bims-librar 2019-01-13 papers

bims-librar

Biomed News

on Biomedical librarianship

Issue of 2019–01–13
nine papers selected by
Thomas Krichel, Open Library Society

PubTerm: a web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records.
Spinning the Genome: Why Science Hype Matters.
Improving Scientific Writing Skills and Publishing Capacity by Developing University-Based Editing System and Writing Programs.
Where college students look for vaping information and what information they believe.
Are All Brain Death Controversies on The Internet Fake Medical News?
Provision of online HIV-related information to gay, bisexual and other men who have sex with men: a health literacy-informed critical appraisal of Canadian agency websites.
Indicators of adolescents' preference to receive oral health information using social media.
Beyond opinion classification: Extracting facts, opinions and experiences from health forums.
Well-being through the lens of the internet.

Database (Oxford). 2019 Jan 01. 2019

PubTerm: a web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records.

José Garcia-Pelaez, David Rodriguez, Roberto Medina-Molina, Gerardo Garcia-Rivas, Carlos Jerjes-Sánchez, Victor Trevino.

Background and objective: Analysis, annotation and curation of biomedical scientific literature is a recurrent task in biomedical research, database curation and clinics. Commonly, the reading is centered on concepts such as genes, diseases or molecules. Database curators may also need to annotate published abstracts related to a specific topic. However, few free and intuitive tools exist to assist users in this context. Therefore, we developed PubTerm, a web tool to organize, categorize, curate and annotate a large number of PubMed abstracts related to biological entities such as genes, diseases, chemicals, species, sequence variants and other related information.
Methods: A variety of interfaces were implemented to facilitate curation and annotation, including the organization of abstracts by terms, by the co-occurrence of terms or by specific phrases. Information includes statistics on the occurrence of terms. The abstracts, terms and other related information can be annotated and categorized using user-defined categories. The session information can be saved and restored, and the data can be exported to other formats.
Results: The pipeline in PubTerm starts by specifying a PubMed query or list of PubMed identifiers. Then, the user can specify three lists of categories and specify what information will be highlighted in which colors. The user then utilizes the `term view' to organize the abstracts by gene, disease, species or other information to facilitate the annotation and categorization of terms or abstracts. Other views also facilitate the exploration of abstracts and connections between terms. We have used PubTerm to quickly and efficiently curate collections of more than 400 abstracts that mention more than 350 genes to generate revised lists of susceptibility genes for diseases. An example is provided for pulmonary arterial hypertension.
Conclusions: PubTerm saves time for literature revision by assisting with annotation organization and knowledge acquisition.

DOI: https://doi.org/10.1093/database/bay137
Perspect Biol Med. 2018 ;61(4): 560-571

Spinning the Genome: Why Science Hype Matters.

Timothy Caulfield.

There is a growing body of literature that describes both the degree to which science is hyped and how and why that hype happens. Hype can be described as an inappropriate exaggeration of the significance or potential value of a particular study or area of science. Evidence tells us that this spin happens throughout the science translation process. There is hype in research grants, peer-reviewed publications, scientific abstracts, institutional press releases, media representations, and, of course, in the associated marketing of a new product. There is also evidence that it has played a particularly significant role in the area of genetic research. Science hype is a complex phenomenon that involves many actors. And it is, at least to some degree, the result of systemic pressures imbedded in the current incentives associated with biomedical research. This article reviews what the evidence says about the sources of hype, the social and scientific harms, and what can be done to nudge us in the right direction.

DOI: https://doi.org/10.1353/pbm.2018.0065
J Korean Med Sci. 2019 Jan 07. 34(1): e9

Improving Scientific Writing Skills and Publishing Capacity by Developing University-Based Editing System and Writing Programs.

Edward Barroga, Hiroshi Mitoma.

  Scholarly article writing and publishing in international peer-reviewed journals can become an overwhelming task for many medical, nursing, and healthcare professionals in a university setting, especially in countries whose native language is not English. To help improve their scientific writing skills and publishing capacity, a university-based editing system and writing programs can be developed as educational platforms. These are delivered by a team of specialist editors composed of tenured faculty members who have a strong medical background and extensive experience in teaching courses on medical research, editing, writing, and publishing. For the editing system, the specialist editors provide comprehensive editing, personalized consultation, full editorial support after peer review, guidance with online submissions/resubmissions, and detailed editorial review at different stages of the manuscript writing. In addition, the specialist editors can develop writing programs such as medical writing and editing internships, academic courses in medical writing or research study designs and reporting standards, special interactive lectures and sessions on predatory publishing, seminars on updated editorial guidance of global editorial associations, academic visits on medical writing and editing, medical writing mentoring program, networking programs in scholarly communication, and publication resources in medical writing and scholarly publishing. These editing system and writing programs can serve as integrated platforms for improving scientific writing skills and publishing capacity by providing continuing education in medical writing, editing, publishing, and publication ethics.

Keywords:  Editing System; Educational Platform; Publishing Capacity; Scientific Writing Skills; Writing Programs

DOI:  https://doi.org/10.3346/jkms.2019.34.e9
J Am Coll Health. 2019 Jan 07. 1-10

Where college students look for vaping information and what information they believe.

Page D Dobbs, Ashley H Clawson, Mary Gowin, Marshall K Cheney.

   OBJECTIVE: This convergent mixed methods study examined how information sources influence college students' beliefs and knowledge about vaping.
PARTICIPANTS: College students either completed a survey (n = 522; January-April, 2016) or were interviewed (n = 33; 2015-2016).
METHODS: College students completed an online survey asking 'where' students had heard about e-cigarette and 'what' they had heard. Responses were quantified and a chi-square analysis was conducted. Additional college student e-cigarette users were interviewed about the credibility of information sources. Thematic analysis was conducted with the coded interviews.
RESULTS: There was a significant relationship between information sources for e-cigarettes (social sources, media, advertising, education/research) and the messages they recalled. Friends who vaped and e-cigarette users were the most credible information sources. Confirmation bias and scientific impotence bias characterized assessment of e-cigarette information.
CONCLUSIONS: Health education specialists working on college campuses should provide accurate information via communication channels most unitized by college students.

Keywords:  E-cigarette; electronic cigarette; information channels; information sources; vaping

DOI:  https://doi.org/10.1080/07448481.2018.1549557
Chest. 2019 Jan;pii: S0012-3692(18)32429-2. [Epub ahead of print]155(1): 238-239

Are All Brain Death Controversies on The Internet Fake Medical News?

Mohamed Y Rady, Joseph L Verheijde, Michael Potts.

DOI: https://doi.org/10.1016/j.chest.2018.08.1068
Sex Health. 2019 Jan 09.

Provision of online HIV-related information to gay, bisexual and other men who have sex with men: a health literacy-informed critical appraisal of Canadian agency websites.

Mark Gilbert, Warren Michelow, Joshun Dulai, Daniel Wexel, Trevor Hart, Ingrid Young, Susan Martin, Paul Flowers, Lorie Donelle, Olivier Ferlatte.

Background:HIV risk and prevention information is increasingly complex and poses challenges for gay, bisexual and other men who have sex with men (GBMSM) seeking to find, understand and apply this information. A directed content analysis of Canadian HIV websites to see what information is provided, how it is presented and experienced by users, was conducted. Methods: Eligible sites provided information relevant for GBMSM on HIV risk or prevention, were from community or government agencies, and were aimed at the public. Sites were found by using a Google search using French and English search terms, from expert suggestions and a review of links. Eligibility and content for review was determined by two reviewers, and coded using a standardised form. Reading grade level and usability scores were assessed through Flesch-Kincaid and LIDA instruments. Results: Of 50 eligible sites, 78% were from community agencies and 26% were focussed on GBMSM. Overall, fewer websites contained information on more recent biomedical advances (e.g. pre-exposure prophylaxis, 10%) or community-based prevention strategies (e.g. seroadaptive positioning, 10%). Many sites had high reading levels, used technical language and relied on text and prose. And 44% of websites had no interactive features and most had poor usability scores for engageability. Conclusions: Overall, less information about emerging topics and a reliance on text with high reading requirements was observed. Our study speaks to potential challenges for agency website operators to maintain information relevant to GBMSM which is up-to-date, understandable for a range of health literacy skills and optimises user experience.

DOI: https://doi.org/10.1071/SH18092
Acta Odontol Scand. 2019 Jan 11. 1-6

Indicators of adolescents' preference to receive oral health information using social media.

Maha El Tantawi, Eman Bakhurji, Asim Al-Ansari, Abdulelah AlSubaie, Hassan A Al Subaie, Abdulhadi AlAli.

   OBJECTIVES: To assess (1) adolescents' preference to use social media (SM) to receive oral health information (OHI) and (2) factors associated with this preference.
MATERIALS AND METHODS: A cross-sectional survey was conducted in 2016, Eastern Province, Saudi Arabia including male middle school students. A questionnaire assessed explanatory variables including background, previous OHI seeking practices, internet use purposes, convenience of using SM for OHI and perceived usefulness of obtained OHI. The outcome variable was respondents' preference to use SM to receive OHI. Simple and multiple logistic regression models were used for statistical analysis.
RESULTS: The response rate was 91.2% (456/500). Of those, 57.5% preferred using SM to receive OHI. The odds for this were significantly associated with being Saudi (OR = 3.12, 95%CI = 1.36, 7.18), previously using Twitter (OR = 4.59, 95%CI = 1.77, 11.89) and Instagram for OHI (OR = 2.60, 95%CI = 1.51, 4.45), frequent use of the internet to obtain OHI (OR = 1.25, 95%CI = 1.02, 1.54) and ease of obtaining OHI using the Internet (OR = 2.69, 95%CI = 1.5, 4.39).
CONCLUSION: Most adolescents preferred using SM to receive OHI. This was associated with previous OHI seeking practices and convenience of using SM. These findings have implications for designing SM-based health education campaigns targeting adolescents.

Keywords:  Saudi Arabia; Social media; adolescents; internet; oral health information

DOI:  https://doi.org/10.1080/00016357.2018.1536803
PLoS One. 2019 ;14(1): e0209961

Beyond opinion classification: Extracting facts, opinions and experiences from health forums.

Jorge Carrillo-de-Albornoz, Ahmet Aker, Emina Kurtic, Laura Plaza.

INTRODUCTION: Surveys indicate that patients, particularly those suffering from chronic conditions, strongly benefit from the information found in social networks and online forums. One challenge in accessing online health information is to differentiate between factual and more subjective information. In this work, we evaluate the feasibility of exploiting lexical, syntactic, semantic, network-based and emotional properties of texts to automatically classify patient-generated contents into three types: "experiences", "facts" and "opinions", using machine learning algorithms. In this context, our goal is to develop automatic methods that will make online health information more easily accessible and useful for patients, professionals and researchers.
MATERIAL AND METHODS: We work with a set of 3000 posts to online health forums in breast cancer, morbus crohn and different allergies. Each sentence in a post is manually labeled as "experience", "fact" or "opinion". Using this data, we train a support vector machine algorithm to perform classification. The results are evaluated in a 10-fold cross validation procedure.
RESULTS: Overall, we find that it is possible to predict the type of information contained in a forum post with a very high accuracy (over 80 percent) using simple text representations such as word embeddings and bags of words. We also analyze more complex features such as those based on the network properties, the polarity of words and the verbal tense of the sentences and show that, when combined with the previous ones, they can boost the results.

DOI: https://doi.org/10.1371/journal.pone.0209961
PLoS One. 2019 ;14(1): e0209562

Well-being through the lens of the internet.

Yann Algan, Fabrice Murtin, Elizabeth Beasley, Kazuhito Higa, Claudia Senik.

We build models to estimate well-being in the United States based on changes in the volume of internet searches for different words, obtained from the Google Trends website. The estimated well-being series are weighted combinations of word groups that are endogenously identified to fit the weekly subjective well-being measures collected by Gallup Analytics for the United States or the biannual measures for the 50 states. Our approach combines theoretical underpinnings and statistical analysis, and the model we construct successfully estimates the out-of-sample evolution of most subjective well-being measures at a one-year horizon. Our analysis suggests that internet search data can be a complement to traditional survey data to measure and analyze the well-being of a population at high frequency and local geographic levels. We highlight some factors that are important for well-being, as we find that internet searches associated with job search, civic participation, and healthy habits consistently predict well-being across several models, datasets and use cases during the period studied.

DOI: https://doi.org/10.1371/journal.pone.0209562