Policy recommendations to ensure that research software is openly accessible and reusable.

Research data is optimized when it can be freely accessed and reused. To maximize research equity, transparency, and reproducibility, policymakers should take concrete steps to ensure that research software is openly accessible and reusable.

The role of collegiality in academic review, promotion, and tenure.

Review, promotion, and tenure (RPT) processes at universities typically assess candidates along three dimensions: research, teaching, and service. In recent years, some have argued for the inclusion of a controversial fourth criterion: collegiality. While collegiality plays a role in the morale and effectiveness of academic departments, it is amorphic and difficult to assess, and could be misused to stifle dissent or enforce homogeneity. Despite this, some institutions have opted to include this additional element in their RPT documents and processes, but it is unknown the extent of this practice and how it varies across institution type and disciplinary units. This study is based on two sets of data: survey data collected as part of a project that explored the publishing decisions of faculty and how these related to perceived importance in RPT processes, and 864 RPT documents collected from 129 universities from the United States and Canada. We analysed these RPT documents to determine the degree to which collegiality and related terms are mentioned, if they are defined, and if and how they may be assessed during the RPT process. Results show that when collegiality and related terms appear in these documents they are most often just briefly mentioned. It is less common for collegiality and related terms to be defined or assessed in RPT documents. Although the terms are mentioned across all types of institutions, there is a statistically significant difference in how prevalent they are at each. Collegiality is more commonly mentioned in the documents of doctoral research-focused universities (60%), than of master's universities and colleges (31%) or baccalaureate colleges (15%). Results from the accompanying survey of faculty also support this finding: individuals from R-Types were more likely to perceive collegiality to be a factor in their RPT processes. We conclude that collegiality likely plays an important role in RPT processes, whether it is explicitly acknowledged in policies and guidelines or not, and point to several strategies in how it might be best incorporated in the assessment of academic careers.

Building capacity through open approaches: Lessons from developing undergraduate electrophysiology practicals.

Background: Electrophysiology has a wide range of biomedical research and clinical applications. As such, education in the theoretical basis and hands-on practice of electrophysiological techniques is essential for biomedical students, including at the undergraduate level. However, offering hands-on learning experiences is particularly difficult in environments with limited resources and infrastructure. Methods: In 2017, we began a project to design and incorporate electrophysiology laboratory practicals into our Biomedical Physics undergraduate curriculum at the Universidad Nacional Autónoma de México. We describe some of the challenges we faced, how we maximized resources to overcome some of these challenges, and in particular, how we used open scholarship approaches to build both educational and research capacity. Results: We succeeded in developing a number of experimental and data analysis practicals in electrophysiology, including electrocardiogram, electromyogram, and electrooculogram techniques. The use of open tools, open platforms, and open licenses was key to the success and broader impact of our project. We share examples of our practicals and explain how we use these activities to strengthen interdisciplinary learning, namely the application of concepts in physics to understanding functions of the human body. Conclusions: Open scholarship provides multiple opportunities for universities to build capacity. Our goal is to provide ideas, materials, and strategies for educators working in similar resource-limited environments.

How faculty define quality, prestige, and impact of academic journals.

Despite the calls for change, there is significant consensus that when it comes to evaluating publications, review, promotion, and tenure processes should aim to reward research that is of high "quality," is published in "prestigious" journals, and has an "impact." Nevertheless, such terms are highly subjective and present challenges to ascertain precisely what such research looks like. Accordingly, this article responds to the question: how do faculty from universities in the United States and Canada define the terms quality, prestige, and impact of academic journals? We address this question by surveying 338 faculty members from 55 different institutions in the U.S. and Canada. While relying on self-reported definitions that are not linked to their behavior, this study's findings highlight that faculty often describe these distinct terms in overlapping ways. Additionally, results show that marked variance in definitions across faculty does not correspond to demographic characteristics. This study's results highlight the subjectivity of common research terms and the importance of implementing evaluation regimes that do not rely on ill-defined concepts and may be context specific.

Why we publish where we do: Faculty publishing values and their relationship to review, promotion and tenure expectations.

Using an online survey of academics at 55 randomly selected institutions across the US and Canada, we explore priorities for publishing decisions and their perceived importance within review, promotion, and tenure (RPT). We find that respondents most value journal readership, while they believe their peers most value prestige and related metrics such as impact factor when submitting their work for publication. Respondents indicated that total number of publications, number of publications per year, and journal name recognition were the most valued factors in RPT. Older and tenured respondents (most likely to serve on RPT committees) were less likely to value journal prestige and metrics for publishing, while untenured respondents were more likely to value these factors. These results suggest disconnects between what academics value versus what they think their peers value, and between the importance of journal prestige and metrics for tenured versus untenured faculty in publishing and RPT perceptions.

Use of the Journal Impact Factor in academic review, promotion, and tenure evaluations.

We analyzed how often and in what ways the Journal Impact Factor (JIF) is currently used in review, promotion, and tenure (RPT) documents of a representative sample of universities from the United States and Canada. 40% of research-intensive institutions and 18% of master's institutions mentioned the JIF, or closely related terms. Of the institutions that mentioned the JIF, 87% supported its use in at least one of their RPT documents, 13% expressed caution about its use, and none heavily criticized it or prohibited its use. Furthermore, 63% of institutions that mentioned the JIF associated the metric with quality, 40% with impact, importance, or significance, and 20% with prestige, reputation, or status. We conclude that use of the JIF is encouraged in RPT evaluations, especially at research-intensive universities, and that there is work to be done to avoid the potential misuse of metrics like the JIF.

How significant are the public dimensions of faculty work in review, promotion and tenure documents?

Much of the work done by faculty at both public and private universities has significant public dimensions: it is often paid for by public funds; it is often aimed at serving the public good; and it is often subject to public evaluation. To understand how the public dimensions of faculty work are valued, we analyzed review, promotion, and tenure documents from a representative sample of 129 universities in the US and Canada. Terms and concepts related to public and community are mentioned in a large portion of documents, but mostly in ways that relate to service, which is an undervalued aspect of academic careers. Moreover, the documents make significant mention of traditional research outputs and citation-based metrics: however, such outputs and metrics reward faculty work targeted to academics, and often disregard the public dimensions. Institutions that seek to embody their public mission could therefore work towards changing how faculty work is assessed and incentivized.

The principles of tomorrow's university.

In the 21st Century, research is increasingly data- and computation-driven. Researchers, funders, and the larger community today emphasize the traits of openness and reproducibility. In March 2017, 13 mostly early-career research leaders who are building their careers around these traits came together with ten university leaders (presidents, vice presidents, and vice provosts), representatives from four funding agencies, and eleven organizers and other stakeholders in an NIH- and NSF-funded one-day, invitation-only workshop titled "Imagining Tomorrow's University." Workshop attendees were charged with launching a new dialog around open research - the current status, opportunities for advancement, and challenges that limit sharing. The workshop examined how the internet-enabled research world has changed, and how universities need to change to adapt commensurately, aiming to understand how universities can and should make themselves competitive and attract the best students, staff, and faculty in this new world. During the workshop, the participants re-imagined scholarship, education, and institutions for an open, networked era, to uncover new opportunities for universities to create value and serve society. They expressed the results of these deliberations as a set of 22 principles of tomorrow's university across six areas: credit and attribution, communities, outreach and engagement, education, preservation and reproducibility, and technologies. Activities that follow on from workshop results take one of three forms. First, since the workshop, a number of workshop authors have further developed and published their white papers to make their reflections and recommendations more concrete. These authors are also conducting efforts to implement these ideas, and to make changes in the university system.  Second, we plan to organise a follow-up workshop that focuses on how these principles could be implemented. Third, we believe that the outcomes of this workshop support and are connected with recent theoretical work on the position and future of open knowledge institutions.

Imagining the "open" university: Sharing scholarship to improve research and education.

Open scholarship, such as the sharing of articles, code, data, and educational resources, has the potential to improve university research and education as well as increase the impact universities can have beyond their own walls. To support this perspective, I present evidence from case studies, published literature, and personal experiences as a practicing open scholar. I describe some of the challenges inherent to practicing open scholarship and some of the tensions created by incompatibilities between institutional policies and personal practice. To address this, I propose several concrete actions universities could take to support open scholarship and outline ways in which such initiatives could benefit the public as well as institutions. Importantly, I do not think most of these actions would require new funding but rather a redistribution of existing funds and a rewriting of internal policies to better align with university missions of knowledge dissemination and societal impact.

CA1 pyramidal cells have diverse biophysical properties, affected by development, experience, and aging.

Neuron types (e.g., pyramidal cells) within one area of the brain are often considered homogeneous, despite variability in their biophysical properties. Here we review literature demonstrating variability in the electrical activity of CA1 hippocampal pyramidal cells (PCs), including responses to somatic current injection, synaptic stimulation, and spontaneous network-related activity. In addition, we describe how responses of CA1 PCs vary with development, experience, and aging, and some of the underlying ionic currents responsible. Finally, we suggest directions that may be the most impactful in expanding this knowledge, including the use of text and data mining to systematically study cellular heterogeneity in more depth; dynamical systems theory to understand and potentially classify neuron firing patterns; and mathematical modeling to study the interaction between cellular properties and network output. Our goals are to provide a synthesis of the literature for experimentalists studying CA1 PCs, to give theorists an idea of the rich diversity of behaviors models may need to reproduce to accurately represent these cells, and to provide suggestions for future research.

How open science helps researchers succeed.

Open access, open data, open source and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about how sharing their work will affect their careers. We review literature demonstrating that open research is associated with increases in citations, media attention, potential collaborators, job opportunities and funding opportunities. These findings are evidence that open research practices bring significant benefits to researchers relative to more traditional closed practices.

Effects of manipulating slowpoke calcium-dependent potassium channel expression on rhythmic locomotor activity in Drosophila larvae.

Rhythmic motor behaviors are generated by networks of neurons. The sequence and timing of muscle contractions depends on both synaptic connections between neurons and the neurons' intrinsic properties. In particular, motor neuron ion currents may contribute significantly to motor output. Large conductance Ca(2+)-dependent K(+) (BK) currents play a role in action potential repolarization, interspike interval, repetitive and burst firing, burst termination and interburst interval in neurons. Mutations in slowpoke (slo) genes encoding BK channels result in motor disturbances. This study examined the effects of manipulating slo channel expression on rhythmic motor activity using Drosophila larva as a model system. Dual intracellular recordings from adjacent body wall muscles were made during spontaneous crawling-related activity in larvae expressing a slo mutation or a slo RNA interference construct. The incidence and duration of rhythmic activity in slo mutants were similar to wild-type control animals, while the timing of the motor pattern was altered. slo mutants showed decreased burst durations, cycle durations, and quiescence intervals, and increased duty cycles, relative to wild-type. Expressing slo RNAi in identified motor neurons phenocopied many of the effects observed in the mutant, including decreases in quiescence interval and cycle duration. Overall, these results show that altering slo expression in the whole larva, and specifically in motor neurons, changes the frequency of crawling activity. These results suggest an important role for motor neuron intrinsic properties in shaping the timing of motor output.

Relating ion channel expression, bifurcation structure, and diverse firing patterns in a model of an identified motor neuron.

Neurons show diverse firing patterns. Even neurons belonging to a single chemical or morphological class, or the same identified neuron, can display different types of electrical activity. For example, motor neuron MN5, which innervates a flight muscle of adult Drosophila, can show distinct firing patterns under the same recording conditions. We developed a two-dimensional biophysical model and show that a core complement of just two voltage-gated channels is sufficient to generate firing pattern diversity. We propose Shab and DmNa v to be two candidate genes that could encode these core currents, and find that changes in Shab channel expression in the model can reproduce activity resembling the main firing patterns observed in MN5 recordings. We use bifurcation analysis to describe the different transitions between rest and spiking states that result from variations in Shab channel expression, exposing a connection between ion channel expression, bifurcation structure, and firing patterns in models of membrane potential dynamics.

Mitigating effects of vaccination on influenza outbreaks given constraints in stockpile size and daily administration capacity.

BACKGROUND: Influenza viruses are a major cause of morbidity and mortality worldwide. Vaccination remains a powerful tool for preventing or mitigating influenza outbreaks. Yet, vaccine supplies and daily administration capacities are limited, even in developed countries. Understanding how such constraints can alter the mitigating effects of vaccination is a crucial part of influenza preparedness plans. Mathematical models provide tools for government and medical officials to assess the impact of different vaccination strategies and plan accordingly. However, many existing models of vaccination employ several questionable assumptions, including a rate of vaccination proportional to the population at each point in time. METHODS: We present a SIR-like model that explicitly takes into account vaccine supply and the number of vaccines administered per day and places data-informed limits on these parameters. We refer to this as the non-proportional model of vaccination and compare it to the proportional scheme typically found in the literature. RESULTS: The proportional and non-proportional models behave similarly for a few different vaccination scenarios. However, there are parameter regimes involving the vaccination campaign duration and daily supply limit for which the non-proportional model predicts smaller epidemics that peak later, but may last longer, than those of the proportional model. We also use the non-proportional model to predict the mitigating effects of variably timed vaccination campaigns for different levels of vaccination coverage, using specific constraints on daily administration capacity. CONCLUSIONS: The non-proportional model of vaccination is a theoretical improvement that provides more accurate predictions of the mitigating effects of vaccination on influenza outbreaks than the proportional model. In addition, parameters such as vaccine supply and daily administration limit can be easily adjusted to simulate conditions in developed and developing nations with a wide variety of financial and medical resources. Finally, the model can be used by government and medical officials to create customized pandemic preparedness plans based on the supply and administration constraints of specific communities.