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Journal of Primary Care & Community... 2024Journal editors depend on peer reviewers to make decisions about submitted manuscripts. These reviewers help evaluate the methods, the results, the discussion of the...
Journal editors depend on peer reviewers to make decisions about submitted manuscripts. These reviewers help evaluate the methods, the results, the discussion of the results, and the overall organization and presentation of the manuscript. In addition, reviewers can help identify important mistakes and possible misconduct. Editors frequently have difficulty obtaining enough peer reviews which are submitted in a timely manner. This increases the workload of editors and journal managers and potentially delays the publication of clinical and research studies. This commentary discusses of the importance of peer reviews and make suggestions which potentially can increase the participation of academic faculty and researchers in this important activity.
Topics: Humans; Periodicals as Topic; Peer Review, Research; Editorial Policies; Peer Review; Publishing
PubMed: 38682542
DOI: 10.1177/21501319241252235 -
Frontiers in Immunology 2023T cell receptors (TR) underpin the diversity and specificity of T cell activity. As such, TR repertoire data is valuable both as an adaptive immune biomarker, and as a...
T cell receptors (TR) underpin the diversity and specificity of T cell activity. As such, TR repertoire data is valuable both as an adaptive immune biomarker, and as a way to identify candidate therapeutic TR. Analysis of TR repertoires relies heavily on computational analysis, and therefore it is of vital importance that the data is standardized and computer-readable. However in practice, the usage of different abbreviations and non-standard nomenclature in different datasets makes this data pre-processing non-trivial. tidytcells is a lightweight, platform-independent Python package that provides easy-to-use standardization tools specifically designed for TR nomenclature. The software is open-sourced under the MIT license and is available to install from the Python Package Index (PyPI). At the time of publishing, tidytcells is on version 2.0.0.
Topics: Receptors, Antigen, T-Cell; Publishing; Software
PubMed: 37954585
DOI: 10.3389/fimmu.2023.1276106 -
F1000Research 2023The rate of science information's spread has accelerated in recent years. In this context, it appears that many scientific disciplines are beginning to recognize the...
The rate of science information's spread has accelerated in recent years. In this context, it appears that many scientific disciplines are beginning to recognize the value and possibility of sharing open access (OA) online manuscripts in their preprint form. Preprints are academic papers that are published but have not yet been evaluated by peers. They have existed in research at least since the 1960s and the creation of ArXiv in physics and mathematics. Since then, preprint platforms-which can be publisher- or community-driven, profit or not for profit, and based on proprietary or free and open source software-have gained popularity in many fields (for example, bioRxiv for the biological sciences). Today, there are many platforms that are either disciplinary-specific or cross-domain, with exponential development over the past ten years. Preprints as a whole still make up a very small portion of scholarly publishing, but a large group of early adopters are testing out these value-adding tools across a much wider range of disciplines than in the past. In this opinion article, we provide perspective on the three main options available for earth scientists, namely EarthArXiv, ESSOAr/ESS Open Archive and EGUsphere.
Topics: Publishing; Publications; Biological Science Disciplines; Scholarly Communication; Earth Sciences
PubMed: 37448860
DOI: 10.12688/f1000research.133612.2 -
Journal of Infection and Public Health Oct 2023Candida auris (CA) is an emerging fungus, classified as an urgent global health threat, that resists common antifungal drugs and decontamination procedures;...
BACKGROUND
Candida auris (CA) is an emerging fungus, classified as an urgent global health threat, that resists common antifungal drugs and decontamination procedures; identification requires specific tools; transmissibility and mortality are high in healthcare settings. Infection and colonisation can be long-lasting, leading to problems in isolation procedures and the risk of outbreaks. This study aims to evaluate publication and citation related metrics, identify major keywords and topics, and assess geographic distribution of published articles.
METHODS
A list of all publications containing "Candida auris" in all fields was extracted from Web Of Science on date 2023/01/02. Bibliometric analysis was conducted using the bibliometrix and biblioshiny packages on RStudio.
RESULTS
Total publications (TP) were 1283 with an annual growth rate of 53.91%. Total citations were 27854, with an average of 21.71 citations per paper. The core sources are 9 out of 322, according to Bradford's law. In only 42 countries where CA was identified, articles on the topic were published (89%). The origin of TP is concentrated in high-income countries (68.22%). Trending topics about CA include epidemiology, identification and resistance.
CONCLUSION
Our analysis shows a growing interest in scientific literature on the topic of CA, led by Europe. In some countries where CA has been identified, no papers have been published. Despite the multidrug-resistance of CA, the topic of therapy is not much debated. Our findings highlight the need to increase focus on CA in order to promote health systems' preparedness and to properly address the spread of this worrisome pathogen.
Topics: Humans; Global Health; Health Promotion; Bibliometrics; Antifungal Agents; Candida
PubMed: 37647837
DOI: 10.1016/j.jiph.2023.08.012 -
Frontiers in Endocrinology 2023Chronic inflammation and fibrosis are significant factors in the pathogenesis of metabolic-associated fatty liver disease (MAFLD). In this study, we conducted a...
Chronic inflammation and fibrosis are significant factors in the pathogenesis of metabolic-associated fatty liver disease (MAFLD). In this study, we conducted a bibliometric analysis of publications on inflammation and fibrogenesis in MAFLD, with a focus on reporting publication trends. Our findings indicate that the USA and China are the most productive countries in the field, with the University of California San Diego being the most productive institution. Over the past 23 years, Prof. Diehl AM has published 25 articles that significantly contributed to the research community. Notably, the research focus of the field has shifted from morbid obesity and adiponectin to metabolic syndrome, genetics, and microbiome. Our study provides a comprehensive and objective summary of the historical characteristics of research on inflammation and fibrogenesis in MAFLD, which will be of interest to scientific researchers in this field.
Topics: Humans; Bibliometrics; Inflammation; Adiponectin; China; Metabolic Syndrome; Non-alcoholic Fatty Liver Disease
PubMed: 37720529
DOI: 10.3389/fendo.2023.1231520 -
Journal of Cachexia, Sarcopenia and... Dec 2023The Journal of Cachexia, Sarcopenia and Muscle (JCSM) aims to publish articles with relevance to wasting disorders and illnesses of the muscle in the broadest sense. In...
The Journal of Cachexia, Sarcopenia and Muscle (JCSM) aims to publish articles with relevance to wasting disorders and illnesses of the muscle in the broadest sense. In order to avoid publication of inappropriate articles and to avoid protracted disputes, the Editors have established ethical guidelines that detail a number of regulations to be fulfilled prior to submission to the journal. This article updates the principles of ethical authorship and publishing in JCSM and its daughter journal JCSM Rapid Communication. We require the corresponding author, on behalf of all co-authors, to certify adherence to the following principles: All authors listed on a manuscript considered for publication have approved its submission and (if accepted) approve publication in the journal; Each named author has made a material and independent contribution to the work submitted for publication. No person who has a right to be recognized as author has been omitted from the list of authors on the submitted manuscript; The submitted work is original and is neither under consideration elsewhere nor that it has been published previously in whole or in part other than in abstract form; All authors certify that the submitted work is original and does not contain excessive overlap with prior or contemporaneous publication elsewhere, and where the publication reports on cohorts, trials, or data that have been reported on before the facts need to be acknowledged and these other publications must be referenced; All original research work has been approved by the relevant bodies such as institutional review boards or ethics committees; All relevant conflicts of interest, financial or otherwise, that may affect the authors' ability to present data objectively, and relevant sources of funding of the research in question have been duly declared in the manuscript; All authors certify that they will submit the original source data to the editorial office upon request; Authors who have used artificial intelligence, language models, machine learning, or similar technologies need to provide a written statement - as part of the manuscript - that details the use of the respective technology; none of the aforementioned technologies can be listed as an author; The manuscript in its published form will be maintained on the servers of the journal as a valid publication only as long as all statements in these guidelines remain true. If any of the aforementioned statements ceases to be true, the authors have a duty to notify as soon as possible the Editor-in-Chief of the journal, so that the available information regarding the published article can be updated and/or the manuscript can be withdrawn.
Topics: Humans; Publishing; Cachexia; Artificial Intelligence; Sarcopenia; Muscles
PubMed: 38148513
DOI: 10.1002/jcsm.13420 -
International Journal of Surgery... Dec 2023Rectal cancer leads a major disease burden worldwide. Total mesorectal excision (TME) is the standard treatment for locally advanced or node-positive rectal cancer,...
BACKGROUND
Rectal cancer leads a major disease burden worldwide. Total mesorectal excision (TME) is the standard treatment for locally advanced or node-positive rectal cancer, while attempts to improve the surgery such as laparoscopic and transanal TME are widely used but have their inherent limitations. This bibliometric study analyzed research trends, cooperation, and knowledge dissemination on TME over the past 20 years to inform future directions.
METHODS
Relevant literature from 2003 to 2023 was extracted from the Web of Science Core Collection and analyzed with VOSviewer, CiteSpace, and R for publication patterns, countries, institutions, authors, and research hotspots.
RESULTS
Five thousand three hundred forty-five related publications were included, with rising annual output and citations. The US and China contributed the most studies, while the Netherlands had greater influence. Leiden University ranked first in publications. The top authors were Heald, Kapiteijn, Sauer, Nagtegaal, and Peeters. Research shifted from cancer-focused to patient-centered care and from radiotherapy/chemotherapy to advanced surgery. Multicenter trials became more common.
CONCLUSION
Although the United States and China have the largest number of publications, it should be noted that the influence of these two countries in the field of TME research is not the highest, which does not match the number of publications. In addition, telemedicine, interdisciplinary, medical-industrial integration, etc. may be potential directions for future research in the field of TME.
Topics: Humans; Rectal Neoplasms; Bibliometrics; China; Laparoscopy; Netherlands
PubMed: 37678311
DOI: 10.1097/JS9.0000000000000681 -
Annals of Internal Medicine Nov 2023
Topics: Humans; Publishing; Authorship
PubMed: 37903368
DOI: 10.7326/M23-2619 -
PLoS Computational Biology Feb 2024CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the...
CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.
Topics: Humans; Artificial Intelligence; Software; Cloud Computing; Publishing
PubMed: 38324613
DOI: 10.1371/journal.pcbi.1011270 -
Journal of Korean Medical Science Dec 2023The concept of research integrity (RI) refers to a set of moral and ethical standards that serve as the foundation for the execution of research activities. Integrity in... (Review)
Review
The concept of research integrity (RI) refers to a set of moral and ethical standards that serve as the foundation for the execution of research activities. Integrity in research is the incorporation of principles of honesty, transparency, and respect for ethical standards and norms throughout all stages of the research endeavor, encompassing study design, data collecting, analysis, reporting, and publishing. The preservation of RI is of utmost importance to uphold the credibility and amplify the influence of scientific research while also preventing and dealing with instances of scientific misconduct. Researchers, institutions, journals, and readers share responsibilities for preserving RI. Researchers must adhere to the highest ethical standards. Institutions have a role in establishing an atmosphere that supports integrity ideals while also providing useful guidance, instruction, and assistance to researchers. Editors and reviewers act as protectors, upholding quality and ethical standards in the dissemination of research results through publishing. Readers play a key role in the detection and reporting of fraudulent activity by critically evaluating content. The struggle against scientific misconduct has multiple dimensions and is continuous. It requires a collaborative effort and adherence to the principles of honesty, transparency, and rigorous science. By supporting a culture of RI, the scientific community may preserve its core principles and continue to contribute appropriately to society's well-being. It not only aids present research but also lays the foundation for future scientific advancements.
Topics: Humans; Publishing; Scientific Misconduct; Research Design; Research Personnel; Biomedical Research
PubMed: 38050915
DOI: 10.3346/jkms.2023.38.e405