Onset of runaway fragmentation of salt marshes

Salt marshes are valuable but vulnerable coastal ecosystems that adapt to relative sea level rise (RSLR) by accumulating organic matter and inorganic sediment. The natural limit of these processes defines a threshold rate of RSLR beyond which marshes drown, resulting in ponding and conversion to open waters. We develop a simplified formulation for sediment transport across marshes to show that pond formation leads to runaway marsh fragmentation, a process characterized by a self-similar hierarchy of pond sizes with power-law distributions. We find the threshold for marsh fragmentation scales primarily with tidal range and that sediment supply is only relevant where tides are sufficient to transport sediment to the marsh interior. Thus the RSLR threshold is controlled by organic accretion in microtidal marshes regardless of the suspended sediment concentration at the marsh edge. This explains the observed fragmentation of microtidal marshes and suggests a tipping point for widespread marsh loss

An Open-Publishing Response to the COVID-19 Infodemic

The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript\u27s figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis

Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS

Motivation: Epistasis, the presence of gene–gene interactions, has been hypothesized to be at the root of many common human diseases, but current genome-wide association studies largely ignore its role. Multifactor dimensionality reduction (MDR) is a powerful model-free method for detecting epistatic relationships between genes, but computational costs have made its application to genome-wide data difficult. Graphics processing units (GPUs), the hardware responsible for rendering computer games, are powerful parallel processors. Using GPUs to run MDR on a genome-wide dataset allows for statistically rigorous testing of epistasis

Is authorship sufficient for today’s collaborative research? A call for contributor roles

Assigning authorship and recognizing contributions to scholarly works is challenging on many levels. Here we discuss ethical, social, and technical challenges to the concept of authorship that may impede the recognition of contributions to a scholarly work. Recent work in the field of authorship shows that shifting to a more inclusive contributorship approach may address these challenges. Recent efforts to enable better recognition of contributions to scholarship include the development of the Contributor Role Ontology (CRO), which extends the CRediT taxonomy and can be used in information systems for structuring contributions. We also introduce the Contributor Attribution Model (CAM), which provides a simple data model that relates the contributor to research objects via the role that they played, as well as the provenance of the information. Finally, requirements for the adoption of a contributorship-based approach are discussed

Sci-Hub provides access to nearly all scholarly literature

The website Sci-Hub enables users to download PDF versions of scholarly articles, including many articles that are paywalled at their journal\u27s site. Sci-Hub has grown rapidly since its creation in 2011, but the extent of its coverage was unclear. Here we report that, as of March 2017, Sci-Hub\u27s database contains 68.9% of the 81.6 million scholarly articles registered with Crossref and 85.1% of articles published in toll access journals. We find that coverage varies by discipline and publisher, and that Sci-Hub preferentially covers popular, paywalled content. For toll access articles, we find that Sci-Hub provides greater coverage than the University of Pennsylvania, a major research university in the United States. Green open access to toll access articles via licit services, on the other hand, remains quite limited. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection, suggesting the toll access business model may become unsustainable

Is Authorship Sufficient for Today’s Collaborative Research? A Call for Contributor Roles

Assigning authorship and recognizing contributions to scholarly works is challenging on many levels. Here we discuss ethical, social, and technical challenges to the concept of authorship that may impede the recognition of contributions to a scholarly work. Recent work in the field of authorship shows that shifting to a more inclusive contributorship approach may address these challenges. Recent efforts to enable better recognition of contributions to scholarship include the development of the Contributor Role Ontology (CRO), which extends the CRediT taxonomy and can be used in information systems for structuring contributions. We also introduce the Contributor Attribution Model (CAM), which provides a simple data model that relates the contributor to research objects via the role that they played, as well as the provenance of the information. Finally, requirements for the adoption of a contributorship-based approach are discussed

Sci-Hub and the Future of Publishing

Join us for tea, cookies and conversation with Daniel Himmelstein, postdoctoral fellow at Penn in Systems Pharmacology & Translational Therapeutics, who will be talking about his recent research on Sci-hub, a pirate site for published research, and how its ubiquity might change academic publishing. You can read his preprint, Sci-hub Provides Access to Nearly All Scholarly Literature, here: https://peerj.com/preprints/3100/. Research teas are an opportunity for informal conversation around ongoing research at Penn. Register: http://libcal.library.upenn.edu/event/3476612?hs=

The hetnet awakens: understanding complex diseases through data integration and open science

Human disease is complex. However, the explosion of biomedical data is providing new opportunities to improve our understanding. My dissertation focused on how to harness the biodata revolution. Broadly, I addressed three questions: how to integrate data, how to extract insights from data, and how to make science more open. To integrate data, we pioneered the hetnet—a network with multiple node and relationship types. After several preludes, we released Hetionet v1.0, which contains 2,250,197 relationships of 24 types. Hetionet encodes the collective knowledge produced by millions of studies over the last half century. To extract insights from data, we developed a machine learning approach for hetnets. In order to predict the probability that an unknown relationship exists, our algorithm identifies influential network patterns. We used the approach to prioritize disease—gene associations and drug repurposing opportunities. By evaluating our predictions on withheld knowledge, we demonstrated the systematic success of our method. After encountering friction that interfered with data integration and rapid communication, I began looking at how to make science more open. The quest led me to explore realtime open notebook science and expose publishing delays at journals as well as the problematic licensing of publicly-funded research data