Development of an Open-Access Webinar Series on Pathways for Global Surgery Engagement for Applicants to US Residency Programs – Journal of Surgical Research

Abstract:  Background

: Global surgery (GS) training pathways in residency are unclear and vary by specialty and program. Furthermore, information on these pathways is not always accessible. To address this gap, we produced a collection of open-access webinars for senior medical students focused on identifying GS training pathways during residency.


: The Global Surgery Student Alliance (GSSA) is a national nonprofit that engages US students and trainees in GS education, research, and advocacy. GSSA organized nine one-hour, specialty-specific webinars featuring residents of surgical specialties, anesthesia, and OBGYN programs. Live webinars were produced via Zoom from August to October 2020, and all recordings were posted to the GSSA YouTube channel. Medical students moderated webinars with predetermined standardized questions and live questions submitted by attendees. Participant data were collected in mandatory registration forms.


: A total of 539 people were registered for 9 webinars. Among registrants, 189 institutions and 36 countries were represented. Registrants reported education/training levels from less than undergraduate education to attending physicians, while medical students represented the majority of registrants. Following the live webinars, YouTube recordings of the events were viewed 839 times. Webinars featuring otolaryngology and general surgery residents accrued the greatest number of registrations, while anesthesia accrued the least.


: Medical students at all levels demonstrated interest in both the live and recorded specialty-specific webinars on GS in residency. To address the gap in developing global surgery practitioners, additional online, open-access education materials and mentorship opportunities are needed for students applying to US residencies.

In?silico selection of cancer blood plasma proteins by integrating genomic and proteomic databases – Chatterjee – – PROTEOMICS – Wiley Online Library

Abstract:  Blood protein markers have been studied for the clinical management of cancer. Due to the large number of the proteins existing in blood, it is often necessary to pre-select potential protein markers before experimental studies. However, to date there is a lack of automated method for in-silico selection of cancer blood proteins that integrates the information from both genetic and proteomic studies in a cancer-specific manner. In this work, we synthesized both genomic and proteomic information from several open access databases and established a bioinformatic pipeline for in-silico selection of blood plasma proteins overexpressed in specific type of cancer. We demonstrated the workflow of this pipeline with an example of breast cancer, while the methodology was applicable for other cancer types. With this pipeline we obtained 10 candidate biomarkers for breast cancer. The proposed pipeline provides a useful and convenient tool for in-silico selection of candidate blood protein biomarkers for a variety of cancer research.


Celebrating the 50th Issue of Qatar Medical Journal: Editorial Letter |

It is with great pride that we celebrate the 50th issue of Qatar Medical Journal (QMJ) that has achieved significant growth recently. Our mission is to encourage authors to submit high-quality and innovative research promoting medical advancements. In the past two years, manuscripts submissions have tripled in number and were enriched by a more diverse pool of authors with global representation, resulting in an increase in the number of published issues moving from being a biannual to a triannual journal. Additionally, the number of articles published in an issue has doubled. QMJ continues to be an open-access peer-reviewed journal, publishing original research work, reviews, editorials, and case reports that are particularly relevant to medicine and free of charge to authors. It is indexed in several renowned and highly ranked platforms such as PubMed Central, Scopus, Scimago, Google Scholar, and the Directory of Open Access Journals. It was also recently indexed in the World Health Organization’s Index Medicus for the Eastern Mediterranean Region (IMEMR). We look forwards to becoming the highest-rated medical journal, in terms of impact factor, regionally.


Can open science follow open access? – Journal of Biological Chemistry

“What does the immediate future hold in store? The implementation of open access raises an equally important aspect of science publishing in 2021 and beyond – open science. The basic premise of open science is that not only should articles be freely accessible to all, but that the primary data contained within them should also be readily available. JBC certainly adheres to this principle, in so much that JBC policy states that all primary data should be available upon request from the authors. The open science movement has gained significant traction over the last decade, and the basic tenets are that articles and data should be published in the fully open access model. Similarly, all primary data, both ‘negative’ and ‘positive’, should be deposited in publicly-accessible repositories, free to all. This is not a particularly heretical concept, after all at JBC and in many other journals, large data sets such as proteomics, RNAseq, functional genomics, and structural data must all be deposited into one of many public repositories as a condition of article acceptance. Why should this not apply to all primary data?

There are numerous ways to define the Open Science movement. One of the most illustrative is the sociologist Robert Merton’s norms from 1942, defining the ethos of science: Communality, Universalism, Disinterestedness, and Organized Skepticism (

). Communality represents the open and transparent sharing of knowledge, the basic tenet of Open Science. Universalism encompasses objective assessments where decisions are driven by data. Disinterestedness speaks to motivation, a scientist should be motivated by knowledge and discovery, which to many of us seems self-evident but in practice is often distorted because of external forces. Finally organized skepticism, where one limits bias and considers all new evidence, even against one’s prior work. After all, the basic premise of the experimental method has always been one in which scientists define a hypothesis and set out experimental approaches to disprove that hypothesis. All of these idealized norms converge, in collaboration with the scientific method, to ensure a high quality of science. I will be looking forward to discussing with the JBC community the ideals and implementation of Open Science.”

Promoting Open Science: A Holistic Approach to Changing Behaviour

In this article, we provide a toolbox of recommendations and resources for those aspiring to promote the uptake of open scientific practices. Open Science encompasses a range of behaviours that aim to improve the transparency of scientific research. This paper is divided into seven sections, each devoted to different groups or institutions in the research ecosystem: colleagues, students, departments and faculties, universities, academic libraries, journals, and funders. We describe the behavioural influences and incentives for each of these stakeholders as well as changes they can make to foster Open Science. Our primary goal, however, is to suggest actions that researchers can take to promote these behaviours, inspired by simple principles of behaviour change: make it easy, social, and attractive. In isolation, a small shift in one person’s behaviour may appear to make little difference, but when combined, many shifts can radically alter shared norms and culture. We offer this toolbox to assist individuals and institutions in cultivating a more open research culture.

Perspectives on Open Science and The Future of Scholarly Communication: Internet Trackers and Algorithmic Persuasion | Research Metrics and Analytics

The current digital content industry is heavily oriented towards building platforms that track users’ behaviour and seek to convince them to stay longer and come back sooner onto the platform. Similarly, authors are incentivised to publish more and to become champions of dissemination. Arguably, these incentive systems are built around public reputation supported by a system of metrics, hard to be assessed. Generally, the digital content industry is permeable to non-human contributors (algorithms that are able to generate content and reactions), anonymity and identity fraud. It is pertinent to present a perspective paper about early signs of track and persuasion in scholarly communication. Building our views, we have run a pilot study to determine the opportunity for conducting research about the use of “track and persuade” technologies in scholarly communication. We collected observations on a sample of 148 relevant websites and we interviewed 15 that are experts related to the field. Through this work, we tried to identify 1) the essential questions that could inspire proper research, 2) good practices to be recommended for future research, and 3) whether citizen science is a suitable approach to further research in this field. The findings could contribute to determining a broader solution for building trust and infrastructure in scholarly communication. The principles of Open Science will be used as a framework to see if they offer insights into this work going forward.

The Future is in Interoperability Not Big Tech: 2021 in Review

“Network effects aren’t anything new in tech. What is new are the legal strictures that prevent interoperability: new ways of applying cybersecurity law, copyright, patents, and other laws and regulations that make it illegal (or legally terrifying) to make new products that plug into existing ones.

That’s why you can’t leave Facebook and still talk to your Facebook friends. It’s why you can’t switch mobile platforms and take your apps with you. It’s why you can’t switch audiobook providers without losing your audiobooks, and why your local merchants don’t just give you a browser plugin that replaces Amazon’s “buy” buttons with information about which store near you has the item you’re looking for on its shelves.

These switching costs are wholly artificial….

Here’s the interop news that excited us this year:

The US Congress took up the ACCESS Act, a law that would require the largest platforms to open up APIs to their rivals;;
The EU launched the Digital Markets Act (DMA), a sweeping pro-competition proposal. The initial draft had a lot of stuff we loved on interop, which was removed from subsequent drafts, and then, in a victory for common sense and good policy, the European Parliament put all the interop stuff back in, and more besides! …”


A step-by-step guide for using Wikipedia for research communication | Impact of Social Sciences

“The Wikipedia community has, over time, developed a complex maze of guidelines to protect the encyclopedia from vandalism and (self-)promotion. With this post we want to offer scholars some guidance towards their first edit. For demo purposes we selected a research article already written by one of us and figured out how to incorporate some of its findings and accompanying sources into Wikipedia. In the following step-by-step guide, we summarize our experiences from this process while drawing on Wikipedia’s help page for researchers….”

An open repository of real-time COVID-19 indicators | PNAS

Abstract:  The COVID-19 pandemic presented enormous data challenges in the United States. Policy makers, epidemiological modelers, and health researchers all require up-to-date data on the pandemic and relevant public behavior, ideally at fine spatial and temporal resolution. The COVIDcast API is our attempt to fill this need: Operational since April 2020, it provides open access to both traditional public health surveillance signals (cases, deaths, and hospitalizations) and many auxiliary indicators of COVID-19 activity, such as signals extracted from deidentified medical claims data, massive online surveys, cell phone mobility data, and internet search trends. These are available at a fine geographic resolution (mostly at the county level) and are updated daily. The COVIDcast API also tracks all revisions to historical data, allowing modelers to account for the frequent revisions and backfill that are common for many public health data sources. All of the data are available in a common format through the API and accompanying R and Python software packages. This paper describes the data sources and signals, and provides examples demonstrating that the auxiliary signals in the COVIDcast API present information relevant to tracking COVID activity, augmenting traditional public health reporting and empowering research and decision-making.


When Studies Don’t Replicate: A Case Study | Psychology Today

“Another standard developed is the open sharing of data and statistical models that scientists use to test their hypotheses. In the past, scientists would ask other scholars to share this information directly, and often they did.

Today, scientists make this material available on websites such as the Open Science Framework so that anyone can access the information. And lately, scientists are beginning to share their data before publication. These changes have increased the transparency of the scientific work being conducted and made it easier to replicate and verify others’ research.


But what happens when open science practices are not followed?…”

Equitable Open Access Publishing: Changing the Financial Power Dynamics in Academia | Global Health: Science and Practice

“Key Messages

Open access publishing is steadily growing but associated with high article processing charges that exacerbate disparities between funded and unfunded researchers.

Early-career and underrepresented researchers often are not eligible for waivers or discounts, thus resulting in either publishing barriers or financial hardship.

Journals should adopt equitable solutions that enable every author to pursue open access publishing regardless of one’s funding status or affiliation.

Publishing companies should rethink open access publishing models to reduce the financial barriers for readers and authors alike….”

Public Engagement with Science via Social Media: A Case of Communicating the Pandemic on Twitter – Knox – 2021 – Proceedings of the Association for Information Science and Technology – Wiley Online Library

Abstract:  The poster describes a project which analyzes interactions between laypeople and experts via social media. Our aim is to understand how experts and the general public interact with each other on social media, and how we can use current data to improve these interactions in the future. We created a Twitter bot to obtain data from 15 COVID-19 experts and 7 federal government-sponsored public health organizations from English-speaking countries. The data were analyzed in R to investigate the relationships among Followers, Favorites, Retweets, and Hashtag Count per tweet. The preliminary analysis indicated statistically significant differences between various variables including: Number of Favorites, Number of Retweets, Number of Hashtags, and Number of Followers; the results shed light on the current relationship between the public and experts on social media.




Postprints-to-preprints linkage to enhance access to scientific literature: Accountability in Research: Vol 0, No ja

“Preprint servers can enhance the access to scientific literature by bidirectional linkage from published papers (postprints) to their counterpart preprint versions. The current state of linkage is to link preprints to their corresponding postprints (peer-reviewed articles published in journals). Here, I suggest an opposite linkage, from postprints to preprints wherever and whenever preprints are posted on a preprint server. Such connection from paid postprints to free versions (preprints) makes sense as it removes the barriers to get access to paywalled publications freely and easily.”

Preprint servers and patent prior art

“Preprint publications are often “prior art” that render later-filed patent applications either lacking in novelty or an inventive step both of which are primary requirements under the patent laws. Prior to their dispersion on the Internet, preprints were only considered primary art if they were “available to the public”, which was not always the case for preprints distributed in closely held conferences. Internet preprint servers, however, change that calculus, making any research results available to everyone, everywhere. This tension between Internet preprints and patents may have nega tive effects on the research enterprise, including encouraging researchers to manufacture a delay in putting their preprints online-a perverse effect of preprint servers’ openness and accessi bility. Researchers should therefore be deliber ate in their choices about placing preliminary research results on preprint servers and, in particular, should investigate whether patents are necessary to achieve their research’s commercial ends, if any.”

Increase in online chatting has adverse effects on reading skills worldwide

The worldwide deterioration of reading skills due to the increase in online chatting is continuing per country. This is the conclusion of a study by researcher Hans Luyten from the University of Twente. He studied the data from the international PISA-surveys (Programme for International Student Assessment) in 2009 and 2018 in 63 countries. This was part of a large-scale comparative research study conducted under the auspices of the OESO. During that period, online chatting increased significantly in almost every country, but the rate of increase varied considerably from country to country. In Japan, for example, the percentage of students chatting daily increased from 9% to 85%, whereas the increase in Russia was much lower (from 42% to 58%).