Experimental design methods for bioengineering applications

Experimental design is a form of process analysis in which certain factors are selected to obtain the desired responses of interest. It may also be used for the determination of the effects of various independent factors on a dependent factor. The bioengineering discipline includes many different areas of scientific interest, and each study area is affected and governed by many different factors. Briefly analyzing the important factors and selecting an experimental design for optimization are very effective tools for the design of any bioprocess under question. This review summarizes experimental design methods that can be used to investigate various factors relating to bioengineering processes. The experimental methods generally used in bioengineering are as follows: full factorial design, fractional factorial design, Plackett–Burman design, Taguchi design, Box–Behnken design and central composite design. These design methods are briefly introduced, and then the application of these design methods to study different bioengineering processes is analyzed.     

Sustainable design indicators: Roadway project as an example

Environmental sustainability has been more examined in the construction industry in recent years. But it is still difficult for engineering designers to incorporate sustainability into their work without practical methods. The design stage is key in the life cycle to integrating sustainability into construction projects. Assessment of sustainable design performance can be an initiative to pursue sustainability.This paper proposes the ratio of items considered/adopted and man-hour spending to measure project sustainable design performance. The two indicators were tested on six roadway projects to validate their applicability on engineering design.The results show that the ratios of items considered and adopted are from 34% to 87%, meaning the many suggested sustainability items can be incorporated into design. The man-hours spent on sustainability are from 2% to 12%, meaning sustainable design initially takes more time than conventional design.The engineering design itself does not cause environmental impact. But the proposed indicators can examine the effort devoted into sustainability in the design stage. This early step helps predict the future environmental performance of designed products.     

Teaching about Scientific Origins: Taking Account of Creationism

The purpose of this study was to develop a model for measuring experimental design ability based on functional magnetic resonance imaging (fMRI) during biological inquiry. More specifically, the researchers developed an experimental design task that measures experimental design ability. Using the developed experimental design task, they measured both the paper experimental design ability and the fMRI experimental design ability of subjects. Subjects’ paper experimental design ability was measured using the quotient equation of experimental design ability, and their fMRI experimental design ability using the brain connectivity coefficient. According to the fMRI results, differences in design ability existed among subjects in terms of brain connectivity coefficient level during the experimental design task. The experimental design ability brain connectivity coefficient level and quotient for each subject were analysed. Statistically significant correlations between subjects’ connectivity strength level among brain activation regions and quotient value guided the establishment of a measuring model. The model measured experimental design ability and could predict an individual’s experimental design ability quotient using his or her brain connectivity coefficient. Hence, the model developed for this study for measuring experimental design ability based on fMRI may serve as a practical measurement of students’ scientific experimental design ability. Furthermore, this study could serve as a founding theory for measuring models of other scientific processing abilities such as observation, question generation, classification, hypothesis generation and hypothesis evaluation.     

Incorporating prior parameter uncertainty in the design of sampling schedules for pharmacokinetic parameter estimation experiments

An experiment design procedure is proposed for nonlinear parameter estimation studies that formally incorporates prior parameter uncertainty. The design criterion derives from information theory considerations and involves an asymptotic interpretation of the expected posterior information provided by an experiment. A pharmacokinetic sample schedule design problem is used to illustrate and evaluate this information theoretic design strategy. The model considered is commonly used to describe the plasma concentration of a drug following its oral administration. The limitations and advantages of the proposed design procedure are discussed in relation to other previously reported design techniques for incorporating parameter uncertainty.     

Principles of the design and operational considerations of large scale high performance liquid chromatography (HPLC) systems for proteins and peptides purification.

This review introduces concepts of design of large scale HPLC systems for purification of proteins and peptides. It is addressed to users of large scale HPLC systems to aid in system selection and help in customizing the design. Major techniques used for large scale HPLC purification of proteins and peptides are briefly reviewed. Engineering aspects of system design are discussed in detail. The review of selected relevant literature is provided as well as author's experience with the existing designs and his own systems. Commercial publications have been used in preparation of this review but only the most significant are listed as examples. The design process for any new system should be related to the performance of existing systems, if possible of a large scale. Laboratory data are also very useful in aiding the design process since they provide a lead, as to which chromatography techniques may succeed in providing required separation levels. The expertise needed for system design and operation comes from many areas: protein and peptide chemistry, chromatographic theory, mass transfer and hydrodynamics, machine design and material science. All these factors have to be blended together during the system design process. The controls must ensure flexibility in adapting to changing system configuration, depending on the operational requirements for various products. Extensive interfacing with the operator during the process run is essential. This work is focused mostly on system design and operation for reversed-phase chromatography and hydrophobic interaction chromatography, but it also covers aspects associated with other chromatographic techniques. The reviewed design principles would also apply to design other than HPLC large scale chromatography systems for biotechnology and pharmaceutical operations.     

生态工程设计研究进展及特点——以黑龙江省肇东市玉米生态工程为例

生态工程设计是生态工程建设的核心。明确生态工程设计的特点,是进行良好的生态工程设计的根本。通过生态设计研究进展的综述,从１０个方面,以肇东市玉米生态工程设计为例,分析了生态工程设计的特点,并在此基础上,提出了今后进行生态工程设计应采取的策略。     

Quality-by-Design II: Application of Quantitative Risk Analysis to the Formulation of Ciprofloxacin Tablets

Qualitative risk assessment methods are often used as the first step to determining design space boundaries; however, quantitative assessments of risk with respect to the design space, i.e., calculating the probability of failure for a given severity, are needed to fully characterize design space boundaries. Quantitative risk assessment methods in design and operational spaces are a significant aid to evaluating proposed design space boundaries. The goal of this paper is to demonstrate a relatively simple strategy for design space definition using a simplified Bayesian Monte Carlo simulation. This paper builds on a previous paper that used failure mode and effects analysis (FMEA) qualitative risk assessment and Plackett-Burman design of experiments to identity the critical quality attributes. The results show that the sequential use of qualitative and quantitative risk assessments can focus the design of experiments on a reduced set of critical material and process parameters that determine a robust design space under conditions of limited laboratory experimentation. This approach provides a strategy by which the degree of risk associated with each known parameter can be calculated and allocates resources in a manner that manages risk to an acceptable level.     

生物防治稻田与普通稻田水体中浮游植物的生态特征研究

通过对大沙镇生物防治稻田及普通稻田水体中浮游植物的调查研究,共检出藻类112种,其中生物防治稻田中82种,普通稻田中89种.稻田水体中的浮游植物以硅藻、裸藻和绿藻占优势.在普通稻田中,硅藻种类数超过生物防治稻田,其优势度最高的5种藻类中除双对栅藻外,其余4种均为硅藻;而在生物防治稻田中,裸藻种类数高于普通稻田,且其优势度最高的5种藻类中有两种为裸藻.通过比较发现,生物防治稻田水体中浮游生物的密度明显高于普通稻田.对水体浮游植物多样性及均匀度的分析表明,稻田水体中的浮游植物自秧苗插上至干田期间,多样性指数略有上升(主要是由于种类数的增加引起的),而均匀度呈下降趋势.     

Self-self hybridization as an alternative experiment design to dye swap for two-color microarrays

Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.     

A unifying family of group sequential test designs

Currently, the design of group sequential clinical trials requires choosing among several distinct design categories, design scales, and strategies for determining stopping rules. This approach can limit the design selection process so that clinical issues are not fully addressed. This paper describes a family of designs that unifies previous approaches and allows continuous movement among the previous categories. This unified approach facilitates the process of tailoring the design to address important clinical issues. The unified family of designs is constructed from a generalization of a four-boundary group sequential design in which the shape and location of each boundary can be independently specified. Methods for implementing the design using error-spending functions are described. Examples illustrating the use of the design family are also presented.     

Paradigms for computational nucleic acid design

The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR-based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free-energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape.     

Specific primer design for the polymerase chain reaction

The design of primers has a major impact on the success of PCR in relation to the specificity and yield of the amplified product. Here, we introduce the applications of PCR as well as the definition and characteristics for PCR primer design. Recent primer design tools based on Primer3, along with several computational intelligence-based primer design methods which have been applied in primer design, are also reviewed. In addition, characteristics of population-based methods used in primer design are discussed in detail.     

Standing wave design and experimental validation of a tandem simulated moving bed process for insulin purification

A tandem simulated moving bed (SMB) process for insulin purification has been proposed and validated experimentally. The mixture to be separated consists of insulin, high molecular weight proteins, and zinc chloride. A systematic approach based on the standing wave design, rate model simulations, and experiments was used to develop this multicomponent separation process. The standing wave design was applied to specify the SMB operating conditions of a lab-scale unit with 10 columns. The design was validated with rate model simulations prior to experiments. The experimental results show 99.9% purity and 99% yield, which closely agree with the model predictions and the standing wave design targets. The agreement proves that the standing wave design can ensure high purity and high yield for the tandem SMB process. Compared to a conventional batch SEC process, the tandem SMB has 10% higher yield, 400% higher throughput, and 72% lower eluant consumption. In contrast, a design that ignores the effects of mass transfer and nonideal flow cannot meet the purity requirement and gives less than 96% yield.     

Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions

Computational design of binding sites in proteins remains difficult, in part due to limitations in our current ability to sample backbone conformations that enable precise and accurate geometric positioning of side chains during sequence design. Here we present a benchmark framework for comparison between flexible-backbone design methods applied to binding interactions. We quantify the ability of different flexible backbone design methods in the widely used protein design software Rosetta to recapitulate observed protein sequence profiles assumed to represent functional protein/protein and protein/small molecule binding interactions. The CoupledMoves method, which combines backbone flexibility and sequence exploration into a single acceptance step during the sampling trajectory, better recapitulates observed sequence profiles than the BackrubEnsemble and FastDesign methods, which separate backbone flexibility and sequence design into separate acceptance steps during the sampling trajectory. Flexible-backbone design with the CoupledMoves method is a powerful strategy for reducing sequence space to generate targeted libraries for experimental screening and selection.     

Design and analysis of a robust genetic Muller C-element

This paper presents results on the design and analysis of a robust genetic Muller C-element. The Muller C-element is a standard logic gate commonly used to synchronize independent processes in most asynchronous electronic circuits. Synthetic biological logic gates have been previously demonstrated, but there remain many open issues in the design of sequential (state-holding) logic operations. Three designs are considered for the genetic Muller C-element: a majority gate, a toggle switch, and a speed-independent implementation. While the three designs are logically equivalent, each design requires different assumptions to operate correctly. The majority gate design requires the most timing assumptions, the speed-independent design requires the least, and the toggle switch design is a compromise between the two. This paper examines the robustness of these designs as well as the effects of parameter variation using stochastic simulation. The results show that robustness to timing assumptions does not necessarily increase reliability, suggesting that modifications to existing logic design tools are going to be necessary for synthetic biology. Parameter variation simulations yield further insights into the design principles necessary for building robust genetic gates. The results suggest that high gene count, cooperativity of at least two, tight repression, and balanced decay rates are necessary for robust gates. Finally, this paper presents a potential application of the genetic Muller C-element as a quorum-mediated trigger.     

Modulator Dynamics Shape the Design Space for Stepwise‐Elution Simulated Moving Bed Chromatographic Separations

For proteins and other biological macromolecules, SMB chromatography is best operated non‐isocratically. However, traditional modes of non‐isocratic SMB operation generate significant mobile‐phase modulator dynamics. The mechanisms by which these modulator dynamics affect a separation's success, and thus frame the design space, have yet to be explained quantitatively. Here, the dynamics of the modulator (e.g., salts in ion exchange and hydrophobic interaction chromatography) are explicitly accounted for. This leads to the elucidation of two new design constraints, presented as dimensionless numbers, which quantify the effects of the modulator phenomena and thus predict the success of a non‐isocratic SMB separation. Consequently, these two new design constraints re‐define the SMB design space. Computational and experimental studies at the boundaries of this design space corroborate the theoretical predictions. The design of efficient and robust operating conditions through use of the new design space is also demonstrated.     

“共享平台”下风景园林专业本科课程设计教学改革研究

“共享平台”下的风景园林专业本科课程设计教学改革,融合同济“风景园林学”与“建筑学”“城乡规划学”三位一体的教学特色,以“风景园林规划设计”课程设计为“突出主线”,通过四项课程改革子项,即“建筑与建成环境设计”课程改革子项、“景观设计”课程改革子项、“景观详细规划设计”课程改革子项、“景观总体规划设计”课程改革子项,进行教学计划调整、教学内容重构、教学组织重组等的深化改革研究。从而建构“主线突出,两翼并重,三级分层,相互协同”复合网络化的风景园林本科专业教学内容组织形式框架,实现风景园林专业人才培养从进口至出口的知识、人格、素质和能力（ KAQP）的全面培养目标。     

De novo design of biocatalysts

The challenging field of de novo enzyme design is beginning to produce exciting results. The application of powerful computational methods to functional protein design has recently succeeded at engineering target activities. In addition, efforts in directed evolution continue to expand the transformations that can be accomplished by existing enzymes. The engineering of completely novel catalytic activity requires traversing inactive sequence space in a fitness landscape, a feat that is better suited to computational design. Optimizing activity, which can include subtle alterations in backbone conformation and protein motion, is better suited to directed evolution, which is highly effective at scaling fitness landscapes towards maxima. Improved rational design efforts coupled with directed evolution should dramatically improve the scope of de novo enzyme design.