Experimental design considerations: a determinant of acute neonatal toxicity

Few studies have investigated the potential developmental differences resulting from treating neonatal rat pups in either split-litter or whole-litter (nested) experimental designs. We directly compared rat pups dosed with triethyl lead (TEL) via both split-litter (representing all dosage groups within a single litter) and nested (all pups randomly assigned to a single litter receive the same dose) designs. The nested design was chosen to produce a uniform behavioral pattern across pups within each litter, whereas the split-litter design was chosen to promote pup competition and differential maternal care. On postpartum day 5, pups were administered either 12, 13, 14, or 15 mg/kg TEL, with each design represented by 12 litters. Although the LD50 values for the two designs were not significantly different, there were significantly more deaths in the 12 mg/kg dosage group within the split-litter design than in the nested design group. Preweaning survival times for split-litter dosed animals were also decreased. In addition, significant growth reduction (7-16%) was observed in the split-litter group, relative to the nested design animals during the preweaning period. These results suggest that neonatal toxicity is not independent from experimental design considerations, and that the factors of littermate competition and/or pup-induced maternal care deserve further study.     

Medium optimization of antifungal activity production by Bacillus amyloliquefaciens using statistical experimental design

In order to overproduce biofungicides agents by Bacillus amyloliquefaciens BLB371, a suitable culture medium was optimized using response surface methodology. Plackett-Burman design and central composite design were employed for experimental design and analysis of the results. Peptone, sucrose, and yeast extract were found to significantly influence antifungal activity production and their optimal concentrations were, respectively, 20 g/L, 25 g/L, and 4.5 g/L. The corresponding biofungicide production was 250 AU/mL, corresponding to 56% improvement in antifungal components production over a previously used medium (160 AU/mL). Moreover, our results indicated that a deficiency of the minerals CuSO(4), FeCl(3) · 6H(2)O, Na(2)MoO(4), KI, ZnSO(4) · 7H(2)O, H(3)BO(3), and C(6)H(8)O(7) in the optimized culture medium was not crucial for biofungicides production by Bacillus amyloliquefaciens BLB371, which is interesting from a practical point of view, particularly for low-cost production and use of the biofungicide for the control of agricultural fungal pests.     

Statistical optimization of medium composition for growth of<Emphasis Type="Italic">Leuconostoc citreum</Emphasis>

Leuconostoc citreum is one of the representative strains ofLeuconostoc spp. that show fast growth rates in fermented vegetables. Sequential experimental designs including the Plackett-Burman design, fractional factorial design, steepest ascent analysis, central composite design and response surface methodology were introduced to optimize and improve the medium forL. citreum. Fifteen medium ingredients were examined and glucose (20 g/L), yeast extract (12.5 g/L), sodium acetate trihydrate (6.12 g/L), potassium phosphate (42.55 g/L) and dibasic ammonium citrate (4.12 g/L) were chosen as the best components to give a critical and positive effect for cell-growth. The biomass was increased to 2.79 g/L (169%), compared to the 1.65 g/L in MRS medium.     

Electricity production in membrane-less microbial fuel cell fed with livestock organic solid waste

Two different MFC configurations designed for handling solid wastes as a feedstock were evaluated in batch mode: a single compartment combined membrane-electrodes (SCME) design; and a twin-compartment brush-type anode electrodes (TBE) design (reversed T-shape MFC with two-air cathode) without a proton exchange membrane (PEM). Cattle manure was tested as a model livestock organic solid waste feedstock. Under steady conditions, voltage of 0.38 V was recorded with an external resistance of 470 Ω. When digested anaerobic sludge was used as the seed in the SCME design, a maximum power density of 36.6 mW/m² was recorded. When hydrogen-generating bacteria (HGB) were used as the seed used in the TBE design, a higher power density of 67 mW/m² was recorded.     

DNA聚合酶与引物/模板的相互作用对PCR效率的影响

PCR是体外酶促合成特异DNA片段的一种方法,引物的优劣直接关系到PCR的特异性与成功与否。传统的PCR引物设计软件基本上忽略了DNA聚合酶与引物/模板的亲和性对PCR效率的影响。为揭示DNA聚合酶与引物/模板的相互作用是否对PCR的效率有影响,通过构建Taq DNA 聚合酶与不同序列引物/模板DNA相互作用的三维结构模型,采用MM/GBSA方法计算复合物的结合自由能,以结合自由能为参数,为人血清白蛋白基因(Human Serum Albumin gene,HSA gene)和结核杆菌pyrF基因(Mycobacterium tuberculosis pyrF gene)设计了PCR引物。PCR实验结果表明,引物的PCR效率与结合自由能相关：引物与聚合酶的结合自由能越低,PCR实验的效率相对越高。这说明DNA聚合酶与引物/模板的相互作用对PCR效率有重要影响。因此,引物/模板DNA与聚合酶的结合自由能可以作为PCR引物设计的新参数。     

Production of thermostable pullulanase by Clostridium thermosulfurogenes SV2 in solid-state fermentation: optimization of enzyme leaching conditions using response surface methodology

The optimization of parameters for the effective leaching of thermostable pullulanase from Clostridium thermosulfurogenes SV2-fermented bran was carried out using response surface methodology based on the central composite rotatable design. The design contains a total of 54 experimental trials with the first 32 organized in a fractional factorial design and experimental trials from 33-40 and 51-54 involving the replication of the central points. The design was employed by selecting solvent to wheat bran ratio (S/BB), process temperature, solvent pH, shaking (RPM) and contact time (h) as model factors. Among the five independent variables studied, the S/BB, solvent pH and shaking were found to be significant. S/BB ratio of 9.0, 200 RPM shaking and solvent pH 6.0 were identified as optimum for the leaching of thermostable pullulanase from the strain SV2-fermented bran.     

Design, synthesis and trypanocidal activity of lead compounds based on inhibitors of parasite glycolysis

The glycolytic pathway has been considered a potential drug target against the parasitic protozoan species of Trypanosoma and Leishmania. We report the design and the synthesis of inhibitors targeted against Trypanosoma brucei phosphofructokinase (PFK) and Leishmania mexicana pyruvate kinase (PyK). Stepwise library synthesis and inhibitor design from a rational starting point identified furanose sugar amino amides as a novel class of inhibitors for both enzymes with IC₅₀ values of 23 μM and 26 μM against PFK and PyK, respectively. Trypanocidal activity also showed potency in the low micromolar range and confirms these inhibitors as promising candidates for the development towards the design of anti-trypanosomal drugs.     

Structural SPR Tunability of Metal@Graphene Core–Shell Nano-Needle and Nano-Disk

Plasmonics - In present paper, a design of the graphene-coated metal (Ag/Au/Cu) nano-disk (2D) and nano-needle (1D) has been studied within the quasi-static approximation. The core@shell...     

Two-layer passive/active anisotropic FSI models with fiber orientation: MRI-based patient-specific modeling of right ventricular response to pulmonary valve insertion surgery

A single-layer patient specific right/left ventricle patch (RV/LV/Patch) combination model with fluid-structure interactions (FSI) was introduced in our previous papers to evaluate and optimize human pulmonary valve replacement/insertion (PVR) surgical procedure and patch design. In this paper, an active anisotropic model with two-layer structure for ventricle wall and tissue fiber orientation was introduced to improve previous isotropic model for more accurate assessment of RV function and potential application in PVR surgery and patch design. A material-stiffening approach was used to model active heart contraction. The computational models were used to conduct "virtual (computational)" surgeries and test the hypothesis that a PVR surgical design with a smaller patch and more aggressive scar tissue trimming would lead to improved RV cardiac function recovery. Results from our models validated by pre-operation data indicated that the small patch design had 11% improvement in RV function as measured by RV ejection fraction, compared to the conventional patch. Maximum Stress-P1 value from the active anisotropic model was 121.2% higher than that from the passive isotropic model. Computational RV volume predictions agreed well with CMR-measured volume data (error < 2%).     

Computer-aided drug design: getting the best results.

There are two major stages in the design of drug molecules: lead-molecule development and lead-molecule optimization. Whereas a variety of computational chemistry and molecular modeling (CC/MM) techniques are now routinely and successfully applied to the optimization stage of drug design, the generation of initial lead compounds has proven a more difficult problem for the CC/MM approach. Only recently has the design of lead molecules by this route become a subject of active research. This article looks at the factors which must be considered carefully when incorporating CC/MM methods into different aspects of drug-design strategies.     

Application of statistical experimental designs for the optimization of medium constituents for the production of citric acid from pineapple waste

Statistical experimental designs were applied for the optimization of medium constituents for citric acid production by Yarrowia lipolytica NCIM 3589 in solid state fermentation (SSF) using pineapple waste as the sole substrate. Using Plackett-Burman design, yeast extract, moisture content of the substrate, KH(2)PO(4) and Na(2)HPO(4) were identified as significant variables which highly influenced citric acid production and these variables were subsequently optimized using a central composite design (CCD). The optimum conditions were found to be yeast extract 0.34 (%w/w), moisture content of the substrate 70.71 (%), KH(2)PO(4) 0.64 (%w/w) and Na(2)HPO(4) 0.69 (%w/w). Citric acid production at these optimum conditions was 202.35 g/kg ds (g citric acid produced/kg of dried pineapple waste as substrate).     

Design of experiments and artificial neural network linked genetic algorithm for modeling and optimization of L-asparaginase production by <Emphasis Type="Italic">Aspergillus terreus</Emphasis> MTCC 1782

The sequential optimization strategy for design of an experimental and artificial neural network (ANN) linked genetic algorithm (GA) were applied to evaluate and optimize media component for L-asparaginase production by Aspergillus terreus MTCC 1782 in submerged fermentation. The significant media components identified by Plackett-Burman design (PBD) were fitted into a second order polynomial model (R² = 0.910) and optimized for maximum L-asparaginase production using a five-level central composite design (CCD). A nonlinear model describing the effect of variables on L-asparaginase production was developed (R² = 0.995) and optimized by a back propagation NN linked GA. Ground nut oil cake (GNOC) flour 3.99% (w/v), sodium nitrate (NaNO₃) 1.04%, L-asparagine 1.84%, and sucrose 0.64% were found to be the optimum concentration with a maximum predicted L-asparaginase activity of 36.64 IU/mL using a back propagation NN linked GA. The experimental activity of 36.97 IU/mL obtained using the optimum concentration of media components is close to the predicted L-asparaginase activity of the ANN linked GA.     

Medium optimization for antifungal active substances production from a newly isolated Paenibacillus sp. using response surface methodology

Statistics based experimental designs were used to optimize the medium for antifungal active substances production from a newly isolated Paenibacillus polymyxa Cp-S316 in shaker flask cultivation. The medium components having significant effect on the production were first identified using a fractional factorial design. Then steepest ascent method was employed to approach the experimental design space, followed by an application of response surface methodology for further optimization. A quadratic model was found to fit the antifungal active substances production. Response surface analysis revealed that the optimum values of the tested variables for the production of active substances were 12.3 (g/l) lactose, 17.5 (g/l) peptone, 0.4 (g/l) sodium nitrate, 4.5 (g/l) magnesium sulfate and 100 (g/l) potato. A production of 4687.71mug/ml, which was in agreement with the prediction, was observed in verification experiment. In comparison to the production of basal medium, 3.05-fold increase had been obtained.     

Hydraulic residence time computation for constructed wetland design

Hydraulic residence time (HRT) is one of the key design parameters controlling the removal efficiency of contaminants and nutrients in stormwater and wastewater wetlands. The paper presents a new approach to the estimation of HRT using the variable residence time (VART) model. The VART model is employed to simulate the major processes (including advection, dispersion, and transient storage of contaminants/nutrients in vegetated zones) affecting HRT and thereby to produce a hydraulic residence time distribution (HRTD) for a design wetland. The HRTD in combination with a moment-based method is then utilized to find a mean design HRT for the design wetland. Methods for estimation of parameters governing the HRTD are proposed. The new approach to HRT computation is demonstrated through a case study for the Tres Rios Demonstration (TRD) Wetlands in Arizona, USA. Modeling results show that the design HRTs for the Hayfield wetland (H1) and the Cobble wetlands (C1 and C2) are 4.04, 4.66, and 2.65 days, respectively. The computed HRTs agree well with those reported by previous studies, confirming the efficacy of the new approach to hydraulic design of constructed wetlands.     

Stance phase control of above-knee prostheses: knee control versus SACH foot design

The mobility of above-knee amputees (A/K) is limited, in part, due to the performance of A/K prostheses during the stance phase. Currently stance phase control of most conventional A/K prostheses can only be achieved through leg alignment and choice of the SACH (Solid Ankle Cushioned Heel) foot. This paper examines the role of the knee controller in relation to a SACH foot during the stance phase of level walking. The three-dimensional gait mechanics were measured under two stance phase conditions. In the first set of trials, the amputee used a prosthesis with a conventional knee controller that allowed the amputee to maintain the knee joint in full extension during the stance phase. In the second set of trials, the prosthetic knee, during stance, echoed the modified kinematics of the amputee's sound (intact) knee that had been recorded during the previous sound stance phase. Analysis and interpretation of the data indicate the following: (1) SACH foot design can strongly influence the walking mechanics independent of the knee controller; (2) knee controller design and SACH foot design are mutually interdependent; and (3) normal kinematics imposed on the prosthetic knee does not necessarily produce normal hip kinematics (e.g. reduce the abnormal rise in the prosthetic side hip trajectory). Future research is necessary to explore and exploit the interdependency of prosthetic knee control and foot design.     

海洋侧孢短芽孢杆菌Brevibacillus laterosporus Lh-1 产抗菌肽R-1的培养条件优化

采用Plackett-Burman(PB)设计和响应面分析(RSM)方法, 对一株海洋侧孢短芽孢杆菌Lh-1产抗菌肽R-1的发酵条件进行了优化。研究中数据的统计和分析均使用MINITAB 15.0。在研究中, 首先使用了Plackett-Burman (PB)设计对影响Lh-1产抗菌肽的15个因素进行了筛选, 得到了影响产量的显著因素为：葡萄糖、蛋白胨和氯化钙。在此基础上采用响应面法对该3个显著因素的最佳水平范围进行研究, 得到的最佳浓度为 15.72 g/L 葡萄糖、6.01 g/L 蛋白胨和3.29     

The thermodynamics of 3'-terminal pyrene and guanosine for the design of isoenergetic 2'-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structure

To facilitate design of short isoenergetic hybridization probes for RNA, we report the influence of adding 5'- or 3'-terminal 2'-O-methylguanosine (GM), LNA-guanosine (GL), or 3'-terminal pyrene pseudo-nucleotide (PPN) on the thermodynamic stability of 2'-O-methyl-RNA/RNA (2'-O-Me-RNA/RNA) duplexes with sequences 5'CMGMGMCMAM/3'AAXGCCGUXAA, where X is A, C, G, or U. A 3'-terminal GM or GL added to the 2'-O-Me-RNA strand to form a G-A, G-G or G-U mismatch enhances thermodynamic stability (DeltaDeltaG degrees 37) of the 2'-O-Me-RNA/RNA duplexes on average by 0.7 and 1.5 kcal/mol, respectively. A 3'-terminal GM or GL in a GM-C or GL-C pair stabilizes the 2'-O-Me-RNA/RNA duplex by 2.6 and 3.4 kcal/mol, respectively. A 5'-terminal GM or GL in a G-A or G-G mismatch provided less stabilization in comparison with a 3'-terminal G-A or G-G mismatch, but more stabilization in a G-C or G-U pair. In contrast to guanosine derivatives, pyrene residue (P) as PPN at the 3'-terminal position enhances thermodynamic stability of the 2'-O-Me-RNA/RNA duplexes on average by 2.3 +/- 0.1 kcal/mol, relatively independent of the type of ribonucleotide placed in the opposite strand. The thermodynamic data can be applied to design 2'-O-Me-RNA/RNA duplexes with enhanced thermodynamic stability that is also sequence independent. This is useful for design of hybridization probes to interrogate RNA structure and/or expression by microarray and other methods.     

Molecular drug targets and structure based drug design: A holistic approach

Access to the complete human genome sequence as well as to the complete sequences of pathogenic organisms provides information that can result in an avalanche of therapeutic targets. Structure-based design is one of the first techniques to be used in drug design. Structure based design refers specifically to finding and complementing the 3D structure (binding and/or active site) of a target molecule such as a receptor protein. The aim of this review is to give an outline of studies in the field of structure based drug design that has helped in the discovery process of new drugs. The emphasis will be on comparative/homology modeling.     

Electro-plasmonic Modal Power Shifting in Metal/Insulator/Semiconductor Structure Tailored as a CMOS-compatible Plasmonic Waveguide

Plasmonics - In this paper, we have proposed a new npn-type design of a CMOS-compatible metal/semiconductor/insulator/metal (MSIM) plasmonic structure, to be used as a different geometry to...     

Optimization of bio-hydrogen production from biodiesel wastes by Klebsiella pneumoniae

Biodiesel wastes containing glycerol were utilized by Klebsiella pneumoniae DSM 2026 to produce hydrogen. The optimization of medium components was performed using both Plackett-Burman and uniform design methods. Using the Plackett-Burman design, glycerol, yeast extract, NH(4)Cl, KCl and CaCl2 were found to be the most important components, which were further investigated by uniform design and second-order polynomial stepwise regression analysis. The optimized medium containing 20.4 g.L(-1) glycerol, 5.7 g.L(-1) KCl, 13.8 g.L(-1) NH(4)Cl, 1.5 g.L(-1) CaCl(2) and 3.0 g.L(-1) yeast extract resulted in 5.0-fold increased level of hydrogen (57.6 mL/50 mL medium) production compared to initial level (11.6 mL/50 mL medium) after 24 h of fermentation The optimization of fermentation condition (pH, temperature and inoculum) was also conducted. When the strain grew in the optimized medium under optimal fermentation condition in a 5-L stirred tank bioreactor for batch production, hydrogen yield and production reached 0.53 mol/mol and 117.8 mmol/L, respectively. The maximum hydrogen evolution rate was 17.8 mmol/(L.h). Furthermore, 1,3-propanediol (6.7 g.L(-1)) was also obtained from the liquid medium as a by-product.