Nominal Data And Factor Analysis: A Comment On Geier

Abstract

Use of nominally coded data in a factor analysis is incorrect. This paper first critiques a recent Plains Anthropologist article incorrectly using nominal data, and then provides a comparative example to illustrate the problem. Several alternatives are discussed briefly.     

新一代高通量RNA测序数据的处理与分析

随着新一代高通量DNA测序技术的快速发展,RNA测序(RNA-seq)已成为基因表达和转录组分析新的重要手段．RNA-seq技术产生的海量数据为生物信息学带来了新的机遇和挑战．有效地对测序数据进行针对性的生物信息学处理和分析,成为RNA-seq技术能否在科学探索中发挥重大作用的关键．以新一代Illumina/Solexa测序平台所产生的数据为例,在扼要介绍高通量RNA-seq测序流程的基础上,对RNA-seq数据处理和分析的方法和现有软件做一个较为全面的综述,并对其中有待进一步研究的问题进行展望．     

The Role of Visual Ornamentation in Female Choice of a Multimodal Male Courtship Display

The courtship behavior of male Schizocosa uetzi wolf spiders incorporates both visual and seismic signals into a multimodal display. These two signals have been shown to interact in such a manner that the seismic signal alters a female's response to the visual signal, leading to a putative increased importance of visual signaling in the presence of a seismic signal. Experiments leading to this attention‐focusing hypothesis relied in part on the video playback technique, eliciting the question of its significance under more biologically relevant conditions. Here, we directly examine female mate choice of males with differing visual signals (foreleg pigmentation) both in the presence and absence of a seismic courtship signal. We first quantified the natural variation of male foreleg pigmentation within a population of S. uetzi. The proportion of the tibia covered in pigmentation was found to be positively correlated with male weight, suggesting that this signal may convey reliable information about male size. Visual signals of live males were then manipulated into two treatments: black and brown male foreleg tibias, representing the extreme ends of the natural variation found. The seismic signaling environment was also manipulated into two treatments: seismic signal present and absent. Mating frequency was higher in the presence of a seismic signal than in its absence, but there was no interaction between the seismic and visual signaling treatments. Females mated with black and brown males equally whether a seismic signal was present or absent. This study suggests that inexperienced females do not distinguish between males of different manipulated foreleg pigmentations in mate‐choice decisions, even when in the presence of a seismic courtship signal.     

Applications of the Repeatability of Quantitative Imaging Biomarkers: A Review of Statistical Analysis of Repeat Data Sets

Repeat imaging data sets performed on patients with cancer are becoming publicly available. The potential utility of these data sets for addressing important questions in imaging biomarker development is vast. In particular, these data sets may be useful to help characterize the variability of quantitative parameters derived from imaging. This article reviews statistical analysis that may be performed to use results of repeat imaging to 1) calculate the level of change in parameter value that may be seen in individual patients to confidently characterize that patient as showing true parameter change, 2) calculate the level of change in parameters value that may be seen in individual patients to confidently categorize that patient as showing true lack of parameter change, 3) determine if different imaging devices are interchangeable from the standpoint of repeatability, and 4) estimate the numbers of patients needed to precisely calculate repeatability. In addition, we recommend a set of statistical parameters that should be reported when the repeatability of continuous parameters is studied.     

A Brief Review: The Z-curve Theory and its Application in Genome Analysis

In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.     

Malaria Diagnosis: A Brief Review

Malaria is a major cause of death in tropical and sub-tropical countries, killing each year over 1 million people globally; 90% of fatalities occur in African children. Although effective ways to manage malaria now exist, the number of malaria cases is still increasing, due to several factors. In this emergency situation, prompt and effective diagnostic methods are essential for the management and control of malaria. Traditional methods for diagnosing malaria remain problematic; therefore, new technologies have been developed and introduced to overcome the limitations. This review details the currently available diagnostic methods for malaria.     

Role of the Liver in Regulation of Body Cysteine and Taurine Levels: A Brief Review

The first-pass metabolism of dietary sulfur amino acids by the liver and the robust upregulation of hepatic cysteine dioxygenase activity in response to an increase in dietary protein or sulfur amino acid level gives the liver a primary role in the removal of excess cysteine and in the synthesis of taurine. Hepatic taurine synthesis is largely restricted by the low availability of cysteinesulfinate as substrate for cysteinesulfinate decarboxylase, and taurine production is increased when cysteinesulfinate increases in response to an increase in the hepatic cysteine concentration and the associated increase in cysteine dioxygenase activity. The upregulation of cysteine dioxygenase in the presence of cysteine is a consequence of diminished ubiquitination of cysteine dioxygenase and a slower rate of degradation by the 26S proteasome.     

Conservation of Grassland Leafhoppers: A Brief Review

The leafhoppers, planthoppers and their allies (collectively known as the Auchenorrhyncha) are presented as a group of insects that are highly appropriate for studying grassland ecology and conservation, evaluating the conservation status of sites and monitoring environmental and habitat change. Semi-natural grasslands typically support dense populations and a wide range of species with diverse ecological strategies. Their numerical dominance in many grasslands means that they have considerable functional significance, both as herbivores and as prey for higher trophic levels. Population and assemblage studies are supported by good ecological knowledge about most species and modern identification keys. Hitherto, most studies have focused on the composition and structure of assemblages and how they are affected by conservation management. However, grasslands support many rare species with small and fragmented populations which deserve conservation attention in their own right, and recent work has started to reflect this. The effects of management on the composition and structure of grassland leafhopper populations and assemblages are described and an assessment is given of the main threats facing individual species and overall diversity. There is a need to synthesise the scattered literature on grassland leafhoppers, to provide a model for how the composition and structure of populations and assemblages respond to major environmental and anthropogenic gradients across large biogeographic areas. Such an analysis could help predict the impact of likely future changes in land use and climate.