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Steps Editors Calling PubMed articles on BioPortfolio. Our PubMed references draw on over 21 million records from the medical literature. Here you can see the latest Steps Editors Calling articles that have been published worldwide.
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The International Committee of Medical Journal Editors (ICMJE) provides recommendations to improve the editorial standards and scientific quality of biomedical journals. These recommendations range from uniform technical requirements to more complex and elusive editorial issues including ethical aspects of the scientific process. Recently, registration of clinical trials, conflicts of interest disclosure, and new criteria for authorship -emphasizing the importance of responsibility and accountability-, have...
A discussion of return of genetic research results requires a common understanding of how final results are generated and what the scope of potential results may be. To this end, we provide a brief overview of the steps by which human genomic data, whether in the clinical or research setting, are generated and interpreted. We cover (1) DNA targeting methods, (2) sequencing, (3) mapping, (4) variant calling, (5) annotation, and (6) interpretation. As powerful as this technology is, we point out technical, sc...
Whole genome sequencing is becoming a diagnostics of choice for the identification of rare inherited and de novo copy number variants in families with various pediatric and late-onset genetic diseases. However, joint variant calling in pedigrees is hampered by the complexity of consensus breakpoint alignment across samples within an arbitrary pedigree structure.
The use of reporting guidelines has an important role in the development of health research, improving the quality and precision of the publications. This study evaluated how dental journals use reporting guidelines. All editors of dental journals registered on the 2013 Journal Citation Reports list (n=81) were invited to participate. The data were collected by a self-reported web-based questionnaire. Information about the profile of journal/editor and on the use of reporting guidelines by journals was gath...
The MinION device by Oxford Nanopore produces very long reads (reads over 100 kBp were reported); however it suffers from high sequencing error rate. We present an open-source DNA base caller based on deep recurrent neural networks and show that the accuracy of base calling is much dependent on the underlying software and can be improved by considering modern machine learning methods. By employing carefully crafted recurrent neural networks, our tool significantly improves base calling accuracy on data from...
Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant calling pipelines are not optimized to run efficiently on large data sets. However, as variant calling in genomic data has become common practice, several methods have been proposed to reduce runtime for DNA-seq analysis through the use of parallel computing. D...
Complementary to reference-based variant detection, recent studies revealed that many novel variants could be detected with de novo assembled genomes. To evaluate the effect of reads coverage and the accuracy of assembly-based variant calling, we simulated short reads containing more than 3 million of single nucleotide variants (SNVs) from the whole human genome and compared the efficiency of SNV calling between the assembly-based and alignment-based calling approaches. We assessed the quality of the assemb...
The International Committee of Medical Journal Editors announces requirements that a data sharing plan be prospectively registered, and a data sharing statement be included in submitted manuscripts, for clinical trials to be published in ICMJE journals.
The collection, management and visualisation of clinical pedigree (family history) data is a core activity in clinical genetics centres. However, clinical pedigree datasets can be difficult to manage, as they are time consuming to capture, and can be difficult to build, manipulate and visualise graphically. Several standalone graphical pedigree editors and drawing applications exist but there are no freely available lightweight graphical pedigree editors that can be easily configured and incorporated into w...
Nursing students are often encouraged or required to submit scholarly work for consideration for publication but most manuscripts or course assignment papers do not meet journal standards and consume valuable resources from editors and peer reviewers. The International Academy of Nursing Editors (INANE) is a group of nurse editors and publishers dedicated to promoting best practices in publishing in the nursing literature. In August 2014, editors at INANE's annual meeting voiced frustrations over multiple q...
The rate of medical emergency team (MET) calling among post-cardiac surgery patients is unknown. We set out to determine what the call frequency would be if MET activation occurred in every instance that the early warning score (EWS) breached our local threshold, what the outcome was for these patients and what the calling rate might be if the proposed New Zealand EWS (NZEWS) system was implemented with 100% adherence.
Distribution-based operational taxonomic unit-calling (dbOTU) improves on other approaches by incorporating information about the input sequences' distribution across samples. Previous implementations of dbOTU presented challenges for users. Here we introduce and evaluate a new implementation of dbOTU that is faster and more user-friendly. We show that this new implementation has theoretical and practical improvements over previous implementations of dbOTU, making the algorithm more accessible to microbial ...
Sports officials can play an important role in concussion safety by calling injury timeouts so that athletic trainers can evaluate athletes with possible concussions. Understanding the determinants of whether officials call an injury timeout when they suspect a concussion has important implications for the design of interventions that better support officials in this role.
The Journal Editors hereby issue this note of an expression of concern for the following publication: Benjamin, A. J., Jr., Kepes, S., & Bushman, B. J. (2017). Effects of weapons on aggressive thoughts, angry feelings, hostile appraisals, and aggressive behavior: A meta-analytic review of the weapons effect literature. Personality and Social Psychology Review. Advance online publication. doi:10.1177/1088868317725419 The authors of this manuscript contacted the editors indicating they had discovered some err...
Precision medicine attempts to individualize cancer therapy by matching tumor-specific genetic changes with effective targeted therapies. A crucial first step in this process is the reliable identification of cancer-relevant variants, which is considerably complicated by the impurity and heterogeneity of clinical tumor samples. We compared the impact of admixture of non-cancerous cells and low somatic allele frequencies on the sensitivity and precision of 19 state-of-the-art SNV callers. We studied both who...