MeSHProbeNet: a self-attentive probe net for MeSH indexing

2019 ◽  
Vol 35 (19) ◽  
pp. 3794-3802 ◽  
Author(s):  
Guangxu Xun ◽  
Kishlay Jha ◽  
Ye Yuan ◽  
Yaqing Wang ◽  
Aidong Zhang
Keyword(s):  
Specific Aspect ◽  
Controlled Vocabulary ◽  
Manual Annotation ◽  
Medical Subject Headings ◽  
Biomedical Knowledge ◽  
Word Level ◽  
Mesh Terms ◽  
Lowest Common Ancestor ◽  
Automatic Mesh ◽  
F Measure

Abstract Motivation MEDLINE is the primary bibliographic database maintained by National Library of Medicine (NLM). MEDLINE citations are indexed with Medical Subject Headings (MeSH), which is a controlled vocabulary curated by the NLM experts. This greatly facilitates the applications of biomedical research and knowledge discovery. Currently, MeSH indexing is manually performed by human experts. To reduce the time and monetary cost associated with manual annotation, many automatic MeSH indexing systems have been proposed to assist manual annotation, including DeepMeSH and NLM’s official model Medical Text Indexer (MTI). However, the existing models usually rely on the intermediate results of other models and suffer from efficiency issues. We propose an end-to-end framework, MeSHProbeNet (formerly named as xgx), which utilizes deep learning and self-attentive MeSH probes to index MeSH terms. Each MeSH probe enables the model to extract one specific aspect of biomedical knowledge from an input article, thus comprehensive biomedical information can be extracted with different MeSH probes and interpretability can be achieved at word level. MeSH terms are finally recommended with a unified classifier, making MeSHProbeNet both time efficient and space efficient. Results MeSHProbeNet won the first place in the latest batch of Task A in the 2018 BioASQ challenge. The result on the last test set of the challenge is reported in this paper. Compared with other state-of-the-art models, such as MTI and DeepMeSH, MeSHProbeNet achieves the highest scores in all the F-measures, including Example Based F-Measure, Macro F-Measure, Micro F-Measure, Hierarchical F-Measure and Lowest Common Ancestor F-measure. We also intuitively show how MeSHProbeNet is able to extract comprehensive biomedical knowledge from an input article.

scholarly journals Search and Graph Database Technologies for Biomedical Semantic Indexing: Experimental Analysis (Preprint)

2017 ◽  
Author(s):  
Isabel Segura Bedmar ◽  
Paloma Martínez ◽  
Adrián Carruana Martín
Keyword(s):  
Search Algorithms ◽  
Biomedical Literature ◽  
Graph Search ◽  
Semantic Indexing ◽  
Graph Database ◽  
Medical Subject Headings ◽  
Support Tool ◽  
Mesh Terms ◽  
Lowest Common Ancestor ◽  
Graph Search Algorithms

BACKGROUND Biomedical semantic indexing is a very useful support tool for human curators in their efforts for indexing and cataloging the biomedical literature. OBJECTIVE The aim of this study was to describe a system to automatically assign Medical Subject Headings (MeSH) to biomedical articles from MEDLINE. METHODS Our approach relies on the assumption that similar documents should be classified by similar MeSH terms. Although previous work has already exploited the document similarity by using a k-nearest neighbors algorithm, we represent documents as document vectors by search engine indexing and then compute the similarity between documents using cosine similarity. Once the most similar documents for a given input document are retrieved, we rank their MeSH terms to choose the most suitable set for the input document. To do this, we define a scoring function that takes into account the frequency of the term into the set of retrieved documents and the similarity between the input document and each retrieved document. In addition, we implement guidelines proposed by human curators to annotate MEDLINE articles; in particular, the heuristic that says if 3 MeSH terms are proposed to classify an article and they share the same ancestor, they should be replaced by this ancestor. The representation of the MeSH thesaurus as a graph database allows us to employ graph search algorithms to quickly and easily capture hierarchical relationships such as the lowest common ancestor between terms. RESULTS Our experiments show promising results with an F1 of 69% on the test dataset. CONCLUSIONS To the best of our knowledge, this is the first work that combines search and graph database technologies for the task of biomedical semantic indexing. Due to its horizontal scalability, ElasticSearch becomes a real solution to index large collections of documents (such as the bibliographic database MEDLINE). Moreover, the use of graph search algorithms for accessing MeSH information could provide a support tool for cataloging MEDLINE abstracts in real time.

Liraglutide for the Treatment of Obesity: Analyzing Published Reviews

2019 ◽  
Vol 25 (15) ◽  
pp. 1783-1790 ◽  
Author(s):  
Rosario Pastor ◽  
Josep A. Tur
Keyword(s):  
Weight Loss ◽  
Clinical Trials ◽  
Systematic Reviews ◽  
Randomized Clinical Trials ◽  
Statistical Tests ◽  
Overweight And Obesity ◽  
Cochrane Library ◽  
Medical Subject Headings ◽  
Mesh Terms ◽  
Treatment Of Obesity

Background: Several drugs have been currently approved for the treatment of obesity. The pharmacokinetic of liraglutide, as well as the treatment of type 2 diabetes mellitus, have been widely described. Objective: To analyze the published systematic reviews on the use of liraglutide for the treatment of obesity. Methods: Systematic reviews were found out through MEDLINE searches, through EBSCO host and the Cochrane Library based on the following terms: "liraglutide" as major term and using the following Medical Subject Headings (MesH) terms: "obesity", "overweight", "weight loss". A total of 3 systematic reviews were finally included to be analyzed. Results: From the three systematic reviews selected, only two included the randomized clinical trials, while the third study reviewed both randomized and non-randomized clinical trials. Only one review performed statistical tests of heterogeneity and a meta-analysis, combining the results of individual studies. Another review showed the results of individual studies with odds ratio and confidence interval, but a second one just showed the means and confidence intervals. In all studies, weight loss was registered in persons treated with liraglutide in a dose dependent form, reaching a plateau at 3.0 mg dose, which was reached just in men. Most usual adverse events were gastrointestinal. Conclusion: More powerful and prospective studies are needed to assess all aspects related to liraglutide in the overweight and obesity treatment.

The Role of Leukotrienes Inhibitors in the Management of Chronic Inflammatory Diseases

2020 ◽  
Vol 14 (1) ◽  
pp. 15-31
Author(s):  
Deepak Meshram ◽  
Khushbo Bhardwaj ◽  
Charulata Rathod ◽  
Gail B. Mahady ◽  
Kapil K. Soni
Keyword(s):  
Respiratory Diseases ◽  
Inflammatory Diseases ◽  
Leukotriene B4 ◽  
Published Data ◽  
Free Text ◽  
Plant Origin ◽  
Medical Subject Headings ◽  
Leukotriene Antagonists ◽  
Mesh Terms ◽  
Mediators Of Inflammation

Background: Leukotrienes are powerful mediators of inflammation and interact with specific receptors in target cell membrane to initiate an inflammatory response. Thus, Leukotrienes (LTs) are considered to be potent mediators of inflammatory diseases including allergic rhinitis, inflammatory bowel disease and asthma. Leukotriene B4 and the series of cysteinyl leukotrienes (C4, D4, and E4) are metabolites of arachidonic acid metabolism that cause inflammation. The cysteinyl LTs are known to increase vascular permeability, bronco-constriction and mucus secretion. Objectives: To review the published data for leukotriene inhibitors of plant origin and the recent patents for leukotriene inhibitors, as well as their role in the management of inflammatory diseases. Methods: Published data for leukotrienes antagonists of plant origin were searched from 1938 to 2019, without language restrictions using relevant keywords in both free text and Medical Subject Headings (MeSH terms) format. Literature and patent searches in the field of leukotriene inhibitors were carried out by using numerous scientific databases including Science Direct, PubMed, MEDLINE, Google Patents, US Patents, US Patent Applications, Abstract of Japan, German Patents, European Patents, WIPO and NAPRALERT. Finally, data from these information resources were analyzed and reported in the present study. Results: Currently, numerous anti-histaminic medicines are available including chloropheneremine, brompheniramine, cetirizine, and clementine. Furthermore, specific leukotriene antagonists from allopathic medicines are also available including zileuton, montelukast, pranlukast and zafirlukast and are considered effective and safe medicines as compared to the first generation medicines. The present study reports leukotrienes antagonistic agents of natural products and certain recent patents that could be an alternative medicine in the management of inflammation in respiratory diseases. Conclusion: The present study highlights recent updates on the pharmacology and patents on leukotriene antagonists in the management of inflammation respiratory diseases.

scholarly journals Evolution of knowledge on meniscal biomechanics: a 40 year perspective

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Amin Mohamadi ◽  
Kaveh Momenzadeh ◽  
Aidin Masoudi ◽  
Kempland C. Walley ◽  
Kenny Ierardi ◽  
...  
Keyword(s):  
Future Research ◽  
Fe Model ◽  
Cruciate Ligaments ◽  
Fe Modeling ◽  
Meniscal Tears ◽  
Medical Subject Headings ◽  
Model Studies ◽  
The Past ◽  
Mesh Terms ◽  
Kinematic Studies

Abstract Background Knowledge regarding the biomechanics of the meniscus has grown exponentially throughout the last four decades. Numerous studies have helped develop this knowledge, but these studies have varied widely in their approach to analyzing the meniscus. As one of the subcategories of mechanical phenomena Medical Subject Headings (MeSH) terms, mechanical stress was introduced in 1973. This study aims to provide an up-to-date chronological overview and highlights the evolutionary comprehension and understanding of meniscus biomechanics over the past forty years. Methods A literature review was conducted in April 2021 through PubMed. As a result, fifty-seven papers were chosen for this narrative review and divided into categories; Cadaveric, Finite element (FE) modeling, and Kinematic studies. Results Investigations in the 1970s and 1980s focused primarily on cadaveric biomechanics. These studies have generated the fundamental knowledge basis for the emergence of FE model studies in the 1990s. As FE model studies started to show comparable results to the gold standard cadaveric models in the 2000s, the need for understanding changes in tissue stress during various movements triggered the start of cadaveric and FE model studies on kinematics. Conclusion This study focuses on a chronological examination of studies on meniscus biomechanics in order to introduce concepts, theories, methods, and developments achieved over the past 40 years and also to identify the likely direction for future research. The biomechanics of intact meniscus and various types of meniscal tears has been broadly studied. Nevertheless, the biomechanics of meniscal tears, meniscectomy, or repairs in the knee with other concurrent problems such as torn cruciate ligaments or genu-valgum or genu-varum have not been extensively studied.

scholarly journals Newer Volatile Anesthetic Agents in Cardiac Anesthesia: Review of Literature

2021 ◽  
Author(s):  
Alka Mandke ◽  
Manjula Sarkar ◽  
Charulata Deshpande ◽  
Arun Maheshwari ◽  
Bhupesh Kumar ◽  
...  
Keyword(s):  
Volatile Anesthetic ◽  
Cochrane Library ◽  
Cochrane Central Register ◽  
Cardiac Anesthesia ◽  
Medical Subject Headings ◽  
Holistic View ◽  
Anesthetic Agents ◽  
Cardiac Anaesthesia ◽  
Mesh Terms ◽  
Inhalational Anaesthesia

AbstractMyocardial protection with volatile anesthetic agents have been suggested by multiple studies. These studies, however, are scattered and are often limited to a particular aspect of cardiac anesthesia. Older inhalational agents like halothane is known to cause significant hepatic damage in patients undergoing long duration surgeries while isoflurane is known to have marked vasodilating properties that also affects the coronary arteries leading to coronary “steal” phenomenon. Additionally, newer agents, like sevoflurane and desflurane, have shown more prominent cardioprotective effects than older agents. We searched ScholarOne, Medline, Embase, and the Cochrane Central Register of Controlled Trials (CENTRAL) in the Cochrane Library. The medical subject headings (MeSH) terms “anaesthesia, inhalational,” “anaesthesia, intravenous, or TIVA,” and “Cardiac anaesthesia or Cardiac Surgery” were used. Additional studies were identified by review of the reference sections of all eligible studies. The aim of this review article is to bring together the evidences with newer inhalational agents and provide a holistic view of their benefits and shortcomings in cardiac anesthesia.

Hyaluronic Acid Fillers for Midface Augmentation: A Systematic Review

2021 ◽  
Author(s):  
Lily N. Trinh ◽  
Amar Gupta
Keyword(s):  
Systematic Review ◽  
Hyaluronic Acid ◽  
Subcutaneous Tissue ◽  
Age Groups ◽  
Medical Subject Headings ◽  
Mesh Terms ◽  
Full Text Review ◽  
Filler Injections ◽  
Subjective Measurements ◽  
Meta Analyses

AbstractInjectable fillers represent one of the most requested minimally invasive treatments to rejuvenate the aging face, and its popularity is steadily rising. A vast majority of filler treatments are with hyaluronic acid (HA). The aim of this systematic review is to evaluate patient outcomes, safety profile, and administration techniques of various HA fillers for malar augmentation. A systematic review of the published literature was conducted in accordance with the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines and included PubMed, Embase, and Science Direct databases. Medical Subject Headings (MeSH) terms used were “cheek” OR “midface” OR “malar” and “filler” OR “hyaluronic acid” OR “Juvederm” OR “Restylane” OR “Perlane” OR “Belotero.” The initial search identified 699 articles; 256 duplicates were removed. Additional 12 studies were identified from reference lists. A total of 455 were screened by title and abstract and 387 studies were eliminated based on criteria. Also, 68 articles underwent full-text review, and 18 articles were included in the final review and involved seven different HA formulations. Men and women from many age groups were highly satisfied with their results following HA treatment for midface augmentation up to 24 months. The most common adverse events included bruising, swelling, and tenderness, and typically lasted no more than 2 weeks. Upper cheek filler injections near the zygoma should be placed in the submuscular plane while lower cheek injections should be placed in the subcutaneous tissue. HA is an attractive choice for midface augmentation due to its high patient satisfaction, long-lasting effects, and low side-effect profile. Due to the variability in technique, level of expertise, and subjective measurements across studies, one optimal regimen could not be concluded. However, midface augmentation treatment should be personalized to each patient. Additional clinical trials are required to more conclusively determine the most appropriate approach for this procedure.

Neurological associations of SARS-CoV-2 infection: A Systematic Review

2021 ◽  
Vol 20 ◽  
Author(s):  
Amaan Javed
Keyword(s):  
Systematic Review ◽  
Case Reports ◽  
Case Series ◽  
Severe Infection ◽  
Cerebrovascular Diseases ◽  
Controlled Vocabulary ◽  
Cochrane Central Register ◽  
Post Traumatic Stress ◽  
Medical Subject Headings ◽  
Reported Data

Background: The current ongoing COVID-19 pandemic has compelled us to scrutinize major outbreaks in the past two decades, severe acute respiratory syndrome (SARS), in 2002, and Middle East respiratory syndrome (MERS), in 2012. We aimed to assess the associated neurological manifestations with SARS CoV-2 infection. Methods: In this systematic review, a search was carried out by key-electronic databases, controlled vocabulary, and indexing of trials to evaluate the available pertinent studies which included both medical subject headings (MeSH) and advance electronic databases comprising of PubMed, Embase, Scopus, Cochrane Central Register of Controlled Trials (CENTRAL). Peer-reviewed studies published in English and Spanish were considered which reported data on the neurological associations of individuals with suspected or laboratory-confirmed SARS-CoV-2 infection. Outcomes were nervous signs or symptoms; symptom severity; and diagnoses. Findings: Our search identified 45 relevant studies, with 21 case reports, 3 case series, 9 observational studies, 1 retrospective study, 9 retrospective reviews, and 2 prospective reviews. This systematic review revealed that most commonly reported neuronal presentations involved headache, nausea, vomiting and muscular symptoms like fibromyalgia. Anosmia and ageusia, defects in clarity or sharpness of vision (error in visual acuity), and pain may occur in parallel. Notable afflictions in the form of anxiety, anger, confusion, post-traumatic stress symptoms, and post-intensive care syndrome were observed in individuals who were kept in quarantine and those with long-stay admissions in healthcare settings. SARS CoV-2 infection may result in cognitive impairment. Patients with more severe infection exhibited uncommon manifestations, such as acute cerebrovascular diseases (intracerebral haemorrhage, stroke), rhabdomyolysis, encephalopathy, Guillain-Barré syndrome. Interpretation: SARS-CoV-2 patients experience neuronal presentations varying with the progression of the infection. Healthcare professionals should be acquainted with the divergent neurological symptoms and to curb misdiagnosis and limit long term sequelae. Health-care planners and policymakers must prepare for this eventuality, while the ongoing studies increase our knowledge base on acute and chronic neurological associations of this pathogen.

scholarly journals Intensity of Task-Specific Training for Functional Ability Post-stroke: Protocol for a Systematic Review

2021 ◽  
Author(s):  
Rabiu Ibrahim ◽  
Isa Usman Lawal ◽  
Conran Joseph
Keyword(s):  
Systematic Review ◽  
Literature Search ◽  
Risk Of Bias ◽  
Controlled Trials ◽  
Cochrane Central Register ◽  
Specific Training ◽  
Medical Subject Headings ◽  
Mesh Terms ◽  
Pubmed Search ◽  
Evidence Database

Abstract Background This study aimed to describe and present detailed protocol of a systematic review aimed at determining available research evidence regarding the intensity, and frequency of task-specific training ( TST ) that can best result in improved motor function and mobility outcomes in both upper and lower extremities in acute, sub-acute and chronic stroke survivors. Methods Literature search strategies were developed using Medical Subject Headings (MeSH) terms and text key words related to stroke rehabilitation and the use of TST to search for relevant randomized controlled trials (RCTs). The Cochrane Central Register of Controlled Trials, MEDLINE (PubMed search engine), Excerpta Medica dataBASE (EMBASE), Physiotherapy Evidence Database (PEDro), Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Google Scholar were searched for eligible articles published from inception to date. Two reviewers independently screened the titles, selected appropriate abstract/studies and extracted relevant data as yielded by the search based on the study inclusion criteria. Assessment of the study risk of bias and quality of included studies were appraised using the Cochrane’s tool for assessing risk of bias or other appropriate tools. Discussion This paper presented the description of the systematic review methods, and it is expected to guide researchers in conducting systematic review in similar fields of research. Sources of literature search terms and reviewers have been determined. Systematic review registration The study protocol has been registered with PROSPERO (130991)

Modeling the co-citation dependence on semantic layers of co-cited documents

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Maryam Yaghtin ◽  
Hajar Sotudeh ◽  
Alireza Nikseresht ◽  
Mahdieh Mirzabeigi
Keyword(s):  
Peer Review ◽  
Language Processing ◽  
Opinion Mining ◽  
Citation Network ◽  
Test Collection ◽  
Medical Subject Headings ◽  
Content Type ◽  
Citation Frequency ◽  
Mesh Terms ◽  
Citation Measures

PurposeCo-citation frequency, defined as the number of documents co-citing two articles, is considered as a quantitative, and thus, an efficient proxy of subject relatedness or prestige of the co-cited articles. Despite its quantitative nature, it is found effective in retrieving and evaluating documents, signifying its linkage with the related documents' contents. To better understand the dynamism of the citation network, the present study aims to investigate various content features giving rise to the measure.Design/methodology/approachThe present study examined the interaction of different co-citation features in explaining the co-citation frequency. The features include the co-cited works' similarities in their full-texts, Medical Subject Headings (MeSH) terms, co-citation proximity, opinions and co-citances. A test collection is built using the CITREC dataset. The data were analyzed using natural language processing (NLP) and opinion mining techniques. A linear model was developed to regress the objective and subjective content-based co-citation measures against the natural log of the co-citation frequency.FindingsThe dimensions of co-citation similarity, either subjective or objective, play significant roles in predicting co-citation frequency. The model can predict about half of the co-citation variance. The interaction of co-opinionatedness and non-co-opinionatedness is the strongest factor in the model.Originality/valueIt is the first study in revealing that both the objective and subjective similarities could significantly predict the co-citation frequency. The findings re-confirm the citation analysis assumption claiming the connection between the cognitive layers of cited documents and citation measures in general and the co-citation frequency in particular.Peer reviewThe peer review history for this article is available at https://publons.com/publon/10.1108/OIR-04-2020-0126.

scholarly journals Heart Rate Variability in Children and Adolescents with Cerebral Palsy—A Systematic Literature Review

2020 ◽  
Vol 9 (4) ◽  
pp. 1141 ◽  
Author(s):  
Jakub S. Gąsior ◽  
Antonio Roberto Zamunér ◽  
Luiz Eduardo Virgilio Silva ◽  
Craig A. Williams ◽  
Rafał Baranowski ◽  
...  
Keyword(s):  
Heart Rate ◽  
Heart Rate Variability ◽  
Cerebral Palsy ◽  
English Language ◽  
Pediatric Patients ◽  
Medical Subject Headings ◽  
Mesh Terms ◽  
Cardiac Autonomic Dysfunction ◽  
Guidelines And Recommendations ◽  
Methodological Guidelines

Cardiac autonomic dysfunction has been reported in patients with cerebral palsy (CP). The aim of this study was to assess the existing literature on heart rate variability (HRV) in pediatric patients with CP and a special attention was paid to the compliance of the studies with the current HRV assessment and interpretation guidelines. A systematic review was performed in PubMed, Web of Science, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) databases searched for English language publications from 1996 to 2019 using Medical Subject Headings (MeSH) terms “heart rate variability” and “cerebral palsy” in conjunction with additional inclusion criteria: studies limited to humans in the age range of 0–18 years and empirical investigations. Out of 47 studies, 12 were included in the review. Pediatric patients with CP presented a significantly higher resting heart rate and reduced HRV, different autonomic responses to movement stimuli compared to children with normal development, but also reduced HRV parameters in the children dependent on adult assistance for mobility compared to those generally independent. None of the included studies contained the necessary details concerning RR intervals acquisition and HRV measurements as recommended by the guidelines. Authors of HRV studies should follow the methodological guidelines and recommendations on HRV measurement, because such an approach may allow a direct comparison of their results.

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