Use of uniform designs in combination with neural networks for viral infection process development

This work aimed to compare the predictive capacity of empirical models, based on the uniform design utilization combined to artificial neural networks with respect to classical factorial designs in bioprocess, using as example the rabies virus replication in BHK‐21 cells. The viral infection process parameters under study were temperature (34°C, 37°C), multiplicity of infection (0.04, 0.07, 0.1), times of infection, and harvest (24, 48, 72 hours) and the monitored output parameter was viral production. A multilevel factorial experimental design was performed for the study of this system. Fractions of this experimental approach (18, 24, 30, 36 and 42 runs), defined according uniform designs, were used as alternative for modelling through artificial neural network and thereafter an output variable optimization was carried out by means of genetic algorithm methodology. Model prediction capacities for all uniform design approaches under study were better than that found for classical factorial design approach. It was demonstrated that uniform design in combination with artificial neural network could be an efficient experimental approach for modelling complex bioprocess like viral production. For the present study case, 67% of experimental resources were saved when compared to a classical factorial design approach. In the near future, this strategy could replace the established factorial designs used in the bioprocess development activities performed within biopharmaceutical organizations because of the improvements gained in the economics of experimentation that do not sacrifice the quality of decisions. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:532–540, 2015     

Partial Root Drying Effects on Biomass Production in Brassica napus and the Significance of Root Responses

Partial root drying (PRD) has been shown to stimulate stomatal-closure response and improve water-use efficiency and thus biomass production and grain yield under water deficiency. While most studies focus on above-ground responses to PRD, we examined how root responses contributed to effects of partial root drying. In particular, in two experiments with oilseed rape (Brassica napus L.) we investigated whether roots were able to forage for patchily distributed water, and how this affected plant growth compared with uniform watering and alternate watering (in which different parts of the roots receive water alternately). The first pot experiment was carried out in the greenhouse and the second outside under a rain-shelter in which also the watering amount was varied. The results indicate that B. napus roots were able to forage for fixed water patches by selective root placement. In the first experiment with small plants, root foraging was equally effective as enhanced water-use efficiency under alternate watering. Both treatments resulted in about 10% higher shoot biomass compared with uniform watering. Alternate watering generally outperformed uniform watering in the second experiment, but the success depended on the time of harvest and the water supply level. Measurements indicated that only the alternate watering regime effectively reduced stomatal conductance, but lead to a higher shoot biomass only under more severe (50%) rather than under milder water deficiency (70% of a well watered control). Water deficiency strongly reduced leaf initiation rates and leaf sizes in B. napus, but for a given level of water supply the supply pattern (uniform control, fixed patchy or alternate watering) hardly influenced these growth parameters. Although also in the second experiment, the plants selectively placed their roots in the wet parts of the pot, root foraging was not as effective as in the first experiment. Possible reasons for these discrepancies are discussed as well as their implications for the application of PRD effects for crop growth.     

MR thermometry characterization of a hyperthermia ultrasound array designed using the k-space computational method

Background  

Ultrasound induced hyperthermia is a useful adjuvant to radiation therapy in the treatment of prostate cancer. A uniform thermal dose (43°C for 30 minutes) is required within the targeted cancerous volume for effective therapy. This requires specific ultrasound phased array design and appropriate thermometry method. Inhomogeneous, acoustical, three-dimensional (3D) prostate models and economical computational methods provide necessary tools to predict the appropriate shape of hyperthermia phased arrays for better focusing. This research utilizes the k-space computational method and a 3D human prostate model to design an intracavitary ultrasound probe for hyperthermia treatment of prostate cancer. Evaluation of the probe includes ex vivo and in vivo controlled hyperthermia experiments using the noninvasive magnetic resonance imaging (MRI) thermometry.     

改进支持向量机在棉铃虫人工饲料配方优化中的应用

发展新的实验设计与分析方法,通过实施尽可能少的实验而获得满意配方对动植物营养、发酵工程等复杂多因素多水平寻优问题极为重要。本研究结合均匀设计（uniform design, UD）与支持向量回归（support vector regression, SVR）,提出了一种新的配方优化实验设计与分析方法UD-SVR,将其应用于棉铃虫Helicoverpa armigera （Hübner）幼虫人工饲料配方优化。结果表明：在考虑6因素时仅通过2轮22个实验,表征配方优劣的指标--平均蛹重即由初始的0.2436 g高效提升至0.3044 g,明显优于二次多项式偏最小二乘回归等经验风险最小参比模型。UD-SVR预测精度高、指导性强、可解释性好、优化高效,有望在多因素多水平配方优化中得到广泛应用。     

Circadian locomotor activity of Musca flies: Recording method and effects of 10 Hz square-wave electric fields

Musca domestica flies that were exposed to a uniform vertical 10 Hz electric square-wave field of 1 kVm⁻¹ changed the period length of their circadian locomotor activity rhythm. Under constant conditions, the clock of short-period flies was slowed down by the field, whereas the clock of long-period flies either was affected only scarcely (experiments at about 19°C) or ran faster (experiments at 25°C). If the field was applied for only 12 h daily, then 30–40% of the flies were synchronized. Thus, the field could function as a weak “Zeitgeber” (synchronizer). If the field was increased to 10 kVm⁻¹, then 50–70% of the flies were synchronized. Flies avoided becoming active around the onset of the 12 h period of exposure to a 10 Hz field. The results of these experiments are discussed with respect to similar experiments by Wever on the effects of exposure to a 10 Hz field on the circadian system of man. © 1996 Wiley-Liss, Inc.     

Individual scent marking of the nest entrance as a mechanism for nest recognition inXylocopa pubescens (Hymenoptera: Anthophoridae)

The mechanism by which female Xylocopa pubescenslocate their nest in a nesting aggregation was investigated. The bees were induced to nest in canes to which uniform nest entrances were attached. The results of nest displacement experiments revealed that the bees use visual cues for proximate orientation,but at very close range they also use olfactory cues. This conclusion was corroborated by the results of experiments in which the nest entrances were either removed or exchanged for alien nest entrances. Moreover, habituation experiments strongly indicated that the bees impart their individual marking at the nest entrance and that they can learn and memorize the individual odors of the neighboring bees.     

The influence of light,darkness, and lack of CO2 on phloem translocation in detached maize leaves

Summary Longitudinal strips from leaf blades of Zea mays L., with veins continuous along their whole length, proved to be a very uniform and convenient material for translocation experiments. Under normal photosynthetic conditions a very strong basipetal assimilate movement was shown. In the dark this movement persisted as long as starch reserves were available. Parts of the strips exposed to darkness or to CO₂-free air, i.e. nonphotosynthetic conditions, became strong sinks which attracted assimilates, darkness having the strongest effect. Microradioautographs showed that transport of assimilates took place in the sieve tubes of the phloem.     

The development of an efficient cultivar-independent plant regeneration system from callus derived from both apical and non-apical root segments of garlic (<Emphasis Type="Italic">Allium sativum</Emphasis> L.)

Summary Callus induction and later plant regeneration were studied in four widely grown garlic (Allium sativum L.) cultivars from Europe. Root segments from in vitro plantlets were used as starting material. In addition to cultivar effects, the effects of auxin and cytokinin levels and the position of the segments on the root were studied. There were no statistically significant differences among cultivars for the number of root segments that induced callus in the two series of experiments. The average induction frequency was 34.7% in the first series of experiments. Callus induction on apical root segments was significantly higher compared to callus induction on non-apical root segments in the second series of experiments. Two months after callus induction, callus lines were transferred to a regeneration medium consisting of Murashige and Skoog basal medium supplemented with 30gl⁻¹ sucrose and 1 mgl⁻¹ (4.6μM) kinetin. Calluses derived from different experiments were quite uniform with respect to their regeneration potential. Also it was found that our regeneration system was cultivar-independent. The average shoot regeneration frequency was 17.9% in the first series of experiments. Highly significant differences were found in the frequency of shoot regeneration among different callus induction treatments. When the cytokinin 6-(γ,γ-dimethylallylamino)purine (0.1mgl⁻¹∶0.5 μM) was present during callus induction, shoot regeneration ranged from 30.10 to 47.60%. Shoot regeneration from callus induced on non-apical segments was higher, although not significant, compared to callus induction from apical root segments in the second series of experiments. All in all, an efficient callus induction and plant regeneration system was developed from both apical and non-apical segments taken along the entire length of the roots. This system has potential to be used for garlic transformation.     

Optimization of Recombinant Cytochrome P450 2C9 Protein Production in Escherichia coli DH5α by Statistically-Based Experimental Design

Cytochrome P450 (CYP) 2C9 is of major importance in drug metabolism. However, the low yield of recombinant CYP2C9 protein in E. coli strains prevents its extensive use in the study of in vitro drug metabolism. In the present study, Taguchi design and desirability function were first used to investigate the effect of medium components (glycerol, δ-ALA, IPTG, ampicillin, chloramphenicol, inoculum density, peptone, thiamine, trace elements, NH₄Cl, and MgSO₄) on recombinant human CYP2C9 production by E. coli DH5α. An L₁₂ (2¹¹) orthogonal array was used to design the experiments to screen out the most influential factors. The CYP concentration and the specific content of CYP were considered as two product quality variables. A desirability function was applied to combine these two qualities as a single objective function. Optimization via central composite design (CCD) was then undertaken to yield the best performance. The confirmation experiments indicated that the expression performance under the optimized conditions was better than those obtained under other conditions. A compromise between conflicting goals, such as achievement of good yield of recombinant CYP2C9 and facility of the following purification, was found by means of the desirability function D. This is the first report that combined Taguchi design and CCD, and performed experiments in a multiresponse framework to optimize the production of human CYP in a recombinant E. coli strain.     

Costs and benefits of defense by tannins in a neotropical tree

Summary The costs and benefits of defense by tannins were investigated for a neotropical tree, Cecropia peltata L. (Moraceae). Seedlings of equal age were grown under uniform conditions in a greenhouse for 18 months. Within a plant, leaf tannin concentrations measured in different years were highly correlated. Tannin concentrations differed substantially among individuals; plants with high tannin content had lower damage levels in herbivory experiments. The effects of tannin on herbivory appeared to be dosage dependent. There was, however, a cost associated with tannin production in terms of reduced leaf production.     

Laccase production from oil palm industry solid waste: Statistical optimization of selected process parameters

Oil palm frond parenchyma tissue was used as a solid substrate for the production of laccase via solid‐state fermentation using the white rot fungus Pycnoporus sanguineus. With a rectangular aluminium tray as solid‐state fermentation bioreactor, process parameters such as bed height, moisture and supplemented nitrogen (as urea solution) levels were studied and optimized using a statistical design of experiment. The moisture level exerted a significant effect on the process. The interaction effect observed between bed height and supplemented nitrogen level suggested that uniform distribution of supplemented nitrogen into the substrate bed was important. The proposed regression model sufficiently predicted the process response over the experimental range tested. The optimum parameter combination for laccase production was a 3‐cm bed height, 72% w/w moisture and 0.21% w/v supplemented nitrogen. Laccase productivity remained constant when the tray size was increased from 1.4 to 3.4‐fold.     

DIRECT SELECTION ON LIFE SPAN IN DROSOPHILA MELANOGASTER

An important issue in the study of the evolution of aging in Drosophila melanogaster is whether decreased early fecundity is inextricably coupled with increased life span in selection experiments on age at reproduction. Here, this problem has been tackled using an experimental design in which selection is applied directly to longevity. Selection appeared successful for short and long life, in females as well as males. Progeny production of females selected for long life was lower than for short-lived females throughout their whole life. No increase of late-life reproduction in long-lived females occurred, as has been found in selection experiments on age at reproduction. This discrepancy is explained in terms of the inadequacy of the latter design to separate selection on life span from selection on late-life fecundity. Moreover, starvation resistance and fat content were lower for adults selected for short life. In general, the data support the negative-pleiotropy–disposable-soma theory of aging, and it is hypothesized that the pleiotropic allocation of resources to maintenance versus to reproduction as implicated in the theory might involve lipid metabolism. It is argued that further research on this suggestion is urgent and should certainly comprise observations on male reproduction because these are for the greater part still lacking. In conclusion, the longevity of D. melanogaster can be genetically altered in a direct-selection design, and such an increase is accompanied by a decreased general reproduction and thus early reproduction.     

N‐terminal guanidinylation of the cyclic 1,4‐ureido‐deltorphin analogues: the synthesis,receptor binding studies,and resistance to proteolytic digestion

The synthesis of a series of N‐guanidinylated cyclic ureidopeptides, analogues of 1,4‐ureido‐deltorphin/dermorphine tetrapeptide is described. The δ‐ and μ‐opioid receptor affinity of new guanidinylated analogues and their non‐guanidinylated precursors was determined by the displacement radioligand binding experiments. Our results indicate that the guanidinylation of cyclic 1,4‐ureidodeltorphin peptide analogues does not exhibit a uniform influence on the opioid receptor binding properties, similarly as reported earlier for some linear peptides. All analogues were also tested for their in vitro resistance to proteolysis during incubation with large excess of chymotrypsin, pepsin, and papain by means of mass spectroscopy. Guanidinylated ureidopeptides 1G–4G showed mixed μ agonist/δ agonist properties and high enzymatic stability indicating their potential as therapeutic agents for treatment of pain. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

Altered dihydrofolate reductase in fol regulatroy mutants of Escherichia coli K12.

Summary Culture of the thymine-dependent mutant of Rhizobium trifolii T37 was synchronized with phenethanol. During bacterial synchronous growth with synchronized replication of DNA, cells were differentially labeled using subsequently ³H-thymidine of low and high specific activity. The grain tracks produced in autoradiographs of chromosomes were denser on both ends than in the middle. In control experiments with bacteria labeled only with ³H-thymidine of low specific activity, the grain density was uniform throughout the grain track. The results constitute clear evidence of bidirectional replication of R. trifolli chromosome.     

Design Efficiency and Estimation for Component Amount Models

Component amount models were introduced by Piepel and Cornell (1985) to describe mixture experiments where the response depends not only on the proportions of the components but also on the total amount. The extended simplex centroid design supported by the barycenters corresponding to the regression functions in the model is D-optimal or fails to be D-optimal depending on the regression model under consideration. For two special component amount models, namely the ν-tic polynomial and the minimum polynomial of degree ν, the efficiency of the simplex centroid design was investigated. This covers the presentation of new results concerning the D-optimality as well as the assessment of the simplex centroid design in non-optimal situations by means of the G-efficiency. Formulae for the least squares estimates as well as their variances are presented.     

Field experiments to estimate optimum fertilizer levels

Summary Field experiments provide a basis for fertilizer recommendations. Some defects of an incomplete factorial scheme are discussed and the complete factorial briefly reviewed. Using the general polynomial of the second degree as the equation of a response surface, composite designs provide a more uniform precision for the coefficients. These designs are basically augmented 2^m factorials. One such design and a variation on it are compared. A method is given for calculating the economic optimal rates for the fertilizers.     

Effect of different manuring and defoliation patterns on broad-leaved dock (Rumex obtusifolius) in grassland

The effects of cutting frequency and cutting height on broad‐leaved dock (Rumex obtusifolius) in Lolium perenne‐based agricultural grassland at two levels of fertiliser input were investigated at North Wyke, Devon, UK. Two micro‐plot field experiments, containing immature dock plants at uniform densities, with a factorial design, were used to compare: (a) ‘organic’ and ‘low‐input’ fertilisation, i.e. cattle slurry only vs slurry plus mineral fertiliser (NPK at 100‐0‐64 kg ha^?1 yr^?1), (b) cutting heights of 5–6 cm vs 10–12 cm, and (c) four harvesting frequencies representative of different grassland management practices (regular 4‐weekly cutting, a ‘hay‐stage’ cutting, and two treatments with ‘silage‐stage’ cutting). Expt 1 was established in 1995 with 13 dock plants m^?2 (from excised dock‐root sections) and Expt 2 established in 1996 with 25 plants m^?2 (as seed‐grown plug plants). Treatments were assessed over the 2 subsequent years to determine treatment effects on total herbage dry matter (DM) yield and dock DM yield, and on in‐situ measures of dock ramets. In both experiments, total DM yield was increased by 1.0–2.01 ha^?1 yr^?1 for treatments receiving NK fertiliser; the proportion of dock was also higher than from slurry‐only treatments. In Expt 1, the dock ramet density, mean dock ramet height, mean leaf length and numbers of dock leaves per m² were also greater on NK fertilised treatments in autumn of yr 1. Height of cut had no consistent effect on dock yield, but dock ramet density and leaf density in autumn were greater on the 5–6 cm than the 10–12 cm cutting treatment, Expt 2 only. In yr 2 of both experiments cutting at 4‐weekly intervals resulted in less dock in the herbage than hay‐stage cutting and, particularly in Expt 1, there were associated differences in leaf density and ramet height in autumn; silage‐stage treatments were intermediate. Results are discussed in relation to requirements for management options where there is a need to avoid or reduce herbicides.     

Temporal modulation of luminance adapts time constant of fly movement detectors

The time constant of movement detectors in the fly visual system has been proposed to adapt in response to moving stimuli (de Ruyter van Steveninck et al. 1986). The objective of the present study is to analyse, whether this adaptation can be induced as well, if the luminance of a stationary uniform field is modulated in time. The experiments were done on motion-sensitive wide-field neurones of the lobula plate, the posterior part of the third visual ganglion of the blowfly, calliphora erythrocephala. These cells are assumed to receive input from large retinotopic arrays of movement detectors. In order to demonstrate that our results concern the properties of the movement detectors rather than those of a particular wide-field cell we recorded from two different types of them, the H1- and the HSE-cell. Both cell types respond to a brief movement stimulus in their preferred direction with a transient excitation. This response decays about exponentially. The time constant of this decay reflects, in a first approximation, the time constant of the presynaptic movement detectors. It was determined after prestimulation of the cell by the following stimuli: (a) periodic stationary grating; (b) uniform field, the intensity of which was modulated sinusoidally in time (flicker stimulation); (c) periodic grating moving front-to-back; (d) periodic grating moving back-to-front. The decay of the response is significantly faster not only after movement but also after flicker stimulation as compared with pre-stimulation with a stationary stimulus. This is interpreted as an adaptation of the movement detector's time constant. The finding that flicker stimulation also leads to an adaptation shows that movement is not necessary for this process. Instead the adaptation of the time constant appears to be governed mainly by the temporal modulation (i.e., contrast frequency) of the signal in each visual channel.     

The use of flavonoid aglycones in in vitro systems to test biological activities: based on bioavailability data,is this a valid approach?

The majority of in vitro assays on biological activities of flavonoids have used the aglycone form as the test compound. This form is readily available from commercial sources and comparable approaches have been used for testing efficacy of drugs. This paper presents the hypothesis that aglycones are only transiently present in vivo at significant concentrations at specific sites. The pathway of metabolism of flavonoids in mammals in vivo, focusing on aglycone formation, is examined to facilitate better design in the future of in vitro cell culture experiments. In vitro experiments using flavonoids and cultured cells require careful consideration of absorption and bioavailability for their appropriate interpretation. This revised version was published online in June 2006 with corrections to the Cover Date.     

On the Information Matrix of Exponential Mixture Models with Long-term Survivors

The aim of this paper is to study the properties of the asymptotic variances of the maximum likelihood estimators of the parameters of the exponential mixture model with long-term survivors for randomly censored data. In addition, we study the asymptotic relative efficiency of these estimators versus those which would be obtained with complete follow-up. It is shown that fixed censoring at time T produces higher precision as well as higher asymptotic relative efficiency than those obtainable under uniform and uniform-exponential censoring distributions over (0, T). The results are useful in planning the size and duration of survival experiments with long-term survivors under random censoring schemes.