Exact Test of Uniform Association in a 2 × 3 Table

In a similar approach to Fisher's exact test of independence (null association) for a 2 × 2 table, this note gives an exact test of uniform association for a 2 × 3 table.     

Methods for Analyzing Odds Ratios in a 2× C Contingency Table

This paper presents produrea for the analysis of the odds ratio and log odds ratio for a 2×C contingency table. The proposed procedurea provide a more unified approach to study of the trend of the odds ratio as a measure of association between a risk indioator and an “outcome” variable than traditional form of analyeis. The methodology is illustrated with an example from the epidemiologic literature.     

His-tag的人胞浆磷脂酶A_2的C2结构域的表达、纯化及性质

带有His tag的人胞浆磷脂酶A2 的C2结构域高效表达 ,用内源荧光的变化测定了其稳定性和其与钙离子结合的结合常数 .结果表明 ,带有His tag的C2结构域仍可有效用于研究其折叠及其与钙离子的协同性结合 ,温度从 2 2℃升高到 35℃时 ,C2结构域和钙离子结合的协同性程度显著增强 .     

A family of functional dissimilarity measures for presence and absence data

Plot‐to‐plot dissimilarity measures are considered a valuable tool for understanding the complex ecological mechanisms that drive community composition. Traditional presence/absence coefficients are usually based on different combinations of the matching/mismatching components of the 2 × 2 contingency table. However, more recently, dissimilarity measures that incorporate information about the degree of functional differences between the species in both plots have received increasing attention. This is because such “functional dissimilarity measures” capture information on the species' functional traits, which is ignored by traditional coefficients. Therefore, functional dissimilarity measures tend to correlate more strongly with ecosystem‐level processes, as species influence these processes via their traits. In this study, we introduce a new family of dissimilarity measures for presence and absence data, which consider functional dissimilarities among species in the calculation of the matching/mismatching components of the 2 × 2 contingency table. Within this family, the behavior of the Jaccard coefficient, together with its additive components, species replacement, and richness difference, is examined by graphical comparisons and ordinations based on simulated data.     

The analysis of three-dimensional data (sites × species × times) in marine ecology

A new numerical model is defined for the partition of three-dimensional data; it is based on the analysis of variance, and is shown to be equivalent to an unstandardized Euclidean distance preceded by a specified form of standardization. The resulting quantity can be used as a dissimilarity measure for classification; it will serve to define a two-way table and provides a simple and elegant method for data-reduction requiring only a single subjective decision. The concept of ‘mean variance per comparison’ is introduced, and it is shown that such mean variances can be used to assess the relative importance of the three dimensions; two important symmetry properties of mean variance are established. The model is applied to a small real-life problem of 15 sites × 56 species × 8 seasons, and is shown to produce ecologically satisfactory results.     

The Power Function of the Test for ‘No Three Factor Interaction’ in 2×2×2 Contingency Tables

Three approximations to the power function of the chi-square test for the hypotheses of ‘no three factor interaction’ in a 2 × 2 × 2 contingency table are introduced and compared. The first method is based on the sampling distribution of the logarithm of the odds ratio, the second-on the non-central X² distribution and the third—on the conditional distribution of a cell entry. The last method is found to provide the closest approximation under various alternative hypotheses and sample sizes.     

Multiple species effects and spatial autocorrelation in detecting species associations

Abstract. The traditional approach to the analysis of species association within a community, based upon co-occurrence in sampling units such as quadrats, has been to test all pairs of species, using a 2 × 2 contingency table for each pair. It has long been recognised that all these tests are not independent of each other, but there is an additional problem in that the association between any particular pair may depend on the combination of the other species that are present or on the environmental factors that determine that combination. We use a 2^k contingency table to examine this problem and find that pairwise associations are not independent of the other species. The second problem that we consider is the effect of spatial autocorrelation in the data which makes the statistical tests too liberal. In the absence of a derived solution for a deflation factor to correct the test statistic calculated from a 2^k table, we describe a Monte Carlo approach that provides an approximate solution to this problem. In our data the amount of deflation that is necessary for a 2^k table is small compared to the amount required for the 2 × 2 tables used to test pairwise association.     

Stratified Fisher's exact test and its sample size calculation

Chi‐squared test has been a popular approach to the analysis of a 2 × 2 table when the sample sizes for the four cells are large. When the large sample assumption does not hold, however, we need an exact testing method such as Fisher's test. When the study population is heterogeneous, we often partition the subjects into multiple strata, so that each stratum consists of homogeneous subjects and hence the stratified analysis has an improved testing power. While Mantel–Haenszel test has been widely used as an extension of the chi‐squared test to test on stratified 2 × 2 tables with a large‐sample approximation, we have been lacking an extension of Fisher's test for stratified exact testing. In this paper, we discuss an exact testing method for stratified 2 × 2 tables that is simplified to the standard Fisher's test in single 2 × 2 table cases, and propose its sample size calculation method that can be useful for designing a study with rare cell frequencies.     

FUNCTIONAL INNOVATIONS AND MORPHOLOGICAL DIVERSIFICATION IN PARROTFISH

The association between diversification and evolutionary innovations has been well documented and tested in studies of taxonomic richness but the impact that such innovations have on the diversity of form and function is less well understood. Using phylogenetically rigorous techniques, we investigated the association between morphological diversity and two design breakthroughs within the jaws of parrotfish. Similar intramandibular joints and other modifications of the pharyngeal jaws have evolved repeatedly in teleost fish and are frequently hypothesized to promote diversity. We quantified morphological diversity within six functionally important oral jaw traits using the Brownian motion rate of evolution to correct for phylogenetic and time‐related biases and compared these rates across clades that did and did not possess the intramandibular joint and the parrotfish pharyngeal jaw. No change in morphological diversity was associated with the pharyngeal jaw modification alone but rates of oral jaw diversification were up to 8× faster in parrotfish species that possessed both innovations. Interestingly, this morphological diversity may not have led to differential resource uses as available data suggest that members of this clade show remarkable homogeneity of diet.     

Chlamydomonas reinhardtii-expressed multimer of Bacteriocin LS2 potently inhibits the growth of bacteria

Bacteriocin LS2 was isolated from the Lactobacillus salivarius BGHO1 strain in 2012. Since then, its antibacterial activity has not been examined. Here, Chlamydomonas reinhardtii was used to express a C-terminal hemagglutinin (HA) and 6×His double tagged three repeats of Bacteriocin LS2 (3×Bacteriocin LS2). 3×Bacteriocin LS2 expression was stable following passaging in C. reinhardtii cells for six months and its yield accounted for 0.28% of total soluble proteins of the host cells. C. reinhardtii-derived 3×Bacteriocin LS2 inhibited the growth of four tested bacteria of both gram-positive and gram-negative with minimum inhibitory concentration (MIC) values between 75 and 90 μg/mL, indicating that this peptide is more potent than other bacteriocins like nesin and bacteriocin MA047A which have a MIC beyond 165 μg/mL in general. The recombinant 3×Bacteriocin LS2 maintained high stability over a wide range of temperature and pHs, showed tolerance to proteases, exhibited low hemolytic activity against rabbit erythrocytes and low cytotoxicity to human embryonic kidney 293 T (HEK 293 T) cells. In addition, C. reinhardtii-derived 3×Bacteriocin LS2 penetrated cell membranes and destroyed the morphology of targeted bacterial cells to different extents. In summary, our study shows that C. reinhardtii can be used as a platform for the production of active Bacteriocin LS2.     

Functional Similarities of Recombinant OLP and Cytokinin-Binding Protein 2

CBP1 and CBP2 are cytokinin-binding proteins isolated from tobacco callus. In particularly, CBP2 is a 26-kDa protein with high affinity (Kd=1.08×10^-6M) for cytokinin[Kobayashi et al. Plant Cell Physiol. 41(2): 148-157 (2000)] and the N-terminal amino acid analysis of CBP2 showed high sequence homology (92.9%) to tobacco osmotin-like protein (OLP). To compare the properties of OLP and CBP2, recombinant OLP was purified, and binding to benzyladenine (BA) was examined. The inclusion bodies of recombinant OLP were solubilized in 8 M urea and purified on an SP-Sepharose column. SDS-PAGE analysis of the purified recombinant OLP revealed a single band of 26 kDa. The Kd of solublized recombinant OLP to BA obtained from a Scachard plot was 1.10×10^-6M, which was similar to the Kd of CBP2 to BA (1.08×10^-6M).     

人β_2m转基因小鼠的制备及鉴定(英文)

 制备人 β2m转基因小鼠 ,研究HLA B2 70 4基因的表达 .应用显微注射将人 β2m基因注入C5 7BL 6×昆明鼠和昆明鼠×昆明鼠F1代受精卵 .出生动物及其后代经PCR筛选 ,采用斑点杂交和Southern杂交对阳性鼠基因组DNA标本进行进一步鉴定和测定整合拷贝数 ,利用RT PCR检测阳性鼠中人 β2m转基因的表达 .6只原代仔鼠及 7只它们的下一代鼠 (F1)带有人 β2m基因 .由微注射基因后移卵出生的 86只小鼠中 ,C5 7BL 6×昆明鼠杂交仔鼠 35只 ,其中 4只阳性 (11 4 % ) ,昆明鼠×昆明鼠杂交仔鼠 5 1只 ,其中 2只阳性 (3 9% ) ,含有人 β2m基因的原代鼠×昆明鼠杂交仔鼠 2 0只 ,其中 7只阳性 .整合的转基因均为单拷贝 .Southern杂交证实上述阳性鼠确有转基因整合 .阳性鼠的皮肤、结肠、睾丸和脾脏组织中均有人β2m转基因mRNA的表达 .在转基因动物制备中 ,C5 7BL 6×昆明鼠F1代明显优于昆明鼠×昆明鼠F1代 .与人HLA B2 70 4基因相比 ,人 β2m基因不易整合 ,其整合率与整合拷贝数均较低 .得到的人 β2m转基因小鼠能够将人 β2m基困传给下一代 ,并可与人HLA B2 70 4转基因鼠交配 ,研究它的致病性     

Statistical Inference For Risk Difference in an Incomplete Correlated 2 × 2 Table

In some infectious disease studies and 2‐step treatment studies, 2 × 2 table with structural zero could arise in situations where it is theoretically impossible for a particular cell to contain observations or structural void is introduced by design. In this article, we propose a score test of hypotheses pertaining to the marginal and conditional probabilities in a 2 × 2 table with structural zero via the risk/rate difference measure. Score test‐based confidence interval will also be outlined. We evaluate the performance of the score test and the existing likelihood ratio test. Our empirical results evince the similar and satisfactory performance of the two tests (with appropriate adjustments) in terms of coverage probability and expected interval width. Both tests consistently perform well from small‐ to moderate‐sample designs. The score test however has the advantage that it is only undefined in one scenario while the likelihood ratio test can be undefined in many scenarios. We illustrate our method by a real example from a two‐step tuberculosis skin test study.     

Differential frequency of NKG2C/<Emphasis Type="Italic">KLRC2</Emphasis> deletion in distinct African populations and susceptibility to Trachoma: a new method for imputation of <Emphasis Type="Italic">KLRC2</Emphasis> genotypes from SNP genotyping data

NKG2C is an activating receptor that is preferentially expressed on natural killer (NK) cells. The gene encoding NKG2C (killer cell lectin-like receptor C2, KLRC2) is present at different copy numbers in the genomes of different individuals. Deletion at the NKG2C locus was investigated in a case–control study of 1522 individuals indigenous to East- and West-Africa and the association with the ocular Chlamydia trachomatis infection and its sequelae was explored. The frequency of homozygous KLRC2 deletion was 13.7 % in Gambians and 4.7 % in Tanzanians. A significantly higher frequency of the deletion allele was found in West-Africans from the Gambia and Guinea-Bissau (36.2 % p = 2.105 × 10^?8, 26.8 % p = 0.050; respectively) in comparison to East-African Tanzanians where the frequency of the deletion is comparable to other human populations (20.9 %). We found no evidence for an association between the numbers of KLRC2 gene copies and the clinical manifestations of trachoma (follicular trachoma or conjunctival scarring). A new method for imputation of KLRC2 genotypes from single nucleotide polymorphism (SNP) data in 2621 individuals from the Gambia further confirmed these results. Our data suggest that NKG2C does not play a major role in trachomatous disease. We found that the deletion allele is present at different frequencies in different populations but the reason behind these differences is currently not understood. The new method offers the potential to use SNP arrays from genome wide association studies to study the frequency of KLRC2 deletion in other populations and its association with other diseases.     

Craniofacial abnormalities result from knock down of nonsyndromic clefting gene,crispld2, in zebrafish

Nonsyndromic cleft lip and palate (NSCLP), a common birth defect, affects 4,000 newborns in the US each year. Previously, we described an association between CRISPLD2 and NSCLP and showed Crispld2 expression in the murine palate. These results suggested that a perturbation in CRISPLD2 activity affects craniofacial development. Here, we describe crispld2 expression and the phenotypic consequence of its loss of function in zebrafish. crispld2 was expressed at all stages of zebrafish morphogenesis examined and localized to the rostral end by 1‐day postfertilization. Morpholino knockdown of crispld2 resulted in significant jaw and palatal abnormalities in a dose‐dependent manner. Loss of crispld2 caused aberrant patterning of neural crest cells (NCC) suggesting that crispld2 is necessary for normal NCC formation. Altogether, we show that crispld2 plays a significant role in the development of the zebrafish craniofacies and alteration of normal protein levels disturbs palate and jaw formation. These data provide support for a role of CRISPLD2 in NSCLP. genesis 50:871–881, 2012. © 2012 Wiley Periodicals, Inc.     

缙云山亚热带栲树林优势种群间联结性研究

本文根据2×2联列表,应用方差分析、X2统计量度量、Ochiai指数、Dice指数和Jaccard指数等系列技术,测定了四川缙云山栲树林的13个优势种群间的联结性。并以半矩阵、全矩阵和星座图等形式表达测定结果。研究表明,缙云山栲树林的种间联结测定使用上述系列技术效果很佳。运用方差分析可揭示出多物种整体间联结性,X2检验表示出各种对联结的显著性程度和性质,Ochiai指数、Dice指数和Jaccard指数标量出种对的联结程度和相伴随出现的机率。同时表明,缙云山栲树林种间联结较复杂,栲树(Castanopsis fargesii)与杜英(Elaeocarpus decipiens )间为极显著正联结,而与大头茶(Gordonia acuminata)间为极显著负联结,与小叶栲(Castanopsis carlesii var.spinulosa)间为显著负联结。表明亲缘关系较近、对环境要求相同、对环境反应相似的种群相伴随出现的机率较大,其联结的性质却不因此而定。     

Novel human sex-typing strategies based on the autism candidate gene NLGN4X and its male-specific gametologue NLGN4Y

The male predominance in the incidence of nasopharyngeal carcinoma (NPC) suggests the contribution of the X chromosome to the susceptibility of NPC. However, no X-linked susceptibility loci have been examined by genome-wide association studies (GWASs) for NPC by far. To understand the contribution of the X chromosome in NPC susceptibility, we conducted an X chromosome-wide association analysis on 1615 NPC patients and 1025 healthy controls of Guangdong Chinese, followed by two validation analyses in Taiwan Chinese (n = 562) and Malaysian Chinese (n = 716). Firstly, the proportion of variance of X-linked loci over phenotypic variance was estimated in the discovery samples, which revealed that the phenotypic variance explained by X chromosome polymorphisms was estimated to be 12.63% (non-dosage compensation model) in males, as compared with 0.0001% in females. This suggested that the contribution of X chromosome to the genetic variance of NPC should not be neglected. Secondly, association analysis revealed that rs5927056 in DMD gene achieved X chromosome-wide association significance in the discovery sample (OR = 0.81, 95% CI 0.73–0.89, P = 1.49 × 10−5). Combined analysis revealed rs5927056 for DMD gene with suggestive significance (P = 9.44 × 10−5). Moreover, the female-specific association of rs5933886 in ARHGAP6 gene (OR = 0.62, 95%CI: 0.47–0.81, P = 4.37 × 10−4) was successfully replicated in Taiwan Chinese (P = 1.64 × 10−2). rs5933886 also showed nominally significant gender × SNP interaction in both Guangdong (P = 6.25 × 10−4) and Taiwan datasets (P = 2.99 × 10−2). Our finding reveals new susceptibility loci at the X chromosome conferring risk of NPC and supports the value of including the X chromosome in large-scale association studies.     

Confirming therapeutic target of protopine using immobilized β2‐adrenoceptor coupled with site‐directed molecular docking and the target‐drug interaction by frontal analysis and injection amount–dependent method

Drug‐protein interaction analysis is pregnant in designing new leads during drug discovery. We prepared the stationary phase containing immobilized β₂‐adrenoceptor (β ₂‐ AR) by linkage of the receptor on macroporous silica gel surface through N ,N ′‐carbonyldiimidazole method. The stationary phase was applied in identifying antiasthmatic target of protopine guided by the prediction of site‐directed molecular docking. Subsequent application of immobilized β ₂‐ AR in exploring the binding of protopine to the receptor was realized by frontal analysis and injection amount–dependent method. The association constants of protopine to β ₂‐ AR by the 2 methods were (1.00 ± 0.06) × 10⁵M⁻¹ and (1.52 ± 0.14) × 10⁴M⁻¹. The numbers of binding sites were (1.23 ± 0.07) × 10⁻⁷M and (9.09 ± 0.06) × 10⁻⁷M, respectively. These results indicated that β ₂‐ AR is the specific target for therapeutic action of protopine in vivo. The target‐drug binding occurred on Ser¹⁶⁹ in crystal structure of the receptor. Compared with frontal analysis, injection amount–dependent method is advantageous to drug saving, improvement of sampling efficiency, and performing speed. It has grave potential in high‐throughput drug‐receptor interaction analysis.     

缙云山风灾迹地恢复群落主要乔木树种种间联结性

应用方差比率法,并通过2×2列联表χ2检验法及利用联结系数AC指数测定法研究了缙云山自然保护区风灾迹地恢复群落自然恢复样地和人工恢复样地中主要乔木树种的种间联结性。结果表明:(1)自然恢复样地主要乔木种群间在总体上呈一定的正关联;而人工恢复样地种群间在总体上呈负关联;(2)2×2列联表的χ2检验共有5个(3)种对为显著正关联(括号内为人工恢复群落的种对数,下同),2个(1)种对为显著负关联;(3)联结系数(AC)指数标量出了自然恢复和人工恢复样地中种对间的联结程度和相伴随出现的机率,两种恢复方式中的多数乔木种群间的联结性不显著且联结程度较低,绝大多数乔木树种之间无显著关联,而且人工恢复比自然恢复无关联性更强;(4)种对间的正关联,主要是由于它们具有相近的生物学特性以及对生境具有相似的生态适应性所致,种对间的负关联主要是由于物种间的空间排斥,适应不同的微环境的结果;(5)人工恢复和自然恢复所在的群落处于演替的不稳定阶段。