Monthly Archives: June 2021

Open Access Publishing Explained: A Discussion With Ros Pyne New Books Network podcast

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In this episode you’ll hear about: Ros Pyne’s path through higher education, how she found her way to her current job, her role at Bloomsbury Publishers, what Open Access [OA] is and is not, how OA can democratize knowledge, and what she’s hopeful about. Our guest is: Ros Pyne, who is the Global Director of Research and Open Access at Bloomsbury Publishers. She has worked in academic publishing since 2007, initially as an editor, and for the last eight years in roles focusing on open access. She has a particular interest in bringing open access to long-form scholarship and to the humanities, and is the co-author of several reports on open access books. She holds a degree in English from the University of Cambridge, and an MA in early modern English literature from King’s College London.

Open Science Conference 2021 | United Nations

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“With the advent of the pandemic, the component of openness in the scientific process has achieved criticality. Since 2019, when the Dag Hammarskjöld Library held the first Open Science Conference in the United Nations headquarters in New York, the global open movement has been significantly enriched with new national and international policies and frameworks as well as daring and visionary initiatives, both private and public. Research and funding institutions, libraries, publishers switched content to open access, in some cases overnight, to ensure unhindered access for researchers and the public, solidifying a tacit understanding of Open Science principles. The roundtable discussion among 19 eminent personalities in Open Science that preceded the Library’s 2019 Conference had resulted in a document of principles elaborating on the necessary elements needed for the creation of a Global Open Science Commons for the SDGs

In the 2nd OPEN SCIENCE CONFERENCE, From Tackling the Pandemic to Addressing Climate Change, policy makers, main IGO actors, librarians, publishers and research practitioners will engage into a public dialogue focusing on what Open Science has learned from COVID-19 and how this can be applied into actions addressing the global climate crisis, at the interface of science, technology, policy and research….”

A Strengths-Based Approach to Evaluation and Transformational Change in Publishing | Educopia Institute

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“When Katherine Skinner and I published the Values and Principles Framework and Checklist last year, we introduced them as mechanisms to hold actors in the scholarly communication system accountable to their stakeholders and demonstrate their commitment to openness in concrete and documentable ways. We conceived the framework and checklist as living, iterative, and adaptable documents. Our first major revision, to be released this fall, reflects a deliberate shift to a strengths-based model of evaluation and change….

The revised framework will include resources that help organizations demonstrate their signature contributions to a more open, equitable, and productive scholarly communication ecosystem and that help them build towards their ideals….”

Journal impact factor gets a sibling that adjusts for scientific field | Science | AAAS

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“The new Journal Citation Indicator (JCI) accounts for the substantially different rates of publication and citation in different fields, Clarivate says. But the move is drawing little praise from the critics, who say the new metric remains vulnerable to misunderstanding and misuse….”

The Sustainability Argument for Open Science

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Abstract:  Ever-increasing anthropogenic greenhouse gas emissions narrow the timeframe for humanity to mitigate the climate crisis. Scientific research activities are resource demanding and, consequently, contribute to climate change; at the same time, scientists have a central role in advancing knowledge, also on climate-related topics. In this opinion piece, we discuss (1) how open science – adopted on an individual as well as on a systemic level – can contribute to making research more environmentally friendly, and (2) how open science practices can make research activities more efficient and thereby foster scientific progress and solutions to the climate crises. While many building blocks are already at hand, systemic changes are necessary in order to create academic environments that support open science practices and encourage scientists from all fields to become more carbon-conscious, ultimately contributing to a sustainable future.

Balancing Investments in Open Access: Sustainability and Innovation · Commonplace

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“Over the past year or so my colleagues at Temple University Libraries and I have been engaged in a project to assess various open access publishing initiatives. Led by myself and Collections Analysis Librarian Karen Kohn, our goal was to develop a plan for how the Libraries might more strategically use the collections budget to support the global transition to open. Towards this end, we organized all-staff discussions, brought in a speaker, and did a lot of reading about what other libraries are doing.

Throughout this project, I have been struck by what I see as the central tension within this work: we want to experiment and support innovative approaches to open access but at the same time we need these initiatives to be sustainable for our organization….

After a year spent learning, thinking, talking, and writing, our group came up with four priorities that will guide future decisions as to which open publishing initiatives we support. These priorities include:

Non-APC or BPC-based models

Initiatives that focus on disciplines that are less likely to have researchers with grant funding

Initiatives spearheaded by university presses or scholarly societies

Models in which the cost is comparable to a similar paywalled product and/or the change in cost over time is predictable…” 

2U, Inc. and edX Agree to Industry-Redefining Combination in Higher Education.

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“2U will acquire substantially all of the assets of edX—a leading nonprofit online learning platform and marketplace—for $800M in cash. Together, 2U and edX will reach over 50 million learners globally, serve more than 230 partners, and offer over 3,500 digital programs on the world’s most comprehensive free-to-degree online education marketplace. The combined scale, reach, capabilities, marketing efficiency, and relationships of 2U and edX will unlock unprecedented opportunity for learners, universities, and employers worldwide….”

 

Openness and Diversity in Journal Editorial Boards

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Abstract:  This study aims to measure diversity in scholarly journals’ editorial board structure and characterize patterns of editorial diversity across types of journals. To accomplish these aims, we integrate multiple sources of data at the journal and editor level to assemble a novel database describing the composition of editors and editorial boards for more than six thousand journals internationally, characterized by discipline, commercial publishing model, and research transparency. We then apply name-based gender imputation, geo-entity extraction analysis, and standardized dispersion measures to evaluate each group’s diversity. This analysis reveals that editorial leadership is more homogenous than editorial boards, and that diversity across both boards and leadership varies substantially (and robustly) across disciplines. Open-access journal’s boards exhibit less gender diversity and more international diversity than their closed-access counterparts. These results also suggest that open access, open science, and diversity, and equity, and inclusion are not strongly correlated and thus require separate measurements.

The big deal this week in online ed.

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“The announcement on Tuesday that 2U will buy the assets of the nonprofit MOOC company edX for $800 million is shaking up the world of online higher ed. It also means I’ll riff on that news for you this week instead of giving you an annotated reading list, per The Edge’s summer programming (back to that next week).

This deal has ramifications in many directions. For starters, it will realign the commercial marketplace for online education, where colleges now pay billions annually to companies known as online-program managers, or OPMs, to help develop, market, and deliver online courses and degrees. The $800 million now headed to a successor nonprofit to edX could also have a huge impact on the future of open-source online options — and maybe breathe new life into the original mission of the nonprofit, which began in 2012 with the goal of democratizing education around the world.

I say “could” because, at this point, we know precious little about what the new nonprofit plans to do with this gargantuan infusion of cash. A joint news release says the money will be “dedicated to reimagining the future of learning for people at all stages of life, addressing educational inequalities, and continuing to advance next-generation learning experiences and platforms.” Lofty, ambitious language to be sure. But $800 million is a lotta clams, and I’m sure the hundreds of colleges and thousands of professors whose own financial and in-kind contributions over the last nine years have helped bring edX to this point would love to know some specifics — perhaps even more than I would….”

Introducing the Modeling Cell Proliferation and the Cell Microenvironment Collection

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In 2020, PLOS ONE announced a Call for Papers on Modeling Cell Proliferation and the Cell Microenvironment. This week, we celebrate the launch of this collection, which includes a number of papers offering new insights into this vital topic. Understanding the cellular microenvironment and how cells proliferate has a number of useful applications, and this collection showcases the breadth of this research area. We are immensely grateful to Guest Editors Aurélie Carlier (Maastricht University), Ravi Iyengar (Icahn School of Medicine at Mount Sinai), Padmini Rangamani (University of California, San Diego) and Vivek Shenoy (University of Pennsylvania), who were instrumental in curating this collection at PLOS ONE.

Bacterial biofilms are present in many different environments, and are important to understand both in order to utilize their properties as well as combating them in problematic settings. Jin and Marshall extend an existing model of biofilm formation to study for the first time how the fimbrial force and extracellular polymeric substance (EPS) flow affect the growth of biofilms. The model incorporates both continuous elements, for modeling the water and EPS, and discrete elements, for modeling the interaction between individual cells. They find that the total cell number is a main driver for colony morphology, and the findings are in good agreement with existing experimental work. The study concludes that the ultimate structure of a bacterial colony is dependent on the interaction of the opposing effects of cell drag from EPS production and the fimbrial force.

The forces that are exerted by cells play a major role in the mechanisms by which cancer metastasis, angiogenesis and other processes operate. Hervas-Rayul and colleagues explore cell surface traction through an experimental study followed by solving the inverse problem iteratively using a finite element model. The model utilizes the displacement field for 3D traction force microscopy as an input for the inverse problem solver. In this way, this study provides a concrete link between experimental and modeling work in the field, and can be applied to any material and geometry.

The shape of a cell is influenced both by its cytoskeleton and the surrounding environment. In a new study, Eroumé and colleagues model the effect of cell shape on cell polarization, specifically by studying how cell shape influences Cdc42 patterns. They find that cell shape and aspect ratio both influence Cdc42 patterns, and that some of these influences are non-intuitive. They find evidence for ‘reverse polarization’ in which the maximal Cdc42 concentration can shift in the direction opposite the initial polarization gradient. Their results call for future experimental validation of the predictions that come out of this work.

Metastasis can arise when circulating tumor cells are transported through the bloodstream to a new secondary location. Understanding how this process works can aid the development of various therapies that block the transport of these circulating tumor cells both as single cells and as clusters. In an effort to study these processes in more detail, Marrella and colleagues have developed a microfluidic device which mimics the wall shear stress experienced in the human vascular system. The device is 3D-printed using a biocompatible photopolymer resin, and their investigations show how increasing wall shear stress can influence morphology and disaggregation of cell clusters.

Uncontrolled cell proliferation is a major factor in tumor growth and progression of colorectal cancer. Vundavilli and colleagues present new results on the underlying mutations that may be influencing colorectal cancer cell proliferation through mathematical and experimental work. They use publicly available gene expression data to identify pathways and mutations that are deregulated in colon cancer, and then apply Boolean modeling to search for drug combinations that may induce cancer cell death.

Taken together, these papers provide new insights into cell signaling, biofilms and cancer metastasis, and provide suggestions for future lines of research within these broader research areas. We will add papers to this collection over time as they are published, so please do keep checking back.

References:

Eroumé K, Vasilevich A, Vermeulen S, de Boer J, Carlier A (2021) On the influence of cell shape on dynamic reaction-diffusion polarization patterns. PLoS ONE 16(3): e0248293. https://doi.org/10.1371/journal.pone.0248293

Hervas-Raluy S, Gomez-Benito MJ, Borau-Zamora C, Cóndor M, Garcia-Aznar JM (2021) A new 3D finite element-based approach for computing cell surface tractions assuming nonlinear conditions. PLoS ONE 16(4): e0249018. https://doi.org/10.1371/journal.pone.0249018

Jin X, Marshall JS (2020) Mechanics of biofilms formed of bacteria with fimbriae appendages. PLoS ONE 15(12): e0243280. https://doi.org/10.1371/journal.pone.0243280

Marrella A, Fedi A, Varani G, Vaccari I, Fato M, Firpo G, et al. (2021) High blood flow shear stress values are associated with circulating tumor cells cluster disaggregation in a multi-channel microfluidic device. PLoS ONE 16(1): e0245536. https://doi.org/10.1371/journal.pone.0245536

Vundavilli H, Datta A, Sima C, Hua J, Lopes R, Bittner M (2021) Targeting oncogenic mutations in colorectal cancer using cryptotanshinone. PLoS ONE 16(2): e0247190. https://doi.org/10.1371/journal.pone.0247190

Image attribution: Ricardo Murga and Rodney Donlan, Public domain, via Wikimedia Commons

The post Introducing the Modeling Cell Proliferation and the Cell Microenvironment Collection appeared first on EveryONE.

Negotiating Open Access Journal Agreements: An Academic Library Case Study | Hosoi | Pennsylvania Libraries: Research & Practice

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Abstract:  The COVID-19 pandemic has presented an opportunity for academic libraries to advance open access (OA) to scholarly articles. Awareness among faculty on the importance of OA has increased significantly during the pandemic, as colleges and universities struggle financially and seek sustainable access to high-quality scholarly journals. Consortia have played an important role in establishing negotiation principles on OA journal agreements. While the number of OA agreements is increasing, case studies involving individual libraries are still limited. This paper reviews existing literature on publisher negotiation principles related to OA journal negotiations and reflects on recent cases at an academic library in Pennsylvania, in order to identify best practices in OA journal negotiations. It provides recommendations on roles, relationships, and processes, as well as essential terms of OA journal agreements. This study’s findings are most relevant to large academic libraries that are interested in negotiating with scholarly journal publishers independently or through consortia.

 

Open Access goes Barcamp, Part 2: How to organise networking online

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by Hannah Schneider (KIM), Andreas Kirchner (KIM) und Maximilian Heber (KIM)

You normally get together for a Barcamp event on site in a relaxed atmosphere, write ideas on whiteboards, pinboards or flipcharts and switch back and forth between the sessions as you see fit. You also naturally get into conversations with others in the kitchenette, in the corridors, during breaks or when having dinner together. All these elements enliven Barcamps and make them what they are. So how do you succeed in transferring a physical setting of this kind into a virtual space while staying true to the character of a Barcamp event?

Choose the right tools for the online Barcamp event

As we wanted the virtual Open Access Barcamp to reflect not only the exchange of information and ideas but also the networking character online, we decided to use gather.town as the technical basis. In our opinion, this tool is better than other videoconferencing software, such as Zoom or BigBlueButton, at facilitating quick conversational exchanges and the independent formation of small groups. A special feature of gather.town is that it offers users the option of moving around freely as a small figure in a space specially created for the respective event. As soon as you approach others, the camera and microphone are activated. This helps participants make a variety of contacts – just like at real meetings. We also considered using wonder.me, but since it does not provide for flexible room design, we ultimately decided against it.

Screenshot 1: The Gather.town room (CC BY 4.0)

We also used the online whiteboard Miro to collaboratively collect topics and for documentation purposes. This gave participants the opportunity to catch up on the contents of the sessions they could not attend. We chose Miro because it offers both a voting function and enough space for different groups to work in different corners at the same time.

Since technical issues and problems are to be expected when using such interactive tools, there were also two people in the conference room who provided technical support throughout the event, in addition to a central helpdesk email address. This proved to be very helpful, especially at the beginning of the event. An illustrated guide on how to use the tools was sent out in advance to help participants prepare for the event.

Screenshot 2: The Miro whitheboard (CC BY 4.0)

A central point of the programme at the beginning of each Barcamp event is the session planning to collectively set the agenda. The aim was to fill the five 45-minute sessions with up to three parallel events. To do so, we first collected topics on Miro and then presented each topic for one minute in an elevator pitch. A vote integrated into Miro then determined which topics should be included in the agenda. Care was taken to ensure that they did not overlap in order to allow as many people as possible to participate in the most popular sessions. The scheduling preference of the people giving the sessions was also taken into account.

Illustration 3: Session planning (CC BY 4.0)

To sweeten the break for the participants while the organisation team finalised the programme, a conference bag containing Open Access items and chocolates was sent to their home office in advance as a “care package”. For this purpose, we had asked the participants to provide their addresses on a voluntary basis during registration and most of them accepted the offer.

Illustration 4: Carepaket (CC BY 4.0)

How to create networking opportunities online

Since networking with other people is often more difficult at online events than at on-site meetings, and brief conversations during the coffee break usually don’t happen during virtual events, we specifically scheduled times for socialising.

Participants were given time to get to know each other better on the first day. For this purpose, three organisational questions were asked, according to which everyone in the gather.town room was asked to line up (for example, “I have already been to a Barcamp event” ? line up in ascending order from never to very often). The resulting groups were then given the opportunity to chat.

A kind of “speed dating” activity also took place allowing participants to talk to one person for five minutes, after which the interlocutors changed partners in order to ensure that each participant could have several different conversations.

We also deliberately left a time slot open on the second day for topics that either had not made it onto the agenda or required more extensive discussion. During this time slot, everyone could gather around “topic tables” to discuss aspects that concern them personally in their everyday work with Open Access. In keeping with the motto “bring-your-own-problem”, this facilitated practice-oriented discussions in smaller groups, for example on the topics of secondary publications, publication funds or Open Access consulting services.

During the evening programme, likewise held in gather.town, the participants were first given the opportunity to put their general knowledge to the test in a pub quiz. They then also had a chance to make or consolidate contacts with other Open Access enthusiasts in an informal setting. Although all the participants had spent the whole day sitting in front of the screen, about 25 people met up again in gather.town in the evening. Even though the quiz could have been a little shorter according to the feedback from some participants, it was a relaxed get-together despite the virtual setting.

The online Barcamp thrived on the active participation

We feel that the virtual Open Access Barcamp was a successful experiment all things considered and are pleased that the community had a lively exchange of ideas in our innovative setting. The two-day online event thrived on the contribution and collaboration of everyone and the active engagement of the participants. Numerous practical aspects and challenges in the everyday work with Open Access were addressed and discussed, and participants looked for solutions together.

We would like to point out that the vast majority of participants saw the video conferencing tool gather.town as very suitable, despite initial technical difficulties. It not only challenged and supported participants with their activities, but also facilitated conversations in the virtual kitchenette or socialising time slots. The combination with an online whiteboard such as Miro has also proven successful for session planning as well as for collaboration and documentation during the Open Access Barcamp. It should be noted, however, that the technical performance of online events is highly dependent on the internet connection and other technical conditions that are difficult to influence as an organiser. The virtual format nevertheless offers all interested parties the opportunity to exchange ideas easily with the Open Access community, regardless of location and without having to travel far or implement other logistical planning measures.

We would like to take this opportunity to thank all participants for their active and lively engagement in the programme. We would also like to thank them for their openness to the unconventional online format and their patience with technical problems. A big thank you also goes out to the entire open-access.network project team for their great teamwork. We are looking forward to #OABarcamp22 next year!

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This text has been translated from German.

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Disturbance of greedy publishing to academia

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Questionable publications have been criticized for their greedy behaviour, yet have not been investigated their influence on academia quantitatively. Here, we probe the impact of questionable publications through the systematic and comprehensive analysis for the various participants in academia compared with their most similar unquestioned counterparts using billions of citation records: the brokers, e.g. journals and publishers, and prosumers, e.g. authors. Our analysis reveals that the questionable publishers decorate their citation score by the publisher-level self-citations to their journals while they control the journal-level self-citations to evade the evaluation of the journal indexing services; thus, it is hard to detect by conventional journal-level metrics, which our novel metric can capture. We also show that both novelty and influence are lower for the questionable publications than their counterparts implying the negative effect of questionable publications in the academic ecosystem, which provides a valuable basis for future policy-making.