scholarly journals Anne O’Tate: Value-added PubMed search engine for analysis and text mining

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248335
Author(s):  
Neil R. Smalheiser ◽  
Dean P. Fragnito ◽  
Eric E. Tirk
Keyword(s):  
Search Engine ◽  
Scientific Community ◽  
Value Added ◽  
Biomedical Literature ◽  
Web Based ◽  
Search Results ◽  
Wide Range ◽  
Pubmed Search ◽  
Study Designs ◽  
Number Of Authors

Over a decade ago, we introduced Anne O’Tate, a free, public web-based tool http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi to support user-driven summarization, drill-down and mining of search results from PubMed, the leading search engine for biomedical literature. A set of hotlinked buttons allows the user to sort and rank retrieved articles according to important words in titles and abstracts; topics; author names; affiliations; journal names; publication year; and clustered by topic. Any result can be further mined by choosing any other button, and small search results can be expanded to include related articles. It has been deployed continuously, serving a wide range of biomedical users and needs, and over time has also served as a platform to support the creation of new tools that address additional needs. Here we describe the current, greatly expanded implementation of Anne O’Tate, which has added additional buttons to provide new functionalities: We now allow users to sort and rank search results by important phrases contained in titles and abstracts; the number of authors listed on the article; and pairs of topics that co-occur significantly more than chance. We also display articles according to NLM-indexed publication types, as well as according to 50 different publication types and study designs as predicted by a novel machine learning-based model. Furthermore, users can import search results into two new tools: e) Mine the Gap!, which identifies pairs of topics that are under-represented within set of the search results, and f) Citation Cloud, which for any given article, allows users to visualize the set of articles that cite it; that are cited by it; that are co-cited with it; and that are bibliographically coupled to it. We invite the scientific community to explore how Anne O’Tate can assist in analyzing biomedical literature, in a variety of use cases.

scholarly journals Tool for filtering PubMed search results by sample size

2018 ◽  
Vol 25 (7) ◽  
pp. 774-779
Author(s):  
Carlos Baladrón ◽  
Alejandro Santos-Lozano ◽  
Javier M Aguiar ◽  
Alejandro Lucia ◽  
Juan Martín-Hernández
Keyword(s):  
Clinical Trials ◽  
Sample Size ◽  
Search Engine ◽  
Sample Sizes ◽  
Search Results ◽  
Estimate Sample Size ◽  
Search Tool ◽  
Pubmed Search ◽  
Meta Analyses ◽  
Validation Tests

Abstract Objective The most used search engine for scientific literature, PubMed, provides tools to filter results by several fields. When searching for reports on clinical trials, sample size can be among the most important factors to consider. However, PubMed does not currently provide any means of filtering search results by sample size. Such a filtering tool would be useful in a variety of situations, including meta-analyses or state-of-the-art analyses to support experimental therapies. In this work, a tool was developed to filter articles identified by PubMed based on their reported sample sizes. Materials and Methods A search engine was designed to send queries to PubMed, retrieve results, and compute estimates of reported sample sizes using a combination of syntactical and machine learning methods. The sample size search tool is publicly available for download at http://ihealth.uemc.es. Its accuracy was assessed against a manually annotated database of 750 random clinical trials returned by PubMed. Results Validation tests show that the sample size search tool is able to accurately (1) estimate sample size for 70% of abstracts and (2) classify 85% of abstracts into sample size quartiles. Conclusions The proposed tool was validated as useful for advanced PubMed searches of clinical trials when the user is interested in identifying trials of a given sample size.

OPTIMASI RISET KEYWORD DENGAN TEKNIK ALLINTITLLE PADA MESIN PENCARI GOOGLE

2018 ◽  
Vol 1 (1) ◽  
pp. 1-5
Author(s):  
Hengki Tamando Sihotang
Keyword(s):  
Search Engine ◽  
Information Needs ◽  
Research Question ◽  
Online Information ◽  
Web Based ◽  
Development Method ◽  
Government Services ◽  
Search Results ◽  
Google Search ◽  
The Web

Online information needs have evolved in the real direction. These needs include the latest information, government services, and commercial products. The research question is how to describe and optimize keyword research with the allintitle technique on the google search engine. The development method used in this research is the prototype method because it is considered able to be evaluated directly on the user. The system testing is done for 3 months by placing keywords on several websites on Google. The conclusion that can be taken is to use the allintitle technique, the search results for the web are easier to find. And this web-based allintitle technique can overcome the challenges of captcha verification from the Google search engine.   Keywords: Allintitle, Google's Search Engine, Keyword competition.

Online Ratings and Reviews by Patients: Should Surgeons use Web-Based Feedback as an Outcome Metric?

2013 ◽  
Vol 95 (6) ◽  
pp. 188-189 ◽  
Author(s):  
Neil Bacon ◽  
Dermot O'Riordan
Keyword(s):  
Clinical Effectiveness ◽  
Patient Reported Outcome ◽  
Web Based ◽  
Outcomes Measures ◽  
Wide Range ◽  
Patient Reported ◽  
Online Ratings ◽  
Quality In Healthcare ◽  
Study Designs ◽  
Outcome Metrics

Patient experience (as distinct from patient-reported outcome metrics, or PrOMs) is known to be an accurate and sensitive metric of patient safety and clinical effectiveness 'for a wide range of disease areas, settings, outcomes measures and study designs' and there is a clear case for it being considered 'one of the central pillars of quality in healthcare'.

scholarly journals The Citation Cloud of a Biomedical Article: Enabling Citation Analysis

2020 ◽  
Author(s):  
Neil R. Smalheiser ◽  
Jodi Schneider ◽  
Vetle I. Torvik ◽  
Dean P. Fragnito ◽  
Eric E. Tirk
Keyword(s):  
Citation Analysis ◽  
Scientific Community ◽  
Value Added ◽  
Search Interface ◽  
Link Type ◽  
Target Article ◽  
Pubmed Search

AbstractUsing open citations provided by iCite and other sources, we have built an extension to PubMed that allows any user to visualize and analyze the “citation cloud” around any target article A: the set of articles cited by A; those which cite A; those which are co-cited with A; and those which are bibliographically coupled to A. This greatly enables the study of citations by the scientific community. The Citation Cloud can be accessed by running any query on the Anne O’Tate value-added PubMed search interface http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi and clicking on the Citations button next to any retrieved article.

scholarly journals Fifty Ways to Tag your Pubtypes: Multi-Tagger, a Set of Probabilistic Publication Type and Study Design Taggers to Support Biomedical Indexing and Evidence-Based Medicine

2021 ◽  
Author(s):  
Aaron M Cohen ◽  
Jodi Schneider ◽  
Yuanxi Fu ◽  
Marian S McDonagh ◽  
Prerna Das ◽  
...  
Keyword(s):  
Study Design ◽  
Value Added ◽  
Mesh Term ◽  
Training Data ◽  
Bibliographic Databases ◽  
Large Set ◽  
Publication Type ◽  
Predictive Probability ◽  
Pubmed Search ◽  
Study Designs

Objective: Indexing articles according to publication types (PTs) and study designs can be a great aid to filtering literature for information retrieval, especially for evidence syntheses. In this study, 50 automated machine learning based probabilistic PT and study design taggers were built and applied to all articles in PubMed. Materials and Methods: PubMed article metadata from 1987-2014 were used as training data, with 2015 used for recalibration. The set of articles indexed with a particular study design MeSH term or PT tag was used as positive training sets. For each PT, the rest of the literature from the same time period was used as its negative training set. Multiple features based on each article title, abstract and metadata were used in training the models. Taggers were evaluated on PubMed articles from 2016 and 2019. A manual analysis was also performed. Results: Of the 50 predictive models that we created, 44 of these achieved an AUC of ~0.90 or greater, with many having performance above 0.95. Of the clinically related study designs, the best performing was SYSTEMATIC_REVIEW with an AUC of 0.998; the lowest performing was RANDOM_ALLOCATION, with an AUC of 0.823. Discussion: This work demonstrates that is feasible to build a large set of probabilistic publication type and study design taggers with high accuracy and ranking performance. Automated tagging permits users to identify qualifying articles as soon as they are published, and allows consistent criteria to be applied across different bibliographic databases. Probabilistic predictive scores are more flexible than binary yes/no predictions, since thresholds can be tailored for specific uses such as high recall literature search, user-adjustable retrieval size, and quality improvement of manually annotated databases. Conclusion: The PT predictive probability scores for all PubMed articles are freely downloadable at http://arrowsmith.psych.uic.edu/evidence_based_medicine/mt_download.html for incorporation into user tools and workflows. Users can also perform PubMed queries at our Anne O'Tate value-added PubMed search engine http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi and filter retrieved articles according to both NLM-annotated and model-predicted publication types and study designs.

Satu Kahkonen and Anthony Lanyi. Institutions, Incentives, and Economic Reforms in India. New Delhi: Sage Publications, 2000. 516 pages. Hardback. Price Indian Rs 595.00.

2001 ◽  
Vol 40 (1) ◽  
pp. 71-74
Author(s):  
Attiya Y. Javed
Keyword(s):  
Reform Process ◽  
New Delhi ◽  
Social Rules ◽  
Reform Agenda ◽  
The Social ◽  
Wide Range ◽  
Rural Governance ◽  
Private And Public ◽  
Economic Landscape ◽  
Number Of Authors

The economic reform process began in India in 1991. However, the reform agenda is still far from its goals as is evident from low per capita income. Thus, this reform effort has not produced the desired outcome of a faster rate of economic and social development in a meaningful way. It is the premise of this volume that to transform the social and economic landscape, the proposed reforms should be broadbased and multi-pronged which take into account incentives for the stockholders in both the private and public sectors. The institutions are the rules that govern economy and include the fundamental legal, political, and social rules that establish the basis for production, exchange, and distribution. The two editors of this volume have received contributions from a number of authors and the wide range of papers are grouped under five main headings: political economy of reforms, reforming public goods delivery, reform issues in agriculture and rural governance, and reforming the district and financial sector.

OPPORTUNITIES FOR STRATEGIC DEVELOPMENT OF BIO-ECONOMY IN THE FOOD AND TOURISM INDUSTRY

2018 ◽  
Vol 28 (5) ◽  
pp. 1681-1684
Author(s):  
Georgi Toskov ◽  
Ana Yaneva ◽  
Stanko Stankov ◽  
Hafize Fidan
Keyword(s):  
National Level ◽  
Value Added ◽  
Tourism Industry ◽  
Small Companies ◽  
Food Sector ◽  
Strategic Development ◽  
Innovation Potential ◽  
Wide Range ◽  
Foreign Brands ◽  
Value Added Products

The European Commission defines the bioeconomy as "the production of renewable biological resources and the conversion of these resources and waste streams into value added products, such as food, feed, bio-based products and bioenergy. Its sectors and industries have strong innovation potential due to their use of a wide range of sciences, enabling and industrial technologies, along with local and implied knowledge." The Bulgarian food industry faces a lot of challenges on the local and national level, which have direct influence on the structure of the production companies. Most of the enterprises from the food sector produce under foreign brands in order to be flexible partners to the large Bulgarian retail chains. The small companies from the food sector are not able to develop as an independent competitive producer on the territory of their local markets. This kind of companies rarely has a working strategy for positioning on new markets. In order to consolidate their already built positions for long period of time, the producers are trying to optimize their operations in a short term. However, the unclear vision of the companies for the business segment does not allow them to fully develop. Tourism in Bulgaria is a significant contributor to the country's economy.

Heterocycle Compounds with Antimicrobial Activity

2020 ◽  
Vol 26 (8) ◽  
pp. 867-904 ◽  
Author(s):  
Maria Fesatidou ◽  
Anthi Petrou ◽  
Geronikaki Athina
Keyword(s):  
Heterocyclic Compounds ◽  
Bacterial Infections ◽  
Scientific Community ◽  
Antimicrobial Agents ◽  
Fungal Infections ◽  
Biological Activities ◽  
Literature Survey ◽  
New Findings ◽  
Wide Range ◽  
Number Of Microorganisms

Background: Bacterial infections are a growing problem worldwide causing morbidity and mortality mainly in developing countries. Moreover, the increased number of microorganisms, developing multiple resistances to known drugs, due to abuse of antibiotics, is another serious problem. This problem becomes more serious for immunocompromised patients and those who are often disposed to opportunistic fungal infections. Objective: The objective of this manuscript is to give an overview of new findings in the field of antimicrobial agents among five-membered heterocyclic compounds. These heterocyclic compounds especially five-membered attracted the interest of the scientific community not only for their occurrence in nature but also due to their wide range of biological activities. Method: To reach our goal, a literature survey that covers the last decade was performed. Results: As a result, recent data on the biological activity of thiazole, thiazolidinone, benzothiazole and thiadiazole derivatives are mentioned. Conclusion: It should be mentioned that despite the progress in the development of new antimicrobial agents, there is still room for new findings. Thus, research still continues.

A Comprehensive Review on C-3 Functionalization of β-Lactams

2019 ◽  
Vol 16 (1) ◽  
pp. 3-16 ◽  
Author(s):  
Reshma Nagpal ◽  
Jitender Bhalla ◽  
Shamsher S. Bari
Keyword(s):  
Scientific Community ◽  
Organometallic Reagent ◽  
Reaction Conditions ◽  
Biological Potential ◽  
Wide Range ◽  
Economic Strategies ◽  
Synthetic Utility ◽  
Recent Advancement ◽  
Equivalent Method ◽  
Made In

Background:A lot of advancement has been made in the area of β-lactams in recent times. Most of the research is targeted towards the synthesis of novel β-lactams, their functionalization and exploring their biological potential. The C-3 functionalization of β-lactams has continued to attract considerable interest of the scientific community due to their utility as versatile intermediates in organic synthesis and their therapeutic applications. This has led to the significant increase in efforts towards developing efficient and economic strategies for C-3 functionalized β-lactams.Objective:The present review aims to highlight recent advancement made in C-3 functionalization of β-lactams.Conclusion:To summarize, functionalization of β-lactams at C-3 is an essential aspect of β-lactam chemistry in order to improve/modify its synthetic utility as well as biological potential. The C-3 carbocation equivalent method has emerged as an important and convenient strategy for C-3 functionalization of β-lactam heterocycles which provides a wide range of β-lactams viz. 3-alkylated β-lactams, 3-aryl/heteroarylated β-lactams, 3- alkoxylated β-lactams. On the other hand, base mediated functionalization of β-lactams via carbanion intermediate is another useful approach but their scope is limited by the requirement of stringent reaction conditions. In addition to this, organometallic reagent mediated α-alkylation of 3-halo/3-keto-β-lactams also emerged as interesting methods for the synthesis of functionalized β-lactams having good yields and diastereoselectivities.

Investigating the Efficacy and Cost-Effectiveness of a Web-based Self-help Program for People With Adjustment Problems After an Accident (SelFIT): Protocol for a Randomized Controlled Trial (Preprint)

2020 ◽  
Author(s):  
Julia Hegy ◽  
Noemi Anja Brog ◽  
Thomas Berger ◽  
Hansjoerg Znoj
Keyword(s):  
Health Care ◽  
Psychological Distress ◽  
Cost Effectiveness ◽  
Well Being ◽  
User Friendliness ◽  
Adjustment Problems ◽  
Health Care Consumption ◽  
Web Based ◽  
Self Help ◽  
Wide Range

BACKGROUND Accidents and the resulting injuries are one of the world’s biggest health care issues often causing long-term effects on psychological and physical health. With regard to psychological consequences, accidents can cause a wide range of burdens including adjustment problems. Although adjustment problems are among the most frequent mental health problems, there are few specific interventions available. The newly developed program SelFIT aims to remedy this situation by offering a low-threshold web-based self-help intervention for psychological distress after an accident. OBJECTIVE The overall aim is to evaluate the efficacy and cost-effectiveness of the SelFIT program plus care as usual (CAU) compared to only care as usual. Furthermore, the program’s user friendliness, acceptance and adherence are assessed. We expect that the use of SelFIT is associated with a greater reduction in psychological distress, greater improvement in mental and physical well-being, and greater cost-effectiveness compared to CAU. METHODS Adults (n=240) showing adjustment problems due to an accident they experienced between 2 weeks and 2 years before entering the study will be randomized. Participants in the intervention group receive direct access to SelFIT. The control group receives access to the program after 12 weeks. There are 6 measurement points for both groups (baseline as well as after 4, 8, 12, 24 and 36 weeks). The main outcome is a reduction in anxiety, depression and stress symptoms that indicate adjustment problems. Secondary outcomes include well-being, optimism, embitterment, self-esteem, self-efficacy, emotion regulation, pain, costs of health care consumption and productivity loss as well as the program’s adherence, acceptance and user-friendliness. RESULTS Recruitment started in December 2019 and is ongoing. CONCLUSIONS To the best of our knowledge, this is the first study examining a web-based self-help program designed to treat adjustment problems resulting from an accident. If effective, the program could complement the still limited offer of secondary and tertiary psychological prevention after an accident. CLINICALTRIAL ClinicalTrials.gov NCT03785912; https://clinicaltrials.gov/ct2/show/NCT03785912?cond=NCT03785912&draw=2&rank=1

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