Progress on reproducibility

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Science  05 Jan 2018:
Vol. 359, Issue 6371, pp. 9
DOI: 10.1126/science.aar8654

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  • The high irreproducibility of cancer studies may be partly the consequence of genomic instability
    • Qiuyun Liu, Professor, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
    • Other Contributors:
      • Zijin Li, Student, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
      • Min Fu, Student, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
      • Sirui Yan, Student, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China

    It was reported that nearly 80% of the cancer studies were irreproducible in replicate attempts (1.2). Genomic instability is a hallmark of cancer cells (3). Dynamic changes such as point mutations, insertions, deletions, duplications and translocations appear in malignant cells constantly. Carcinogenesis may be triggered by the local buildup of HCl, as calcium supplement capable of neutralizing acids substantially reduced cancer risks (4,5). The alteration in the genome can result in variations in protein sequences, leading to changes in secondary chemical bonding such as hydrogen bonding. The augmented or reduced proton traffic has direct impact on cell metabolism and biochemical networks. The changes in the number of charged amino acids alter ion traffic, and change cell homeostasis. Genomic alterations in malignant tumor cells affect functional networks, DNA replications, transcriptome, proteome, etc. Therefore, part of the pronounced irreproducibility of cancer data may be the consequence of genomic alteration ongoing in cancer cells.

    Zijin Li, Min Fu, Sirui Yan, Qiuyun Liu*
    Biomedical Center, Guangdong Provincial Key Laboratory of Improved Variety Reproduction in Aquatic Economic Animals, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
    *Correspondence author.
    E-mail address: lsslqy@mail.sysu.edu.cn

    1. L. P. Fre...

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    Competing Interests: None declared.
  • An issue of reproducibility in the trans-disciplinary fields

    Jeremy Berg reported progress on the reproducibility (1).
    Data science is being used for research across various fields. However, when studying in a trans-disciplinary team, reproducibility in computer science and reproducibility in economics represented different things. The result by statistics and the result by machine learning are distinguished from each other in computer science, so the method is described. Meanwhile, researchers in economics said that they did not mind either method if results were obtained, and the description about method was required to be skipped. For computer science researchers, to be honest, the way of economics does not make their research achievements in computer science. Both are not wrong but, for example, it is like a gap between those who develop software and those who use it.
    Then, how can computer science researchers in social science field implement reproducibility into their publications? In 2014, a large research disguise was discovered and reproducibility became a large issue. At that time, doubts about review system in sciences were also applied to reviewers and editors who adopted the manuscript. So, main academic journals have placed more importance on reproducibility now. When I refer to that example, in fact, co-author agreed about a slight improvement in the description of the method.
    As another example, in the latter half of the 1990s when computers began to be used in general, an analysis was carried out w...

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    Competing Interests: None declared.

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