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1. Opening the Door to Registered Reports: Census of Journals Publishing Registered Reports (2013–2020)

   https://doi.org/10.1525/collabra.24404  

   Montoya, Amanda Kay ; Krenzer, William Leo ; Fossum, Jessica Louise ( January 2021 , Collabra: Psychology)

   Registered reports are a new publication workflow where the decision to publish is made prior to data collection and analysis and thus cannot be dependent on the outcome of the study. An increasing number of journals have adopted this new mechanism, but previous research suggests that submission rates are still relatively low. We conducted a census of journals publishing registered reports (N = 278) using independent coders to collect information from submission guidelines, with the goal of documenting journals’ early adoption of registered reports. Our results show that the majority of journals adopting registered reports are in psychology, and it typically takes about a year to publish the first registered report after adopting. Still, many journals have not published their first registered report. There is high variability in impact of journals adopting registered reports. Many journals do not include concrete information about policies that address concerns about registered reports (e.g., exploratory analysis); however, those that do typically allow these practices with some restrictions. Additionally, other open science practices are commonly encouraged or required as part of the registered report process, especially open data and materials. Overall, many journals did not include many of the fields coded by the research team, which could be a barrier to submission for some authors. Though the majority of journals allow authors to be anonymous during the review process, a sizable portion do not, which could also be a barrier to submission. We conclude with future directions and implications for authors of registered reports, journals that have already adopted registered reports, and journals that may consider adopting registered reports in the future. 

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2. Making expert cognitive processes visible: planning and preliminary analysis in theoretical physics research

   https://doi.org/10.1119/perc.2022.pr.Verostek  

   Verostek, Michael ; Griston, Molly ; Botello, Jesus ; Zwickl, Benjamin M. ( September 2022 , Physics Education Research Conference 2022)

   Frank, Brian W. ; Jones, Dyan L. ; Ryan, Qing X. (Ed.)

   Many of the activities and cognitive processes that physicists use while solving problems are "invisible" to students, which can hinder their acquisition of important expert-like skills. Whereas the detailed calculations performed by researchers are often published in journals and textbooks, other activities such as those undertaken while planning how to approach a problem are rarely discussed in published research. Hence, these activities are especially hidden from students. To better understand how physicists solve problems in their professional research, we leveraged the framework of cognitive task analysis to conduct semi-structured interviews with theoretical physicists (N=11). Here we elucidate the role of planning and preliminary analysis in theorists' work. Theorists described using a variety of activities in order to decide if their project was doable while also generating possible solution paths. These actions included doing cursory calculations, reflecting on previous knowledge, gaining intuition and understanding by studying prior work, and reproducing previous results. We found that theorists typically did not pursue projects unless they had a clear idea of what the outcome of their project would be, or at least knew that they would be able to make progress on the problem. Thus, this preliminary design and analysis phase was highly important for theorists despite being largely hidden from students. We conclude by suggesting potential ways to incorporate our findings into the classroom to give students more numerous opportunities to engage in these expert-like practices. 

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3. Pain and Laboratory Animals: Publication Practices for Better Data Reproducibility and Better Animal Welfare

   https://doi.org/10.1371/journal. pone.0155001  

   Larry Carbone, Jamie Austin ( May 2016 , PloS one)

   Scientists who perform major survival surgery on laboratory animals face a dual welfare and methodological challenge: how to choose surgical anesthetics and post-operative analgesics that will best control animal suffering, knowing that both pain and the drugs that manage pain can all affect research outcomes. Scientists who publish full descriptions of animal procedures allow critical and systematic reviews of data, demonstrate their adherence to animal welfare norms, and guide other scientists on how to conduct their own studies in the field. We investigated what information on animal pain management a reasonably diligent scientist might find in planning for a successful experiment. To explore how scientists in a range of fields describe their management of this ethical and methodological concern, we scored 400 scientific articles that included major animal survival surgeries as part of their experimental methods, for the completeness of information on anesthesia and analgesia. The 400 articles (250 accepted for publication pre-2011, and 150 in 2014–15, along with 174 articles they reference) included thoracotomies, craniotomies, gonadectomies, organ transplants, peripheral nerve injuries, spinal laminectomies and orthopedic procedures in dogs, primates, swine, mice, rats and other rodents. We scored articles for Publication Completeness (PC), which was any mention of use of anesthetics or analgesics; Analgesia Use (AU) which was any use of post-surgical analgesics, and Analgesia Completeness (a composite score comprising intra-operative analgesia, extended post-surgical analgesia, and use of multimodal analgesia). 338 of 400 articles were PC. 98 of these 338 were AU, with some mention of analgesia, while 240 of 338 mentioned anesthesia only but not postsurgical analgesia. Journals’ caliber, as measured by their 2013 Impact Factor, had no effect on PC or AU. We found no effect of whether a journal instructs authors to consult the ARRIVE publishing guidelines published in 2010 on PC or AC for the 150 mouse and rat articles in our 2014–15 dataset. None of the 302 articles that were silent about analgesic use included an explicit statement that analgesics were withheld, or a discussion of how pain management or untreated pain might affect results. We conclude that current scientific literature cannot be trusted to present full detail on use of animal anesthetics and analgesics. We report that publication guidelines focus more on other potential sources of bias in experimental results, under-appreciate the potential for pain and pain drugs to skew data, PLOS ONE | DOI:10.1371/journal.pone.0155001 May 12, 2016 1 / 24 a11111 OPEN ACCESS Citation: Carbone L, Austin J (2016) Pain and Laboratory Animals: Publication Practices for Better Data Reproducibility and Better Animal Welfare. PLoS ONE 11(5): e0155001. doi:10.1371/journal. pone.0155001 Editor: Chang-Qing Gao, Central South University, CHINA Received: December 29, 2015 Accepted: April 22, 2016 Published: May 12, 2016 Copyright: © 2016 Carbone, Austin. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Authors may be contacted for further information. Funding: This study was funded by the United States National Science Foundation Division of Social and Economic Sciences. Award #1455838. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. and thus mostly treat pain management as solely an animal welfare concern, in the jurisdiction of animal care and use committees. At the same time, animal welfare regulations do not include guidance on publishing animal data, even though publication is an integral part of the cycle of research and can affect the welfare of animals in studies building on published work, leaving it to journals and authors to voluntarily decide what details of animal use to publish. We suggest that journals, scientists and animal welfare regulators should revise current guidelines and regulations, on treatment of pain and on transparent reporting of treatment of pain, to improve this dual welfare and data-quality deficiency. 

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4. Relating referential clarity and phonetic clarity in infant‐directed speech

   https://doi.org/10.1111/desc.13442  

   Beech, Caroline ; Swingley, Daniel ( August 2023 , Developmental Science)

   Psycholinguistic research on children's early language environments has revealed many potential challenges for language acquisition. One is that in many cases, referents of linguistic expressions are hard to identify without prior knowledge of the language. Likewise, the speech signal itself varies substantially in clarity, with some productions being very clear, and others being phonetically reduced, even to the point of uninterpretability. In this study, we sought to better characterize the language‐learning environment of American English‐learning toddlers by testing how well phonetic clarity and referential clarity align in infant‐directed speech. Using an existing Human Simulation Paradigm (HSP) corpus with referential transparency measurements and adding new measures of phonetic clarity, we found that the phonetic clarity of words’ first mentions significantly predicted referential clarity (how easy it was to guess the intended referent from visual information alone) at that moment. Thus, when parents’ speech was especially clear, the referential semantics were also clearer. This suggests that young children could use the phonetics of speech to identify globally valuable instances that support better referential hypotheses, by homing in on clearer instances and filtering out less‐clear ones. Such multimodal “gems” offer special opportunities for early word learning.

   In parent‐infant interaction, parents’ referential intentions are sometimes clear and sometimes unclear; likewise, parents’ pronunciation is sometimes clear and sometimes quite difficult to understand.

   We find that clearer referential instances go along with clearer phonetic instances, more so than expected by chance.

   Thus, there are globally valuable instances (“gems”) from which children could learn about words’ pronunciations and words’ meanings at the same time.

   Homing in on clear phonetic instances and filtering out less‐clear ones would help children identify these multimodal “gems” during word learning.

    

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5. Data from: Parallel processing in speech perception with local and global representations of linguistic context

   https://doi.org/10.5061/dryad.nvx0k6dv0  

   Brodbeck, Christian ; Bhattasali, Shohini ; Cruz Heredia, Aura A. ; Resnik, Philip ; Simon, Jonathan Z. ; Lau, Ellen ( January 2022 , Dryad)

   Speech processing is highly incremental. It is widely accepted that human listeners continuously use the linguistic context to anticipate upcoming concepts, words, and phonemes. However, previous evidence supports two seemingly contradictory models of how a predictive context is integrated with the bottom-up sensory input: Classic psycholinguistic paradigms suggest a two-stage process, in which acoustic input initially leads to local, context-independent representations, which are then quickly integrated with contextual constraints. This contrasts with the view that the brain constructs a single coherent, unified interpretation of the input, which fully integrates available information across representational hierarchies, and thus uses contextual constraints to modulate even the earliest sensory representations. To distinguish these hypotheses, we tested magnetoencephalography responses to continuous narrative speech for signatures of local and unified predictive models. Results provide evidence that listeners employ both types of models in parallel. Two local context models uniquely predict some part of early neural responses, one based on sublexical phoneme sequences, and one based on the phonemes in the current word alone; at the same time, even early responses to phonemes also reflect a unified model that incorporates sentence-level constraints to predict upcoming phonemes. Neural source localization places the anatomical origins of the different predictive models in nonidentical parts of the superior temporal lobes bilaterally, with the right hemisphere showing a relative preference for more local models. These results suggest that speech processing recruits both local and unified predictive models in parallel, reconciling previous disparate findings. Parallel models might make the perceptual system more robust, facilitate processing of unexpected inputs, and serve a function in language acquisition. MEG Data MEG data is in FIFF format and can be opened with MNE-Python. Data has been directly converted from the acquisition device native format without any preprocessing. Events contained in the data indicate the stimuli in numerical order. Subjects R2650 and R2652 heard stimulus 11b instead of 11. Predictor Variables The original audio files are copyrighted and cannot be shared, but the make_audio folder contains make_clips.py which can be used to extract the exact clips from the commercially available audiobook (ISBN 978-1480555280). The predictors directory contains all the predictors used in the original study as pickled eelbrain objects. They can be loaded in Python with the eelbrain.load.unpickle function. The TextGrids directory contains the TextGrids aligned to the audio files. Source Localization The localization.zip file contains files needed for source localization. Structural brain models used in the published analysis are reconstructed by scaling the FreeSurfer fsaverage brain (distributed with FreeSurfer) based on each subject's `MRI scaling parameters.cfg` file. This can be done using the `mne.scale_mri` function. Each subject's MEG folder contains a `subject-trans.fif` file which contains the coregistration between MEG sensor space and (scaled) MRI space, which is used to compute the forward solution. 

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