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Language Barriers in Organismal Biology: What Can Journals Do Better?
Synopsis In the field of organismal biology, as in much of academia, there is a strong incentive to publish in internationally recognized, highly regarded, English-language journals to promote career advancement. This expectation has created a linguistic hegemony in scientific publishing, whereby scholars for whom English is an additional language face additional barriers to achieving the same scientific recognition as scholars who speak English as a first language. Here, we surveyed the author guidelines of 230 journals in organismal biology with impact factors of 1.5 or greater for linguistically inclusive and equitable practices and policies. We looked for efforts that reflect first steps toward reducing barriers to publication for authors globally, including the presence of statements that encouraged submissions from authors of diverse nationalities and backgrounds, policies regarding manuscript rejection based on perceived inadequacies of the English language, the existence of bias-conscious reviewer practices, whether translation and editing resources or services are available, allowance for non-English abstracts, summaries, or translations, and whether journals offer license options that would permit authors (or other scholars) to translate their work and publish it elsewhere. We also directly contacted a subset of journals to verify whether the information on their author guidelines page accurately reflects their policies and the accommodations they would make. We reveal that journals and publishers have made little progress toward beginning to recognize or reduce language barriers. Counter to our predictions, journals associated with scientific societies did not appear to have more inclusive policies compared to non-society journals. Many policies lacked transparency and clarity, which can generate uncertainty, result in avoidable manuscript rejections, and necessitate additional time and effort from both prospective authors and journal editors. We highlight examples of equitable policies and summarize actions that journals can take to begin to alleviate barriers to scientific publishing.
The Journal of Open Source Software (JOSS): Bringing Open-Source Software Practices to the Scholarly Publishing Community for Authors, Reviewers, Editors, and Publishers
Open-source software (OSS) is a critical component of open science, but contributions to the OSS ecosystem are systematically undervalued in the current academic system. The Journal of Open Source Software (JOSS) contributes to addressing this by providing a venue (that is itself free, diamond open access, and all open-source, built in a layered structure using widely available elements/services of the scholarly publishing ecosystem) for publishing OSS, run in the style of OSS itself. A particularly distinctive element of JOSS is that it uses open peer review in a collaborative, iterative format, unlike most publishers. Additionally, all the components of the process—from the reviews to the papers to the software that is the subject of the papers to the software that the journal runs—are open. We describe JOSS’s history and its peer review process using an editorial bot, and we present statistics gathered from JOSS’s public review history on GitHub showing an increasing number of peer reviewed papers each year. We discuss the new JOSSCast and use it as a data source to understand reasons why interviewed authors decided to publish in JOSS. JOSS’s process differs significantly from traditional journals, which has impeded JOSS’s inclusion in indexing services such as Web of Science. In turn, this discourages researchers within certain academic systems, such as Italy’s, which emphasize the importance of Web of Science and/or Scopus indexing for grant applications and promotions. JOSS is a fully diamond open-access journal with a cost of around US$\$$5 per paper for the 401 papers published in 2023. The scalability of running JOSS with volunteers and financing JOSS with grants and donations is discussed.
Space Weather: New Directions for a Maturing Field and Journal
As space weather has significantly matured as a field, the Space Weather journal is implementing two major changes: a new scope and a new Editor-in-Chief (EiC). As part of the revised scope, the novelty of submitted manuscripts is now a major quality to be assessed by the editors and reviewers. The goal of the journal remains primarily to advance our understanding of fundamental space phenomena that have direct impact on technology, to improve the forecasting of such phenomena, and to provide space environment climatology models. This new scope is the last major change implemented by the departing EiC who will be succeeded in January 2026 by Dr. Steven K. Morley. The new EiC will now oversee a large editorial board and a journal with over 400 submissions in 2025.
Athena-I CUBIT Journal Files
The Monte Carlo N-Particle (MCNP)1 transport code version 6 (also known as MCNP6) has the capability for tracking particles on unstructured mesh (UM) geometry models embedded into con structive solid geometry (CSG) cells. This feature has been developed for performing calculations of complex geometry models because manually creating CSG models is a time-consuming and error prone process as the complexities of geometries increase. The UM capability was originally designed to work with UM models created with the Abaqus software and ASCII input files that it generates. The MCNP code version 6.0 and later can process UM models formatted as Abaqus input files. Starting with version 6.3, MCNP can also process HDF5 mesh input files. External codes must be used to generate Abaqus input files for MCNP UM calculations. CUBIT, the Sandia National Laboratory automated mesh generation toolkit, can generate a UM model formatted as an Abaqus input file. However, the Abaqus input files exported from CUBIT cannot be used for MCNP simulations because it lacks the proper syntax. A Python script was developed to convert an Abaqus file created by CUBIT to an Abaqus file format that MCNP can process. Creating UM models for complex geometries is not an easy task. The process of creating UM models in CUBIT for MCNP simulations is detailed in. CUBIT provides several user interface options including a graphical user interface (GUI) and a command line interface. A GUI provides an easy way to use CUBIT without learning the CUBIT command syntax. When using CUBIT with either interface option, command lines are written into an ASCII file known as a journal file; this journal file can be edited and archived so that it can be played back in CUBIT to automatically generate a UM model. This report describes the CUBIT journal files of the UM models developed for Athena-I. The Athena platform, an energy-tuning assembly, was developed to spectrally shape the National Ignition Facility (NIF) deuterium-tritium fusion neutron source to a thermonuclear (fusion) plus prompt fission neutron spectrum with capability to act as a short-pulse neutron source. MCNP6 was used for the Athena experiment design analysis.
Medical Physics Leadership Academy Journal Club (Leadership Club) program: Two-year review in building a community of leaders
The American Association of Physicists in Medicine began the Medical Physics Leadership Academy Journal Club in the fall of 2020. The initiative was launched to provide a forum for medical physicists to learn about leadership topics using published material, discuss and reflect on the material, and consider incorporating the discussed skills into their professional practice. This report presents the framework for the MPLA Journal Club program, describes the lessons learned over the last 2 years, summarizes the data collected from attendees, and highlights the roadmap for the program moving forward.
Heavy-tailed distribution of the number of papers within scientific journals
Scholarly publications represent at least two benefits for the study of the scientific community as a social group. First, they attest to some form of relation between scientists (collaborations, mentoring, heritage, …), useful to determine and analyze social subgroups. Second, most of them are recorded in large databases, easily accessible and including a lot of pertinent information, easing the quantitative and qualitative study of the scientific community. Understanding the underlying dynamics driving the creation of knowledge in general, and of scientific publication in particular, can contribute to maintaining a high level of research, by identifying good and bad practices in science. In this article, we aim to advance this understanding by a statistical analysis of publication within peer-reviewed journals. Namely, we show that the distribution of the number of papers published by an author in a given journal is heavy-tailed, but has a lighter tail than a power law. Interestingly, we demonstrate (both analytically and numerically) that such distributions match the result of a modified preferential attachment process, where, on top of a Barabási-Albert process, we take the finite career span of scientists into account.
Can Sex and Seniority Predict the Quality of a Journal Reviewer's Manuscript Critique?
To evaluate reviewers’ timeliness and review quality for the International Journal of Radiation Oncology, Biology, Physics (IJROBP) by sex and seniority.
Constructing Self-Labeled Materials Imaging Datasets from Open Access Scientific Journals with EXSCLAIM!
Due to recent improvements in image resolution and acquisition speeds, materials microscopy is experiencing an explosion in imaging data. Yet, despite the volume of images generated, the overall accessibility landscape is highly fragmented, as researchers who do release images to the public, often only do so as snapshots of their larger private dataset in context of scientific journal publications. The effort to automatically consolidate images and descriptive information from web-based platforms has garnered broad attention from the computer vision, language technologies, and chemistry/materials informatics communities. However, these methods are problematic for scientific figures because over 30% of figures are compound in nature, and it is the individual images themselves, paired with relevant context, that are necessary for construction a proper labeled dataset. To this end, we outline in this paper the design of a software pipeline for the automatic EXtraction, Separation, and Caption-based natural Language Annotation of IMages from scientific figures (EXSCLAIM!). Successful consolidation of materials imaging across literature sources will enhance navigation and searchability of materials microscopy images for both novice and experienced researchers, as well as establish the framework necessary for users to search by images, text, or some combination of both.
Comment on “Thermodynamic Models for the (HClO 4 + NaClO 4 ){aq} and (HBr + NaBr){aq} Systems at 298.15 K and 0.1 MPa” Authored by Oakes, C. S., Ward, A. L., Chugunov, N. Journal of Chemical & Engineering Data , 68 , 2554–2562
Oakes et al. (2023) published a review article in this journal. In that paper, Oakes et al. (2023) developed thermodynamic models to describe electrolyte solutions for HClO 4 –NaClO 4 –H 2 O and HBr–NaBr–H 2 O systems, based on literature data. In their paper, previously published work from researchers in the field was criticized; some of it is ours. Here, in this brief Comment, we first comment on their models, and then we briefly provide a technical response to that criticism.
Cited Reference Analysis in a National Laboratory to Assess Journal Usage
Librarians at a large, federally funded, multidisciplinary research organization sought to assess the value provided by the library’s collections. One method for capturing this value includes determining how well their library’s collections meet researcher needs, as expressed by the materials those researchers choose to cite in the production of new scholarly communications. A cited reference analysis was performed on the publications originating from the institution to provide the necessary data for the assessment, as well as to aid in the creation of a core list of journals which will inform future collection development efforts. Overall, this paper fills a gap in the library and information science literature by addressing the citation behaviors of researchers at a large multidisciplinary government research facility, a setting that has not been examined previously.
Who Should Read This Journal?
We are excited and pleased that from this volume (Volume 45, published in 2020), the Annual Review of Environment and Resources joins the ranks of the first handful of Annual Reviews journals that are converting to open access. The conversion uses a new model: Subscribe to Open (S2O). All articles in this volume will be permanently open access to the whole world, and so long as S2O continues, all articles in all past volumes of the Annual Review of Environment and Resources will also be kept accessible to all without a paywall.
Data and interactive visualization for "The economic accessibility of CO2 sequestration through bioenergy with carbon capture and sequestration (BECCS) in the US" submitted to the journal "Land", 2020
Detailed outputs and interactive visualization to accompany the manuscript titled "The economic accessibility of CO2 sequestration through bioenergy with carbon capture and sequestration (BECCS) in the US" submitted to the journal "Land" in 2020. https://public.tableau.com/profile/billion.ton.2016#!/vizhome/ORNLBECCS2020/CO2EMITANDCAPTURE2
In silico evolution of oscillatory gene dynamics formerly Code sharing for a manuscript to be submitted to the journal iScience
The disclosure is about the numerical simulations and visualization implemented in general-purpose language Python and C++. The simulations were in-silico evolution of hypothetical gene circuits that potentially admit oscillatory dynamics. The aim of the study, which was invited to be submitted to a special issue "Timekeeping, noise and development across kingdoms" in the journal iScience, is to demonstrate that in contrast to common belief, noise in gene expression dynamics could significantly facilitate the evolutionary process for searching oscillatory dynamics, which are essential for developing circadian rhythm in living organisms.
Physical Review Journal Club: Structural uncertainty assessment for fire-engulfed objects in crosswind: Establishing credibility for a multiphysics wall-modeled large-eddy simulation paradigm
This is an invited presentation for APS's monthly Journal Club where important papers that have recently been accepted for publication are highlighted in a seminar-like setting. The presentation will be "live" (May 1, 2025) and streamed across the world (including an archived recording).
Message From the MTS Journal Editor
This is my foreword for the next general issue of the Marine Technology Society Journal.
Message from the MTS Journal Editor
Foreword for the upcoming general issue of the Marine Technology Society Journal (of which I am the general editor)
Foreword: Message from the MTS Journal Editor
Foreword for upcoming general issue of the Marine Technology Society Journal of which I am the general editor.