scholarly journals The thin ret(raction) line: biomedical journal responses to incorrect non-targeting nucleotide sequence reagents in human gene knockdown publications

2021 ◽  
Author(s):  
Jennifer A. Byrne ◽  
Yasunori Park ◽  
Rachael A. West ◽  
Amanda Capes-Davis ◽  
Bertrand Favier ◽  
...  

AbstractThe capacity of the scientific literature to self-correct is of vital importance, but few studies have compared post-publication journal responses to specific error types. We have compared journal responses to a specific reagent error in 31 human gene knockdown publications, namely a non-targeting or negative control nucleotide sequence that is instead predicted to target a human gene. The 31 papers published by 13 biomedical journals generated 26 published responses (14 retractions, 5 expressions of concern, 7 author corrections which included one resolved expression of concern) as well as 6 stated decisions to take no action. Variations in published responses were noted both between journals and by 4 journals that published different responses to at least 2 papers. A subset of published responses revealed conflicting explanations for the wrongly identified control reagent, despite 30/31 papers obtaining their gene knockdown reagents from the same external supplier. Viewed collectively, different journal responses to human gene knockdown publications with a common reagent error type suggest that editorial staff require more support to interpret post-publication notifications of incorrect nucleotide sequence reagents. We propose a draft template to facilitate the communication, interpretation and investigation of published errors, including errors affecting research reagents.

2006 ◽  
Vol 12 (2) ◽  
pp. 159-165 ◽  
Author(s):  
MERVIN BLAIR ◽  
ANDREW KERTESZ ◽  
PAUL MCMONAGLE ◽  
WILDA DAVIDSON ◽  
NIKOLETTA BODI

The clock drawing test (CDT) is a widely used cognitive screening test. It is useful in identifying focal lesions and cognitive deficits in dementia groups. Lately, several studies attempted its use to differentiate between dementia subtypes. Although many studies have examined the CDT in dementia populations, research into the use of clock drawing in frontotemporal dementia (FTD) is limited. We examined quantitative (global) and qualitative (specific error type) differences on the CDT between FTD (n = 36) and Alzheimer's disease (AD; n = 25) patients and controls without dementia (n = 25). Results showed significantly lower overall scores in the dementia groups compared to the control group, whereas FTD patients scored significantly higher than the AD group. On qualitative analysis, the FTD group had fewer stimulus bound responses, conceptual deficits, and spatial or planning errors compared to the AD group. In conclusion, both global and error analysis of the CDT helped discriminate the FTD group from controls and AD patients. (JINS, 2006, 12, 159–165.)


Plant Disease ◽  
2013 ◽  
Vol 97 (10) ◽  
pp. 1388-1388 ◽  
Author(s):  
Y. Qin ◽  
Z. Zhang ◽  
Z. Qiao ◽  
Q. Qiao ◽  
D. Zhang ◽  
...  

Begomoviruses infecting sweet potato (Ipomoea batatas) are phylogenetically distinct from other members of the genus Begomovirus, and have been named “sweepoviruses” (1). Sweepoviruses cause sweet potato yield losses and cultivar decline, and have been found in China (1,3). In 2011, a survey was conducted to determine the incidence, genetic diversity, and distribution of sweepoviruses in China. Thirty sweet potato cuttings showing upward leaf curl, leaf roll, chlorosis, and stunting were collected from fields in Jiangsu, Guangxi, Guizhou, Shanxi, Henan, and Hebei Provinces. Five-leaf growth stage I. setosa plants were inoculated by side-grafting with scions from these samples, and grown in an insect-proof greenhouse in 20-cm-diameter clay pots. Each sample was grafted onto three replicate plants. Healthy, non-grafted I. setosa plants were used as the negative control treatment. Total nucleic acids were extracted from 100 mg fresh leaves harvested 30 days post-inoculation (dpi) from symptomatic and negative control plants using the Universal Genomic DNA Extraction Kit (TaKaRa, Dalian, China). Universal primers for amplification of Geminiviruses (BM-V [5′-KSGGGTCGACGTCATCAATGACGTTRTAC-3′] and BM-C [5′-AARGAATTCATKGGGGCCCARARRGACTGGC-3′]) (2) were used to amplify the begomovirus A component by PCR assay. A DNA fragment of the expected size (2.8 kb) was obtained from grafted leaf samples of the Hebei Province plant, and was cloned into the pMD-19T vector (TaKaRa). The recombinant plasmid was transformed into competent cells of Escherichia coli strain JM109, and the inserted fragment sequenced. The nucleotide sequence obtained (GenBank Accession No. JX448368) was 2,785 nt long, and contained two open reading frames (ORFs) in the virion sense, and four ORFs in the complementary sense, similar to other monopartite begomoviruses (1). The sequence was compared with sequences in GenBank using BLAST. The results revealed the greatest nucleotide sequence identity, 90.8%, with that of the Sweet potato leaf curl Georgia virus (SPLCGV) from Georgia, United States (AF326775). The sequence also shared identities of <89% with other sweepoviruses, and was therefore designated SPLCGV-China: Hebei: 2011. Comparison of the complete genome sequence of SPLCGV-China: Hebei: 2011 with SPLCGV revealed an 18 nucleotide insertion between AV-1 and AC-3. The results confirmed that the sweet potato sample from which SPLCGV-China: Hebei: 2011 was obtained was infected with SPLCGV. To our knowledge, this is the first report of the natural occurrence of SPLCGV in China. This study will assist with understanding the presence of this virus and genetic diversity of sweepoviruses in China. References: (1) H. P. Bi and P. Zhang. Arch. Virol. 157:441, 2012. (2) R. W. Briddon and P. G. Markham. Mol. Biotechnol. 1:202, 1994. (3) Y. S. Luan et al. Virus Genes 35:379, 2007.


2018 ◽  
Vol 13 (10) ◽  
pp. 1587-1597 ◽  
Author(s):  
Allison Tong ◽  
Deidra C. Crews ◽  
Jane O. Schell ◽  
Ian H. de Boer ◽  
Michel Chonchol ◽  
...  

The digital era has seen rapid changes in how information is consumed. Traditional dissemination of scholarly work through biomedical journals may not be optimally tailored to the preferences of younger clinicians and researchers. We aimed to describe the perspectives of young clinicians and researchers in kidney disease on consuming scientific information. Three focus groups were conducted during the 2017 American Society of Nephrology Kidney Week with a total of 29 nephrologists and researchers (ages 40 years old and younger) purposively sampled through our networks and the American Society of Nephrology registration database. Data were analyzed thematically. Of the 72 participants invited, 29 participated from 28 centers across 13 countries. Five themes were identified: capturing and retaining attention (with subthemes of triggering interest, optimizing readability, and navigation to sustain motivation); having discernible relevance (resonating with clinical and research interests, supporting professional development, action-oriented and readily applicable, able to disseminate, contextualizing the study, and filtering out informational noise); immediacy and efficiency in processing information (requiring instantaneous and easy access, enabling rapid understanding, and facilitating comprehension of complex concepts); trusting legitimate and credible sources (authoritative indicator of importance and quality, reputable experts broadening perspective, certainty and confidence with collegial input, accurate framing and translation of the message, ascertaining methodologic detail and nuances, and integrating the patient perspective); and social dialoguing and debate. Immediate and digitally optimized access motivated young kidney professionals to consume scientific information. Mechanisms that enable them to distil relevant and new evidence, appraise and apply information to clinical practice and research, disseminate studies to colleagues, and engage in discussion and debate may enhance their comprehension, confidence, interpretation, and use of scientific literature.


1987 ◽  
Vol 15 (23) ◽  
pp. 10051-10051 ◽  
Author(s):  
Koichi Ishida ◽  
Tomio Morino ◽  
Kenkichi Takagi ◽  
Yoshikazu Sukenaga

Gene ◽  
1991 ◽  
Vol 108 (2) ◽  
pp. 293-298 ◽  
Author(s):  
Haider Mehdi ◽  
Michael Nunn ◽  
Diana M. Steel ◽  
Alexander S. Whitehead ◽  
Mary Perez ◽  
...  

2022 ◽  
Vol 5 (4) ◽  
pp. e202101203
Author(s):  
Yasunori Park ◽  
Rachael A West ◽  
Pranujan Pathmendra ◽  
Bertrand Favier ◽  
Thomas Stoeger ◽  
...  

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.


1996 ◽  
Vol 43 (3) ◽  
pp. 575-578 ◽  
Author(s):  
B Przybojewska ◽  
G Płucienniczak

The c-H-ras-1 gene of an B6C3F1 mouse was isolated and nucleotide sequence determined. Our study has revealed that this c-H-ras-1 gene consists of four exons, separated by three introns ranging in size from 150 to 649 bp. The coding parts of the sequence of mouse c-H-ras-1 gene show no important differences as compared with those of the rat, hamster and human gene. More numerous changes were found in introns. The identity of mouse c-H-ras-1 gene with rat, hamster and human ones at the nucleotide level is 86.40%, 80.04% and 67.87%, respectively. Comparison of amino acids in protein sequence of c-H-ras gene of mouse, rat, hamster and human points to high degree of conservation of the gene.


2022 ◽  
Author(s):  
Akshay Markanday ◽  
Sungho Hong ◽  
Junya Inoue ◽  
Erik De Schutter ◽  
Peter Thier

Both the environment and our body keep changing dynamically. Hence, ensuring movement precision requires adaptation to multiple demands occurring simultaneously. Here we show that the cerebellum performs the necessary multi-dimensional computations for the flexible control of different movement parameters depending on the prevailing context. This conclusion is based on the identification of a manifold-like activity in both mossy fibers (MF, network input) and Purkinje cells (PC, output), recorded from monkeys performing a saccade task. Unlike MFs, the properties of PC manifolds developed selective representations of individual movement parameters. Error feedback-driven climbing fiber input modulated the PC manifolds to predict specific, error type-dependent changes in subsequent actions. Furthermore, a feed-forward network model that simulated MF-to-PC transformations revealed that amplification and restructuring of the lesser variability in the MF activity is a pivotal circuit mechanism. Therefore, flexible control of movement by the cerebellum crucially depends on its capacity for multi-dimensional computations.


Gene ◽  
1997 ◽  
Vol 186 (2) ◽  
pp. 285-292 ◽  
Author(s):  
Koji Nata ◽  
Toshinari Takamura ◽  
Tadahiro Karasawa ◽  
Tomoko Kumagai ◽  
Wataru Hashioka ◽  
...  

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1928-1928
Author(s):  
Nancy Day ◽  
Janet Ayello ◽  
Carmella van de Ven ◽  
Megan S Lim ◽  
Sherrie L. Perkins ◽  
...  

Abstract Abstract 1928 Poster Board I-951 Background: Burkitt lymphoma (BL) represents approximately 40% of all childhood or adolescent NHL (Cairo et al., Blood, 2007). Following a multivariate analysis for known prognostic factors, we have identified a subgroup of BL patients with a 13q deletion who had a significantly poorer outcome despite aggressive short, intensive multiagent chemotherapy (Poirel/Cairo et al Leukemia 2009). More recently, we identified in a subset analysis that children with BL and a 13q14.3 deletion by FISH analysis have a significant inferior OS (Nelson/Cairo/Perkins/Sanger et al BJHaem, In Press). DLEU1, a gene within the Burkitt classifier genes as reported by Dave/Staudt et al. NEJM, 2006, is located within the region of 13q14.3. In addition, DLEU1 is recognized to interact with c-Myc, histone acetylase (HTATIP), tumor antigen p53, histone-lysine N-methyltransferase (SETDB1), Tubulin beta-2C (TUBB2C), RASSF1A, and E3 ubiquitin-protein ligase (UBR1). We have previously reported that DLEU1 may in part function as a potential tumor suppressor gene. When DLEU1 is down regulated by a DLEU1 siRNA, the spontaneous apoptotic rate was decreased with concomitant significantly reduced levels of UBR1 and TUBB2C gene expression (Day/Cairo et al SIOP 2008). In gene array profiling studies, we also found that the expression levels of RASSF1, ERG, UBR1, and TUBB2C were significantly higher in BL than in DLBCL (Day/Cairo et al, AACR 2008). Objective: In this study, we sought to examine the percent of apoptosis induced by CY and/or rituximab in DLEU1 siRNA transfected BL cells. Methods: Ramos BL cell lines were transiently transfected (24 hrs) with DLEU1 siRNA as previously described (5'-AUACUUGGCAUGAAUGAACUUAUGU-3' and 3'-UAUGAACCGUACUUACUUGAAUACA-5') (Day/Cairo SIOP 2008). Stealth RNAi whose GC content is similar to that of this DLEU1 siRNA was used as negative control. The siRNA transfected cells were then treated with CY (0, 89.5, 895, 8950 nM) and/or rituximab (0, 4, 40, 400 mg/mL) for additional 4 hrs. Cells were evaluated for percent apoptosis using Annexin V-FITC and Propidium Iodide followed by FACS using BD LSRII. Statistics was conducted by one-way ANOVA followed by Dunnett multiple comparisons test. Results: There was a significant reduction in apoptosis in the CY treated BL transfected DLEU1 siRNA vs mock control cells (89.5 nM CY: 10.26±0.23% reduction, p<0.05 to negative control; 895 nM CY, 10.86±0.67% reduction, p<0.01; 8950 nM, 9.85±0.32% reduction, p<0.05. There was a similar significant reduction in rituximab induced apoptosis in the BL transfected DLEU1 siRNA vs mock control cells (4 mg/mL Rituximab: 25.45±2.55% reduction, p<0.01 to negative control; 40 mg/mL Rituximab, 18.31±5.13% reduction, p<0.04; 400 mg/mL Rituximab, 32.33±1.77% reduction, p<0.02). There was no additive effect when combining CY (895 nM) and Rituximab (4 mg/mL) in DLEU1 siRNA transfected BL cells: 17.96±3.35 vs 29.85±1.83 vs 31.74±2.44 (Figure). Conclusion: In summary, we have demonstrated that DLEU1 may in part regulate programmed cell death in BL. DLEU1 siRNA gene knockdown studies resulted in significantly less apoptosis in CY and rituximab treated BL cells. Deletion of 13q14.3, which contains DLEU1, in pediatric BL may confer a phenotype of drug resistance and predispose pediatric patients with BL to a significantly decreased EFS following intensive multiagent chemotherapy. Disclosures: No relevant conflicts of interest to declare.


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