Aqueous solutions that model the cytosol: studies on polarity, chemical reactivity and enzyme kineticsElectronic supplementary information (ESI) available: further results and discussion and tables of experimental data. See http://www.rsc.org/suppdata/ob/b4/b402886d/

Multicomponent adsorption of benzene, toluene, ethylbenzene, and xylene (BTEX) was assessed in aqueous solutions by montmorillonite modified with tetradecyl trimethyl ammonium bromide (TTAB-Mt). Batch experiments were conducted to determine the influences of parameters including loading rates of surfactant, contact time, pH, adsorbate concentration, and temperature on the adsorption efficiency. Scanning electron microscope (SEM) and X-ray diffractometer (XRD) were used to determine the adsorbent properties. Results showed that the modification of the adsorbent via the surfactant causes structural changes of the adsorbent. It was found that the optimum adsorption condition achieves with the surfactant loading rate of 200% of the cation exchange capacity (CEC) of the adsorbent for a period of 24 h. The sorption of BTEX by TTAB-Mt was in the order ofB<T<E<X. The experimental data were fitted by many kinetic and isotherm models. The results also showed that the pseudo-second-order kinetic model and Freundlich isotherm model could, respectively, be fitted to the experimental data better than other available kinetic and isotherm models. The thermodynamic study indicated that the sorption of BTEX with TTAB-Mt was achieved spontaneously and the adsorption process was endothermic as well as physical in nature. The regeneration results of the adsorbent also showed that the adsorption capacity of adsorbent after one use was 51% to 70% of original TTAB-Mt.

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Measurement and Prediction of Densities of Ternary Aqueous Mixtures Involving Sodium Polyacrylate

ASEAN Journal of Chemical Engineering ◽

10.22146/ajche.50851 ◽

2004 ◽

Vol 4 (1) ◽

pp. 64

Author(s):

Z. A. Noor Fadzlina ◽

T. T. Teng ◽

M. Abdul Rahman

Keyword(s):

Experimental Data ◽

Aqueous Solutions ◽

Percentage Error ◽

Sodium Polyacrylate ◽

Aqueous Systems ◽

Aqueous Mixtures ◽

Density Prediction ◽

Density Values ◽

Good Agreement

The densities of the binary aqueous solutions of sodium polyacrylate (NaPM) at 20°C, 25°C, and 300C up to 0.17 m and LiCI at 25°C and 300C up to 3.13 m were measured using a vibrating tube digital densitimeter. The measured experimental data were then fitted to the polynomial d = do + IA;m'. The densities of the ternary aqueous systems NaPM-NaCI, NaPM-LiCI, and NaPM-sucrose were also =1 measured from 20°C to 30°C. The isopycnotic equation, Imi / moi was used to predict the densities of the ternary aqueous systems mentioned. The results show that predicted and observed density values are in good agreement. The overall percentage error of density prediction for the system NaPM-NaCI-H20 is 0.067. For the system NaPM-LiCI-HP,the overall percentage error is 0.074; and, for the system NaPM-sucrose-H20, the overall percentage error is 0.065.

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Haplotype assembly of autotetraploid potato using integer linear programing

Bioinformatics ◽

10.1093/bioinformatics/btz060 ◽

2019 ◽

Vol 35 (18) ◽

pp. 3279-3286 ◽

Cited By ~ 4

Author(s):

Enrico Siragusa ◽

Niina Haiminen ◽

Richard Finkers ◽

Richard Visser ◽

Laxmi Parida

Keyword(s):

Experimental Data ◽

Experimental Studies ◽

Simulated Data ◽

Supplementary Information ◽

Linear Programs ◽

Plant Genomics ◽

Optimal Method ◽

Haplotype Assembly ◽

Open Issue ◽

Removal Model

Abstract Summary Haplotype assembly of polyploids is an open issue in plant genomics. Recent experimental studies on highly heterozygous autotetraploid potato have shown that available methods do not deliver satisfying results in practice. We propose an optimal method to assemble haplotypes of highly heterozygous polyploids from Illumina short-sequencing reads. Our method is based on a generalization of the existing minimum fragment removal model to the polyploid case and on new integer linear programs to reconstruct optimal haplotypes. We validate our methods experimentally by means of a combined evaluation on simulated and experimental data based on 83 previously sequenced autotetraploid potato cultivars. Results on simulated data show that our methods produce highly accurate haplotype assemblies, while results on experimental data confirm a sensible improvement over the state of the art. Availability and implementation Executables for Linux at http://github.com/Computational Genomics/HaplotypeAssembler. Supplementary information Supplementary data are available at Bioinformatics online.

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Sugar Industry: Effect of Dextran Concentrations on the Sucrose Crystallization in Aqueous Solutions

Journal of Engineering ◽

10.1155/2019/7987369 ◽

2019 ◽

Vol 2019 ◽

pp. 1-6 ◽

Cited By ~ 1

Author(s):

Abdelali Borji ◽

Fatima-Ezzahra Borji ◽

Abdelaziz Jourani

Keyword(s):

Experimental Data ◽

Aqueous Solutions ◽

Growth Process ◽

Sugar Industry ◽

Nucleation Kinetics ◽

Metastable Zone Width ◽

Zone Width ◽

Industry Effect ◽

Instantaneous Nucleation ◽

Metastable Zone

Using the spectrophotometric method, as a new method, the influence of dextran on the sucrose solubility and metastable zone width has been studied. In agreement with the literature the experimental data show that the dextran has a negligible effect on the sucrose solubility. The results also show that this impurity decreases the sucrose metastable zone width. The study of the nucleation kinetics performed, using Nyvlt’s approach, shows that the dextran accelerates the nucleation and that the nuclei are formed in the solution by instantaneous nucleation. The presence of dextran in the system causes a decrease in the growth rate of sucrose. The growth process of sucrose is governed by a Birth and Spread mechanism. The kinetic parameters of sucrose growth in aqueous solutions without and with dextran were estimated.

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Modeling cell proliferation in human acute myeloid leukemia xenografts

Bioinformatics ◽

10.1093/bioinformatics/btz063 ◽

2019 ◽

Vol 35 (18) ◽

pp. 3378-3386 ◽

Cited By ~ 5

Author(s):

Marco S Nobile ◽

Thalia Vlachou ◽

Simone Spolaor ◽

Daniela Bossi ◽

Paolo Cazzaniga ◽

...

Keyword(s):

Experimental Data ◽

Cell Proliferation ◽

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Time Series Data ◽

Supplementary Information ◽

Series Data ◽

Proliferative Potential ◽

Proliferating Cells ◽

Acute Myeloid

Abstract Motivation Acute myeloid leukemia (AML) is one of the most common hematological malignancies, characterized by high relapse and mortality rates. The inherent intra-tumor heterogeneity in AML is thought to play an important role in disease recurrence and resistance to chemotherapy. Although experimental protocols for cell proliferation studies are well established and widespread, they are not easily applicable to in vivo contexts, and the analysis of related time-series data is often complex to achieve. To overcome these limitations, model-driven approaches can be exploited to investigate different aspects of cell population dynamics. Results In this work, we present ProCell, a novel modeling and simulation framework to investigate cell proliferation dynamics that, differently from other approaches, takes into account the inherent stochasticity of cell division events. We apply ProCell to compare different models of cell proliferation in AML, notably leveraging experimental data derived from human xenografts in mice. ProCell is coupled with Fuzzy Self-Tuning Particle Swarm Optimization, a swarm-intelligence settings-free algorithm used to automatically infer the models parameterizations. Our results provide new insights on the intricate organization of AML cells with highly heterogeneous proliferative potential, highlighting the important role played by quiescent cells and proliferating cells characterized by different rates of division in the progression and evolution of the disease, thus hinting at the necessity to further characterize tumor cell subpopulations. Availability and implementation The source code of ProCell and the experimental data used in this work are available under the GPL 2.0 license on GITHUB at the following URL: https://github.com/aresio/ProCell. Supplementary information Supplementary data are available at Bioinformatics online.

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HypercubeME: two hundred million combinatorially complete datasets from a single experiment

Bioinformatics ◽

10.1093/bioinformatics/btz841 ◽

2019 ◽

Author(s):

Laura Avino Esteban ◽

Lyubov R Lonishin ◽

Daniil Bobrovskiy ◽

Gregory Leleytner ◽

Natalya S Bogatyreva ◽

...

Keyword(s):

Experimental Data ◽

High Throughput ◽

Recursive Algorithm ◽

Random Mutagenesis ◽

Higher Order ◽

Supplementary Information ◽

Single Experiment ◽

Manual Curation ◽

Complete Dataset ◽

Genotype Space

Abstract Motivation Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a “combinatorially complete dataset”. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. Results We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199,847,053 unique combinatorially complete genotype combinations of dimensionality ranging from two to twelve. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data. Availability https://github.com/ivankovlab/HypercubeME.git Supplementary information Supplementary data are available at Bioinformatics online.

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