TeamTree analysis: A new approach to evaluate scientific production.
Ontology highlight
ABSTRACT:
SUBMITTER: Pfrieger FW
PROVIDER: S-EPMC8294527 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The factual value of genome-wide association studies (GWAS) for the understanding of multifactorial diseases is a matter of intense debate. Practical consequences for the development of more effective therapies do not seem to be around the corner. Here we propose a pragmatic and objective evaluation of how much new biology is arising from these studies, with particular attention to the information that can help prioritize therapeutic targets. We chose multiple sclerosis (MS) as a paradigm disease and assumed that, in pre-GWAS candidate-gene studies, the knowledge behind the choice of each gene reflected the understanding of the disease prior to the advent of GWAS. Importantly, this knowledge was based mainly on non-genetic, phenotypic grounds. We performed single-gene and pathway-oriented comparisons of old and new knowledge in MS by confronting an unbiased list of candidate genes in pre-GWAS association studies with those genes exceeding the genome-wide significance threshold in GWAS published from 2007 on. At the single gene level, the majority (94 out of 125) of GWAS-discovered variants had never been contemplated as plausible candidates in pre-GWAS association studies. The 31 genes that were present in both pre- and post-GWAS lists may be of particular interest in that they represent disease-associated variants whose pathogenetic relevance is supported at the phenotypic level (i.e. the phenotypic information that steered their selection as candidate genes in pre-GWAS association studies). As such they represent attractive therapeutic targets. Interestingly, our analysis shows that some of these variants are targets of pharmacologically active compounds, including drugs that are already registered for human use. Compared with the above single-gene analysis, at the pathway level GWAS results appear more coherent with previous knowledge, reinforcing some of the current views on MS pathogenesis and related therapeutic research. This study presents a pragmatic approach that helps interpret and exploit GWAS knowledge.
| S-EPMC3743868 | biostudies-literature
Project description:BackgroundAs the amount of scientific data grows, peer-reviewed Scientific Data Analysis Resources (SDARs) such as published software programs, databases and web servers have had a strong impact on the productivity of scientific research. SDARs are typically linked to using an Internet URL, which have been shown to decay in a time-dependent fashion. What is less clear is whether or not SDAR-producing group size or prior experience in SDAR production correlates with SDAR persistence or whether certain institutions or regions account for a disproportionate number of peer-reviewed resources.MethodsWe first quantified the current availability of over 26,000 unique URLs published in MEDLINE abstracts/titles over the past 20 years, then extracted authorship, institutional and ZIP code data. We estimated which URLs were SDARs by using keyword proximity analysis.ResultsWe identified 23,820 non-archival URLs produced between 1996 and 2013, out of which 11,977 were classified as SDARs. Production of SDARs as measured with the Gini coefficient is more widely distributed among institutions (.62) and ZIP codes (.65) than scientific research in general, which tends to be disproportionately clustered within elite institutions (.91) and ZIPs (.96). An estimated one percent of institutions produced 68% of published research whereas the top 1% only accounted for 16% of SDARs. Some labs produced many SDARs (maximum detected = 64), but 74% of SDAR-producing authors have only published one SDAR. Interestingly, decayed SDARs have significantly fewer average authors (4.33 +/- 3.06), than available SDARs (4.88 +/- 3.59) (p < 8.32 × 10-4). Approximately 3.4% of URLs, as published, contain errors in their entry/format, including DOIs and links to clinical trials registry numbers.ConclusionSDAR production is less dependent upon institutional location and resources, and SDAR online persistence does not seem to be a function of infrastructure or expertise. Yet, SDAR team size correlates positively with SDAR accessibility, suggesting a possible sociological factor involved. While a detectable URL entry error rate of 3.4% is relatively low, it raises the question of whether or not this is a general error rate that extends to additional published entities.
| S-EPMC4251054 | biostudies-literature
Project description:MotivationTo understand the molecular mechanisms involved in cancer development, significant efforts are being invested in cancer research. This has resulted in millions of scientific articles. An efficient and thorough review of the existing literature is crucially important to drive new research. This time-demanding task can be supported by emerging computational approaches based on text mining which offer a great opportunity to organize and retrieve the desired information efficiently from sizable databases. One way to organize existing knowledge on cancer is to utilize the widely accepted framework of the Hallmarks of Cancer. These hallmarks refer to the alterations in cell behaviour that characterize the cancer cell.ResultsWe created an extensive Hallmarks of Cancer taxonomy and developed automatic text mining methodology and a tool (CHAT) capable of retrieving and organizing millions of cancer-related references from PubMed into the taxonomy. The efficiency and accuracy of the tool was evaluated intrinsically as well as extrinsically by case studies. The correlations identified by the tool show that it offers a great potential to organize and correctly classify cancer-related literature. Furthermore, the tool can be useful, for example, in identifying hallmarks associated with extrinsic factors, biomarkers and therapeutics targets.Availability and implementationCHAT can be accessed at: http://chat.lionproject.net. The corpus of hallmark-annotated PubMed abstracts and the software are available at: http://chat.lionproject.net/about.Contactsimon.baker@cl.cam.ac.uk.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC5860084 | biostudies-literature
Project description:The scientific community has classified COVID-19 as the worst pandemic in human history. The damage caused by the new disease was direct (e.g., deaths) and indirect (e.g., closure of economic activities). Within the latter category, we find infodemic phenomena such as the adoption of generic and stigmatizing names used to identify COVID-19 and the related novel coronavirus 2019 variants. These monikers have fostered the spread of health disinformation and misinformation and fomented racism and segregation towards the Chinese population. In this regard, we present a comprehensive infodemiological picture of Italy from the epidemic outbreak in December 2019 until September 2021. In particular, we propose a new procedure to examine in detail the web interest of users in scientific and infodemic monikers linked to the identification of COVID-19. To do this, we exploited the online tool Google Trends. Our findings reveal the widespread use of multiple COVID-19-related names not considered in the previous literature, as well as a persistent trend in the adoption of stigmatizing and generic terms. Inappropriate names for cataloging novel coronavirus 2019 variants of concern have even been adopted by national health agencies. Furthermore, we also showed that early denominations influenced user behavior for a long time and were difficult to replace. For these reasons, we suggest that the assignments of scientific names to new diseases are more timely and advise against mass media and international health authorities using terms linked to the geographical origin of the novel coronavirus 2019 variants.
| S-EPMC8801192 | biostudies-literature
Project description:Critical thinking is the process by which people make decisions about what to trust and what to do. Many undergraduate courses, such as those in biology and physics, include critical thinking as an important learning goal. Assessing critical thinking, however, is non-trivial, with mixed recommendations for how to assess critical thinking as part of instruction. Here we evaluate the efficacy of assessment questions to probe students' critical thinking skills in the context of biology and physics. We use two research-based standardized critical thinking instruments known as the Biology Lab Inventory of Critical Thinking in Ecology (Eco-BLIC) and Physics Lab Inventory of Critical Thinking (PLIC). These instruments provide experimental scenarios and pose questions asking students to evaluate what to trust and what to do regarding the quality of experimental designs and data. Using more than 3000 student responses from over 20 institutions, we sought to understand what features of the assessment questions elicit student critical thinking. Specifically, we investigated (a) how students critically evaluate aspects of research studies in biology and physics when they are individually evaluating one study at a time versus comparing and contrasting two and (b) whether individual evaluation questions are needed to encourage students to engage in critical thinking when comparing and contrasting. We found that students are more critical when making comparisons between two studies than when evaluating each study individually. Also, compare-and-contrast questions are sufficient for eliciting critical thinking, with students providing similar answers regardless of if the individual evaluation questions are included. This research offers new insight on the types of assessment questions that elicit critical thinking at the introductory undergraduate level; specifically, we recommend instructors incorporate more compare-and-contrast questions related to experimental design in their courses and assessments.
| S-EPMC9426932 | biostudies-literature
Project description:The Consider, Read, Elucidate hypotheses, Analyze and interpret data, Think of the next Experiment (CREATE) strategy for teaching and learning uses intensive analysis of primary literature to improve students' critical-thinking and content integration abilities, as well as their self-rated science attitudes, understanding, and confidence. CREATE also supports maturation of undergraduates' epistemological beliefs about science. This approach, originally tested with upper-level students, has been adapted in Introduction to Scientific Thinking, a new course for freshmen. Results from this course's initial semesters indicate that freshmen in a one-semester introductory course that uses a narrowly focused set of readings to promote development of analytical skills made significant gains in critical-thinking and experimental design abilities. Students also reported significant gains in their ability to think scientifically and understand primary literature. Their perceptions and understanding of science improved, and multiple aspects of their epistemological beliefs about science gained sophistication. The course has no laboratory component, is relatively inexpensive to run, and could be adapted to any area of scientific study.
| S-EPMC3587857 | biostudies-other
Project description:The search for effective vaccines to stop the COVID-19 pandemic has led to an unprecedented amount of global scientific production and activity. This study aimed to analyze global scientific production on the different vaccine types (mRNA and conventional) that were validated for COVID-19 during the years 2020-2021. The scientific production generated on COVID-19 vaccines during the period 2020-2021 totaled the enormous amount of 20,459 studies published. New mRNA vaccines clearly showed higher production levels than conventional vaccines (viral and inactivated vectors), with 786 and 350 studies, respectively. The USA is the undisputed leader in the global production on COVID-19 vaccines, with Israel and Italy also playing an important role. Among the journals publishing works in this field, the New England Journal of Medicine, the British Medical Journal, and Vaccines stand out from the rest as the most important. The keyword 'immunogenicity' and its derivatives have been more researched for the new mRNA vaccines, while thrombosis has been more studied for conventional vaccines. The massive scientific production generated on COVID-19 vaccines in only two years has shown the enormous gravity of the pandemic and the extreme urgency to find a solution. This high scientific production and the main keywords found for the mRNA vaccines indicate the great potential that these vaccines have against COVID-19 and future infectious diseases. Moreover, this study provides valuable information for guiding future research lines and promoting international collaboration for an effective solution.
| S-EPMC9213638 | biostudies-literature
Project description:Systematically evaluating scientific literature is a time consuming endeavor that requires hours of coding and rating. Here, we describe a method to distribute these tasks across a large group through online crowdsourcing. Using Amazon's Mechanical Turk, crowdsourced workers (microworkers) completed four groups of tasks to evaluate the question, "Do nutrition-obesity studies with conclusions concordant with popular opinion receive more attention in the scientific community than do those that are discordant?" 1) Microworkers who passed a qualification test (19% passed) evaluated abstracts to determine if they were about human studies investigating nutrition and obesity. Agreement between the first two raters' conclusions was moderate (κ = 0.586), with consensus being reached in 96% of abstracts. 2) Microworkers iteratively synthesized free-text answers describing the studied foods into one coherent term. Approximately 84% of foods were agreed upon, with only 4 and 8% of ratings failing manual review in different steps. 3) Microworkers were asked to rate the perceived obesogenicity of the synthesized food terms. Over 99% of responses were complete and usable, and opinions of the microworkers qualitatively matched the authors' expert expectations (e.g., sugar-sweetened beverages were thought to cause obesity and fruits and vegetables were thought to prevent obesity). 4) Microworkers extracted citation counts for each paper through Google Scholar. Microworkers reached consensus or unanimous agreement for all successful searches. To answer the example question, data were aggregated and analyzed, and showed no significant association between popular opinion and attention the paper received as measured by Scimago Journal Rank and citation counts. Direct microworker costs totaled $221.75, (estimated cost at minimum wage: $312.61). We discuss important points to consider to ensure good quality control and appropriate pay for microworkers. With good reliability and low cost, crowdsourcing has potential to evaluate published literature in a cost-effective, quick, and reliable manner using existing, easily accessible resources.
| S-EPMC4079692 | biostudies-literature
Project description:Survival analyzes are usually based on a single point in time predefined event. Dissatisfied with this approach to evaluating maintenance treatment outcomes, we developed the Multi-state Outcome Analysis of Treatments (MOAT) methodology using a combined database from two FDA registration studies of lamotrigine, lithium and placebo. MOAT partitions total survival time into clinically distinct periods operationally defined by cutpoints on rating scales. For bipolar disorder (BD), the clinical states are remission, subsyndromal and syndromal mania, mixed states or depression. MOAT results can be crossed with information about tolerability and functioning to yield an outcome system integrating efficacy and tolerability. As found in the original analysis, both drugs were associated with longer time in study compared with the placebo. MOAT supplements this by finding that both drugs increased the time remitted compared with placebo. However, a substantial amount of time in all three treatments was spent in subsyndromal depression. Time with manic symptoms was reduced with lithium, but not lamotrigine. Patients on placebo neither benefitted nor had adverse effects from the assignment but experienced more syndromal levels of symptoms and were terminated from the study sooner than either drug treated group. Lithium was associated with both benefit in time manic and worse tolerability compared with placebo. In summary, lamotrigine was associated with limited therapeutic benefit but not harm; lithium with both benefit and harm; and placebo with neither. MOAT describes not only quantity but also quality of time spent in longitudinal studies, providing a more clinically informative picture than Kaplan-Meier survival analysis.
| S-EPMC4573671 | biostudies-other
Project description:In the past, milk whey was only a by-product of cheese production, but currently, it has a high commercial value for use in the food industries. However, the regulation of whey management (i.e., storage and hygienic properties) has not been updated, and as a consequence, its microbiological quality is very challenging for food safety. The Next Generation Sequencing (NGS) technique was applied to several whey samples used for Ricotta production to evaluate the microbial community composition in depth using both RNA and DNA as templates for NGS library construction. Whey samples demonstrating a high microbial and aerobic spore load contained mostly Firmicutes; although variable, some samples contained a relevant amount of Gammaproteobacteria. Several lots of whey acquired as raw material for Ricotta production presented defective organoleptic properties. To define the volatile compounds in normal and defective whey samples, a headspace gas chromatography/mass spectrometry (GC/MS) analysis was conducted. The statistical analysis demonstrated that different microbial communities resulted from DNA or cDNA library sequencing, and distinguishable microbiota composed the communities contained in the organoleptic-defective whey samples.
| S-EPMC4987355 | biostudies-literature