Biomedical Journal Articles Research Articles

A systematic review of retractions in biomedical research publications: reasons for retractions and their citations in Indian affiliations

Retractions of peer-reviewed biomedical journal articles with Indian authorship have been on the rise for many years. Our study aimed to investigate the reason behind these retractions, namely plagiarism, falsification, fabrication, duplicate publication, author conflicts, ethical issues, fake peer-reviews, and data-related issues, besides providing year-wise trends regarding retraction, authorship, impact factor, and citations. We retrieved retracted publications with Indian affiliations indexed in MEDLINE between 1 January 1990 to 31 December 2021. During this period a total of 619 papers from 372 different journals with median values (interquartile range) pertaining to impact factor [3.2 (1.5, 5.2)], retraction time [24 (10, 51)] months, pre-retraction citations [4 (1, 12)], and post-retraction citations [4 (2, 12)] were retracted. While retractions still account for a small fraction of all publications (0.1%), the overall rate of retractions, that is, the number of retractions relative to the number of newly published journal articles in a given year, has been increasing. The reasons for retractions included plagiarism (27%), falsification and fabrication (26%), duplicate publication (21%), erroneous data (12%), authorship issues (4%), fake-peer reviews (3%), and ethical and funding issues (2%). We have analysed these reasons separately and compared them with each other. Besides a spurt in retraction due to plagiarism, instances of falsification have been escalating over the past decade. Half of the papers retracted on grounds of falsification were published by repeat offender authors in high-impact journals. Furthermore, 82% of retracted papers continued to accumulate citations even after the release of the journal retraction notices. The increase in retractions raises concerns over research quality as well as the wastage of scientific resources, which is especially pressing considering the present environment of scarce funding. The problem of retractions due to reasons such as plagiarism, duplicate publication, authorship issues, and, ethical issues as well as post-retraction citations can be mitigated by educating and raising awareness on publication ethics and responsible research conduct of researchers and journal publishers. Retractions due to fabrication, falsification, and fake peer reviews are more challenging to difficult to address and require further research for the identification of effective solutions.

Literature-Based Discovery Predicts Antihistamines Are a Promising Repurposed Adjuvant Therapy for Parkinson's Disease.

Parkinson's disease (PD) is a movement disorder caused by a dopamine deficit in the brain. Current therapies primarily focus on dopamine modulators or replacements, such as levodopa. Although dopamine replacement can help alleviate PD symptoms, therapies targeting the underlying neurodegenerative process are limited. The study objective was to use artificial intelligence to rank the most promising repurposed drug candidates for PD. Natural language processing (NLP) techniques were used to extract text relationships from 33+ million biomedical journal articles from PubMed and map relationships between genes, proteins, drugs, diseases, etc., into a knowledge graph. Cross-domain text mining, hub network analysis, and unsupervised learning rank aggregation were performed in SemNet 2.0 to predict the most relevant drug candidates to levodopa and PD using relevance-based HeteSim scores. The top predicted adjuvant PD therapies included ebastine, an antihistamine for perennial allergic rhinitis; levocetirizine, another antihistamine; vancomycin, a powerful antibiotic; captopril, an angiotensin-converting enzyme (ACE) inhibitor; and neramexane, an N-methyl-D-aspartate (NMDA) receptor agonist. Cross-domain text mining predicted that antihistamines exhibit the capacity to synergistically alleviate Parkinsonian symptoms when used with dopamine modulators like levodopa or levodopa-carbidopa. The relationship patterns among the identified adjuvant candidates suggest that the likely therapeutic mechanism(s) of action of antihistamines for combatting the multi-factorial PD pathology include counteracting oxidative stress, amending the balance of neurotransmitters, and decreasing the proliferation of inflammatory mediators. Finally, cross-domain text mining interestingly predicted a strong relationship between PD and liver disease.

Some unconventional fate of the letter to the editor in response to a published article and appraisal to the journal editors.

Some unconventional fate of the letter to the editor in response to a published article and appraisal to the journal editors.

The NLM indexer assignment dataset: a new large-scale dataset for reviewer assignment research.

MEDLINE is the National Library of Medicine's (NLM) journal citation database. It contains over 28 million references to biomedical and life science journal articles, and a key feature of the database is that all articles are indexed with NLM Medical Subject Headings (MeSH). The library employs a team of MeSH indexers, and in recent years they have been asked to index close to 1 million articles per year in order to keep MEDLINE up to date. An important part of the MEDLINE indexing process is the assignment of articles to indexers. High quality and timely indexing is only possible when articles are assigned to indexers with suitable expertise. This paper introduces the NLM indexer assignment dataset: a large dataset of 4.2 million indexer article assignments for articles indexed between 2011 and 2019. The dataset is shown to be a valuable testbed for expert matching and assignment algorithms, and indexer article assignment is also found to be useful domain-adaptive pre-training for the closely related task of reviewer assignment.

Free MEDLINE access worldwide.

When Donald A.B. Lindberg M.D. was sworn in as Director of the National Library of Medicine (NLM) in 1984, MEDLINE, NLM’s online database of citations and abstracts to biomedical journal articles, was searched primarily by librarians trained to use its command language interface. There were fees for searching, primarily to recover the cost of using commercial value-added telecommunications networks. Thirteen years later, in 1997, MEDLINE became free to anyone with an Internet connection and a Web browser. This chapter provides an insider’s view of how Dr. Lindberg’s vision and leadership - combined with new technology, astute handling of policy issues, and key help from political supporters and influential advocates - enabled a tremendous expansion in access to biomedical and health information for scientists, health professionals, patients, and the public.

Expert-recommended biomedical journal articles: Their retractions or corrections, and post-retraction citing

Faculty Opinions has provided recommendations of important biomedical publications by domain experts (FMs) since 2001. The purpose of this study is two-fold: (1) identify the characteristics of the expert-recommended articles that were subsequently retracted and (2) investigate what happened after retraction. We examined a set of 232 recommended, later retracted or corrected articles. These articles were classified as New Finding (43%), Interesting Hypothesis (16%), and so on. More than 71% of the articles acknowledged funding support; the National Institutes of Health, USA (NIH) was a top funder (64%). The top reasons for retractions were Errors of various types (28%); Falsification/fabrication of data, image, or results (20%); Unreliable data, image, or results (16%); and Results not reproducible (16%). Retractions took from less than 2 months to more than 15 years. Only 15% of recommendations were withdrawn either after dissents were made by other FMs or after retractions. Most of the retracted articles continue to be cited post-retraction, especially those published in Nature, Science, and Cell. Significant positive correlations were observed between post-retraction citations and pre-retraction citations, between post-retraction citations and peak citations, and between post-retraction citations and the post-retraction citing span. A significant negative correlation was also observed between the post-retraction citing span and years taken to reach peak citations. Literature recommendation systems need to update the changing status of the recommended articles in a timely manner; invite the recommending experts to update their recommendations; and provide a personalised mechanism to alert users who have accessed the recommended articles on their subsequent retractions, concerns, or corrections.

Free MEDLINE Access Worldwide.

When Donald A.B. Lindberg M.D. was sworn in as Director of the National Library of Medicine (NLM) in 1984, MEDLINE, NLM's online database of citations and abstracts to biomedical journal articles, was searched primarily by librarians trained to use its command language interface. There were fees for searching, primarily to recover the cost of using commercial value-added telecommunications networks. Thirteen years later, in 1997, MEDLINE became free to anyone with an Internet connection and a Web browser. This chapter provides an insider's view of how Dr. Lindberg's vision and leadership - combined with new technology, astute handling of policy issues, and key help from political supporters and influential advocates - enabled a tremendous expansion in access to biomedical and health information for scientists, health professionals, patients, and the public.

Smart watches: A review of evolution in bio-medical sector

Smartwatch (SW) is a wearable gadget used in everyday life. It is equivalent to a customary wristwatch and offers features similar to a smartphone. These features include access to the internet, making a call, weather updates, text or video messages, GPS navigation, health, physical fitness information, etc. The market for wearable gadgets and SWs is increasing day by day. There are many benefits and drawbacks of smartwatches in medical environments. This article aims to review the existing literature on smartwatch applications in the biomedical sector. As a result, this paper compiles all the information regarding SW technology in the biomedical sector and related journal articles, conference proceedings, web materials, market survey reports, and history in one place. The review shows that the demand rate of SWs in India is less as compared to other countries. It is increasing with the years, but the overall rate of demand is not as expected. It varies with the user’s choice. The vital author keyword and index keywords are presented. The abstract and title words are also analyzed with Vosviewer 1.6.16 software. The attributes/criteria associated with SWs are also discussed, which helps in purchasing them. The paper also discusses the flaws and problems that need to be resolved in the present situation and several potential alternatives for prospective research projects.

ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts.

Analysis of high-throughput experiments in the life sciences frequently relies upon standardized information about genes, gene products, and other biological entities. To provide this information, expert curators are increasingly relying on text mining tools to identify, extract and harmonize statements from biomedical journal articles that discuss findings of interest. For determining reliability of the statements, curators need the evidence used by the authors to support their assertions. It is important to annotate the evidence directly used by authors to qualify their findings rather than simply annotating mentions of experimental methods without the context of what findings they support. Text mining tools require tuning and adaptation to achieve accurate performance. Many annotated corpora exist to enable developing and tuning text mining tools; however, none currently provides annotations of evidence based on the extensive and widely used Evidence and Conclusion Ontology. We present the ECO-CollecTF corpus, a novel, freely available, biomedical corpus of 84 documents that captures high-quality, evidence-based statements annotated with the Evidence and Conclusion Ontology.

Uprooting race-based assumptions in biomedical journal articles.

Coronavirus disease 2019 (COVID-19) has exacerbated the structural inequities in healthcare and the challenges of translating research into public discourse. This article highlights key antiracist considerations, presents previously noted core challenges, and provides recommendations for writing and reporting. Importantly, this article contributes to combating racialized science in the biomedical community.

Biomedical article authorship: A proposal to enhance the meaningful assignment of authorship

The authorship of articles in biomedical journals has proliferated despite efforts of publishers and editors to require justification of authorship. A proposal is made, herein, to resolve that matter by applying the “one paper: one citation” concept, so as to adhere to the thermodynamic principle of conservation of mass. This proposal provides (i) a means to allow authors to agree on their relative contribution, (ii) an incentive to assign only significant contributors to authorship, and (iii) the appropriate fractional contribution of each author when there are multiple authors. As a result, the sum of citations for any one paper shall be one paper. I believe this proposal the only method suggested, thus far, to make authorship of a biomedical paper authentic.

Knowledge and motivations of researchers publishing in presumed predatory journals: a survey

ObjectivesTo develop effective interventions to prevent publishing in presumed predatory journals (ie, journals that display deceptive characteristics, markers or data that cannot be verified), it is helpful to understand the...

Opinion: Strategy of Semi-Automatically Annotating Full Text Corpus of Genomics & Informatics.

There is a communal need for an annotated corpus consisting of the full texts of biomedical journal articles. In response to community needs, a prototype version of the full-text corpus of Genomics & Informatics, called GNI version 1.0, has recently been published, with 499 annotated full-text articles available as a corpus resource. However, GNI needs to be updated, as the texts were shallow-parsed and annotated with several existing parsers. I list issues associated with upgrading annotations and give an opinion on the methodology for developing the next version of the GNI corpus, based on a semi-automatic strategy for more linguistically rich corpus annotation.

The functional anatomy of the human spermatozoon: relating ultrastructure and function.

The Internet, magazine articles, and even biomedical journal articles, are full of cartoons of spermatozoa that bear minimal resemblance to real spermatozoa, especially human spermatozoa, and this had led to many misconceptions about what spermatozoa look like and how they are constituted. This review summarizes the historical and current state of knowledge of mammalian sperm ultrastructure, with particular emphasis on and relevance to human spermatozoa, combining information obtained from a variety of electron microscopic (EM) techniques. Available information on the composition and configuration of the various ultrastructural components of the spermatozoon has been related to their mechanistic purpose and roles in the primary aspects of sperm function and fertilization: motility, hyperactivation, capacitation, the acrosome reaction and sperm-oocyte fusion.

Role of supplementary material in biomedical journal articles: surveys of authors, reviewers and readers

ObjectiveMany journals permit authors to submit supplementary material for publication alongside the article. We explore the value, use and role of this material in biomedical journal articles from the perspectives...

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

BackgroundCoreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature. In order to better understand the nature of the phenomenon of coreference in biomedical publications and to increase performance on the task, we annotated the Colorado Richly Annotated Full Text (CRAFT) corpus with coreference relations.ResultsThe corpus was manually annotated with coreference relations, including identity and appositives for all coreferring base noun phrases. The OntoNotes annotation guidelines, with minor adaptations, were used. Interannotator agreement ranges from 0.480 (entity-based CEAF) to 0.858 (Class-B3), depending on the metric that is used to assess it. The resulting corpus adds nearly 30,000 annotations to the previous release of the CRAFT corpus. Differences from related projects include a much broader definition of markables, connection to extensive annotation of several domain-relevant semantic classes, and connection to complete syntactic annotation. Tool performance was benchmarked on the data. A publicly available out-of-the-box, general-domain coreference resolution system achieved an F-measure of 0.14 (B3), while a simple domain-adapted rule-based system achieved an F-measure of 0.42. An ensemble of the two reached F of 0.46. Following the IDENTITY chains in the data would add 106,263 additional named entities in the full 97-paper corpus, for an increase of 76% percent in the semantic classes of the eight ontologies that have been annotated in earlier versions of the CRAFT corpus.ConclusionsThe project produced a large data set for further investigation of coreference and coreference resolution in the scientific literature. The work raised issues in the phenomenon of reference in this domain and genre, and the paper proposes that many mentions that would be considered generic in the general domain are not generic in the biomedical domain due to their referents to specific classes in domain-specific ontologies. The comparison of the performance of a publicly available and well-understood coreference resolution system with a domain-adapted system produced results that are consistent with the notion that the requirements for successful coreference resolution in this genre are quite different from those of the general domain, and also suggest that the baseline performance difference is quite large.

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus.

Gold-standard annotated corpora have become important resources for the training and testing of natural-language-processing (NLP) systems designed to support biocuration efforts, and ontologies are increasingly used to facilitate curational consistency and semantic integration across disparate resources. Bringing together the respective power of these, the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of full-length, open-access biomedical journal articles with extensive manually created syntactic, formatting and semantic markup, was previously created and released. This initial public release has already been used in multiple projects to drive development of systems focused on a variety of biocuration, search, visualization, and semantic and syntactic NLP tasks. Building on its demonstrated utility, we have expanded the CRAFT Corpus with a large set of manually created semantic annotations relying on Uberon, an ontology representing anatomical entities and life-cycle stages of multicellular organisms across species as well as types of multicellular organisms defined in terms of life-cycle stage and sexual characteristics. This newly created set of annotations, which has been added for v2.1 of the corpus, is by far the largest publicly available collection of gold-standard anatomical markup and is the first large-scale effort at manual markup of biomedical text relying on the entirety of an anatomical terminology, as opposed to annotation with a small number of high-level anatomical categories, as performed in previous corpora. In addition to presenting and discussing this newly available resource, we apply it to provide a performance baseline for the automatic annotation of anatomical concepts in biomedical text using a prominent concept recognition system. The full corpus, released with a CC BY 3.0 license, may be downloaded from http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml. Database URL: http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml

A text feature-based approach for literature mining of lncRNA–protein interactions

Long non-coding RNAs (lncRNAs) play important roles in regulating transcriptional and post-transcriptional levels. Currently, Knowledge of lncRNA and protein interactions (LPIs) is crucial for biomedical researches that are related to lncRNA. Many freshly discovered LPIs are stored in biomedical literature. With over one million new biomedical journal articles published every year, just keeping up with the novel finding requires automatically extracting information by text mining. To address this issue, we apply a text feature-based text mining approach to efficiently extract LPIs from biomedical literatures. Our approach consists of four steps. By employ natural language processing (NLP) technologies, this approach extracts text features from sentences that can precisely reflect the real LPIs. Our approach involves four steps including data collection, text pre-processing, structured representation, features extraction and training model and classification. The F-score performance of our approach achieves 79.5%, and the results indicate that the proposed approach can efficiently extract LPIs from biomedical literature.

Reproducible Research Practices and Transparency across the Biomedical Literature.

There is a growing movement to encourage reproducibility and transparency practices in the scientific community, including public access to raw data and protocols, the conduct of replication studies, systematic integration of evidence in systematic reviews, and the documentation of funding and potential conflicts of interest. In this survey, we assessed the current status of reproducibility and transparency addressing these indicators in a random sample of 441 biomedical journal articles published in 2000–2014. Only one study provided a full protocol and none made all raw data directly available. Replication studies were rare (n = 4), and only 16 studies had their data included in a subsequent systematic review or meta-analysis. The majority of studies did not mention anything about funding or conflicts of interest. The percentage of articles with no statement of conflict decreased substantially between 2000 and 2014 (94.4% in 2000 to 34.6% in 2014); the percentage of articles reporting statements of conflicts (0% in 2000, 15.4% in 2014) or no conflicts (5.6% in 2000, 50.0% in 2014) increased. Articles published in journals in the clinical medicine category versus other fields were almost twice as likely to not include any information on funding and to have private funding. This study provides baseline data to compare future progress in improving these indicators in the scientific literature.

Coreference resolution improves extraction of Biological Expression Language statements from texts.

We describe a system that automatically extracts biological events from biomedical journal articles, and translates those events into Biological Expression Language (BEL) statements. The system incorporates existing text mining components for coreference resolution, biological event extraction and a previously formally untested strategy for BEL statement generation. Although addressing the BEL track (Track 4) at BioCreative V (2015), we also investigate how incorporating coreference resolution might impact event extraction in the biomedical domain. In this paper, we report that our system achieved the best performance of 20.2 and 35.2 in F-score for the full BEL statement level on both stage 1, and stage 2 using provided gold standard entities, respectively. We also report that our results evaluated on the training dataset show benefit from integrating coreference resolution with event extraction.