On Sample Size of the Kruskal–Wallis Test with Application to a Mouse Peritoneal Cavity Study

Summary As the nonparametric generalization of the one‐way analysis of variance model, the Kruskal–Wallis test applies when the goal is to test the difference between multiple samples and the underlying population distributions are nonnormal or unknown. Although the Kruskal–Wallis test has been widely used for data analysis, power and sample size methods for this test have been investigated to a much lesser extent. This article proposes new power and sample size calculation methods for the Kruskal–Wallis test based on the pilot study in either a completely nonparametric model or a semiparametric location model. No assumption is made on the shape of the underlying population distributions. Simulation results show that, in terms of sample size calculation for the Kruskal–Wallis test, the proposed methods are more reliable and preferable to some more traditional methods. A mouse peritoneal cavity study is used to demonstrate the application of the methods.     

暴露评估中样本采集量的模拟研究

选择暴露评估常用的4种右偏分布,就评估关注的高百分位数估计与采样量的关系进行模拟研究;又以对数正态分布为代表,从分布形态和变异的角度做了细致探讨.结果表明：（1）对右偏分布来说,百分位数越高,准确估计所需的采样容量就越大.而其估计值都随采样量的增大而趋近理论值,精度也随之增大,采样量500时,本文考察的4种右偏分布除P99.9外的其它百分位数都得到了较为准确的估计.（2）估计相同的百分位数,对数正态分布所需的样本容量要比正态分布大得多;而其分布变异越大,所需的采样量也就越大.本研究可为暴露评估中数据的采样调查提供借鉴.     

Sample Size Calculation for Intraclass Correlation in the Presence of Random Loss of Sampled Patients

When a trial involves an invasive laboratory test procedure or requires patients to make a commitment to follow a restrictive test schedule, we can often lose a great proportion of our sampled patients due to refusal of participation into our study. Therefore, incorporating the possible loss of patients into sample size calculation is certainly important in the planning stage of a study. In this paper, we have generalized the sample size calculation procedure for intraclass correlation by accounting for the random loss of patients in the beginning of a trial. We have demonstrated that the simple ad hoc procedure, that raises the estimated sample size in the absence of loss of patients by the factor 1/p_o, where p_o is the retention probability for a randomly selected patient, is adequate when p_o is large (=0.80). When p_o is small (i.e., a high refusal rate), however, use of this simple ad hoc procedure tends to underestimate the required sample size. Furthermore, we have found that if the individual retention probability varied substantially among patients, then the magnitude of the above underestimation could even be critical and therefore, the application of the simple direct adjustment procedure in this situation should be avoided.     

Estimating the Number of Droplets and Drug Particles Emitted from MDIs

The objective of this paper is to assess the number of drug particles or droplets contained in metered dose inhaler (MDI) aerosols. Equations were developed to estimate this. The number of drug particles was estimated to be as high as about 300 million for QVAR solution MDIs and as low as 670,000 for Beclovent MDIs. The number of particles in MDI aerosols was shown to be highly dependent on the mass median aerodynamic diameter (MMAD) and geometric standard deviation, and to a lesser extent the total mass of the aerosol. It was demonstrated that when the number of particles are calculated assuming that the aerosol is monodisperse and using the MMAD as the particle size, the number of particles are significantly underestimated. The number of droplets atomized from HFA-134a MDIs was estimated to range from about 220 million to about 1.1 billion droplets per actuation. For solution MDIs, each of the atomized droplets contains drug and thus the number of drug particles is the same as the number of atomized droplets. However, for suspension MDI formulations many of the droplets do not contain any micronized drug particles and the number of drug particles is much lower than the number of atomized droplets.     

t-Tests for Single Means of Autocorrelated Data — A Simulation Study —

A simulation study is reported in which the effect of positive and negative autocorrelation on the quantiles of Student's t-test variable is investigated. It is shown that negative autocorrelations lead to smaller quantiles. Positive autocorrelations lead to larger quantiles.     

省藤属四种植物的核型分析

报道了省藤属 (Calamus) 4种植物的核型 :小省藤 (C gracilis)的核型公式为 2n =2x =16m 10sm ,盈江省藤 (C nambariensisvar yingjiangensis)为 2n =2x =16m 10sm ,宽刺藤 (C platyacanthus)为 2n =2x =14m 12sm ,高地省藤 (C nambariensisvar alpinus)为 2n =2x =14m 12sm。其体细胞染色体数均为 2n =2 6 ,核型不对称性类型为 2B ,说明其种间染色体核型差异小。但小省藤臂比值大于 2的染色体占 12 % ,而宽刺藤、盈江省藤和高地省藤为 30 % ,说明在系统发育中 ,前者可能更为原始     

A Comparison of Formulae for Calculating Cost‐Efficient Sample Sizes of Case‐Control Studies with an Internal Validation Scheme

When a case‐control study is planned to include an internal validation study, the sample size of the study and the proportion of validated observations has to be calculated. There are a variety of alternative methods to accomplish this. In this article some possible procedures will be compared in order to clarify whether considerable differences in the suggested optimal designs occur, dependent on the used method.     

Random Fields Approach to the Study of DNA Chains

We apply the random field theory tothe study of DNA chains which we assume tobe trajectories of a stochastic process. Weconstruct statistical potential betweennucleotides corresponding to theprobabilities of those trajectories thatcan be obtained from the DNA data basecontaining millions of sequences. It turnsout that this potential has aninterpretation in terms of quantitiesnaturally arrived at during the study ofevolution of species i.e. probabilities ofmutations of codons. Making use of recentlyperformed statistical investigations of DNAwe show that this potential has differentqualitative properties in coding andnoncoding parts of genes. We apply ourmodel to data for various organisms andobtain a good agreement with the resultsjust presented in the literature. We alsoargue that the coding/noncoding boundariescan corresponds to jumps of the potential.     

不同方法检测鸡蛋表面菌落总数的相关性研究

研究了ATP生物荧光检测法与国标法《GB4789.2-2010食品卫生微生物学检验菌落总数测定》检测鸡蛋壳表面细菌总数的相关性。采用ATP生物荧光检测法和国标法对40个混合样品表面细菌总数进行检测,以log CFU/个蛋壳为横坐标(x),以logRLU/个蛋壳为纵坐标(y),分别进行线性、对数、乘幂、指数拟合。结果表明,ATP荧光检测法与国标法检测结果 Pearson相关系数为0.912,线性模型y=0.7306x-1.0041(R2=0.8322)拟合度较高。该试验结果为ATP荧光检测法在鸡蛋壳表面细菌总数快速检测中应用的可行性提供了依据。     

Upslope movements and large scale expansions: the taxonomy and biogeography of the Coenonympha arcania –C. d arwiniana –C. gardetta butterfly species complex

Sibling species groups are suitable models for the understanding of inter‐ and intraspecific processes in taxonomy and biogeography. We analysed 262 individuals from the Alps of the Coenonympha arcania/gardetta species complex by allozyme electrophoresis. These taxa showed high variance amongst populations (F_ST: 0.391) and strong intertaxon genetic differentiation (F_CT: 0.376). Although morphologically similar, Coenonympha gardetta and Coenonympha arcania clearly differ in their genetic characteristics; the morphologically intermediate taxa Coenonympha darwiniana darwiniana and Coenonympha darwiniana macromma are genetically well distinguished from each other and the two other taxa. Coenonympha arcania and C. d. macromma most probably share a common ancestor and evolved by cladogenesis, whereas the taxonomic situation of C. d. darwiniana is still unresolved: This taxon might be the result of hybridization between C. arcania and C. gardetta or it might have a common ancestor together with C. gardetta. We suggest species rank for all four taxa. The distribution of genetic diversity of these populations and the differentiation amongst populations suggest rather different biogeographical scenarios: C. arcania most probably is of Mediterranean origin with postglacial range expansion northwards; C. gardetta survived the last ice age in peripheral refugia of the Alps and has spread all over this high mountain system in the postglacial; C. darwiniana and C. macromma survived the Würm in geographic proximity to their actual distribution areas and only have performed moderate uphill translocations during postglacial warming. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 890–904.     

Design,synthesis, and conformational studies of the hGM‐CSF derived peptide (13–27)–Gly–(75–87)

An analogue of the human granulocyte–macrophage colony‐stimulating factor (hGM‐CSF), hGM‐CSF(13–27)–Gly–(75–87) was synthesized by solid phase methodology. This analogue was designed to comprise helices A and C of the native growth factor, linked by a glycine bridge. Helices A and C form half of a four‐helix bundle motif in the crystal structure of the native factor and are involved in the interaction with α‐ and β‐chains of the heterodimeric receptor. A conformational analysis of the synthetic analogue by CD, two‐dimensional nmr spectroscopy, and molecular dynamics calculations is reported. The analogue is in a random structure in water and assumes a partially α‐helical conformation in a 1 : 1 trifluoroethanol/water mixture. The helix content in this medium is ∼ 70%. By 2D‐nmr spectroscopy, two helical segments were identified in the sequences corresponding to helices A and C. In addition to medium‐ and short‐range NOESY connectivities, a long‐range cross peak was found between the Cβ proton of Val¹⁶ and NH proton of His⁸⁷ (using the numbering of the native protein). Experimentally derived interproton distances were used as restraints in molecular dynamics calculations, utilizing the x‐ray coordinates as the initial structure. The final structure is characterized by two helical segments in close spatial proximity, connected by a loop region. This structure is similar to that of the corresponding domain in the x‐ray structure of the native growth factor in which helices A and C are oriented in an antiparallel fashion. The N‐terminal residues Gly–Pro of helix C are involved in an irregular turn connecting the two helical segments. As a consequence, helix C is appreciably shifted and slightly rotated with respect to helix A compared to the x‐ray structure of the native growth factor. These small differences in the topology of the two helices could explain the lower biological activity of this analogue with respect to that of the native growth factor. © 1999 John Wiley & Sons, Inc. Biopoly 50: 545–554, 1999     

The Color Loci of Mice – A Genetic Century

Color loci in mammals are those genetic loci in which mutations can affect pigmentation of the hair, skin, and/or eyes. In the mouse, over 800 phenotypic alleles are now known, at 127 identified color loci. As the number of color loci passed 100 only recently, we celebrate this ‘century’ with an overview of these loci, especially the 59 that have been cloned and sequenced. These fall into a number of functional groups representing melanocyte development and differentiation, melanosomal components, organelle biogenesis, organelle transport, control of pigment‐type switching, and some systemic effects. A human ortholog has been identified in all cases, and the majority of these human genes are found to be loci for human disorders, often affecting other body systems as well as pigmentation. We expect that a significant number of color loci remain to be identified. Nonetheless, the large number known already provide a treasury of resources for reconstruction of the mechanisms, at the subcellular, cellular and tissue levels, that produce a functional pigmentary system and contribute to the normal development and functioning of many other organ systems. The mutant mice also provide valuable models for the study of human disease.     

A divalent FHA/BRCT‐binding mechanism couples the MRE11–RAD50–NBS1 complex to damaged chromatin

The MRE11–RAD50–NBS1 (MRN) complex accumulates at sites of DNA double‐strand breaks in large chromatin domains flanking the lesion site. The mechanism of MRN accumulation involves direct binding of the Nijmegen breakage syndrome 1 (NBS1) subunit to phosphorylated mediator of the DNA damage checkpoint 1 (MDC1), a large nuclear adaptor protein that interacts directly with phosphorylated H2AX. NBS1 contains an FHA domain and two BRCT domains at its amino terminus. Here, we show that both of these domains participate in the interaction with phosphorylated MDC1. Point mutations in key amino acid residues of either the FHA or the BRCT domains compromise the interaction with MDC1 and lead to defects in MRN accumulation at sites of DNA damage. Surprisingly, only mutation in the FHA domain, but not in the BRCT domains, yields a G2/M checkpoint defect, indicating that MDC1‐dependent chromatin accumulation of the MRN complex at sites of DNA breaks is not required for G2/M checkpoint activation.     

Mutational tests of the NMR-docked structure of the staphylococcal nuclease–metal–3′,5′-pdTp complex

In the X-ray structure of the staphylococcal nuclease–Ca²⁺ ?3′,5′-pdTp complex, the conformation of the inhibitor 3′,5′-pdTp is distroteed Lys-70* and Lys-71* from an adjacent molecule of staphylococcal nuclease (Loll, P.J., Lattman, E.E. Proteins 5 : 183-201, 1989). In order to correct this crystal packing problem, the solution conformation of enzyme-bound 3′,5′-pdTp in the staphylococcal nuclease–metal–pdTp Complex determined by NMR methods was docked into the X-ray structure of the enzyme [Weber, D. J., Serpersu, E. H., Gittis, A. G., Lattman, E. E., Mildvan, A. S. (preceding paper)]. In the NMR-docked structure, the 5′-phophate of 3′,5′-pdTp overlaps with that in the X-ray Structure. However the 3′-phosphate accepts a hydrogen bond from Lys-49 (2.89Å) rather than from Lys-84 (8.63 Å), and N3 of thymine donates a hydrogen bond to the OH of Tyr-115 (3.16 Å) which does not occur in the X-ray structure (5.28 Å). These interactions have been tested by binding studies of 3′,5′-pdTp, Ca²⁺, and Mn²⁺ to the K49A, K84A, and Y115A mutants of staphylococcal nuclease using water proton relaxation rate and EPR methods. Each mutant was fully active and structurally intact, as found by CD and two-dimensional NMR spectroscopy, but bound Ca²⁺ 9.1- to 9.9-fold more weakly than the wild-type enzyme. While thye K84A mutation did not significantly weaken 3′,5′-pdTp binding to the enzyme (1.5 ± 0.7 fold), the K49A mutation weakened 3′,5′-pdTp binding to the enzyme by the factor of 4.4 ± 1.8-fold. Similarly, the Y115A mutation weakened 3′,5′-pdTp binding to the enzyme 3.6 ± 1.6-fold. Comparable weakening effects of these mutations were found on the binding of Ca²⁺-3′,5′-pdTp. These results are more readily explained by the NMR-docked structure of staphylococcal nuclease-metal-3′,5′-pdTp than by the X-ray structure. © 1993 Wiley-Liss, Inc.     

A Fluorescence Polarization Assay for the Identification of Inhibitors of the p53–DM2 Protein–Protein Interaction

Improper function of the tumor suppressor protein p53 is a contributing factor in many human cancers. In normal cells, p53 acts to arrest the cell cycle in response to DNA damage or nucleotide depletion. One mechanism of regulating the amount of p53 in the cell is through the action of the Double Minute 2 protein, DM2 (also known as MDM2), which ubiquitinates p53 and targets it for proteosomal degradation. In a number of human cancers, the DM2 gene is amplified or overexpressed, leading to inadequate levels of p53 for cell cycle arrest or apoptosis. With the goal of restoring p53 function in cancers that overexpress DM2, we are developing inhibitors of the p53-DM2 protein-protein interaction that structurally mimic the N-terminal segment of p53 that binds to DM2. To assist this effort, we have devised a fluorescence polarization assay that quantifies the interaction between the N-terminal regions of both proteins in 384-well microtiter plates. Using this assay, we have demonstrated that a peptide with a nonhydrolyzable beta-amino acid substitution binds DM2 with an affinity comparable to a p53 peptide that is composed of only alpha-amino acids.