Editorial Process Research Articles

Peer Review: Insights Gleaned From Observing the Editorial Process at Annals of Internal Medicine

Peer Review: Insights Gleaned From Observing the Editorial Process at <i>Annals of Internal Medicine</i>

Learnings From 1000 Rejections

AbstractThe Review of Finance aimed to significantly increase its standards over my 6 years as managing editor and 1 year as editor. To comply with these new standards, I had to reject nearly 1000 manuscripts. This paper aims to use these rejections constructively by distilling common reasons for rejection to guide future research. They are divided into three categories: contribution, execution, and exposition. Beyond extracts from decision letters that give reasons for rejection, this paper also shares excerpts that shed light on the editorial process, such as how an editor weighs up feedback to reach a decision, as well as emails to authors outside formal letters in response to queries on the process.

VRTree: Example‐Based 3D Interactive Tree Modeling in Virtual Reality

AbstractWe present VRTree, an example‐based interactive virtual reality (VR) system designed to efficiently create diverse 3D tree models while faithfully preserving botanical characteristics of real‐world references. Our method employs a novel representation called Hierarchical Branch Lobe (HBL), which captures the hierarchical features of trees and serves as a versatile intermediary for intuitive VR interaction. The HBL representation decomposes a 3D tree into a series of concise examples, each consisting of a small set of main branches, secondary branches, and lobe‐bounded twigs. The core of our system involves two key components: (1) We design an automatic algorithm to extract an initial library of HBL examples from real tree point clouds. These HBL examples can be optionally refined according to user intentions through an interactive editing process. (2) Users can interact with the extracted HBL examples to assemble new tree structures, ensuring the local features align with the target tree species. A shape‐guided procedural growth algorithm then transforms these assembled HBL structures into highly realistic, finegrained 3D tree models. Extensive experiments and user studies demonstrate that VRTree outperforms current state‐of‐the‐art approaches, offering a highly effective and easy‐to‐use VR tool for tree modeling.

The Beauty and Importance of Scientific Journals

For more than 300 years, academic journals have been the main means of communication in all disciplines to disseminate scientific discoveries and advances, both theoretical and methodological, through scientific article, since they have covered all the functions of knowledge generation. Writing articles is the highlight of the research process and through it we not only share ideas and foster the spirit of free and cooperative exchange of information, but also fuel the process of self-correction that makes science powerful. To be shared with the community, articles must go through a process of attribution of authorship, certification of validity, dissemination, distribution and archiving of knowledge. Throughout history, scientific journals have gone through different stages and through different problems inherent to the editorial process. In this essay on scientific publications, we will reflect on the nature of publications, their importance and usefulness both social and economic, their less luminous side as well as their role, as a systemic and almost irreplaceable mechanism, in the generation and transmission of scientific culture, of our knowledge and understanding about the world and about ourselves.

CRISPR-Cas9: Revolutionizing Gene Therapy for Genetic Disorders

Faulty or mutated genes cause multiple human disorders such as cancer, neurogenerative disorders, and cardiovascular diseases. These mutations in genes are usually inherited. Many treatments have been established to cure such diseases, but gene therapy is the most promising strategy. It’s an application of biotechnology that is based on correcting and replacing the mutated gene with the healthy gene, providing the genes for the proper expression of desired proteins required for curing the disease. In clinical settings, gene therapy has proved itself as a very promising treatment but has some drawbacks. Traditionally, these methods involved viral vectors that are used to deliver correct genes and replace them with the mutated genes, in patients. These approaches have somehow potential to cure diseases but often off-target effects, limitations in the editing process, and immune responses caused by patients’ immune systems are the main challenges that are the main shortcomings of this method. However, the discovery of the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease protein 9 (Cas9) genome editing system (CRISPR/Cas9) in 2012 and its development have increased the value of gene therapy in the therapeutic world [1]. CRISPR/Cas9 is a revolutionizing tool that has been in gene therapy for knocking in and out gene to correct the mutation associated with many genetic diseases. This system has evolved greatly and has many isomers using different strategies to improve both applied, basic research and its clinical application. The ability of CRISPR-Cas9 to target various genetic diseases is one of its greatest advantages. Mutation in single gene results in monogenic diseases such as cystic fibrosis, muscular dystrophy, and sickle cell anemia, and this system has shown the potential to edit or fix the defective genes, causing these diseases. Even in the case of complex disorders caused by the mutation in multiple genes such as several types of cancer, and cardiovascular diseases, CRISPR has shown very positive results. The application of CRISPR-Cas9 in gene therapy is very promising and has tremendous potential to give cures for many complex disorders. The ethical issue regarding the editing of human DNA and the inheritance of modified DNA into the next generation is still under discussion and causing hurdles in uncovering the full potential of this system. Researchers are working to increase its efficiency and specificity to reduce the off-target sequences so that only targeted modification can be achieved. Moreover, they are trying to give possible results to reduce ethical concerns. CRISPR has evolved greatly and has many isomers using different strategies to improve both applied, basic research and its clinical application in the future.

CRISPR System and Its Applications in Medicine and Stem Cell Engineering

Context: The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system is a groundbreaking gene-editing tool that shows great promise for modifying genomes. Derived from prokaryotic adaptive immune defense mechanisms, this technique has been used in research on human diseases, demonstrating remarkable therapeutic potential. Through CRISPR, specific genetic mutations in patients can be corrected during gene therapy, offering a solution for treating diseases that were previously untreatable using conventional methods. This review explores the recent progress and future prospects of the CRISPR system, focusing on its applications in medicine and stem cell engineering. Special emphasis is placed on medical applications, the latest target design or analysis tools for genome editing, advancements in stem cell engineering, and associated innovations and challenges. Evidence Acquisition: This study reviewed articles indexed in ISI, SID, PubMed, and PubMed Central from 2007 to 2024. Results: Cas9, a key protein in CRISPR gene editing, is an endonuclease capable of targeting and cutting specific DNA sequences, guided by short RNA sequences. The gene editing process involves homology-directed repair (HDR), non-homologous end joining (NHEJ), and base editing pathways. Base editing, which modifies the epigenome without inducing DNA breaks, is gaining increasing attention. However, CRISPR still faces technical challenges, and the development of more efficient "super" CRISPR technology will likely require time. This article reviews the effectiveness, limitations, and applications of the CRISPR system. Conclusions: CRISPR/Cas9 tools allow for the creation of precise models, leading to more effective treatment options for patients.

Academic journal website from the user’s perspective

Professional community recommendations on the content of academic journal websites mostly include criteria for indexing in databases, however these recommendations do not consider the authors’ and reviewers’ perspective on the website contents and design. To address this, we analyzed these recommendations through a survey of 198 Russian academic journal authors and reviewers, using a continuous sampling technique. The survey took place in April and May 2024. The questionnaire was based on the Principles of Transparency and Best Practice in Scholarly Publishing by COPE, DOAJ etc. The survey also focused on the journal website content, design, mobile version, and publication strategy of academic journal website users. We analyzed the survey results for two partially overlapping sets of authors who published in journals indexed in the Web of Science Core Collection, Scopus, and Russian Citation Science Index Core, or in journals listed by the Higher Attestation Commission of Russian Federation. The study revealed that both COPE’s recommendations and users of academic websites value information regarding aims and scope of the journal, copyright fees, review policies, timelines for the editorial and publication process, and licensing. However, Russian authors and reviewers put less emphasis on website sections that address ethical principles and authorship criteria. They prioritize having an online editorial office, security certification, scientific journal indexing and abstracting information, additional educational materials, and the ability to customize the website for devices with different screen sizes. We also discuss the importance of HTML meta tags for promoting the journal’s website. The findings of the research may contribute to promotion of Russian academic journals in international databases, improve the efficiency of communication between authors, reviewers and editors, and develop a set of recommendations that complement international publishing conventions.

Empirical Inferences Under Bayesian Framework to Identify Cellwise Outliers

Outliers are typically identified using frequentist methods. The data are classified as “outliers” or “not outliers” based on a test statistic that measures the magnitude of the difference between a value and the majority part of the data. The threshold for a data value to be an outlier is typically defined by the user. However, a subjective choice of the threshold increases the uncertainty associated with outlier status for each data value. A cellwise outlier detection algorithm named FuzzyHRT is used to automate the editing process in repeated surveys. This algorithm uses Bienaymé–Chebyshev’s inequality and fuzzy logic to detect four different types of outliers resulting from format inconsistencies, historical, tail, and relational anomalies. However, fuzzy logic is not suited for probabilistic reasoning behind the identification of anomalous cells. Bayesian methods are well suited for quantifying the uncertainty associated with the identification of outliers. Although, as suggested by the literature, there exist well-developed Bayesian methods for record-level outlier detection, Bayesian methods for identifying outliers within individual records (i.e., at the cell level) remain unexplored. This paper presents two approaches from the Bayesian perspective to study the uncertainty associated with identifying outliers. A Bayesian bootstrap approach is explored to study the uncertainty associated with the output scores from the FuzzyHRT algorithm. Empirical likelihoods in a Bayesian setting are also considered for probabilistic reasoning behind the identification of anomalous cells. NASS survey data for livestock and major crop yield (such as corn) are considered for comparing the performances of the two proposed approaches with recent cellwise outlier methods.

Analisis Peran Artifical Intelligence pada Konten Tiktok @dimulai.id

Current era of development, AI technology plays a big role in creating content in a short time. With the current AI technology, anyone can create an interesting content, because AI (Artificial Intelligence) technology, offers a new discovery when creating content on social media, this technology can also speed up the process of editing and creating content in the form of images, graphics, videos, etc..This research method uses Descriptive Qualitative method. This research approach is Phenomenology, which is the general focus of this research to examine/examine the essence or structure of experience into human consciousness by means of interviews.The role of AI (Artificial Intelligence) in content is to simplify and shorten the time in creating interesting and creative content. When explored more deeply, AI technology has many benefits and has a role in a content in the form of images or videos. This AI technology can make it easier for us to create interesting content, but keep in mind that applying it requires original creativity that comes from human ideas to create interesting content.

Pedagogical Approaches in Music and Audio Education for Deaf and Hard-of-Hearing Students

Learning about music, sound or audio can present significant challenges for individuals who are deaf and hard of hearing (DHH). Given the advancements in technology and the increasing emphasis on equality, diversity and inclusion (EDI) in education, this article proposes pedagogical approaches aimed at facilitating the learning process for DHH students in the areas of music and audio production. These approaches encompass sound visualisation, haptic feedback, automated transcription, tactics in non-linear editing and digital signal processing. Importantly, these approaches do not necessitate advanced technical skills or substantial additional resources, thus lowering barriers for DHH students to overcome challenges in music and audio production. Furthermore, these strategies would enable content creation and editing for individuals with DHH, who may have previously been excluded from participating in music and audio production. Recommendations are provided for the implementation of these approaches in diverse educational settings to promote the integration of EDI in music and audio education.

‘Texting Scarlatti’: unlocking a standard edition with a digital toolkit

Editing musical texts requires a great deal of artistic, intellectual and commercial investment but, once published, an edition tends to become inert, a form of musical still life. ‘Texting Scarlatti’ explores ways of unlocking the value of a standard edition using a variety of digital tools. For as long as the editorial process in music begins and ends with analogue graphical notation, a digital music edition will inevitably be hybrid to some extent. But our project examines each stage in that process from input to output, showing how scholarly insight, performance-based musicology, data science, HCI-inspired crowdsourcing techniques and information systems can together form the basis of an open, rich digital edition for future development. Key outputs will be an extremely large machine-readable dataset consisting of more than 310,000 bars of music, together with structured, searchable apparatus for each of the 555 sonatas in the Scarlatti canon. Musicology has been a notable absentee from recent developments in artificial intelligence and machine learning (AIML) and there is a great deal of catching-up to do. In our conclusion, we urge more scholars and publishers to make similarly large, and largely hidden, datasets more openly available for machine learning and suggest some practical steps to facilitate this.

Measuring the Prevalence of Earnings Manipulations: A Novel Approach

ABSTRACTWe provide prevalence estimates for five forms of earnings manipulation based on executives’ reports about their firms’ actual reporting practices. After preregistering our methods and analyses via the Journal of Accounting Research’s registration‐based editorial process, we recruit nearly a thousand executives from firms listed in the Russell 3000 Index to participate in either a survey or a list experiment; the hallmark of the latter being additional privacy protections designed to promote honest disclosure about self‐incriminating information. In our survey, 26.8% of executives disclose at least one form of earnings manipulation at their firm in the 2018–2023 period: 18.0% report changing an operational activity to meet a near‐term earnings target at the expense of long‐term value (i.e., real earnings management), 8.8% report intentionally obfuscating unfavorable information, 6.6% report manipulating accruals, 3.9% report withholding material information, and 0.0% report accounting fraud. Our list experiment produces an economically higher result in two cases, estimating that 29.9% of firms engaged in real earnings management and 12.4% committed accounting fraud over the same time period. We conclude that while a traditional survey can provide credible lower‐bound estimates for the prevalence of many forms of earnings manipulation, list experiments encourage more honest disclosure in some cases.

An undergraduate research experience in CRISPR-Cas9 mediated eukaryotic genome editing to teach fundamental biochemistry techniques.

CRISPR-Cas9 technology is an established, powerful tool for genome editing through the ability to target specific DNA sequences of interest for introduction of desired genetic modifications. CRISPR-Cas9 is utilized for a variety of purposes, ranging from a research molecular biology tool to treatment for human diseases. Due to its prominence across a variety of applications, it is critical that undergraduates in the life sciences are educated on CRISPR-Cas9 technology. To this end, we created an intensive eight-week long course-based undergraduate research experience (CURE) designed for students to understand CRISPR-Cas9 genome editing and perform it in Saccharomyces cerevisiae. Students enrolled in the CURE participate in 2, 3-h sessions a week and are engaged in the entire process of CRISPR-Cas9 genome editing, from preparation of genome editing reagents to characterization of mutant yeast strains. During the process, students master fundamental techniques in the life sciences, including sterile technique, Polymerase Chain Reaction (PCR), primer design, sequencing requirements, and data analysis. The course is developed with flexibility in the schedule for repetition of techniques in the event of a failed experiment, providing an authentic research experience for the students. Additionally, we have developed the course to be easily modified for the editing of any yeast gene, offering the potential to expand the course in research-driven classroom or laboratory settings.

Assembly and comparative analysis of the complete mitochondrial genome of tea-scented China rose

Plant mitochondrial (mt) genomes enable better understanding of cellular processes and phylogenetic relationships. Tea-scented China rose ‘Hume's Blush Tea-scented China’ is the ancestor of the modern hybrid tea rose and has had an important and lasting influence on the breeding of the modern horticultural rose, but a comprehensive description of its mt genome is not yet available. In this study, mature leaves were used to determine the sequence of the rose mt genome. The mt genome of ‘Hume's Blush Tea-scented China’ is a circular sequence 277 730 bp in length and includes 30 protein-coding genes, 19 tRNA genes, and 3 rRNA genes. We analyzed repeat sequences, codon preferences, and RNA editing processes. In addition, we detected the transfer of 25 chloroplast genes to the mt genome, indicating intracellular genes transferred frequently from chloroplasts to mitochondria in ‘Hume's Blush Tea-scented China’. The phylogenetic analysis of the ‘Hume's Blush Tea-scented China’ mt genome and those of 26 other plant groups reflects its taxonomic status. The Ka/Ks of most genes was less than 1, indicating that most coding genes underwent negative selection, while pi was greater than 0.01, confirming highly diverse genetic variation. This work lays a foundation for future investigation of genetic variation in ‘Hume's Blush Tea-scented China’.

Analyzing the relationship between processing speed impairment and Rey-15 item test performance

ABSTRACT Objective This study investigated the relationship between processing speed impairment severity and performance on the Rey 15-Item Test (RFIT) and RFIT + Recognition. Method Cross-sectional data from 285 examinees (228 valid/57 invalid) referred for neuropsychological assessment who were administered the RFIT, Weschler Adult Intelligence Scale-Fourth Edition (WAIS-IV) Processing Speed Index (PSI), Brief Visuospatial Memory Test – Revised, Rey Auditory Verbal Learning Test, and three independent criterion PVTs were included. PSI bands were operationalized as Intact (≥85SS; n = 163), Reduced/Possibly Impaired (77-84SS; n = 36), or Impaired (≤76 SS; n = 29). Receiver operator characteristic (ROC) curve analyses tested the RFIT and RFIT + Recognition’s classification accuracy for detecting invalid performance for the overall sample and by PSI impairment status. Results Those with intact processing speed performed significantly better on the RFIT and RFIT + Recognition than those with reduced/possibly impaired and impaired processing speed. Though verbal/visual memory predicted RFIT scores independently, PSI contributed additional variance. ROC curves for RFIT and RFIT + Recognition were significant (AUC=.64-.84). Optimal cut-scores yielded modest sensitivity (30%-63%) and high specificity (89%-93%) among those with intact and reduced processing speed but yielded unacceptable accuracy in those with impaired speed (AUC=.59-.62). Conclusions Although the RFIT and RFIT + Recognition demonstrated acceptable classification accuracy in those with intact processing speed, accuracy diminished with increasing speed impairment. This finding was more pronounced for RFIT + Recognition compared to the traditional RFIT. As such, the RFIT may have limited clinical utility in examinees with more significant processing speed deficits.

Sources and development of the Kalevala as an example for the quantitative analysis of literary editions and sources

This paper describes ongoing work to quantitatively analyse the development of the Finnish national epic Kalevala. The analysis targets both the oral poetry sources used and the development of the final edition through multiple preparatory publications and manuscripts. In terms of methodological development, the paper relates to prior research on how to visualise relations between texts. However, the particular nature of oral poetry and the editing process at play here precludes using the established methods directly, leading instead to the development of complementary approaches.

Indigenous Voices in the Knowledge Production

In Brazil, in recent years, we have observed an increase in the access of indigenous people in Higher Education and Postgraduate Studies. They demand recognition as producers of scientific knowledge, overcoming the colonial paradigms that objectify them in the production of knowledge. However, in the case of Public Health, persists a very low visibility of indigenous participation in academia. This experience report presents the project “Indigenous Voices in the Production of Knowledge”, carried out through a partnership between a collective of indigenous researchers from different regions of the country and researchers from “Academic Institution”. A network of 20 indigenous researchers was organized, who met in 2019 and highlighted the need to “give recognition to indigenous knowledge” as a scientific expression; the difficulties of mastering the Portuguese language; the collective character of indigenous authorship and the need to make indigenous identities visible in authorship in scientific productions. An Indigenous Editorial Board was formed and prepared a public call for indigenous authors, which resulted in an open access publication with 21 texts. The editorial process sought to qualify the editorial board in the editorial production process; indigenous researchers carried out the peer review of the submitted texts; and virtual meetings were held with the authors to discuss the opinions. In addition to a quality academic production by indigenous authors, the project strengthened the network of indigenous researchers in collective health area, involving them in other events and initiatives, and triggered institutional changes at “Academic Institution”.

Comparative mitochondrial genomics of Terniopsis yongtaiensis in Malpighiales: structural, sequential, and phylogenetic perspectives

BackgroundTerniopsis yongtaiensis, a member of the Podostemaceae family, is an aquatic flowering plant displaying remarkable adaptive traits that enable survival in submerged, turbulent habitats. Despite the progressive expansion of chloroplast genomic information within this family, mitochondrial genome sequences have yet to be reported.ResultsIn current study, the mitochondrial genome of the T. yongtaiensis was characterized by a circular genome of 426,928 bp encoding 31 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNA genes. Our comprehensive analysis focused on gene content, repeat sequences, RNA editing processes, intracellular gene transfer, phylogeny, and codon usage bias. Numerous repeat sequences were identified, including 130 simple sequence repeats, 22 tandem repeats, and 220 dispersed repeats. Phylogenetic analysis positioned T. yongtaiensis (Podostemaceae) within the Malpighiales order, showing a close relationship with the Calophyllaceae family, which was consistent with the APG IV classification. A comparative analysis with nine other Malpighiales species revealed both variable and conserved regions, providing insights into the genomic evolution within this order. Notably, the GC content of T. yongtaiensis was distinctively lower compared to other Malpighilales, primarily due to variations in non-coding regions and specific protein-coding genes, particularly the nad genes. Remarkably, the number of RNA editing sites was low (276), distributed unevenly across 27 PCGs. The dN/dS analysis showed only the ccmB gene of T. yongtaiensis was positively selected, which plays a crucial role in cytochrome c biosynthesis. Additionally, there were 13 gene-containing homologous regions between the mitochondrial and chloroplast genomes of T. yongtaiensis, suggesting the gene transfer events between these organellar genomes.ConclusionsThis study assembled and annotated the first mitochondrial genome of the Podostemaceae family. The comparison results of mitochondrial gene composition, GC content, and RNA editing sites provided novel insights into the adaptive traits and genetic reprogramming of this aquatic eudicot group and offered a foundation for future research on the genomic evolution and adaptive mechanisms of Podostemaceae and related plant families in the Malpighiales order.

GPT Alumni AI Pesquisa: A Practical Tutorial for the Adoption and Ethical Use of AI in Scientific Research

Objective: This tutorial introduces the use of Alumni AI Pesquisa, a chatbot based on GPT-4, publicly available on the OpenAI platform, designed to support the ethical and transparent use of Artificial Intelligence (AI) in academic research. The aim is to guide authors, editors, and reviewers in the responsible application of AI, ensuring scientific integrity throughout the editorial process. Method: The tutorial provides a step-by-step guide on how to access and utilize Alumni AI Pesquisa. The GPT-4 offers guidance on the ethical use of AI in academic writing, the oversight of editorial decisions assisted by AI, as well as compliance with editorial guidelines and manuscript formatting. Correct usage of AI is promoted through practical examples and references to global best practices. Results: Alumni AI Pesquisa provides immediate support tailored to different user profiles (authors, editors, and reviewers), encouraging transparent AI use in manuscripts. The tool ensures that AI-assisted decisions are validated by human supervisors, guaranteeing adherence to ethical and technical standards. Conclusions: Publicly available on the OpenAI platform, Alumni AI Pesquisa, powered by GPT-4, significantly contributes to the promotion of scientific integrity by facilitating responsible AI use in the academic environment. It is recommended that the use of the tool be cited in publications, explicitly mentioning the version (GPT-4).

CONNECTION BETWEEN ARTISTIC EDITING AND ARTISTIC TRANSLATION

This scientific article investigates the necessity of adhering to linguistic norms and existing editorial principles when editing literary translations from foreign languages, taking into account the shared aspects of translation and editorial criteria. The study focuses on the quality of editing the Uzbek translation of the novel The Alchemist, compared to its English and Russian versions. It examines issues such as preserving the semantic features of the text during the editing process and provides suggestions and recommendations for addressing shortcomings that arise in the editorial process.