scholarly journals search.bioPreprint: a discovery tool for cutting edge, preprint biomedical research articles

2016 ◽  
Author(s):  
Carrie L. Iwema ◽  
John LaDue ◽  
Angela Zack ◽  
Ansuman Chattopadhyay

AbstractThe time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1) to make their research immediately and freely available and (2) to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing on any website to be integrated with articles from preprint servers. The bioPreprint search engine is publicly available at http://www.hsls.pitt.edu/resources/preprint.

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1396 ◽  
Author(s):  
Carrie L. Iwema ◽  
John LaDue ◽  
Angela Zack ◽  
Ansuman Chattopadhyay

The time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1) to make their research immediately and freely available and (2) to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing to with articles from preprint servers. This tool, search.bioPreprint, is publicly available at http://www.hsls.pitt.edu/resources/preprint.


F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1396
Author(s):  
Carrie L. Iwema ◽  
John LaDue ◽  
Angela Zack ◽  
Ansuman Chattopadhyay

The time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1) to make their research immediately and freely available and (2) to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing on any web site to be integrated with articles from preprint servers. This tool, search.bioPreprint, is publicly available at http://www.hsls.pitt.edu/resources/preprint.


Publications ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 14
Author(s):  
Eirini Delikoura ◽  
Dimitrios Kouis

Recently significant initiatives have been launched for the dissemination of Open Access as part of the Open Science movement. Nevertheless, two other major pillars of Open Science such as Open Research Data (ORD) and Open Peer Review (OPR) are still in an early stage of development among the communities of researchers and stakeholders. The present study sought to unveil the perceptions of a medical and health sciences community about these issues. Through the investigation of researchers` attitudes, valuable conclusions can be drawn, especially in the field of medicine and health sciences, where an explosive growth of scientific publishing exists. A quantitative survey was conducted based on a structured questionnaire, with 179 valid responses. The participants in the survey agreed with the Open Peer Review principles. However, they ignored basic terms like FAIR (Findable, Accessible, Interoperable, and Reusable) and appeared incentivized to permit the exploitation of their data. Regarding Open Peer Review (OPR), participants expressed their agreement, implying their support for a trustworthy evaluation system. Conclusively, researchers need to receive proper training for both Open Research Data principles and Open Peer Review processes which combined with a reformed evaluation system will enable them to take full advantage of the opportunities that arise from the new scholarly publishing and communication landscape.


Author(s):  
Theresia Devi Indriasari ◽  
Kusworo Anindito ◽  
Eddy Julianto ◽  
Bertha Laroha Paraya Pangaribuan

<span>Indonesia is a country located on top of some tectonic plates that bring potential natural disasters. Disaster management system is considered essential in controlling the situation in the site both before and after the disaster takes place. In disaster situation, the government and society are involved in a volunteer team in order to help minimize victims and support survivors. However, the volunteering activities are often hindered since there are problems in the disaster site. One of the problems is late responses due to poor coordination among volunteers that drives the delay in disaster relief. Therefore, it is necessary to have an application that maps the positions of volunteers in a disaster site, so that the disaster management coordinator can disseminate volunteers to disaster areas based on needs. The purpose of the study is to propose an application called ‘MyMapVolunteers’ that effectively and efficiently detects the position of the volunteers in order to improve disaster management service. In this case, real time and location based service technology will able to detect the position of each volunteer. ‘MyMapVolunteers’ is composed of two platforms, which are mobile and web applications. Mobile platform is an application that uses GPS function provided by the smartphone to find the volunteers’ location coordinates and then send the data of the location automatically and manually. The web platform is used to receive volunteers’ location data and to present them in google map, therefore disaster management coordinator can monitor the positions of and search for volunteers faster.</span>


2020 ◽  
Vol 19 (10) ◽  
pp. 1602-1618 ◽  
Author(s):  
Thibault Robin ◽  
Julien Mariethoz ◽  
Frédérique Lisacek

A key point in achieving accurate intact glycopeptide identification is the definition of the glycan composition file that is used to match experimental with theoretical masses by a glycoproteomics search engine. At present, these files are mainly built from searching the literature and/or querying data sources focused on posttranslational modifications. Most glycoproteomics search engines include a default composition file that is readily used when processing MS data. We introduce here a glycan composition visualizing and comparative tool associated with the GlyConnect database and called GlyConnect Compozitor. It offers a web interface through which the database can be queried to bring out contextual information relative to a set of glycan compositions. The tool takes advantage of compositions being related to one another through shared monosaccharide counts and outputs interactive graphs summarizing information searched in the database. These results provide a guide for selecting or deselecting compositions in a file in order to reflect the context of a study as closely as possible. They also confirm the consistency of a set of compositions based on the content of the GlyConnect database. As part of the tool collection of the Glycomics@ExPASy initiative, Compozitor is hosted at https://glyconnect.expasy.org/compozitor/ where it can be run as a web application. It is also directly accessible from the GlyConnect database.


Acta Naturae ◽  
2018 ◽  
Vol 10 (2) ◽  
pp. 24-29
Author(s):  
I. V. Mizgirev ◽  
D. R. Safina ◽  
I. V. Demidyuk ◽  
S. V. Kostrov

Development and implementation of adequate organism-level models is one of the key elements in biomedical research that focuses on experimental oncology. Over the last decade, studies using Zebrafish (Danio rerio) have gained in popularity in this area of research. This review describes the various approaches that have been used in developing highly effective models for oncological (clinical term, better cancer or tumor) studies based on D. rerio. Priority is given to transplantation models of cancer and their application to optically transparent D. rerio lines, including clonal ones, and utilization tumors of various origins bearing fluorescent labels. The combination of tumor transplantation at organism-level models in transparent clonal D. rerio lines with fluorescent microscopy, FACS-fractionation of tumor cell subsets, and transcription analysis can result in one of the most promising research approaches in providing new information on tumor formation and growth.


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