Electrophoresis gel image processing and analysis using the KODAK 1D software.

The present article reports on the performance of the KODAK 1D Image Analysis Software for the acquisition of information from electrophoresis experiments and highlights the utility of several mathematical functions for subsequent image processing, analysis, and presentation. Digital images of Coomassie-stained polyacrylamide protein gels containing molecular weight standards and ethidium bromide stained agarose gels containing DNA mass standards are acquired using the KODAK Electrophoresis Documentation and Analysis System 290 (EDAS 290). The KODAK 1D software is used to optimize lane and band identification using features such as isomolecular weight lines. Mathematical functions for mass standard representation are presented, and two methods for estimation of unknown band mass are compared. Given the progressive transition of electrophoresis data acquisition and daily reporting in peer-reviewed journals to digital formats ranging from 8-bit systems such as EDAS 290 to more expensive 16-bit systems, the utility of algorithms such as Gaussian modeling, which can correct geometric aberrations such as clipping due to signal saturation common at lower bit depth levels, is discussed. Finally, image-processing tools that can facilitate image preparation for presentation are demonstrated.     

A comprehensive and user-friendly framework for 3D-data visualisation in invertebrates and other organisms

Methods for 3D-imaging of biological samples are experiencing unprecedented development, with tools such as X-ray micro-computed tomography (μCT) becoming more accessible to biologists. These techniques are inherently suited to small subjects and can simultaneously image both external and internal morphology, thus offering considerable benefits for invertebrate research. However, methods for visualising 3D-data are trailing behind the development of tools for generating such data. Our aim in this article is to make the processing, visualisation and presentation of 3D-data easier, thereby encouraging more researchers to utilise 3D-imaging. Here, we present a comprehensive workflow for manipulating and visualising 3D-data, including basic and advanced options for producing images, videos and interactive 3D-PDFs, from both volume and surface-mesh renderings. We discuss the importance of visualisation for quantitative analysis of invertebrate morphology from 3D-data, and provide example figures illustrating the different options for generating 3D-figures for publication. As more biology journals adopt 3D-PDFs as a standard option, research on microscopic invertebrates and other organisms can be presented in high-resolution 3D-figures, enhancing the way we communicate science.     

数据挖掘在生物信息学中的应用——文献计量学视角

基因组和蛋白质结构与功能方面已积累了海量数据。如何从海量数据中获取有效信息成为生物信息学迫切要解决的问题。本文以相关主题词检索文献,分析了该领域历年文章数量、发文最多的机构和作者、被引用频次居前论文、期刊载文量,并对关键词和被引用频次居前论文的作者进行共现分析。我们发现,生物信息学中运用数据挖掘方法的文献逐年增多,该领域30.1%的文献发表在十个期刊上,分类、聚类、特征选择和支持向量机等数据挖掘方法使用较多。本研究描绘了生物信息学与数据挖掘这一交叉领域的研究概况,为后续数据挖掘方法与生物信息学研究相结合提供帮助。     

Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm

Figures in scientific publications are critically important because they often show the data supporting key findings. Our systematic review of research articles published in top physiology journals (n = 703) suggests that, as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies. Papers rarely included scatterplots, box plots, and histograms that allow readers to critically evaluate continuous data. Most papers presented continuous data in bar and line graphs. This is problematic, as many different data distributions can lead to the same bar or line graph. The full data may suggest different conclusions from the summary statistics. We recommend training investigators in data presentation, encouraging a more complete presentation of data, and changing journal editorial policies. Investigators can quickly make univariate scatterplots for small sample size studies using our Excel templates.     

动物栖息地选择评估的常用统计方法

利用合适的统计学方法能够更准确地理解动物的栖息地选择。本文通过对2003~2012年期间,10个国际期刊所发表的177篇关于鸟类和兽类栖息地选择论文的30种统计学方法进行分析,简要概述了目前流行的栖息地选择统计学分析方法及特点,同时对同时期的中文文献也进行了简要分析。目前关于动物栖息地选择较为流行的分析方法主要有逻辑斯蒂回归、资源选择函数、成分分析、广义线性模型、多元方差分析、基于欧几里德距离的方法、广义线性混合模型、生态位因子分析、基于个体模型、典型相关分析、物种分布模型等。广义线性模型、逻辑斯蒂回归、多元方差分析和基于欧几里德距离这些方法可以很灵活地用来分析数据,但是缺乏一个有生态学意义的理论框架。资源选择函数和生态位因子分析各自为栖息地选择研究提供了一个统一的理论框架。基于个体的模型是一个自下而上的过程,很难在系统水平形成理论。232篇国内文章中使用较多的方法是主成分分析、Mann-Whitney U检验、t检验、卡方检验、判别分析、方差分析、Vanderloeg选择系数和Scavia选择指数、逻辑斯蒂回归、Kruskal-Wallis H检验和多元回归分析等。在实际研究中,应根据所要解决的研究问题,选择切实可行的分析方法。     

Questionable papers in citation databases as an issue for literature review

In recent years, the academic world has been faced with much academic misconduct. Examples involve plagiarizing papers, manipulating data, and launching predatory or hijacked journals. The literature exposing these activities is growing exponentially, and so is the presentation of criteria or guidelines for counteracting the problem. Most of the research is focused on predatory or hijacked journal detection and providing suitable warnings. Overlooked in all this is the fact that papers published in these journals are questionable, but nevertheless show up in standard citation databases. We need some way to flag them so future researchers will be aware of their questionable nature and prevent their use in literature review.     

Multiple Component Analysis of Plasma Growth Hormone in Children with Standard and Short Stature

Growth hormone (GH) concentrations (in ng/ml) were determined by radioimmunoassay, in plasma obtained at about 3-hr intervals during a 24-hr sampling span, from 42 boys and 12 girls of short stature (2-4 standard deviations below their peer group mean), and 13 boys and 9 girls of standard stature. Subjects had 11.20 0.37 years of age at the time of study, and were living on a diurnal waking (∼07:30 to ∼22:30), nocturnal resting routine during sampling. Analysis of these data by single and population-mean cosinor methods as well as by analysis of variance revealed circadian and ultradian prominent components characterizing most groups. Accordingly, a multiple component analysis was undertaken for data of each group separately, as well as for all subjects. A comparison of circadian parameters indicates similar characteristics between short and standard children, whether one compares boys [P=0.674, 0.371 and 0.749 for comparison of rhythm adjusted means (M), amplitudes (A) and acrophases (), respectively], girls (P=0.993,0.914 and 0.397), or all children (P=0.859,0.712 and 0.865). Differences are found, however, in circasemidian characteristics as well as in the prominent 8-hr ultradian component documented for the short but not for the standard children. These ultradian components should be taken into consideration in the design and later evaluation of a time-specified treatment of children of short stature.     

Research Data in Core Journals in Biology,Chemistry, Mathematics,and Physics

This study takes a stratified random sample of articles published in 2014 from the top 10 journals in the disciplines of biology, chemistry, mathematics, and physics, as ranked by impact factor. Sampled articles were examined for their reporting of original data or reuse of prior data, and were coded for whether the data was publicly shared or otherwise made available to readers. Other characteristics such as the sharing of software code used for analysis and use of data citation and DOIs for data were examined. The study finds that data sharing practices are still relatively rare in these disciplines’ top journals, but that the disciplines have markedly different practices. Biology top journals share original data at the highest rate, and physics top journals share at the lowest rate. Overall, the study finds that within the top journals, only 13% of articles with original data published in 2014 make the data available to others.     

Easily assembled digital data acquisition system for the analytical ultracentrifuge

A system for the acquisition of digital data from the analytical ultracentrifuge which uses a commercially available data acquisition board, a standard IBM compatible personal computer (PC), and an interface circuit has been developed. The system uses the signal from the standard Beckman scanner. Preliminary analysis and data reduction are performed at the PC within minutes of data acquisition using simple commercially available software, and final data fitting is performed with a mainframe computer. Procedures are described which allow approach to equilibrium to be followed and attainment of equilibrium to be demonstrated. Data density of 200 points per millimeter column height (500 points per 100 μ1 of sample) allows the use of short columns and hence short run times. Only 2 min are required to collect a complete scan, which is recorded in a format suitable for direct analysis by standard spreadsheet software. This allows multiple sequential scans to be quickly recorded at equilibrium and averaged to reduce noise prior to analysis. The combination of characteristics allows molecular weight determinations to be performed relatively quickly with only a few micrograms of protein. The system is inexpensive and easy to assemble given the centrifuge and a PC.     

Use of balance methods for assessment of short-term changes in body composition

Balance methods reveal changes in body energy, nitrogen, macro‐ and micronutrients as well as fluid in response to different feeding regimens. Under metabolic ward conditions, where physical activity is restricted and activity and food intake are controlled, the errors of estimates of energy intake, energy expenditure, and energy losses are about 2, 4, and 2%, respectively. Balance techniques can be used to validate techniques of in vivo body composition analysis (BCA). This is necessary since immediate and transient changes in body composition in response to a change in diet adversely affect the validity of techniques by violating the assumptions underlying standard methods (i.e., a constant composition or hydration of lean mass). Using two compartment reference methods, like densitometry, dual X‐ray absorptiometry (DXA) or deuterium dilution, changes in fat mass with caloric restriction and overfeeding can be measured with a minimal detectable change (MDC) of 1.0–2.0 kg. However, when compared against balance data, the validity of these techniques to measure short‐term changes in body composition is poor. The noninvasive and rapid new quantitative magnetic resonance (QMR) technique has a high precision with a MDC of 0.18 kg of fat mass. The validity of QMR to assess short‐term changes in fat mass is challenged by comparison to balance data. Today, techniques used for in vivo BCA should be related to steady state conditions only, while in the nonsteady state, the use of balance methods is recommended to assess short‐term changes in body composition.     

Statistical Tools and Status Symbols

This paper sets the stage for a series of edited papers which follow. It is argued that obvious statistical blunders (mortal sins) have not dissappeared entirely from the aging literature, but that the most frequent error now is that of choosing a less powerful analytic solution when a more powerful (and equally applicable) one is at hand (a venial sin). Clearly, it is argued, power must be considered in relationship to the theoretical model, the condition of the data set, and the research question. Editors and reviewers, it is argued, must cut through the “glitter” of new fads and the security of tradition in order to objectively consider the merits of new statistical applications. More importantly, without knowledge of the issues, limitations, and advantages of contemporary and emerging analytic techniques, authors cannot make good analytic choices and defend them effectively. The time between presentation of innovative approaches in the quantitative journals and application in the aging literature contributes to traditionalism in data analysis. Overzealousness by advocates of new approaches often contributes to premature embracing of them. Thus the papers that follow were designed to bring new methods to the “working-researcher” with a frank appraisal of assumptions, proper and improper applications, and limitations. Authors of these papers were challenged to communicate in plain and understandable terms and to provide practical examples.     

Not seeing is not believing: improving the visibility of your fluorescence images

The digital age has brought both technical advances and ethical quandaries regarding data acquisition and image presentation in the field of cell biology. Image manipulation has drawn considerable attention in the past decade, leading to general guidelines for ethical data processing. However, effective methods of image presentation have been discussed only cursorily and have been largely overlooked. Under standard viewing conditions, the human visual system imposes limitations for readers analyzing fluorescence images. In this paper, I discuss the advantages and limitations of image-manipulation techniques with respect to the human visual system, including contrast stretching, nonlinear grayscale transformations, and pseudocoloring. While online data viewing presents innovative ways to access image information, most images continue to be viewed in static publications, in which image presentation is critical for effective information transmission.     

Approach to assessing determinants of glucose homeostasis in the conscious mouse

Obesity and type 2 diabetes lessen the quality of life of those afflicted and place considerable burden on the healthcare system. Furthermore, the detrimental impact of these pathologies is expected to persist or even worsen. Diabetes is characterized by impaired insulin action and glucose homeostasis. This has led to a rapid increase in the number of mouse models of metabolic disease being used in the basic sciences to assist in facilitating a greater understanding of the metabolic dysregulation associated with obesity and diabetes, the identification of therapeutic targets, and the discovery of effective treatments. This review briefly describes the most frequently utilized models of metabolic disease. A presentation of standard methods and technologies on the horizon for assessing metabolic phenotypes in mice, with particular emphasis on glucose handling and energy balance, is provided. The article also addresses issues related to study design, selection and execution of metabolic tests of glucose metabolism, the presentation of data, and interpretation of results.     

Short column gas chromatography–mass spectrometry and principal component analysis for the identification of coeluted substances in doping control analysis

The identification of four doping control substances in an artificial mixture, using short column gas chromatography–mass spectrometry (GC–MS) analysis was examined. Two chromatographic peaks were recorded in the chromatogram, using a short capillary column (1.8 m) at an oven temperature of 180°C. The first peak was associated with a mixture of a solvent derivative and an artifact. The second one corresponded to the mixture of four control substances. Principal component analysis was applied on a selected GC–MS data set of the latter peak to determine clear full spectra of pure substances from mixture spectra. The time of GC–MS analysis was significantly reduced to less than 1 min from 30 min which is a typical GC–MS analysis time, using standard methods of doping control analysis.     

Publishing proteomic data

Scientific publications should provide sufficient detail in terms of methodology and presented data to enable the community to reproduce the methodology to generate similar data and arrive at the same conclusion, if an identical sample is provided for analysis. The advent of high-throughput methods in biological experimentation impose some unique challenges both in data presentation in classical print format, as well as in describing methodology and data analysis in sufficient detail to conform to good publication practice. To facilitate this process, Proteome Science is adopting a set of methodology and data presentation guidelines to enable both peer reviewers, as well as the scientific community, to better evaluate high-throughput proteomic studies.     

Specialized hidden markov model databases for microbial genomics

As hidden Markov models (HMMs) become increasingly more important in the analysis of biological sequences, so too have databases of HMMs expanded in size, number and importance. While the standard paradigm a short while ago was the analysis of one or a few sequences at a time, it has now become standard procedure to submit an entire microbial genome. In the future, it will be common to submit large groups of completed genomes to run simultaneously against a dozen public databases and any number of internally developed targets. This paper looks at some of the readily available HMM (or HMM-like) algorithms and several publicly available HMM databases, and outlines methods by which the reader may develop custom HMM targets.     

Symbols and Terminology in Biometry

The many biologists whose work requires statistical science must be concerned for sound management and interpretation of quantitative data. Biometricians also need increased care for literacy and clarity in speech and writing, with precise phrasing for every numerical statement. This paper illustrates common confusions that arise from inexact terminology, or from words and symbols used without adequate definition. Careless statements on quantitative relations, or on probabilities, may be ambiguous; bad practices seriously pollute scientific journals and obstruct transmission of information. Such faults can affect daily life for a modern citizen. Pedantry is unwanted, and to be dogmatic about corrective measures would be stupid. This paper suggests that biologists and biometricians should examine the practicability of a system yet to be devised for standardizing use of symbols and the generally accepted terminology for the methods, techniques, and processes of statistical analysis. The outcome should influence all that we biometricians say and do — as authors, as consultants, and as referees for journals.     

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles)

Policies supporting the rapid and open sharing of proteomic data are being implemented by the leading journals in the field. The proteomics community is taking steps to ensure that data are made publicly accessible and are of high quality, a challenging task that requires the development and deployment of methods for measuring and documenting data quality metrics. On September 18, 2010, the United States National Cancer Institute convened the "International Workshop on Proteomic Data Quality Metrics" in Sydney, Australia, to identify and address issues facing the development and use of such methods for open access proteomics data. The stakeholders at the workshop enumerated the key principles underlying a framework for data quality assessment in mass spectrometry data that will meet the needs of the research community, journals, funding agencies, and data repositories. Attendees discussed and agreed up on two primary needs for the wide use of quality metrics: 1) an evolving list of comprehensive quality metrics and 2) standards accompanied by software analytics. Attendees stressed the importance of increased education and training programs to promote reliable protocols in proteomics. This workshop report explores the historic precedents, key discussions, and necessary next steps to enhance the quality of open access data. By agreement, this article is published simultaneously in the Journal of Proteome Research, Molecular and Cellular Proteomics, Proteomics, and Proteomics Clinical Applications as a public service to the research community. The peer review process was a coordinated effort conducted by a panel of referees selected by the journals.