Biological Journals Research Articles

’Gypsies’, Natural Monogamy, and Violence Full of Love

The paper examines modern knowledge about non-human primates in Czech travel narratives concerning Africa and biological journals from the late nineteenth century to the end of the interwar period. Particular attention is given to the way discourse on primates and anthropological discourse mutually influenced each other. Inspired by the intersection of human – animal studies, critical race theory, and gender studies, the paper emphasizes the anthropomorphizing character of biological discourse and popular travel narratives. At the time, presentations of primates created a specific anthropological resource and, in addition, helped to naturalize the dominant racial and gender ideologies. In the context of the Austrian–Hungarian and Czechoslovakian relative inability to obtain colonial possessions in the way western powers did, the representations of anthropomorphized non-human primates can also be interpreted as a specific field where Czech colonial fantasies about dominance were expressed.

Different open access routes, varying societal impacts: evidence from the Royal Society biological journals

Different open access routes, varying societal impacts: evidence from the Royal Society biological journals

25 years of the Natura Sloveniae journal

The article presents the history of the journal Natura Sloveniae over the 25 years, from 1999–2023, of its publication. The main aim of the journal is highlighted, as well as a brief analysis of the number of contributions and authors, the taxonomic groups covered in the articles, including an overview of the citation success of the articles published in the journal. In 25 years, 286 articles by 320 authors have been published in the journal. Over the years, the geographical scope of published articles has expanded from Slovenia to SE and Central Europe. A brief statistical analysis of the published articles shows the highest popularity of articles presenting species lists or new records for Slovenia. A considerable share of the contributions are focused on individual taxa, mostly insects, including butterflies and dragonflies. In its 25th year of publication, the journal, which is jointly published by the Biotechnical Faculty at University of Ljubljana and the National Institute of Biology, is switching to the digital submission and review system of the University of Ljubljana Press. In this year, a third, thematic issue is being published for the first time. After a quarter of a century of continuous publication, the journal occupies an important niche among Slovenian scientific biological journals and continues its mission to publish original scientific contributions in the field of biogeographical, biodiversity and ecological research in Central and Southeastern Europe and to encourage young authors to publish their field observations.

Comparison of article processing times in biological journals with different financial models

The article processing time is currently one of the main characteristics that authors take into account when choosing a journal. In a competitive environment, journals, especially those with low rankings, need to process articles quickly to be attractive to authors. Most charge-free journals are significantly slower in terms of speed than journals with article processing charges (APC), and this is not only due to the fact that some journals with APC publish articles without peer reviewing and editing, but also because paid journals with peer reviewing and editing employ specialists who deal exclusively with the journal. Many domestic journals cannot afford to hire such free-from-other duties specialists, so the articles are processed by employees of the founding organization, who are also involved in scientific and educational work, which is why editorial processes are uneven. Also, article publication time is increased by volume restrictions related to the obligations of subscription publications and publication of the journal strictly by issues (especially if journal publishes issues every two months, quarterly, or less often). This paper compares the article processing time in four biology journals with different financial models from four countries. As expected, the article processing time in journals with APC was expectedly shorter than in charge-free ones. There is a noticeably long wait for paper publication after its acceptance in the journal, which publishes a printed version and releases articles not as they are ready but only as part of the finished issue. The article discusses possible ways to reduce processing time in charge-free journals. However, such a reduction should be adequate; editorial processes should not be expedited at the expense of the quality of editing and peer review.

Beware of scientific scams! Hints to avoid predatory publishing in biological journals

Our motivation for writing this editorial is to alert the academic community about the risks of predatory publishing in Biology. By piggy-backing on the open access (OA) movement and taking advantage of the “publish or perish” culture in a system that prioritises quantity over quality, predatory publishing has grown exponentially in recent years and spread across all areas of knowledge. Thousands of predatory journals and books have emerged and (provided a fee is paid) they publish scientific papers and chapters without submitting them to rigorous peer review. Now there are even predatory meetings, which promise to accept talks and publish complete works for a fee, also without reviewing them properly. These profit-making machines can damage both academia and society, putting at risk the quality of science and public trust in it, the well-being of the population, the conservation of biodiversity and the mitigation of climate change. We show the modus operandi behind invitations to contribute to predatory journals, books and meetings and suggest ways to separate the wheat from the chaff. Finally, we discuss the need to create regulatory agencies that perform a careful and systematic evaluation of the activities carried out by publishers.

Chemists Focus on Probes, Biologists on Cells—But Who Talks about Probe-Cell Interactions? A Critical Account of the Suboptimal Reporting of Novel Fluorescent Imaging Probes, Using Lipid Droplet Stains as a Case Study

Many current reports in the scientific literature describe novel fluorescent probes intended to provide information on various structures or properties of live cells by using microscopic imaging. Unfortunately, many such reports fail to provide key information regarding the staining process. It is often the case that neither the necessary minimum technical detail (probe concentration, solvent and cosolute, temperature and time of staining, and details of post-staining washes) nor a discussion of the proposed staining mechanism are provided. Such omissions make it unnecessarily difficult for biomedical end-users to try out reported novel probes in their own laboratories. The validity of these criticisms is explored and demonstrated by a detailed analysis of 75 non-cherry-picked articles describing novel fluorescent probes for the detection of lipid droplets in live cells. This dataset also suggests that papers from journals with high journal impact factors or from better-known research groups are no more likely to provide better protocol information or discussion of the mechanism than papers from less prestigious sources. Comments on possible reasons for this suboptimal reporting are offered. The use of a suitable information/feature checklist, following best practice in many leading chemical and biological journals, is suggested as a mechanism for ameliorating this situation, with a draft checklist being provided.

Error analysis of Syntactical errors and style errors in scientific articles submitted for publication in Iraqi biological journals

Most of the Iraqi researchers in the biology field write their scientific articles in English although it is not their native language. Linguistic errors can be expected in these articles particularly in verbs, tenses, conjunctions, adverbs, adjective, punctuation marks, spelling, pronouns, and plurals. Hence this study investigates linguistic errors in scientific articles written by those researchers, and published in Iraqi biological journals. The main aim of this study is to promote the level of their scientific writing in linguistic aspects and the linguistic difficulties they face in this genre of writing. The linguistic errors were identified and analyzed in 24 scientific articles from two issues of Iraqi journal of cancer and medical genetics. These scientific articles are not linguistically reviewed. This study focuses on certain syntactical errors and other errors involved punctuation ,capitalization, spelling of writing The results show that errors are committed including verbs forms ,tenses ,active and passive, adverb and adjective, conjunction, auxiliaries, down to spelling punctuation and capitalization, articles , preposition, pronouns, and finally the misuse of plural. Although there are variations between these ,on basis of, of analyzing result data that there are errors committed in these scientific articles.all samples have errors. Some errors are recurrent in forms of tenses, passive voice, and active, adverb, adjective, spelling, punctuation, etc. A big observation was recorded that some researchers strongly need to improve their English level when they write their articles.

Hierarchical Bayesian classification methods to identify topics by journal quartile with an application in biological sciences

This manuscript builds on a novel, automatic, freely-available Bayesian approach to extract information in abstracts and titles to classify research topics by quartile. This approach is demonstrated for all N= 149,129 ISI-indexed publications in biological sciences journals during 2017. A Bayesian multinomial inverse regression approach is used to extract rankings of topics without the need of a pre-defined dictionary. Bigrams are used for extraction of research topics across manuscripts, and rankings of research topics are constructed by quartile. Worldwide and local results (e.g., comparison between two peer/aspirational research institutions in Colombia) are provided, and differences are explored both at the global and local levels. Some topics persist across quartiles, while the relevance of others is quartile-specific. Challenges in sustainable development appear as more prevalent in top quartile journals across institutions, while the two Colombian institutions favour plant and microorganism research. This approach can reduce information inequities, by allowing young/incipient researchers in biological sciences, especially within lower income countries or universities with limited resources, to freely assess the state of the literature and the relative likelihood of publication in higher impact journals by research topic. This can also serve institutions of higher education to identify missing research topics and areas of competitive advantage.

Indexing of the Russian biomedical journals in MEDLINE and PubMed: analysis of the positive and negative experience

The MEDLINE database and PubMed.com web-platform are the world’s best-known and most used sources for search scientific information in biology and medicine. Indexing in MEDLINE and making a journal searchable through PubMed.com is a most powerful tool to promote it worldwide. No other databases, even Scopus and Web of Science, can be compared with MEDLINE in terms of its effect on the readability and availability in web-search results. At the same time, medical and biological journals from Russia have serious problems with the MEDLINE indexation results in an extremely low presence of publications from Russian journals in this database. Over the past decade, the number of Russian journals indexed in MEDLINE has significantly decreased. Present article discusses the main characteristics of the MEDLINE database and PubMed.com, their journal selection process and the reasons for their high importance in scientific journals promotion, as well as the experience of submitting journals for peer review to be indexed in this database. Both positive and negative experience of preparing a journal for indexing in MEDLINE is considered, this can help the editors and publishers of all biology and medicine journals in Russia in solving this task.

КОРОНАВИРУСЫ (СТРУКТУРА ГЕНОМА, РЕПЛИКАЦИЯ)

The overview presented in the article is a continuation of the publication on coronaviruses. The paper examines modern data on the structure of the genome and the replication process in various types of coronaviruses that cause diseases in humans and are of medical importance. The structure of the genomes of coronaviruses and the functions of genes that encode the structure of viral particles are presented; describes the function of structural genes and auxiliary genes; the role of genes encoding non-structural proteins in the structure of the viral particle and replication of coronaviruses is shown. The analysis of published studies made it possible to comparatively characterize the genomes of highly dangerous coronaviruses: SARS-CoV, MERS-CoV, SARS-CoV-2, describe their differences in structure and in the process of replication. The review analyzes the structure of the genome and the replication process of coronaviruses at the molecular level, taking into account the characteristics of different types of coronaviruses. To analyze the genetic structures and replication of coronaviruses, modern literary sources, articles in the world’s leading medical and biological journals were used.

КОРОНАВИРУСЫ (ТАКСОНОМИЯ, СТРУКТУРА ВИРУСА)

The review is devoted to the little-known and insufficiently studied until recently taxonomic group of viruses - coronaviruses. The publication provides definitions: «coronaviruses» and «coronavirus infection». The issues of modern taxonomy of coronaviruses and its development from the discovery of the first coronavirus to the emergence of the last pandemic species - SARS-CoV-2 are discussed. The modern results of studying the morphology, structure and structure of the viral cell in coronaviruses, the characteristics of various representatives that cause diseases in humans and are of medical importance are described. The differences in the structure and structure of viruses of different types are pointed out and it is proposed to conditionally divide into «especially dangerous» and «banal» groups of coronaviruses. To analyze virological problems, modern literary sources, the opinion of international organizations, articles in the world’s leading medical and biological journals were used. In subsequent publications, the topic of coronaviruses and coronavirus infection will be continued.

Періодичні видання НАН України з фізико-технічних і математичних наук: рівень монополізованості

This is the third article in the cycle of publications on the monopolization level of scientific periodicals of National Academy of Sciences of Ukraine. It is devoted to the journals of Section of Physical, Engineering and Mathematical Sciences. The paper finishes the first stage of research aimed at revealing the breadth of the authors’ community of the NAS of Ukraine journals during 2015–2017. As well as in the previous articles of this cycle, the estimation of the authors’ community and its monopolization level is made by the Herfindahl–Hirschman Index calculation. Thus, the quantitative weighted distribution of affiliation is made for each journal. The analysis of the journals of Section of Social Sciences and Humanities and the Section of Chemical and Biological Sciences is made in the articles previously published in the “Herald of the National Academy of Sciences of Ukraine” (2018, No. 9 and 2019, No. 10). It was shown that the chemical and biological journals of NAS of Ukraine have the lowest monopolization level — there are only 23% of middle-monopolized and 27% of low-monopolized ones. Meanwhile, only 19% of journals of the Section of Social Sciences and Humanities have the moderate monopolization level and the rest have the high one. Journals of the Section of Physical, Engineering and Mathematical Sciences are more like chemical and biological ones. They mostly have high monopolization level (54%), however 17% are moderately monopolized and 25% are low-monopolized.

Comparing the topological rank of journals in Web of Science and Mendeley

Recently, there has been a surge of interest in new data emerged due to the rapid development of the information technologies in scholarly communication. Since the 2010s, altmetrics has become a common trend in scientometric research. However, researchers have not treated in much detail the question of the probability distributions underlying these new data. The principal objective of this study was to investigate one of the classic problems of scientometrics—the problem of citation and readership distributions. The study is based on the data obtained from two information systems: Web of Science and Mendeley. Here we based on the concept of the cumulative empirical distribution function to explore the differences and similarities between citations and readership counts of biological journals indexed in Web of Science and Mendeley. The basic idea was to determine, for any journal, a “size” (it is said to be the topological rank) of citation and readership empirical cumulative distributions, and then to compare distributions of the topological ranks of Web of Science and Mendeley. In order to verify our model, we employ it to the bibliometric and altmetric research of 305 biological journals indexed in Journal Citation Reports 2015. The findings show that both distributions of the topological rank of biological journals are statistically close to the Wakeby distribution. The findings presented in this study add to our understanding of information processes of the scholarly communication in the new digital environment.

Citation Metrics and Impact Factors Fail as Measures of Scientific Quality, in Particular in Taxonomy, and are Biased by Biological Discipline and by Geographic and Taxonomic Factors

Based on my experience and analyses of citation frequencies of papers published in various biological journals, I discuss the use of citation counts and journal Impact Factors as measures of scientific quality. I conclude that citation frequency differs not only among biological sub-disciplines such as ecology and taxonomy, but also among taxonomic papers on highly similar topics, and that these latter differences largely depend on the organismal group (cryptogams vs. vascular plants and species-rich vs small genera and families) and the geographic region concerned. As a result, journals with a broad biological scope face difficulties in competing in terms of Impact Factors, and thus in competing for the best manuscripts, with journals specialized on particular sub-disciplines that attract many citations. However, since papers on “hot” topics also tend to be short-lived, these differences, at least in part, would be much reduced if citations were counted for longer periods of time or were compensated based on the average age of cited papers in the particular field. In particular in taxonomy, factors such as originality and innovativeness, generally regarded as measures of scientific quality, appear to be inversely correlated with citation frequency. I, therefore, conclude that scientific editors would be able to significantly increase the Impact Factors of taxonomic journals, not by choosing for publication the most scientifically valuable and supreme articles, but by picking manuscripts based the taxonomic position and geographic distribution of the organisms concerned. Still, the author sincerely hopes that no editor will ever take such measures!

TOPOISOMERASES: FEATURES OF THE ACTION, CLASSIFICATION, CELL FUNCTIONS, INHIBITION, ANTHRAFURANDION

Introduction. Topoisomerases influence on DNA topology and are capable of running down their super spiraling molecules by importation of one- or two-chained ruptures with the subsequent restitution and also the negative super rounds or catenae’s. Topoisomerases are known to be targets for antineoplastic therapy. Inhibitors of these enzymes of various nature and chemical structure are widely used for the suppression of tumor Topoisomerase I and/or II activity with the blocking cells in the phase G2 and a delay of their introduction in mitosis. Such difficult curable tumors as colorectal cancer, carcinoma of the stomach, non-small cell lung cancer and so forth are the most sensitive to these drugs. The search of perspective antineoplastic inhibitors is implemented generally in ranks of the non-camptothecin agents among which heterocyclic condensed nitrogenous compounds, in particular, anthrafurandiones show the most significant results. The review of thematic literature from 2011 to 2018 is devoted to the description of properties of topoisomerase as targets and their inhibitors from perspective classes. Objectives: 1. The analysis of signal characteristics of topoisomerases as targets for anticancer non-camptothecin inhibitors. 2. Identification of structure-activity relationship in the ranks of potential inhibitors of topoisomerases. 3. The choice of the most perspective non-camptothecin topoisomerase inhibitors among heterocyclic condensed nitrogenous compounds on the basis of the comparative analysis of structure and properties. Material and methods. Materials of 79 scientific articles published in the leading biological, biochemical and chemical journals of the different countries within the 8 last years are subjected to the analysis. The structure of the review meets the purpose and tasks of the scientific analysis. Results. The analysis of the thematic literature showed topoisomerases to be relevant targets for antineoplastic therapy of severe oncological pathology. In this regard, intensive search of various pharmaceuticals among topoisomerase inhibitors is performed in recent years. Researchers modify the known basic structures as well as synthesize new compounds. The discovery of a top-directional effect of the known medicines expands the data on their mechanism of the action. To identify the topoisomerase inhibitory activity of the drug the methods with the use of plasmid DNA is applied. The cytotoxic activity, apoptosis induction, including the caspases activation, modification of mitochondrial potential, influence on p53 and others are examined in parallel studies. The research directed on the identification of new effective non-camptothecin oral topoisomerase inhibitors among the anthracyclines derivatives are of undoubted relevance. Such agents, in contrast to Doxorubicin (anthracycline antibiotic widely used for tumor therapy), have moderate toxicity and allow to control the growth of solid tumors and leukemia in mono-therapy mode. Conclusion. In terms of searching of original antineoplastic agents, a class of heterocyclic condensed nitrogenous compounds, first of all, the anthraquinones showing properties of topoisomerase inhibitors is one of the most promising. The results of chemical and biological research of the compounds of this series were laid in a basis of the design of medicinal substances and their drug formulations. Prognostically significant data obtained in preclinical testing allow us to hope that obtained antitumor agents will be highly effective on a clinical stage of trials.

Statistics in a Horticultural Journal: Problems and Solutions

We examined all articles in volume 139 and the first issue of volume 140 of the Journal of the American Society for Horticultural Science (JASHS) for statistical problems. Slightly fewer than half appeared to have problems. This is consistent with what has been found for other biological journals. Problems ranged from inappropriate analyses and statistical procedures to insufficient (or complete lack of) information on how the analyses were performed. A common problem arose from taking many measurements from the same plant, which leads to correlated test results, ignored when declaring significance at P = 0.05 for each test. In this case, experiment-wise error control is lacking. We believe that many of these problems could and should have been caught in the writing or review process; i.e., identifying them did not require an extensive statistics background. This suggests that authors and reviewers have not absorbed nor kept current with many of the statistical basics needed for understanding their own data, for conducting proper statistical analyses, and for communicating their results. For a variety of reasons, graduate training in statistics for horticulture majors appears inadequate; we suggest that researchers in this field actively seek out opportunities to improve and update their statistical knowledge throughout their careers and engage a statistician as a collaborator early when unfamiliar methods are needed to design or analyze a research study. In addition, the ASHS, which publishes three journals, should assist authors, reviewers, and editors by recognizing and supporting the need for continuing education in quantitative literacy.

Statistics in a Horticultural Journal: Problems and Solutions

We examined all articles in volume 139 and the first issue of volume 140 of the Journal of the American Society for Horticultural Science (JASHS) for statistical problems. Slightly fewer than half appeared to have problems. This is consistent with what has been found for other biological journals. Problems ranged from inappropriate analyses and statistical procedures to insufficient (or complete lack of) information on how the analyses were performed. A common problem arose from taking many measurements from the same plant, which leads to correlated test results, ignored when declaring significance at P = 0.05 for each test. In this case, experiment-wise error control is lacking. We believe that many of these problems could and should have been caught in the writing or review process; i.e., identifying them did not require an extensive statistics background. This suggests that authors and reviewers have not absorbed nor kept current with many of the statistical basics needed for understanding their own data, for conducting proper statistical analyses, and for communicating their results. For a variety of reasons, graduate training in statistics for horticulture majors appears inadequate; we suggest that researchers in this field actively seek out opportunities to improve and update their statistical knowledge throughout their careers and engage a statistician as a collaborator early when unfamiliar methods are needed to design or analyze a research study. In addition, the ASHS, which publishes three journals, should assist authors, reviewers, and editors by recognizing and supporting the need for continuing education in quantitative literacy.

Statistics in a Horticultural Journal: Problems and Solutions

We examined all articles in volume 139 and the first issue of volume 140 of the Journal of the American Society for Horticultural Science (JASHS) for statistical problems. Slightly fewer than half appeared to have problems. This is consistent with what has been found for other biological journals. Problems ranged from inappropriate analyses and statistical procedures to insufficient (or complete lack of) information on how the analyses were performed. A common problem arose from taking many measurements from the same plant, which leads to correlated test results, ignored when declaring significance at P = 0.05 for each test. In this case, experiment-wise error control is lacking. We believe that many of these problems could and should have been caught in the writing or review process; i.e., identifying them did not require an extensive statistics background. This suggests that authors and reviewers have not absorbed nor kept current with many of the statistical basics needed for understanding their own data, for conducting proper statistical analyses, and for communicating their results. For a variety of reasons, graduate training in statistics for horticulture majors appears inadequate; we suggest that researchers in this field actively seek out opportunities to improve and update their statistical knowledge throughout their careers and engage a statistician as a collaborator early when unfamiliar methods are needed to design or analyze a research study. In addition, the ASHS, which publishes three journals, should assist authors, reviewers, and editors by recognizing and supporting the need for continuing education in quantitative literacy.

Predatory Practices Are Increasing among Some Open Access Medical and Biological Journals

* Corresponding author. e-mail: Dadkhah80@gmail.com. Sanjay A Pai discussed important problem in the academic world and warns researchers about predatory publishers [1]. Devnani and his colleagues believe that low-income countries must devote more resources and more researcher support to aid in dealing with predatory journals [2]. According to these Authors, predatory journals are not indexed journals or, at least, they lack reputable indexes (such as “PubMed” [3]). These Journals declare, e.g. We have contacted you earlier through email. Since we have not received any response from you regarding your valuable manuscript submission, we are taking the liberty of resending the invitation as we are aware that you may be engaged in other activities or my message may not have successfully reached you. I request you to submit a Research, Review, Case report or a Short commentary for December Issue. The impact factor of the journal is 1.9*. What’s that*? Nothing. It is written in the e-mail you have received, but if you go to their websites, you see that the declared IF is an unofficial IF. A fake Impact Factor, one of the stringent criteria to define a predatory journal by Beall Jeffrey [4]: it uses some made up measures, so claiming exaggerated international standing. We are now observing that predatory practices are also emerging among some reputable, indexed journals. Some Scopus, PubMed and Thomson Reuters indexed journals (especially journals indexed in Thomson Reuters' Zoological Index) seem to act like predatory journals, e.g., having unclear review processes and hidden publication fees. In effect, reviewing the last updates in Beall’s list of predatory journals, we can find such journals [5]. It can undermine the credibility of research results and damage public trust in biological/medical journals. In particular, we have observed questionable “special issues” in reputable indexed journals, as example of these predatory practices [6]. It seems that some reputable indexed journals create special issues and publish many papers outside of the journal’s scope apparently only to make money. Some open access journals which do not have a publication fee and have been supported by Universities or Institutes create these questionable “special issues” and publish many papers only to generate revenue. Figure 1 shows the number of published papers in questionable special issues by some reputable, indexed journals in the first half of 2015.

On Credibility, Clarity, and Compliance

On Credibility, Clarity, and Compliance