Robust inference for the stepped wedge design

Stepped wedge designed trials are a type of cluster-randomized study in which the intervention is introduced to each cluster in a random order over time. This design is often used to assess the effect of a new intervention as it is rolled out across a series of clinics or communities. Based on a permutation argument, we derive a closed-form expression for an estimate of the intervention effect, along with its standard error, for a stepped wedge design trial. We show that these estimates are robust to misspecification of both the mean and covariance structure of the underlying data-generating mechanism, thereby providing a robust approach to inference for the intervention effect in stepped wedge designs. We use simulations to evaluate the type 1 error and power of the proposed estimate and to compare the performance of the proposed estimate to the optimal estimate when the correct model specification is known. The limitations, possible extensions, and open problems regarding the method are discussed.     

地黄SCoT分子标记体系的建立和指纹图谱的构建

该研究采用L_(25)(5~6)正交设计和单因素两种方法,对影响地黄SCoT-PCR反应的5个因素(模板DNA浓度,引物浓度,ddH_2O和Mix的用量以及退火温度)进行了优化。结果表明:优化后的反应体系总体积为25μL,含有8μL ddH_2O,1μL模板DNA(80 ng·μL~(-1)),1μL引物(8μmol·L~(-1))和15μL Mix,退火温度为45℃。运用30份地黄种质材料,对优化的SCoT-PCR正交体系进行多次重复验证,获得了多态性丰富、条带清晰的扩增图谱,证明该反应体系稳定可靠。利用该体系对32条SCoT引物进行两次筛选,得到14个扩增产物清晰、重复性好且多态性条带相对较高的引物。利用SCoT_4等5条引物构建了上述地黄2个种共30份种质的SCoT指纹图谱。利用这5个SCoT引物指纹图谱可将7个地黄常用栽培品种区分开。这表明SCoT分子标记体系适用于地黄主要品种亲缘关系及遗传多样性的研究,所构建的指纹图谱也为地黄常见的7个栽培品种的区分提供参考依据。     

微卫星标记在大熊猫研究中的应用进展

大熊猫是我国保护最为成功、研究最为深入的珍稀动物之一,可以为其它珍稀濒危物种的保护研究工作提供参考。20世纪70年代末期借助无线电颈圈,大熊猫的生态学研究工作取得了突破性进展,近20年来微卫星标记和非损伤性遗传取样技术的联合使用,将大熊猫的保护研究工作提升到一个崭新的高度。本文在综合所有已发表大熊猫微卫星标记的基础上,梳理了微卫星标记在圈养大熊猫亲子鉴定与遗传管理,野生大熊猫个体识别与种群数量调查、遗传多样性评估、扩散和种群遗传结构研究中的应用情况,并着重介绍了其中29个重要的微卫星标记。同时指出目前微卫星标记的使用存在标记选择不统一、等位基因读数无统一规程等问题,并对应用前景进行了前瞻。     

Female and male Texas cichlids (Herichthys cyanoguttatum) do not fight by the same rules

Selection usually acts differently on males and females duringintrasexual competition for resources and/or mates. Nevertheless,agonistic behavior has been examined both theoretically andempirically mostly in males. Our research questions whethermales and females follow the same rules of engagement in intrasexualcontests as predicted by the sequential assessment model (SAM).The SAM predicts negative correlations between contest intensityand duration and the magnitude of asymmetry in resource holdingpower (RHP) between the contestants, such that the most escalatedcontests are those between similarly endowed individuals. Westaged male and female intrasexual contests with varying degreesof body size asymmetry under a round robin design using themonogamous Texas cichlid fish (Herichthys cyanoguttatum) asa study case. We used Mantel's matrix analysis to compare howthe behavioral content, duration, structure, and outcome ofmale and female contests were affected by the relative bodysize of the contestants. In the case of males, relative sizein each contest predicted outcome, duration, and frequency ofconventional and escalated behaviors according to prevailingtheory. Female contest structure and outcome, however, werenot predicted by the relative size of contestants. We discussour results in terms of other asymmetries that might be importantin structuring female contests, and we propose potential approachesto study female–female aggression.     

Comparison of two different stool antigen tests for the primary diagnosis of Helicobacter pylori infection in turkish patients with dyspepsia

AIM: To assess the reliability of two different enzyme immunoassays in detecting the Helicobacter pylori status in stool specimens of Turkish patients with dyspepsia. MATERIALS AND METHODS: One hundred and fifty-one patients [74 with nonulcer dyspepsia (NUD), 64 with duodenal ulcer (DU) and 13 with gastric cancer] who were admitted to the endoscopy unit of Istanbul University, Cerrahpasa Medical Faculty for upper gastrointestinal endoscopy because of dyspepsia were enrolled in the study. Helicobacter pylori infection was confirmed in all patients by histology, rapid urease test and culture. A patient was classified as being H. pylori-positive if the culture alone or both the histology and the rapid urease test were positive and as negative only if all of these tests remained negative. Stool samples were obtained from patients to assess the reliability of a monoclonal (FemtoLab H. pylori) and a polyclonal (Premier Platinum HpSA) stool antigen test and to compare the diagnostic accuracies of these two tests. A chi2 test was used for statistical comparisons. RESULTS: Using cut-off values of 0.19 for FemtoLab H. pylori and 0.16 for Premier Platinum HpSA, the sensitivity, specificity, positive predictive value, negative predictive value and diagnostic accuracy were 93%, 90%, 98%, 68% and 93% for the monoclonal test and 84%, 67%, 94%, 40% and 81% for the polyclonal test, respectively. The sensitivity, specificity, negative predictive value and diagnostic accuracy of the monoclonal test were significantly greater than those of the polyclonal test (chi2 = 3.98; p < .05 for sensitivity and chi2 = 15.67; p = .000 for specificity, chi2 = 15.78; p = .000 for negative predictive value and chi2 = 6.37; p = .012 for diagnostic accuracy). The bacterial load did not affect the sensitivity of either test. CONCLUSIONS: The monoclonal FemtoLab H pylori test, using a cut-off 0.19, is a very sensitive, specific and easy to perform diagnostic tool for the primary diagnosis of H. pylori infection in Turkish patients with dyspepsia.     

家畜试验中的一种相关扰动回归模型

本文根据数量遗传学原理,从家畜群体中同一家系内的个体之间存在的遗传相关性出发,建立了扰动项相关的回归模型,运用回归理论讨论一类相关样本的统计推断及其应用。     

Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences

DNA replication in vertebrate mitochondria is usually directional, leaving different portions of the genome single-stranded for different periods of time. During this time, mutations resulting from deaminations of cytosines to thymines and adenines to guanines accumulate on the heavy strand. Therefore, T/C and G/A ratios increase along mitochondrial genomes, proportionally to the time spent single-stranded during replication. Such trends exist at third codon positions for base ratios averaged across genes in individual genomes as well as for gene-specific and site-specific substitution frequencies estimated using phylogenetic methods. We use multiple regressions to test for the potential functioning of all 12 tRNA clusters in 19 primate mitochondrial genomes as alternative origins of light strand replication (OL). We provide a general algorithm for calculating time spent single stranded by a given site for any possible locations of the site and OL. For codon positions 1, 2, and 3, respectively, 23%, 9% and 35% of tRNA gene clusters have significant (p < 0.05) deamination gradients originating from them. The strength of the deamination gradient originating from tRNA gene clusters varies among species, and for five clusters, correlates with the tendency of tRNA genes in each of these clusters to form secondary structures that resemble the OL's structure. This is notably true for all codon positions for tRNA-Lys, which in absence of nuclear regulation, forms secondary structures resembling the hairpin structure of OL. For two tRNA gene clusters, correlations were statistically significant, but opposite to the direction expected by the known unidirectional replication, putatively compatible with bi-directional replication. Few substitutions in tRNA sequences can be neutral at the level of cloverleaf structure and function, yet significantly alter capacities to form OL-like structures, causing sudden evolution of genome-wide nucleotide contents.     

Construction of a sensitive pyrogen-testing cell model by site-specific knock-in of multiple genes

A pyrogen test is crucial for evaluating the safety of drugs and medical equipment, especially those involved in injections. As existing pyrogen tests, including the rabbit pyrogen test, the limulus amoebocyte lysate (LAL) test and the monocyte activation test have limitations, development of new models for pyrogen testing is necessary. Here we develop a sensitive cell model for pyrogen test based on the lipopolysaccharides (LPS) signal pathway. TLR4, MD2, and CD14 play key roles in the LPS-mediated pyrogen reaction. We established a new TLR4/MD2/CD14-specific overexpressing knock-in cell model using the CRISPR/CAS9 technology and homologous recombination to detect LPS. Stimulation of our TLR4/CD14/MD2 knock-in cell line model with LPS leads to the release of the cytokines IL-6 and TNF-alpha, with a detection limit of 0.005 EU/ml, which is greatly lower than the lower limit of 0.015 EU/ml detected by the Tachypleus amebocyte lysate (TAL) assay.