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Is it time for a paper mill blacklist?
Naunyn Schmiedebergs Arch Pharmacol
January 2025
Independent researcher, Ikenobe 3011-2, Miki-cho, Kagawa-ken, 761-0799, Japan.
Paper mills represent one of science's greatest threats to the integrity of the entire scientific enterprise because they have become entrenched in a culture of the commercialization and corruption of science's assets, whether these be authorships, data sets, entire papers, editorial positions, or influence during editorial processes to favor a culture of unfair publication practices. This journal, which has taken proactive and exemplary steps to deal with this plague of fakery, is no stranger to the workings of such academic criminality, as exemplified by a string of retractions resulting from paper mill interference and association. This letter posits that a public database, and blacklist, of known paper mills is needed, as well as of authors who have a track record of using paper mills, but recognizes that the establishment of such a blacklist may pose practical, legal, and ethical challenges to its implementation and maintenance.
View Article and Find Full Text PDFscNanoSeq-CUT&Tag: a single-cell long-read CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells.
Nat Methods
November 2024
School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing, China.
Article Synopsis
- Chromatin modifications are key epigenetic markers that influence how the genome functions, but studying them in complex and repetitive genomic areas has been tough.
- The research introduces scNanoSeq-CUT&Tag, a new method that combines nanopore sequencing with CUT&Tag to profile chromatin modifications at the single-cell level.
- This approach allows for accurate detection of histone marks and transcription factor activities, even in difficult-to-study regions of the genome, including repetitive elements in both human and mouse cells.
Is orthodontic research falling prey to obscure and predatory journals? A bibliometric study.
Eur J Orthod
October 2024
Division of Public and Child Dental Health, Dublin Dental School and Hospital, Dublin D02 F859, Ireland.
Aims: To evaluate where orthodontic research papers are published and to explore potential relationships between the journal of publication and the characteristics of the research study and authorship.
Methods: An online literature search of seven research databases was undertaken to identify orthodontic articles published in English language over a 12-month period (1 January-31 December 2022) (last search: 12 June 2023). Data extracted included journal, article, and author characteristics.
Forecasting potential invaders to prevent future biological invasions worldwide.
Glob Chang Biol
July 2024
School of Biological Sciences, Faculty of Science, Monash University, Clayton, Victoria, Australia.
The ever-increasing and expanding globalisation of trade and transport underpins the escalating global problem of biological invasions. Developing biosecurity infrastructures is crucial to anticipate and prevent the transport and introduction of invasive alien species. Still, robust and defensible forecasts of potential invaders are rare, especially for species without known invasion history.
View Article and Find Full Text PDFCharacterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome.
BMC Genomics
March 2024
Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China.
Article Synopsis
- Hybridization capture-based targeted next generation sequencing (NGS) is becoming crucial in cancer diagnostics, with DNA library preparation being key for quality data.
- The study found that enzymatic fragmentation produced more artifact variants compared to sonication, with distinct types of sequencing errors identified for each method.
- A new hypothesis model (PDSM) was proposed to explain these sequencing errors, and an algorithm was developed to filter out these artifacts for more reliable genomic analyses.
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