THE EFFECT OF UNMEASURED CONFOUNDERS ON THE ABILITY TO ESTIMATE A TRUE PERFORMANCE OR SELECTION GRADIENT (AND OTHER PARTIAL REGRESSION COEFFICIENTS)

Multiple regression of observational data is frequently used to infer causal effects. Partial regression coefficients are biased estimates of causal effects if unmeasured confounders are not in the regression model. The sensitivity of partial regression coefficients to omitted confounders is investigated with a Monte‐Carlo simulation. A subset of causal traits is “measured” and their effects are estimated using ordinary least squares regression and compared to their expected values. Three major results are: (1) the error due to confounding is much larger than that due to sampling, especially with large samples, (2) confounding error shrinks trivially with sample size, and (3) small true effects are frequently estimated as large effects. Consequently, confidence intervals from regression are poor guides to the true intervals, especially with large sample sizes. The addition of a confounder to the model improves estimates only 55% of the time. Results are improved with complete knowledge of the rank order of causal effects but even with this omniscience, measured intervals are poor proxies for true intervals if there are many unmeasured confounders. The results suggest that only under very limited conditions can we have much confidence in the magnitude of partial regression coefficients as estimates of causal effects.     

Chromosome Studies of 10 Species of Aconitum in China

This paper deals with chromosomal numbers and morphology of 10 species of Aconitum in China. According to the basic number of the genus (x=8), these species can be referred to diploid, tetraploid, hexaploid and octoploid. Correlation is found between chromosomal numbers, sizes and structures. The perennial species with a rhizome are mostly diploid, with chromosomes larger than those in the biennial species with a tuber, and their chromosome pairs 3-7 are mostly subterminal ones, whereas most biennial species are polyploid, and their chromosome pairs 3-7 are almost submetacentric. The evolutionary trends of chromosome from diploid to polyploid, large to small, st to sm are considered possible. The data are agreed with the idea that rhizomal species are more primitive than tuberous ones. The existence of two types of karyotypes in these 10 species is a further support of taxonomic division of two subgenera, subgen. Paraconitum and subgen. Aconitum. In addition, some species are taxonomically discussed.     

一种基于Wilson-Cowan双节点耦合振子模型的图像增强方法

针对模拟大脑节律现象的Wilson-Cowan双节点耦合振子模型,选取满足该模型产生极限环振荡条件的参数,采用连续灰度阶图像块作为输入,兴奋性亚群节点响应作为图像增强的输出,做出刺激响应曲线,发现该曲线与图像处理领域中用于图像增强的Gamma校正曲线相似,说明Wilson-Cowan双节点耦合振子模型可以作为一种新的图像增强方法,同时也为基于Gamma校正曲线的图像增强提供了一种神经机制。将新方法与Retinex算法做对比,表现出了更好的图像增强性能。     

The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific to H. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Two cdc6 genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H(2)S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-type cas gene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment.     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

Educational Degrees and Adult Mortality Risk in the United States

We present the first published estimates of U. S. adult mortality risk by detailed educational degree, including advanced postsecondary degrees. We use the 1997–2002 National Health Interview Survey (NHIS) Linked Mortality Files and Cox proportional hazards models to reveal wide graded differences in mortality by educational degree. Compared to adults who have a professional degree, those with an MA are 5 percent, those with a BA are 26 percent, those with an AA are 44 percent, those with some college are 65 percent, high school graduates are 80 percent, and those with a GED or 12 or fewer years of schooling are at least 95 percent more likely to die during the follow-up period, net of sociodemographic controls. These differentials vary by gender and cohort. Advanced educational degrees are associated not only with increased workforce skill level but with a reduced risk of death.     

Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins

The prediction of protein 3D structures close to insertions and deletions or, more generally, loop prediction, is still one of the major challenges in homology modeling projects. In this article, we developed ranking criteria and selection filters to improve knowledge-based loop predictions. These criteria were developed and optimized for a test data set containing 678 insertions and deletions. The examples are, in principle, predictable from the used loop database with an RMSD < 1 A and represent realistic modeling situations. Four noncorrelated criteria for the selection of fragments are evaluated. A fast prefilter compares the distance between the anchor groups in the template protein with the stems of the fragments. The RMSD of the anchor groups is used for fitting and ranking of the selected loop candidates. After fitting, repulsive close contacts of loop candidates with the template protein are used for filtering, and fragments with backbone torsion angles, which are unfavorable according to a knowledge-based potential, are eliminated. By the combined application of these filter criteria to the test set, it was possible to increase the percentage of predictions with a global RMSD < 1 A to over 50% among the first five ranks, with average global RMSD values for the first rank candidate that are between 1.3 and 2.2 A for different loop lengths. Compared to other examples described in the literature, our large numbers of test cases are not self-predictions, where loops are placed in a protein after a peptide loop has been cut out, but are attempts to predict structural changes that occur in evolution when a protein is affected by insertions and deletions.     

拟除虫菊酯类杀虫剂对蜜蜂的毒性和影响

蜜蜂是最重要的农业授粉昆虫之一,蜜蜂在授粉过程中极有可能接触到广泛使用的广谱杀虫剂-拟除虫菊酯,大多数拟除虫菊酯对蜜蜂等农业授粉昆虫有较高的毒性.本文对拟除虫菊酯类杀虫剂的作用机理进行了综述;总结了蜂群及蜂产品中拟除虫菊酯类杀虫剂的残留现状、拟除虫菊酯对蜜蜂的急性毒性以及亚致死效应,讨论了拟除虫菊酯类杀虫剂复配农药对蜜...     

红褐斑腿蝗血细胞的形态与分类

利用光学显微镜和显微数码拍照系统,对红褐斑腿蝗Catantops pinguis(Stal)血细胞的形态进行观察和分类。结果在红褐斑腿蝗血淋巴中观察到5种血细胞,分别是原血胞、浆血胞、粒血胞、珠血胞和囊血胞。原血胞为小型圆形细胞,边缘圆滑、清晰,核质比例很大。粒血胞多为中型,形状不规则,边缘凹突不平,内含较大的异质性溶酶体颗粒。浆血胞多为中型,刚离体时形状较规则,常呈圆形、卵圆形。浆血胞内缺乏大的颗粒,细胞核大而圆形,细胞质内具许多小型颗粒状物质。浆血胞离体后形状变化较多,常发展出伪足,呈丝状、短芒状、钩状或片状伪足。珠血胞多为大、中型,外形大体呈圆形,但边缘由于大小不等的珠形内含物突出,呈花瓣状。囊血胞多为中型,圆形或椭圆形,细胞质内具有大小不一的带有折光性的颗粒或块状物,细胞边缘比较光滑。     

Postcanine dental form in the mustelidae and viverridae (Carnivora: Mammalia)

This study investigates whether the gross morphology of mustelid and viverrid postcanine dentitions corresponds with differences in diet. For each species, the predominant foods ingested are used to form predictions of dental form and measurements of the carnassial and molar teeth determine the extent of shearing and crushing surfaces on the postcanine teeth. Principal components analysis distinguishes species according to morphological differences in the dentition and these differences are compared with predictions of dental form based on diet. Dietarily specialized species are more likely to be correspondingly specialized in the dentition and species with varied food sources are more likely to possess dental characteristics that are generalized in function. Consumers of foods with high fracture resistance, such as vertebrate tissue and hard-surfaced invertebrates, possess specialized shearing or crushing postcanine teeth. On the other hand, species that consume foods of lesser fracture resistance, such as fruit and soft invertebrates, differ greatly in dental form and are more generalized in dental function. A few species possess postcanine dentitions that do not correspond with diet; the absence of dental-dietary correlation in these species suggests that other factors, such as phylogeny, are important in determining dental form.     

Book Reviews

Abstract

A study of the attitudes and actions of 281 dog owners towards neutering their animals is reported from New Providence, The Bahamas. Owner attitudes towards neutering are associated with different sterilization rates of dogs. While owners' gender is associated with differences in attitudes, these differences are not necessarily associated with owner behavior with respect to neutering their animals. Men, more than women, want to have animals for long-term breeding. No evidence is found to support the belief that men are less likely to neuter their dogs than women, but younger owners are less likely than older owners to neuter their dogs. A comparison with a study from Australia suggests that Bahamians are more likely to project human traits on to their animals and so appear more reluctant to have their dogs neutered.     

Electron microscopy morphology of the mitochondrial network in human cancer

Mitochondria have been implicated in the process of carcinogenesis, which includes alterations of cellular metabolism and cell death pathways. The aim of this review is to describe and analyze the electron microscopy morphology of the mitochondrial network in human cancer. The structural mitochondrial alterations in human tumors are heterogeneous and not specific for any neoplasm. These findings could be representing an altered structural and functional mitochondrial network. The mitochondria in cancer cells, independently of histogenesis, predominantly are seen with lucent-swelling matrix associated with disarrangement and distortion of cristae and partial or total cristolysis and with condensed configuration in minor scale. Mitochondrial changes are associated with mitochondrial-DNA mutations, tumoral microenvironment conditions and mitochondrial fusion–fission disequilibrium. Functionally, the structural alterations suppose the presence of hypoxia-tolerant and hypoxia-sensitive cancer cells. Possibly, hypoxia-tolerant cells are related with mitochondrial condensed appearance and are competent to produce adequate amount of ATP by mitochondrial respiration. Hypoxia-sensitive cells are linked with lucent-swelling and cristolysis mitochondria profile and have an inefficient or null oxidative phosphorylation, which consequently use the glycolytic pathway to generate energy. Additionally, mitochondrial fragmentation is associated with apoptosis; however, alterations in the mitochondrial network are linked with the reduction in sensitivity to apoptosis induces and/or pro-apoptotic conditions. Pharmacological approaches designed to act on both glycolysis and oxidative phosphorylation can be considered as a new approach to selectively kill cancer cells.     

安徽珍稀濒危植物区系探讨

在深入调查的基础上,对安徽珍稀濒危植物区系组成和地理成分进行了详细的统计分析,探讨了该区系的组成特点及地理分布特征。结果表明,该区系属温带亚热带性植物区系,具有珍稀濒危物种丰富,古老、孑遗植物众多;地理成分复杂,区系联系广泛;过渡性质明显,温带亚热带成分占优;特有现象显著,华东区系特征典型等基本特征。在植物区系亲缘上,该区系隶属东亚植物区、中国-日本森林植物亚区、华东地区,与华中植物区系关系密切,受西南植物区系影响深刻。     

Associations between lycaenid butterflies and ants in Australia

A comprehensive and critical review of all available literature on associations between Australian lycaenid butterflies and ants was undertaken to establish an accurate database of the partners involved. Collections and observations of lycaenids and ants were used to augment this review, resulting in a significant number of newly documented association (and non-association) records. Twenty published records considered to be erroneous or doubtful are noted, with justifications given for their deletion from the association database. In total, 265 different associations between lycaenids and ants, plus 65 non-attendance records are documented for Australia. Nearly 80% of the lycaenid species in Australia, for which the early stages are known, are recorded associating with ants and half of these are obligately ant-associated. Patterns of association are examined from the perspective of both lycaenids and ants, with a focus on ant systematics and ecology. Lycaenids are recorded with five ant subfamilies, including the first record of an association with the Pseudomyrmecinae. The Dolichoderinae, and to some extent the Formicinae, have a disproportionately high percentage of genera that associate with lycaenid butterflies. All ant species that tend lycaenids spend at least some portion of their time foraging on vegetation to collect plant and insect nectar. There is a robust relationship between the competitive status of ants within a community, and their frequency and degree of association with lycaenids. Obligate ant-association is accompanied by a high degree of specificity for ant partner, but two notable exceptions, Ogyris aenone and O. amaryllis are discussed. Facultative myrmecophiles tend to associate with a broad range of ants, although interactions with ecologically dominant ants are less frequent than might be expected based on the abundance of dominant ant species in Australian communities.     

Microarray analysis: basic strategies for successful experiments

Microarrays offer a powerful approach to the analysis of gene expression that can be used for a wide variety of experimental purposes. However, there are several types of microarray platforms that are available. In addition, microarray experiments are expensive and generate complicated data sets that can be difficult to interpret. Success with microarray approaches requires a sound experimental design and a coordinated and appropriate use of statistical tools. Here, the advantages and pitfalls of utilizing microarrays are discussed, as are practical strategies to help novice users succeed with this method that can empower them with the ability to assay changes in gene expression at the whole genome level.     

Peculiar Epibionts in Euplotidium itoi (Ciliata, Hypotrichida)

ABSTRACT. Euplotidium itoi share with some other species of the same genus a peculiar feature: the presence of a band of particles running along the right and left borders of the cell body and forming a sort of "scarf" at the dorsal anterior end. The ultrastructural analysis, here performed, revealed that these particles (reported in the literature as extrusomes) are always external to the cell and are inserted in matching depressions on the euplotidium cortex. They are present in two different forms: type I, whose ultrastructure recalls that of bacteria, are able to reproduce by binary fission; type II are not able to divide and contain peculiar structures (a granular dome-shaped zone, a complex extrusive apparatus and a network of regularly arranged fibrils) which render them more complicated with respect to the majority of prokaryotic organisms. These observations, together with the finding that these particles contain DNA, indicate that we are dealing with epibionts, that will be referred to as "epixenosomes" (ecto-organisms), rather than extrusomes. Some ideas about the nature of "epixenosomes" and their relationship with the host cell are proposed and discussed.     

Macrolepidoptera diversity in the Indo-Australian tropics: geographic, biotopic and taxonomic variations

Data are presented on the richness of Macrolepidoptera faunas in the Indo-Australian tropics, and on the proportional representation of the various families. Both overall diversity and diversity of families decline with latitude and also with isolation from major land areas. Exceptions are noted.
Measures of alpha-diversity from quantitative light-trap samples indicate that diversity within the tropics is often greatest at altitudes around 1000 m, declining above that level. Diversity is much lower in Pacific archipelagos. Loss of diversity through disturbance and conversion to agriculture is evident and marked. Problems in the measurement of diversity with light-traps are discussed, exemplified by results obtained using different trap types.
Changes in family proportions with habitat type are examined. Family diversity generally decreased with altitude and with disturbance and conversion to agriculture, though there are exceptions to this decline.     

THE MAINTENANCE OF GYNODIOECY AND ANDRODIOECY IN A METAPOPULATION

Males and females are at a selective disadvantage relative to hermaphrodites (cosexuals) in species with a colonizing habit, as only cosexuals are able to establish new colonies on their own. The implications of this disadvantage are assessed by means of a computer model of metapopulation dynamics, in which individual colonies are established through different rates of immigration and suffer different rates of local extinction. Results are given for simulations of an island model, a stepping-stone model, and for a partial analysis of the island model with simplifying assumptions. It is shown that: (1) unisexual frequencies in a metapopulation can be reasonably approximated by a linear function of the logarithm of the ratio of the immigration rate to the colony extinction rate; (2) metapopulation dynamics favor the maintenance of females (gynodioecy) over males (androdioecy) with cosexuals when they would otherwise be equally likely in a panmictic situation; (3) the way in which extinction and immigration rates affect unisexual frequencies at metapopulation equilibrium interacts with whether sterility is determined by a dominant or a recessive allele; and (4) unisexual frequencies are affected in a qualitatively similar way by the dynamics of a metapopulation when cosexuals are self-incompatible to when they are self-compatible, although only in the former case are high frequencies of unisexuals maintained when extinction and colonization rates approach the threshold at which the metapopulation goes extinct. These results are discussed with reference to existing data from species with nuclear male or female sterility.