On the Comparison of Two Observed Frequencies

A significance measure essentially due to Liebermeister and dating back to 1877 may be preferable to Fisher's Exact Test, a conservative but commonly applied test when the sample sizes are small. We show that Liebermeister's measure is less conservative than Fisher's P‐value and just as easy to calculate, while retaining the important features of a significance measure. We also compare Liebermeister's measure with Lancaster's mid‐P, which has gained increasing acceptance as a replacement for Fisher's P‐value. Application is made to a recent striking medical study on appendicitis symptoms for which the Fisher test does not give significance.     

Size,longevity and cancer: age structure

There is significant recent interest in Peto''s paradox and the related problem of the evolution of large, long-lived organisms in terms of cancer robustness. Peto''s paradox refers to the expectation that large, long-lived organisms have a higher lifetime cancer risk, which is not the case: a paradox. This paradox, however, is circular: large, long-lived organisms are large and long-lived because they are cancer robust. Lifetime risk, meanwhile, depends on the age distributions of both cancer and competing risks: if cancer strikes before competing risks, then lifetime risk is high; if not, not. Because no set of competing risks is generally prevalent, it is instructive to temporarily dispose of competing risks and investigate the pure age dynamics of cancer under the multistage model of carcinogenesis. In addition to augmenting earlier results, I show that in terms of cancer-free lifespan large organisms reap greater benefits from an increase in cellular cancer robustness than smaller organisms. Conversely, a higher cellular cancer robustness renders cancer-free lifespan more resilient to an increase in size. This interaction may be an important driver of the evolution of large, cancer-robust organisms.     

Do peacock's trains advertise age?

Manning (1987 and 1989) found a positive correlation between several measured aspects of the male's upper tail coverts and male age in a sample of males measured at several different sites. Here we test whether or not the trains of individuals from the same population increase between years. There is no evidence from the data presented that variation in the degree of train elaboration amongst male peacocks is age-dependent beyond 4 years or that peahens always prefer to mate with older males; one young male in his first year of displaying achieved high mating success and was preferred by several females over other older males present. It therefore appears unlikely that the peacock's train acts as an age-indicator.     

Evolutionary stasis of a heritable morphological trait in a wild fish population despite apparent directional selection

Comparing observed versus theoretically expected evolutionary responses is important for our understanding of the evolutionary process, and for assessing how species may cope with anthropogenic change. Here, we document directional selection for larger female size in Atlantic salmon, using pedigree‐derived estimates of lifetime reproductive success as a fitness measure. We show the trait is heritable and, thus, capable of responding to selection. The Breeder's Equation, which predicts microevolution as the product of phenotypic selection and heritability, predicted evolution of larger size. This was at odds, however, with the observed lack of either phenotypic or genetic temporal trends in body size, a so‐called “paradox of stasis.” To investigate this paradox, we estimated the additive genetic covariance between trait and fitness, which provides a prediction of evolutionary change according to Robertson's secondary theorem of selection (STS) that is unbiased by missing variables. The STS prediction was consistent with the observed stasis. Decomposition of phenotypic selection gradients into genetic and environmental components revealed a potential upward bias, implying unmeasured factors that covary with trait and fitness. These results showcase the power of pedigreed, wild population studies—which have largely been limited to birds and mammals—to study evolutionary processes on contemporary timescales.     

Overnight Dexamethasone Suppression Test: A Reliable Screen for Cushing's Syndrome in the Obese

Objective: Reevaluation of the validity of the 1-mg overnight dexamethasone suppression test (ODST) as a screening test for Cushing's syndrome in obese patients. Research Methods and Procedures: Eighty-six obese patients (body mass index, 30 to 53 kg/m²) that were referred to a general endocrine outpatient clinic for evaluation of simple obesity, diabetes mellitus, hypertension, polycystic ovary disease, or pituitary tumor. One milligram dexamethasone was administered orally at 11:00 pm , and serum cortisol levels were measured the following morning between 8:00 am and 9:00 am . Suppression of serum cortisol to <80 nM (3 μg/dL) was chosen as the cut-off point for normal suppression. Patients with serum cortisol levels ≥80 nM were evaluated for Cushing's syndrome. Results: Suppression of morning cortisol levels to <80 nM occurred in 79 of the 86 obese patients. Seven patients had serum cortisol levels higher than 80 nM; five were eventually diagnosed with Cushing's syndrome and two were considered false positive results in view of normal 24-hour free urinary cortisol and normal suppression on a low dose dexamethasone suppression test (0.5 mg of dexamethasone every 6 hours for 2 days). We found a false positive rate of 2.3% for the ODST using a cut-off serum cortisol of 80 nM. Discussion: The ODST is a valid screening test for Cushing's syndrome in the obese population. The false positive rate was 2.3%, even when using a strict cut-off serum cortisol of 80 nM. Abnormal cortisol suppression in obese patients should be investigated and not be considered false positive results.     

Tests for Homogeneity of Variances Using Robust Weighted Likelihood Estimates

The classical normal-theory tests for testing the null hypothesis of common variance and the classical estimates of scale have long been known to be quite nonrobust to even mild deviations from normality assumptions for moderate sample sizes. Levene (1960) suggested a one-way ANOVA type statistic as a robust test. Brown and Forsythe (1974) considered a modified version of Levene's test by replacing the sample means with sample medians as estimates of population locations, and their test is computationally the simplest among the three tests recommended by Conover , Johnson , and Johnson (1981) in terms of robustness and power. In this paper a new robust and powerful test for homogeneity of variances is proposed based on a modification of Levene's test using the weighted likelihood estimates (Markatou , Basu , and Lindsay , 1996) of the population means. For two and three populations the proposed test using the Hellinger distance based weighted likelihood estimates is observed to achieve better empirical level and power than Brown-Forsythe's test in symmetric distributions having a thicker tail than the normal, and higher empirical power in skew distributions under the use of F distribution critical values.     

Modification of the Minimum Logit Chi-Squared Estimator in Simple Linear Logistic Regression

A new modification of Berkson's minimum logit chi-squared estimator in simple linear logistic regression is suggested in order to achieve reduction of first order bias of the estimator as well as in the model. Furthermore, unlike estimators currently available, our procedure is quite simple to apply in practice and is valid even in the presence of zero frequencies in the table.     

Conservation Reserve Program Benefits on Henslow's Sparrows Within the United States

ABSTRACT Henslow's sparrow (Ammodramus henslowii) is one of North America's fastest declining songbirds. Population declines combined with a small global population have led to heightened conservation concern. I used data from the North American Breeding Bird Survey to assess the impact that the Conservation Reserve Program (CRP) has had on Henslow's sparrows throughout their United States breeding range. My analysis suggests local Henslow's sparrow population trends are correlated with CRP enrollment, with populations increasing more in areas with relatively high local CRP enrollment, and that CRP appears to be playing a significant role in reversing long-term population declines.     

The multiple facets of Peto's paradox: a life-history model for the evolution of cancer suppression

Large animals should have higher lifetime probabilities of cancer than small animals because each cell division carries an attendant risk of mutating towards a tumour lineage. However, this is not observed—a (Peto''s) paradox that suggests large and/or long-lived species have evolved effective cancer suppression mechanisms. Using the Euler–Lotka population model, we demonstrate the evolutionary value of cancer suppression as determined by the ‘cost’ (decreased fecundity) of suppression verses the ‘cost’ of cancer (reduced survivorship). Body size per se will not select for sufficient cancer suppression to explain the paradox. Rather, cancer suppression should be most extreme when the probability of non-cancer death decreases with age (e.g. alligators), maturation is delayed, fecundity rates are low and fecundity increases with age. Thus, the value of cancer suppression is predicted to be lowest in the vole (short lifespan, high fecundity) and highest in the naked mole rat (long lived with late female sexual maturity). The life history of pre-industrial humans likely selected for quite low levels of cancer suppression. In modern humans that live much longer, this level results in unusually high lifetime cancer risks. The model predicts a lifetime risk of 49% compared with the current empirical value of 43%.     

塔克尔莫乎尔沙漠银沙槐群落主要植物的种间关系

根据野外调查的样地数据资料,运用2×2列联表的Fisher精确检验、Pearson相关系数和Spearman秩相关系数检验,并结合DCA排序,分析塔克尔莫乎尔沙漠银沙槐群落主要植物种群之间的种间关系。结果表明:Fisher精确检验有3个种对呈显著正关联,3个种对呈显著负关联;Pearson相关系数检验有1个种对呈显著正相关,12个种对呈显著负相关;Spearman秩相关系数检验,有14个种对存在显著相关,其中负相关13对,占所有种对数的14.29%,正相关1对,占所有种对数的1.1%。银沙槐群落种间关系相对松散,反映出植物群落随着环境变化其物种组成也发生相应变化,正向着相对稳定独立的无关联方向发展。     

A Revisit on Comparing the Asymptotic Interval Estimators of Odds Ratio in a Single 2 × 2 Table

It is well known that Cornfield 's confidence interval of the odds ratio with the continuity correction can mimic the performance of the exact method. Furthermore, because the calculation procedure of using the former is much simpler than that of using the latter, Cornfield 's confidence interval with the continuity correction is highly recommended by many publications. However, all these papers that draw this conclusion are on the basis of examining the coverage probability exclusively. The efficiency of the resulting confidence intervals is completely ignored. This paper calculates and compares the coverage probability and the average length for Woolf s logit interval estimator, Gart 's logit interval estimator of adding 0.50, Cornfield 's interval estimator with the continuity correction, and Cornfield 's interval estimator without the continuity correction in a variety of situations. This paper notes that Cornfield 's interval estimator with the continuity correction is too conservative, while Cornfield 's method without the continuity correction can improve efficiency without sacrificing the accuracy of the coverage probability. This paper further notes that when the sample size is small (say, 20 or 30 per group) and the probability of exposure in the control group is small (say, 0.10) or large (say, 0.90), using Cornfield 's method without the continuity correction is likely preferable to all the other estimators considered here. When the sample size is large (say, 100 per group) or when the probability of exposure in the control group is moderate (say, 0.50), Gart 's logit interval estimator is probably the best.     

Evidence for a Recent Henslow's Sparrow Population Increase in Illinois

Abstract: The Henslow's sparrow (Ammodramus henslowii) is a species of high conservation concern due to long-term population declines and a small global population. Habitat loss is considered to be the most likely cause of Henslow's sparrow declines and the recent establishment of large acreages of undisturbed grasslands through the Conservation Reserve Program is considered to have the potential to benefit populations. I used data from Illinois' Spring Bird Count to estimate recent population trends and examine the association that changes in land-use, especially the establishment of Conservation Reserve Program lands, have had on local Henslow's sparrow population trends. My analysis shows that Henslow's sparrow populations have increased substantially within Illinois, USA over the last 10 years and that this population increase strongly coincides with the establishment of >400,000 ha of grasslands within the state by the Conservation Reserve Program. New rules allowing for managed haying and grazing on Conservation Reserve Program grasslands have the potential to reduce the suitability of program fields for this species and, thus, Henslow's sparrow use of program fields should be monitored as the new rules are implemented.     

A radiographic approach to childhood illness in precolumbian inhabitants of southern Peru

A total of 108 individuals from six different cultures found in the Department of Ica, Peru, were studied for the presence of Harris's Lines. Such lines or “bone scars” are formed due to cessation of bone growth due to episodes of starvation or illness and possibly other causes. These individuals covered a span of time of nearly 2,600 years. The individuals from mountain cultures had fewer lines and possibly a healthier childhood than those from coastal cultures. The modern population surveyed in this series still show a pattern of Harris's Lines similar to people from the Inca culture of 450 years ago.     

Functional adaptation rather than ecogeographical rules determine body-size metrics along a thermal cline with elevation in the Chinese pygmy dormouse (Typhlomys cinereus)

Phenotypic plasticity is crucial for how organisms respond to variation in their environment, affecting their diversity and distribution, especially in the light of rapid environmental change. Ecogeographical rules predict an association between specific adaptive morphological and physiological traits with cooler conditions due to higher latitude, elevation, or climate change. Such ecogeographical effects are often most evident in ancient species due to continuous selective adaptation occurring over long periods of time. Here, we use the suitably ancient Chinese pygmy dormouse (Typhlomys cinereus) to test whether body-size, appendage length and heart size vary in accordance with Bergmann's, Allen's and Hesse's rule, respectively. Based on a sample of 67 adult individuals (female, n = 29; male n = 38) trapped at 37 sites transcending an elevational range from 414 to 1757 m, we tested for trait concordance with Bergmann's rule (body mass, length and SMI), Allen's rule (length of tail, foot, ear, snout), and Hesse's rule (wet and dry heart mass). Effects of elevation (and thus temperature lapse rate; calculated as 0.61 °C per 100 m) on body size, appendage length and heart size, were tested by fitting Standardized Major Axis (SMA) models. We observed substantial heterogeneity in morphometric traits allowing for the detection of ecogeographical clines. However, none conformed with Bergmann's, Allen's (except ear size), or Hesse's rule. However, our results indicate some support for Geist's rule of net primary productivity. We conclude that pervasive functional life-history adaptations in this blind, arboreal, echolocating ancient species exceeded selection for morphological energy efficiency constraints, with the notable exception of reduced ear pinnae size at colder, elevated sites. This is an important consideration for predicting how species, and populations in general, may adapt to human induced rapid environmental change, contrary to expectations of warming driving selection for smaller body-size.     

基于加权Ripley's K-function的多尺度景观格局分析——以江苏盐城滨海湿地为例

以1987,1992,1997,2002,2007年的遥感影像为例,首次尝试使用加权Ripley's K-function的多尺度格局分析方法,计算了20年来景观异质性在江苏盐城滨海湿地的时间变化和空间分布趋势。通过对研究区的样带划分以及景观类型的点状化处理,建立滨海湿地样带图层和1987—2007年间各类型景观的点格局数据库,从而分析滨海湿地不同类型景观的空间聚集特征变化。基于加权Ripley's K-function的计算表明,在各级空间尺度和时间变化上,各类型湿地的斑块都呈现出空间聚集分布状态,且1987年以来,不同湿地类型的聚集空间特征尺度和空间分布强度均出现了大幅的增减变化,除互花米草滩之外的自然湿地的聚集空间特征尺度和强度都有明显下降甚至少到无法被检测到,而人工湿地却呈现聚集特征尺度和强度的双增长,且该聚集程度有逐渐增强的趋势。分析表明,既考虑样点的空间位置信息又考虑样点分布范围的加权Ripley's K-function方法能很好地表征湿地景观在多尺度上的变异,且与传统空间景观指数等分析方法的结论在一定程度上保持一致。     

SEX REVERSAL: A FOUNTAIN OF YOUTH FOR SEX CHROMOSOMES?

Nonrecombining Y chromosomes are expected to degenerate through the progressive accumulation of deleterious mutations. In lower vertebrates, however, most species display homomorphic sex chromosomes. To address this, paradox I propose a role for sex reversal, which occasionally occurs in ectotherms due to the general dependence of physiological processes on temperature. Because sex‐specific recombination patterns depend on phenotypic, rather than genotypic sex, homomorphic X and Y chromosomes are expected to recombine in sex‐reversed females. These rare events should generate bursts of new Y haplotypes, which will be quickly sorted out by natural or sexual selection. By counteracting Muller's ratchet, this regular purge should prevent the evolutionary decay of Y chromosomes. I review empirical data supporting this suggestion, and propose further investigations for testing it.     

Paradoxical Survival: Examining the Parrondo Effect across Biology

Parrondo's paradox, in which losing strategies can be combined to produce winning outcomes, has received much attention in mathematics and the physical sciences; a plethora of exciting applications has also been found in biology at an astounding pace. In this review paper, the authors examine a large range of recent developments of Parrondo's paradox in biology, across ecology and evolution, genetics, social and behavioral systems, cellular processes, and disease. Intriguing connections between numerous works are identified and analyzed, culminating in an emergent pattern of nested recurrent mechanics that appear to span the entire biological gamut, from the smallest of spatial and temporal scales to the largest—from the subcellular to the complete biosphere. In analyzing the macro perspective, the pivotal role that the paradox plays in the shaping of biological life becomes apparent, and its identity as a potential universal principle underlying biological diversity and persistence is uncovered. Directions for future research are also discussed in light of this new perspective.     

Nonparametric Two-Sample Tests for General Clinical Data

Starting from the discussion of a practical example a unifying concept for the derivation of meaningfully interpretable nonparametric tests for the two-sample case is developed which may well be adapted for other designs, too. This methodology covers other well-known procedures, e.g. Fisher's exact test, the Wilcoxon-Mann-Whitney and Gehan's tests, and may furthermore be extended to all situations sharing the same fundamental structural property of the sample space, namely its strict order induced by the substantial problem under study. The resulting test procedure is discussed for a randomization argument, exact and approximate, as well as for the general specific test problem. A numerical example is provided.     

Burning mouth in Parkinson's Disease sufferers

Objective . The purpose of the study was to determine the prevalence of burning mouth (BM) in a population of Parkinson's Disease (PD) sufferers and also to assess the use of pain profiles in identifying the type of burning sensation experienced. Design. Subjects were surveyed by means of a one shot postal questionnaire for which ethical approval had previously been granted. Anonymity was guaranteed and therefore no attempt was made to follow up non-respondents. Main outcome. BM was reported by 24% of respondents. The pain profiles were completed by 17 BM sufferers. Conclusion. Burning mouth is reported to occur in 24% of PD sufferers which is 5 times greater than that of the general population. The reason for this is uncertain but the result has implications for the future care of PD patients and indicates the need for increased dental input at PD outpatient clinics.     

Determining Consistency of Spatial Dispersion of Nematodes in Small Plots

Nematode population densities in field plots were estimated by collecting samples consisting of 12 soil cores. Plots encompassed a variety of plant hosts and sampling dates, and provided data on the population densities of seven species of plant-parasitic nematodes. Three separate samples were collected per plot on each sampling date to obtain estimates of the mean and variance of numbers for each species. For each nematode species, these estimates were used to derive the Taylor''s Power Law regression over plots having identical hosts and sampling dates. For some nematode species, comparisons of regression equations among different sampling dates on the same host revealed similarities in values of a and b from Taylor''s Power Law. Parameters of Taylor''s Power Law relationships were used to develop sampling plans and to obtain estimates of sample precision. Precision estimates from specific and general sampling plans are illustrated for Belonolaimus longicaudatus.