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PubMed2001

Time-series analysis of delta13C from tree rings. I. Time trends and autocorrelation.

Univariate time-series analyses were conducted on stable carbon isotope ratios obtained from tree-ring cellulose. We looked for the presence and structure of autocorrelation. Significant autocorrelation violates the statistical independence assumption and biases hypothesis tests. Its presence would indicate the existence of lagged physiological effects that persist for longer than the current year. We analyzed data from 28 trees (60-85 years old; mean = 73 years) of western white pine (Pinus monticola Dougl.), ponderosa pine (Pinus ponderosa Laws.), and Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. glauca) growing in northern Idaho. Material was obtained by the stem analysis method from rings laid down in the upper portion of the crown throughout each tree's life. The sampling protocol minimized variation caused by changing light regimes within each tree. Autoregressive moving average (ARMA) models were used to describe the autocorrelation structure over time. Three time series were analyzed for each tree: the stable carbon isotope ratio (delta(13)C); discrimination (delta); and the difference between ambient and internal CO(2) concentrations (c(a) - c(i)). The effect of converting from ring cellulose to whole-leaf tissue did not affect the analysis because it was almost completely removed by the detrending that precedes time-series analysis. A simple linear or quadratic model adequately described the time trend. The residuals from the trend had a constant mean and variance, thus ensuring stationarity, a requirement for autocorrelation analysis. The trend over time for c(a) - c(i) was particularly strong (R(2) = 0.29-0.84). Autoregressive moving average analyses of the residuals from these trends indicated that two-thirds of the individual tree series contained significant autocorrelation, whereas the remaining third were random (white noise) over time. We were unable to distinguish between individuals with and without significant autocorrelation beforehand. Significant ARMA models were all of low order, with either first- or second-order (i.e., lagged 1 or 2 years, respectively) models performing well. A simple autoregressive (AR(1)), model was the most common. The most useful generalization was that the same ARMA model holds for each of the three series (delta(13)C, delta, c(a) - c(i)) for an individual tree, if the time trend has been properly removed for each series. The mean series for the two pine species were described by first-order ARMA models (1-year lags), whereas the Douglas-fir mean series were described by second-order models (2-year lags) with negligible first-order effects. Apparently, the process of constructing a mean time series for a species preserves an underlying signal related to delta(13)C while canceling some of the random individual tree variation. Furthermore, the best model for the overall mean series (e.g., for a species) cannot be inferred from a consensus of the individual tree model forms, nor can its parameters be estimated reliably from the mean of the individual tree parameters. Because two-thirds of the individual tree time series contained significant autocorrelation, the normal assumption of a random structure over time is unwarranted, even after accounting for the time trend. The residuals of an appropriate ARMA model satisfy the independence assumption, and can be used to make hypothesis tests.

Carbon Isotopes↗
PubMed1985

Comparison of distance matrices in studies of population structure and genetic microdifferentiation: quadratic assignment.

Questions concerning the relative effects of various evolutionary forces in molding the genetic variability exhibited by groups of human populations have typically been investigated by comparing a variety of genetic and cultural/historical "distance" matrices. A major methodological difficulty has been the lack of formal testing procedures with which to assess the degree of confirmation or disconfirmation of an estimated measure of relationship between such matrices. In this paper, we examine a very flexible matrix combinatorial procedure which generates statistical significance levels for correlational measures of pattern similarity between distance matrices. A recent generalization of the basic procedure to the three-matrix case allows questions concerning which of two matrices best fits a third matrix to be formally tested. Applications of these hypothesis testing and inference procedures to two separate sets of genetic, geographic, and cultural distance matrices illustrates their potential for finally solving a long-standing problem in anthropological genetics.

Anthropometry↗
PubMed2005

Do feathered dinosaurs exist? Testing the hypothesis on neontological and paleontological evidence.

The origin of birds and avian flight from within the archosaurian radiation has been among the most contentious issues in paleobiology. Although there is general agreement that birds are related to theropod dinosaurs at some level, debate centers on whether birds are derived directly from highly derived theropods, the current dogma, or from an earlier common ancestor lacking suites of derived anatomical characters. Recent discoveries from the Early Cretaceous of China have highlighted the debate, with claims of the discovery of all stages of feather evolution and ancestral birds (theropod dinosaurs), although the deposits are at least 25 million years younger than those containing the earliest known bird Archaeopteryx. In the first part of the study we examine the fossil evidence relating to alleged feather progenitors, commonly referred to as protofeathers, in these putative ancestors of birds. Our findings show no evidence for the existence of protofeathers and consequently no evidence in support of the follicular theory of the morphogenesis of the feather. Rather, based on histological studies of the integument of modern reptiles, which show complex patterns of the collagen fibers of the dermis, we conclude that "protofeathers" are probably the remains of collagenous fiber "meshworks" that reinforced the dinosaur integument. These "meshworks" of the skin frequently formed aberrant patterns resembling feathers as a consequence of decomposition. Our findings also draw support from new paleontological evidence. We describe integumental structures, very similar to "protofeathers," preserved within the rib area of a Psittacosaurus specimen from Nanjing, China, an ornithopod dinosaur unconnected with the ancestry of birds. These integumental structures show a strong resemblance to the collagenous fiber systems in the dermis of many animals. We also report the presence of scales in the forearm of the theropod ornithomimid (bird mimic) dinosaur, Pelecanimimus, from Spain. In the second part of the study we examine evidence relating to the most critical character thought to link birds to derived theropods, a tridactyl hand composed of digits 1-2-3. We maintain the evidence supports interpretation of bird wing digit identity as 2,3,4, which appears different from that in theropod dinosaurs. The phylogenetic significance of Chinese microraptors is also discussed, with respect to bird origins and flight origins. We suggest that a possible solution to the disparate data is that Aves plus bird-like maniraptoran theropods (e.g., microraptors and others) may be a separate clade, distinctive from the main lineage of Theropoda, a remnant of the early avian radiation, exhibiting all stages of flight and flightlessness.

Animals↗
PubMed2006

Conditional power calculations for clinical trials with historical controls.

A trial of a new therapy is to be compared to results from a previous trial of patients treated with a standard therapy. For a given sample size for the trial of the new therapy, we desire the power, against a specific alternative hypothesis, for the hypothesis test of the null hypothesis that the therapies are equivalent. Alternatively, the sample size required for the trial of the new therapy is needed for a target power. We explain why a popular method for doing these calculations is wrong, and discuss alternative methods in the context of normal outcomes, binary outcomes, and time-to-event outcomes.

Clinical Trials as Topic↗
PubMed1991

Two-dimensional diffusion of F1F0-ATP synthase and ADP/ATP translocator. Testing a hypothesis for ATP synthesis in the mitochondrial inner membrane.

We report here the first experimentally determined lateral diffusion coefficients of the F1F0-ATP synthase and the ADP/ATP translocator in isolated inner membranes of rat liver mitochondria. Rabbit IgG developed against the F1F0-ATP synthase isolated from rat liver mitochondria was determined to be immunospecific for the synthase subunits, notably the alpha-beta doublet, gamma and delta subunits of F1 and subunits two, three and four of F0. This IgG, conjugated with lissamine-rhodamine, was used as a fluorescent probe to monitor the diffusion of the synthase in the membrane. IgG to cytochrome bc1 complex, prepared and labeled similarly, was used as a fluorescent probe for diffusion of this redox component. Eosin maleimide was determined to specifically label the ADP/ATP translocator in the isolated inner membrane and was used as a specific probe for the diffusion of the translocator. Using fluorescence recovery after photobleaching, the experimental average lateral diffusion coefficient of the F1F0-ATP synthase was determined to be 8.4 x 10(-10) cm2/s or twice that of cytochrome bc1 complex while the diffusion coefficient of the ADP/ATP translocator was 1.7 x 10(-9) cm2/s or four times that of cytochrome bc1 complex suggesting that all three components are independent two-dimensional diffusants. Using these diffusion coefficients and applying a number of basic assumptions, we calculated the theoretical two-dimensional diffusion-controlled collision frequencies and derived collision efficiencies (protons transferred per collision) between each of the three proton-transferring redox complexes and both the F1F0-ATP synthase and ADP/ATP translocator by treating the redox components as proton donors and the synthase and translocator as proton acceptors. These collision efficiencies support the physical possibility of a diffusion-based, random collision process of proton transfer and ATP synthesis in the mitochondrial inner membrane.

Adenosine Triphosphate↗
PubMed1982

A comment on confusion in open-field studies: abuse of null-hypothesis significance test.

The confusion in open-field studies which has resulted from a misinterpretation of statistical results was examined. Several discrepant results obtained on the basis of significance tests have revealed that the discrepancy was not so serious as had been thought. Examples of highly reliable but substantially small experimental effects were presented to indicate the erroneous impression given. The expectation that consistent results can always be obtained from even a small sample size was criticized. In order to reduce some of this confusion, the use of strength of association (eta2) together with consideration for statistical power in the interpretation of open-field results was recommended.

Analysis of Variance↗
PubMed1990

Global in vivo replacement of choline by N-aminodeanol. Testing a hypothesis about progressive degenerative dementia: I. Dynamics of choline replacement.

Severe disruption of certain cholinergic pathways is a characteristic feature of Alzheimer's disease. Attempts to establish animal models by interfering with cholinergic function have not been very successful. We now present data which show a substantial and progressive replacement of free and phospholipid-bound choline by the novel choline isostere N-amino-N,N-dimethylaminoethanol during its dietary administration in place of choline. Free choline in blood fell to approximately 20% of controls after 10 to 30 days on diet. Phospholipid-bound choline in plasma was reduced to less than 15%, and in erythrocytes to about 22%. After 120 days of diet free and bound choline were reduced in most tissues to approximately 30% of controls. Only liver retained more than 80% of free choline. Acetylcholine was decreased to 33 to 50% of control. Total true and false transmitter in experimental animals was in all tissues less that acetylcholine in controls, suggesting that muscarinic transmission would be impaired. Moderate reduction of choline acetyltransferase activity was seen in striatum and myenteric plexus, and of QNB-binding in hippocampus, striatum and myenteric plexus.

Acetylation↗
PubMed1990

Global in vivo replacement of choline by N-aminodeanol. Testing a hypothesis about progressive degenerative dementia: II. Physiological and behavioral effects.

We have examined the progressive effects of replacement of dietary choline with NADe for a period of 120 days on a broad spectrum of behavioral and physiological functions known to involve the cholinergic system. The magnitudes of these effects tended to increase with time on the NADe diet, but those related to learning and memory were largely confined to the 60-120-day period. Neurochemical effects were concomitant with the replacement of Ch by NADe, being consistent with a hypocholinergic state as found in such progressive degenerative dementias as Alzheimer's disease. As cholinergic functioning was progressively impaired, basic physiological ("vegetative") processes appeared not to be affected. Apparently the rate at which the hypofunctional state developed was sufficiently slow for adjustments to occur, allowing the animal to adapt at a survival level to neurochemical changes. More complex behavioral functions were affected progressively, cognitive processes (e.g., learning and memory) being most sensitive and showing the least adaptability. We propose that the syndrome generated by NADe replacement of Ch represents an experimental model of progressive degenerative dementia.

Alzheimer Disease↗
PubMed1985

The ecophysiological significance of calcium bicarbonate in the urine of subterranean rodents: testing a hypothesis.

1. A comparative study of calcium and bicarbonate in the urine was carried out on the subterranean mole rat Cryptomys hottenttus and the terrestrial vlei rat Otomys irroratus. 2. The two species were kept on two different diets; carrots, a high calcium diet (41 mg/ 100 kg) or potatoes, a low calcium diet (14 mg/ 100g). 3. The results show that the urine of the mole rat contained high values of calcium bicarbonate on either diet. 4. The urine of the vlei rat showed high values of calcium bicarbonate only when kept on the high calcium diet. 5. From these results we assume that in subterranean rodents excretion of calcium bicarbonate is an adaptive mechanism to unload CO2 without increasing its concentration in the hypercapnic environment.

Adaptation, Physiological↗
PubMed2002

Longitudinal assessment of the middle cerebral artery peak systolic velocity in healthy fetuses and in fetuses at risk for anemia.

OBJECTIVE: Our purpose was to assess the feasibility of longitudinal assessment of the middle cerebral artery peak systolic velocity (MCA-PSV) to predict fetuses who will have severe anemia. STUDY DESIGN: Doppler measurement of MCA-PSV was serially performed in 15 healthy fetuses (99 measurements; range: 4-9 per fetus), 8 fetuses who were mildly anemic (41 measurements; range: 3-10 per fetus), and 11 who were severely anemic (50 measurements; range: 2-7 per fetus) at their first cordocenteses. Linear models were fitted to the data from individual fetuses and the slopes were determined. The average rate of change (slope) of MCA-PSV as a function of gestational age in the 3 groups was calculated from these data. Estimated average slopes were computed using restricted maximum likelihood. F tests were used for hypothesis tests, with the degrees of freedom based on the Kenward and Roger approximation. The values of MCA-PSV and hemoglobin were expressed as multiples of the median (MoM). A P <.05 indicated statistical significance. RESULTS: Gestational age at the time of the Doppler studies ranged from 15.1 to 41 weeks in the healthy fetuses. It was between 15 and 33.4 weeks in the fetuses who became anemic. The estimated average slopes increased with the degree of anemia (P =.03). The difference in mean slope between the severely anemic sample and the healthy sample was statistically significant (estimated difference = 2.2, SE =.65, P =.01). The difference in mean slope between the mildly anemic and healthy samples was not statistically significant (estimated difference = 1.1, SE =.06; P =.08). CONCLUSIONS: We have demonstrated that the MCA-PSV slope is an excellent tool for identifying those fetuses who will become severely anemic and, therefore, need to be followed up more closely during the pregnancy. Our findings expand the clinical applications to which Doppler ultrasonography can be applied in monitoring pregnancies at risk for fetal anemia.

Anemia↗