scholarly journals An OpenData portal to share COVID-19 drug repurposing data in real time

Author(s):  
Kyle R. Brimacombe ◽  
Tongan Zhao ◽  
Richard T. Eastman ◽  
Xin Hu ◽  
Ke Wang ◽  
...  

AbstractThe National Center for Advancing Translational Sciences (NCATS) has developed an online open science data portal for its COVID-19 drug repurposing campaign – named OpenData – with the goal of making data across a range of SARS-CoV-2 related assays available in real-time. The assays developed cover a wide spectrum of the SARS-CoV-2 life cycle, including both viral and human (host) targets. In total, over 10,000 compounds are being tested in full concentration-response ranges from across multiple annotated small molecule libraries, including approved drug, repurposing candidates and experimental therapeutics designed to modulate a wide range of cellular targets. The goal is to support research scientists, clinical investigators and public health officials through open data sharing and analysis tools to expedite the development of SARS-CoV-2 interventions, and to prioritize promising compounds and repurposed drugs for further development in treating COVID-19.

2021 ◽  
Author(s):  
Julian Hocker ◽  
Taryn Bipat ◽  
David W. McDonald ◽  
Mark Zachry

Abstract Qualitative science methods have largely been omitted from discussions of open science. Platforms focused on qualitative science that support open science data and method sharing are rare. Sharing and exchanging coding schemas has great potential for supporting traceability in qualitative research as well as for facilitating the re-use of coding schemas. In this study, we describe and evaluate QualiCO, an ontology for qualitative coding schemas. QualiCO is designed to describe a wide range of qualitative coding schemas. Twenty qualitative researchers used QualiCO to complete two coding tasks. In our findings, we present task performance and interview data that focus participants’ attention on the ontology. Participants used QualiCO to complete the coding tasks, decreasing time on task, while improving accuracy, signifying that QualiCO enabled the reuse of qualitative coding schemas. Our discussion elaborates some issues that participants had and highlights how conceptual and prior practice frames their interpretation of how QualiCo can be used.


2020 ◽  
Author(s):  
George Abi Younes ◽  
Charles Ayoubi ◽  
Omar Ballester ◽  
Gabriele Cristelli ◽  
Gaetan de Rassenfosse ◽  
...  

The present document provides the take of innovation economists on the current pandemic. It is addressed to the general public and focuses on questions related to the Science, Technology, and Innovation (STI) ecosystem. It does not present new research findings. Instead, it provides a reading of current real-world developments using economic reasoning and relying on existing economic research.The first part of the report explains the root causes for a general underinvestment in Research and Development (R&D), with a particular focus on vaccines. These causes include an insufficient demand for vaccines in normal times and the very characteristics of R&D. Governments can intervene to mitigate these problems, but government intervention comes with its own set of issues. We discuss three of them, namely free riding, setting research priorities, and acting on scientific knowledge.The second part discusses several aspects related to current STI policy reactions. First, we observe a sizable shift of funds towards research on SARS-CoV-2. Aren’t we wasting money by allocating so much of it on one single scientific problem? Using the concept of the ‘elasticity of science,’ we argue that we are far from a situation where additional funding would represent a waste of money.Second, we also observe an unprecedented level of cooperation among researchers but also an intense competition to find therapeutic solutions and vaccines. We seek to make sense of this apparent antonymy, highlighting how both cooperative and competitive forces might accelerate research.Third, we focus on one policy tool, namely patents, and we discuss whether the existence of patents hampers the search for a solution. We argue that it might, but we provide ways in which patents can be beneficial. They can accelerate research (such as through patent pools) or ensure greater access to innovations (such as with compulsory licensing).Fourth, we notice that the whole STI ecosystem has been rapidly refocusing on SARS-CoV-2 in a way similar to mission-oriented R&D (MOR) programs such as the Manhattan Project in the 1940s. We highlight the fundamental differences between MOR and the present situation. Today’s response is characterized by a proliferation of a wide range of innovative solutions offered by a complex set of institutions and actors with great intellectual freedom and decentralized competition.The third part of the report assesses some potential long-term impacts of the COVID-19 pandemic. We firstly discuss its impact on R&D investment. We explain how innovation might be negatively affected by a prolonged economic downturn and highlight the crucial role of stimulus packages in confronting the recession. We also address the influence of the crisis on ICT, arguing that it has been a formidable catalyst for ICT adoption. Next, we focus on clean technologies, another major societal challenge besides the pandemic. There are strong reasons for why cleantech investment may suffer. However, the crisis also offers significant opportunities to accelerate the green transition. Finally, we focus on open science, in particular on open access and open data. The current crisis could be a catalyst for the adoption of FAIR (Findable, Accessible, Interoperable, and Reusable) Data Practices.The last part of the report offers some concluding thoughts. The STI policy response cannot be limited to the urgent need for ‘technological fixes.’ A second line of response involves the production of new knowledge to prevent outbreaks (ex-ante) or mitigate their effects (ex-post). Furthermore, the current crisis is a reminder that all branches of science matter. The pandemic has many facets, and a significant number of scientific disciplines can contribute to dealing with it. We conclude with a forward-looking note, arguing that the most substantial impact of the pandemic may lie outside of the public health realm or the science system. It offers a unique opportunity to adapt the set of rules that govern our society.


2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
C. Pommier ◽  
C. Michotey ◽  
G. Cornut ◽  
P. Roumet ◽  
E. Duchêne ◽  
...  

GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems.


2020 ◽  
Author(s):  
George Abi Younes ◽  
Charles Ayoubi ◽  
Omar Ballester ◽  
Gabriele Cristelli ◽  
Gaetan de Rassenfosse ◽  
...  

The present document provides the take of innovation economists on the current pandemic. It is addressed to the general public and focuses on questions related to the Science, Technology, and Innovation (STI) ecosystem. It does not present new research findings. Instead, it provides a reading of current real-world developments using economic reasoning and relying on existing economic research.The first part of the report explains the root causes for a general underinvestment in Research and Development (R&D), with a particular focus on vaccines. These causes include an insufficient demand for vaccines in normal times and the very characteristics of R&D. Governments can intervene to mitigate these problems, but government intervention comes with its own set of issues. We discuss three of them, namely free riding, setting research priorities, and acting on scientific knowledge.The second part discusses several aspects related to current STI policy reactions. First, we observe a sizable shift of funds towards research on SARS-CoV-2. Aren’t we wasting money by allocating so much of it on one single scientific problem? Using the concept of the ‘elasticity of science,’ we argue that we are far from a situation where additional funding would represent a waste of money.Second, we also observe an unprecedented level of cooperation among researchers but also an intense competition to find therapeutic solutions and vaccines. We seek to make sense of this apparent antonymy, highlighting how both cooperative and competitive forces might accelerate research.Third, we focus on one policy tool, namely patents, and we discuss whether the existence of patents hampers the search for a solution. We argue that it might, but we provide ways in which patents can be beneficial. They can accelerate research (such as through patent pools) or ensure greater access to innovations (such as with compulsory licensing).Fourth, we notice that the whole STI ecosystem has been rapidly refocusing on SARS-CoV-2 in a way similar to mission-oriented R&D (MOR) programs such as the Manhattan Project in the 1940s. We highlight the fundamental differences between MOR and the present situation. Today’s response is characterized by a proliferation of a wide range of innovative solutions offered by a complex set of institutions and actors with great intellectual freedom and decentralized competition.The third part of the report assesses some potential long-term impacts of the COVID-19 pandemic. We firstly discuss its impact on R&D investment. We explain how innovation might be negatively affected by a prolonged economic downturn and highlight the crucial role of stimulus packages in confronting the recession. We also address the influence of the crisis on ICT, arguing that it has been a formidable catalyst for ICT adoption. Next, we focus on clean technologies, another major societal challenge besides the pandemic. There are strong reasons for why cleantech investment may suffer. However, the crisis also offers significant opportunities to accelerate the green transition. Finally, we focus on open science, in particular on open access and open data. The current crisis could be a catalyst for the adoption of FAIR (Findable, Accessible, Interoperable, and Reusable) Data Practices.The last part of the report offers some concluding thoughts. The STI policy response cannot be limited to the urgent need for ‘technological fixes.’ A second line of response involves the production of new knowledge to prevent outbreaks (ex-ante) or mitigate their effects (ex-post). Furthermore, the current crisis is a reminder that all branches of science matter. The pandemic has many facets, and a significant number of scientific disciplines can contribute to dealing with it. We conclude with a forward-looking note, arguing that the most substantial impact of the pandemic may lie outside of the public health realm or the science system. It offers a unique opportunity to adapt the set of rules that govern our society.


2018 ◽  
Author(s):  
Dick Bierman ◽  
Jacob Jolij

We have tested the feasibility of a method to prevent the occurrence of so-called Questionable Research Practices (QRP). A part from embedded pre-registration the major aspect of the system is real-time uploading of data on a secure server. We outline the method, discuss the drop-out treatment and compare it to the Born-open data method, and report on our preliminary experiences. We also discuss the extension of the data-integrity system from secure server to use of blockchain technology.


2019 ◽  
Vol 14 (2) ◽  
pp. 133-143 ◽  
Author(s):  
Hidayat Hussain ◽  
Ivan R. Green ◽  
Muhammad Saleem ◽  
Khanzadi F. Khattak ◽  
Muhammad Irshad ◽  
...  

Background: Cucurbitacins belong to a group of tetracyclic triterpenoids that display a wide range of biological effects. In the past, numerous cucurbitacins have been isolated from natural sources and many active compounds have been synthesized using the privileged scaffold in order to enhance its cytotoxic effects. Objective: his review covers patents on the therapeutic effects of natural cucurbitacins and their synthetic analogs published during the past decade. By far, the majority of patents published are related to cancer and Structure-Activity Relationships (SAR) of these compounds are included to lend gravitas to this important class of natural products. Methods: The date about the published patents was downloaded via online open access patent databases. Results: Cucurbitacins display significant cytotoxic properties, in particular cucurbitacins B and D which possess very potent effects towards a number of cancer cells. Numerous cucurbitacins isolated from natural sources have been derivatized through chemical modification at the C(2)-OH and C(25)- OH groups. Most importantly, an acyl ester of the C(25)-OH and, iso-propyl, n-propyl and ethyl ether groups of the C(2)-OH demonstrated the most increased cytotoxic activity. Conclusion: The significant cytotoxic effects of natural and semi-synthetic cucurbitacins make them attractive as new drug candidates. Moreover, cucurbitacins have the capability to form conjugates with other anticancer drugs which will synergistically enhance their anticancer effects. The authors believe that in order to get lead compounds, there should be a greater focus on the synthesis of homodimers, heterodimers, and halo derivatives of cucurbitacins. In the opinion of the authors the analysis of the published patents on the cucurbitacins indicates that these compounds can be developed into a regimen to treat a wide spectrum of cancers.


2021 ◽  
Vol 9 ◽  
pp. 205031212110225
Author(s):  
Mark A Pianka ◽  
Joseph Serino ◽  
Steven F DeFroda ◽  
Blake M Bodendorfer

Greater trochanteric pain syndrome is a common cause of lateral hip pain, encompassing a spectrum of disorders, including trochanteric bursitis, abductor tendon pathology, and external coxa saltans. Greater trochanteric pain syndrome is primarily a clinical diagnosis, and careful clinical examination is essential for accurate diagnosis and treatment. A thorough history and physical exam may be used to help differentiate greater trochanteric pain syndrome from other common causes of hip pain, including osteoarthritis, femoroacetabular impingement, and lumbar stenosis. Although not required for diagnosis, plain radiographs and magnetic resonance imaging may be useful to exclude alternative pathologies or guide treatment of greater trochanteric pain syndrome. The majority of patients with greater trochanteric pain syndrome respond well to conservative management, including physical therapy, non-steroidal anti-inflammatory drugs, and corticosteroid injections. Operative management is typically indicated in patients with chronic symptoms refractory to conservative therapy. A wide range of surgical options, both open and endoscopic, are available and should be guided by the specific etiology of pain. The purpose of this review is to highlight pertinent clinical and radiographic features used in the diagnosis and management of greater trochanteric pain syndrome. In addition, treatment indications, techniques, and outcomes are described.


Publications ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 31
Author(s):  
Manh-Toan Ho ◽  
Manh-Tung Ho ◽  
Quan-Hoang Vuong

This paper seeks to introduce a strategy of science communication: Total SciComm or all-out science communication. We proposed that to maximize the outreach and impact, scientists should use different media to communicate different aspects of science, from core ideas to methods. The paper uses an example of a debate surrounding a now-retracted article in the Nature journal, in which open data, preprints, social media, and blogs are being used for a meaningful scientific conversation. The case embodied the central idea of Total SciComm: the scientific community employs every medium to communicate scientific ideas and engages all scientists in the process.


Nanophotonics ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 1831-1853
Author(s):  
Jaeho Jeon ◽  
Yajie Yang ◽  
Haeju Choi ◽  
Jin-Hong Park ◽  
Byoung Hun Lee ◽  
...  

AbstractTwo-dimensional (2D) layers of transition metal carbides, nitrides, or carbonitrides, collectively referred to as MXenes, are considered as the new family of 2D materials for the development of functional building blocks for optoelectronic and photonic device applications. Their advantages are based on their unique and tunable electronic and optical properties, which depend on the modulation of transition metal elements or surface functional groups. In this paper, we have presented a comprehensive review of MXenes to suggest an insightful perspective on future nanophotonic and optoelectronic device applications based on advanced synthesis processes and theoretically predicted or experimentally verified material properties. Recently developed optoelectronic and photonic devices, such as photodetectors, solar cells, fiber lasers, and light-emitting diodes are summarized in this review. Wide-spectrum photodetection with high photoresponsivity, high-yield solar cells, and effective saturable absorption were achieved by exploiting different MXenes. Further, the great potential of MXenes as an electrode material is predicted with a controllable work function in a wide range (1.6–8 eV) and high conductivity (~104 S/cm), and their potential as active channel material by generating a tunable energy bandgap is likewise shown. MXene can provide new functional building blocks for future generation nanophotonic device applications.


2021 ◽  
Vol 13 (10) ◽  
pp. 1884
Author(s):  
Jingjing Hu ◽  
Yansong Bao ◽  
Jian Liu ◽  
Hui Liu ◽  
George P. Petropoulos ◽  
...  

The acquisition of real-time temperature and relative humidity (RH) profiles in the Arctic is of great significance for the study of the Arctic’s climate and Arctic scientific research. However, the operational algorithm of Fengyun-3D only takes into account areas within 60°N, the innovation of this work is that a new technique based on Neural Network (NN) algorithm was proposed, which can retrieve these parameters in real time from the Fengyun-3D Hyperspectral Infrared Radiation Atmospheric Sounding (HIRAS) observations in the Arctic region. Considering the difficulty of obtaining a large amount of actual observation (such as radiosonde) in the Arctic region, collocated ERA5 data from European Centre for Medium-Range Weather Forecasts (ECMWF) and HIRAS observations were used to train the neural networks (NNs). Brightness temperature and training targets were classified using two variables: season (warm season and cold season) and surface type (ocean and land). NNs-based retrievals were compared with ERA5 data and radiosonde observations (RAOBs) independent of the NN training sets. Results showed that (1) the NNs retrievals accuracy is generally higher on warm season and ocean; (2) the root-mean-square error (RMSE) of retrieved profiles is generally slightly higher in the RAOB comparisons than in the ERA5 comparisons, but the variation trend of errors with height is consistent; (3) the retrieved profiles by the NN method are closer to ERA5, comparing with the AIRS products. All the results demonstrated the potential value in time and space of NN algorithm in retrieving temperature and relative humidity profiles of the Arctic region from HIRAS observations under clear-sky conditions. As such, the proposed NN algorithm provides a valuable pathway for retrieving reliably temperature and RH profiles from HIRAS observations in the Arctic region, providing information of practical value in a wide spectrum of practical applications and research investigations alike.All in all, our work has important implications in broadening Fengyun-3D’s operational implementation range from within 60°N to the Arctic region.


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