Motivation: Immune cell dynamics is a critical factor of disease-associated pathology (immunopathology) that also impacts the levels of mRNAs in diseased tissue. Deconvolution algorithms attempt to infer cell quantities in a tissue/organ sample based on gene expression profiles and are often evaluated using artificial, non-complex samples. Their accuracy on estimating cell counts given temporal tissue gene expression data remains not well characterized and has never been characterized when using diseased lung. Further, how to remove the effects of cell migration on transcript counts to improve discovery of disease factors is an open question. Results: Four cell count inference (i.e., deconvolution) tools are evaluated using microarray data from influenza-infected lung sampled at several time points post-infection. The analysis finds that inferred cell quantities are accurate only for select cell types and there is a tendency for algorithms to have a good relative fit (R 2 ) but... [more]

The presented work describes the method of preparation of thermosensitive chitosan hydrogels using calcium β-glycerophosphate salt as the only pH neutralizing agent and supporting the crosslinking process. The presence of calcium ions instead of sodium ions is particularly important in the case of scaffolds in bone tissue engineering. Rheological and physicochemical properties of low concentrated chitosan solutions with the addition of calcium β-glycerophosphate were investigated using rotational rheometry techniques, Zeta potential (by electrophoresis), XPS, and SEM analysis together with an EDS detector. It was found to be possible to prepare colloidal solutions of chitosan containing only calcium β-glycerophosphate (without sodium ions) undergoing a sol-gel phase transition at the physiological temperature of the human body. It has also been shown that it is possible to further enrich the obtained cellular scaffolds with calcium ions. Using the addition of calcium carbonate, hydroge... [more]

Recombinant proteins produced by the baculovirus expression vector system (BVES) have been widely applied in the agricultural and medical fields. However, the procedure for protein expression is inefficient and needs to be improved. Herein, we propose a simple construct that incorporates a selectable marker (enhanced green fluorescent protein, EGFP) and a picorna viral-derived “self-cleaving” 2A-like peptide to separate the EGFP and target proteins in a monocistronic baculovirus vector to facilitate isolation of the recombinant baculovirus in the BVES. In this study, porcine adiponectin (ADN), a secreted, multimeric protein with insulin-sensitizing properties, was used to demonstrate its utility in our EGFP-2A-based expression system. EGFP and ADN were simultaneously expressed by a recombinant alphabaculovirus. Co-expression of EGFP facilitates the manipulation of the following processes, such as determining expression kinetics and harvesting ADN. The results showed that the 2A “self-c... [more]

The increasing rate of diabetes is found across the planet. Therefore, the diagnosis of pre-diabetes and diabetes is important in populations with extreme diabetes risk. In this study, a machine learning technique was implemented over a data mining platform by employing Rule classifiers (PART and Decision table) to measure the accuracy and logistic regression on the classification results for forecasting the prevalence in diabetes mellitus patients suffering simultaneously from other chronic disease symptoms. The real-life data was collected in Nigeria between December 2017 and February 2019 by applying ten non-intrusive and easily available clinical variables. The results disclosed that the Rule classifiers achieved a mean accuracy of 98.75%. The error rate, precision, recall, F-measure, and Matthew’s correlation coefficient MCC were 0.02%, 0.98%, 0.98%, 0.98%, and 0.97%, respectively. The forecast decision, achieved by employing a set of 23 decision rules (DR), indicates that age, ge... [more]

Tyrosine kinase receptor (RTK) ligation and dimerization is a key mechanism for translating external cell stimuli into internal signaling events. This process is critical to several key cell and physiological processes, such as in angiogenesis and embryogenesis, among others. While modulating RTK activation is a promising therapeutic target, RTK signaling axes have been shown to involve complicated interactions between ligands and receptors both within and across different protein families. In angiogenesis, for example, several signaling protein families, including vascular endothelial growth factors and platelet-derived growth factors, exhibit significant cross-family interactions that can influence pathway activation. Computational approaches can provide key insight to detangle these signaling pathways but have been limited by the sparse knowledge of these cross-family interactions. Here, we present a framework for studying known and potential non-canonical interactions. We construct... [more]

Genome-scale models have become indispensable tools for the study of cellular growth. These models have been progressively improving over the past two decades, enabling accurate predictions of metabolic fluxes and key phenotypes under a variety of growth conditions. In this work, an efficient computational method is proposed to incorporate genome-scale models into superstructure optimization settings, introducing them as viable growth models to simulate the cultivation section of biorefinaries. We perform techno-economic and life-cycle analyses of an algal biorefinery with five processing sections to determine optimal processing pathways and technologies. Formulation of this problem results in a mixed-integer nonlinear program, in which the net present value is maximized with respect to mass flowrates and design parameters. We use a genome-scale metabolic model of Chlamydomonas reinhardtii to predict growth rates in the cultivation section. We study algae cultivation in open ponds, in... [more]

Many drugs have a propensity for agglomeration, resulting in poor flowability. Spherical crystallization can be used to improve product properties including flowability and particle size. In this work, two methods were developed and utilized to successfully make two kinds of azithromycin spherical particles, namely solid and hollow spheres. The resultant product exhibited regular spherical shape, large particle size, narrow particle size distribution and excellent flowability. The formation mechanism of these different spherical crystals was investigated with the help of a particle vision microscope (PVM). The immersion mechanism and the counter diffusion mechanism were proposed as the formation mechanisms for solid and hollow spheres, respectively. The effects of crystallization parameters on the spherical crystallization processes were investigated systematically. Furthermore, the tablet properties were evaluated to verify that the spherical particles obtained in this work can be dir... [more]

Ultrasonic-assisted extraction (UAE) was optimized using response surface methodology (RSM) to maintain the cyto-protective activity of M.toringoides against oxidative stress. The optimal conditions for UAE were a 58 mL/g liquid-solid ratio, a 38 °C extraction temperature, an 85% solvent concentration, and a 19-min extraction time, which resulted in a protection rate of 54.57% against hydrogen peroxide-induced oxidative stress in human umbilical vein endothelial cells (HUVECs). These results were comparable to the predicted value of 53.75%. The extracts showed excellent antioxidant activity, and phlorizin was detected in the dried leaves of Malus.toringoides. The highest yield of phlorizin (101.239 mg/g) was also obtained using these conditions. Taken together, these results showed that the method successfully integrated RSM and partial least squares regression methods to optimize M.toringoides extraction to yield the highest cyto-protective activity and effectively increase the yield... [more]

A simple method for obtaining pure and well-defined oligosaccharides was established by hydrolyzing agar with β-agarase from Vibrio natriegens. The conditions for enzymolysis were optimized as follows: a temperature of 45 °C, a pH of 8.5, a substrate concentration of 0.3%, an enzyme amount of 100 U/g and an enzymolysis time of 20 h. Neoagaro-oligosaccharides with different degrees of polymerization were obtained by hydrolyzing agar with β-agarase for different lengths of time. After removing pigments using activated carbon and salts by dialyzing, the enzyme hydrolysis solution was separated with Bio-Gel P2 column chromatography. Neoagaro-oligosaccharides with different degrees of polymerization were acquired. By comparing with authentic standard substances, along with further confirmation by FTIR, MS and NMR, structures of the purified neoagaro-oligosaccharides were identified as neoagarobiose (NA2), neoagaroteraose (NA4), neoagarohexaose (NA6), neoagarooctaose (NA8), neoagaro-decaose... [more]

The constraint-based rMeCBM-KU50 model of cassava storage root growth was analyzed to evaluate its sensitivity, with respect to reaction flux distribution and storage root growth rate, to changes in model inputted data and constraints, including sucrose uptake rate-related data—photosynthetic rate, total leaf area, total photosynthetic rate, storage root dry weight, and biomass function-related data. These mainly varied within ±90% of the model default values, although exceptions were made for the carbohydrate (−90% to 8%) and starch (−90% to 9%) contents. The results indicated that the predicted storage root growth rate was highly affected by specific sucrose uptake rates through the total photosynthetic rate and storage root dry weight variations; whereas the carbon flux distribution, direction and partitioning inclusive, was more sensitive to the variation in biomass content, particularly the carbohydrate content. This study showed that the specific sucrose uptake rate based on the... [more]

The Powder-Activated Carbon (PAC) under optimum conditions from a new low-cost precursor Date Palm Fibre (DPF) biomass through a carbonization followed by KOH activation has been synthesized by response surface methodology (RSM) combined with central composite design (CCD). The special effects of activation temperature, time, and impregnation ratio on bio-PAC Aluminum (Al3+) removal and uptake capacity were examined. The optimum conditions for synthesized bio-PAC were found to be 99.4% and 9.94 mg·g−1 for Al3+ removal and uptake capacity, respectively at activation temperature 650 °C, activation time 1h and impregnation ratio 1. The optimum bio-PAC was characterized and analyzed using FESEM, FTIR, XRD, TGA, BET, and Zeta potential. RSM-CCD experimental design was used to optimize removal and uptake capacity of Al3+ on bio-PAC. Optimum conditions were found to be at bio-PAC dose of 5 mg with pH 9.48 and contact time of 117 min. Furthermore, at optimized conditions of Al3+ removal, kinet... [more]

The exhaustion of natural resources has increased petroleum prices and the environmental impact of oil has stimulated the search for an alternative source of energy such as biodiesel. Waste cooking oil is a potential replacement for vegetable oils in the production of biodiesel. Biodiesel is synthesized by direct transesterification of vegetable oils, which is controlled by several inputs or process variables, including the dosage of catalyst, process temperature, mixing speed, mixing time, humidity and impurities of waste cooking oil that was studied in this case. Yield, turbidity, density, viscosity and higher heating value are considered as outputs. This paper used multi-response surface methodology (MRS) with desirability functions to find the best combination of input variables used in the transesterification reactions to improve the production of biodiesel. In this case, several biodiesel optimization scenarios have been proposed. They are based on a desire to improve the biodies... [more]

This research investigates ethanol production from waste lignocellulosic material (sugarcane bagasse). The bagasse was first pretreated using chemicals and ultrasound techniques. These pretreatment techniques were applied separately and combined. The pretreated bagasse was then fermented anaerobically for biofuel production without enzymatic hydrolysis. The results showed higher ethanol production than those reported in the literature. The maximum ethanol production of 820 mg/L was achieved with a combination of ultrasound (60 amplitude level, 127 W) and acid (3% H₂SO₄ concentration). The combination of two-step pretreatment such as an ultrasound (50 amplitude level, 109 W) with acid (3% H₂SO₄ concentration) and then an ultrasound with alkaline (23% NaOH concentration) generated 911 mg/L of ethanol.

Global Sensitivity Analysis (GSA) is a technique that numerically evaluates the significance of model parameters with the aim of reducing the number of parameters that need to be estimated accurately from experimental data. In the work presented herein, we explore different methods and criteria in the sensitivity analysis of a recently developed mathematical model to describe Chinese hamster ovary (CHO) cell metabolism in order to establish a strategic, transferable framework for parameterizing mechanistic cell culture models. For that reason, several types of GSA employing different sampling methods (Sobol’, Pseudo-random and Scrambled-Sobol’), parameter deviations (10%, 30% and 50%) and sensitivity index significance thresholds (0.05, 0.1 and 0.2) were examined. The results were evaluated according to the goodness of fit between the simulation results and experimental data from fed-batch CHO cell cultures. Then, the predictive capability of the model was tested against four different... [more]

Deep eutectic solvents (DESs) are increasingly receiving interest as a new type of green and sustainable alternative to hazardous organic solvents. In this work, a novel DES based on levulinic acid (La) and 1,4-butanediol (Buta) as an extraction media was developed for extracting the bioactive alkaloid rutaecarpine from the unripe fruits of Tetradium ruticarpum. 24 different DESs consisting of choline chloride, betaine, sugar alcohols, organic acids, amides, and sugars were prepared and tailored to test their extraction efficiency. After initial screening, a hydrophilic DES composed of La and Buta with 1:0.5 molar ratio containing 25% water was tailored for the highest extraction efficiency, followed by the optimizations of molar ratio and water content. The interaction between the molecules of La-Buta DES was investigated by nuclear magnetic resonance spectroscopy in order to confirm its deep eutectic supermolecular structure feature. The extraction conditions were optimized by single... [more]

Intensified and accelerated development processes are being demanded by the market, as innovative biopharmaceuticals such as virus-like particles, exosomes, cell and gene therapy, as well as recombinant proteins and peptides will possess no available platform approach. Therefore, methods that are able to accelerate this development are preferred. Especially, physicochemical rigorous process models, based on all relevant effects of fluid dynamics, phase equilibrium, and mass transfer, can be predictive, if the model is verified and distinctly quantitatively validated. In this approach, a macroscopic kinetic model based on Monod kinetics for mammalian cell cultivation is developed and verified according to a general valid model validation workflow. The macroscopic model is verified and validated on the basis of four decision criteria (plausibility, sensitivity, accuracy and precision as well as equality). The process model workflow is subjected to a case study, comprising a Chinese hamst... [more]

Aiming to further improve the dust suppression performance of the dust suppressant, the present study independently develops a new type of biodegradable environmentally-friendly dust suppressant. Specifically, the naturally occurring biodegradable soybean protein isolate (SPI) is selected as the main material, which is subject to an anionic surfactant, i.e., sodium dodecyl sulfonate (SDS) for modification with the presence of additives including carboxymethylcellulose sodium and methanesiliconic acid sodium. As a result, the SDS-SPI cementing dust suppressant is produced. The present study experimentally tests solutions with eight different dust suppressant concentrations under the same experimental condition, so as to evaluate their dust suppression performances. Key metrics considered include water retention capability, cementing power and dust suppression efficiency. The optimal concentration of dust suppressant solution is determined by collectively comparing these metrics. The exp... [more]

In the past decades, dyes waste waters produced from industries have become a major source of environmental pollution causing the destruction of aquatic communities in the ecosystem and greatly threatened human health. Herein, a novel magnetic adsorbent was synthesized by carbonizing iron (III) 2,4-pentanedionate (Fe(acac)3) pre-enriched forestry waste wood at a pyrolysis temperature of 1000 °C. The characterization of the adsorbent conducted via SEM, EDS, VSM, XRD, XPS, and FT-IR spectroscopy. The adsorption trend followed the pseudo-second order kinetics model. The corresponding adsorption performance was efficient with an equilibrium time of only 1 min. Affect factors on the adsorption performance, such as adsorbent dosage, contact time and temperature, were investigated. The magnetic bio-char showed a high adsorption capacity and an efficient adsorption toward RhB, implying great potential application in the treatment of colored wastewaters.

Sweet sorghum juice, a potential bioethanol feedstock, can be incorporated into the dry-grind ethanol process to improve sugar utilization efficiency, thereby enhancing ethanol yields. The juice is normally obtained by pressing the stalk through roller mills in tandem. Juice extraction by this process is known to be labor intensive, less efficient, and susceptible to considerable fermentable sugar loss due to microbial activities when stored at room temperature. Sweet sorghum juice extraction via diffusion has recently been proposed to improve sugar recovery efficiency. In this study, extraction kinetics based on the optimized diffusion parameters (8% grain loading, 85 °C, and 120 min) were determined to describe the mass transfer of sugars in sweet sorghum biomass during the diffusion process. Diffusion parameters obtained from previous studies were used to extract free sugars and convert them into ethanol using granular starch hydrolyzing enzymes (GSHE) and traditional enzymes. Ethan... [more]

Diabetic kidney disease (DKD) is a major cause of renal failure. Podocytes are terminally differentiated renal epithelial cells that are key targets of damage due to DKD. Podocytes express a glucose-stimulated local renin-angiotensin system (RAS) that produces angiotensin II (ANG II). Local RAS differs from systemic RAS, which has been studied widely. Hyperglycemia increases the production of ANG II by podocyte cells, leading to podocyte injury. Angiotensin-converting enzyme (ACE) is involved in the production of ANG II, and ACE inhibitors are drugs used to suppress elevated ANG II concentration. As systemic RAS differs from the local RAS in podocytes, ACE inhibitor drugs should act differently in local versus systemic contexts. Experimental and computational studies have considered the pharmacokinetics (PK) and pharmacodynamics (PD) of ACE inhibition of the systemic RAS. Here, a PK/PD model for ACE inhibition is developed for the local RAS in podocytes. The model takes constant or dyn... [more]

The treatment of nitrate and phosphate ions in fresh water such as streams, rivers, lakes, reservoirs, and wetlands through biological treatment has been getting more crucial and popular in recent years. This paper reports the reduction of nitrate and phosphate ions in modified low salinity fresh water via the cultivation of a microalgae strain, e.g., Tetraspora sp. and Spirogyra sp. The low salinity fresh water (9054 to 9992 ppm) was modified with the addition of organic fertiliser (VermiCompost Tea) and used as the cultivation medium to grow microalgae. The microalgae strains were grown under controlled conditions in an indoor laboratory for 14 days. The initial concentrations of nitrate and phosphate ions in the modified fresh water sample were 1.17 mg/L and 0.10 mg/L, respectively. The reduction of nitrate and phosphate ions associated with the effect of cultivation of Tetraspora sp. and Spirogyra sp. in ambient air (0.03% of CO2) and 15% of CO2 was investigated. In ambient air, th... [more]

The purpose of this study was to investigate how the properties of Mexican kefir grains (MKG) are affected by the operating parameters used in the freeze-drying process. The factors investigated were the freezing time (3−9 h), freezing temperature (−20 to −80 °C), pressure (0.2−0.8 mbar), and lyophilization time (5−20 h). The maximum range of change and one-way analysis of variance showed that lyophilization time and freezing time significant affects (p < 0.05) the response variables, residual moisture content and water activity, and pressure had a significant effect on the color difference and survival rate of probiotic microorganisms. The best drying conditions were a freezing time of 3 h, a freezing temperature of −20 °C, a pressure of 0.6 mbar, and a lyophilization time of 15 h. Under these conditions, we obtained a product with residual moisture content below 6%, water activity below 0.2, and survival rates above 8.5 log cfu per gram of lactic acid bacteria and above 8.6 log fo... [more]

Brewers’ spent grain (BSG) is the most abundant by-product of the brewing process. BSG is currently disposed of or used as a supplement for animal feed, although it contains significant amounts of bioactive compounds of great interest to the pharmaceutical, cosmetic and food sectors. In this study we investigate the feasibility of using a simple solvent extraction procedure to recover phenolic antioxidants from BSG. Acetone−water and ethanol−water mixtures were used as extraction solvents. Phenolic extracts obtained by treatment of BSG with the two solvent systems were characterized in terms of total phenolics and antioxidant activity. For both systems, the extraction yield was maximum at 60% (v/v) organic solvent concentration. At all solvent compositions, mixtures containing acetone provided higher extraction yields. As suggested by the strong correlation between the antioxidant activity of BSG extracts and their phenolic content, the antioxidant capacity of the extracts can be mainl... [more]

Viscose, a cellulose-based commodity fibre, is produced by pulping and bleaching of wood, yielding a high quality “dissolving pulp” which is then spun. During pulping and bleaching, effective hemicellulose extraction is required to allow fibre production. We present a design of experiments (DoE) approach to optimise caustic extraction in a total chlorine free (TCF) bleaching sequence (O-CE-Z-P) of beech wood sulphite pulp. Temperature and sodium hydroxide concentration were varied to identify highest xylan extraction yield, and a maximum xylan removal of 83% was achieved at 20 °C and 120 g/L NaOH. Additionally, caustic extraction conditions were derived from the DoE model that led to pulps with high yield, high alpha cellulose content or uniform cellulose molecular weight distribution. Pulps from verification experiments exhibited good reactivity in viscose application tests. Hence, the presented O-CE-Z-P bleaching sequence can be considered as suitable for integrated viscose fibre pro... [more]

Accurate predictive mathematical models are urgently needed in synthetic biology to support the bottom-up design of complex biological systems, minimizing trial-and-error approaches. The majority of models used so far adopt empirical Hill functions to describe activation and repression in exogenously-controlled inducible promoter systems. However, such equations may be poorly predictive in practical situations that are typical in bottom-up design, including changes in promoter copy number, regulatory protein level, and cell load. In this work, we derived novel mechanistic steady-state models of the lux inducible system, used as case study, relying on different assumptions on regulatory protein (LuxR) and cognate promoter (Plux) concentrations, inducer-protein complex formation, and resource usage limitation. We demonstrated that a change in the considered model assumptions can significantly affect circuit output, and preliminary experimental data are in accordance with the simulated ac... [more]