Bias-corrected maximum likelihood estimator of the negative binomial dispersion parameter

We derive a first-order bias-corrected maximum likelihood estimator for the negative binomial dispersion parameter. This estimator is compared, in terms of bias and efficiency, with the maximum likelihood estimator investigated by Piegorsch (1990, Biometrics46, 863-867), the moment and the maximum extended quasi-likelihood estimators investigated by Clark and Perry (1989, Biometrics45, 309-316), and a double-extended quasi-likelihood estimator. The bias-corrected maximum likelihood estimator has superior bias and efficiency properties in most instances. For ease of comparison we give results for the two-parameter negative binomial model. However, an example involving negative binomial regression is given.     

Modeling late entry bias in survival analysis

In a failure time analysis, we sometimes observe additional study subjects who enter during the study period. These late entries are treated as left-truncated data in the statistical literature. However, with real data, there is a substantial possibility that the delayed entries may have extremely different hazards compared to the other standard subjects. We focus on a situation in which such entry bias might arise in the analysis of survival data. The purpose of the present article is to develop an appropriate methodology for making inference about data including late entries. We construct a model that includes parameters for the effect of delayed entry bias having no specification for the distribution of entry time. We also discuss likelihood inference based on this model and derive the asymptotic behavior of estimates. A simulation study is conducted for a finite sample size in order to compare the analysis results using our method with those using the standard method, where independence between entry time and failure time is assumed. We apply this method to mortality analysis among atomic bomb survivors defined in a geographical study region.     

Transient response of aerobic and anoxic activated sludge activities to sudden substrate concentration changes

The state-of-the-art understanding of activated sludge processes as summarized in activated sludge models (ASMs) predicts an instantaneous increase in the biomass activity (which is measured, e.g., by the corresponding respiration rate OUR, NUR, etc.) under sudden substrate concentration changes. Experimental data (e.g., short-term batch respiration experiments under aerobic or anoxic conditions) collected for the calibration of the dynamic models (ASMs) often exhibit a transient phenomenon while attaining maximum activity, which cannot be explained by the current understanding of the activated sludge process. That transient phenomenon exhibits itself immediately upon addition of a substrate source to an endogenously respiring activated sludge sample and it usually takes a few minutes until the activated sludge reaches its maximum possible rate under given environmental conditions. This discrepancy between the state-of-the-art model and the experimental data is addressed in detail in this investigation. It is shown that the discrepancy is not caused by an error in the experimental set-up/data but it is rather due to model inadequacy. Among the hypotheses proposed, it appears that this transient response of the activated sludge most likely results from the sequence of intracellular reactions involved in substrate degradation by the activated sludge. Results from studies performed elsewhere with pure cultures (S. cerevisae and E. coli) support the hypothesis. The transient phenomenon can be described by a dynamic metabolic network model or by a simple first-order model, as adopted in this study. The transient phenomenon occurring in short-term batch respiration experiments is shown to interfere severely with parameter estimation if not modeled properly (2.8%, 11.5%, and 16.8% relative errors [average of three experiments] on Y(H), micro(maxH), and K(S), respectively). Proper modeling of this transient phenomenon whose time constant is on the order of minutes (1 to 3 min) is expected to contribute fundamentally to a better understanding and modeling of Orbal, carousel, and SBR-type treatment plants with fast-alternating process conditions, although such studies are beyond the scope of this report.     

低温弱光胁迫及恢复对切花菊光合作用和叶绿素荧光参数的影响

以切花菊品种‘神马’为试材,在偏低温弱光(16℃/12℃,PFD100μmol.m-2.s-1)和临界低温弱光(12℃/8℃,PFD60μmol.m-2.s-1)下分别胁迫11d,然后转入正常条件(22℃/18℃,PFD450μmol.m-2.s-1)恢复11d,研究不同低温弱光强度及恢复对菊花光合作用和叶绿素荧光参数的影响.结果表明:低温弱光导致菊花叶片的净光合速率(Pn)和气孔限制值(Ls)下降,而胞间CO2浓度(Ci)上升.偏低温弱光胁迫下菊花叶片暗适应下最大光化学效率(Fv/Fm)和初始荧光(Fo)无明显变化,但光适应下最大光化学效率(Fv′/Fm′)在处理前期略有下降,后期则有所回升;而临界低温弱光处理的Fo明显升高,Fv/Fm和Fv′/Fm′显著降低.PSⅡ光合电子传递量子效率(ΦPSⅡ)、光化学猝灭系数(qP)和表观光合电子传递速率(ETR)均随着低温弱光胁迫程度的增加和时间的延长而降低;偏低温弱光处理植株在解除胁迫后能迅速恢复到对照水平,而临界低温弱光处理植株回升速度较慢;同时,低温弱光胁迫下吸收光强用于分配光化学反应部分(Prate)的比例减少,而天线热耗散(Drate)和反应中心的能量耗散(Ex)比例上升,但天线热耗散为过剩光能的主要分配途径.     

基于图论模型的蛋白质结构类型的研究

提出了基于图论模型的H系数分类蛋白质结构为H结型和NH结型的方法.论述了蛋白质结构中序列不相邻的C_α原子之间的空间距离与序列相邻的C_α原子之间空间距离的关系.用此方法对PDB的66个单链蛋白质结构进行分类,结果显示H结型占18.2%.H结在全α型中出现比例较高,在全β型中出现比例较小,所以H结倾向出现在含有α螺旋的蛋白质结构中.     

淮河淮南段与巢湖水质污染对鲫鱼（Carassius auratus）的毒性效应

研究了枯水期淮河淮南段及巢湖西半湖水质污染对鲫鱼的毒性效应。从淮河淮南段与巢湖采集鱼类样本,并以未受人为污染的安丰塘鱼类为对照,分析了鲫鱼肝脏丙二醛（Malondialdehyde,MDA）含量、超氧化物歧化酶（Superoxide dismutase,SOD）活性、谷胱甘肽硫转移酶（Glutathione S-transferase,GST）活性、7-乙氧基异吩恶唑-O-脱乙基酶（7-ethoxyresorufin-O-deethylase,EROD）活性及DNA单链损伤情况,结果表明,淮河淮南段鲫鱼肝脏MDA含量、SOD活性、GST活性、EROD活性均高于对照组,分别是对照组的2.88、1.48、2.03和3.93倍;巢湖鲫鱼肝脏MDA含量、SOD活性、EROD活性均高于对照组,分别是对照组的2.28、1.85和2.74倍。肝细胞DNA单链断裂的测定显示淮河淮南段与巢湖的水质污染均对鲫鱼有遗传毒性。     

Voltammetry of half-sandwich manganese group complexes of η-PhC3B7H9 and η-C60Bn2PhH2, two ligands that are cyclopentadienyl mimicks

The potentials of a series of one-electron oxidation and reduction reactions have been determined for manganese group half-sandwich complexes of the tricarbadecaboranyl ligand PhC₃B₇H₉ and the penta-organo fullerene ligand C₆₀Bn₂PhH₂ (Bn = benzyl). The anodic processes were studied in CH₂Cl₂ and the cathodic processes were studied in both CH₂Cl₂ and THF, the supporting electrolyte being [NBu₄][B(C₆F₅)₄]. The manganese complex Mn(CO)₂(PMe₃)(PhC₃B₇H₉) (1) is a member of a three-electron transfer series which includes oxidation to 1⁺ (0.51 V versus ferrocene) and successive reductions to 1⁻ (−1.66 V) and 1²⁻ (−1.77 V). Both the oxidation and reduction of the closely-related complex Mn(CO)₂(PPh₃)(PhC₃B₇H₉) (2) are chemically irreversible under slow-scan cyclic voltammetry conditions. The rhenium complex Re(CO)₂(PPh₃)(PhC₃B₇H₉) (3) oxidizes (E_1/2 = 0.82 V versus ferrocene) to a radical cation which, unlike its cyclopentadienyl analogue, shows no evidence of dimerization. Oxidation of the fullerene-based complex Re(CO)₃(C₆₀Bn₂PhH₂) is more facile than that of its cyclopentadienyl analogue, in contrast to previous findings in this class of metal-fullerene derivatives. An electrochemical ligand factor, E_L, of 0.63 is calculated for the PhC₃B₇H₉ ligand in manganese group half-sandwich complexes.     

An unbiased sensitivity analysis reveals important parameters controlling periodicity of circadian clock

To assess the importance of model parameters in kinetic models, sensitivity analysis is generally employed to provide key measures. However, it is quite often that no information is available for a significant number of parameters in biochemical models. Therefore, the results of sensitivity analysis that heavily rely on the accuracy of parameters are largely ambiguous. In this study, we propose a computational approach to determine the relative importance of parameters controlling the performance of the circadian clock in Drosophila. While previous attempts to sensitivity analysis largely depend on the knowledge of model parameters which are generally unknown, our study depicts a consistent picture of sensitivity assessment for a large number of parameters, even when the values of these parameters are not available in vivo. The resulting parametric sensitivity analysis suggests that PER/TIM negative loop is critical to maintain the stable periodicity of the circadian clock, which is consistent to the previously experimental and computational findings. Furthermore, our analysis generates a rich hypothesis of important parameters in the circadian clock that can be further tested experimentally. This approach can also be extended to assess the sensitivity of parameters in any biochemical system where a large number of parameters have unknown values. Biotechnol. Bioeng. 2010; 105: 250–259. © 2009 Wiley Periodicals, Inc.     

Cell membrane fluidity related to electroporation and resealing

In this paper, we report the results of a systematic attempt to relate the intrinsic plasma membrane fluidity of three different cell lines to their electroporation behaviour, which consists of reversible and irreversible electroporation. Apart from electroporation behaviour of given cell lines the time course required for membrane resealing was determined in order to distinguish the effect of resealing time from the cell’s ability to survive given electric pulse parameters. Reversible, irreversible electroporation and membrane resealing were then related to cell membrane fluidity as determined by electron paramagnetic resonance spectroscopy and computer characterization of membrane domains. We found that cell membrane fluidity does not have significant effect on reversible electroporation although there is a tendency for the voltage required for reversible electroporation to increase with increased membrane fluidity. Cell membrane fluidity, however, may affect irreversible electroporation. Nevertheless, this effect, if present, is masked with different time courses of membrane resealing found for the different cell lines studied. The time course of cell membrane resealing itself could be related to the cell’s ability to survive.