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Sale JE, Stoddard BL. Fifty years of Nucleic Acids Research. Nucleic Acids Res 2024; 52:1-3. [PMID: 38178306 PMCID: PMC10783492 DOI: 10.1093/nar/gkad1156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Affiliation(s)
- Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., Seattle WA 98109, USA
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2
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Kronzucker HJ, Qiu QS, Sonnewald U. The good and the bad of preprint servers in plant physiology. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153661. [PMID: 35240511 DOI: 10.1016/j.jplph.2022.153661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Preprint servers allow rapid publication of research findings by eliminating the time gap between submission and publication associated with editorial and peer review of scientific works. Consequently, non-peer-reviewed articles are essentially accessible immediately to researchers and the public. There are many valid justifications for sharing work on preprint servers, such as the ability to collect feedback from the research community and improve work prior to journal submission and a reduced risk of work being "scooped" by competitors. Rapid access to the latest scientific developments can furthermore expedite progress in important research areas. Significant downsides of preprint servers, however, are that the public, including members of the media and policy makers, cannot judge the quality of such non-reviewed publications and that misinformation may be spread. Balancing the good and the bad of preprint servers as opposed to classic peer review, we provide guidance for authors of the Journal of Plant Physiology.
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Affiliation(s)
- Herbert J Kronzucker
- School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia; Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Quan-Sheng Qiu
- School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China.
| | - Uwe Sonnewald
- Department of Biology, Division of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstrasse 5, 91058, Erlangen, Germany.
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3
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Soderberg CK, Errington TM, Nosek BA. Credibility of preprints: an interdisciplinary survey of researchers. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201520. [PMID: 33204484 DOI: 10.31222/osf.io/kabux] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 05/28/2023]
Abstract
Preprints increase accessibility and can speed scholarly communication if researchers view them as credible enough to read and use. Preprint services do not provide the heuristic cues of a journal's reputation, selection, and peer-review processes that, regardless of their flaws, are often used as a guide for deciding what to read. We conducted a survey of 3759 researchers across a wide range of disciplines to determine the importance of different cues for assessing the credibility of individual preprints and preprint services. We found that cues related to information about open science content and independent verification of author claims were rated as highly important for judging preprint credibility, and peer views and author information were rated as less important. As of early 2020, very few preprint services display any of the most important cues. By adding such cues, services may be able to help researchers better assess the credibility of preprints, enabling scholars to more confidently use preprints, thereby accelerating scientific communication and discovery.
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Affiliation(s)
| | | | - Brian A Nosek
- Center for Open Science, Charlottesville VA, USA
- Department of Psychology, University of Virginia, Charlottesville VA, USA
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Soderberg CK, Errington TM, Nosek BA. Credibility of preprints: an interdisciplinary survey of researchers. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201520. [PMID: 33204484 PMCID: PMC7657885 DOI: 10.1098/rsos.201520] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
Preprints increase accessibility and can speed scholarly communication if researchers view them as credible enough to read and use. Preprint services do not provide the heuristic cues of a journal's reputation, selection, and peer-review processes that, regardless of their flaws, are often used as a guide for deciding what to read. We conducted a survey of 3759 researchers across a wide range of disciplines to determine the importance of different cues for assessing the credibility of individual preprints and preprint services. We found that cues related to information about open science content and independent verification of author claims were rated as highly important for judging preprint credibility, and peer views and author information were rated as less important. As of early 2020, very few preprint services display any of the most important cues. By adding such cues, services may be able to help researchers better assess the credibility of preprints, enabling scholars to more confidently use preprints, thereby accelerating scientific communication and discovery.
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Affiliation(s)
| | | | - Brian A. Nosek
- Center for Open Science, Charlottesville VA, USA
- Department of Psychology, University of Virginia, Charlottesville VA, USA
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5
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Fraser N, Momeni F, Mayr P, Peters I. The relationship between bioRxiv preprints, citations and altmetrics. QUANTITATIVE SCIENCE STUDIES 2020. [DOI: 10.1162/qss_a_00043] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
A potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences. We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently published in peer-reviewed journals. Citation data from Scopus and altmetric data from Altmetric.com were used to compare citation and online sharing behavior of bioRxiv preprints, their related journal articles, and nondeposited articles published in the same journals. We found that bioRxiv-deposited journal articles had sizably higher citation and altmetric counts compared to nondeposited articles. Regression analysis reveals that this advantage is not explained by multiple explanatory variables related to the articles’ publication venues and authorship. Further research will be required to establish whether such an effect is causal in nature. bioRxiv preprints themselves are being directly cited in journal articles, regardless of whether the preprint has subsequently been published in a journal. bioRxiv preprints are also shared widely on Twitter and in blogs, but remain relatively scarce in mainstream media and Wikipedia articles, in comparison to peer-reviewed journal articles.
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Affiliation(s)
- Nicholas Fraser
- ZBW - Leibniz Information Centre for Economics, Kiel, Germany
| | - Fakhri Momeni
- GESIS - Leibniz Institute for the Social Sciences, Cologne, Germany
| | - Philipp Mayr
- GESIS - Leibniz Institute for the Social Sciences, Cologne, Germany
| | - Isabella Peters
- ZBW - Leibniz Information Centre for Economics, Kiel, Germany
- Kiel University, Kiel, Germany
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Wu J, Ma C, Tang X, Shi Y, Liu Z, Chai X, Tang Q, Li L, Hann SS. The regulation and interaction of PVT1 and miR181a-5p contributes to the repression of SP1 expression by the combination of XJD decoction and cisplatin in human lung cancer cells. Biomed Pharmacother 2020; 121:109632. [PMID: 31707347 DOI: 10.1016/j.biopha.2019.109632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022] Open
Abstract
The Chinese herbal prescription Xiaoji decoction (XJD) has been used as an adjuvant treatment of cancer for decades. However, the molecular mechanisms underlying XJD enhancement of the efficiency of chemotherapy were undetermined. In this study, we observed that combination of XJD and cisplatin (DDP) showed a greater inhibition on growth and induced a high magnitude of apoptosis in non-small cell lung cancer (NSCLC) cells. We also found that XJD decreased lncRNA PVT1 and increased miR181a-5p expressions. There was a reciprocal interaction between PVT1 and miR181a-5p. XJD decreased SP1 protein, which were overcame by overexpressed PVT1 and inhibitors of miR181a-5p. Overexpressed SP1 reversed the inhibitory effect of XJD on cell growth. Importantly, XJD and DDP exhibited synergy on regulation of PVT1, miR181a-5p, and SP1 expressions. The similar results were observed in one in vivo model. In conclusions, XJD inhibits NSCLC cell growth via reciprocal interaction of PVT1 and miR181a-5p followed by reducing SP1 expression. XJD and DDP exhibit synergy. This study provides a novel mechanism by which XJD enhances the anti-cancer effect of DDP in NSCLC cells.
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Affiliation(s)
- Jingjing Wu
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - ChangJu Ma
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - XiaoJuan Tang
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - Yao Shi
- Department of Cerebrovascular Disease, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - Zheng Liu
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - XiaoShu Chai
- Department of Medical Oncology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - Qing Tang
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - Liuning Li
- Department of Medical Oncology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
| | - Swei Sunny Hann
- Laboratory of Tumor Biology, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Collage of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, China.
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8
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Das J, Kelley SO. High-Performance Nucleic Acid Sensors for Liquid Biopsy Applications. Angew Chem Int Ed Engl 2019; 59:2554-2564. [PMID: 31332937 DOI: 10.1002/anie.201905005] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/21/2019] [Indexed: 12/18/2022]
Abstract
Circulating tumour nucleic acids (ctNAs) are released from tumours cells and can be detected in blood samples, providing a way to track tumors without requiring a tissue sample. This "liquid biopsy" approach has the potential to replace invasive, painful, and costly tissue biopsies in cancer diagnosis and management. However, a very sensitive and specific approach is required to detect relatively low amounts of mutant sequences linked to cancer because they are masked by the high levels of wild-type sequences. This review discusses high-performance nucleic acid biosensors for ctNA analysis in patient samples. We compare sequencing- and amplification-based methods to next-generation sensors for ctDNA and ctRNA (including microRNA) profiling, such as electrochemical methods, surface plasmon resonance, Raman spectroscopy, and microfluidics and dielectrophoresis-based assays. We present an overview of the analytical sensitivity and accuracy of these methods as well as the biological and technical challenges they present.
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Affiliation(s)
- Jagotamoy Das
- Department of Pharmaceutical Sciences, Department of Chemistry, University of Toronto, Toronto, ON, M5S 3M2, Canada
| | - Shana O Kelley
- Department of Pharmaceutical Sciences, Department of Chemistry, University of Toronto, Toronto, ON, M5S 3M2, Canada
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9
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Liu Z, Ma C, Tang X, Tang Q, Lou L, Yu Y, Zheng F, Wu J, Yang XB, Wang W, Hann SS. The Reciprocal Interaction Between LncRNA CCAT1 and miR-375-3p Contribute to the Downregulation of IRF5 Gene Expression by Solasonine in HepG2 Human Hepatocellular Carcinoma Cells. Front Oncol 2019; 9:1081. [PMID: 31681610 PMCID: PMC6813207 DOI: 10.3389/fonc.2019.01081] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/30/2019] [Indexed: 01/17/2023] Open
Abstract
Solasonine (SS), a natural glycoalkaloid component, has been shown to have potent inhibitory activity and cytotoxicity against many cancer types. However, the precise mechanisms underlying this, particularly in hepatocellular carcinoma (HCC) are poorly understood. In this study, we showed that SS inhibited growth of HCC cells. Mechanistically, we observed that SS increased the expression of miR-375-3p, whereas reducing levels of long non-coding RNAs (lncRNAs) CCAT1 was noticed in HepG2 HCC and other cells. In addition, we found that SS repressed transcription factors, SP1 and interferon regulatory factor 5 (IRF5), protein expressions. There was a reciprocal interaction among miR-375-3p, CCAT1, and SP1. Moreover, SS inhibited IRF5 promoter activity, which was not observed in cells transfected with excessive expressed SP1 vectors. Interestingly, exogenously expressed IRF5 was shown to reverse expressions of SS-inhibited CCAT1 and induced-miR-375-3p; and neutralized SS-inhibited growth of HCC cells. Similar results were also found in vivo mouse model. Collectively, our results show that SS inhibits HepG2 HCC growth through the reciprocal regulation between the miR-375-3p and lncRNA CCAT1, and this results in transcription factor SP1-mediated reduction of IRF5 expression. The regulations and interactions among miR-375-3p, CCAT1, SP1, and IRF5 axis unveil a novel molecular mechanism underlying the anti-HCC growth by SS. IRF5 may be a potential target for treatment of HCC.
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Affiliation(s)
- Zheng Liu
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - ChangJu Ma
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - XiaoJuan Tang
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qing Tang
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - LiJie Lou
- Department of Gastrointestinal Surgery, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yaya Yu
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fang Zheng
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - JingJing Wu
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiao-Bo Yang
- Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Wang
- Department of Gastrointestinal Surgery, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Swei Sunny Hann
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.,Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
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