Initial Value Dependence: A Comparison of Two Methods For Its Study

This article is concerned with the comparison of slope estimator precision in regression analysis and the structural relationships approach (e.g., Humak, 1983, ch. 3; Kendall and Stuart, 1977), as it is relevant for their applications when testing for initial value dependence in biomedical and behavioral contexts of repeated assessments (e.g., Blomqvist, 1977; Wall, 1977). As a basis for the comparison of the two methods, the mean square error is adopted. In the general case, it is argued for an informed (data-dependent) choice between regression analysis and the structural relationships approach. For the apparent majority of biomedical and behavioral studies of the phenomenon of initial value depenence, this comparison suggests that structural relationships is the preferable approach leading to more trustworthy substantive conclusions.     

黄土丘陵沟壑区黄土坡面侵蚀过程及其影响因素

降雨强度、坡长、坡度是影响坡面产流产沙的重要因素。为定量分析降雨强度、坡长、坡度对黄土丘陵沟壑区安塞黄土坡面侵蚀过程的影响,本研究基于室内人工模拟降雨试验,分析2个坡长(5、10 m)、3个坡度(5°、10°、15°)、2个降雨强度(60、90 mm·h^-1)下安塞黄土坡面产流产沙规律。结果表明: 初始产流时间随坡长增加呈减小趋势,但总体变化不大;初始产流时间随降雨强度增加而减小,与60 mm·h^-1相比,90 mm·h^-1下缩短5.7～18 min;10°坡度上的径流起始时间最快。随降雨历时延长,产流率先快速增加,最终逐渐稳定在某一产流率值上下波动;产沙率在产流初期短时间内突然升高,达到最大值后减小,再逐渐达到稳定。产流率和产沙率随坡长和降雨强度的增加而增加,但随坡度变化规律不明显。随着降雨强度、坡长和坡度的增加,总产沙量相应增加。在降雨强度90 mm·h^-1时,坡长和坡度分别为10 m和15°的坡面产生了细沟,导致总侵蚀量最大(11885.66 g)。降雨强度为60 mm·h^-1时,随着坡长增加单位面积侵蚀量减小,在5～10 m坡段存在临界侵蚀坡长。坡长、坡度和降雨强度对坡面径流过程均有促进作用,降雨强度、坡长和两者之间交互作用对产流率和总侵蚀量的贡献率较大,其中,对产流率贡献最大的影响因素是降雨强度,贡献率为49.8%;坡长对总侵蚀的贡献率最大,为37.8%。     

Tempo and mode of sequence evolution in mitochondrial DNA of HawaiianDrosophila

Summary Sequence comparisons were made for up to 667 bp of DNA cloned from 14 kinds of HawaiianDrosophila and five other dipteran species. These sequences include parts of the genes for NADH dehydrogenase (subunits 1, 2, and 5) and rRNA (from the large ribosomal subunit). Because the times of divergence among these species are known approximately, the sequence comparisons give insight into the evolutionary dynamics of this molecule. Transitions account for nearly all of the differences between sequences that have diverged by less than 2%; for these sequences the mean rate of divergence appears to be about 2%/Myr. In comparisons involving greater divergence times and greater sequence divergence, relatively more of the sequence differences are due to transversions. Specifically, the fraction of these differences that are counted as transversions rises from an initial value of less than 0.1 to a plateau value of nearly 0.6. The time required to reach half of the plateau value, about 10 Myr, is similar to that for mammalian mtDNA. The mtDNAs of flies and mammals are also alike in the shape of the curve relating the percentage of positions at which there are differences in protein-coding regions to the time of divergence. For both groups of animals, the curve has a steep initial slope ascribable to fast accumulation of synonymous substitutions and a shallow final slope resulting from the slow accumulation of substitutions causing amino acid replacements. However, the percentage of all sites that can experience a high rate of substitution appears to be only about 8% for fly mtDNA compared to about 20% for mammalian mtDNA. The low percentage of hypervariable sites may be a consequence of a functional constraint associated with the low content of guanine and cytosine in fly mtDNA.     

Natural selection and genetic variation for reproductive reaction norms in a wild bird population

Many morphological and life-history traits show phenotypic plasticity that can be described by reaction norms, but few studies have attempted individual-level analyses of reaction norms in the wild. We analyzed variation in individual reaction norms between laying date and three climatic variables (local temperature, local rainfall, and North Atlantic Oscillation) of 1126 female collared flycatchers (Ficedula albicollis) with a restricted maximum likehood linear mixed model approach using random-effect best linear unbiased predictor estimates for the elevation (i.e., expected laying date in the average environment) and slope (i.e., adjustment in laying date as a function of environment) of females' reaction norms. Variation in laying date was best explained by local temperature, and individual females differed in both the elevation and the slope of their laying date-temperature reaction norms. As revealed by animal model analyses, there was weak evidence for additive genetic variance of elevation (h2 +/- SE = 0.09 +/- 0.09), whereas there was no evidence for heritability of slope (h2 +/- SE = 0.00 +/- 0.01). Selection analysis, using a female's lifetime production of fledglings or recruits as an estimate of her fitness, revealed significant selection for a lower phenotypic value and breeding value for elevation (i.e., earlier laying date at the average temperature). There was selection for steeper phenotypic values of slope (i.e., greater plasticity in the adjustment of laying date to temperature), but no significant selection on the breeding values of slope. Although these results suggest that phenotypic laying date is influenced by additive genetic factors, as well as by an interaction with the environment, selection on plasticity would not produce an evolutionary response.     

Time–frequency and principal-component methods for the analysis of EMGs recorded during a mildly fatiguing exercise on a cycle ergometer

Electromyographic signals contain the information on muscle activity and have to be frequently averaged, compared, classified or details need to be extracted. A time–frequency analysis, based on wavelets, was previously presented. The analysis transformed an EMG signal into an EMG-intensity-pattern showing the intensities at any point in time for the frequencies filtered out by the wavelets. The purpose of the present study was:

1. to define and apply a new EMG-pattern-space for the analysis of EMG-intensity-patterns; and

2. to determine the variation of EMG-intensity-patterns while getting mildly fatigued by cycling on a cycle-ergometer.

The coordinates spanning the pattern space were principal components of the measured EMG-intensity-patterns. A point in pattern-space thus represented an EMG-intensity-pattern. Fatigue resulted in points moving along a line in pattern space. The line was characterized by an intercept at time 0 and a slope. Thus mild fatigue caused a shift from an initial intensity-pattern representing the intercept to a final intensity-pattern adding gradually larger amounts of the pattern representing the slope. The intensity-pattern of the slope revealed the physiologically important individual strategies for coping with mild fatigue. Changes were observed at different times and at different frequencies during the cycling movement.     

Optimal conditions for immunohistochemical determination of the in vitro DNA synthesis labelling index with bromodeoxyuridine in head and neck cancer

The in vitro DNA synthesis labelling index was assessed immunohistochemically in 24 freshly obtained specimens of head and neck cancer using bromodeoxyuridine (BrdUrd) as the DNA precursor to determine the influence of BrdUrd concentration on labelling index (LI). Initially, tumour fragments were incubated in varying concentrations of BrdUrd from 2 to 100 microM for 2 h, and BrdUrd was detected with an anti-BrdUrd monoclonal antibody using immunoperoxidase labelling. There was a dose-response gradient with mean LI varying from 1.6% at 2 microM BrdUrd to 8.8% at 100 microM. The concentration-response gradient best fit a quadratic model when LI was plotted against log BrdUrd concentration (r = 0.65, P less than 0.0001). Eleven additional tumours were then studied to determine whether LI increased for BrdUrd concentrations above 100 microM. The mean LI at 125 microM and at 150 microM in these 11 tumours did not differ from the value at 100 microM, suggesting a plateau at this level. The gradient effect accounted for 17% of the variance in LI, while 60% of the variance was explained by between tumour differences. Within individual tumours, three response patterns were observed: (i) LI rose at a constant rate to the highest concentration tested (n = 8), (ii) the LI plateaued or declined at high BrdUrd concentrations (n = 6); and (iii) there was a biphasic slope slope in which the rate of rise in the LI increased at the higher BrdUrd concentrations (n = 2). The data show that BrdUrd concentration is an important variable in the immunohistochemical assessment of the in vitro LI in head and neck cancer.     

Experimentally reducing clutch size reveals a fixed upper limit to egg size in snakes, evidence from the king ratsnake, Elaphe carinata

Snakes are free of the pelvic girdle's constraint on maximum offspring size, and therefore present an opportunity to investigate the upper limit to offspring size without the limit imposed by the pelvic girdle dimension. We used the king ratsnake (Elaphe carinata) as a model animal to examine whether follicle ablation may result in enlargement of egg size in snakes and, if so, whether there is a fixed upper limit to egg size. Females with small sized yolking follicles were assigned to three manipulated, one sham-manipulated and one control treatments in mid-May, and two, four or six yolking follicles in the manipulated females were then ablated. Females undergoing follicle ablation produced fewer, but larger as well as more elongated, eggs than control females primarily by increasing egg length. This finding suggests that follicle ablation may result in enlargement of egg size in E. carinata. Mean values for egg width remained almost unchanged across the five treatments, suggesting that egg width is more likely to be shaped by the morphological feature of the oviduct. Clutch mass dropped dramatically in four- and six-follicle ablated females. The function describing the relationship between size and number of eggs reveals that egg size increases with decreasing clutch size at an ever-decreasing rate, with the tangent slope of the function for the six-follicle ablation treatment being -0.04. According to the function describing instantaneous variation in tangent slope, the maximum value of tangent slope should converge towards zero. This result provides evidence that there is a fixed upper limit to egg size in E. carinata.     

Long-term repeatability of behaviours in zebrafish (Danio rerio)

Animal personality is defined as individual variation in behaviour that is consistent over time and/or across contexts. Animal personality is now considered a fundamental aspect in the fields of animal behaviour and behavioural ecology, yet the majority of studies assess repeatability of behaviours over only relatively short time periods (e.g. a week) using just two measures. Understanding whether behavioural traits are repeatable over longer periods is important for the assessment of individual differences in behaviour. Using zebrafish (Danio rerio), we investigated the repeatability of activity and exploratory behaviours, including distance travelled, time spent in the bottom of the arena, stationary time and overall exploration of the novel arena over a 28-week period, using five intervals. All measures were repeatable over 28 weeks, but the repeatability estimates were much lower when comparing the initial week one and week two behaviours. There were clear sex differences in aspects of activity, with males more active than females. Importantly, our behavioural assays suggest that zebrafish require an initial “tank experience,” prior to the main phenotyping session, to ensure that behaviours being measured are repeatable—these effects are often not considered, but have implications for the many studies that measure behaviour at a single time point only.     

A new measure of cooperativity in protein-ligand binding

An allosteric binding system consisting of a single ligand and a nondissociating macromolecule having multiple binding sites can be represented by a binding polynomial. Various properties of the binding process can be obtained by analyzing the coefficients of the binding polynomial and such functions as the binding curve and the Hill plot. The Hill plot has an asymptote of unit slope at each end and the departure of the slope from unity at any point can be used to measure the effective interaction free energy at that point. Of particular interest in detecting and measuring cooperativity are extrema of the Hill slope and its value at the half-saturation point. If the binding polynomial is symmetric, then there is an extremum of the Hill slope at the half-saturation point. This value, the Hill coefficient, is a convenient measure of cooperativity. The purpose of this paper is to express the Hill coefficient for symmetric binding polynomials in terms of the roots of the polynomial and to give an interpretation of cooperativity in terms of the geometric pattern of the roots in the complex plane. This interpretation is then applied to the binding polynomials for the MWC (Monod-Wyman-Changeux) and KNF (Koshland-Nemethy-Filmer) models.     

A comparative study of satellite and ground-based phenology

Long time series of ground-based plant phenology, as well as more than two decades of satellite-derived phenological metrics, are currently available to assess the impacts of climate variability and trends on terrestrial vegetation. Traditional plant phenology provides very accurate information on individual plant species, but with limited spatial coverage. Satellite phenology allows monitoring of terrestrial vegetation on a global scale and provides an integrative view at the landscape level. Linking the strengths of both methodologies has high potential value for climate impact studies. We compared a multispecies index from ground-observed spring phases with two types (maximum slope and threshold approach) of satellite-derived start-of-season (SOS) metrics. We focus on Switzerland from 1982 to 2001 and show that temporal and spatial variability of the multispecies index correspond well with the satellite-derived metrics. All phenological metrics correlate with temperature anomalies as expected. The slope approach proved to deviate strongly from the temporal development of the ground observations as well as from the threshold-defined SOS satellite measure. The slope spring indicator is considered to indicate a different stage in vegetation development and is therefore less suited as a SOS parameter for comparative studies in relation to ground-observed phenology. Satellite-derived metrics are, however, very susceptible to snow cover, and it is suggested that this snow cover should be better accounted for by the use of newer satellite sensors.     

间歇降雨和多场次降雨条件下黄土坡面土壤水分入渗特性

基于可控的坡面间歇降雨和多场次降雨试验,对黄土坡面土壤水分入渗及分布特征进行了研究.结果表明：间歇降雨条件下,两次降雨期间的累积径流量均随降雨历时的延长呈近似线性增加,湿润锋也随降雨时间的延长而增加;在两次降雨的间歇期,湿润锋增加缓慢.入渗率随着坡度的增大而减小,第2次降雨的入渗率随时间而减小的趋势更明显;15°坡面的累积入渗量比25°大,分别为178和88 mm.多场次降雨条件下,各场次降雨的初始入渗率均较高,其中第1场降雨的土壤入渗率、累积入渗量在各时段均明显高于其他场次,后3场降雨的入渗率差异不大;降雨场次越多,湿润锋越深.     

Discontinuous formation and desorption of clusters during particles adsorption at surfaces

A theoretical model was derived to describe the discontinuous formation and desorption of clusters during particle adsorption at surfaces. Two steps were investigated: (1) time-dependent adsorption, where we found that the initial slope and the limiting magnitude of an adsorption isotherm depend on the clusters' distribution. A higher magnitude of both the adsorption and desorption rates appear to contract the time scale and hence increase the initial slope. Decreasing the geometrical parameter, q, which represents the shape of an adsorbed cluster, enhances the growth of large clusters on the surface. (2) A concentration dependence model shows that the number of adsorbed molecules increases with increases in the value of n (nucleation capacity). Furthermore, higher rates of adsorption provide steeper initial slopes (higher affinity of, molecules to surface). Decreasing q from 2 to 1, i.e. from a circular to a linear cluster formation, slightly decreases the magnitude of the isotherms.     

Repeatable inter‐individual variation in the thermal sensitivity of metabolic rate

Assessing whether trait variations among individuals are consistent over time and among environmental conditions is crucial to understand evolutionary responses to new selective pressures such as climate change. According to the universal thermal dependence hypothesis, thermal sensitivity of metabolic rate should not vary strongly and consistently among organisms, implying limited evolutionary response for metabolic traits under climate change. However, this hypothesis has been rarely tested at an individual level, leaving a gap in our understanding of climate change impacts on metabolic responses and their potential evolution. Using the amphipod Gammarus fossarum, we investigated the variability and repeatability of individual metabolic thermal reaction norms over time. We found large variations in both the thermal sensitivity (i.e. slope) and expression level (i.e. intercept) of individual metabolic reaction norms. Moreover, differences among individuals were consistent over time, and therefore repeatable. Inter‐individual variations in body mass resulted in a high repeatability of metabolic expression level but had no significant effect on the repeatability of thermal sensitivity. Overall, our results highlight that inter‐individual variability and repeatability of thermal reaction norms can be substantial. We conclude that these consistent differences among individuals should not be overlooked when apprehending the ecological and evolutionary effects of climate change.     

Mass,length and growth rate in single cells

A heuristic model for the time course of elongation and mass increase of a population of single cells with generation times different from the mean is considered. The fundamental assumption is that the dynamics governing the fluctuations around the mean are the same as those describing the mean itself. Cell length is assumed to depend on cell mass by a $\text{1}\text{3}$ power law. The final cell length and mass are obtained by demanding that a daughter cell's initial length and mass obey the same equation as those of the mother cell when the mother cell was born. An exponential time course is assumed for simplicity, although most of the results depend only on the initial and final values, not the actual time behavior. The aspect ratio (length/radius) is found to be a constant for all cells at birth, and twice that value at maturity. Thus the individual generation time is a doubling time for the aspect ratio, even though neither mass nor length double in general. Oscillations in ancestor/progeny generation times are derived, and their stability considered. The model yields a non-hereditary determinant of individual generation time. The well-known skewness in the distribution of individual generation times and the “β-plots” of the transition probability model find a natural explanation in the inequality of cell division.     

Generalized norms of reaction for ecological developmental biology

A standard norm of reaction (NoR) is a graphical depiction of the phenotypic value of some trait of an individual genotype in a population as a function an environmental parameter. NoRs thus depict the phenotypic plasticity of a trait. The topological properties of NoRs for sets of different genotypes can be used to infer the presence of (nonlinear) genotype-environment interactions. Although it is clear that many NoRs are adaptive, it is not yet settled whether their evolutionary etiology should be explained by selection on the mean phenotypic trait values in different environments or whether there are specific genes conferring plasticity. If the second alternative is true, the NoR is itself an object of selection. Generalized NoRs depict plasticity at the level of populations or subspecies within a species, species within a genus, or taxa at higher levels. Historically, generalized NoRs have routinely been drawn though rarely explicitly recognized as such. Such generalized NoRs can be used to make evolutionary inferences at higher taxonomic levels in a way analogous to how standard NoRs are used for microevolutionary inferences.     

Making the case for human life extension: personal arguments

In the close to medium future, the life sciences might permit a vast extension of the human life span. I will argue that this is a very desirable development for the individual person. The question whether death is a harm to the dying is irrelevant here. All it takes is that being alive is good for the living person and not being alive is not good for anyone. Thus, living persons who expect to live on happily are rationally required to want to stay alive. Eventual uncertainty whether it will be possible to be happy in the future provides no objection, but rather an incentive to try. This view, however, may be naive in assuming that persons are unchanging entities that exist separately from their psychological information. Objections have been derived from reductionistic views that value our future experiences in a way that declines with time, so that there will be a future point beyond which only negligible value accrues. If we adopt such a view, then we cannot now be concerned to have experiences beyond that point. I argue that these arguments fail to take into account all the reasons we might have to be concerned for the future and all kinds of such concern that come from them. The adoption of a plausible reductionistic account can arguably weaken our concern for the future and certainly change its quality in important ways. But this provides no objection to the desire to live forever, nor to live at all.     

Regression analysis of doubly censored failure time data with frailty

In doubly censored failure time data, the survival time of interest is defined as the elapsed time between an initial event and a subsequent event, and the occurrences of both events cannot be observed exactly. Instead, only right- or interval-censored observations on the occurrence times are available. For the analysis of such data, a number of methods have been proposed under the assumption that the survival time of interest is independent of the occurrence time of the initial event. This article investigates a different situation where the independence may not be true with the focus on regression analysis of doubly censored data. Cox frailty models are applied to describe the effects of covariates and an EM algorithm is developed for estimation. Simulation studies are performed to investigate finite sample properties of the proposed method and an illustrative example from an acquired immune deficiency syndrome (AIDS) cohort study is provided.     

Rubisco, Rubisco activase, and global climate change

Global warming and the rise in atmospheric CO(2) will increase the operating temperature of leaves in coming decades, often well above the thermal optimum for photosynthesis. Presently, there is controversy over the limiting processes controlling photosynthesis at elevated temperature. Leading models propose that the reduction in photosynthesis at elevated temperature is a function of either declining capacity of electron transport to regenerate RuBP, or reductions in the capacity of Rubisco activase to maintain Rubisco in an active configuration. Identifying which of these processes is the principal limitation at elevated temperature is complicated because each may be regulated in response to a limitation in the other. Biochemical and gas exchange assessments can disentangle these photosynthetic limitations; however, comprehensive assessments are often difficult and, for many species, virtually impossible. It is proposed that measurement of the initial slope of the CO(2) response of photosynthesis (the A/C(i) response) can be a useful means to screen for Rubisco activase limitations. This is because a reduction in the Rubisco activation state should be most apparent at low CO(2) when Rubisco capacity is generally limiting. In sweet potato, spinach, and tobacco, the initial slope of the A/C(i) response shows no evidence of activase limitations at high temperature, as the slope can be accurately modelled using the kinetic parameters of fully activated Rubisco. In black spruce (Picea mariana), a reduction in the initial slope above 30 degrees C cannot be explained by the known kinetics of fully activated Rubisco, indicating that activase may be limiting at high temperatures. Because black spruce is the dominant species in the boreal forest of North America, Rubisco activase may be an unusually important factor determining the response of the boreal biome to climate change.     

Influence of interelectrode distance and force level on the spectral parameters of surface electromyographic recordings from the lumbar muscles.

In order to study the influence of interelectrode distance and force level on the electromyographic (EMG) spectral parameters and on their reliability, bipolar surface EMG measurements were performed on the lumbar muscles of 15 subjects. Two test contractions (45 s) at 40% of maximal voluntary contraction (MVC) were performed, one with 2 cm interelectrode distance and the other with 4 cm, followed by two contractions at 80% MVC with the same change in interelectrode distance. Increasing the interelectrode distance from 2 to 4 cm caused a significant mean decrease (about 8%) in the initial median frequency. It is shown that this shift is of an order of magnitude that may be expected from the bipolar electrode filter factor, and we further conclude that the observed individual variations in the shift are likely to be connected to fluctuations in the shape of the power spectrum and to variations in conduction velocity. No significant change was found for the median frequency slope when changing the interelectrode distance. Increasing the force (from 40 to 80% MVC) also caused a significant mean decrease (about 10%) in the initial median frequency. The median frequency slope became significantly more negative by more than 200%. We conclude, however, that torque fluctuations during the fatigue contractions should have had only minor influence on the standard error of measurement of the initial median frequency and of the median frequency slope.     

Increasing human tooth length between birth and 5.4 years

Most previous studies of tooth development have used fractional stages of tooth formation to construct growth standards suitable for aging juvenile skeletal material. A simple alternative for determining dental age is to measure tooth length throughout development. In this study, data on tooth length development are presented from 63 individuals of known age at death, between birth and 5.4 years, from an archeological population recovered from the crypt of Christ Church, Spitalfields, London. Isolated developing teeth (304 deciduous, 269 permanent) were measured in millimeters and plotted against individual age. Regression equations to estimate age from a given tooth length, are presented for each deciduous maxillary and mandibular tooth type and for permanent maxillary and mandibular incisors, canines, and first permanent molars. Data on the earliest age of root completion of deciduous teeth and initial mineralization and crown completion of some permanent teeth in this sample are given, as well as the average crown height and total tooth length from a small number of unworn teeth. This method provides an easy, quantitative and objective measure of dental formation appropriate for use by archeologists and anthropologists. © 1993 Wiley-Liss, Inc.