Confidence regions and hypothesis tests for topologies using generalized least squares

A confidence region for topologies is a data-dependent set of topologies that, with high probability, can be expected to contain the true topology. Because of the connection between confidence regions and hypothesis tests, implicitly or explicitly, the construction of confidence regions for topologies is a component of many phylogenetic studies. Existing methods for constructing confidence regions, however, often give conflicting results. The Shimodaira-Hasegawa test seems too conservative, including too many topologies, whereas the other commonly used method, the Swofford-Olsen-Waddell-Hillis test, tends to give confidence regions with too few topologies. Confidence regions are constructed here based on a generalized least squares test statistic. The methodology described is computationally inexpensive and broadly applicable to maximum likelihood distances. Assuming the model used to construct the distances is correct, the coverage probabilities are correct with large numbers of sites.     

A Study of Distribution-free Tests for Umbrella Alternatives

In this paper we are concerned with test procedures for umbrella alternatives in the k-sample location problem. Distribution-free tests are considered for both cases where the peak of the umbrella is known or unknown. Comparative results of a Monte Carlo power study are presented.     

Gaining insight into the response logic of Saccharomyces cerevisiae to heat shock by combining expression profiles with metabolic pathways

Extensive alteration of gene expression and metabolic remodeling enable the budding yeast Saccharomyces cerevisiae to ensure cellular homeostasis and adaptation to heat shock. The response logic of the cells to heat shock is still not entirely clear. In this study, we combined the expression profiles with metabolic pathways to investigate the logical relations between heat shock response metabolic pathways. The results showed that the heat-stressed S. cerevisiae cell accumulated trehalose and glycogen, which protect cellular proteins against denaturation, and modulate its phospholipid structure to sustain stability of the cell wall. The TCA cycle was enhanced, and the heat shock-induced turnover of amino acids and nucleotides served to meet the extra energy requirement due to heat-induced protein metabolism and modification. The enhanced respiration led to oxidative stress, and subsequently induced the aldehyde detoxification system. These results indicated that new insight into the response logic of S. cerevisiae to heat shock can be gained by integrating expression profiles and the logical relations between heat shock response metabolic pathways.     

Comparing Two Samples of Response Curves by Nonparamètric Tests of Predicted Order

Starting from MOSTELLER'S (1955) one-sample test of predicted order, some two-sample versions are proposed for comparing nonparametrically a treatment group (m response curves) with a control group (n response curves) as to a predicted shape represented by a specified rank order. The tests are applied to two groups of learning curves.     

A Multivariate Permutation Test for the Analysis of Arbitrarily Censored Survival Data

The exact generalization of GEHAN's (1965) two-sample test for arbitrarily censored survival data has been overlooked by subsequent work on the multisample problem. We give this general covariance matrix and show how it may be used in test procedures. While this permutation test is less powerful than its competitors in cases where both apply, it may be used on types of data not previously discussed.     

A calibration method to generate seasonal hatching profiles for the fiddler crabs Uca pugnax (Smith, 1870) and Uca minax (LeConte, 1855) (Decapoda : Brachyura)

A statistical method for generating seasonal egg hatching profiles is applied to the brachyuran crabs Uca pugnax (Smith) and U. minax (LeConte) in New Jersey. Calibration experiments quantified the time course of egg development, using serial egg sampling at 1- to 2- day intervals from marked ovigerous females maintained in cages in the field. Egg stage was ranked from 1 to 10, based on morphological changes during development. Equations for predicting the number of days remaining until hatching from egg developmental stage were obtained from the calibration experiments, using stepwise polynomial regression. To cover the reproductive season, three consecutive calibration experiments using 15 or more females were run for U. pugnax; two for U. minax. Significant seasonal differences in the time course of egg development were detected. Weekly collections of females for each species were made; the date of larval release for each ovigerous female was predicted from the proximate calibration equation, yielding weekly hatching profiles. Weekly hatching profiles were summed to obtain seasonal hatching profiles. The average number of broods produced per female over the reproductive season was 1.9 for U. pugnax and 1.6 for U. minax. Hatching peaks for both species were associated with spring tides. The merits of this and other methods used to estimate daily variation in egg hatching of crabs are discussed.     

Isozyme profiles associated with the hypersensitive response of Chenopodium foetidum to plum pox virus infection

Isozyme profiles of esterases (E.C. 3.1.1.1), glutamate oxaloacetate transaminase (E.C. 2.6.1.1) and peroxidases (E.C. 1.11.1.7) have been determined in healthy tissues of Chenopodium foetidum as well as their modifications during leaf development. The effect of plum pox virus infection on the isozyme profiles has also been studied. Virus-induced necrotic lesions displayed a peroxidase (POX) pattern that has not been found in any other tissue of the plant so far analyzed. The pattern was similar to that of old yellow leaves, except that POX-B, which was detected in the necrotic lesions, has not been detected in any developmental stage of healthy leaves. Changes in the peroxidase profile seem to begin early during infection, even before necrosis is visible. We suggest that senescence is established at necrotic lesions extending from there to the rest of the infected leaf affecting the peroxidase isozyme pattern. However, other changes, which induce POX-B, must also take place at necrotic lesions. These do not extend to the rest of the infected leaves. Plum pox virus infection has less effect on the glutamate oxaloacetate transaminase and esterase isozyme patterns, inducing an almost normal senescence pattern.     

老年认知障碍常用神经心理测验的应用进展

随着医学进步,人类平均寿命不断延长,人口老龄化问题越来越突出,老年认知障碍患者不断增加。而神经心理测验在不同程度认知功能损害的诊断中的作用已日益引起重视。就认知功能损害诊断常用的神经心理测验进行综述,为临床认知功能检查提供依据。     

Comparisons of tests for aneuploidy

The fundamental problems that face us in the development of suitable assay systems for the detection of potentially aneugenic (aneuploidy-inducing) chemicals include: (a) the diversity of cellular targets and mechanisms where perturbations of structure and function may give rise to changes in chromosome number, and (b) the phylogenetic differences that exist between species in their mechanism and kinetics of cell division and their metabolic profiles. A diverse range of assay systems have been developed, which have been shown to have potential for use in the detection of either changes in chromosome number or of perturbations of the events which may be causal in the induction of aneuploidy.

Chromosome number changes may be detected cytologically by karyotypic analysis, or by the use of specialised strains in which aneuploid progeny may be observed due to phenotypic differences with aneuploid parental cells or whole organisms. Techniques for the detection of cellular target modifications range from in vitro studies of tubulin polymerisation to observations of the behaviour of various cellular organelles and their fidelity of action during the division cycle.

The diversity of mechanisms which may give rise to aneuploidy and the qualitative relevance of events observed in experimental organisms compared to man make it unlikely that the detection and risk assessment of the aneugenic activity of chemicals will be possible using a single assay system. Optimal screening and assessment procedures will thus be dependent upon the selection of an appropriate battery of predictive tests for the measurement of the potentially damaging effects of aneuploidy induction.     

Compound tests for the detection of hitchhiking under positive selection

Many statistical tests have been developed for detecting positive selection. Most of these tests draw conclusions based on significant deviations from the patterns of polymorphism predicted by the neutral model. However, many non-equilibrium forces may cause similar deviations, and thus the tests usually have low statistical specificity to positive selection. The main challenge is hence to construct test statistics that are reasonably powerful in detecting positive selection, but are relatively insensitive to other forces. Recently, Zeng et al. (2006) proposed a new test, DH, which is a compound of Tajima's D and Fay and Wu's H, and showed that DH has reasonably high statistical specificity to positive selection. In this report, we expand the idea of a compound test by combining Fay and Wu's H or DH with the Ewens-Watterson (EW) test. We refer to these 2 new tests as HEW and DHEW, respectively. Compared to the DH test, HEW and DHEW are more robust against the presence of recombination, and are also more powerful in detecting positive selection. Furthermore, the DHEW test, similar to DH, is also relatively insensitive to background selection and demography. The HEW test, on the other hand, tends to be somewhat less conservative than DH and DHEW in some cases.     

A rapid controller of temperature for use in determining Arrhenius profiles in biomembrane systems

To minimize artifacts in temperature-velocity (Arrhenius) profiles due to aging of preparations of biological membranes, a rapid controller of temperature was developed for spectrophotometric or polarographic (O₂ electrode) measurements. The reaction mixture is cooled or heated through contact with Peltier elements. One Pt temperature sensor in the cuvette or electrode holder controls current flow into the Peltier units, and another Pt temperature sensor in the reaction mixture is used to read out the sample temperature on a meter or recorder, and to provide feedback control. The sample temperature can be reproducibly set to within 0.1°C, with a noise level of 0.04°C or less; a change of 4°C takes 1 min.On leave at the Arrhenius Laboratory, University of Stockholm.     

The relevance of various tests for the study of specificity in immunocytochemical staining: a review

Factors determining the specificity of immunocytochemical (ICC) tissue stainings as well as the various tests to study these factors are discussed. Since every specificity test only deals with particular aspects of the ICC procedure, a practical sequence of known test methods is proposed, which enables the determination of the specificity of the ICC tissue staining and, after possibly needed antiserum purification steps, may result in a monospecific staining. It is made clear that such a sequence has always to include a tissue-spectrum affinity test, in which the spectrum of tissue antigens is controlled for antibody binding. A variety of such tests, consisting of separation of tissue compounds, fixation, and ICC detection, are discussed as well as their pros and cons with respect to their predictability for the actual serum specificity in the tissue section.     

Assessing the response of open-habitat bird species to landscape changes in Mediterranean mosaics

In Mediterranean landscapes, wildfires and land abandonment lead to major landscape modifications primarily by favouring the presence of open, shrub-like habitats. At present, we know very little of how these changes affect patterns of species occurrence at the landscape scale. In this work, we analyse the impact of these landscape changes on the occurrence patterns of eight open-habitat species by using presence/absence data collected in the Catalan Breeding Bird Atlas (NE Spain). We compared the species occurrence patterns along habitat gradients for three different landscape settings: a semi-permanent farmland–forest landscape (i.e. with variable proportions of farmland and forests) and two landscape settings which mimic those favoured by land abandonment and fire: farmland–shrubland landscapes and mosaic landscapes (i.e. variable proportions of farmland and forest coexisting with a shrubby matrix). In the forest–farmland landscape, we found a dominant negative effect of adjacent forest on species occurrence rates. This overall effect mostly disappeared in farmland–shrubland landscapes composed by two habitats with more similar vegetation structure. In mosaic landscapes, the general negative effect of forest habitats also appeared to be partially compensated by the presence of a shrubby matrix. Our results suggest that landscape gradients induced by fire and to some degree also land abandonment, mainly favouring availability of shrublands may potentially enhance the resilience of threatened open-habitat species at the landscape scale by increasing the range of potential habitats used. The analysis of species-occurrence patterns along predefined habitat gradients appears as a useful tool to predict potential species responses to land use change.     

A graphical model for the evaluation of cross-transfer evidence in DNA profiles

The role of graphical models in the assessment of transfer evidence is described with particular reference to the role of cross-transfer evidence. The issues involved in the determination of factors (nodes), associations (links) and probabilities to be included are discussed. Four types of subjective probabilities are of particular interest: those for transfer, persistence and recovery; innocent acquisition; relevance; innocent presence. Examples are given to illustrate the roles of various aspects of the suspect's and victim's lifestyle and the investigation of the evidence found on the suspect and victim in assessing the probability of ultimate issue, that the suspect committed the crime.     

A comparison of tests for independence in the FBI RFLP data bases

Several tests of independence of alletic frequencies within and between loci have been compared, and it has been found that Fisher's exact test is the best test to use. When this test is applied to RFLP databases established by the FBI, paying no attention to the single-band problem, there is generally evidence for independence at one locus but not at two loci. When the test is restricted to double-banded entries in the databases; there is overall evidence for independence.     

Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein

The ribose-binding protein (RBP) is a sugar-binding bacterial periplasmic protein whose function is associated with a large allosteric conformational change from an open to a closed conformation upon binding to ribose. The crystal structures of RBP in open and closed conformations have been solved. It has been hypothesized that the open and closed conformations exist in a dynamic equilibrium in solution, and that sugar binding shifts the population from open conformations to closed conformations. Here, we study by computer simulations the thermodynamic changes that accompany this conformational change, and model the structural changes that accompany the allosteric transition, using umbrella sampling molecular dynamics and the weighted histogram analysis method. The open state is comprised of a diverse ensemble of conformations; the open ribose-free X-ray crystal conformations being representative of this ensemble. The unligated open form of RBP is stabilized by conformational entropy. The simulations predict detectable populations of closed ribose-free conformations in solution. Additional interdomain hydrogen bonds stabilize this state. The predicted shift in equilibrium from the open to the closed state on binding to ribose is in agreement with experiments. This is driven by the energetic stabilization of the closed conformation due to ribose-protein interactions. We also observe a significant population of a hitherto unobserved ribose-bound partially open state. We believe that this state is the one that has been suggested to play a role in the transfer of ribose to the membrane-bound permease complex.