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Records with Subject: Biosystems
Showing records 1 to 25 of 92. [First] Page: 1 2 3 4 Last
Study on Mass Transfer Kinetics of Sugar Extraction from Sweet Sorghum Biomass via Diffusion Process and Ethanol Yield Using SSF
Nana Baah Appiah-Nkansah, Jun Li, Ke Zhang, Meng Zhang, Donghai Wang
July 17, 2019 (v1)
Subject: Biosystems
Keywords: bioethanol, diffusion, ethanol fermentation, kinetic model, mass transfer, sweet sorghum juice
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]
A Glucose-Dependent Pharmacokinetic/ Pharmacodynamic Model of ACE Inhibition in Kidney Cells
Minu R. Pilvankar, Hui Ling Yong, Ashlee N. Ford Versypt
July 11, 2019 (v1)
Subject: Biosystems
Keywords: benazepril, diabetic kidney disease, diabetic nephropathy, PK/PD, podocytes, renin-angiotensin system
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]
High Nitrate and Phosphate Ions Reduction in Modified Low Salinity Fresh Water through Microalgae Cultivation
Ahmad Rozaimee Mustaffa, Ku Halim Ku Hamid, Mohibah Musa, Juferi Idris, Roslina Ramli
July 11, 2019 (v1)
Subject: Biosystems
Keywords: biodiesel, Carbon Dioxide, fresh water, low salinity, nitrate ions, phosphate ions, Spirogyra sp., Tetraspora sp.
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]
Effect of the Freeze-Drying Process on the Physicochemical and Microbiological Properties of Mexican Kefir Grains
Alicia Águeda Conde-Islas, Maribel Jiménez-Fernández, Denis Cantú-Lozano, Galo Rafael Urrea-García, Guadalupe Luna-Solano
July 11, 2019 (v1)
Subject: Biosystems
Keywords: freeze-drying, kefir grains, operating parameters, probiotic, properties
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]
Water−Organic Solvent Extraction of Phenolic Antioxidants from Brewers’ Spent Grain
Antonio Zuorro, Annalaura Iannone, Roberto Lavecchia
July 11, 2019 (v1)
Subject: Biosystems
Keywords: brewers’ spent grain, phenolic compounds, solvent extraction, waste valorization
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]
Effects of Caustic Extraction on Properties of Viscose Grade Dissolving Pulp
Cindy Friebel, Robert H. Bischof, Gabriele Schild, Karin Fackler, Ireen Gebauer
July 5, 2019 (v1)
Subject: Biosystems
Keywords: caustic extraction, cellulosic fibres, dissolving pulp, pulp, textile fibres, viscose, wood
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]
Mechanistic Models of Inducible Synthetic Circuits for Joint Description of DNA Copy Number, Regulatory Protein Level, and Cell Load
Lorenzo Pasotti, Massimo Bellato, Davide De Marchi, Paolo Magni
July 5, 2019 (v1)
Subject: Biosystems
Keywords: bottom-up design, cell load, copy number, inducible promoter, mathematical modeling, mechanistic model, synthetic biology
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]
Biomaterial Implants in Abdominal Wall Hernia Repair: A Review on the Importance of the Peritoneal Interface
Verónica Gómez-Gil, Gemma Pascual, Juan M. Bellón
June 10, 2019 (v1)
Subject: Biosystems
Keywords: abdominal wall, hernia recurrence, hernia repair, omentum, peritoneal adhesions, peritoneum, polypropylene, surgical mesh
Biomaterials have long been used to repair defects in the clinical setting, which has led to the development of a wide variety of new materials tailored to specific therapeutic purposes. The efficiency in the repair of the defect and the safety of the different materials employed are determined not only by the nature and structure of their components, but also by the anatomical site where they will be located. Biomaterial implantation into the abdominal cavity in the form of a surgical mesh, such as in the case of abdominal hernia repair, involves the contact between the foreign material and the peritoneum. This review summarizes the different biomaterials currently available in hernia mesh repair and provides insights into a series of peculiarities that must be addressed when designing the optimal mesh to be used in this interface.
Accelerating Biologics Manufacturing by Modeling or: Is Approval under the QbD and PAT Approaches Demanded by Authorities Acceptable without a Digital-Twin?
Steffen Zobel-Roos, Axel Schmidt, Fabian Mestmäcker, Mourad Mouellef, Maximilian Huter, Lukas Uhlenbrock, Martin Kornecki, Lara Lohmann, Reinhard Ditz, Jochen Strube
June 10, 2019 (v1)
Subject: Biosystems
Keywords: biologics, continuous bioprocessing, manufacturing, Modelling, modular plants, Process Intensification, Renewable and Sustainable Energy
Innovative biologics, including cell therapeutics, virus-like particles, exosomes, recombinant proteins, and peptides, seem likely to substitute monoclonal antibodies as the main therapeutic entities in manufacturing over the next decades. This molecular variety causes a growing need for a general change of methods as well as mindset in the process development stage, as there are no platform processes available such as those for monoclonal antibodies. Moreover, market competitiveness demands hyper-intensified processes, including accelerated decisions toward batch or continuous operation of dedicated modular plant concepts. This indicates gaps in process comprehension, when operation windows need to be run at the edges of optimization. In this editorial, the authors review and assess potential methods and begin discussing possible solutions throughout the workflow, from process development through piloting to manufacturing operation from their point of view and experience. Especially,... [more]
Relationship Between MiRKAT and Coefficient of Determination in Similarity Matrix Regression
Xiang Zhan
June 8, 2019 (v1)
Subject: Biosystems
Keywords: coefficient of determination R2, fraction of variance explained, microbiome association analysis, MiRKAT, similarity matrix regression
The Microbiome Regression-based Kernel Association Test (MiRKAT) is widely used in testing for the association between microbiome compositions and an outcome of interest. The MiRKAT statistic is derived as a variance-component score test in a kernel machine regression-based generalized linear mixed model. In this brief report, we show that the MiRKAT statistic is proportional to the R 2 (coefficient of determination) statistic in a similarity matrix regression, which characterizes the fraction of variability in outcome similarity, explained by microbiome similarity (up to a constant).
Comparison of Three Deoxidation Agents for Ozonated Broths Used in Anaerobic Biotechnological Processes
Ewelina Pawlikowska, Jaroslaw Domanski, Piotr Dziugan, Joanna Berlowska, Weronika Cieciura-Wloch, Krzysztof Smigielski, Dorota Kregiel
May 16, 2019 (v1)
Subject: Biosystems
Keywords: deoxidation, iron sulfate, Metschnikowia sp., ozonation, ultrasound
Anaerobic fermentation of organic compounds is used in many biotechnological processes and has been the subject of much research. A variety of process conditions and different growth media can be used to obtain microbial metabolites. The media must be free from contamination before fermentation. Sterilization is most often achieved by applying heat or other treatments, such as ozonation. Sterilization of liquid media using ozone can be very beneficial, but this method introduces high concentrations of residual oxygen, which inhibit anaerobic processes. Deoxidation is therefore necessary to remove the oxygen from ozonated broths. This study evaluates the effectiveness of three deoxidation agents for two kinds of fermentation media based on malt or molasses: ultrasound, iron(II) sulfate, and Metschnikowia sp. yeast. The time needed for deoxidation varied, depending on the kind of broth and the deoxidation agent. In general, the dynamics of oxygen removal were faster in malt broth. A comp... [more]
Integrated Hydrolysis of Mixed Agro-Waste for a Second Generation Biorefinery Using Nepenthes mirabilis Pod Digestive Fluids
Nkosikho Dlangamandla, Seteno Karabo Obed Ntwampe, Justine Oma Angadam, Elie Fereche Itoba-Tombo, Boredi Silas Chidi, Lukhanyo Mekuto
May 16, 2019 (v1)
Subject: Biosystems
Keywords: agro-waste, biorefinery, carboxylesterases, cellulases, Nepenthes mirabilis, total reducing sugars, xylanase, β-glucosidase
To sustainably operate a biorefinery with a low cost input in a commercial setting, the hydrolysis of lignocellulosic biomass must be undertaken in a manner which will impart environmental tolerance while reducing fermenter inhibitors from the delignification process. The challenge lies with the highly recalcitrant lignin structure, which limits the conversion of the holocelluloses to fermentable total reducing sugars (TRS). Due to these challenges, sustainable and innovative methods to pre-treat biomass must be developed for delignocellulolytic operations. Herein, Nepenthes mirabilis digestive fluids shown to have ligninolytic, cellulolytic and xylanolytic activities were used as an enzyme cocktail to hydrolyse mixed agro-waste constituted by Citrus sinensis (orange), Malus domestica (apple) peels, cobs from Zea mays (maize) and Quercus robur (oak) yard waste. The digestive fluids contained carboxylesterases (529.41 ± 30.50 U/L), β-glucosidases (251.94 ± 11.48 U/L) and xylanases (36.0... [more]
Effect of Supercritical Fluid Extraction Process on Chemical Composition of Polianthes tuberosa Flower Extracts
Javier C. Fragoso-Jiménez, Ernesto Tapia-Campos, Mirna Estarron-Espinosa, Rodrigo Barba-Gonzalez, Ma. Claudia Castañeda-Saucedo, Gustavo A. Castillo-Herrera
May 16, 2019 (v1)
Subject: Biosystems
Keywords: chemical composition, Polianthes tuberosa, supercritical fluid extraction
Supercritical fluid extracts from flowers of Polianthes tuberosa var. double were ob tained using carbon dioxide as a solvent. Yield extract obtained was 2.5%. The effects of the pressure process (18 MPa, 28 MPa, and 38 MPa) and temperature process (313 K, 323 K, and 333 K) on the volatile composition of tuberose flowers extracts were evaluated, and a significant variation in chemical composition was found. Characteristic compounds of tuberose as methyl isoeugenol, benzyl benzoate, methyl anthranilate, pentacosene, and heptacosene were obtained mainly at 18 MPa and 333 K process conditions, and could be used in the perfume or fragrance industry. Components such as geraniol, farnesol, and methyl eugenol were also obtained, these extracts could be used in the development of cosmeceutical products. This work allowed to identification of the chemical composition profile and evaluation of the changes in tuberose extracts due to the extraction process.
The Study on Extraction Process and Analysis of Components in Essential Oils of Black Pepper (Piper nigrum L.) Seeds Harvested in Gia Lai Province, Vietnam
Thien Hien Tran, Le Ke Ha, Duy Chinh Nguyen, Tan Phat Dao, Le Thi Hong Nhan, Dai Hai Nguyen, Trinh Duy Nguyen, Dai-Viet N. Vo, Quoc Toan Tran, Long Giang Bach
May 16, 2019 (v1)
Subject: Biosystems
Keywords: black pepper (Piper nigrum L.), essential oils, chemical composition analysis, GC-MS, hydrodistillation
Black pepper (Piper nigrum L.) is a tropical crop with extensive medicinal potential in ethnomedicine and nutraceutical applications. The essential oil of black pepper finds wide applications in inhabitation of respiratory infections and soothing of muscular pains due to its warming and energizing property. The pungent bioactive piperine is responsible for this function, and therefore, efficient technology is required for an optimal extraction process of this compound. In the present article, we have developed a procedure for extracting black pepper essential oil from Vietnam, optimizing conditions that affect the extraction process. The effect of process parameters, namely material size, preservation method, the concentration of sodium chloride, the concentration of soak time, the ratio of material to water, temperature extraction, time extraction on the extraction yield, and relative efficiency were investigated. Results demonstrated that 20 g of black pepper milled with a mesh size... [more]
Pilot Plant Data Assessment in Anaerobic Digestion of Organic Fraction of Municipal Waste Solids
Massimo Migliori, Enrico Catizzone, Girolamo Giordano, Adolfo Le Pera, Miriam Sellaro, Alessandro Lista, Giuseppe Zanardi, Luciano Zoia
April 15, 2019 (v1)
Subject: Biosystems
Keywords: biogas, dry anaerobic digestion, municipal waste, wet anaerobic digestion
In this paper, a preliminary study of anaerobic digestion of organic fraction of municipal solid wastes (OFMSW) in presented with the aim to compare the performances of both wet- and dry-type reactors. The treatment of OFMSW via anaerobic digestion (AD) producing biogas is a process that is receiving a growing interest because two different needs can be coupled: the request of sustainable municipal waste treatments and increasing demand renewable energy. This paper aims to offer experimental results comparing batch test and continuous experimental reactors under different conditions of humidity and solid content. Results show that both the investigated configurations may be used for converting OFMSW into a high quality biogas and that the increase of dry matter in the continuous process still allows to achieve significant biogas production rates. A slight reduction of the methane content was observed (less than 5% relative) that can be also related to the change in the level of volatil... [more]
Characterization, Expression Profiling, and Functional Analyses of a 4CL-Like Gene of Populus trichocarpa
Hui Wei, Chen Xu, Ali Movahedi, Weibo Sun, Qiang Zhuge
April 15, 2019 (v1)
Subject: Biosystems
Keywords: 4CL-like, ACS, box I domain, box II domain, CL, Populus trichocarpa, PTS
Adenosine 5′-monophosphate (AMP) (adenylate)-forming acetyl-CoA synthetase (ACS) catalyzes the formation of acetyl-coenzyme A (CoA), and the ACS family is closely related to the 4-coumarate CoA ligase (4CL) family. In this study, a 4CL-like gene was cloned from Populus trichocarpa and named Pt4CL-like. Characterization of Pt4CL-like, using bioinformatics, showed that it contained box I and box II domains at the end of the C-terminal sequence, and there is a characteristic sequence of ACS, namely, peroxisome-targeting sequence (PTS). Real-time PCR results showed that the 4CL-like gene was expressed in all tissues tested, and was highly expressed in the stems. A denaturation and renaturation process was conducted, and the recombinant Pt4CL-like protein was purified through HisTrapTM high performance affinity chromatography. It showed Pt4CL-like protein did not catalyze substrates of 4CL, but could significantly catalyzed sodium acetate. These results indicate that Pt4CL-like protein belo... [more]
Catastrophic Health Expenditures and Its Inequality in Households with Cancer Patients: A Panel Study
Munjae Lee, Kichan Yoon
April 15, 2019 (v1)
Subject: Biosystems
Keywords: cancer patient households, catastrophic health expenditure, healthcare spending, Korea Health Panel, panel logit analysis
This study aims to examine the determinants of catastrophic health expenditure in households with cancer patients by conducting a panel analysis of three-year data. Data are adopted from surveys administered by Korea Health Panel for 2012⁻2014. We conducted correspondence and conditional transition probability analyses to examine households that incurred catastrophic health expenditure, followed by a panel logit analysis. The analyses reveal three notable results. First, the occurrence of catastrophic health expenditure differs by age group, that is, the probability of incurring catastrophic health expenditure increases with age. Second, this probability is higher in households with National Health Insurance than those receiving medical care benefits. Finally, households without private health insurance report a higher occurrence rate. The findings suggest that elderly people with cancer have greater medical coverage and healthcare needs. Private health insurance contributes toward pro... [more]
Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment
Kerri-Ann Norton, Chang Gong, Samira Jamalian, Aleksander S. Popel
April 15, 2019 (v1)
Subject: Biosystems
Keywords: computational biology, immune checkpoint inhibitor, immuno-oncology, immunotherapy, mathematical modeling, multiscale systems biology, quantitative systems pharmacology (QSP)
Multiscale systems biology and systems pharmacology are powerful methodologies that are playing increasingly important roles in understanding the fundamental mechanisms of biological phenomena and in clinical applications. In this review, we summarize the state of the art in the applications of agent-based models (ABM) and hybrid modeling to the tumor immune microenvironment and cancer immune response, including immunotherapy. Heterogeneity is a hallmark of cancer; tumor heterogeneity at the molecular, cellular, and tissue scales is a major determinant of metastasis, drug resistance, and low response rate to molecular targeted therapies and immunotherapies. Agent-based modeling is an effective methodology to obtain and understand quantitative characteristics of these processes and to propose clinical solutions aimed at overcoming the current obstacles in cancer treatment. We review models focusing on intra-tumor heterogeneity, particularly on interactions between cancer cells and strom... [more]
Combining Microwave Pretreatment with Iron Oxide Nanoparticles Enhanced Biogas and Hydrogen Yield from Green Algae
Asad A. Zaidi, Ruizhe Feng, Adil Malik, Sohaib Z. Khan, Yue Shi, Asad J. Bhutta, Ahmer H. Shah
April 15, 2019 (v1)
Subject: Biosystems
Keywords: algae, anaerobic digestion, biogas, biohydrogen, energy assessment, kinetic models, microwave, nanoparticles, pretreatment
The available energy can be effectively upgraded by adopting smart energy conversion measures. The biodegradability of biomass can be improved by employing pretreatment techniques; however, such methods result in reduced energy efficiency. In this study, microwave (MW) irradiation is used for green algae (Enteromorpha) pretreatment in combination with iron oxide nanoparticles (NPs) which act as a heterogeneous catalyst during anaerobic digestion process for biogas enhancement. Batch-wise anaerobic digestion was carried out. The results showed that MW pretreatment and its combination with Fe₃O₄ NPs produced highest yields of biogas and hydrogen as compared to the individual ones and control. The biogas amount and hydrogen % v/v achieved by MW pretreatment + Fe₃O₄ NPs group were 328 mL and 51.5%, respectively. The energy analysis indicated that synergistic application of MW pretreatment with Fe₃O₄ NPs produced added energy while consuming less input energy than MW pretreatment alone. The... [more]
Model for Thin Layer Drying of Lemongrass (Cymbopogon citratus) by Hot Air
Thi Van Linh Nguyen, My Duyen Nguyen, Duy Chinh Nguyen, Long Giang Bach, Tri Duc Lam
April 15, 2019 (v1)
Subject: Biosystems
Keywords: activation energy, convection drying, Cymbopogon citratus, lemongrass, mathematical modeling, moisture diffusivity
Lemongrass is a plant that contains aromatic compounds (myrcene and limonene), powerful deodorants, and antimicrobial compounds (citral and geraniol). Identifying a suitable drying model for the material is crucial for establishing an initial step for the development of dried products. Convection drying is a commonly used drying method that could extend the shelf life of the product. In this study, a suitable kinetic model for the drying process was determined by fitting moisture data corresponding to four different temperature levels: 50, 55, 60 and 65 °C. In addition, the effect of drying temperature on the moisture removal rate, the effective diffusion coefficient and activation energy were also estimated. The results showed that time for moisture removal increases proportionally with the air-drying temperature, and that the Weibull model is the most suitable model for describing the drying process. The effective diffusion coefficient ranges from 7.64 × 10−11 m²/s to 1.48 × 10−10 m²... [more]
Early Afterdepolarisations Induced by an Enhancement in the Calcium Current
André H. Erhardt
April 15, 2019 (v1)
Subject: Biosystems
Keywords: bifurcation analysis, calcium current, canard-induced EADs, geometric singular perturbation theory, multiple time scales, nonlinear dynamics
Excitable biological cells, such as cardiac muscle cells, can exhibit complex patterns of oscillations such as spiking and bursting. Moreover, it is well known that an enhancement in calcium currents may yield certain kind of cardiac arrhythmia, so-called early afterdepolarisations (EADs). The presence of EADs strongly correlates with the onset of dangerous cardiac arrhythmia. In this paper we study mathematically and numerically the dynamics of a cardiac muscle cell with respect to the calcium current by investigating a simplistic system of differential equations. For the study of this phenomena, we use bifurcation theory, numerical bifurcation analysis, geometric singular perturbation theory and computational methods to investigate a nonlinear multiple time scales system. It will turn out that EADs related to an enhanced calcium current are canard⁻induced and that we have to combine these theories to derive a better understanding of the dynamics behind EADs. Moreover, a suitable time... [more]
Supercritical CO₂ Transesterification of Triolein to Methyl-Oleate in a Batch Reactor: Experimental and Simulation Results
Geetanjali Yadav, Leonard A. Fabiano, Lindsay Soh, Julie Zimmerman, Ramkrishna Sen, Warren D. Seider
April 9, 2019 (v1)
Subject: Biosystems
Keywords: biodiesel, methyl-oleate, multiphase equilibrium, RK-ASPEN, supercritical CO2
In earlier work (Silva et al., 2016; Soh et al., 2014a; Soh et al., 2015), the supercritical CO₂ transesterification of triolein to methyl-oleate using Nafion solid-acid catalyst and large methanol/triolein molar feed ratios was carried out. Herein, these ratios are adjusted (from 50⁻550) to evaluate the yield of fatty acid methyl esters in batch laboratory reactors as temperature is varied from 80⁻95 °C and pressure is varied from 8.0⁻9.65 MPa. Also, to better understand the effect of varying these operating parameters, batch reactor simulations using the Soave-Redlich-Kwong Equation of State (RK-ASPEN EOS) in ASPEN PLUS are carried-out. A single-reaction kinetic model is used and phase equilibrium is computed as the reactions proceed. Experimental data are compared with these results.
A Model-Based Investigation of Cytokine Dynamics in Immunotherapies
Brooks Hopkins, Yiming Pan, Matthew Tucker, Zuyi (Jacky) Huang
April 9, 2019 (v1)
Subject: Biosystems
Keywords: cytokine release syndrome, hierarchical clustering, immunotherapy, Monte Carlo sampling, principal component analysis, sensitivity analysis
With the advent of effective immunotherapies to battle cancers and diseases, an obstacle in recovery has become the potential side effects, specifically cytokine release syndrome (CRS). As there is little quantitative understanding of risks for developing CRS and the degree of its severity, this work explored a model-based approach to produce a library of in silico patients through sensitivity analysis of cytokine interaction parameters and a Monte Carlo sampling. The objective of producing the in silico patients was to correlate a known grading system of cytokine release syndrome severity and thus design a new formula for grading CRS. Using our CRS grading system as the foundation, this work produced not only a formula which related the in silico patient data to the different grades, but we effectively demonstrated a selective approach to reduce the grade of CRS with sequential cytokine inhibition targets. We achieved the reduction of grades by applying the insight from the sensitivit... [more]
High-Throughput Microfiltration Membranes with Natural Biofouling Reducer Agent for Food Processing
Panggulu Ahmad R. Utoro, Agung Sukoyo, Sandra Sandra, Nimatul Izza, Shinta Rosalia Dewi, Yusuf Wibisono
April 9, 2019 (v1)
Subject: Biosystems
Keywords: biofouling, cellulose acetate, microfiltration, mixed matrix membrane, Moringa oleifera
The effect of natural antibiotics Moringa oleifera seeds powder in cellulose acetate membranes as biofouling reducer agent was investigated. Mixed matrix membranes (MMM) were synthesized by adding 100 mesh M. oleifera seeds powder with variation of three concentrations (1 wt%, 2 wt%, and 3 wt%), into a mix polymer solution of CA (cellulose acetate) and two different solvents, i.e., DMF (dimethylformamide) and DMAc (dimethylacetamide). The synthesized membranes morphology was observed under scanning electron microscopy and from the images can be seen that the membranes made of DMAc formed rather large macrovoid as compared to DMF-based membranes. The microstructure affected the water flux through the membranes, in which the DMAc membranes provided a higher flux value and served as high-throughput microfiltration membranes. Antibacterial properties of MMM were tested using Escherichia coli adhesion onto membrane surfaces. The results showed that M. oleifera has been proven to eradicate E... [more]
Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology
Philipp Boeing, Miriam Leon, Darren N. Nesbeth, Anthony Finkelstein, Chris P. Barnes
April 8, 2019 (v1)
Subject: Biosystems
Keywords: aspect-oriented software engineering, CAD, host context, mathematical modelling, modularity, SynBioWeaver, synthetic biology
Work on synthetic biology has largely used a component-based metaphor for system construction. While this paradigm has been successful for the construction of numerous systems, the incorporation of contextual design issues—either compositional, host or environmental—will be key to realising more complex applications. Here, we present a design framework that radically steps away from a purely parts-based paradigm by using aspect-oriented software engineering concepts. We believe that the notion of concerns is a powerful and biologically credible way of thinking about system synthesis. By adopting this approach, we can separate core concerns, which represent modular aims of the design, from cross-cutting concerns, which represent system-wide attributes. The explicit handling of cross-cutting concerns allows for contextual information to enter the design process in a modular way. As a proof-of-principle, we implemented the aspect-oriented approach in the Python tool, SynBioWeaver, which e... [more]
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