Luminescence Literature

The journal provides comprehensive literature searches on all aspects of luminescence which will be published in most issues. These lists have been produced regularly since 1986—some by year and some by specialized topic. This survey of papers on Obelia, Renilla, Aequorea and Gonyaulax is drawn from the 2000 literature and covers the biology of these organisms and the applications of genes and proteins from these organisms in analysis.     

Luminescence Literature 2000

The journal provides comprehensive literature searches on all aspects of luminescence which will be published in most issues. These lists have been produced regularly since 1986—some by year and some by specialized topic. This survey of papers on Firefly and marine bacterial bioluminescence is drawn from the 2000 literature and covers the biology of these organisms and the applications of genes and proteins from these organisms in analysis.     

Luminescence Literature

The journal provides comprehensive literature searches on all aspects of luminescence which will be published in most issues. These lists have been produced regularly since 1986—some by year and some by specialized topic. This survey of papers on green fluorescent protein and imaging is drawn from the 2000 literature and covers reagents, assay development and validation, and applications and supplements the previous survey (J. Biolumin. Chemilumin. 1997; 12 : 113–34). The 2000 Literature Compiled by L. J. Kricka (kricka@mail.med.upenn.edu) and P. E. Stanley (stanley@lumiweb.com)     

Photosystem 2 and the oxygen evolving complex: a brief overview

These special issues of photosynthesis research present papers documenting progress in revealing the many aspects of photosystem 2, a unique, one-of-a-kind complex system that can reduce a plastoquinone to a plastoquinol on every second flash of light and oxidize 2 H₂O to an O₂ on every fourth flash. This overview is a brief personal assessment of the progress observed by the author over a four-decade research career, including a discussion of some remaining unsolved issues. It will come as no surprise to readers that there are remaining questions given the complexity of PS2, and the efforts that have been needed so far to uncover its secrets. In fact, most readers will have their own lists of outstanding questions.

     

Capture-recapture, epidemiology, and list mismatches: two lists

In recent years, capture-recapture methods for closed populations have been extensively applied to epidemiology. For example, suppose we have several incomplete lists of diabetics and we wish to estimate the total number of diabetics by estimating the number missing from all the lists. A major problem is that the information about individuals on the lists may have been given incorrectly or the information may have been typed incorrectly so that some list matches are missed. Using the concept of tag loss borrowed from animal population studies, we consider methods for estimating both the probabilities of making list errors and the population size for just two independent lists. The effect of heterogeneity on the errors is examined. The methods are applied to a large data set of diabetic persons consisting of a list obtained from a survey and a list obtained from doctors' records. It was found that the error rates were high and that ignoring the errors led to a gross overestimate of the total number of diabetic persons.     

IVth International Symposium on Quantitative Luminescence Spectrometry in Biomedical Sciences

This meeting (Chairman, W. R. G. Baeyens) was held on 27—31 May 1991 at the State University of Ghent, Belgium. Abstracts of papers and posters from this meeting on the topics of bioluminescence and chemiluminescence are reproduced in the following sections. The abstracts have been classified under the main topic headings used in the ‘Bioluminescence and Chemiluminescence Literature’ section of this journal, and are listed alphabetically by first author.     

Human urine proteomics: building a list of human urine cancer biomarkers

In the last decade, several reports have focused on the identification and characterization of proteins present in urine. In an effort to build a list of proteins of interest as biomarkers, we reviewed the largest urine proteomes and built two updated lists of proteins of interest (available as supplementary tables). The first table includes a consensus list of 443 proteins found in urine by independent laboratories and reported on the top three largest urine proteomes currently published. This consensus list of proteins could serve as biomarkers to diagnose, monitor and manage a number of diseases. Here, we focus on a reduced list of 35 proteins with potential interest as cancer biomarkers in urine following two criteria: first, proteins previously detected in urine using bottom-up proteomic experiments, and second, those suggested as cancer protein biomarkers in human plasma. In an effort to standardize the information presented and its use in future studies, here we include the updated International Protein Index (v. 3.80) and primary Swiss-Prot accession numbers, official gene symbols and recommended full names. The main variables that influence urine proteomic experiments are also discussed.     

Survey of the 2009 commercial optical biosensor literature

We took a different approach to reviewing the commercial biosensor literature this year by inviting 22 biosensor users to serve as a review committee. They set the criteria for what to expect in a publication and ultimately decided to use a pass/fail system for selecting which papers to include in this year's reference list. Of the 1514 publications in 2009 that reported using commercially available optical biosensor technology, only 20% passed their cutoff. The most common criticism the reviewers had with the literature was that "the biosensor experiments could have been done better." They selected 10 papers to highlight good experimental technique, data presentation, and unique applications of the technology. This communal review process was educational for everyone involved and one we will not soon forget.     

AGRA: analysis of gene ranking algorithms

Often, the most informative genes have to be selected from different gene sets and several computer gene ranking algorithms have been developed to cope with the problem. To help researchers decide which algorithm to use, we developed the analysis of gene ranking algorithms (AGRA) system that offers a novel technique for comparing ranked lists of genes. The most important feature of AGRA is that no previous knowledge of gene ranking algorithms is needed for their comparison. Using the text mining system finding-associated concepts with text analysis. AGRA defines what we call biomedical concept space (BCS) for each gene list and offers a comparison of the gene lists in six different BCS categories. The uploaded gene lists can be compared using two different methods. In the first method, the overlap between each pair of two gene lists of BCSs is calculated. The second method offers a text field where a specific biomedical concept can be entered. AGRA searches for this concept in each gene lists' BCS, highlights the rank of the concept and offers a visual representation of concepts ranked above and below it. AVAILABILITY AND IMPLEMENTATION: Available at http://agra.fzv.uni-mb.si/, implemented in Java and running on the Glassfish server. CONTACT: simon.kocbek@uni-mb.si.     

Disproportional Representation of Primates in the Ecological Literature

We address the question why papers dealing with the ecology of primates are so sparsely represented in the general ecological literature. A literature analyses based on entries in Web of Science and PrimateLit reveals that despite a large number of papers published on primates in general and on the ecology of primates, only a very small fraction of these papers is published in high-ranking international ecological journals. We discuss a number of potential reasons for the disproportion and highlight the problems associated with experimental research on wild primates and constraints on sample size as major issues.     

不懈探索, 努力引领中国生物多样性科学发展——《生物多样性》创刊三十周年回顾

为更好地推动我国生物多样性科学的发展, 提升期刊服务能力, 并庆祝创刊30周年, 我们梳理了《生物多样性》2013-2022年的主要进展。(1)近10年中, 期刊的特色进一步凸显。围绕学科前沿、国家重大行动计划、履约等领域共策划出版56个专辑/专题, 新设立编者按、生物编目、数据论文、保护与治理对策、生物文化多样性等特色栏目, 通过发表数据论文、生物编目等文章推动数据共享, 以及通过鼓励学术争鸣、探索中文期刊的国际传播等举措使期刊的特色进一步凸显。(2)期刊载文量快速增加, 报道的内容不断拓展。研究方向由前20年的61个增加为目前的78个, 90%左右的文章聚焦于生物多样性保护、环境科学/生态学等领域; 植物学、动物学、微生物学的稿件分别占41.79%、47.48%和4.61%。基于关键词的文献计量分析表明, 近10年刊登的文章关键词聚类为遗传多样性、群落结构、红外相机、红色名录、生物多样性公约、国家公园、植物多样性、分类学和地理分布等9个子领域。培养了大批生物多样性人才, 10年中共有4,665位作者署名(作者记录数6,295), 发表文章最多的前20位作者主要来自中国科学院相关研究所、中国环境科学研究院、北京大学等机构, 其中60%为编委。(3)刊登的论文被广泛引用和下载。根据中国知网数据(排除了学位论文和会议论文, 2022年10月18日), 近10年刊登的文章有1,211篇累计被引用13,507次, 平均每篇被引11次以上; 网上下载量从2012年的6.64万次增加到2021年的23.85万次。有5篇文章入选中国科协优秀科技论文或中国百篇最具影响国内学术论文; 以国家公园、红外相机、红色名录、多功能性、生物入侵为关键词的文章是受关注的热点。《生物多样性》的影响因子和总被引频次在生物学领域一直排名前列; 是《科技期刊世界影响力指数(WJCI)报告》中全球保护生物学领域唯一的中国期刊, 2019年和2020年分别位列23/48和25/49位。最后我们探讨了今后如何继续引领中国生物多样性研究和保护、建设一流科技期刊面临的挑战和对策以及如何进一步提升科学传播能力。     

Elusive data underlying debate at the prokaryote-eukaryote divide

Background

The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature.

Results

We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure.

Conclusion

The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution.

Reviewers

This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.

     

List mania: interpreting microarray results with the L2L server

A new server for interpreting microarray results, list to list(L2L), is described. This tool offers a unique approach to understandthe meaning of microarray results, based on comparing them topreviously identified lists of differentially expressed genes.The usefulness of the server is demonstrated by studying differentialexpression in primary tumours versus metastases in colon cancer.     

Using simple species lists to monitor trends in animal populations: new methods and a comparison with independent data

There is an urgent need to develop simple and inexpensive methods for monitoring wildlife populations in resource-poor countries. List-based methods have been advocated as simple yet potentially useful biodiversity monitoring tools, and systems have recently been launched in a number of countries to collect species lists. We attempt to advance the use of systematic list-based monitoring by (1) suggesting improvements to the way in which list reporting rates are calculated; (2) assessing the extent to which degrading effort-corrected measures of abundance into simple species lists results in loss of information on population trends; (3) comparing long-term trends in list reporting rates with population trends from a wholly independent monitoring scheme. Daily species lists of birds were derived from regular trapping at a nature reserve in southern England. Most species showed a strong correlation across years between the proportion of lists on which they occurred, adjusted for list length (adjusted list reporting rate; ALRR), and an effort-corrected measure of abundance (captures per unit effort; CPUE). ALRR revealed almost as much about annual variation in abundance as CPUE for all but the most frequently captured species. Long-term (>20 years) trends in ALRRs at the nature reserve were positively correlated with UK national population trends recorded over the same period by an independent, labour-intensive monitoring scheme that counted birds at a large number of widely spread sites. Our results support previous claims that simple species lists could generate data useful for monitoring long-term population trends, particularly where such lists are collected systematically. However, further research on the efficiency of list reporting rates relative to more sophisticated methods is necessary, before list-based methods can be advocated for dedicated monitoring schemes in resource-poor regions.     

Are species lists derived from modeled species range maps appropriate for macroecological studies? A case study on data from BIEN

Because survey-based species lists for fine-scale areas are generally lacking, ecologists have been using species lists derived from modeled range maps in macroecological studies. Here I evaluate whether it is appropriate to use species lists derived from modeled range maps in macroecological studies. I compared species lists derived from about 90,000 range maps in the Botanical Information and Ecology Network (BIEN) for over 180 geographic regions (12 broad regions covering the whole of the New World; 172 smaller regions, i.e. Taxonomic Databases Working Group units) with those representing complete or nearly complete species lists obtained from the literature for the regions. I determined the completeness of native species composition and proportion of false presences and exotic (non-native) species in species lists derived from range maps in BIEN. I determined whether errors in species lists derived from modeled range maps affect macroecological inferences by comparing the relationships of α- and β-diversity with geographic and climatic variables between different datasets (i.e. species lists derived from range maps versus complete or nearly complete species lists derived from the literature). The completeness for native species lists derived from range maps was 60–74%, depending on spatial scale. On average, 65% of the species in a species list derived from BIEN for a geographic area are false presences or non-native species to the area. The relationships of α- and β-diversity derived from the BIEN dataset with geographic and climatic variables differ significantly from those derived from complete species lists. This study shows that the results of a macroecological study based on species lists derived from modeled range maps may be substantially incorrect due to high percentages of missing native species, and high numbers of non-native species and false presences. Thus, it may not be appropriate to use species lists derived from modeled range maps in the macroecological studies that require complete or nearly complete species lists.     

Reference bias in reports of drug trials.

Articles published before 1985 describing double blind trials of two or more non-steroidal anti-inflammatory drugs in rheumatoid arthritis were examined to see whether there was any bias in the references they cited. Althogether 244 articles meeting the criteria were found through a Medline search and through examining the reference lists of the articles retrieved. The drugs compared in the studies were classified as new or as control drugs and the outcome of the trial as positive or not positive. The reference lists of all papers with references to other trials on the new drug were then examined for reference bias. Positive bias was judged to have occurred if the reference list contained a higher proportion of references with a positive outcome for that drug than among all the articles assumed to have been available to the authors (those published more than two years earlier than the index article). Altogether 133 of the 244 articles were excluded for various reasons--for example, 44 because of multiple publication and 19 because they had no references. Among the 111 articles analysed bias was not possible in the references of 35 (because all the references gave the same outcome); 10 had a neutral selection of references, 22 a negative selection, and 44 a positive selection--a significant positive bias. This bias was not caused by better scientific standing of the cited articles over the uncited ones. Thus retrieving literature by scanning reference lists may produce a biased sample of articles, and reference bias may also render the conclusions of an article less reliable.     

Multi-list methods using incomplete lists in closed populations

Multi-list methods have become a common application of capture-recapture methodology to estimate the size of human populations, and have been successfully applied to estimating prevalence of diabetes, human immunodeficiency virus (HIV), and drug abuse. A key assumption in multi-list methods is that individuals have a unique "tag" that allows them to be matched across all lists. This article develops multi-list methodology that relaxes the assumption of a single tag common to all lists. Estimates are found using estimating functions. An example illustrates its application for estimating the prevalence of diabetes, and a simulation study investigates conditions under which the methodology is robust to different list and population sizes.