layers. The recurrence of the X-shaped flares might be attributed to the repetitive formation and dissipation of the CS, as driven by the photospheric footpoint motions. These results demonstrate the power of a data-constrained MHD model in reproducing a CS in the corona as well as providing insight into the magnetic mechanism of solar flares.

iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states

Directory of Open Access Journals (Sweden)

Palsson Bernhard O

2011-07-01

Full Text Available Abstract Background The development of high-throughput technologies capable of whole cell measurements of genes, proteins, and metabolites has led to the emergence of systems biology. Integrated analysis of the resulting omic data sets has proved to be hard to achieve. Metabolic network reconstructions enable complex relationships amongst molecular components to be represented formally in a biologically relevant manner while respecting physical constraints. In silico models derived from such reconstructions can then be queried or interrogated through mathematical simulations. Proteomic profiling studies of the mature human erythrocyte have shown more proteins present related to metabolic function than previously thought; however the significance and the causal consequences of these findings have not been explored. Results Erythrocyte proteomic data was used to reconstruct the most expansive description of erythrocyte metabolism to date, following extensive manual curation, assessment of the literature, and functional testing. The reconstruction contains 281 enzymes representing functions from glycolysis to cofactor and amino acid metabolism. Such a comprehensive view of erythrocyte metabolism implicates the erythrocyte as a potential biomarker for different diseases as well as a 'cell-based' drug-screening tool. The analysis shows that 94 erythrocyte enzymes are implicated in morbid single nucleotide polymorphisms, representing 142 pathologies. In addition, over 230 FDA-approved and experimental pharmaceuticals have enzymatic targets in the erythrocyte. Conclusion The advancement of proteomic technologies and increased generation of high-throughput proteomic data have created the need for a means to analyze these data in a coherent manner. Network reconstructions provide a systematic means to integrate and analyze proteomic data in a biologically meaning manner. Analysis of the red cell proteome has revealed an unexpected level of complexity in

Validity of proxy data obtained by different psychological autopsy information reconstruction techniques.

Science.gov (United States)

Fang, L; Zhang, J

2010-01-01

Two informants were interviewed for each of 416 living controls (individuals sampled from the normal population) interviewed in a Chinese case-control psychological autopsy study. The validity of proxy data, obtained using seven psychological autopsy information reconstruction techniques (types 1, 2 and A - E), was evaluated, with living controls' self reports used as the gold-standard. Proxy data for reconstruction technique types 1, 2 and D on the Impulsivity Inventory Scale (total impulsivity score) were no different from the living controls' self report gold standard, whereas data for types A and E were smaller than data from living controls. On the 'acceptance or resignation' sub-scale of the avoidance coping dimension of the Moos Coping Response Inventory, information obtained by reconstruction technique types 1 and D was not significantly different from the living controls' self reports, whereas proxy data from types 2, A and E were smaller than those from the living controls. No statistically significant differences were identified for other proxy data obtained by reconstruction technique types 1, 2, A, D and E. These results indicate that using a second informant does not significantly enhance information reconstruction for the target.

Reconstructing phylogeny by aligning multiple metabolic pathways using functional module mapping

NARCIS (Netherlands)

Huang, Yiran; Zhong, Cheng; Lin, H.X.; Wang, Jianyi; Peng, Yuzhong

2018-01-01

Comparison of metabolic pathways provides a systematic way for understanding the evolutionary and phylogenetic relationships in systems biology. Although a number of phylogenetic methods have been developed, few efforts have been made to provide a unified phylogenetic framework that sufficiently

Bayesian 3D X-ray computed tomography image reconstruction with a scaled Gaussian mixture prior model

International Nuclear Information System (INIS)

Wang, Li; Gac, Nicolas; Mohammad-Djafari, Ali

2015-01-01

In order to improve quality of 3D X-ray tomography reconstruction for Non Destructive Testing (NDT), we investigate in this paper hierarchical Bayesian methods. In NDT, useful prior information on the volume like the limited number of materials or the presence of homogeneous area can be included in the iterative reconstruction algorithms. In hierarchical Bayesian methods, not only the volume is estimated thanks to the prior model of the volume but also the hyper parameters of this prior. This additional complexity in the reconstruction methods when applied to large volumes (from 512 3 to 8192 3 voxels) results in an increasing computational cost. To reduce it, the hierarchical Bayesian methods investigated in this paper lead to an algorithm acceleration by Variational Bayesian Approximation (VBA) [1] and hardware acceleration thanks to projection and back-projection operators paralleled on many core processors like GPU [2]. In this paper, we will consider a Student-t prior on the gradient of the image implemented in a hierarchical way [3, 4, 1]. Operators H (forward or projection) and H t (adjoint or back-projection) implanted in multi-GPU [2] have been used in this study. Different methods will be evalued on synthetic volume 'Shepp and Logan' in terms of quality and time of reconstruction. We used several simple regularizations of order 1 and order 2. Other prior models also exists [5]. Sometimes for a discrete image, we can do the segmentation and reconstruction at the same time, then the reconstruction can be done with less projections

Metabolic engineering tools in model cyanobacteria.

Science.gov (United States)

Carroll, Austin L; Case, Anna E; Zhang, Angela; Atsumi, Shota

2018-03-26

Developing sustainable routes for producing chemicals and fuels is one of the most important challenges in metabolic engineering. Photoautotrophic hosts are particularly attractive because of their potential to utilize light as an energy source and CO 2 as a carbon substrate through photosynthesis. Cyanobacteria are unicellular organisms capable of photosynthesis and CO 2 fixation. While engineering in heterotrophs, such as Escherichia coli, has result in a plethora of tools for strain development and hosts capable of producing valuable chemicals efficiently, these techniques are not always directly transferable to cyanobacteria. However, recent efforts have led to an increase in the scope and scale of chemicals that cyanobacteria can produce. Adaptations of important metabolic engineering tools have also been optimized to function in photoautotrophic hosts, which include Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9, 13 C Metabolic Flux Analysis (MFA), and Genome-Scale Modeling (GSM). This review explores innovations in cyanobacterial metabolic engineering, and highlights how photoautotrophic metabolism has shaped their development. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

CT angiography after carotid artery stenting: assessment of the utility of adaptive statistical iterative reconstruction and model-based iterative reconstruction

Energy Technology Data Exchange (ETDEWEB)

Kuya, Keita; Shinohara, Yuki; Fujii, Shinya; Ogawa, Toshihide [Tottori University, Division of Radiology, Department of Pathophysiological Therapeutic Science, Faculty of Medicine, Yonago (Japan); Sakamoto, Makoto; Watanabe, Takashi [Tottori University, Division of Neurosurgery, Department of Brain and Neurosciences, Faculty of Medicine, Yonago (Japan); Iwata, Naoki; Kishimoto, Junichi [Tottori University, Division of Clinical Radiology Faculty of Medicine, Yonago (Japan); Kaminou, Toshio [Osaka Minami Medical Center, Department of Radiology, Osaka (Japan)

2014-11-15

Follow-up CT angiography (CTA) is routinely performed for post-procedure management after carotid artery stenting (CAS). However, the stent lumen tends to be underestimated because of stent artifacts on CTA reconstructed with the filtered back projection (FBP) technique. We assessed the utility of new iterative reconstruction techniques, such as adaptive statistical iterative reconstruction (ASIR) and model-based iterative reconstruction (MBIR), for CTA after CAS in comparison with FBP. In a phantom study, we evaluated the differences among the three reconstruction techniques with regard to the relationship between the stent luminal diameter and the degree of underestimation of stent luminal diameter. In a clinical study, 34 patients who underwent follow-up CTA after CAS were included. We compared the stent luminal diameters among FBP, ASIR, and MBIR, and performed visual assessment of low attenuation area (LAA) in the stent lumen using a three-point scale. In the phantom study, stent luminal diameter was increasingly underestimated as luminal diameter became smaller in all CTA images. Stent luminal diameter was larger with MBIR than with the other reconstruction techniques. Similarly, in the clinical study, stent luminal diameter was larger with MBIR than with the other reconstruction techniques. LAA detectability scores of MBIR were greater than or equal to those of FBP and ASIR in all cases. MBIR improved the accuracy of assessment of stent luminal diameter and LAA detectability in the stent lumen when compared with FBP and ASIR. We conclude that MBIR is a useful reconstruction technique for CTA after CAS. (orig.)

CT angiography after carotid artery stenting: assessment of the utility of adaptive statistical iterative reconstruction and model-based iterative reconstruction

International Nuclear Information System (INIS)

Kuya, Keita; Shinohara, Yuki; Fujii, Shinya; Ogawa, Toshihide; Sakamoto, Makoto; Watanabe, Takashi; Iwata, Naoki; Kishimoto, Junichi; Kaminou, Toshio

2014-01-01

Follow-up CT angiography (CTA) is routinely performed for post-procedure management after carotid artery stenting (CAS). However, the stent lumen tends to be underestimated because of stent artifacts on CTA reconstructed with the filtered back projection (FBP) technique. We assessed the utility of new iterative reconstruction techniques, such as adaptive statistical iterative reconstruction (ASIR) and model-based iterative reconstruction (MBIR), for CTA after CAS in comparison with FBP. In a phantom study, we evaluated the differences among the three reconstruction techniques with regard to the relationship between the stent luminal diameter and the degree of underestimation of stent luminal diameter. In a clinical study, 34 patients who underwent follow-up CTA after CAS were included. We compared the stent luminal diameters among FBP, ASIR, and MBIR, and performed visual assessment of low attenuation area (LAA) in the stent lumen using a three-point scale. In the phantom study, stent luminal diameter was increasingly underestimated as luminal diameter became smaller in all CTA images. Stent luminal diameter was larger with MBIR than with the other reconstruction techniques. Similarly, in the clinical study, stent luminal diameter was larger with MBIR than with the other reconstruction techniques. LAA detectability scores of MBIR were greater than or equal to those of FBP and ASIR in all cases. MBIR improved the accuracy of assessment of stent luminal diameter and LAA detectability in the stent lumen when compared with FBP and ASIR. We conclude that MBIR is a useful reconstruction technique for CTA after CAS. (orig.)

How Are We Measuring Patient Satisfaction After Anterior Cruciate Ligament Reconstruction?

Science.gov (United States)

Kahlenberg, Cynthia A; Nwachukwu, Benedict U; Ferraro, Richard A; Schairer, William W; Steinhaus, Michael E; Allen, Answorth A

2016-12-01

Reconstruction of the anterior cruciate ligament (ACL) is one of the most common orthopaedic operations in the United States. The long-term impact of ACL reconstruction is controversial, however, as longer term data have failed to demonstrate that ACL reconstruction helps alter the natural history of early onset osteoarthritis that occurs after ACL injury. There is significant interest in evaluating the value of ACL reconstruction surgeries. To examine the quality of patient satisfaction reporting after ACL reconstruction surgery. Systematic review; Level of evidence, 4. A systematic review of the MEDLINE database was performed using the PubMed interface. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines as well as the PRISMA checklist were employed. The initial search yielded 267 studies. The inclusion criteria were: English language, US patient population, clinical outcome study of ACL reconstruction surgery, and reporting of patient satisfaction included in the study. Study quality was assessed using the Newcastle-Ottawa scale. A total of 22 studies met the inclusion criteria. These studies comprised a total of 1984 patients with a mean age of 31.9 years at the time of surgery and a mean follow-up period of 59.3 months. The majority of studies were evidence level 4 (n = 18; 81.8%), had a mean Newcastle-Ottawa scale score of 5.5, and were published before 2006 (n = 17; 77.3%); 5 studies (22.7%) failed to clearly describe their method for determining patient satisfaction. The most commonly used method for assessing satisfaction was a 0 to 10 satisfaction scale (n = 11; 50.0%). Among studies using a 0 to 10 scale, mean satisfaction ranged from 7.4 to 10.0. Patient-reported outcome and objective functional measures for ACL stability and knee function were positively correlated with patient satisfaction. Degenerative knee change was negatively correlated with satisfaction. The level of evidence for studies reporting patient

Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica

Science.gov (United States)

Chatterjee, Ankita; Kundu, Sudip

2015-01-01

Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air. PMID:26443104

Current Limitations of Surgical Robotics in Reconstructive Plastic Microsurgery

Directory of Open Access Journals (Sweden)

Youri P. A. Tan

2018-03-01

Full Text Available Surgical robots have the potential to provide surgeons with increased capabilities, such as removing physiologic tremor, scaling motion and increasing manual dexterity. Several surgical specialties have subsequently integrated robotic surgery into common clinical practice. Plastic and reconstructive microsurgical procedures have not yet  benefitted significantly from technical developments observed over the last two decades. Several studies have successfully demonstrated the feasibility of utilising surgical robots in plastic surgery procedures, yet limited work has been done to identify and analyse current barriers that have prevented wide-scale adaptation of surgical robots for microsurgery. Therefore, a systematic review using PubMed, MEDLINE, Embase and Web of Science databases was performed, in order to evaluate current state of surgical robotics within the field of reconstructive microsurgery and their limitations. Despite the theoretical potential of surgical robots, current commercially available robotic systems are suboptimal for plastic or reconstructive microsurgery. Absence of bespoke microsurgical instruments, increases in operating time, and high costs associated with robotic-assisted provide a barrier to using such systems effectively for reconstructive microsurgery. Consequently, surgical robots provide currently little overall advantage over conventional microsurgery. Nevertheless, if current barriers can be addressed and systems are specifically designed for microsurgery, surgical robots may have the potential of meaningful impact on clinical outcomes within  this surgical subspeciality.

Current Limitations of Surgical Robotics in Reconstructive Plastic Microsurgery

Science.gov (United States)

Tan, Youri P. A.; Liverneaux, Philippe; Wong, Jason K. F.

2018-01-01

Surgical robots have the potential to provide surgeons with increased capabilities, such as removing physiologic tremor, scaling motion and increasing manual dexterity. Several surgical specialties have subsequently integrated robotic surgery into common clinical practice. Plastic and reconstructive microsurgical procedures have not yet  benefitted significantly from technical developments observed over the last two decades. Several studies have successfully demonstrated the feasibility of utilising surgical robots in plastic surgery procedures, yet limited work has been done to identify and analyse current barriers that have prevented wide-scale adaptation of surgical robots for microsurgery. Therefore, a systematic review using PubMed, MEDLINE, Embase and Web of Science databases was performed, in order to evaluate current state of surgical robotics within the field of reconstructive microsurgery and their limitations. Despite the theoretical potential of surgical robots, current commercially available robotic systems are suboptimal for plastic or reconstructive microsurgery. Absence of bespoke microsurgical instruments, increases in operating time, and high costs associated with robotic-assisted provide a barrier to using such systems effectively for reconstructive microsurgery. Consequently, surgical robots provide currently little overall advantage over conventional microsurgery. Nevertheless, if current barriers can be addressed and systems are specifically designed for microsurgery, surgical robots may have the potential of meaningful impact on clinical outcomes within  this surgical subspeciality. PMID:29740585

Self-prior strategy for organ reconstruction in fluorescence molecular tomography.

Science.gov (United States)

Zhou, Yuan; Chen, Maomao; Su, Han; Luo, Jianwen

2017-10-01

The purpose of this study is to propose a strategy for organ reconstruction in fluorescence molecular tomography (FMT) without prior information from other imaging modalities, and to overcome the high cost and ionizing radiation caused by the traditional structural prior strategy. The proposed strategy is designed as an iterative architecture to solve the inverse problem of FMT. In each iteration, a short time Fourier transform (STFT) based algorithm is used to extract the self-prior information in the space-frequency energy spectrum with the assumption that the regions with higher fluorescence concentration have larger energy intensity, then the cost function of the inverse problem is modified by the self-prior information, and lastly an iterative Laplacian regularization algorithm is conducted to solve the updated inverse problem and obtains the reconstruction results. Simulations and in vivo experiments on liver reconstruction are carried out to test the performance of the self-prior strategy on organ reconstruction. The organ reconstruction results obtained by the proposed self-prior strategy are closer to the ground truth than those obtained by the iterative Tikhonov regularization (ITKR) method (traditional non-prior strategy). Significant improvements are shown in the evaluation indexes of relative locational error (RLE), relative error (RE) and contrast-to-noise ratio (CNR). The self-prior strategy improves the organ reconstruction results compared with the non-prior strategy and also overcomes the shortcomings of the traditional structural prior strategy. Various applications such as metabolic imaging and pharmacokinetic study can be aided by this strategy.

High-throughput metabolic state analysis: The missing link in integrated functional genomics of yeasts

DEFF Research Database (Denmark)

Villas-Bôas, Silas Granato; Moxley, Joel. F; Åkesson, Mats Fredrik

2005-01-01

that achieve comparable throughput, effort and cost compared with DNA arrays. Our sample workup method enables simultaneous metabolite measurements throughout central carbon metabolism and amino acid biosynthesis, using a standard GC-MS platform that was optimized for this Purpose. As an implementation proof......-of-concept, we assayed metabolite levels in two yeast strains and two different environmental conditions in the context of metabolic pathway reconstruction. We demonstrate that these differential metabolite level data distinguish among sample types, such as typical metabolic fingerprinting or footprinting. More...

Algorithm of hadron energy reconstruction for combined calorimeters in the DELPHI detector

International Nuclear Information System (INIS)

Gotra, Yu.N.; Tsyganov, E.N.; Zimin, N.I.; Zinchenko, A.I.

1989-01-01

The algorithm of hadron energy reconstruction from responses of electromagnetic and hadron calorimeters is described. The investigations have been carried out using the full-scale prototype of the hadron calorimeter cylindrical part modules. The supposed algorithm allows one to improve energy resolution by 5-7% with conserving the linearly of reconstructed hadron energy. 5 refs.; 4 figs.; 1 tab

Mastectomy Skin Necrosis After Breast Reconstruction: A Comparative Analysis Between Autologous Reconstruction and Implant-Based Reconstruction.

Science.gov (United States)

Sue, Gloria R; Lee, Gordon K

2018-05-01

Mastectomy skin necrosis is a significant problem after breast reconstruction. We sought to perform a comparative analysis on this complication between patients undergoing autologous breast reconstruction and patients undergoing 2-stage expander implant breast reconstruction. A retrospective review was performed on consecutive patients undergoing autologous breast reconstruction or 2-stage expander implant breast reconstruction by the senior author from 2006 through 2015. Patient demographic factors including age, body mass index, history of diabetes, history of smoking, and history of radiation to the breast were collected. Our primary outcome measure was mastectomy skin necrosis. Fisher exact test was used for statistical analysis between the 2 patient cohorts. The treatment patterns of mastectomy skin necrosis were then analyzed. We identified 204 patients who underwent autologous breast reconstruction and 293 patients who underwent 2-stage expander implant breast reconstruction. Patients undergoing autologous breast reconstruction were older, heavier, more likely to have diabetes, and more likely to have had prior radiation to the breast compared with patients undergoing implant-based reconstruction. The incidence of mastectomy skin necrosis was 30.4% of patients in the autologous group compared with only 10.6% of patients in the tissue expander group (P care in the autologous group, only 3.2% were treated with local wound care in the tissue expander group (P skin necrosis is significantly more likely to occur after autologous breast reconstruction compared with 2-stage expander implant-based breast reconstruction. Patients with autologous reconstructions are more readily treated with local wound care compared with patients with tissue expanders, who tended to require operative treatment of this complication. Patients considering breast reconstruction should be counseled appropriately regarding the differences in incidence and management of mastectomy skin

Snapshot of iron response in Shewanella oneidensis by gene network reconstruction

Energy Technology Data Exchange (ETDEWEB)

Yang, Yunfeng; Harris, Daniel P.; Luo, Feng; Xiong, Wenlu; Joachimiak, Marcin; Wu, Liyou; Dehal, Paramvir; Jacobsen, Janet; Yang, Zamin; Palumbo, Anthony V.; Arkin, Adam P.; Zhou, Jizhong

2008-10-09

Background: Iron homeostasis of Shewanella oneidensis, a gamma-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of S. oneidensis. Results: We show that the iron response in S. oneidensis is a rapid process. Temporal gene expression profiles were examined for iron depletion and repletion, and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways. Conclusions: Using a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion. Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor (SO1415) with a

An Integrative Approach to Energy Carbon and Redox Metabolism In Cyanobacterium Synechocystis

Energy Technology Data Exchange (ETDEWEB)

Dr. Ross Overbeek

2003-06-30

The main objectives for the first year were to produce a detailed metabolic reconstruction of synechocystis sp.pcc6803 especially in interrelated arrears of photosynthesis respiration and central carbon metabolism to support a more complete understanding and modeling of this organism. Additionally, IG, Inc. provided detailed bioinformatic analysis of selected functional systems related to carbon and energy generation and utilization, and of the corresponding pathways functional roles and individual genes to support wet lab experiments by collaborators.

A Standardized Precipitation Evapotranspiration Index Reconstruction in the Taihe Mountains Using Tree-Ring Widths for the Last 283 Years.

Directory of Open Access Journals (Sweden)

Yongyong Ma

Full Text Available Tree-ring samples from Chinese Pine (Pinus tabulaeformis Carr. that were collected in the Taihe Mountains on the western Loess Plateau, China, were used to analyze the effects of climate and drought on radial growth and to reconstruct the mean April-June Standardized Precipitation Evapotranspiration Index (SPEI during the period 1730-2012 AD. Precipitation positively affected tree growth primarily during wet seasons, while temperature negatively affected tree growth during dry seasons. Tree growth responded positively to SPEI at long time scales most likely because the trees were able to withstand water deficits but lacked a rapid response to drought. The 10-month scale SPEI was chosen for further drought reconstruction. A calibration model for the period 1951-2011 explained 51% of the variance in the modeled SPEI data. Our SPEI reconstruction revealed long-term patterns of drought variability and captured some significant drought events, including the severe drought of 1928-1930 and the clear drying trend since the 1950s which were widespread across northern China. The reconstruction was also consistent with two other reconstructions on the western Loess Plateau at both interannual and decadal scales. The reconstructed SPEI series showed synchronous variations with the drought/wetness indices and spatial correlation analyses indicated that this reconstruction could be representative of large-scale SPEI variability in northern China. Period analysis discovered 128-year, 25-year, 2.62-year, 2.36-year, and 2.04-year cycles in this reconstruction. The time-dependency of the growth response to drought should be considered in further studies of the community dynamics. The SPEI reconstruction improves the sparse network of long-term climate records for an enhanced understanding of climatic variability on the western Loess Plateau, China.

A Standardized Precipitation Evapotranspiration Index Reconstruction in the Taihe Mountains Using Tree-Ring Widths for the Last 283 Years

Science.gov (United States)

Ma, Yongyong; Liu, Yu; Song, Huiming; Sun, Junyan; Lei, Ying; Wang, Yanchao

2015-01-01

Tree-ring samples from Chinese Pine (Pinus tabulaeformis Carr.) that were collected in the Taihe Mountains on the western Loess Plateau, China, were used to analyze the effects of climate and drought on radial growth and to reconstruct the mean April-June Standardized Precipitation Evapotranspiration Index (SPEI) during the period 1730–2012 AD. Precipitation positively affected tree growth primarily during wet seasons, while temperature negatively affected tree growth during dry seasons. Tree growth responded positively to SPEI at long time scales most likely because the trees were able to withstand water deficits but lacked a rapid response to drought. The 10-month scale SPEI was chosen for further drought reconstruction. A calibration model for the period 1951–2011 explained 51% of the variance in the modeled SPEI data. Our SPEI reconstruction revealed long-term patterns of drought variability and captured some significant drought events, including the severe drought of 1928–1930 and the clear drying trend since the 1950s which were widespread across northern China. The reconstruction was also consistent with two other reconstructions on the western Loess Plateau at both interannual and decadal scales. The reconstructed SPEI series showed synchronous variations with the drought/wetness indices and spatial correlation analyses indicated that this reconstruction could be representative of large-scale SPEI variability in northern China. Period analysis discovered 128-year, 25-year, 2.62-year, 2.36-year, and 2.04-year cycles in this reconstruction. The time-dependency of the growth response to drought should be considered in further studies of the community dynamics. The SPEI reconstruction improves the sparse network of long-term climate records for an enhanced understanding of climatic variability on the western Loess Plateau, China. PMID:26207621

Large-scale building scenes reconstruction from close-range images based on line and plane feature

Science.gov (United States)

Ding, Yi; Zhang, Jianqing

2007-11-01

Automatic generate 3D models of buildings and other man-made structures from images has become a topic of increasing importance, those models may be in applications such as virtual reality, entertainment industry and urban planning. In this paper we address the main problems and available solution for the generation of 3D models from terrestrial images. We first generate a coarse planar model of the principal scene planes and then reconstruct windows to refine the building models. There are several points of novelty: first we reconstruct the coarse wire frame model use the line segments matching with epipolar geometry constraint; Secondly, we detect the position of all windows in the image and reconstruct the windows by established corner points correspondences between images, then add the windows to the coarse model to refine the building models. The strategy is illustrated on image triple of college building.

Multiproxy summer and winter surface air temperature field reconstructions for southern South America covering the past centuries

Energy Technology Data Exchange (ETDEWEB)

Neukom, R.; Grosjean, M.; Wanner, H. [University of Bern, Oeschger Centre for Climate Change Research (OCCR), Bern (Switzerland); University of Bern, Institute of Geography, Climatology and Meteorology, Bern (Switzerland); Luterbacher, J. [Justus Liebig University of Giessen, Department of Geography, Climatology, Climate Dynamics and Climate Change, Giessen (Germany); Villalba, R.; Morales, M.; Srur, A. [CONICET, Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales (IANIGLA), Mendoza (Argentina); Kuettel, M. [University of Bern, Oeschger Centre for Climate Change Research (OCCR), Bern (Switzerland); University of Bern, Institute of Geography, Climatology and Meteorology, Bern (Switzerland); University of Washington, Department of Earth and Space Sciences, Seattle (United States); Frank, D. [Swiss Federal Research Institute WSL, Birmensdorf (Switzerland); Jones, P.D. [University of East Anglia, Climatic Research Unit, School of Environmental Sciences, Norwich (United Kingdom); Aravena, J.-C. [Centro de Estudios Cuaternarios de Fuego Patagonia y Antartica (CEQUA), Punta Arenas (Chile); Black, D.E. [Stony Brook University, School of Marine and Atmospheric Sciences, Stony Brook (United States); Christie, D.A.; Urrutia, R. [Universidad Austral de Chile Valdivia, Laboratorio de Dendrocronologia, Facultad de Ciencias Forestales y Recursos Naturales, Valdivia (Chile); D' Arrigo, R. [Earth Institute at Columbia University, Tree-Ring Laboratory, Lamont-Doherty Earth Observatory, Palisades, NY (United States); Lara, A. [Universidad Austral de Chile Valdivia, Laboratorio de Dendrocronologia, Facultad de Ciencias Forestales y Recursos Naturales, Valdivia (Chile); Nucleo Cientifico Milenio FORECOS, Fundacion FORECOS, Valdivia (Chile); Soliz-Gamboa, C. [Utrecht Univ., Inst. of Environmental Biology, Utrecht (Netherlands); Gunten, L. von [Univ. of Bern (Switzerland); Univ. of Massachusetts, Climate System Research Center, Amherst (United States)

2011-07-15

We statistically reconstruct austral summer (winter) surface air temperature fields back to ad 900 (1706) using 22 (20) annually resolved predictors from natural and human archives from southern South America (SSA). This represents the first regional-scale climate field reconstruction for parts of the Southern Hemisphere at this high temporal resolution. We apply three different reconstruction techniques: multivariate principal component regression, composite plus scaling, and regularized expectation maximization. There is generally good agreement between the results of the three methods on interannual and decadal timescales. The field reconstructions allow us to describe differences and similarities in the temperature evolution of different sub-regions of SSA. The reconstructed SSA mean summer temperatures between 900 and 1350 are mostly above the 1901-1995 climatology. After 1350, we reconstruct a sharp transition to colder conditions, which last until approximately 1700. The summers in the eighteenth century are relatively warm with a subsequent cold relapse peaking around 1850. In the twentieth century, summer temperatures reach conditions similar to earlier warm periods. The winter temperatures in the eighteenth and nineteenth centuries were mostly below the twentieth century average. The uncertainties of our reconstructions are generally largest in the eastern lowlands of SSA, where the coverage with proxy data is poorest. Verifications with independent summer temperature proxies and instrumental measurements suggest that the interannual and multi-decadal variations of SSA temperatures are well captured by our reconstructions. This new dataset can be used for data/model comparison and data assimilation as well as for detection and attribution studies at sub-continental scales. (orig.)

Hypothenar hammer syndrome: long-term results of vascular reconstruction.

Science.gov (United States)

Endress, Ryan D; Johnson, Craig H; Bishop, Allen T; Shin, Alexander Y

2015-04-01

To evaluate long-term patency rates and related outcomes after vascular reconstruction of hypothenar hammer syndrome and identify patient- or treatment-related factors that may contribute to differences in outcome. We used color flow ultrasound to determine the patency of 18 vein graft reconstructions of the ulnar artery at the wrist in 16 patients. Validated questionnaires evaluated patients' functional disability with the Disabilities of the Arm, Shoulder, and Hand score, pain with the visual analog scale, and cold intolerance with the Cold Intolerance Symptom Severity survey. Patient demographics, clinical data, and surgical factors were analyzed for association with graft failure. Patients were asked to grade the result of treatment on a scale of 0 to 10. Of 18 grafts, 14 (78%) were occluded at a mean of 118 months postoperatively. Patients with patent grafts had significantly less disability related to cold intolerance according to the Cold Intolerance Symptom Severity survey in addition to significantly less pain on the visual analog scale. There was no statistical difference in Disabilities of the Arm, Shoulder, and Hand scores between patients with patent or occluded grafts. Patients graded the result significantly higher in patent reconstructions. We noted a higher incidence of graft occlusion than previously reported at a mean follow-up of 9.8 years, which represents a long-duration follow-up study of surgical treatment of hypothenar hammer syndrome. Despite a high percentage of occlusion, overall, patients remained satisfied with low functional disability and all would recommend surgical reconstruction. This study suggests that improved outcomes may result from patent grafts in the long term. Prognostic IV. Copyright © 2015 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

Sparse/Low Rank Constrained Reconstruction for Dynamic PET Imaging.

Directory of Open Access Journals (Sweden)

Xingjian Yu

Full Text Available In dynamic Positron Emission Tomography (PET, an estimate of the radio activity concentration is obtained from a series of frames of sinogram data taken at ranging in duration from 10 seconds to minutes under some criteria. So far, all the well-known reconstruction algorithms require known data statistical properties. It limits the speed of data acquisition, besides, it is unable to afford the separated information about the structure and the variation of shape and rate of metabolism which play a major role in improving the visualization of contrast for some requirement of the diagnosing in application. This paper presents a novel low rank-based activity map reconstruction scheme from emission sinograms of dynamic PET, termed as SLCR representing Sparse/Low Rank Constrained Reconstruction for Dynamic PET Imaging. In this method, the stationary background is formulated as a low rank component while variations between successive frames are abstracted to the sparse. The resulting nuclear norm and l1 norm related minimization problem can also be efficiently solved by many recently developed numerical methods. In this paper, the linearized alternating direction method is applied. The effectiveness of the proposed scheme is illustrated on three data sets.

Tomographic reconstruction of OH* chemiluminescence in two interacting turbulent flames

International Nuclear Information System (INIS)

Worth, Nicholas A; Dawson, James R

2013-01-01

The tomographic reconstruction of OH* chemiluminescence was performed on two interacting turbulent premixed bluff-body stabilized flames under steady flow conditions and acoustic excitation. These measurements elucidate the complex three-dimensional (3D) vortex–flame interactions which have previously not been accessible. The experiment was performed using a single camera and intensifier, with multiple views acquired by repositioning the camera, permitting calculation of the mean and phase-averaged volumetric OH* distributions. The reconstructed flame structure and phase-averaged dynamics are compared with OH planar laser-induced fluorescence and flame surface density measurements for the first time. The volumetric data revealed that the large-scale vortex–flame structures formed along the shear layers of each flame collide when the two flames meet, resulting in complex 3D flame structures in between the two flames. With a fairly simple experimental setup, it is shown that the tomographic reconstruction of OH* chemiluminescence in forced flames is a powerful tool that can yield important physical insights into large-scale 3D flame dynamics that are important in combustion instability. (paper)

Tree Morphologic Plasticity Explains Deviation from Metabolic Scaling Theory in Semi-Arid Conifer Forests, Southwestern USA.

Directory of Open Access Journals (Sweden)

Tyson L Swetnam

Full Text Available A significant concern about Metabolic Scaling Theory (MST in real forests relates to consistent differences between the values of power law scaling exponents of tree primary size measures used to estimate mass and those predicted by MST. Here we consider why observed scaling exponents for diameter and height relationships deviate from MST predictions across three semi-arid conifer forests in relation to: (1 tree condition and physical form, (2 the level of inter-tree competition (e.g. open vs closed stand structure, (3 increasing tree age, and (4 differences in site productivity. Scaling exponent values derived from non-linear least-squares regression for trees in excellent condition (n = 381 were above the MST prediction at the 95% confidence level, while the exponent for trees in good condition were no different than MST (n = 926. Trees that were in fair or poor condition, characterized as diseased, leaning, or sparsely crowned had exponent values below MST predictions (n = 2,058, as did recently dead standing trees (n = 375. Exponent value of the mean-tree model that disregarded tree condition (n = 3,740 was consistent with other studies that reject MST scaling. Ostensibly, as stand density and competition increase trees exhibited greater morphological plasticity whereby the majority had characteristically fair or poor growth forms. Fitting by least-squares regression biases the mean-tree model scaling exponent toward values that are below MST idealized predictions. For 368 trees from Arizona with known establishment dates, increasing age had no significant impact on expected scaling. We further suggest height to diameter ratios below MST relate to vertical truncation caused by limitation in plant water availability. Even with environmentally imposed height limitation, proportionality between height and diameter scaling exponents were consistent with the predictions of MST.

Tree Morphologic Plasticity Explains Deviation from Metabolic Scaling Theory in Semi-Arid Conifer Forests, Southwestern USA.

Science.gov (United States)

Swetnam, Tyson L; O'Connor, Christopher D; Lynch, Ann M

2016-01-01

A significant concern about Metabolic Scaling Theory (MST) in real forests relates to consistent differences between the values of power law scaling exponents of tree primary size measures used to estimate mass and those predicted by MST. Here we consider why observed scaling exponents for diameter and height relationships deviate from MST predictions across three semi-arid conifer forests in relation to: (1) tree condition and physical form, (2) the level of inter-tree competition (e.g. open vs closed stand structure), (3) increasing tree age, and (4) differences in site productivity. Scaling exponent values derived from non-linear least-squares regression for trees in excellent condition (n = 381) were above the MST prediction at the 95% confidence level, while the exponent for trees in good condition were no different than MST (n = 926). Trees that were in fair or poor condition, characterized as diseased, leaning, or sparsely crowned had exponent values below MST predictions (n = 2,058), as did recently dead standing trees (n = 375). Exponent value of the mean-tree model that disregarded tree condition (n = 3,740) was consistent with other studies that reject MST scaling. Ostensibly, as stand density and competition increase trees exhibited greater morphological plasticity whereby the majority had characteristically fair or poor growth forms. Fitting by least-squares regression biases the mean-tree model scaling exponent toward values that are below MST idealized predictions. For 368 trees from Arizona with known establishment dates, increasing age had no significant impact on expected scaling. We further suggest height to diameter ratios below MST relate to vertical truncation caused by limitation in plant water availability. Even with environmentally imposed height limitation, proportionality between height and diameter scaling exponents were consistent with the predictions of MST.

Nutrient Uptake and Metabolism Along a Large Scale Tropical Physical-Chemical Gradient

Science.gov (United States)

Tromboni, F.; Neres-Lima, V.; Saltarelli, W. A.; Miwa, A. C. P.; Cunha, D. G. F.

2016-12-01

Nutrient spiraling is a whole-system approach for estimating nutrient uptake that can be used to assess aquatic ecosystems' responses to environmental change and anthropogenic impacts. Historically research on nutrient dynamic uptake in streams has focused on single nutrient dynamics and only rarely the stoichiometric uptake has been considered and linked to carbon metabolism driven by autotrophic and heterotrophic production. We investigated the relationship between uptake of phosphate (PO43-), nitrate (NO3-) ammonium (NH4+) and total dissolve nitrogen (DIN)/ PO43-; and gross primary production (GPP), respiration (R), and net ecosystem productivity (NEP) in six relatively pristine streams with differences regarding canopy cover and physical characteristics, located in a large scale gradient from tropical Atlantic Forest to an Atlantic forest/Cerrado (Brazilian Savanna) transition. We carried out whole stream instantaneous additions of PO43-, NO3- and NH4+ added to each stream in combination, using the TASCC (Tracer Additions for Spiraling Curve Characterization) method. Metabolism measurements were performed in the same streams right after uptake was measured, using one-station open channel method and re-aeration estimations for those sites. We found different background concentrations in the streams located in the Atlantic forest compared with the transition area with Cerrado. In general PO43- and NO3- uptake increased with the decreasing of canopy cover, while a positive relation with background concentration better explained NH4+uptake. DIN/PO43- uptake increased with increasing R and NEP. Little work on functional characteristics of pristine streams has been conducted in this region and this work provides an initial characterization on nitrogen and phosphorus dynamics as well as their stoichiometric uptake in streams.

Database Constraints Applied to Metabolic Pathway Reconstruction Tools

Directory of Open Access Journals (Sweden)

Jordi Vilaplana

2014-01-01

Full Text Available Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (reannotation of proteomes, to properly identify both the individual proteins involved in the process(es of interest and their function. It also enables the sets of proteins involved in the process(es in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.

Database constraints applied to metabolic pathway reconstruction tools.

Science.gov (United States)

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.

The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture.

Science.gov (United States)

Caetano-Anollés, Gustavo; Kim, Hee Shin; Mittenthal, Jay E

2007-05-29

Metabolism represents a complex collection of enzymatic reactions and transport processes that convert metabolites into molecules capable of supporting cellular life. Here we explore the origins and evolution of modern metabolism. Using phylogenomic information linked to the structure of metabolic enzymes, we sort out recruitment processes and discover that most enzymatic activities were associated with the nine most ancient and widely distributed protein fold architectures. An analysis of newly discovered functions showed enzymatic diversification occurred early, during the onset of the modern protein world. Most importantly, phylogenetic reconstruction exercises and other evidence suggest strongly that metabolism originated in enzymes with the P-loop hydrolase fold in nucleotide metabolism, probably in pathways linked to the purine metabolic subnetwork. Consequently, the first enzymatic takeover of an ancient biochemistry or prebiotic chemistry was related to the synthesis of nucleotides for the RNA world.

Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling

Directory of Open Access Journals (Sweden)

Dorines Rosario

2018-06-01

Full Text Available Dysbiosis in the gut microbiome composition may be promoted by therapeutic drugs such as metformin, the world’s most prescribed antidiabetic drug. Under metformin treatment, disturbances of the intestinal microbes lead to increased abundance of Escherichia spp., Akkermansia muciniphila, Subdoligranulum variabile and decreased abundance of Intestinibacter bartlettii. This alteration may potentially lead to adverse effects on the host metabolism, with the depletion of butyrate producer genus. However, an increased production of butyrate and propionate was verified in metformin-treated Type 2 diabetes (T2D patients. The mechanisms underlying these nutritional alterations and their relation with gut microbiota dysbiosis remain unclear. Here, we used Genome-scale Metabolic Models of the representative gut bacteria Escherichia spp., I. bartlettii, A. muciniphila, and S. variabile to elucidate their bacterial metabolism and its effect on intestinal nutrient pool, including macronutrients (e.g., amino acids and short chain fatty acids, minerals and chemical elements (e.g., iron and oxygen. We applied flux balance analysis (FBA coupled with synthetic lethality analysis interactions to identify combinations of reactions and extracellular nutrients whose absence prevents growth. Our analyses suggest that Escherichia sp. is the bacteria least vulnerable to nutrient availability. We have also examined bacterial contribution to extracellular nutrients including short chain fatty acids, amino acids, and gasses. For instance, Escherichia sp. and S. variabile may contribute to the production of important short chain fatty acids (e.g., acetate and butyrate, respectively involved in the host physiology under aerobic and anaerobic conditions. We have also identified pathway susceptibility to nutrient availability and reaction changes among the four bacteria using both FBA and flux variability analysis. For instance, lipopolysaccharide synthesis, nucleotide sugar

Multifractal signal reconstruction based on singularity power spectrum

International Nuclear Information System (INIS)

Xiong, Gang; Yu, Wenxian; Xia, Wenxiang; Zhang, Shuning

2016-01-01

Highlights: • We propose a novel multifractal reconstruction method based on singularity power spectrum analysis (MFR-SPS). • The proposed MFR-SPS method has better power characteristic than the algorithm in Fraclab. • Further, the SPS-ISE algorithm performs better than the SPS-MFS algorithm. • Based on the proposed MFR-SPS method, we can restructure singularity white fractal noise (SWFN) and linear singularity modulation (LSM) multifractal signal, in equivalent sense, similar with the linear frequency modulation(LFM) signal and WGN in the Fourier domain. - Abstract: Fractal reconstruction (FR) and multifractal reconstruction (MFR) can be considered as the inverse problem of singularity spectrum analysis, and it is challenging to reconstruct fractal signal in accord with multifractal spectrum (MFS). Due to the multiple solutions of fractal reconstruction, the traditional methods of FR/MFR, such as FBM based method, wavelet based method, random wavelet series, fail to reconstruct fractal signal deterministically, and besides, those methods neglect the power spectral distribution in the singular domain. In this paper, we propose a novel MFR method based singularity power spectrum (SPS). Supposing the consistent uniform covering of multifractal measurement, we control the traditional power law of each scale of wavelet coefficients based on the instantaneous singularity exponents (ISE) or MFS, simultaneously control the singularity power law based on the SPS, and deduce the principle and algorithm of MFR based on SPS. Reconstruction simulation and error analysis of estimated ISE, MFS and SPS show the effectiveness and the improvement of the proposed methods compared to those obtained by the Fraclab package.

Post-disaster housing reconstruction: Perspectives of the NGO and local authorities on delay issues

Science.gov (United States)

Khalid, Khairin Norhashidah; Nifa, Faizatul Akmar Abdul; Ismail, Risyawati Mohamed; Lin, Chong Khai

2016-08-01

Post disaster reconstruction is complex, dynamic and chaotic in nature and as such represents many challenges because it is unlike normal construction. However, the time scale of reconstruction is shorter than the normal construction, but it often deals with uncertainties and the scale of the construction activities required is relatively high. After a disaster impacts a country, many governments, institutions and aid organizations cooperate and involved with the reconstruction process. This is seen as a tool for applying policies and programs designed to remedy the weakness in developmental policies, infrastructure and institutional arrangements. This paper reports a part of an on-going research on post-disaster housing reconstruction in Malaysia. An extensive literature review and pilot interviews were undertaken to establish the factors that contribute to the delay in post-disaster reconstruction project. Accordingly, this paper takes the perspective of recovery from non-government organization (NGO) and local authorities which act as providers of social services, builders of infrastructure, regulators of economic activity and managers of the natural environment. As a result, it is important on how those decisions are made, who is involved in the decision-making, and what are the consequences of this decision.

Reconstructions with identical filling (RIF) of the heart: a physiological approach to image reconstruction in coronary CT angiography

International Nuclear Information System (INIS)

Reinartz, S.D.; Diefenbach, B.S.; Kuhl, C.K.; Mahnken, A.H.; Allmendinger, T.

2012-01-01

To compare image quality in coronary artery computed tomography angiography (cCTA) using reconstructions with automated phase detection and Reconstructions computed with Identical Filling of the heart (RIF). Seventy-four patients underwent ECG-gated dual source CT (DSCT) between November 2009 and July 2010 for suspected coronary heart disease (n = 35), planning of transcatheter aortic valve replacement (n = 34) or evaluation of ventricular function (n = 5). Image data sets by the RIF formula and automated phase detection were computed and evaluated with the AHA 15-segment model and a 5-grade Likert scale (1: poor, 5: excellent quality). Subgroups regarding rhythm (sinus rhythm = SR; arrhythmia = ARR) and potential premedication were evaluated by a per-segment, per-vessel and per-patient analysis. RIF significantly improved image quality in 10 of 15 coronary segments (P < 0.05). More diagnostic segments were provided by RIF regarding the entire cohort (n = 693 vs. 590, P < 0.001) and all of the subgroups (e.g. ARR: n = 143 vs. 72, P < 0.001). In arrhythmic patients (n = 19), more diagnostic vessels (e.g. LAD: n = 10 vs. 3; P < 0.014) and complete data sets (n = 7 vs. 1; P < 0.001) were produced. RIF reconstruction is superior to automatic diastolic non-edited reconstructions, especially in arrhythmic patients. RIF theory provides a physiological approach for determining the optimal image reconstruction point in ECG-gated CT angiography. (orig.)

Genome-scale metabolic modeling to provide insight into the production of storage compounds during feast-famine cycles of activated sludge.

Science.gov (United States)

Tajparast, Mohammad; Frigon, Dominic

2013-01-01

Studying storage metabolism during feast-famine cycles of activated sludge treatment systems provides profound insight in terms of both operational issues (e.g., foaming and bulking) and process optimization for the production of value added by-products (e.g., bioplastics). We examined the storage metabolism (including poly-β-hydroxybutyrate [PHB], glycogen, and triacylglycerols [TAGs]) during feast-famine cycles using two genome-scale metabolic models: Rhodococcus jostii RHA1 (iMT1174) and Escherichia coli K-12 (iAF1260) for growth on glucose, acetate, and succinate. The goal was to develop the proper objective function (OF) for the prediction of the main storage compound produced in activated sludge for given feast-famine cycle conditions. For the flux balance analysis, combinations of three OFs were tested. For all of them, the main OF was to maximize growth rates. Two additional sub-OFs were used: (1) minimization of biochemical fluxes, and (2) minimization of metabolic adjustments (MoMA) between the feast and famine periods. All (sub-)OFs predicted identical substrate-storage associations for the feast-famine growth of the above-mentioned metabolic models on a given substrate when glucose and acetate were set as sole carbon sources (i.e., glucose-glycogen and acetate-PHB), in agreement with experimental observations. However, in the case of succinate as substrate, the predictions depended on the network structure of the metabolic models such that the E. coli model predicted glycogen accumulation and the R. jostii model predicted PHB accumulation. While the accumulation of both PHB and glycogen was observed experimentally, PHB showed higher dynamics during an activated sludge feast-famine growth cycle with succinate as substrate. These results suggest that new modeling insights between metabolic predictions and population ecology will be necessary to properly predict metabolisms likely to emerge within the niches of activated sludge communities. Nonetheless

Least Square NUFFT Methods Applied to 2D and 3D Radially Encoded MR Image Reconstruction

Science.gov (United States)

Song, Jiayu; Liu, Qing H.; Gewalt, Sally L.; Cofer, Gary; Johnson, G. Allan

2009-01-01

Radially encoded MR imaging (MRI) has gained increasing attention in applications such as hyperpolarized gas imaging, contrast-enhanced MR angiography, and dynamic imaging, due to its motion insensitivity and improved artifact properties. However, since the technique collects k-space samples nonuniformly, multidimensional (especially 3D) radially sampled MRI image reconstruction is challenging. The balance between reconstruction accuracy and speed becomes critical when a large data set is processed. Kaiser-Bessel gridding reconstruction has been widely used for non-Cartesian reconstruction. The objective of this work is to provide an alternative reconstruction option in high dimensions with on-the-fly kernels calculation. The work develops general multi-dimensional least square nonuniform fast Fourier transform (LS-NUFFT) algorithms and incorporates them into a k-space simulation and image reconstruction framework. The method is then applied to reconstruct the radially encoded k-space, although the method addresses general nonuniformity and is applicable to any non-Cartesian patterns. Performance assessments are made by comparing the LS-NUFFT based method with the conventional Kaiser-Bessel gridding method for 2D and 3D radially encoded computer simulated phantoms and physically scanned phantoms. The results show that the LS-NUFFT reconstruction method has better accuracy-speed efficiency than the Kaiser-Bessel gridding method when the kernel weights are calculated on the fly. The accuracy of the LS-NUFFT method depends on the choice of scaling factor, and it is found that for a particular conventional kernel function, using its corresponding deapodization function as scaling factor and utilizing it into the LS-NUFFT framework has the potential to improve accuracy. When a cosine scaling factor is used, in particular, the LS-NUFFT method is faster than Kaiser-Bessel gridding method because of a quasi closed-form solution. The method is successfully applied to 2D and

Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification.

Science.gov (United States)

Cankorur-Cetinkaya, Ayca; Dikicioglu, Duygu; Oliver, Stephen G

2017-11-01

Genome-scale metabolic models are valuable tools for the design of novel strains of industrial microorganisms, such as Komagataella phaffii (syn. Pichia pastoris). However, as is the case for many industrial microbes, there is no executable metabolic model for K. phaffiii that confirms to current standards by providing the metabolite and reactions IDs, to facilitate model extension and reuse, and gene-reaction associations to enable identification of targets for genetic manipulation. In order to remedy this deficiency, we decided to reconstruct the genome-scale metabolic model of K. phaffii by reconciling the extant models and performing extensive manual curation in order to construct an executable model (Kp.1.0) that conforms to current standards. We then used this model to study the effect of biomass composition on the predictive success of the model. Twelve different biomass compositions obtained from published empirical data obtained under a range of growth conditions were employed in this investigation. We found that the success of Kp1.0 in predicting both gene essentiality and growth characteristics was relatively unaffected by biomass composition. However, we found that biomass composition had a profound effect on the distribution of the fluxes involved in lipid, DNA, and steroid biosynthetic processes, cellular alcohol metabolic process, and oxidation-reduction process. Furthermore, we investigated the effect of biomass composition on the identification of suitable target genes for strain development. The analyses revealed that around 40% of the predictions of the effect of gene overexpression or deletion changed depending on the representation of biomass composition in the model. Considering the robustness of the in silico flux distributions to the changing biomass representations enables better interpretation of experimental results, reduces the risk of wrong target identification, and so both speeds and improves the process of directed strain development

Color-coded volume rendering for three-dimensional reconstructions of CT data

International Nuclear Information System (INIS)

Rieker, O.; Mildenberger, P.; Thelen, M.

1999-01-01

Purpose: To evaluate a technique of colored three-dimensional reconstructions without segmentation. Material and methods: Color-coded volume rendered images were reconstructed from the volume data of 25 thoracic, abdominal, musculoskeletal, and vascular helical CT scans using commercial software. The CT volume rendered voxels were encoded with color in the following manner. Opacity, hue, lightness, and chroma were assigned to each of four classes defined by CT number. Color-coded reconstructions were compared to the corresponding grey-scale coded reconstructions. Results: Color-coded volume rendering enabled realistic visualization of pathologic findings when there was sufficient difference in CT density. Segmentation was necessary in some cases to demonstrate small details in a complex volume. Conclusion: Color-coded volume rendering allowed lifelike visualisation of CT volumes without the need of segmentation in most cases. (orig.) [de

Control of fluxes in metabolic networks

Science.gov (United States)

Basler, Georg; Nikoloski, Zoran; Larhlimi, Abdelhalim; Barabási, Albert-László; Liu, Yang-Yu

2016-01-01

Understanding the control of large-scale metabolic networks is central to biology and medicine. However, existing approaches either require specifying a cellular objective or can only be used for small networks. We introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. We identify the driver reactions facilitating control of 23 metabolic networks from all kingdoms of life. We find that unicellular organisms require a smaller degree of control than multicellular organisms. Driver reactions are under complex cellular regulation in Escherichia coli, indicating their preeminent role in facilitating cellular control. In human cancer cells, driver reactions play pivotal roles in malignancy and represent potential therapeutic targets. The developed framework helps us gain insights into regulatory principles of diseases and facilitates design of engineering strategies at the interface of gene regulation, signaling, and metabolism. PMID:27197218

Perturbation theory for BAO reconstructed fields: One-loop results in the real-space matter density field

Science.gov (United States)

Hikage, Chiaki; Koyama, Kazuya; Heavens, Alan

2017-08-01

We compute the power spectrum at one-loop order in standard perturbation theory for the matter density field to which a standard Lagrangian baryonic acoustic oscillation (BAO) reconstruction technique is applied. The BAO reconstruction method corrects the bulk motion associated with the gravitational evolution using the inverse Zel'dovich approximation (ZA) for the smoothed density field. We find that the overall amplitude of one-loop contributions in the matter power spectrum substantially decreases after reconstruction. The reconstructed power spectrum thereby approaches the initial linear spectrum when the smoothed density field is close enough to linear, i.e., the smoothing scale Rs≳10 h-1 Mpc . On smaller Rs, however, the deviation from the linear spectrum becomes significant on large scales (k ≲Rs-1 ) due to the nonlinearity in the smoothed density field, and the reconstruction is inaccurate. Compared with N-body simulations, we show that the reconstructed power spectrum at one-loop order agrees with simulations better than the unreconstructed power spectrum. We also calculate the tree-level bispectrum in standard perturbation theory to investigate non-Gaussianity in the reconstructed matter density field. We show that the amplitude of the bispectrum significantly decreases for small k after reconstruction and that the tree-level bispectrum agrees well with N-body results in the weakly nonlinear regime.

A computational geometry framework for the optimisation of atom probe reconstructions

Energy Technology Data Exchange (ETDEWEB)

Felfer, Peter [Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006 (Australia); Institute for General Materials Properties, Department of Materials Science, Friedrich-Alexander University Erlangen-Nürnberg, 91058 Erlangen (Germany); Cairney, Julie [Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006 (Australia)

2016-10-15

In this paper, we present pathways for improving the reconstruction of atom probe data on a coarse (>10 nm) scale, based on computational geometry. We introduce a way to iteratively improve an atom probe reconstruction by adjusting it, so that certain known shape criteria are fulfilled. This is achieved by creating an implicit approximation of the reconstruction through a barycentric coordinate transform. We demonstrate the application of these techniques to the compensation of trajectory aberrations and the iterative improvement of the reconstruction of a dataset containing a grain boundary. We also present a method for obtaining a hull of the dataset in both detector and reconstruction space. This maximises data utilisation, and can be used to compensate for ion trajectory aberrations caused by residual fields in the ion flight path through a ‘master curve’ and correct for overall shape deviations in the data. - Highlights: • An atom probe reconstruction can be iteratively improved by using shape constraints. • An atom probe reconstruction can be inverted using barycentric coordinate transforms. • Hulls for atom probe datasets can be obtained from 2D detector outlines that are co-reconstructed with the data. • Ion trajectory compressions caused by instrument-specific residual fields in the drift tube can be corrected.

Ekofisk chalk: core measurements, stochastic reconstruction, network modeling and simulation

Energy Technology Data Exchange (ETDEWEB)

Talukdar, Saifullah

2002-07-01

This dissertation deals with (1) experimental measurements on petrophysical, reservoir engineering and morphological properties of Ekofisk chalk, (2) numerical simulation of core flood experiments to analyze and improve relative permeability data, (3) stochastic reconstruction of chalk samples from limited morphological information, (4) extraction of pore space parameters from the reconstructed samples, development of network model using pore space information, and computation of petrophysical and reservoir engineering properties from network model, and (5) development of 2D and 3D idealized fractured reservoir models and verification of the applicability of several widely used conventional up scaling techniques in fractured reservoir simulation. Experiments have been conducted on eight Ekofisk chalk samples and porosity, absolute permeability, formation factor, and oil-water relative permeability, capillary pressure and resistivity index are measured at laboratory conditions. Mercury porosimetry data and backscatter scanning electron microscope images have also been acquired for the samples. A numerical simulation technique involving history matching of the production profiles is employed to improve the relative permeability curves and to analyze hysteresis of the Ekofisk chalk samples. The technique was found to be a powerful tool to supplement the uncertainties in experimental measurements. Porosity and correlation statistics obtained from backscatter scanning electron microscope images are used to reconstruct microstructures of chalk and particulate media. The reconstruction technique involves a simulated annealing algorithm, which can be constrained by an arbitrary number of morphological parameters. This flexibility of the algorithm is exploited to successfully reconstruct particulate media and chalk samples using more than one correlation functions. A technique based on conditional simulated annealing has been introduced for exact reproduction of vuggy

Industrial dynamic tomographic reconstruction; Reconstrucao tomografica dinamica industrial

Energy Technology Data Exchange (ETDEWEB)

Oliveira, Eric Ferreira de

2016-07-01

The state of the art methods applied to industrial processes is currently based on the principles of classical tomographic reconstructions developed for tomographic patterns of static distributions, or is limited to cases of low variability of the density distribution function of the tomographed object. Noise and motion artifacts are the main problems caused by a mismatch in the data from views acquired in different instants. All of these add to the known fact that using a limited amount of data can result in the presence of noise, artifacts and some inconsistencies with the distribution under study. One of the objectives of the present work is to discuss the difficulties that arise from implementing reconstruction algorithms in dynamic tomography that were originally developed for static distributions. Another objective is to propose solutions that aim at reducing a temporal type of information loss caused by employing regular acquisition systems to dynamic processes. With respect to dynamic image reconstruction it was conducted a comparison between different static reconstruction methods, like MART and FBP, when used for dynamic scenarios. This comparison was based on a MCNPx simulation as well as an analytical setup of an aluminum cylinder that moves along the section of a riser during the process of acquisition, and also based on cross section images from CFD techniques. As for the adaptation of current tomographic acquisition systems for dynamic processes, this work established a sequence of tomographic views in a just-in-time fashion for visualization purposes, a form of visually disposing density information as soon as it becomes amenable to image reconstruction. A third contribution was to take advantage of the triple color channel necessary to display colored images in most displays, so that, by appropriately scaling the acquired values of each view in the linear system of the reconstruction, it was possible to imprint a temporal trace into the regularly

Nasoseptal flap for palatal reconstruction after hemi-maxillectomy: case report.

Science.gov (United States)

Alwashahi, M K; Battaglia, P; Turri-Zanoni, M; Castelnuovo, P

2018-01-01

Palatal reconstruction following maxillectomy is a surgical challenge, and a nasoseptal flap is a feasible approach. This paper reports the first known successful clinical case of a nasoseptal pedicle flap applied for the reconstruction of maxillary bone following hemi-maxillectomy. This report describes hemi-maxillectomy in a 60-year-old Italian male diagnosed with stage IV squamous cell carcinoma of the left maxilla. Endoscopic transnasal extended medial maxillectomy was performed, followed by a transoral modified midfacial degloving technique for removal of the maxillary bone. The contralateral nasoseptal pedicle flap was used to reconstruct the defect. The case was followed up prospectively for the assessment of flap reception and healing. The locally accessible nasoseptal flap is a viable alternative for palatal reconstruction; therefore, a second surgical procedure with its associated donor site morbidity can be avoided. Large-scale studies may help in establishing the cosmetic and functional outcomes.

Clinical update on metabolic syndrome

Directory of Open Access Journals (Sweden)

Juan Diego Hernández-Camacho

2017-12-01

Full Text Available Metabolic syndrome has been defined as a global issue since it affects a lot of people. Numerous factors are involved in metabolic syndrome development. It has been described that metabolic syndrome has negative consequences on health. Consequently, a lot of treatments have been proposed to palliate it such as drugs, surgery or life style changes where nutritional habits have shown to be an important point in its management. The current study reviews the literature existing about the actual epidemiology of metabolic syndrome, the components involucrate in its appearance and progression, the clinical consequences of metabolic syndrome and the nutritional strategies reported in its remission. A bibliographic search in PubMed and Medline was performed to identify eligible studies. Authors obtained that metabolic syndrome is present in population from developed and undeveloped areas in a huge scale. Environmental and genetic elements are involucrate in metabolic syndrome development. Metabolic syndrome exponentially increased risk of cardiovascular disease, some types of cancers, diabetes mellitus type 2, sleep disturbances, etc. Nutritional treatments play a crucial role in metabolic syndrome prevention, treatment and recovery.

The study of urban metabolism and its applications to urban planning and design

International Nuclear Information System (INIS)

Kennedy, C.; Pincetl, S.; Bunje, P.

2011-01-01

Following formative work in the 1970s, disappearance in the 1980s, and reemergence in the 1990s, a chronological review shows that the past decade has witnessed increasing interest in the study of urban metabolism. The review finds that there are two related, non-conflicting, schools of urban metabolism: one following Odum describes metabolism in terms of energy equivalents; while the second more broadly expresses a city's flows of water, materials and nutrients in terms of mass fluxes. Four example applications of urban metabolism studies are discussed: urban sustainability indicators; inputs to urban greenhouse gas emissions calculation; mathematical models of urban metabolism for policy analysis; and as a basis for sustainable urban design. Future directions include fuller integration of social, health and economic indicators into the urban metabolism framework, while tackling the great sustainability challenge of reconstructing cities. - This paper presents a chronological review of urban metabolism studies and highlights four areas of application.

GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

Directory of Open Access Journals (Sweden)

Radhakrishnan Mahadevan

2012-10-01

With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

Regime Behavior in Paleo-Reconstructed Streamflow: Attributions to Atmospheric Dynamics, Synoptic Circulation and Large-Scale Climate Teleconnection Patterns

Science.gov (United States)

Ravindranath, A.; Devineni, N.

2017-12-01

Studies have shown that streamflow behavior and dynamics have a significant link with climate and climate variability. Patterns of persistent regime behavior from extended streamflow records in many watersheds justify investigating large-scale climate mechanisms as potential drivers of hydrologic regime behavior and streamflow variability. Understanding such streamflow-climate relationships is crucial to forecasting/simulation systems and the planning and management of water resources. In this study, hidden Markov models are used with reconstructed streamflow to detect regime-like behaviors - the hidden states - and state transition phenomena. Individual extreme events and their spatial variability across the basin are then verified with the identified states. Wavelet analysis is performed to examine the signals over time in the streamflow records. Joint analyses of the climatic data in the 20th century and the identified states are undertaken to better understand the hydroclimatic connections within the basin as well as important teleconnections that influence water supply. Compositing techniques are used to identify atmospheric circulation patterns associated with identified states of streamflow. The grouping of such synoptic patterns and their frequency are then examined. Sliding time-window correlation analysis and cross-wavelet spectral analysis are performed to establish the synchronicity of basin flows to the identified synoptic and teleconnection patterns. The Missouri River Basin (MRB) is examined in this study, both as a means of better understanding the synoptic climate controls in this important watershed and as a case study for the techniques developed here. Initial wavelet analyses of reconstructed streamflow at major gauges in the MRB show multidecadal cycles in regime behavior.

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

DEFF Research Database (Denmark)

Herrgard, Markus; Swainston, Neil; Dobson, Paul

2008-01-01

and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology...

Genome-reconstruction for eukaryotes from complex natural microbial communities.

Science.gov (United States)

West, Patrick T; Probst, Alexander J; Grigoriev, Igor V; Thomas, Brian C; Banfield, Jillian F

2018-04-01

Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities. © 2018 West et al.; Published by Cold Spring Harbor Laboratory Press.

A novel neural network based image reconstruction model with scale and rotation invariance for target identification and classification for Active millimetre wave imaging

Science.gov (United States)

Agarwal, Smriti; Bisht, Amit Singh; Singh, Dharmendra; Pathak, Nagendra Prasad

2014-12-01

Millimetre wave imaging (MMW) is gaining tremendous interest among researchers, which has potential applications for security check, standoff personal screening, automotive collision-avoidance, and lot more. Current state-of-art imaging techniques viz. microwave and X-ray imaging suffers from lower resolution and harmful ionizing radiation, respectively. In contrast, MMW imaging operates at lower power and is non-ionizing, hence, medically safe. Despite these favourable attributes, MMW imaging encounters various challenges as; still it is very less explored area and lacks suitable imaging methodology for extracting complete target information. Keeping in view of these challenges, a MMW active imaging radar system at 60 GHz was designed for standoff imaging application. A C-scan (horizontal and vertical scanning) methodology was developed that provides cross-range resolution of 8.59 mm. The paper further details a suitable target identification and classification methodology. For identification of regular shape targets: mean-standard deviation based segmentation technique was formulated and further validated using a different target shape. For classification: probability density function based target material discrimination methodology was proposed and further validated on different dataset. Lastly, a novel artificial neural network based scale and rotation invariant, image reconstruction methodology has been proposed to counter the distortions in the image caused due to noise, rotation or scale variations. The designed neural network once trained with sample images, automatically takes care of these deformations and successfully reconstructs the corrected image for the test targets. Techniques developed in this paper are tested and validated using four different regular shapes viz. rectangle, square, triangle and circle.

Image quality of iterative reconstruction in cranial CT imaging: comparison of model-based iterative reconstruction (MBIR) and adaptive statistical iterative reconstruction (ASiR)

Energy Technology Data Exchange (ETDEWEB)

Notohamiprodjo, S.; Deak, Z.; Meurer, F.; Maertz, F.; Mueck, F.G.; Geyer, L.L.; Wirth, S. [Ludwig-Maximilians University Hospital of Munich, Institute for Clinical Radiology, Munich (Germany)

2015-01-15

The purpose of this study was to compare cranial CT (CCT) image quality (IQ) of the MBIR algorithm with standard iterative reconstruction (ASiR). In this institutional review board (IRB)-approved study, raw data sets of 100 unenhanced CCT examinations (120 kV, 50-260 mAs, 20 mm collimation, 0.984 pitch) were reconstructed with both ASiR and MBIR. Signal-to-noise (SNR) and contrast-to-noise (CNR) were calculated from attenuation values measured in caudate nucleus, frontal white matter, anterior ventricle horn, fourth ventricle, and pons. Two radiologists, who were blinded to the reconstruction algorithms, evaluated anonymized multiplanar reformations of 2.5 mm with respect to depiction of different parenchymal structures and impact of artefacts on IQ with a five-point scale (0: unacceptable, 1: less than average, 2: average, 3: above average, 4: excellent). MBIR decreased artefacts more effectively than ASiR (p < 0.01). The median depiction score for MBIR was 3, whereas the median value for ASiR was 2 (p < 0.01). SNR and CNR were significantly higher in MBIR than ASiR (p < 0.01). MBIR showed significant improvement of IQ parameters compared to ASiR. As CCT is an examination that is frequently required, the use of MBIR may allow for substantial reduction of radiation exposure caused by medical diagnostics. (orig.)

Image quality of iterative reconstruction in cranial CT imaging: comparison of model-based iterative reconstruction (MBIR) and adaptive statistical iterative reconstruction (ASiR)

International Nuclear Information System (INIS)

Notohamiprodjo, S.; Deak, Z.; Meurer, F.; Maertz, F.; Mueck, F.G.; Geyer, L.L.; Wirth, S.

2015-01-01

The purpose of this study was to compare cranial CT (CCT) image quality (IQ) of the MBIR algorithm with standard iterative reconstruction (ASiR). In this institutional review board (IRB)-approved study, raw data sets of 100 unenhanced CCT examinations (120 kV, 50-260 mAs, 20 mm collimation, 0.984 pitch) were reconstructed with both ASiR and MBIR. Signal-to-noise (SNR) and contrast-to-noise (CNR) were calculated from attenuation values measured in caudate nucleus, frontal white matter, anterior ventricle horn, fourth ventricle, and pons. Two radiologists, who were blinded to the reconstruction algorithms, evaluated anonymized multiplanar reformations of 2.5 mm with respect to depiction of different parenchymal structures and impact of artefacts on IQ with a five-point scale (0: unacceptable, 1: less than average, 2: average, 3: above average, 4: excellent). MBIR decreased artefacts more effectively than ASiR (p < 0.01). The median depiction score for MBIR was 3, whereas the median value for ASiR was 2 (p < 0.01). SNR and CNR were significantly higher in MBIR than ASiR (p < 0.01). MBIR showed significant improvement of IQ parameters compared to ASiR. As CCT is an examination that is frequently required, the use of MBIR may allow for substantial reduction of radiation exposure caused by medical diagnostics. (orig.)

Effect of vibration on osteoblastic and osteoclastic activities: Analysis of bone metabolism using goldfish scale as a model for bone

Science.gov (United States)

Suzuki, N.; Kitamura, K.; Nemoto, T.; Shimizu, N.; Wada, S.; Kondo, T.; Tabata, M. J.; Sodeyama, F.; Ijiri, K.; Hattori, A.

In osteoclastic activity during space flight as well as hind limb unloading by tail suspension, inconsistent results have been reported in an in vivo study. The bone matrix plays an important role in the response to physical stress. However, there is no suitable in vitro co-culture system of osteoblasts and osteoclasts including bone matrix. On the other hand, fish scale is a calcified tissue that contains osteoblasts, osteoclasts, and bone matrix, all of which are similar to those found in human bones. Recently, we developed a new in vitro model system using goldfish scale. This system can detect the activities of osteoclasts and osteoblasts with tartrate-resistant acid phosphatase and alkaline phosphatase as the respective markers and precisely analyze the co-relationship between osteoblasts and osteoclasts. Using this system, we analyzed the bone metabolism under various degrees of acceleration (0.5-, 1-, 2-, 4-, and 6-G) by vibration with a G-load apparatus. After loading for 5 and 10 min, the scales were incubated for 6 and 24 h. The osteoblastic and osteoclastic activities were then measured. The osteoblastic activities gradually increased corresponding to 1-G to 6-G acceleration. In addition, ER mRNA expression was the highest under 6-G acceleration. On the other hand, the osteoclastic activity decreased at 24 h of incubation under low acceleration (0.5- and 1-G). This change coincided with TRAP mRNA expression. Under 2-G acceleration, the strength of suppression in osteoclastic activity was the highest. The strength of the inhibitory action under 4- and 6-G acceleration was lower than that under 2-G acceleration. In our co-culture system, osteoblasts and osteoclasts in the scale sensitively responded to several degrees of acceleration. Therefore, we strongly believe that our in vitro co-culture system is useful for the analysis of bone metabolism under loading or unloading.

Parallel MR image reconstruction using augmented Lagrangian methods.

Science.gov (United States)

Ramani, Sathish; Fessler, Jeffrey A

2011-03-01

Magnetic resonance image (MRI) reconstruction using SENSitivity Encoding (SENSE) requires regularization to suppress noise and aliasing effects. Edge-preserving and sparsity-based regularization criteria can improve image quality, but they demand computation-intensive nonlinear optimization. In this paper, we present novel methods for regularized MRI reconstruction from undersampled sensitivity encoded data--SENSE-reconstruction--using the augmented Lagrangian (AL) framework for solving large-scale constrained optimization problems. We first formulate regularized SENSE-reconstruction as an unconstrained optimization task and then convert it to a set of (equivalent) constrained problems using variable splitting. We then attack these constrained versions in an AL framework using an alternating minimization method, leading to algorithms that can be implemented easily. The proposed methods are applicable to a general class of regularizers that includes popular edge-preserving (e.g., total-variation) and sparsity-promoting (e.g., l(1)-norm of wavelet coefficients) criteria and combinations thereof. Numerical experiments with synthetic and in vivo human data illustrate that the proposed AL algorithms converge faster than both general-purpose optimization algorithms such as nonlinear conjugate gradient (NCG) and state-of-the-art MFISTA.

Monthly paleostreamflow reconstruction from annual tree-ring chronologies

Science.gov (United States)

Stagge, J. H.; Rosenberg, D. E.; DeRose, R. J.; Rittenour, T. M.

2018-02-01

Paleoclimate reconstructions are increasingly used to characterize annual climate variability prior to the instrumental record, to improve estimates of climate extremes, and to provide a baseline for climate-change projections. To date, paleoclimate records have seen limited engineering use to estimate hydrologic risks because water systems models and managers usually require streamflow input at the monthly scale. This study explores the hypothesis that monthly streamflows can be adequately modeled by statistically decomposing annual flow reconstructions. To test this hypothesis, a multiple linear regression model for monthly streamflow reconstruction is presented that expands the set of predictors to include annual streamflow reconstructions, reconstructions of global circulation, and potential differences among regional tree-ring chronologies related to tree species and geographic location. This approach is used to reconstruct 600 years of monthly streamflows at two sites on the Bear and Logan rivers in northern Utah. Nash-Sutcliffe Efficiencies remain above zero (0.26-0.60) for all months except April and Pearson's correlation coefficients (R) are 0.94 and 0.88 for the Bear and Logan rivers, respectively, confirming that the model can adequately reproduce monthly flows during the reference period (10/1942 to 9/2015). Incorporating a flexible transition between the previous and concurrent annual reconstructed flows was the most important factor for model skill. Expanding the model to include global climate indices and regional tree-ring chronologies produced smaller, but still significant improvements in model fit. The model presented here is the only approach currently available to reconstruct monthly streamflows directly from tree-ring chronologies and climate reconstructions, rather than using resampling of the observed record. With reasonable estimates of monthly flow that extend back in time many centuries, water managers can challenge systems models with a

TREE STEM RECONSTRUCTION USING VERTICAL FISHEYE IMAGES: A PRELIMINARY STUDY

Directory of Open Access Journals (Sweden)

A. Berveglieri

2016-06-01

Full Text Available A preliminary study was conducted to assess a tree stem reconstruction technique with panoramic images taken with fisheye lenses. The concept is similar to the Structure from Motion (SfM technique, but the acquisition and data preparation rely on fisheye cameras to generate a vertical image sequence with height variations of the camera station. Each vertical image is rectified to four vertical planes, producing horizontal lateral views. The stems in the lateral view are rectified to the same scale in the image sequence to facilitate image matching. Using bundle adjustment, the stems are reconstructed, enabling later measurement and extraction of several attributes. The 3D reconstruction was performed with the proposed technique and compared with SfM. The preliminary results showed that the stems were correctly reconstructed by using the lateral virtual images generated from the vertical fisheye images and with the advantage of using fewer images and taken from one single station.

Robust, Efficient Depth Reconstruction With Hierarchical Confidence-Based Matching.

Science.gov (United States)

Sun, Li; Chen, Ke; Song, Mingli; Tao, Dacheng; Chen, Gang; Chen, Chun

2017-07-01

In recent years, taking photos and capturing videos with mobile devices have become increasingly popular. Emerging applications based on the depth reconstruction technique have been developed, such as Google lens blur. However, depth reconstruction is difficult due to occlusions, non-diffuse surfaces, repetitive patterns, and textureless surfaces, and it has become more difficult due to the unstable image quality and uncontrolled scene condition in the mobile setting. In this paper, we present a novel hierarchical framework with multi-view confidence-based matching for robust, efficient depth reconstruction in uncontrolled scenes. Particularly, the proposed framework combines local cost aggregation with global cost optimization in a complementary manner that increases efficiency and accuracy. A depth map is efficiently obtained in a coarse-to-fine manner by using an image pyramid. Moreover, confidence maps are computed to robustly fuse multi-view matching cues, and to constrain the stereo matching on a finer scale. The proposed framework has been evaluated with challenging indoor and outdoor scenes, and has achieved robust and efficient depth reconstruction.

Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality

DEFF Research Database (Denmark)

Kim, Hyun Uk; Kim, Byoungjin; Seung, Do Young

2014-01-01

reactions are more frequently introduced into various microbial hosts. The genome-scale metabolic simulations of Escherichia coli strains engineered to produce 1,4-butanediol, 1,3-propanediol, and amorphadiene suggest that microbial metabolism shows much different responses to the introduced heterologous...... reactions in a strain-specific manner than typical gene knockouts in terms of the energetic status (e.g., ATP and biomass generation) and chemical production capacity. The 1,4-butanediol and 1,3-propanediol producers showed greater metabolic optimality than the wild-type strains and gene knockout mutants...... for the energetic status, while the amorphadiene producer was metabolically less optimal. For the optimal chemical production capacity, additional gene knockouts were most effective for the strain producing 1,3-propanediol, but not for the one producing 1,4-butanediol. These observations suggest that strains having...

Tree-ring temperature reconstructions for the northeastern United States from Chamaecyparis thyoides

Science.gov (United States)

Anchukaitis, K. J.; Pederson, N.; Pearl, J. K.; Donnelly, J. P.

2014-12-01

Over the last century, the northeastern United States has warmed by over 1C, with the region of strongest warming found in coastal Massachusetts, Connecticut, and Rhode Island. These states are amongst the fastest warming in the entire country and the region as a whole is also warming faster than the national average. While these records all appear exceptional in the context of the last century, it is not known how these compare on longer time scales, to potential preindustrial late Holocene warm epochs, and in the context of decadal-scale variability in regional climate. Here, we develop a January through August temperature reconstruction using three Chamaecyparis thyoides (Atlantic White Cedar) chronologies in Massachusetts and Maine. The chronologies show a strong winter-spring-summer temperature signal representative of temperature variability from southern New York to northeastern Maine. The reconstruction is skillful and tracks upwards temperature trends since the early 19th century, reproducing decadal scale variability associated with warming from the 1920s through 1940s, cooling in the region from the 1940s until the 1960s, and warming since that time. No year since at least the middle of the 19th century is as warm as the Janaury through August temperatures seen in the exceptionally warm 2012. Recent modeling experiments simulate a range of decadal warming trends for the northeastern United States that is slightly higher than the reconstructed and instrumental trends. Atlantic White Cedar holds the potential to develop multicentury temperature reconstructions from this heavily-populated region.

Algebraic reconstruction techniques for spectral reconstruction in diffuse optical tomography

International Nuclear Information System (INIS)

Brendel, Bernhard; Ziegler, Ronny; Nielsen, Tim

2008-01-01

Reconstruction in diffuse optical tomography (DOT) necessitates solving the diffusion equation, which is nonlinear with respect to the parameters that have to be reconstructed. Currently applied solving methods are based on the linearization of the equation. For spectral three-dimensional reconstruction, the emerging equation system is too large for direct inversion, but the application of iterative methods is feasible. Computational effort and speed of convergence of these iterative methods are crucial since they determine the computation time of the reconstruction. In this paper, the iterative methods algebraic reconstruction technique (ART) and conjugated gradients (CGs) as well as a new modified ART method are investigated for spectral DOT reconstruction. The aim of the modified ART scheme is to speed up the convergence by considering the specific conditions of spectral reconstruction. As a result, it converges much faster to favorable results than conventional ART and CG methods

Psychological Factors Associated With Anterior Cruciate Ligament Reconstruction Recovery.

Science.gov (United States)

Christino, Melissa A; Fleming, Braden C; Machan, Jason T; Shalvoy, Robert M

2016-03-01

Psychological factors may have underappreciated effects on surgical outcomes after anterior cruciate ligament (ACL) reconstruction; however, few studies have investigated the relationship between specific psychological factors, objective clinical data, and patient-oriented outcomes. Psychological factors are significantly associated with patient perceptions and functional outcomes after ACL reconstruction. The purpose of this study was to demonstrate relationships between self-esteem, health locus of control, and psychological distress with objective clinical outcomes, patient-oriented outcomes, and return to sport. Cross-sectional study; Level of evidence, 3. Twenty-seven patients who were 6 to 24 months post-computer-assisted ACL reconstruction by a single surgeon consented to participate in the study (52% response rate). Participants had a 1-time visit with a physician consisting of: a physical examination, a single-leg hop test, KT-1000 arthrometer measurements, and survey completion. Psychological measures included the Multidimensional Health Locus of Control Scale, Rosenberg Self-Esteem Scale, and Brief Profile of Mood States. Outcome measures included the Tegner activity scale, International Knee Documentation Committee (IKDC) Subjective Knee Score, Knee injury and Osteoarthritis Outcome Score-Quality of Life subscale (KOOS-QOL), and Short Form-36 (SF-36). Patient charts were also reviewed for pertinent operative details. The mean age of patients (±SD) was 25.7 ± 8.4 years, and the mean duration of time since surgery was 16.5 ± 5.9 months. The majority (89%) of the patients identified themselves as athletes, and of these, 65% reported returning to sports at a competitive level. Sport returners were found to have higher levels of self-esteem (P = .002) and higher reported KOOS-QOL scores (P = .02). Self-esteem was significantly associated with IKDC scores (r = 0.46, P Self-esteem levels and locus of control had significant relationships with functional

Coronary CT angiography: Comparison of a novel iterative reconstruction with filtered back projection for reconstruction of low-dose CT—Initial experience

International Nuclear Information System (INIS)

Takx, Richard A.P.; Schoepf, U. Joseph; Moscariello, Antonio; Das, Marco; Rowe, Garrett; Schoenberg, Stefan O.; Fink, Christian; Henzler, Thomas

2013-01-01

Objective: To prospectively compare subjective and objective image quality in 20% tube current coronary CT angiography (cCTA) datasets between an iterative reconstruction algorithm (SAFIRE) and traditional filtered back projection (FBP). Materials and methods: Twenty patients underwent a prospectively ECG-triggered dual-step cCTA protocol using 2nd generation dual-source CT (DSCT). CT raw data was reconstructed using standard FBP at full-dose (Group 1 a) and 80% tube current reduced low-dose (Group 1 b). The low-dose raw data was additionally reconstructed using iterative raw data reconstruction (Group 2 ). Attenuation and image noise were measured in three regions of interest and signal-to-noise-ratio (SNR) as well as contrast-to-noise-ratio (CNR) was calculated. Subjective diagnostic image quality was evaluated using a 4-point Likert scale. Results: Mean image noise of group 2 was lowered by 22% on average when compared to group 1 b (p 2 compared to group 1 b (p 2 (1.88 ± 0.63) was also rated significantly higher when compared to group 1 b (1.58 ± 0.63, p = 0.004). Conclusions: Image quality of 80% tube current reduced iteratively reconstructed cCTA raw data is significantly improved when compared to standard FBP and consequently may improve the diagnostic accuracy of cCTA

Predictors of satisfaction and quality of life following post-mastectomy breast reconstruction.

Science.gov (United States)

Matthews, Hannah; Carroll, Natalie; Renshaw, Derek; Turner, Andrew; Park, Alan; Skillman, Jo; McCarthy, Kate; Grunfeld, Elizabeth A

2017-11-01

Breast reconstruction is associated with multiple psychological benefits. However, few studies have identified clinical and psychological factors associated with improved satisfaction and quality of life. This study examined factors, which predict satisfaction with breast appearance, outcome satisfaction and quality of life following post-mastectomy breast reconstruction. Women who underwent post-mastectomy breast reconstruction between 2010 and 2016 received a postal questionnaire consisting of The BREAST-Q Patient Reported Outcomes Instrument, The European Organisation for Research and Treatment of Cancer QLQ-30 Questionnaire, The Patient and Observer Scar Assessment Scale, and a series of Visual-Analogue Scales. One hundredforty-eight women completed the questionnaire, a 56% response rate. Hierarchical multiple regression analyses revealed psychosocial factors accounted for 75% of the variance in breast satisfaction, 68% for outcome satisfaction, and 46% forquality of life. Psychosocial well-being emerged as a significant predictor of satisfaction with breast appearance (β = .322) and outcome satisfaction (β = .406). Deep inferior epigastric perforator flap patients reported greater satisfaction with breast appearance (β = .120) and outcome satisfaction (β = .167). This study extends beyond the limited research by distinguishing between satisfaction with breast appearance and outcome satisfaction. The study provides evidence for the role of psychosocial factors predicting key patient reported outcomes and demonstrates the importance of psychosocial well-being and reconstruction type. The findings also highlight the need for healthcare providers to consider the psychosocial well-being of patients both preoperatively and post operatively and provide preliminary evidence for the use of deep inferior epigastric perforator reconstructions over other types of reconstructive procedures. Copyright © 2017 John Wiley & Sons, Ltd.

Automatic selection of optimal systolic and diastolic reconstruction windows for dual-source CT coronary angiography

International Nuclear Information System (INIS)

Seifarth, H.; Puesken, M.; Wienbeck, S.; Maintz, D.; Heindel, W.; Juergens, K.U.; Fischbach, R.

2009-01-01

The aim of this study was to assess the performance of a motion-map algorithm that automatically determines optimal reconstruction windows for dual-source coronary CT angiography. In datasets from 50 consecutive patients, optimal systolic and diastolic reconstruction windows were determined using the motion-map algorithm. For manual determination of the optimal reconstruction window, datasets were reconstructed in 5% steps throughout the RR interval. Motion artifacts were rated for each major coronary vessel using a five-point scale. Mean motion scores using the motion-map algorithm were 2.4 ± 0.8 for systolic reconstructions and 1.9 ± 0.8 for diastolic reconstructions. Using the manual approach, overall motion scores were significantly better (1.9 ± 0.5 and 1.7 ± 0.6, p 90% of cases using either approach. Using the automated approach, there was a negative correlation between heart rate and motion scores for systolic reconstructions (ρ = -0.26, p 80 bpm (systolic reconstruction). (orig.)

Accelerated gradient methods for total-variation-based CT image reconstruction

DEFF Research Database (Denmark)

Jørgensen, Jakob Heide; Jensen, Tobias Lindstrøm; Hansen, Per Christian

2011-01-01

incorporates several heuristics from the optimization literature such as Barzilai-Borwein (BB) step size selection and nonmonotone line search. The latter uses a cleverly chosen sequence of auxiliary points to achieve a better convergence rate. The methods are memory efficient and equipped with a stopping...... reconstruction can in principle be found by any optimization method, but in practice the large scale of the systems arising in CT image reconstruction preclude the use of memory-demanding methods such as Newton’s method. The simple gradient method has much lower memory requirements, but exhibits slow convergence...

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.

Science.gov (United States)

Sun, Eric I; Leyn, Semen A; Kazanov, Marat D; Saier, Milton H; Novichkov, Pavel S; Rodionov, Dmitry A

2013-09-02

In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels.An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis. A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations. The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome

BigNeuron: Large-scale 3D Neuron Reconstruction from Optical Microscopy Images

OpenAIRE

Peng, Hanchuan; Hawrylycz, Michael; Roskams, Jane; Hill, Sean; Spruston, Nelson; Meijering, Erik; Ascoli, Giorgio A.

2015-01-01

textabstractUnderstanding the structure of single neurons is critical for understanding how they function within neural circuits. BigNeuron is a new community effort that combines modern bioimaging informatics, recent leaps in labeling and microscopy, and the widely recognized need for openness and standardization to provide a community resource for automated reconstruction of dendritic and axonal morphology of single neurons. Understanding the structure of single neurons is critical for unde...

Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora.

Science.gov (United States)

Valadez-Cano, Cecilio; Olivares-Hernández, Roberto; Resendis-Antonio, Osbaldo; DeLuna, Alexander; Delaye, Luis

2017-04-14

Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations. In this work, we analyzed the evolution of the metabolism of the chromatophore of Paulinella chromatophora by in silico modeling. We asked whether genome reduction is driven by metabolic engineering strategies resulted from the interaction with the host. As its widely known, the loss of enzyme coding genes leads to metabolic network restructuring sometimes improving the production rates. In this case, the production rate of reduced-carbon in the metabolism of the chromatophore. We reconstructed the metabolic networks of the chromatophore of P. chromatophora CCAC 0185 and a close free-living relative, the cyanobacterium Synechococcus sp. WH 5701. We found that the evolution of free-living to host-restricted lifestyle rendered a fragile metabolic network where >80% of genes in the chromatophore are essential for metabolic functionality. Despite the lack of experimental information, the metabolic reconstruction of the chromatophore suggests that the host provides several metabolites to the endosymbiont. By using these metabolites as intracellular conditions, in silico simulations of genome evolution by gene lose recover with 77% accuracy the actual metabolic gene content of the chromatophore. Also, the metabolic model of the chromatophore allowed us to predict by flux balance analysis a maximum rate of reduced-carbon released by the endosymbiont to the host. By inspecting the central metabolism of the chromatophore and the free-living cyanobacteria we found that by

Accelerated gradient methods for total-variation-based CT image reconstruction

Energy Technology Data Exchange (ETDEWEB)

Joergensen, Jakob H.; Hansen, Per Christian [Technical Univ. of Denmark, Lyngby (Denmark). Dept. of Informatics and Mathematical Modeling; Jensen, Tobias L.; Jensen, Soeren H. [Aalborg Univ. (Denmark). Dept. of Electronic Systems; Sidky, Emil Y.; Pan, Xiaochuan [Chicago Univ., Chicago, IL (United States). Dept. of Radiology

2011-07-01

Total-variation (TV)-based CT image reconstruction has shown experimentally to be capable of producing accurate reconstructions from sparse-view data. In particular TV-based reconstruction is well suited for images with piecewise nearly constant regions. Computationally, however, TV-based reconstruction is demanding, especially for 3D imaging, and the reconstruction from clinical data sets is far from being close to real-time. This is undesirable from a clinical perspective, and thus there is an incentive to accelerate the solution of the underlying optimization problem. The TV reconstruction can in principle be found by any optimization method, but in practice the large scale of the systems arising in CT image reconstruction preclude the use of memory-intensive methods such as Newton's method. The simple gradient method has much lower memory requirements, but exhibits prohibitively slow convergence. In the present work we address the question of how to reduce the number of gradient method iterations needed to achieve a high-accuracy TV reconstruction. We consider the use of two accelerated gradient-based methods, GPBB and UPN, to solve the 3D-TV minimization problem in CT image reconstruction. The former incorporates several heuristics from the optimization literature such as Barzilai-Borwein (BB) step size selection and nonmonotone line search. The latter uses a cleverly chosen sequence of auxiliary points to achieve a better convergence rate. The methods are memory efficient and equipped with a stopping criterion to ensure that the TV reconstruction has indeed been found. An implementation of the methods (in C with interface to Matlab) is available for download from http://www2.imm.dtu.dk/~pch/TVReg/. We compare the proposed methods with the standard gradient method, applied to a 3D test problem with synthetic few-view data. We find experimentally that for realistic parameters the proposed methods significantly outperform the standard gradient method. (orig.)

Multiscale study on stochastic reconstructions of shale samples

Science.gov (United States)

Lili, J.; Lin, M.; Jiang, W. B.

2016-12-01

Shales are known to have multiscale pore systems, composed of macroscale fractures, micropores, and nanoscale pores within gas or oil-producing organic material. Also, shales are fissile and laminated, and the heterogeneity in horizontal is quite different from that in vertical. Stochastic reconstructions are extremely useful in situations where three-dimensional information is costly and time consuming. Thus the purpose of our paper is to reconstruct stochastically equiprobable 3D models containing information from several scales. In this paper, macroscale and microscale images of shale structure in the Lower Silurian Longmaxi are obtained by X-ray microtomography and nanoscale images are obtained by scanning electron microscopy. Each image is representative for all given scales and phases. Especially, the macroscale is four times coarser than the microscale, which in turn is four times lower in resolution than the nanoscale image. Secondly, the cross correlation-based simulation method (CCSIM) and the three-step sampling method are combined together to generate stochastic reconstructions for each scale. It is important to point out that the boundary points of pore and matrix are selected based on multiple-point connectivity function in the sampling process, and thus the characteristics of the reconstructed image can be controlled indirectly. Thirdly, all images with the same resolution are developed through downscaling and upscaling by interpolation, and then we merge multiscale categorical spatial data into a single 3D image with predefined resolution (the microscale image). 30 realizations using the given images and the proposed method are generated. The result reveals that the proposed method is capable of preserving the multiscale pore structure, both vertically and horizontally, which is necessary for accurate permeability prediction. The variogram curves and pore-size distribution for both original 3D sample and the generated 3D realizations are compared

Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.

Directory of Open Access Journals (Sweden)

Christian L Barrett

2006-05-01

Full Text Available The number of complete, publicly available genome sequences is now greater than 200, and this number is expected to rapidly grow in the near future as metagenomic and environmental sequencing efforts escalate and the cost of sequencing drops. In order to make use of this data for understanding particular organisms and for discerning general principles about how organisms function, it will be necessary to reconstruct their various biochemical reaction networks. Principal among these will be transcriptional regulatory networks. Given the physical and logical complexity of these networks, the various sources of (often noisy data that can be utilized for their elucidation, the monetary costs involved, and the huge number of potential experiments approximately 10(12 that can be performed, experiment design algorithms will be necessary for synthesizing the various computational and experimental data to maximize the efficiency of regulatory network reconstruction. This paper presents an algorithm for experimental design to systematically and efficiently reconstruct transcriptional regulatory networks. It is meant to be applied iteratively in conjunction with an experimental laboratory component. The algorithm is presented here in the context of reconstructing transcriptional regulation for metabolism in Escherichia coli, and, through a retrospective analysis with previously performed experiments, we show that the produced experiment designs conform to how a human would design experiments. The algorithm is able to utilize probability estimates based on a wide range of computational and experimental sources to suggest experiments with the highest potential of discovering the greatest amount of new regulatory knowledge.

3D prostate histology image reconstruction: Quantifying the impact of tissue deformation and histology section location

Directory of Open Access Journals (Sweden)

Eli Gibson

2013-01-01

Full Text Available Background: Guidelines for localizing prostate cancer on imaging are ideally informed by registered post-prostatectomy histology. 3D histology reconstruction methods can support this by reintroducing 3D spatial information lost during histology processing. The need to register small, high-grade foci drives a need for high accuracy. Accurate 3D reconstruction method design is impacted by the answers to the following central questions of this work. (1 How does prostate tissue deform during histology processing? (2 What spatial misalignment of the tissue sections is induced by microtome cutting? (3 How does the choice of reconstruction model affect histology reconstruction accuracy? Materials and Methods: Histology, paraffin block face and magnetic resonance images were acquired for 18 whole mid-gland tissue slices from six prostates. 7-15 homologous landmarks were identified on each image. Tissue deformation due to histology processing was characterized using the target registration error (TRE after landmark-based registration under four deformation models (rigid, similarity, affine and thin-plate-spline [TPS]. The misalignment of histology sections from the front faces of tissue slices was quantified using manually identified landmarks. The impact of reconstruction models on the TRE after landmark-based reconstruction was measured under eight reconstruction models comprising one of four deformation models with and without constraining histology images to the tissue slice front faces. Results: Isotropic scaling improved the mean TRE by 0.8-1.0 mm (all results reported as 95% confidence intervals, while skew or TPS deformation improved the mean TRE by <0.1 mm. The mean misalignment was 1.1-1.9΀ (angle and 0.9-1.3 mm (depth. Using isotropic scaling, the front face constraint raised the mean TRE by 0.6-0.8 mm. Conclusions: For sub-millimeter accuracy, 3D reconstruction models should not constrain histology images to the tissue slice front faces and

Calibration of reconstruction parameters in atom probe tomography using a single crystallographic orientation

International Nuclear Information System (INIS)

Suram, Santosh K.; Rajan, Krishna

2013-01-01

The purpose of this work is to develop a methodology to estimate the APT reconstruction parameters when limited crystallographic information is available. Reliable spatial scaling of APT data currently requires identification of multiple crystallographic poles from the field desorption image for estimating the reconstruction parameters. This requirement limits the capacity of accurately reconstructing APT data for certain complex systems, such as highly alloyed systems and nanostructured materials wherein more than one pole is usually not observed within one grain. To overcome this limitation, we develop a quantitative methodology for calibrating the reconstruction parameters in an APT dataset by ensuring accurate inter-planar spacing and optimizing the curvature correction for the atomic planes corresponding to a single crystallographic orientation. We validate our approach on an aluminum dataset and further illustrate its capabilities by computing geometric reconstruction parameters for W and Al–Mg–Sc datasets. - Highlights: ► Quantitative approach is developed to accurately reconstruct APT data. ► Curvature of atomic planes in APT data is used to calibrate the reconstruction. ► APT reconstruction parameters are determined from a single crystallographic axis. ► Quantitative approach is demonstrated on W, Al and Al–Mg–Sc systems. ► Accurate APT reconstruction of complex materials is now possible

Random sampling of elementary flux modes in large-scale metabolic networks.

Science.gov (United States)

Machado, Daniel; Soons, Zita; Patil, Kiran Raosaheb; Ferreira, Eugénio C; Rocha, Isabel

2012-09-15

The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis. However, their application to large networks has been hampered by the combinatorial explosion in the number of modes. In this work, we develop a method for generating random samples of EMs without computing the whole set. Our algorithm is an adaptation of the canonical basis approach, where we add an additional filtering step which, at each iteration, selects a random subset of the new combinations of modes. In order to obtain an unbiased sample, all candidates are assigned the same probability of getting selected. This approach avoids the exponential growth of the number of modes during computation, thus generating a random sample of the complete set of EMs within reasonable time. We generated samples of different sizes for a metabolic network of Escherichia coli, and observed that they preserve several properties of the full EM set. It is also shown that EM sampling can be used for rational strain design. A well distributed sample, that is representative of the complete set of EMs, should be suitable to most EM-based methods for analysis and optimization of metabolic networks. Source code for a cross-platform implementation in Python is freely available at http://code.google.com/p/emsampler. dmachado@deb.uminho.pt Supplementary data are available at Bioinformatics online.

3D reconstruction software comparison for short sequences

Science.gov (United States)

Strupczewski, Adam; Czupryński, BłaŻej

2014-11-01

Large scale multiview reconstruction is recently a very popular area of research. There are many open source tools that can be downloaded and run on a personal computer. However, there are few, if any, comparisons between all the available software in terms of accuracy on small datasets that a single user can create. The typical datasets for testing of the software are archeological sites or cities, comprising thousands of images. This paper presents a comparison of currently available open source multiview reconstruction software for small datasets. It also compares the open source solutions with a simple structure from motion pipeline developed by the authors from scratch with the use of OpenCV and Eigen libraries.

Reconstructed Temperature And Precipitation On A Millennial Timescale From Tree-Rings In The Southern Colorado Plateau, U.S.A.

Energy Technology Data Exchange (ETDEWEB)

Salzer, M.W. [Laboratory of Tree-Ring Research, The University of Arizona, Tucson, Arizona, 85721 (United States); Kipfmueller, K.F. [Department of Geography, University of Minnesota, Minneapolis, MN, 55455 (United States)

2005-06-01

Two independent calibrated and verified climate reconstructions from ecologically contrasting tree-ring sites in the southern Colorado Plateau, U.S.A. reveal decadal-scale climatic trends during the past two millennia. Combining precisely dated annual mean-maximum temperature and October through July precipitation reconstructions yields an unparalleled record of climatic variability. The approach allows for the identification of thirty extreme wet periods and thirty-five extreme dry periods in the 1,425-year precipitation reconstruction and 30 extreme cool periods and 26 extreme warm periods in 2,262-year temperature reconstruction. In addition, the reconstructions were integrated to identify intervals when conditions were extreme in both climatic variables (cool/dry, cool/wet, warm/dry, warm/wet). Noteworthy in the reconstructions are the post-1976 warm/wet period, unprecedented in the 1,425-year record both in amplitude and duration, anomalous and prolonged late 20th century warmth, that while never exceeded, was nearly equaled in magnitude for brief intervals in the past, and substantial decadal-scale variability within the Medieval Warm Period and Little Ice Age intervals.

CRUCIATE LIGAMENT RECONSTRUCTION