scholarly journals Model-based metabolism design: constraints for kinetic and stoichiometric models

2018 ◽  
Vol 46 (2) ◽  
pp. 261-267 ◽  
Author(s):  
Egils Stalidzans ◽  
Andrus Seiman ◽  
Karl Peebo ◽  
Vitalijs Komasilovs ◽  
Agris Pentjuss
Keyword(s):  
Design Development ◽  
Experimental Conditions ◽  
Total Enzyme Activity ◽  
Optimization Constraints ◽  
Model Based ◽  
Cellular Analysis ◽  
General Constraints ◽  
Balance Energy ◽  
Set Up ◽  
Stoichiometric Models

The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-based designs of metabolic pathways in organisms. Some constraints (mass balance, energy balance, and steady-state assumption) serve as a basis for many modelling approaches. There are others (total enzyme activity constraint and homeostatic constraint) proposed decades ago, but which are frequently ignored in design development. Several new approaches of cellular analysis have made possible the application of constraints like cell size, surface, and resource balance. Constraints for kinetic and stoichiometric models are grouped according to their applicability preconditions in (1) general constraints, (2) organism-level constraints, and (3) experiment-level constraints. General constraints are universal and are applicable for any system. Organism-level constraints are applicable for biological systems and usually are organism-specific, but these constraints can be applied without information about experimental conditions. To apply experimental-level constraints, peculiarities of the organism and the experimental set-up have to be taken into account to calculate the values of constraints. The limitations of applicability of particular constraints for kinetic and stoichiometric models are addressed.

scholarly journals A Study of Coherent Radiation Generated in an Ablative Capillary Discharge

10.14311/1787 ◽  
2013 ◽  
Vol 53 (2) ◽  
Author(s):  
Jakub Hübner ◽  
Pavel Vrba
Keyword(s):  
Physical Model ◽  
Spontaneous Emission ◽  
Amplified Spontaneous Emission ◽  
Coherent Radiation ◽  
Capillary Discharge ◽  
Mhd Equations ◽  
One Dimensional ◽  
X Ray ◽  
Model Based ◽  
Set Up

Feasible soft-X-ray amplification in the CVI and NVII Balmer transition is investigated in a capillary discharge. The best conditions and parameters for the experimental set-up are found for an ablative capillary. The most optimistic results have shown that the gain would be greater than one, which is the condition for successful ASE (Amplified spontaneous emission) in capillary discharges. The capillary discharge evolution is modeled using the NPINCH program, employing a one-dimensional physical model based on MHD equations. The information about the capillary discharge evolution is processed in the FLY, FLYPAPER, FLYSPEC programs, enabling the population to be modeled on specific levels during capillary discharge.

Antibiotic treatment of the breadcrumb sponge Halichondria panicea and subsequent recolonization v1

2021 ◽  
Author(s):  
Lara Schmittmann ◽  
Ute U Hentschel
Keyword(s):  
Antibiotic Treatment ◽  
Recovery Phase ◽  
Phase 3 ◽  
Experimental Conditions ◽  
Host Environment ◽  
Halichondria Panicea ◽  
Set Up ◽  
Bacterial Recolonization ◽  
Sponge Halichondria Panicea

This protocol generates sponges (Halichondria panicea) with a disturbed microbiome under controlled experimental conditions, in order to study bacterial recolonization dynamics. Bacteria-bacteria interactions can be analysed with this set-up within the host environment aiming at a better understanding of sponge-microbe symbiosis in vivo. It is divided into the sections 1) preparation, 2) antibiotic treatment and recovery phase, 3) recolonization with the natural microbiome and 4) sampling.

scholarly journals A Multi-Objective Permanent Basic Farmland Delineation Model Based on Hybrid Particle Swarm Optimization

2020 ◽  
Vol 9 (4) ◽  
pp. 243 ◽  
Author(s):  
Hua Wang ◽  
Wenwen Li ◽  
Wei Huang ◽  
Ke Nie
Keyword(s):  
Particle Swarm Optimization ◽  
Fitness Function ◽  
Particle Swarm ◽  
Research Area ◽  
Swarm Optimization ◽  
Multi Objective ◽  
Model Based ◽  
Hybrid Particle Swarm Optimization ◽  
General Rules ◽  
Set Up

The delimitation of permanent basic farmland is essentially a multi-objective optimization problem. The traditional demarcation methods cannot simultaneously take into account the requirements of cultivated land quality and the spatial layout of permanent basic farmland, and it cannot balance the relationship between agriculture and urban development. This paper proposed a multi-objective permanent basic farmland delimitation model based on an immune particle swarm optimization algorithm. The general rules for delineating the permanent basic farmland were defined in the model, and the delineation goals and constraints have been formally expressed. The model introduced the immune system concepts to complement the existing theory. This paper describes the coding and initialization methods for the algorithm, particle position and speed update mechanism, and fitness function design. We selected Xun County, Henan Province, as the research area and set up control experiments that aligned with the different targets and compared the performance of the three models of particle swarm optimization (PSO), artificial immune algorithm (AIA), and the improved AIA-PSO in solving multi-objective problems. The experiments proved the feasibility of the model. It avoided the adverse effects of subjective factors and promoted the scientific rationality of the results of permanent basic farmland delineation.

scholarly journals UHPLC-UV/Vis Quantitative Analysis of Hydroxylated and O-prenylated Coumarins in Pomegranate Seed Extracts

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1963 ◽  
Author(s):  
Serena Fiorito ◽  
Federica Ianni ◽  
Francesca Preziuso ◽  
Francesco Epifano ◽  
Luca Scotti ◽  
...  
Keyword(s):  
Punica Granatum ◽  
Biologically Active ◽  
Experimental Conditions ◽  
Analytical Methodology ◽  
Extraction Solvent ◽  
Versatile Technique ◽  
Efficient Extraction ◽  
Pomegranate Seed ◽  
Set Up ◽  
Seed Extracts

A simple and rapid analytical UHPLC methodology with spectrophotometric (UV/Vis) detection, coupled with different extraction procedures, has been perfected to investigate the presence of biologically active O-prenylated umbelliferone derivatives, such as auraptene and umbelliprenin, in pomegranate (Punica granatum L.) seed extracts. Absolute ethanol was the most efficient extraction solvent in terms of yields, after a short ultrasound-assisted. The highest concentration values recorded under these experimental conditions were 1.99 μg/g of dry extract and 6.53 μg/g for auraptene and umbelliprenin, respectively. The parent metabolite umbelliferone was also detected (0.67 μg/g). The extraction and UHPLC analytical methodology set up in the present study proved to be an efficient, powerful, and versatile technique for the simultaneous qualitative analysis and quantification of oxyprenylated coumarins in pomegranate seed extracts. The characterization of such secondary metabolites in the mentioned phytopreparation represents, to the best of our knowledge, the first example in the literature.

scholarly journals DESIGN, DEVELOPMENT AND EVALUATION OF DILTIAZEM HYDROCHLORIDE LOADED NANOSPONGES FOR ORAL DELIVERY

2020 ◽  
pp. 116-122
Author(s):  
B. NARASIMHA RAO ◽  
K. RAVINDRA REDDY ◽  
S. RAHATH FATHIMA ◽  
P. PREETHI
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Surface Morphology ◽  
Oral Delivery ◽  
Ethyl Cellulose ◽  
Design Development ◽  
Diltiazem Hydrochloride ◽  
Drug Content ◽  
Set Up ◽  
Scanning Electron

Objective: In the current investigation,nanosponges were set up by emulsion solvent diffusion technique utilizing ethyl cellulose and β-cyclodextrin as polymers. Methods: Diltiazem hydrochloride is taken as model medication for considering different nanosponge formulations. The similarity of different formulation segments was set up by Fourier Transform Infra-Red (FTIR) spectroscopy. Molecular size, surface morphology, entrapment efficiency and drug content of nanosponges were analyzed. Shape and surface morphology of the nanosponges were inspected utilizing scanning electron microscopy. Results: Molecule size of formulated nanosponges was seen in the scope of 186 to 476 nm. Scanning electron microscopy uncovered the permeable, round nature of the nanosponges. The drug content of nanosponges for ethyl cellulose containing formulations was seen as in the scope of 62.25 to 85.11% and for the β-cyclodextrin containing details were seen as in the scope of 65.18-89.67%. The percentage entrapment effectiveness of nanosponges for ethyl cellulose containing formulations were seen as in the scope of 54.18 to 79.49% and for the β-cyclodextrin containing details were seen as in the scope of 58.21-83.45%. In vitro drugreleasefindings demonstrated that at 12 h ethyl cellulose containing formulations discharged the drug in the scope of 57.27-89.09% and for the β-cyclodextrin containing formulations discharged in the scope of 73.94-93.26%. Conclusion: Sustained drugreleasefrom formulations is supported if there is an occurrence of ethyl cellulose in the formulations rather with plans containing β-cyclodextrin.

Experimental study on the effect of pressure and flow rate on cavitation in a poppet throttle valve

2019 ◽  
Vol 72 (5) ◽  
pp. 629-636
Author(s):  
Jian Zhang ◽  
Tingting Luo
Keyword(s):  
Flow Rate ◽  
Pressure Difference ◽  
High Speed ◽  
High Speed Camera ◽  
Experimental Conditions ◽  
Content Type ◽  
Experimental Support ◽  
Throttle Valve ◽  
Set Up

Purpose The purpose of this paper is to study the variation of cavitation scale with pressure and flow in poppet throttle valve, to obtain the cavitation scale under pressure and flow conditions and to provide experimental support for the research of suppressing throttle valve cavitation and cavitation theory. Design/methodology/approach A hydraulic cavitation platform was set up, a valve was manufactured with highly transparent PMMA material and a high-speed camera was used to observe the change in cavitation scale. Findings Through experiments, it is found that the pressure difference between inlet and outlet of throttle valve affects the cavitation scale, and the more the pressure difference is, the easier the cavitation will be formed. Under the condition of small pressure difference, the cavitation is not obvious and reducing the pressure difference can effectively suppress the cavitation; the flow rate also affects the cavitation scale, the smaller the flow rate, the more difficult the cavitation will be formed and the lower the flow rate, the more the cavitation will be suppressed. Research limitations/implications Because of the magnification factor of the high-speed camera lens, the morphology of smaller bubbles cannot be observed in this study, and the experimental conditions need to be improved in the follow-up study. Originality/value This study can provide experimental support for the study of throttle valve cavitation suppression methods and cavitation theory.

scholarly journals Analytical challenges of untargeted GC-MS-based metabolomics and the critical issues in selecting the data processing strategy

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 967 ◽  
Author(s):  
Ting-Li Han ◽  
Yang Yang ◽  
Hua Zhang ◽  
Kai P. Law
Keyword(s):  
Quality Control ◽  
Data Processing ◽  
Epidemiological Study ◽  
Internal Standard ◽  
Analytical Techniques ◽  
Experimental Conditions ◽  
Data Set ◽  
Raw Data ◽  
Model Based ◽  
Critical Issues

Background: A challenge of metabolomics is data processing the enormous amount of information generated by sophisticated analytical techniques. The raw data of an untargeted metabolomic experiment are composited with unwanted biological and technical variations that confound the biological variations of interest. The art of data normalisation to offset these variations and/or eliminate experimental or biological biases has made significant progress recently. However, published comparative studies are often biased or have omissions. Methods: We investigated the issues with our own data set, using five different representative methods of internal standard-based, model-based, and pooled quality control-based approaches, and examined the performance of these methods against each other in an epidemiological study of gestational diabetes using plasma. Results: Our results demonstrated that the quality control-based approaches gave the highest data precision in all methods tested, and would be the method of choice for controlled experimental conditions. But for our epidemiological study, the model-based approaches were able to classify the clinical groups more effectively than the quality control-based approaches because of their ability to minimise not only technical variations, but also biological biases from the raw data. Conclusions: We suggest that metabolomic researchers should optimise and justify the method they have chosen for their experimental condition in order to obtain an optimal biological outcome.

scholarly journals Changes in Geochemical Composition of Groundwater Due to CO2 Leakage in Various Geological Media

Water ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2597
Author(s):  
Jisu Jeong ◽  
Sung-Wook Jeen ◽  
Hyoun-Tae Hwang ◽  
Kang-Kun Lee
Keyword(s):  
Cation Exchange ◽  
Exchange Capacity ◽  
Co2 Leakage ◽  
Experimental Conditions ◽  
Geochemical Composition ◽  
Ph Buffering ◽  
Physico Chemical ◽  
High Concentrations ◽  
Set Up ◽  
One Year

This study evaluated the effects of CO2 leakage on the geochemical composition of groundwater in various geological media through long-term column experiments. Four columns were set up with soil representing a silicate aquifer; clean sand; a sand and limestone mixture; and alluvium soil, respectively. The experiments were conducted under the same experimental conditions for approximately one year. As the CO2-saturated synthetic groundwater was introduced into the columns, a decrease in pH and increases in electrical conductivity (EC), alkalinity, and concentrations of cations and trace elements were observed in all geological media. However, different patterns of changes were also observed depending on the mineralogical and physico-chemical characteristics of each material. As the column operation continued, while the pH decreased and low alkalinity values were more evident in the silicate soil and clean sand columns, the carbonate column continued to show high alkalinity and EC values in addition to high concentrations of most cations. The alluvium soil showed distinctive cation-exchange behaviors during the initial introduction of CO2. The results indicate that changes in the geochemical composition of groundwater will depend on the characteristic of the geological medium such as pH buffering capacity and cation exchange capacity. This study can be useful for monitoring and managing the impacts of CO2 leakage in various aquifer environments.

Multi-Loss WCVaR Risk Decision Optimization Based On Weight for Centralized Supply Problem of Direct Chain Enterprises

2019 ◽  
Vol 36 (02) ◽  
pp. 1940007
Author(s):  
Xu Leiyan ◽  
Zhiqing Meng
Keyword(s):  
Production Volume ◽  
Total Production ◽  
Supply Risk ◽  
Model Based ◽  
Distribution Density Function ◽  
Decision Optimization ◽  
Robust Model ◽  
Supply Problem ◽  
Set Up ◽  
Risk Decision

In recent years, the centralized supply strategy has been widely adopted by direct chain enterprises (DCEs) and become an indispensable means of operation. First, a general probability distribution density function cluster is used to describe the uncertainty demand from all retailers of the DCE. Second, a multi-loss WCVaR centralized supply risk decision optimization robust model based on weight is presented for the DCE. We prove that this model is equivalent to an single-objective optimization model. Finally, we set up a single-period multi-loss WCVaR centralized supply risk decision optimization robust model based on weight for production allocation problem for a centralized-supply direct chain food enterprise. The numerical results illustrate that the DCE may obtain the approximately robust total production volume and the robust retail volume allocated to all retailers, which is the minimal total supply loss for the DCE.

Criteria for analysis of arterial and venous occlusion

1991 ◽  
Vol 70 (2) ◽  
pp. 665-675 ◽  
Author(s):  
T. S. Hakim
Keyword(s):  
Autologous Blood ◽  
Venous Pressure ◽  
Venous Occlusion ◽  
Pressure Gradients ◽  
Experimental Conditions ◽  
Pressure System ◽  
Arterial Inflow ◽  
Outflow Rate ◽  
Set Up

To provide a better understanding of analysis of arterial (AO) and venous occlusion (VO) tracings, using a constant and nonpulsatile perfusion pressure system, we set up an isolated in situ dog lobe preparation perfused with autologous blood. Four signals were recorded: arterial pressure, arterial inflow rate, venous pressure, and venous outflow rate. The four signals were recorded into the memory of a computer. When flow into the lobe was abruptly stopped (AO), flow out of the lung continued unchanged for approximately 150 ms and then decreased slowly to zero. Likewise, when flow out of the lung was abruptly stopped (VO), the flow into the lung continued unchanged for approximately 130 ms and then decreased slowly to zero. A monoexponential curve was fitted to different stretches of data between 0.1 and 5 s postocclusion and extrapolated to the instant of occlusion (defined here as the instant when flow at the site of occlusion becomes zero). The results indicate that 1) the first 150 ms postocclusion should be avoided because of the oscillatory artifacts generated by the occlusion maneuver, 2) use of a long segment of postocclusion data (5 s) tends to underestimate the middle pressure gradient and overestimate the arterial and venous pressure gradients, and 3) the changes in segmental vascular resistance under different experimental conditions were found to be unaffected by the criteria of analysis. Analysis of the postocclusion (AO and VO) tracings was found to be most compatible with the double-occlusion capillary pressure by fitting a stretch of data between 0.2 and 2.5 s postocclusion and extrapolating back to the instant when flow becomes zero at the site of occlusion but no earlier.

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