植物病原菌物学—不能抛弃的形态分类与不能拒绝的分子分析

本期菌物学报“植物病原菌物学专刊”刊登了22篇文章,其中关于菌物种类调查、鉴定及形态描述的文章11篇,关于植物病原菌生理和遗传分化的文章5篇,关于植物病原菌侵染结构和组织学的文章2篇,关于植物病原菌致病基因克隆及功能基因分析的文章4篇。作者作了简要的启发式总结。     

International collaboration in freshwater ecology

1. International collaboration in freshwater ecology was examined using authorship affiliations of articles published in thirty-three specialized journals. Most are published in Europe. 2. Researchers from four to thirty-seven different countries were represented in the 100 articles examined for each journal. Only 29% of articles were single-authored; multicountry authors' addresses (indicating international collaboration) were found for 9% (range 0–23% per journal) of articles examined. 3. Five of the eighty-nine countries listed in the addresses of the 3300 articles together contributed >50% of total articles: United States (24.9%), Canada (8.6%), Germany (7.6%), Commonwealth of Independent States (7.0%) and Poland (5.9%). Of the fifteen countries that each produced >2.5% of total articles, the percentage representing international collaboration was highest for France (34.9%) and Canada (24.0%). The seventy-four countries that each contributed <2.5% of total articles generally had higher rates of international collaboration. 4. Researchers in the United States and Canada collaborate internationally almost twice as often in freshwater ecology than in all science. Much of France's extensive international collaboration is with countries that produce few articles in freshwater ecology, and their international collaboration is often exclusively with France. 5. Three journals publishing both marine and freshwater ecology articles contain more articles on the former topic, but more countries are represented in the publication of freshwater than marine research. 6. The percentage of articles that represent international collaboration is higher in freshwater ecology than in medicine, biology, chemistry and engineering, and approximates that in physics.     

晚清报刊所载真菌类专篇汇录

晚清时期传入中国的西方真菌学知识对于近代中国真菌学的建立和发展具有启蒙作用.在全面分析其影响之前,有必要先对相关文献进行全面的整理,而这些文献中大部分都分布于多种晚清报刊.经过整理和统计,本文共辑得89份真菌类专篇文章,其中大型真菌类44篇、霉菌类27篇、酵母菌类18篇,分布于26种报刊.这些文章中注明是译作的只有28篇,但其余的文章中涉及西方真菌科学知识的实际上都属于介译性质.这些真菌学知识部分是通过日文图书或期刊文献间接引入,部分是直接译自西方的科学文献.     

Elementary and middle level biology topics: a content analysis of Science and Children and Science Scope from 1990 to 2014

Science and Children and Science Scope are peer-reviewed science practitioner journals that publish articles for science educators who teach children of ages 5–10 years and 10–13 years, respectively. As such, these articles are a reflection of the science concepts that are being communicated to science educators. This comprehensive literature review was completed to determine the extent to which the articles included in these journals from 1990 to 2014 focused on biology topics, incorporated other non-science subjects and science disciplines, and encouraged inquiry-based learning. The results indicate that out of the 2701 total articles, 557 (21%) focused on biology. The biology topic covered most often by both journals was animals. The biology topics covered least often were fungi, photosynthesis, respiration and viruses. The findings are taken into consideration and the educational implications for the journals and educators are discussed.     

Why Has the Number of Scientific Retractions Increased?

Background

The number of retracted scientific publications has risen sharply, but it is unclear whether this reflects an increase in publication of flawed articles or an increase in the rate at which flawed articles are withdrawn.

Methods and Findings

We examined the interval between publication and retraction for 2,047 retracted articles indexed in PubMed. Time-to-retraction (from publication of article to publication of retraction) averaged 32.91 months. Among 714 retracted articles published in or before 2002, retraction required 49.82 months; among 1,333 retracted articles published after 2002, retraction required 23.82 months (p<0.0001). This suggests that journals are retracting papers more quickly than in the past, although recent articles requiring retraction may not have been recognized yet. To test the hypothesis that time-to-retraction is shorter for articles that receive careful scrutiny, time-to-retraction was correlated with journal impact factor (IF). Time-to-retraction was significantly shorter for high-IF journals, but only ∼1% of the variance in time-to-retraction was explained by increased scrutiny. The first article retracted for plagiarism was published in 1979 and the first for duplicate publication in 1990, showing that articles are now retracted for reasons not cited in the past. The proportional impact of authors with multiple retractions was greater in 1972–1992 than in the current era (p<0.001). From 1972–1992, 46.0% of retracted papers were written by authors with a single retraction; from 1993 to 2012, 63.1% of retracted papers were written by single-retraction authors (p<0.001).

Conclusions

The increase in retracted articles appears to reflect changes in the behavior of both authors and institutions. Lower barriers to publication of flawed articles are seen in the increase in number and proportion of retractions by authors with a single retraction. Lower barriers to retraction are apparent in an increase in retraction for “new” offenses such as plagiarism and a decrease in the time-to-retraction of flawed work.     

Primary literature as a basis for a high-school biology curriculum

Textbooks, research news from the media, and review articles from popular journals are the most common sources of texts used for high-school biology education. We attempted to adopt primary literature as a means of developing scientific literacy among high-school biology majors. For that purpose, we developed and implemented a primary literature-based curriculum in developmental biology. The process of adapting original research articles to the high-school level, as well as a conversational model developed for learning through research articles, are discussed.     

Growth and development of biofeedback: a bibliographic analysis

A computerized search was performed, and a bibliography was prepared on the subject of biofeedback covering the years from 1964 to 1985. Growth curves were produced for various publication media. The search produced references to 2,431 journal articles, 102 books, 79 popular magazine articles, and 551 doctoral dissertations. The journal articles were sorted according to the country of publication, language, and primary topic of the journal. Citations were found from 35 countries, written in 18 languages. All the media studied showed a period of rapid growth during the early to middle 1970s, but there was a tendency for leveling off or slight decline during the early 1980s. Publication of articles in medical journals has shown the greatest growth, and more articles are published yearly in medical journals than in journals of any other discipline or all specialty journals combined. Publication in psychological journals has shown a decline since 1977. Dental, nursing, and educational journals have shown a low rate of publication of biofeedback articles, indicating little or no growth.     

Misuse of odds ratios in obesity literature: an empirical analysis of published studies

Odds ratios (ORs) are widely used in scientific research to demonstrate the associations between outcome variables and covariates (risk factors) of interest, and are often described in language suitable for risks or probabilities, but odds and probabilities are related, not equivalent. In situations where the outcome is not rare (e.g., obesity), ORs no longer approximate the relative risk ratio (RR) and may be misinterpreted. Our study examines the extent of misinterpretation of ORs in Obesity and International Journal of Obesity. We reviewed all 2010 issues of these journals to identify all articles that presented ORs. Included articles were then primarily reviewed for correct presentation and interpretation of ORs; and secondarily reviewed for article characteristics that may have been associated with how ORs are presented and interpreted. Of the 855 articles examined, 62 (7.3%) presented ORs. ORs were presented incorrectly in 23.2% of these articles. Clinical articles were more likely to present ORs correctly than social science or basic science articles. Studies with outcome variables that had higher relative prevalence were less likely to present ORs correctly. Overall, almost one-quarter of the studies presenting ORs in two leading journals on obesity misinterpreted them. Furthermore, even when researchers present ORs correctly, the lay media may misinterpret them as relative RRs. Therefore, we suggest that when the magnitude of associations is of interest, researchers should carefully and accurately present interpretable measures of association--including RRs and risk differences--to minimize confusion and misrepresentation of research results.     

Publication trends in zoo biology: A brief analysis of the first 15 years

Zoo Biology has completed 15 years as a professional journal dedicated to exsitu wildlife research. To assess the journal's representation of zoo and aquarium research, we examined some aspects of its publication record, based on analyses of 395 research articles. The taxonomic representation of Zoo Biology is heavily skewed toward research articles on mammals (73%), with articles on birds, reptiles, and invertebrates contributing only 10%, 7%, and 7%, respectively. Behavior and reproduction (sensu latu) are the predominating disciplinary themes of research, with heavy reliance on non-invasive endocrine methodology using RIA and EIA. The relatively small number of articles dealing with demography and genetics is surprising when one considers the eminent role such analyses have played in Species Survival Plans. Most contributions are multi-authored and arise from U.S. institutions, with collaborative ventures between zoos and universities accounting for 26% of all articles. The academic community, however, contributed nearly one third of Zoo Biology's articles as non-collaborative contributions. University and aquarium affiliations are known to exist, but the products of such cooperation are not appearing in the pages of Zoo Biology. We conclude the taxonomic trends reflect a shortage of research-oriented staff in the zoo and aquarium profession, and a tendency for a significant number of zoo biologists to publish in taxon-oriented journals. Zoo Biol 16:3–8, 1997. © 1997 Wiley-Liss, Inc.     

Review of Cognitive Therapy and Dreams.

In this article I review the book, "Cognitive Therapy and Dreams" (see record 2004-00029-000). I came across this book as I was recently searching psychological abstracts for dreams and cognitive-behavioral therapy (CBT) and for hypnosis and CBT. Of the 9 references I found on dreams and CBT, all were in one issue of the Journal of Cognitive Psychotherapy: An International Quarterly (Vol. 16, No. 1). I read a good number of the hypnosis-CBT articles and books, and all were written to integrate CBT into the field of hypnosis. Conversely, the dream articles integrating dream work and CBT were written by a range of people, some with a primary interest in dreams, but some with a more central interest in cognitive therapy. Apparently, a few cognitive-behavioral therapists and researchers have taken some interest in dream work, whereas the hypnosis interest in CBT continues mostly outside the domain of CBT. The collection of the nine articles published in the journal was an impressive enough accomplishment that eight articles of this collection plus four additional articles are now published in this book. The fact that these articles are now in a book may encourage researchers to perform the necessary therapy outcome research to validate the integration of dream work and CBT. The book adds significantly to the journal by drawing a distinction between objectivist approaches (Part II) and constructivist approaches (Part III), a distinction that unifies the articles in this book. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Information extraction from full text scientific articles: Where are the keywords?

Background  

To date, many of the methods for information extraction of biological information from scientific articles are restricted to the abstract of the article. However, full text articles in electronic version, which offer larger sources of data, are currently available. Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant.     

Growth and development of biofeedback: A bibliographic analysis

A computerized search was performed, and a bibliography was prepared on the subject of biofeedback covering the years from 1964 to 1985. Growth curves were produced for various publication media. The search produced references to 2,431 journal articles, 102 books, 79 popular magazine articles, and 551 doctoral dissertations. The journal articles were sorted according to the country of publication, language, and primary topic of the journal. Citations were found from 35 countries, written in 18 languages. All the media studied showed a period of rapid growth during the early to middle 1970s, but there was a tendency for leveling off or slight decline during the early 1980s. Publication of articles in medical journals has shown the greatest growth, and more articles are published yearly in medical journals than in journals of any other discipline or all specialty journals combined. Publication in psychological journals has shown a decline since 1977. Dental, nursing, and educational journals have shown a low rate of publication of biofeedback articles, indicating little or no growth.We thank Ken Hartman for his assistance in performing this study.     

Scholarly Context Not Found: One in Five Articles Suffers from Reference Rot

The emergence of the web has fundamentally affected most aspects of information communication, including scholarly communication. The immediacy that characterizes publishing information to the web, as well as accessing it, allows for a dramatic increase in the speed of dissemination of scholarly knowledge. But, the transition from a paper-based to a web-based scholarly communication system also poses challenges. In this paper, we focus on reference rot, the combination of link rot and content drift to which references to web resources included in Science, Technology, and Medicine (STM) articles are subject. We investigate the extent to which reference rot impacts the ability to revisit the web context that surrounds STM articles some time after their publication. We do so on the basis of a vast collection of articles from three corpora that span publication years 1997 to 2012. For over one million references to web resources extracted from over 3.5 million articles, we determine whether the HTTP URI is still responsive on the live web and whether web archives contain an archived snapshot representative of the state the referenced resource had at the time it was referenced. We observe that the fraction of articles containing references to web resources is growing steadily over time. We find one out of five STM articles suffering from reference rot, meaning it is impossible to revisit the web context that surrounds them some time after their publication. When only considering STM articles that contain references to web resources, this fraction increases to seven out of ten. We suggest that, in order to safeguard the long-term integrity of the web-based scholarly record, robust solutions to combat the reference rot problem are required. In conclusion, we provide a brief insight into the directions that are explored with this regard in the context of the Hiberlink project.     

《蛇志》文章2年回顾分析

本文对《蛇志》1989、1990两年8期所刊载的文章进行了统计分析.结果表明:两年来共开辟栏目24个、刊载文章344篇,其中专业性学术文章157篇(45.6%),其他文章187篇(54.4%)。157篇学术文章中来源于县级以下医疗单位41篇(26.1%)、省市级以上医疗单位60篇(38.2%)、部队及其他单位56篇(35.7%)。平均编辑过程119.2天。《蛇志》创刊两年来,坚持了正确的办刊宗旨、突出了“蛇”的特色、栏目众多、图文并茂,溶知识性、趣味性于一体。可读性强.真正填补了我国科技领域中关于蛇类知识的空白。同时笔者建议,今后要更进一步地面向基层、面向农村,多刊登专业性学术文章,使作为我国唯一介绍蛇类知识的综合性刊物——《蛇志》办得更好。     

How good are articles on adverse drug reactions?

A study was carried out of the quality and completeness of articles on adverse drug reactions: 5737 articles from 80 countries published between 1972 and 1979 were studied. Only 61% of the articles included information on the number of patients treated and the number with adverse drug reactions, yet these are essential for calculating the incidence of adverse reactions. In only 55% could the incidence of a particular adverse reaction be calculated. Great importance is placed on articles on adverse reactions, particularly those that report on many patients. Authors and editors should ensure that articles include the following information: drug regimens, numbers of patients treated, numbers of patients developing adverse reactions, and nature and incidence of adverse reactions.     

Analysis of acanthocephalan literature published since 1900.

The data for this study are based on more than 6000 articles that mention Acanthocephala. The results indicate: (1) the difficulty in being current on world literature. It took about 3 years beyond the date of publication to discover many articles. (2) Except for World Wars I and II there has been a sustained increase in the number of articles. At present this rate exceeds 1000 titles per 5-year period. (3) Investigator interest, as measured by multiple publications by a given author, has remained very small. (4) Most publications have originated in the U.S.S.R. and U.S.A. followed by Great Britain and Germany. (5) Number of authors per title has increased dramatically. Currently, there are more four-author than single-author articles. (6) Fish are host animals most likely to be mentioned as containing acanthocephalans.     

Developmental Patterns and Hypotheses of Homology in the Antennules of Thecostracan Nauplius Larvae (Crustacea)

Abstract Antennular development is summarized for non–brooded nauplius larvae of the Ascothoracida (families Lauridae and Petrarcidae) and for selected nauplii of the Facetotecta. In the Cirripedia Thoracica, nauplii of the Lepadomorpha and Scalpellomorpha/Sessilia are shown to differ in their patterns of antennular setal addition and division into articles, and one or two possible apomorphies for each group are identified. Several variations of the scalpellomorphan/sessilian pattern are outlined. These data on the Ascothoracida, Facetotecta, and Cirripedia provide the basis for modifying an earlier proposal of structural homologies among the naupliar antennules of thecostracan maxillopodans. ‘Virtual’ articles (ones that are never completely free) are invoked to account for setae that ‘jump’ across article boundaries at molts and for supposedly homologous setae found on adjacent articles in different taxa. The identities of the preaxial setae in the Cirripedia are ambiguous and force consideration of two models for that group and for the thecostracan antennular Bauplan; the latter may have included up to 11 or 12 articles, more than the previously supposed 8 or 9. The scoring of characters used in an earlier cladistic study of thecostracan and other maxillopodan taxa is not seriously affected. A comparison with the Cambrian maxillopodan Bredocarissuggests that division of the antennule into discrete articles in extant thecostracans is an apomorphic state and that yet one more apical article once existed in the maxillopodan antennule.     

The value of protein structure classification information—Surveying the scientific literature

The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP–extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012–2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non‐SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings. Proteins 2015; 83:2025–2038. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.