A survey of the availability of primary bioinformatics web resources

The explosive growth of the bioinformatics field has led to a large amount of data and software applications publicly available as web resources. However, the lack of persistence of web references is a barrier to a comprehensive shared access. We conducted a study of the current availability and other features of primary bioinforo matics web resources （such as software tools and databases）. The majority （95%） of the examined bioinformatics web resources were found running on UNIX/Linux operating systems, and the most widely used web server was found to be Apache （or Apache-related products）. Of the overall 1,130 Uniform Resource Locators （URLs） examined, 91% were highly available （more than 90% of the time）, while only 4% showed low accessibility （less than 50% of the time） during the survey. Furthermore, the most common URL failure modes are presented and analyzed.     

Identifying relevant studies for systematic reviews.

OBJECTIVE--To examine the sensitivity and precision of Medline searching for randomised clinical trials. DESIGN--Comparison of results of Medline searches to a "gold standard" of known randomised clinical trials in ophthalmology published in 1988; systematic review (meta-analysis) of results of similar, but separate, studies from many fields of medicine. POPULATIONS--Randomised clinical trials published in 1988 in journals indexed in Medline, and those not indexed in Medline and identified by hand search, comprised the gold standard. Gold standards for the other studies combined in the meta-analysis were based on: randomised clinical trials published in any journal, whether indexed in Medline or not; those published in any journal indexed in Medline; or those published in a selected group of journals indexed in Medline. MAIN OUTCOME MEASURE--Sensitivity (proportion of the total number of known randomised clinical trials identified by the search) and precision (proportion of publications retrieved by Medline that were actually randomised clinical trials) were calculated for each study and combined to obtain weighted means. Searches producing the "best" sensitivity were used for sensitivity and precision estimates when multiple searches were performed. RESULTS--The sensitivity of searching for ophthalmology randomised clinical trials published in 1988 was 82%, when the gold standard was for any journal, 87% for any journal indexed in Medline, and 88% for selected journals indexed in Medline. Weighted means for sensitivity across all studies were 51%, 77%, and 63%, respectively. The weighted mean for precision was 8% (median 32.5%). Most searchers seemed not to use freetext subject terms and truncation of those terms. CONCLUSION--Although the indexing terms available for searching Medline for randomised clinical trials have improved, sensitivity still remains unsatisfactory. A mechanism is needed to "''register" known trials, preferably by retrospective tagging of Medline entries, and incorporating trials published before 1966 and in journals not indexed by Medline into the system.     

Trends in HSPB5 research: a 36-year bibliometric analysis

HSPB5 (heat shock protein B5), also known as αB-crystallin, is one of the most widespread and populous of the ten human small heat shock proteins (sHsps). Over the past decades, extensive research has been conducted on HSPB5. However, few studies have statistically analyzed these publications. Herein, we conducted a bibliometric analysis to track the global research trend and current development status of HSPB5 research from the Web of Science Core Collection (WoSCC) database between 1985 and 2020. Our results demonstrate that 1220 original articles cited 54,778 times in 391 scholarly journals were published. Visualization analyses reveal that the Journal of Biological Chemistry was the most influential journal with 85 articles. The USA dominated this field with 520 publications (42.62%), followed by Japan with 149 publications (12.21%), and Kato contributed the largest number of publications. Most related publications were published in journals focusing on biochemistry molecular biology, cell biology, neurosciences neurology, and ophthalmology. In addition, keyword co-occurrence analyses identify three predominant research topics: expression of HSPB5, chaperone studies for HSPB5, and pathological studies of HSPB5. This study provides valuable guidance for researchers and leads to collaborative opportunities between diverse research interests to be integrated for HSPB5 research.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12192-021-01220-6.     

Developing a register of randomised controlled trials in primary care.

OBJECTIVE--To determine the number, nature, site of publication, and feasibility of identifying randomised controlled trials relevant to primary care. DESIGN--Review of literature using three strategies: approaching journal editors, Medline search, and manual search of individual journals. SETTING--Journals containing publications of studies based in primary care. MAIN OUTCOME MEASURES--The number, site of publication, and subject of trials identified. RESULTS--No journal had a system which enabled identification of all the randomised controlled trials it published. 266 trials relevant to primary care were identified from 110 different journals during 1987-91 by Medline. Of these, only 62 trials were published in primary care journals. Hand searching of seven major primary care research journals showed that between 13% and 38% of the trials had been missed by the Medline search. Of the trials identified, 47 (18%) were concerned with mental disease (including neuroses, tobacco misuse and alcohol misuse) and 43 (16%) were concerned with hypertension. CONCLUSION--Given the diversity of publication sources and topics, this supports the need for a centrally based register of randomised controlled trials that may be relevant to primary care overviews in the future.     

Evaluating research and impact: a bibliometric analysis of research by the NIH/NIAID HIV/AIDS clinical trials networks

Evaluative bibliometrics uses advanced techniques to assess the impact of scholarly work in the context of other scientific work and usually compares the relative scientific contributions of research groups or institutions. Using publications from the National Institute of Allergy and Infectious Diseases (NIAID) HIV/AIDS extramural clinical trials networks, we assessed the presence, performance, and impact of papers published in 2006-2008. Through this approach, we sought to expand traditional bibliometric analyses beyond citation counts to include normative comparisons across journals and fields, visualization of co-authorship across the networks, and assess the inclusion of publications in reviews and syntheses. Specifically, we examined the research output of the networks in terms of the a) presence of papers in the scientific journal hierarchy ranked on the basis of journal influence measures, b) performance of publications on traditional bibliometric measures, and c) impact of publications in comparisons with similar publications worldwide, adjusted for journals and fields. We also examined collaboration and interdisciplinarity across the initiative, through network analysis and modeling of co-authorship patterns. Finally, we explored the uptake of network produced publications in research reviews and syntheses. Overall, the results suggest the networks are producing highly recognized work, engaging in extensive interdisciplinary collaborations, and having an impact across several areas of HIV-related science. The strengths and limitations of the approach for evaluation and monitoring research initiatives are discussed.     

I Publish in I Edit? - Do Editorial Board Members of Urologic Journals Preferentially Publish Their Own Scientific Work?

Scientists who are members of an editorial board have been accused of preferentially publishing their scientific work in the journal where they serve as editor. Reputation and academic standing do depend on an uninterrupted flow of published scientific work and the question does arise as to whether publication mainly occurs in the self-edited journal. This investigation was designed to determine whether editorial board members of five urological journals were more likely to publish their research reports in their own rather than in other journals. A retrospective analysis was conducted for all original reports published from 2001–2010 by 65 editorial board members nominated to the boards of five impact leading urologic journals in 2006. Publications before editorial board membership, 2001–2005, and publications within the period of time as an editorial board member, 2006–2010, were identified. The impact factors of the journals were also recorded over the time period 2001–2010 to see whether a change in impact factor correlated with publication locality. In the five journals as a whole, scientific work was not preferentially published in the journal in which the scientists served as editor. However, significant heterogeneity among the journals was evident. One journal showed a significant increase in the amount of published papers in the ‘own’ journal after assumption of editorship, three journals showed no change and one journal showed a highly significant decrease in publishing in the ‘own’ journal after assumption of editorship.     

Entomology and the Australian Entomological Society

Abstract   The Australian Entomological Society was founded in 1965 and provides a journal of world-class and annual scientific meetings for members. The world-wide impact of entomology publications is growing faster than that of the Australian Journal of Entomology , and membership of the society is declining slowly. In a recent survey members were generally happy with the society, but much of the exciting research involving insects is probably being published in specialist journals. Challenges identified for the future include building membership through greater connection with amateur entomologists and with students interested in ecology and insects. The growth area for entomology is seen to be in the application of insect biodiversity to the sustainable management of Australia's ecosystems. This special issue of the journal includes 10 papers illustrating the breadth and depth of entomology in the society.     

Indexation of psychiatric journals from low‐ and middle‐income countries: a survey and a case study

There is a marked underepresentation of low- and middle-income countries (LAMIC) in the psychiatric literature, which may reflect an overall low representation of LAMIC publications in databases of indexed journals. This paper investigates the worldwide distribution of indexed psychiatric journals. A survey in both Medline and ISI Web of Science was performed in order to identify journals in the field of psychiatry according to their country of origin. Two hundred and twenty-two indexed psychiatric journals were found. Of these, 213 originated from high-income countries and only nine (4.1%) from middle-income countries. None were found in low-income countries. We also present the experience of a LAMIC psychiatric journal, the Revista Brasileira de Psiquiatria, in its recent indexation process. This case study may serve as an example for other LAMIC journals to pursue indexation in major databases as a strategy to widen the international foundation of psychiatric research. There is an important need for the inclusion of LAMIC psychiatric publications in the major indexation databases. This process will require multiple agents to partner with journals from LAMIC to improve their quality and strengthen their chances of being indexed.     

Negative changes in the scientific publication process in ecology: potential causes and consequences

1. Increasingly viewed to have societal impact and value, science is affected by complex changes such as globalisation and the increasing dominance of commercial interest. As a result, technical advancements, financial concerns, institutional prestige and journal proliferation have created challenges for ecological and other scientific journals and affected the perception of both researchers and the public about the science that they publish. 2. Journals are now used for more than dissemination of scientific research. Institutions use journal rankings for a variety of purposes and often require a pre‐established number of articles in hiring and budgetary decisions. Consequently, journal impact factors have achieved greater importance, and the splitting of articles into smaller parcels of information (‘salami‐slicing’) to increase numbers of publications has become more frequent. 3. Journals may prescribe upper limits to article length, even though the average length of articles for several ecological journals examined has increased over time. There are clear signs, however, that journals without length limits for articles will become rarer. In contrast to ecological journals, taxonomic journals are not following this trend. 4. Two case histories demonstrate how splitting longer ecological articles into a series of shorter ones results in both redundancy of information and actually increases the journal space used overall. Furthermore, with current rejection rates of ecological journals (often ～80%), many thin salami‐sliced articles jam the peer‐review system much longer (through resubmission after rejection) than unsliced articles previously did (e.g. when rejection rates were ～50%). In our experience, the increased pressure to publish many articles in ‘high‐impact’ journals also may decrease the attractiveness of a future scientific career in ecology to young people. 5. ‘Gatekeeping’ of journal quality has shifted from editors to reviewers, and several recent trends are apparent including: bias about appropriate statistical methods; reviewers being more rigid overall; non‐native English writers being criticised for poor communications skills; and favourable reviews being signed more often than unfavourable ones. In terms of production, outsourcing of copy editing has increased the final error rate of published material. 6. We supplemented our perceptions with those of older colleagues (～100 experienced ecologists) that responded to an informal survey on this topic (response rate: 81%). In the opinion of almost 90% of our respondents, the overall review process has changed and for 20% among them the professional quality of reviews has declined. 7. We, and many older colleagues, are convinced there have been some negative changes in the scientific publication process. If younger colleagues share this concern, we can collectively counter this deteriorating situation, because we are the key to the publishing and evaluation process.     

Passing the Red Pen: EvoS Journal Offers an Early Education in Peer Review

EvoS Journal: The Journal of the Evolutionary Studies Consortium is the open-access, peer-reviewed journal borne of the EvoS (Evolutionary Studies) Consortium movement. The journal has two separate, yet related goals: to publish scholarly articles regarding the intersection of higher education and evolutionary theory, and to publish articles written and reviewed by undergraduates that incorporate an evolutionary perspective. Undergraduates who publish and review for EvoS Journal get the chance to see their work published alongside that of experts within the field of evolutionary studies, and to see the interdisciplinary and widespread applications of evolutionary theory to human life and beyond. The current study examines whether the interdisciplinary nature of EvoS Journal and its initiation of students into the peer-review process set EvoS Journal apart from more traditional undergraduate journals. EvoS Journal was compared to other journals listed by the Council for Undergraduate Research. While EvoS Journal mirrors many traditional undergraduate journals in their employment of student reviewers and publishing work originating from any U.S. institution, it differs by both its interdisciplinary focus and by serving as an outlet for both student and professional publications. The implications are discussed in terms of the benefits of interdisciplinary and peer-review training to students in the classroom, including improvements in writing, interpersonal relations, and real-world skills.     

SCI收录的真菌学核心期刊介绍

以表格的形式汇总介绍了SC I收录的12种真菌学类目核心期刊的英文刊名、中文刊名、出版国和最新影响因子,并详细介绍了这12种期刊的出版周期、出版者、联系地址、最新期刊网址及期刊描述等全方位的期刊信息。期刊描述内容包括：期刊的创刊年以及期刊的发展,期刊刊载的主要内容,网站可免费获取的该刊目次和文摘及全文信息等。     

2020-2021年世界甲螨亚目新分类单元和近15年中国发表新种概况——纪念中国甲螨学开创100周年

甲螨是土壤动物主要的三大类群之一, 数量庞大且种类丰富。截至2020年, 中国已报道的甲螨仅占世界所有已知甲螨种类的7.6%, 这与我国已知甲螨种类真实物种状况仍有较大的差距。值此中国甲螨学开创100周年之际, 本研究以甲螨亚目为研究对象, 分别基于世界2020-2021年度和中国2007-2021年度发表的分类学文献资料, 编制了世界新增分类单元名录和近15年中国发表甲螨新种名录, 分析了新分类单元的地理分布、学者贡献和出版刊物情况。研究结果表明, 2020-2021年, 世界甲螨亚目共描述238个新分类单元, 包括新属及新亚属21个, 新种217个; 新分类单元发表的热点地区在埃塞俄比亚界、东洋界和新热带界; 描述的新分类单元由27位作者所贡献, 其中外国学者贡献占比高; 论文均发表在国外期刊上, Systematic and Applied Acarology是新分类单元发表的主要期刊。2007-2021年, 中国发表甲螨亚目新种183个, 无新科和新属发表; 新种发表的热点地区在华南区和西南区; 描述的新种由24位作者所贡献, 中国学者占主要贡献; 论文多发表在国外期刊上, Systematic and Applied Acarology和Zootaxa是新分类单元发表的主要期刊。基于以上结果, 本文认为目前从事甲螨分类学研究的学者相对较少, 发表的新分类单元在类群分布和区域分布上均表现出极不均衡的现象。传统分类学未来的发展将面临机遇和挑战。     

Informe: análisis de las publicaciones de socios de la Sociedad Española de Geriatría y Gerontología del año 2006 al 2011

Data is presented from the survey conducted by the Sociedad Española de Geriatría y Gerontología (SEGG) (Spanish Society of Geriatrics and Gerontology) among its members in order to assess their scientific production between 2006 and 2011, specifically articles in journals that are indexed in the Science Citation Index. The scientific quality of the publications was quantified using the number of times every article was cited and the journal's impact factor. A total of 162 out of the 2450 members responded (6.6%), reporting a total of 903 individual articles, 335 (37%) of them in geriatrics-specific journals, and 568 (63%) in other journals of other specialties. The number of publications increased yearly from 128 in 2006 to 201 in 2010. The scientific quality could be calculated for 530 articles. On average, publications have been cited 8.2 times (median: 2), with the range of citations being from 0 to 242. The average impact factor was 3.1 (median 2.4), ranging from 0 to 53.5. A number of articles have been published in some of the largest impact factor journals, in those of general-interest, as well as geriatrics-specific and basic science journals.     

Agreements and Discrepancies between FDA Reports and Journal Papers on Biologic Agents Approved for Rheumatoid Arthritis: A Meta-Research Project

Background

Sponsors that seek to commercialize new drugs apply to the Food and Drug Administration (FDA) which independently analyzes the raw data and reports the results on its website.

Objectives

This study sought to determine if there are differences between the FDA assessments and journal reports on biologic agents developed for the treatment of rheumatoid arthritis.

Methods

Available data on FDA-approved drugs were extracted from the website, and a systematic literature search was conducted to identify matching studies in peer-reviewed medical journals. Outcome measures were the American College of Rheumatology response criteria ACR20 (efficacy) and withdrawal due to adverse events (safety). As effect size odds ratios were estimated for each active trial arm vs. control arm (i.e. for both sources: FDA and journal report), followed by calculation of the ratios of the FDA and journal report odds ratios. A ratio of odds ratios not equal to 1 was categorized as a discrepancy.

Results

FDA reports were available for 8 of 9 FDA-approved biologic agents for rheumatoid arthritis; all identified trials (34) except one were published in peer-reviewed journals. Overall, discrepancies were noted for 20 of the 33 evaluated trials. Differences in the apparent benefit reporting were found in 39% (24/61) pairwise comparisons and in 11 cases these were statistically significant; the FDA report showed greater benefit than the journal publication in 15 comparisons and lesser benefit in 9. Differences in the reported harms were found in 51% (28/55) pairwise comparisons and were statistically significant in 5. The “signal” in FDA reports showed a less harmful effect than the journal publication in 17 comparisons whereas a more harmful effect in 11. The differences were attributed to differences in analytic approach, patient inclusion, rounding effect, and counting discrepancies. However, no differences were categorized as critical.

Conclusion

There was no empirical evidence to suggest biased estimates between the two sources. Increased and detailed transparency in publications would improve the understanding and credibility of published results. Further, the FDA report was found to be a useful source when data are missing in the published report (i.e. reporting bias).     

Qualitative and quantitative aspects of recent research on helminth parasites

Relationships between the species diversity of different taxa, the mean number of articles published per year on each taxon, and the mean impact factor of the journals in which they appear, were examined across six taxa of helminths: Nematomorpha, Acanthocephala, Monogenea, Trematoda, Cestoda and Nematoda, the latter including only animal parasitic nematodes. The mean annual output of scientific articles per taxon was not related to the species diversity of these taxa or, at least, not significantly. Thus, the large volume of publications on nematodes is not merely a reflection of their estimated diversity. There were significant differences among taxa in the mean impact factor of the journals in which papers on each taxon appeared, with nematodes having the highest mean score, followed by trematodes and cestodes. In addition, across the six taxa, the mean journal impact factor correlated positively and significantly with the mean annual number of papers published: not only are there more papers published on nematodes and trematodes than on nematomorphs or acanthocephalans, but they are also generally published in higher-ranking journals. These results suggest that there is an increasing gap in the quantity and general importance of the research carried out on different helminth taxa.     

Arboreal tropical forest vertebrates: current knowledge and research trends

We review the ecology and specialized methods required for studying arboreal mammals, birds, reptiles and amphibians, and use faunal checklists from 12 tropical wet forest sites and an analysis of all articles published during the past ten years in 14 major journals to assess current knowledge and general research trends for these groups. The percentage of arboreal vertebrates was remarkably similar at the different sites (76.2 ± 3.9%). Birds were the most arboreal group and amphibians and reptiles the least. The review of journals showed that primates were overwhelmingly the most studied group (336 papers), followed by bats (105), passeriform birds (73) and rodents (55). Judging by their portion of the arboreal vertebrate community and the number of papers surveyed, birds and amphibians and reptiles are vastly understudied compared to mammals, but this is largely due to the great number of primate studies. The number of publications on arboreal vertebrates has remained relatively stable over the last 10 years for all taxa except primates, which have seen a growth in publications. Canopy vertebrates from Brazil had by far the most publications (120), followed by Madagascar (61), Costa Rica (55) and Indonesia (42). We conclude by highlighting the priorities we see for future studies on tropical canopy vertebrates.