Identification of human gene research articles with wrongly identified nucleotide sequences

Nucleotide sequence reagents underpin molecular techniques that have been applied across hundreds of thousands of publications. We have previously reported wrongly identified nucleotide sequence reagents in human research publications and described a semi-automated screening tool Seek & Blastn to fact-check their claimed status. We applied Seek & Blastn to screen >11,700 publications across five literature corpora, including all original publications in Gene from 2007 to 2018 and all original open-access publications in Oncology Reports from 2014 to 2018. After manually checking Seek & Blastn outputs for >3,400 human research articles, we identified 712 articles across 78 journals that described at least one wrongly identified nucleotide sequence. Verifying the claimed identities of >13,700 sequences highlighted 1,535 wrongly identified sequences, most of which were claimed targeting reagents for the analysis of 365 human protein-coding genes and 120 non-coding RNAs. The 712 problematic articles have received >17,000 citations, including citations by human clinical trials. Given our estimate that approximately one-quarter of problematic articles may misinform the future development of human therapies, urgent measures are required to address unreliable gene research articles.

Human Versus Machine: A Comparison of Robo-Analyst and Traditional Research Analyst Investment Recommendations

We provide the first comprehensive analysis of the properties of investment recommendations generated by “Robo-Analysts,” which are human-analyst-assisted computer programs conducting automated research analysis. Our results indicate that Robo-Analyst recommendations differ from those produced by traditional “human” research analysts across several important dimensions. First, Robo-Analysts produce a more balanced distribution of buy, hold, and sell recommendations than do human analysts and are less likely to recommend “glamour” stocks and firms with prospective investment banking business. Second, automation allows Robo-Analysts to revise their recommendations more frequently than human analysts and incorporate information from complex periodic filings. Third, while Robo-Analysts’ recommendations exhibit weak short-window return reactions, they have long-term investment value. Specifically, portfolios formed based on the buy recommendations of Robo-Analysts significantly outperform those of human analysts. Overall, our results suggest that automation in the sell-side research industry can benefit investors.

Seeking Approval from Universities to Research the Views of Their Staff. Do Gatekeepers Provide a Barrier to Ethical Research?

A “gatekeeper” controls access to an organization; “gatekeeper approval” is often needed before external research can take place within an organization. We explore the need for gatekeeper approval for research with university staff employing, as a case study, a project which collected data in Australia. This case study addresses known issues, seemingly rarely addressed in the literature. The Human Research Ethics Committee (HREC)'s requirement for approval from individual universities to approach their staff brought significant consequences, exacerbated by the lack of university procedures for such approvals. Simultaneously, since invitations could legitimately be distributed via other avenues, such approval was superfluous. We recommend the HREC's blanket requirement for institutional approval instead be considered on a case-by-case basis depending on the risk of the research, and perhaps waived for low-risk research where participants are able to provide informed consent, and that universities establish processes to deal with requests from external researchers.

LUMOS - Low and Intermediate Grade Glioma Umbrella Study of Molecular Guided TherapieS at relapse: Protocol for a pilot study

IntroductionGrades 2 and 3 gliomas (G2/3 gliomas), when combined, are the second largest group of malignant brain tumours in adults. The outcomes for G2/3 gliomas at progression approach the dismal outcomes for glioblastoma (GBM), yet there is a paucity of trials for Australian patients with relapsed G2/3 gliomas compared with patients with GBM. LUMOS will be a pilot umbrella study for patients with relapsed G2/3 gliomas that aims to match patients to targeted therapies based on molecular screening with contemporaneous tumour tissue. Participants in whom no actionable or no druggable mutation is found, or in whom the matching drug is not available, will form a comparator arm and receive standard of care chemotherapy. The objective of the LUMOS trial is to assess the feasibility of this approach in a multicentre study across five sites in Australia, with a view to establishing a national molecular screening platform for patient treatment guided by the mutational analysis of contemporaneous tissue biopsiesMethods and analysisThis study will be a multicentre pilot study enrolling patients with recurrent grade 2/3 gliomas that have previously been treated with radiotherapy and chemotherapy at diagnosis or at first relapse. Contemporaneous tumour tissue at the time of first relapse, defined as tissue obtained within 6 months of relapse and without subsequent intervening therapy, will be obtained from patients. Molecular screening will be performed by targeted next-generation sequencing at the reference laboratory (PathWest, Perth, Australia). RNA and DNA will be extracted from representative formalin-fixed paraffin embedded tissue scrolls or microdissected from sections on glass slides tissue sections following a review of the histology by pathologists. Extracted nucleic acid will be quantified by Qubit Fluorometric Quantitation (Thermo Fisher Scientific). Library preparation and targeted capture will be performed using the TruSight Tumor 170 (TST170) kit and samples sequenced on NextSeq 550 (Illumina) using NextSeq V.2.5 hi output reagents, according to the manufacturer’s instructions. Data analysis will be performed using the Illumina BaseSpace TST170 app v1.02 and a custom tertiary pipeline, implemented within the Clinical Genomics Workspace software platform from PierianDx (also refer to section 3.2). Primary outcomes for the study will be the number of patients enrolled and the number of patients who complete molecular screening. Secondary outcomes will include the proportion of screened patients enrolled; proportion of patients who complete molecular screening; the turn-around time of molecular screening; and the value of a brain tumour specific multi-disciplinary tumour board, called the molecular tumour advisory panel as measured by the proportion of patients in whom the treatment recommendation was refined compared with the recommendations from the automated bioinformatics platform of the reference laboratory testing.Ethics and disseminationThe study was approved by the lead Human Research Ethics Committee of the Sydney Local Health District: Protocol No. X19-0383. The study will be conducted in accordance with the principles of the Declaration of Helsinki 2013, guidelines for Good Clinical Practice and the National Health and Medical Research Council National Statement on Ethical Conduct in Human Research (2007, updated 2018 and as amended periodically). Results will be disseminated using a range of media channels including newsletters, social media, scientific conferences and peer-reviewed publications.Trial registration numberACTRN12620000087954; Pre-results.

Emotional Well-Being Human Studies

Early evidence indicates an association between EWB and underlying brain processes, and that those processes change with both normal and pathological brain aging. However, the nature of these associations, the mechanisms by which EWB and its component domains change with brain aging, and how those changes may be associated with common neuropathologies in ADRD, are largely unexplored. We propose an appraisal-adaptation model in understanding relationships between EWB and ADRD. For human models, we encourage the use of well-established measures that directly assess eudaimonic and hedonic EWB, including abnormal scenarios (e.g., neuropsychiatric symptoms, anhedonia, loneliness, etc.), as well as older adults with exceptional cognition (i.e., superagers or supernormals). Dr. Lin will review premises associated with the appraisal-adaptation model in conducting human research on EWB, aging, and ADRD.

Human Research Ethics Committee Experiences and Views About Children’s Participation in Research: Results From the MESSI Study

As part of a larger study, Australian Human Research Ethics Committee (HREC) members and managers were surveyed about their decision-making and views about social research studies with child participants. Responses of 229 HREC members and 42 HREC managers are reported. While most HREC members had received ethical training, HREC training and guidelines specific to research involving children were rare. Most applications involving children had to go through a full ethical review, but few adverse events were reported to HRECs regarding the conduct of the studies. Revisions to study proposals requested by HRECs were mostly related to consent processes and age-appropriate language. One-third of HREC members said that they would approve research on any topic. Most were also concerned that the methodology was appropriate, and the risks and benefits were clearly articulated. Specific training and guidance are needed to increase HREC members’ confidence to judge ethical research with children.