Experimental multivariable adaptive optimization of the steady-state cellular productivity of a continuous baker's yeast culture

A multivariable adaptive optimization algorithm that uses transient data to improve the optimization speed was successfully implemented on-line to maximize the steady-state cellular productivity of a continuous culture of baker's yeast. The algorithm was shown to be stable even during periods of oscillatory growth and was able to reoptimize the culture when planned disturbances were introduced. Although adaptive tuning of the forgetting factor improved the performance, further refinements in the adaptive forgetting factor algorithm are necessary for completely satisfactory results.     

Experimental and simulation studies of multivariable adaptive optimization of continuous bioreactors using bilevel forgetting factors

A multivariable on-line adaptive optimization algorithm using a bilevel forgetting factor method was developed and applied to a continuous baker's yeast culture in simulation and experimental studies to maximize the cellular productivity by manipulating the dilution rate and the temperature. The algorithm showed a good optimization speed and a good adaptability and reoptimization capability. The algorithm was able to stably maintain the process around the optimum point for an extended period of time. Two cases were investigated: an unconstrained and a constrained optimization. In the constrained optimization the ethanol concentration was used as an index for the baking quality of yeast cells. An equality constraint with a quadratic penalty was imposed on the ethanol concentration to keep its level close to a hypothetical "optimum" value. The developed algorithm was experimentally applied to a baker's yeast culture to demonstrate its validity. Only unconstrained optimization was carried out experimentally. A set of tuning parameter values was suggested after evaluating the results from several experimental runs. With those tuning parameter values the optimization took 50-90 h. At the attained steady state the dilution rate was 0.310 h(-1) the temperature 32.8 degrees C, and the cellular productivity 1.50 g/L/h.     

Fertilization in vitro of bovine oocytes after various sperm procedures

Fertilization in vitro of bovine follicular oocytes cultured in vitro was attempted after various procedures on frozen-thawed bull spermatozoa. The frozen-thawed semen was diluted at 1 : 15 and treated with one of eight methods as follows: 1) no washing, 2) washing, 3) passing through a glass wool column, 4) washing and bovine follicular fluid (BFF), 5) Ham's F-12 based medium and BFF (1 : 1), 6) BFF only, 7) a high ionic strength (HIS) treatment and the medium, or 8) HIS treatment and BFF. A total of 766 oocytes was examined for the identification of fertilization (the presence of the pronuclei and a sperm midpiece in the oocyte cytoplasm and the second polar body) and cleavage at 24 h after insemination. The sperm procedures by BFF treatment with or without washing showed significantly higher rates of fertilization (P<0.05) than the other methods tested, except after HIS treatment. The highest fertilization rate (46.2%) was obtained by the treatment with BFF only. The results indicate that BFF could favorably affect capacitation of frozen-thawed bull spermatozoa and its subsequent fertilization in vitro.     

Network Intrusion Detection Based on a General Regression Neural Network Optimized by an Improved Artificial Immune Algorithm

To effectively and accurately detect and classify network intrusion data, this paper introduces a general regression neural network (GRNN) based on the artificial immune algorithm with elitist strategies (AIAE). The elitist archive and elitist crossover were combined with the artificial immune algorithm (AIA) to produce the AIAE-GRNN algorithm, with the aim of improving its adaptivity and accuracy. In this paper, the mean square errors (MSEs) were considered the affinity function. The AIAE was used to optimize the smooth factors of the GRNN; then, the optimal smooth factor was solved and substituted into the trained GRNN. Thus, the intrusive data were classified. The paper selected a GRNN that was separately optimized using a genetic algorithm (GA), particle swarm optimization (PSO), and fuzzy C-mean clustering (FCM) to enable a comparison of these approaches. As shown in the results, the AIAE-GRNN achieves a higher classification accuracy than PSO-GRNN, but the running time of AIAE-GRNN is long, which was proved first. FCM and GA-GRNN were eliminated because of their deficiencies in terms of accuracy and convergence. To improve the running speed, the paper adopted principal component analysis (PCA) to reduce the dimensions of the intrusive data. With the reduction in dimensionality, the PCA-AIAE-GRNN decreases in accuracy less and has better convergence than the PCA-PSO-GRNN, and the running speed of the PCA-AIAE-GRNN was relatively improved. The experimental results show that the AIAE-GRNN has a higher robustness and accuracy than the other algorithms considered and can thus be used to classify the intrusive data.     

Comparison of colony-formation efficiency of bovine fetal fibroblast cell lines cultured with low oxygen, hydrocortisone, L-carnosine, bFGF, or different levels of FBS

A comparison of colony-formation efficiency (CFE) was made between six independent bovine fetal fibroblast (BFF) cell lines used in somatic cell nuclear transfer. Variation in CFE was assessed under different culture conditions. The conditions examined were ambient atmosphere (approximately 20% oxygen) culture versus 5% oxygen culture, three levels of fetal bovine serum (FBS) in the medium (5%, 10% or 20%), and the amendment of 10% FBS medium with basic fibroblast growth factor (1 ng/mL), L-carnosine (20 mM), or hydrocortisone (1 microM). The six BFF cell lines showed significant differences from one another in CFE. No significant difference in CFE was found with reduced oxygen culture. L-Carnosine also had no significant effect on CFE. A FBS concentration of 10% was found to produce the best overall CFE. Hydrocortisone treatment reduced the size of colonies although the number of colonies formed was not affected. Basic FGF increased the size of colonies but the number of colonies formed was not affected. The results showed that different BFF cell lines varied significantly in their CFE. Also, some medium supplements or culture conditions that have shown positive CFE effects on the fibroblasts of other species failed to show significant positive CFE effects on the BFF cell lines tested.     

Theoretical study on the structure and stability of [1,2,5] oxadiazolo [3,4-e] [1,2,3,4]-tetrazine-4,6-Di-N-dioxide (FTDO)

In protein–ligand docking, an optimization algorithm is used to find the best binding pose of a ligand against a protein target. This algorithm plays a vital role in determining the docking accuracy. To evaluate the relative performance of different optimization algorithms and provide guidance for real applications, we performed a comparative study on six efficient optimization algorithms, containing two evolutionary algorithm (EA)-based optimizers (LGA, DockDE) and four particle swarm optimization (PSO)-based optimizers (SODock, varCPSO, varCPSO-ls, FIPSDock), which were implemented into the protein–ligand docking program AutoDock. We unified the objective functions by applying the same scoring function, and built a new fitness accuracy as the evaluation criterion that incorporates optimization accuracy, robustness, and efficiency. The varCPSO and varCPSO-ls algorithms show high efficiency with fast convergence speed. However, their accuracy is not optimal, as they cannot reach very low energies. SODock has the highest accuracy and robustness. In addition, SODock shows good performance in efficiency when optimizing drug-like ligands with less than ten rotatable bonds. FIPSDock shows excellent robustness and is close to SODock in accuracy and efficiency. In general, the four PSO-based algorithms show superior performance than the two EA-based algorithms, especially for highly flexible ligands. Our method can be regarded as a reference for the validation of new optimization algorithms in protein–ligand docking.     

SVM-Based Synthetic Fingerprint Discrimination Algorithm and Quantitative Optimization Strategy

Synthetic fingerprints are a potential threat to automatic fingerprint identification systems (AFISs). In this paper, we propose an algorithm to discriminate synthetic fingerprints from real ones. First, four typical characteristic factors—the ridge distance features, global gray features, frequency feature and Harris Corner feature—are extracted. Then, a support vector machine (SVM) is used to distinguish synthetic fingerprints from real fingerprints. The experiments demonstrate that this method can achieve a recognition accuracy rate of over 98% for two discrete synthetic fingerprint databases as well as a mixed database. Furthermore, a performance factor that can evaluate the SVM''s accuracy and efficiency is presented, and a quantitative optimization strategy is established for the first time. After the optimization of our synthetic fingerprint discrimination task, the polynomial kernel with a training sample proportion of 5% is the optimized value when the minimum accuracy requirement is 95%. The radial basis function (RBF) kernel with a training sample proportion of 15% is a more suitable choice when the minimum accuracy requirement is 98%.     

Adaptive control of dissolved oxygen concentration in a bioreactor

A new adaptive DO (dissolved oxygen) concentration control algorithm considering DO electrode dynamics with response time delay has been developed. A system model with two time-varying parameters was used to relate the DO concentration with two control variables: air flow rate and agitation speed. Parameters of this model were estimated on-line using a regularized constant trace recursive least-squares method. An extended Kalman filter was used to remove the effect of noises from the DO concentration measurements and thus to improve control performance. A discrete one-step ahead control scheme was adopted to determine control actions based on the parameter estimation results. Experimental results showed that the new adaptive DO concentration control algorithm performed better than other algorithms tested, a PID controller and adaptive algorithms without the DO electrode dynamics.     

On the applicability of adaptive bioprocess state estimators

This article presents an industrial case study, examining the application of a novel adaptive biomass estimator to an industrial microfungi production process. It is our intention that this contribution should focus upon the implementation issues of the algorithm, in preference to a rigorous theoretical development. The novel algorithm adopted is developed from Adaptive Inferential Estimation studies of Guilandoust and co-workers. The technique utilizes input-output process measurements obtained at different frequencies, thereby providing more frequent estimates of biomass concentration than are otherwise available from off-line laboratory analyses. The algorithm is particularly suited to the biotechnology industry, as it is capable of utilizing irregular assay measurements with varying delays.Although this article demonstrates the encouraging industrial implications of the adaptive algorithm, like all adaptive techniques currently developed, it is restricted by the inability to perform robust on-line system identification. The ultimate selection of a "suboptimal" "fixed parameter" algorithm for on-line implementation, is therefore directly attributable to these inadequacies. Aspects of data acquisition, data pretreatment, and data quality are critical for real process applications, and while some practical approaches are adopted here, many important implementation problems remain unresolved. (c) 1993 John Wiley & Sons, Inc.     

Biflavonoids from Brazilian pine Araucaria angustifolia as potentials protective agents against DNA damage and lipoperoxidation

A biflavonoid fraction (BFF) obtained from Araucaria angustifolia needles was effective to quench singlet oxygen (1O2), to protect plasmid DNA against single strand break (ssb) caused by 1O2 or Fenton reaction and to inhibit Fenton or UV radiation-induced lipoperoxidation in phosphatidylcholine liposomes. The activity of the biflavonoid fraction (BFF) was compared with quercetin, rutin (flavonoids), ginkgetin, amentoflavone (biflavonoids), alpha-tocopherol and Trolox. The BFF displayed a higher quenching rate constant compared to flavonoids and biflavonoids and protected against ssb induced by 1O2. Although the BFF was not as efficient as either flavonoids, alpha-tocopherol or Trolox in protection against ssb induced by Fenton-reaction or lipoperoxidation, these scavenging properties suggest that BFF is still an excellent candidate for successful employment as an antioxidant and photoprotector.     

Fast and Accurate Construction of Ultra-Dense Consensus Genetic Maps Using Evolution Strategy Optimization

Our aim was to develop a fast and accurate algorithm for constructing consensus genetic maps for chip-based SNP genotyping data with a high proportion of shared markers between mapping populations. Chip-based genotyping of SNP markers allows producing high-density genetic maps with a relatively standardized set of marker loci for different mapping populations. The availability of a standard high-throughput mapping platform simplifies consensus analysis by ignoring unique markers at the stage of consensus mapping thereby reducing mathematical complicity of the problem and in turn analyzing bigger size mapping data using global optimization criteria instead of local ones. Our three-phase analytical scheme includes automatic selection of ~100-300 of the most informative (resolvable by recombination) markers per linkage group, building a stable skeletal marker order for each data set and its verification using jackknife re-sampling, and consensus mapping analysis based on global optimization criterion. A novel Evolution Strategy optimization algorithm with a global optimization criterion presented in this paper is able to generate high quality, ultra-dense consensus maps, with many thousands of markers per genome. This algorithm utilizes "potentially good orders" in the initial solution and in the new mutation procedures that generate trial solutions, enabling to obtain a consensus order in reasonable time. The developed algorithm, tested on a wide range of simulated data and real world data (Arabidopsis), outperformed two tested state-of-the-art algorithms by mapping accuracy and computation time.     

Parameter Identification of Robot Manipulators: A Heuristic Particle Swarm Search Approach

Parameter identification of robot manipulators is an indispensable pivotal process of achieving accurate dynamic robot models. Since these kinetic models are highly nonlinear, it is not easy to tackle the matter of identifying their parameters. To solve the difficulty effectively, we herewith present an intelligent approach, namely, a heuristic particle swarm optimization (PSO) algorithm, which we call the elitist learning strategy (ELS) and proportional integral derivative (PID) controller hybridized PSO approach (ELPIDSO). A specified PID controller is designed to improve particles’ local and global positions information together with ELS. Parameter identification of robot manipulators is conducted for performance evaluation of our proposed approach. Experimental results clearly indicate the following findings: Compared with standard PSO (SPSO) algorithm, ELPIDSO has improved a lot. It not only enhances the diversity of the swarm, but also features better search effectiveness and efficiency in solving practical optimization problems. Accordingly, ELPIDSO is superior to least squares (LS) method, genetic algorithm (GA), and SPSO algorithm in estimating the parameters of the kinetic models of robot manipulators.     

Biomimicry of symbiotic multi-species coevolution for discrete and continuous optimization in RFID networks

In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS²Os, which extend the single population particle swarm optimization (PSO) algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations. According to different symbiotic interrelationships, four versions of PS²O are initiated to mimic mutualism, commensalism, predation, and competition mechanism, respectively. In the experiments, with five benchmark problems, the proposed algorithms are proved to have considerable potential for solving complex optimization problems. The coevolutionary dynamics of symbiotic species in each PS²O version are also studied respectively to demonstrate the heterogeneity of different symbiotic interrelationships that effect on the algorithm’s performance. Then PS²O is used for solving the radio frequency identification (RFID) network planning (RNP) problem with a mixture of discrete and continuous variables. Simulation results show that the proposed algorithm outperforms the reference algorithms for planning RFID networks, in terms of optimization accuracy and computation robustness.     

Learning with slight forgetting optimizes sensorimotor transformation in redundant motor systems

Recent theoretical studies have proposed that the redundant motor system in humans achieves well-organized stereotypical movements by minimizing motor effort cost and motor error. However, it is unclear how this optimization process is implemented in the brain, presumably because conventional schemes have assumed a priori that the brain somehow constructs the optimal motor command, and largely ignored the underlying trial-by-trial learning process. In contrast, recent studies focusing on the trial-by-trial modification of motor commands based on error information suggested that forgetting (i.e., memory decay), which is usually considered as an inconvenient factor in motor learning, plays an important role in minimizing the motor effort cost. Here, we examine whether trial-by-trial error-feedback learning with slight forgetting could minimize the motor effort and error in a highly redundant neural network for sensorimotor transformation and whether it could predict the stereotypical activation patterns observed in primary motor cortex (M1) neurons. First, using a simple linear neural network model, we theoretically demonstrated that: 1) this algorithm consistently leads the neural network to converge at a unique optimal state; 2) the biomechanical properties of the musculoskeletal system necessarily determine the distribution of the preferred directions (PD; the direction in which the neuron is maximally active) of M1 neurons; and 3) the bias of the PDs is steadily formed during the minimization of the motor effort. Furthermore, using a non-linear network model with realistic musculoskeletal data, we demonstrated numerically that this algorithm could consistently reproduce the PD distribution observed in various motor tasks, including two-dimensional isometric torque production, two-dimensional reaching, and even three-dimensional reaching tasks. These results may suggest that slight forgetting in the sensorimotor transformation network is responsible for solving the redundancy problem in motor control.     

新型图形硬件支持下的动态规划局部比对算法加速研究

为探索准确、高效、低成本、通用性并存的生物序列局部比对方法。将点阵图算法、启发式算法等各种序列局部比对算法中准确性最高的动态规划局部比对算法在计算机中实现,并通过流式模型将其映射到图形硬件上以实现算法加速,再通过实例比对搜索数据库完成比对时间和每秒百万次格点更新（MCUPS）性能值评测。结果表明,该加速算法在保证比对准确性的同时,能显著提升比对速度。与目前最快的启发式算法相比,比对平均加速为14.5倍,最高加速可达22.9倍。     

Differential evolution for protein folding optimization based on a three-dimensional AB off-lattice model

This paper presents a differential evolution algorithm that is adapted for the protein folding optimization on a three-dimensional AB off-lattice model. The proposed algorithm is based on a self-adaptive differential evolution that improves the algorithm efficiency and reduces the number of control parameters. A mutation strategy for the fast convergence is used inside the algorithm. A temporal locality is used in order to speed up the algorithm convergence additionally and to find amino-acid conformations with the lowest free energy values. Within this mechanism a new vector is calculated when the trial vector is better than the corresponding vector from the population. This new vector is likely better than the trial vector and this accelerates convergence speed. Because of the fast convergence the algorithm has some chance to be trapped into the local optima. To mitigate this problem the algorithm includes reinitialization. The proposed algorithm was tested on amino-acid sequences that are used frequently in literature. The obtained results show that the proposed algorithm is superior to the algorithms from the literature and the obtained amino-acid sequences have significantly lower free energy values.

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Graphical Abstract Protein folding optimization on a three-dimensional AB off-lattice model using the differential evolution algorithm.

     

A Normative Theory of Forgetting: Lessons from the Fruit Fly

Recent experiments revealed that the fruit fly Drosophila melanogaster has a dedicated mechanism for forgetting: blocking the G-protein Rac leads to slower and activating Rac to faster forgetting. This active form of forgetting lacks a satisfactory functional explanation. We investigated optimal decision making for an agent adapting to a stochastic environment where a stimulus may switch between being indicative of reward or punishment. Like Drosophila, an optimal agent shows forgetting with a rate that is linked to the time scale of changes in the environment. Moreover, to reduce the odds of missing future reward, an optimal agent may trade the risk of immediate pain for information gain and thus forget faster after aversive conditioning. A simple neuronal network reproduces these features. Our theory shows that forgetting in Drosophila appears as an optimal adaptive behavior in a changing environment. This is in line with the view that forgetting is adaptive rather than a consequence of limitations of the memory system.     

Effects of bovine follicular fluid on maturation of bovine oocytes

Three experiments were conducted to determine the effects of follicular fluid and media on bovine oocyte maturation. Experiments 1 and 3 test the effects of follicular fluid obtained at different times after the LH surge on bovine oocyte maturation in vitro, while Experiment 2 was designed to compare TALP and Medium 199 as serum-free maturation media. Bovine follicular fluid (BFF) was obtained from preovulatory follicles either before (0 h BFF) or at 4, 8, 12 or 20 h after a GnRH-induced LH surge. Oocytes were obtained from follicles 1 to 6 mm in diameter from ovaries retrieved from a slaughterhouse. In Experiment 1, both 0 h and 4 h BFF inhibited resumption of meiosis, whereas BFF collected at 8, 12 and 20 h did not. When oocytes were cultured in media that contained equal portions of 0 and 8 h BFF, meiosis was not inhibited. In Experiment 2, Medium 199 supplemented with bovine serum albumin (BSA) was superior to Tyrode's medium with albumin, lactate and pyruvate for oocyte maturation. In Experiment 3, a higher percentage (P<0.05) of oocytes cultured for 18 h in 40% 20 h BFF in Medium 199 reached Metaphase-II (64%) than those cultured in 0 h BFF (41%) or control medium (39%). There was a transient meiotic arrest due to 0 h BFF as evidenced by the higher percentage of oocytes with germinal vesicles at 8 h of incubation (35% with 0 h vs 20% with 20 h; P<0.05). Furthermore, expansion of cumulus cells was induced in 8 and 20 h BFF, but not 0 h BFF.     

Optimization of culture conditions for the production of Pleuromutilin from Pleurotus Mutilus using a hybrid method based on central composite design, neural network, and particle swarm optimization

This study aims at optimizing the culture conditions (agitation speed, temperature and pH) of the Pleuromutilin production by Pleurotus mutilus. A hybrid methodology including a central composite design (CCD), an artificial neural network (ANN), and a particle swarm optimization algorithm (PSO) was used. Specifically, the CCD and ANN were used for conducting experiments and modeling the non-linear process, respectively. The PSO was used for two purposes: Replacing the standard back propagation in training the ANN (PSONN) and optimizing the process. In comparison to the response surface methodology (RSM) and to the Bayesian regularization neural network (BRNN), PSONN model has shown the highest modeling ability. Under this hybrid approach (PSONN-PSO), the optimum levels of culture conditions were: 242 rpm agitation speed; temperature 26.88 and pH 6.06. A production of 10,074 ± 500 ??g/g, which was in very good agreement with the prediction (10,149 ??g/g), was observed in verification experiment. The hybrid PSONN-PSO gave a yield of 27.5% greater than that obtained by the hybrid BRNN-PSO. This work shows that the combination of PSONN with the generic PSO algorithm has a good predictability and a good accuracy for bio-process optimization. This hybrid approach is sufficiently general and thus can be helpful for modeling and optimization of other industrial bio-processes.