Tracking the Evolution of Research Topics in Healthcare Informatics Research Using Keywords and MeSH Terms

Librarians, informationists, researchers, health policymakers, and health care professionals retrieve reports of health technology assessments (HTAs) to review the evidence on medical, socioeconomic, and ethical implications of health care and health care investments [1]. These assessments are a useful type of gray literature that include cost-benefit analyses of health interventions, syntheses of intervention research findings, and discussion of the economic implications of health care and medical technology [2]. The HTA Database Canadian Repository is a new, valuable tool that aggregates these assessments and makes them findable via a convenient search interface. This international repository includes records for in-progress and published reports of HTAs, reviews, guidelines, protocols, journals, and articles. Launched in January of 2015, the database includes records beginning in 2003. The HTA Database is funded by the United Kingdom's National Institute for Health Research (NIHR) and administered by the University of York Centre for Reviews and Dissemination. The Canadian repository aggregates HTA records from Ontario, Quebec, Alberta, and pan-Canadian agencies (CADTH) in addition to records from the International Network of Agencies for Health Technology Assessment (INAHTA). The database includes reports from 93 INAHTA and other international repositories [3]. All records and documents are translated into English, French, and/or Spanish, representing about 20 source languages. As of May 2015, the Canadian repository contains over 14,000 unique records; approximately 2,400 are Canadian. Canadian search interface The Canadian interface for the HTA Database is free for noncommercial use [4]. The basic search can include title, full text, province, author, agency, and funder. Additional options allow the user to limit searches to Canadian databases, Canadian and international HTA databases, the Database of Abstracts of Reviews of Effects (DARE), Cochrane reviews, and the National Health Service Economic Evaluation Database (NHS EED) of assessed economic evaluations. While items in the DARE and NHS EED databases are critically appraised—in other words, reviewed for trustworthiness, value, and contextual relevance—items in the HTA database are not. However, if a critical appraisal exists, it is linked with the HTA database record [1]. Other search criteria include record date, publication year, and Medical Subject Headings (MeSH) term search. While search text can be truncated and wildcards accepted, special characters, such as the German umlaut, are not. Search results include year—although it is unclear if this indicates publication or record year—source database, source agency, and title. Although additional metadata exist for each record, search queries are limited to the basic metadata only. The Boolean operators AND, OR, and NOT are available, as well as the proximity operators NEAR and ADJ. Using proximity operators and restricting searches to specific fields (e.g., author [:au], title [:ti], language [:lp], source journal [:so], and funding [xfu]) are particularly helpful when performing advanced, full-text, and keyword searches. The MeSH terminology search is also helpful, if not ideal. MeSH terms can be searched by string (permut), stemming, or tree criteria, but combinations of terms cannot be selected for post-coordinated searching by index concept. Terms selected for searching are not visible in the interface for review or modification; using the interface can be frustrating when executing a high volume of advanced or expert searches. Also, terms cannot be exploded, and MeSH terms are not accompanied by MeSH tree numbers. This is significant for content and keyword analysis, because the tree number indicates the context of the MeSH term. Overall, the MeSH terminology search will not hinder basic or advanced terminology searches but may hinder expert searches. Records can be exported in hypertext markup language (HTML) format; however, downloading full-text reports, when available, must be done one-by-one on a case-by-case basis. Metadata Each record notes the title, agency location, publisher, year of publication, publication type, agency-assigned MeSH terms, HTA accession number, language, source database, and uniform resource locator (URL), along with other metadata. Some metadata are unique to the database from which they derive. For example, metadata vary in records from DARE, NHS EED, or HTA. Conformity of metadata is primarily applied when agencies upload records and input their metadata through the HTA interface. Considerations and advantages For record inclusion, the HTA Database has an “extremely flexible definition of what constitutes a health technology assessment,” which, although potentially beneficial to a variety of users, does not provide a reliable description of publications included in the database [3]. As a result, the database also contains records such as protocols for systematic reviews and care guidelines. Also, documentation is incomplete for metadata fields and database coverage, and there are no descriptions of governance policies. For example, in reviewing a sample of records, we found that not all metadata fields include the same type of information; however, this was a minor occurrence. As a final note, records appear to be added weekly, but since agencies add content on a voluntary basis, frequency of updates varies. The HTA Database Canadian repository and its interface will be helpful to librarians who support HTA investigators and policymakers, as well as patrons interested in assessments of health and health technologies. This new resource facilitates information retrieval and research and may reduce costly duplication of effort by enabling queries of both Canadian and international databases via one search interface. Additionally, the search interface enables discovery of gray literature that is otherwise unavailable or subject to purchase. Although its interface does not support expert searching, the superior aggregation of content makes the HTA Database Canadian Repository a valuable resource.

To what extent do MeSH (Medical Subject Headings) terms improve search effectiveness of different kinds of users? We observed four different kinds of searchers using an experimental information retrieval (IR) system: (1) search novices; (2) domain experts; (3) search experts and (4) medical librarians. The information needs were a subset of the relatively difficult topics originally created for the Text REtrieval Conference (TREC). By experimental design, we used 20 search topics in an IR user experiment to alleviate search topic variability. Effectiveness of retrieval was based on the relevance judgments set provided by TREC. Thirty-two participants searched either using a version of the system in which abstracts and MeSH terms were displayed or another version in which they had to formulate their own terms based only on the display of abstracts. We found that MeSH terms were more useful for domain experts than for search experts in terms of the precision measure, even though domain experts did not perceive that MeSH terms were useful. We speculate that because of the technical topics, only the domain experts had the knowledge to understand and therefore make use of the MeSH terms. The primary contributions of this research are: (1) assessment of relative impact of searchers characteristics of domain knowledge and search training on search effectiveness and (2) design and methodology for assessing the usefulness of controlled vocabulary. The effort to create MeSH terms is worthwhile for domain experts' searches on technical topics.

Research on acute pancreatitis (AP) has been ongoing for a long time. It is necessary to summarize and investigate the history of AP research. Publications related to AP research were retrieved from PubMed. Medical Subject Headings (MeSH) terms, countries, journals, and publication dates were analyzed. Co-occurrence analysis was conducted to illustrate the holistic trend in AP research. A dynamic bar graph, heat maps, and line charts were created to illustrate change trends of MeSH terms. In total, 28,222 publications with 8558 MeSH terms were retrieved from 1941 to 2020. Among these, 16,575 publications with 7228 MeSH terms were from 2001 to 2020. The top 10 MeSH terms showed a considerable change from 1941 to 1970 but remained stable since the 1970s. Four clusters obtained from the co-occurrence analysis were "experiments on animals," "diagnosis and treatment," "prognosis and expectation," and "protein and enzyme." From 1941 to 2020, 33 MeSH terms with increasing trends (MH-I) and 15 MeSH terms with decreasing trends (MH-D) were selected to create a heat map (every decade). Meanwhile, 16 MH-I and 41 MH-D were selected to create the heat map from 2001 to 2020 (every 2 years). Over the past 80 years, the pathogenesis, treatment, risk management, and experimental model were the main research highlights. Optimal supportive management, minimally invasive treatment, and prediction of prognosis are subjects of interest for clinical practitioners; signal transduction to identify a target for precise treatment is the focus of experimental research in AP.

With the recent advancements in internet facilities, selection of effective keywords has now become an easy task.[1] These keywords help in indexing published literature in a journal. The success of any published literature depends on the number of citations of an article. A wise selection of keywords by the authors help in the wider dissemination of an article. Medical Subject Headings (MeSH) are standardised keywords present in the MeSH database to index articles in MEDLINE/PubMed.[2] The MeSH database is a vocabulary thesaurus developed by the National Library of Medicine (NLM) for indexing articles in PubMed.[3] MeSH terms provide information on the content of an article. Changes in medical terminology in published literature is reflected by MeSH headings which are regularly updated by the NLM. Four terms are included in the MeSH vocabulary. These are MeSH headings, subheadings, supplementary concept records (SCR) and publication type. The concept mentioned in biomedical literature is called 'MeSH headings' (descriptors). Attached to the MeSH headings are 'subheadings' (qualifiers) that clearly describe a definite aspect of a concept. Chemicals, drugs, and rare diseases are labelled as 'SCR'. 'Publication type' describes the type of research that is indexed. The next question that arises in the mind of the researcher is to how to search for MeSH keywords on the PubMed database. Currently, authors use mainly three methods to search for said keywords: first, using the MeSH browser; second, using MeSH keywords from the selected PubMed articles; and third, using the MeSH on Demand tool. In the MeSH browser method, you can open the PubMed home page and then look for 'Explore' or 'More Resources' and click on the MeSH database link. The window showing the word 'MeSH' on the left-hand side of the ribbon will be seen. From here, look for the horizontal panel where you can type words for direct search of MeSH terms. You can type any word related to your research; for example, you can type in 'nerve block' and then click on 'Search'. The next page will show the definition of the word that was typed (if it is a PubMed MeSH keyword), or else it will suggest an existing MeSH keyword to you.[4] The second method for finding MeSH keywords in PubMed is to open an abstract of the relevant article and look below the abstract for MeSH terms. It will show all of the MeSH terms related to that article. The third method involves the MeSH on Demand tool in which you can copy and paste up to 10,000 characters. Following this, MeSH terms are highlighted using natural language processing and the NLM Medical Text Indexer. This method assists authors in looking up MeSH keywords even without having done the MeSH indexing or even in looking up any downloads of MeSH for the article. You can start by pasting the link (https://meshb.nlm.nih.gov /MeSHonDemand) on the browser to open MeSH on Demand. After copying and pasting the concerned text or abstract, press the button that reads 'Find MeSH term'. All MeSH terms will be highlighted in the paragraph and a list of ranked MeSH words or an alphabetical list of MeSH terms will be displayed on the right side of the screen.[5] The impact of using MeSH terms for keywords in publications are that it increases the scientific visibility of the article and its chances of it being retrieved by authors who are performing a literature search for relevant topics.[6] The MeSH database has a hierarchy or tree structure because of which both broader and more specific searches yield better results.[7,8] The terms are annually updated in the English language to reflect changes in terminology and account for variations in language, synonyms, and alternate spellings. MeSH terms provide a universal article labelling system. The official words or phrases that are labelled as MeSH terms represent a particular biomedical concept in MEDLINE. The official MeSH list provides terms for indexers to label an article. This particularly helps in locating an article specific to a topic. Efficient search is facilitated by MeSH terms. If MeSH terms are not used as keywords by authors and the journal does not insist on its use, this leads to poor visibility of the article, thereby reducing the chances of the article being cited. The impact of this is dual: for the author, there are less chances of their paper being cited and them being recognised and acknowledged for their research; and for the journal, there is a lower impact factor. The impact factor is calculated by the number of articles that are cited from the journal in the last two years.[9] The MeSH browser has certain limitations.[10] One may not be able to retrieve an article that was recently published and that is yet to be indexed on MEDLINE due to the short lag time between the citations that are entered into the PubMed database and their description with MeSH terms. As MeSH terms are not available for most genes, it is difficult to find research topics with gene names. MeSH terms may not be added to the latest emerging research. The articles are also difficult to retrieve if they are not indexed for MEDLINE. For any further questions or queries regarding PubMed MeSH keywords, the authors can send them to at [email protected]

The surge in the number of publications on psoriasis has posed significant challenges for researchers in effectively managing the vast amount of information. However, due to the lack of tools to process metadata, no comprehensive bibliometric analysis has been conducted. This study is to evaluate the trends and current hotspots of psoriatic research from a macroscopic perspective through a bibliometric analysis assisted by machine learning based semantic analysis. Publications indexed under the Medical Subject Headings (MeSH) term "Psoriasis" from 2003 to 2022 were extracted from PubMed. The generative statistical algorithm latent Dirichlet allocation (LDA) was applied to identify specific topics and trends based on abstracts. The unsupervised Louvain algorithm was used to establish a network identifying relationships between topics. A total of 28,178 publications were identified. The publications were derived from 176 countries, with United States, China, and Italy being the top three countries. For the term "psoriasis", 9,183 MeSH terms appeared 337,545 times. Among them, MeSH term "Severity of illness index", "Treatment outcome", "Dermatologic agents" occur most frequently. A total of 21,928 publications were included in LDA algorithm, which identified three main areas and 50 branched topics, with "Molecular pathogenesis", "Clinical trials", and "Skin inflammation" being the most increased topics. LDA networks identified "Skin inflammation" was tightly associated with "Molecular pathogenesis" and "Biological agents". "Nail psoriasis" and "Epidemiological study" have presented as new research hotspots, and attention on topics of comorbidities, including "Cardiovascular comorbidities", "Psoriatic arthritis", "Obesity" and "Psychological disorders" have increased gradually. Research on psoriasis is flourishing, with molecular pathogenesis, skin inflammation, and clinical trials being the current hotspots. The strong association between skin inflammation and biologic agents indicated the effective translation between basic research and clinical application in psoriasis. Besides, nail psoriasis, epidemiological study and comorbidities of psoriasis also draw increased attention.

In recent years, many epidemiological and toxicological studies have investigated the adverse effects of air particulate matter (PM) on the cardiovascular system. However, it is difficult for the researchers to have a timely and effective overall command of the latest characteristics and popular topics in such a wide field. Different from the previous reviews, in which the research characteristics and trends are empirically concluded by experts, we try to have a comprehensive evaluation of the above topics for the first time by bibliometric analysis, a quantitative tool in information exploration. This study aims to introduce the bibliometric method into the field of PM and cardiovascular system. The articles were selected by searching PubMed/MEDLINE (from 2007 to 2012) using Medical Subject Headings (MeSH) terms “particulate matter” and “cardiovascular system”. A total of 935 eligible articles and 1895 MeSH terms were retrieved and processed by the software Thomson Data Analyzer (TDA). The bibliographic information and the MeSH terms of these articles were classified and analyzed to summarize the research characteristics. The top 200 high-frequency MeSH terms (the cumulative frequency percentage was 74.2%) were clustered for popular-topic conclusion. We summarized the characteristics of published articles, of researcher collaborations and of the contents. Ten clusters of MeSH terms are presented. Six popular topics are concluded and elaborated for reference. Our study presents an overview of the characteristics and popular topics in the field of PM and cardiovascular system in the past five years by bibliometric tools, which may provide a new perspective for future researchers.

The Medical Subject Headings (MeSH) term search is typical data-gathering method in biomedical text mining. However, it has two problems: the allocation delay of the MeSH term and missing valuable literature sources. Since MeSH term allocation is performed by a human being, the allocation process has delay. In addition, even if a literature source was allocated with a MeSH term, there is a still the problem that valuable literature sources are missed during the data-gathering process. There are literature sources that are not indexed to the MeSH term of a keyword, even though it contains valuable information related to the MeSH term. The MeSH term search misses these valuable literature sources. In order to resolve these problems, we propose a novel method to gather rich data using a one-class support vector machine (SVM) and relevance rule. The term frequency-inverse document frequency (TF-IDF) and paragraph vector are examined as text vectorization methods with various parameters and relevance factors. We apply our method to lung cancer, prostate cancer, breast cancer, and Alzheimer's disease. As a result, up to 26% of keyword data and 35% of target data are gathered with high quality (a C-score of at least 0.948).

The embedding of Medical Subject Headings (MeSH) terms has become a foundation for many downstream bioinformatics tasks. Recent studies employ different data sources, such as the corpus (in which each document is indexed by a set of MeSH terms), the MeSH term ontology, and the semantic predications between MeSH terms (extracted by SemMedDB), to learn their embeddings. While these data sources contribute to learning the MeSH term embeddings, current approaches fail to incorporate all of them in the learning process. The challenge is that the structured relationships between MeSH terms are different across the data sources, and there is no approach to fusing such complex data into the MeSH term embedding learning. In this paper, we study the problem of incorporating corpus, ontology, and semantic predications to learn the embeddings of MeSH terms. We propose a novel framework, Corpus, Ontology, and Semantic predications-based MeSH term embedding (COS), to generate high-quality MeSH term embeddings. COS converts the corpus, ontology, and semantic predications into MeSH term sequences, merges these sequences, and learns MeSH term embeddings using the sequences. Extensive experiments on different datasets show that COS outperforms various baseline embeddings and traditional non-embedding-based baselines.

After being indexed in National Library of Medicine (NLM) Catalog and PubMed Central in 2012, Healthcare Informatics Research (HIR) took another step forward in 2013 with its new position as a listed journal in Scopus. We also finished our application for Science Citation Index (SCI) at beginning of this year and are now in process of being evaluated. We are also happy to announce that HIR was recognized as one of best academic journals in Korea by The Korean Federation of Science and Technology Societies, as it was in previous years. At last, Issue 4 of Volume 19 is now officially published, ready to be read. The collaboration of this issue with International CODATA Conference marks another move forward in our development. In April 2013, Dr. William T. F. Goossen, an Editorial Board member of HIR, suggested publishing a set of papers presented in CODATA Conference held in Taipei, Taiwan in 2012. The CODATA is a conference organized by Committee on Data for Science and Technology of International Council for Science, and focus of conference is dealing with topic and methods used for preservation of data in Electronic Health Record (EHR). The HIR Editorial Committee decided to publish this special issue with a focus on aspects of preservation of data in EHR, because electronic health-related data and information is vital for clinical care as well as healthcare research, but systems interoperability for preservation, storage, and accessibility of such health data have not yet been established for If preservation of healthcare information is not addressed, valuable and irreplaceable information will become inaccessible or even disappear over time with disastrous consequences for patient care and research. Thus challenge is to preserve and provide access to electronic clinical data as EHR for a sufficiently long period of time to maximize value to patients, caregivers, and scientists. Healthcare informatics is a data-intensive scientific field, and HIR can highlight role that data-intensive science plays in transforming raw observations into applicable, intelligible results and discoveries. For health care, such discoveries will be increasingly based on observational data that come from EHR and clinical data warehouses. Of course, this development implies storage of petabytes, exabytes, zettabytes and even more of patient related data. This data must be stored for lifetimes of individuals and grouped into meaningful datamarts for population research. An additional issue is need to integrate diverse health records that have been captured in different settings and different EHR systems and data from various source systems and in recent smartphone apps and other e-Health applications. Hence question regarding permanence of clinical data becomes obvious. Consequently, hardware on which data is stored and software used become less significant compared to informational structures and meta-data about clinical data. Hence for health care, preservation of EHR and other health-related data is a very important theme. To publish this special issue, papers that we accepted fell under two categories. For articles from CODATA Conference, authors were requested to rewrite their article following HIR author guideline in format of either their original article or case report and submit it through on-line submission system. In other category, a public invitation was put out to send in articles covering theme of preservation of data in All manuscripts submitted from both categories underwent standard HIR peer-review procedure by three anonymous reviewers in order to guarantee quality and originality of research and its clinical and scientific significance. Therefore, only three of seven recommended articles from CODATA Conference were included. This issue consists of twelve unique contributions on topic EHR data preservation: One review article, five original research papers, five case reports, and one book review. The review article by Schultza, et al. clarifies challenges in biomedical knowledge research and describes how focus of research has moved from medical concept representation to medical ontologies. The first original paper by Singh, et al. uses Medical Subject Heading (MeSH) terms to find expert systems required for specific IT healthcare related projects, and paper by Kobayashi, et al. discusses use of Ruby programming language in implementation of OpenEHR specifications and archetypes. The other three original articles deal with topics of reusability of EHR data, use of health insurance claim data, and smartphone applications. The remaining five case reports discuss EHR interoperability through ISO 13606, health information exchange connectivity with legacy systems, semantic interoperability in electronic nursing record systems, mobile EHR applications, and Web-based integrated public healthcare information systems. These contributions state that besides overall structure of EHR, close attention must be paid to data definitions and data semantics in order to obtain sustainable EHR and improve quality of healthcare and research. The methods described here can be applicable to many areas of expertise. This issue is result of collaborating with CODATA Conference on topic of the preservation of data in EHR. To ascertain current practices for preservation and management of EHR, further studies should be conducted to establish an interoperability framework that supports a wide variety of data types, formats, records, and data delivery mechanisms, and to provide technology-independent infrastructures that acquire, store, search, retrieve, migrate, replicate, and distribute EHRs over time. It is our hope that we can continue to collaborate with conferences, workshops, colloquiums, and other academic dialogues in order to realize these goals.

The massive increase in the number of published scientific articles enhances knowledge but makes it more complicated to summarize results. The Medical Subject Headings (MeSH) thesaurus was created in the mid-20th century with the aim of systematizing article indexing and facilitating their retrieval. Despite the advent of search engines, few studies have questioned the relevance of the MeSH thesaurus, and none have done so systematically. The objective of this study was to estimate the added value of using MeSH terms in PubMed queries for systematic reviews (SRs). SRs published in 4 high-impact medical journals in general medicine over the past 10 years were selected. Only SRs for which a PubMed query was provided were included. Each query was transformed to obtain 3 versions: the original query (V1), the query with free-text terms only (V2), and the query with MeSH terms only (V3). These 3 queries were compared with each other based on their sensitivity and positive predictive values. In total, 59 SRs were included. The suppression of MeSH terms had an impact on the number of relevant articles retrieved for 24 (41%) out of 59 SRs. The median (IQR) sensitivities of queries V1 and V2 were 77.8% (62.1%-95.2%) and 71.4% (42.6%-90%), respectively. V1 queries provided an average of 2.62 additional relevant papers per SR compared with V2 queries. However, an additional 820.29 papers had to be screened. The cost of screening an additional collected paper was therefore 313.09, which was slightly more than triple the mean reading cost associated with V2 queries (88.67). Our results revealed that removing MeSH terms from a query decreases sensitivity while slightly increasing the positive predictive value. Queries containing both MeSH and free-text terms yielded more relevant articles but required screening many additional papers. Despite this additional workload, MeSH terms remain indispensable for SRs.

This research applied the Literature-based Discovery approach and supervised link prediction methods to predict previously unknown research links between medical subject headings (MeSH) terms in Zika and CRISPR research. Both Zika and CRISPR research was extracted from the PubMed dataset and analyzed respectively. For Zika research, the timeframe for the data extraction was between 1952 and 2017, containing 1,939 research articles and 2,546 distinct MeSH terms. For CRISPR research, the data were collected from 2002 to 2016, including 4,572 research articles and 4,203 distinct MeSH terms. The link prediction measures, Common Neighbor, Jaccard’s Coefficient, Adamic/Adr, Preferential Attachment, and Resource Allocation Index, were generated as input variables to predict whether a non-linkage between two MeSH terms is formed in the future. This research applied the Logistic Regression, Naive Bayes, Decision Tree, and Random Forests algorithms to build classification models. Because the outcome variables are highly unbalanced, the stratified sampling and under/over-sampling methods were used to generate representative training and testing sets. The results indicate that the Logistic Regression has better performance for predicting a MeSH link in Zika research. In contrast, the Naive Bayes has better performance for predicting a MeSH link in CRISPR research. Thus, the methods proposed by this research can be used to discover possible research areas of MeSH terms and new research directions. For biomedical policymakers, the results can be considered as an evidence-based source for the decisions of public fund allocation.

Irritable bowel syndrome (IBS) and chronic idiopathic constipation ((CIC) also referred to as functional constipation) are two of the most common functional gastrointestinal disorders worldwide. IBS is a global problem, with anywhere from 5 to 15% of the general population experiencing symptoms that would satisfy a definition of IBS (1,2). In a systematic review on the global prevalence of IBS, Lovell and Ford (1) documented a pooled prevalence of 11% with all regions of the world suffering from this disorder at similar rates. Given its prevalence, the frequency of symptoms, and their associated debility for many patients and the fact that IBS typically occurs in younger adulthood, an important period for furthering education, embarking on careers, and/or raising families, the socioeconomic impact of IBS is considerable. These indirect medical costs are frequently compounded by the direct medical costs related to additional medical tests and the use of various medical and nonmedical remedies that may have limited impact. CIC is equally common; in another systematic review, Suares and Ford (3) reported a pooled prevalence of 14%, and also noted that constipation was more common in females, in older subjects, and those of lower socioeconomic status (3). Chronic constipation has also been linked to impaired quality of life (4), most notably among the elderly (5). Neither IBS nor CIC are associated with abnormal radiologic or endoscopic abnormalities, nor are they associated with a reliable biomarker; diagnosis currently rests entirely, therefore, on clinical grounds. Although a number of clinical definitions of both IBS and CIC have been proposed, the criteria developed through the Rome process, currently in its third iteration, have been those most widely employed in clinical trials and, therefore, most relevant to any review of the literature on the management of these disorders. According to Rome III, IBS is defined on the basis of the presence of: Recurrent abdominal pain or discomfort at least 3 days/month in the past 3 months associated with two or more of the following: Improvement with defecation Onset associated with a change in frequency of stool Onset associated with a change in form (appearance) of stool These criteria should be fulfilled for the past 3 months with symptom onset at least 6 months before diagnosis (6). Rome III defines functional constipation as: the presence of two or more of the following: Straining during at least 25% of defecations Lumpy or hard stools in at least 25% of defecations Sensation of incomplete evacuation for at least 25% of defecations Sensation of anorectal obstruction/blockage for at least 25% of defecations Manual maneuvers to facilitate at least 25% of defecations (e.g., digital evacuation, support of the pelvic floor) Fewer than three defecations per week Furthermore, loose stools are rarely present without the use of laxatives and there are insufficient criteria for IBS. Again, these criteria should be fulfilled for the past 3 months with symptom onset at least 6 months before diagnosis (6). In Rome III, IBS is subtyped according to predominant bowel habit as IBS with constipation (IBS-C), IBS with diarrhea (IBS-D), mixed type (IBS-M), and unclassified (IBS-U). The definition of bowel habit type is, in turn, based on the patient's description of stool form by referring to the Bristol Stool Scale (7). The recognition that IBS sufferers segregate into subtypes according to predominant bowel habit, together with research findings suggesting that IBS-C and IBS-D may be pathophysiologically distinct entities (8,9,10), led to the development of therapies specifically directed at each of these subtypes. Nonetheless, it is worth noting that symptoms may not be stable over a lifetime and individuals may exhibit one IBS subtype during a period, and then a different IBS subtype during another period in their lives. However, although there is general awareness of the Rome criteria, they are infrequently employed in the assessment of IBS and CIC in clinical practice (11). To provide more "clinician friendly" definitions, as well as to permit inclusion of studies that predated the Rome process, American College of Gastroenterology Task Forces suggested the following definitions in prior systematic reviews: IBS is defined by: abdominal discomfort associated with altered bowel habits (12). Constipation is defined as: a symptom-based disorder defined as unsatisfactory defecation and is characterized by infrequent stools, difficult stool passage, or both. Difficult stool passage includes straining, a sense of difficulty passing stool, incomplete evacuation, hard/lumpy stools, prolonged time to stool, or need for manual maneuvers to pass stool. CIC is defined as the presence of these symptoms for at least 3 months (13). It is important to note that the Rome III criteria state that individuals with chronic constipation do not fulfill criteria for IBS, with pain or discomfort being a major determinant in the latter. In practice, a clear separation between CIC and IBS with constipation may be challenging and studies have shown, not only considerable overlap between these entities (14,15,16), but also a significant tendency for patients to migrate between these diagnoses over time (15). It is appropriate therefore that in this update of prior American College of Gastroenterology monographs on IBS and CIC, these entities be addressed in the same exercise (12,13,17). The goal of this exercise, therefore, was to update the most recent systematic reviews commissioned by the American College of Gastroenterology on IBS from 2009 (17) and CIC from 2005 (13). METHODS We have conducted a series of systematic reviews on the efficacy of therapy in IBS and CIC. There have been several systematic reviews of therapy for IBS and CIC published in the past 5 years (18,19,20,21,22). There have been considerable data published in the intervening time, and hence we have, therefore, updated all these systematic reviews of IBS and CIC and synthesized the data, including the information from new trials, where appropriate. The primary objective of this exercise was to assess the efficacy of available therapies in treating IBS and CIC compared with placebo or no treatment. The secondary objectives included assessing the efficacy of available therapies in treating IBS according to predominant stool pattern reported (IBS with constipation, IBS with diarrhea, and mixed IBS), as well as assessing adverse events with therapies for both IBS and CIC. Systematic review methodology We evaluated manuscripts that studied adults (aged >16 years) using any definition of IBS or CIC. For IBS, this included a clinician-defined diagnosis, the Manning criteria (23), the Kruis score (24), or Rome I (25), II (26), or III (6) criteria. For CIC, this included symptoms diagnosed by any of the Rome criteria (6,25,26), as well as a clinician-defined diagnosis. We included only parallel-group randomized controlled trials (RCTs) comparing active intervention with either placebo or no therapy. Crossover trials were eligible for inclusion, provided extractable data were provided at the end of the first treatment period, before crossover. For IBS, the following treatments were considered: Diet and dietary manipulation Fiber Interventions that modify the microbiota: probiotics, prebiotics, antibiotics Antispasmodics Peppermint oil Loperamide Antidepressants Psychological therapies, including hypnotherapy Serotonergic agents Prosecretory agents Polyethylene glycol For CIC, the following were considered: Fiber Osmotic and stimulant laxatives 5-HT4 agonists Prosecretory agents Biofeedback Bile acid transporter inhibitors Probiotics Subjects needed to be followed up for at least 1 week. To be eligible, trials needed to include one or more of the following outcome measures: Global assessment of improvement in IBS or CIC symptoms Improvement in abdominal pain for IBS Global IBS symptom or abdominal pain scores for IBS Mean number of stools per week during therapy for CIC Search strategy for identification of studies MEDLINE (1946 to October 2013), EMBASE and EMBASE Classic (1947 to October 2013), and the Cochrane central register of controlled trials were searched. Studies on IBS were identified with the terms irritable bowel syndrome and functional diseases, colon (both as medical subject headings (MeSH) and free text terms), and IBS, spastic colon, irritable colon, and functional adj5 bowel (as free text terms). For RCTs of dietary manipulation, these were combined using the set operator AND with studies identified with the terms: diet, fat-restricted, diet, protein-restricted, diet, carbohydrate-restricted, diet, gluten-free, diet, macrobiotic, diet, vegetarian, diet, Mediterranean, diet fads, gluten, fructose, lactose intolerance, or lactose (both as MeSH and free text terms), or the following free text terms: FODMAP$, glutens, food adj5 intolerance, food allergy, or food hypersensitivity. For RCTs of fiber, antispasmodics, and peppermint oil, these were combined using the set operator AND with studies identified with the terms: dietary fiber, cereals, psyllium, methylcellulose, sterculia, karaya gum, parasympatholytics, hyoscyamine, scopolamine, trimebutine, muscarinic antagonists, or butylscopolammonium bromide (both as MeSH and free text terms), or the following free text terms: bulking agent, psyllium fiber, fiber, husk, bran, ispaghula, wheat bran, calcium polycarbophil, spasmolytics, spasmolytic agents, antispasmodics, mebeverine, alverine, pinaverium bromide, otilonium bromide, cimetropium bromide, hyoscine butyl bromide, butylscopolamine, peppermint oil, or colpermin. For RCTs of probiotics, these were combined using the set operator AND with studies identified with the terms: Saccharomyces, Lactobacillus, Bifidobacterium, Escherichia coli, or probiotics (both as MeSH and free text terms). For RCTs of prebiotics and synbiotics, these were combined using the set operator AND with studies identified with the term: prebiotic (both MeSH and free text terms) or synbiotic (both MeSH and free text terms). For RCTs of antibiotics, these were combined using the set operator AND with studies identified with the terms: anti-bacterial agents, penicillins, cephalosporins, rifamycins, quinolones, nitroimidazoles, tetracycline, doxycycline, amoxicillin, ciprofloxacin, metronidazole, or tinidazole (both as MeSH and free text terms), or the following free text terms: antibiotic or rifamixin. For RCTs of loperamide, these were combined using the set operator AND with studies identified with the terms: loperamide or antidiarrheals (both as MeSH and free text terms), or the following free text terms: imodium or lopex. For RCTs of antidepressants and psychological therapies, including hypnotherapy, these were combined using the set operator AND with studies identified with the terms: psychotropic drugs, antidepressive agents, antidepressive agents (tricyclic), desipramine, imipramine, trimipramine, doxepin, dothiepin, nortriptyline, amitriptyline, selective serotonin reuptake inhibitors, paroxetine, sertraline, fluoxetine, citalopram, venlafaxine, cognitive therapy, psychotherapy, behavior therapy, relaxation techniques, or hypnosis (both as MeSH and free text terms), or the following free text terms: behavioral therapy, relaxation therapy, or hypnotherapy. For RCTs of serotonergic agents, these were combined using the set operator AND with studies identified with the terms: serotonin antagonists, serotonin agonists, cisapride, receptors (serotonin, 5-HT3), or receptors (serotonin, 5-HT4) (both as MeSH and free text terms), or the following free text terms: 5-HT3, 5-HT4, alosetron, cilansetron, ramosetron, prucalopride, mosapride, or renzapride. For RCTs of pro-secretory agents, these were combined using the set operator AND with studies identified with the following free text terms: linaclotide or lubiprostone. For RCTs of polyethylene glycol (PEG), these were combined using the set operator AND with studies identified with the term polyethylene glycol (both as a MeSH and free text term). Studies on CIC were identified with the terms constipation or gastrointestinal transit (both as MeSH and free text terms), or functional constipation, idiopathic constipation, chronic constipation, or slow transit (as free text terms). For the search involving biofeedback, the free text terms dyssynergia, pelvic floor dysfunction, anismus, and outlet obstruction were also added. For RCTs of fiber, these were combined using the set operator AND with studies identified with the terms: dietary fiber, cellulose, plant extracts, psyllium, cereals, plantago, or methylcellulose (both as MeSH and free text terms), or the following free text terms: fiber, soluble fiber, insoluble fiber, bran, ispaghula, metamucil, fybogel, or ispaghula. For RCTs of osmotic and stimulant laxatives, these were combined using the set operator AND with studies identified with the terms: laxatives, cathartics, anthraquinones, phenolphthaleins, indoles, phenols, lactulose, polyethylene glycol, senna plant, senna extract, bisacodyl, phosphates, dioctyl sulfosuccinic acid, magnesium, magnesium hydroxide, sorbitol, poloxamer (both as MeSH and free text terms), or the following free text terms: sodium picosulphate, docusate, milk of magnesia, danthron, senna, and poloxalkol. For RCTs of 5-HT4 agonists, these were combined using the set operator AND with studies identified with the terms: serotonin agonists, receptors, or serotonin, 5-HT4 (both as MeSH and free text terms), or the following free text terms: prucalopride, velusetrag, or naronapride. For RCTs of pro-secretory agents, these were combined using the set operator AND with studies identified with the following free text terms: lubiprostone or linaclotide. For RCTs of biofeedback, these were combined using the set operator AND with studies identified with the MESH terms biofeedback and psychology and the following free text terms: biofeedback or neuromuscular training. For RCTs of bile acid transporter inhibitors, these were combined using the set operator AND with studies identified with the following free text terms: bile acid transporter, elobixibat, or A3309. For RCTs of probiotics, these were combined using the set operator AND with studies identified with the terms: Saccharomyces, Lactobacillus, Bifidobacterium, E. coli, or probiotics (both as MeSH and free text terms). For RCTs of prebiotics and synbiotics, these were combined using the set operator AND with studies identified with the term: prebiotic (both MESH and free text terms) or synbiotic (both MESH and free text terms). The search was limited to humans. No restrictions were applied with regard to language of publication. A recursive search of the bibliography of relevant articles was also conducted. DDW (Digestive Diseases Week) and UEGW (United European Gastroenterology Week) abstract books were hand searched between 2000 and 2013. Authors of trial reports that did not give enough detail for adequate data extraction were contacted and asked to contribute full data sets. Experts in the field were contacted for leads on unpublished studies. Trials were assessed for risk of bias according to the methods described in the Cochrane handbook [27] using the following characteristics: method used to generate the randomization schedule, method used to conceal treatment allocation, implementation of masking, completeness of follow-up, and conduct of an intention-to-treat analysis. Eligibility, quality, and outcome data were extracted by the lead reviewer (Alexander Ford) and by a masked second reviewer (Paul Moayyedi) on to specially developed forms. Any discrepancy was resolved by discussion between the two reviewers in order to reach a consensus. Data were extracted as intention-to-treat analyses, where all dropouts were assumed to be treatment failures, wherever trial reporting allowed this. Data synthesis For IBS, whenever possible, any improvement of global IBS symptoms as a binary outcome was taken as the primary outcome measure. If this was not available, improvement in abdominal pain was used. For CIC, any improvement of global CIC symptoms as a binary outcome was taken as the primary outcome measure. The impact of interventions was expressed as a relative risk (RR) of IBS or CIC symptoms not improving, together with 95% confidence intervals (CIs). If there were sufficient data, RRs were combined using the DerSimonian and Laird random effects model (28) to give a more conservative estimate of the efficacy of individual IBS therapies. For continuous data, such as global IBS symptom scores or individual IBS symptom scores, a standardized mean difference, with 95% CIs, was calculated. It should be noted that some treatments may be beneficial in IBS or CIC because of the effects on outcomes other than global symptoms or abdominal pain, but this was not evaluated and was outside of the scope of this review. Tests of heterogeneity were reported (29). When the test of heterogeneity was significant (P<0.10 and/or I2>25%), the reasons for this were explored by evaluating differences in study population, study design, or study end points in subgroup analyses. Publication bias or other causes of small study effects were evaluated using tests for funnel plot asymmetry (30), where sufficient studies were identified (31). The number needed to treat (NNT), which is the number of patients who would need to receive active therapy, over and above the control therapy, for one to experience an improvement in symptoms, and the number needed to harm (NNH), which is the number of patients who would need to receive active therapy, over and above the control therapy, for one to experience an adverse event were calculated as the inverse of the risk difference from the meta-analysis and checked using the formula: NNT = 100 / RRR × BR, where BR is baseline risk and RRR is relative risk reduction. Methodology for assessing levels of evidence and grading recommendations We used the GRADE (Grading of Recommendations Assessment, Development and Evaluation) system for grading the quality of evidence and strength of recommendation for each medical intervention (32). The system has been widely used in evidence-based guidelines and is endorsed by all major gastrointestinal societies (http://www.gradeworkinggroup.org). The quality of the evidence is based on the study design, as well as the extent of risk of bias, inconsistency, indirectness, imprecision, and publication bias that exists for the evidence supporting the intervention (33). Quality of evidence is described as high to very low, depending on the extent to which further evidence would change the estimate of treatment effect (Box 1). The grading scheme also classifies recommendations as strong or weak, according to the quality of the evidence, applicability to all patient groups, balance of benefits and risks, patient preferences, and cost. With this graded recommendation, the clinician receives guidance about whether or not recommendations should be applied to most patients, and whether or not recommendations are likely to change in the future after production of new evidence. "Strong" recommendations represent a "recommendation that can apply to most patients in most circumstances and further evidence is unlikely to change our confidence in the estimate of treatment effect." The summary of the evidence for IBS is presented in Table 1, the reasons for the decision on the quality of that evidence in Table 2, and the reasons for the strength of recommendation in Table 3. Similarly, the summary of the evidence for CIC is presented in Table 4, the reasons for the decision on quality of the evidence in Table 5, and the reasons for the strength of recommendation in Table 6.Box 1.: Interpretation of the grading of the quality of evidenceTable 1: Summary of results of monograph on interventions for IBSTable 2: Reasons for quality of evidence of assessment for IBS data according to GRADE criteriaTable 2: Continued.Table 3: Reasons for strength of recommendation for IBS therapies according to GRADE criteriaTable 4: Summary of results of monograph on interventions for CICTable 5: Reasons for quality of evidence of assessment of data on CIC according to GRADE criteriaTable 6: Reasons for strength of recommendation for treatments of CIC according to GRADE criteriaRESULTS Irritable bowel syndrome 1. Diet and dietary manipulation in IBS (a) Role of diet in IBS: Although food intake is one of the most common precipitants of symptoms in IBS (34), responses to food and with of the diet have not typically in the of a on their IBS sufferers have their to this or guidance from dietary IBS patients that they have an to although food are in IBS although the prevalence of food in societies is between 1 and in of gastrointestinal patients that that their symptoms food or food IBS symptoms to represent food intolerance, although only of patients can the food in a on their with and a of objective evidence to a studies have that a of IBS patients dietary to an extent that may their Role of dietary manipulation in may symptoms in individual IBS Quality of very We identified RCTs that evaluated dietary intervention in IBS to data of relevant symptom data and an intervention week three RCTs involving patients The first of these addressed the impact of in IBS. In a patients with IBS were randomized to either on a diet or to receive of on of an In the reported that their symptoms were not controlled as compared with in the placebo symptom scores for abdominal pain, with stool and were in those who a The second of these studies the of food or as not by but by In a parallel-group IBS patients were randomized to either an diet based on the presence of to various or a were followed for and symptoms assessed using a global impact score and the IBS with in the diet in the diet intervention noted a significant improvement in The reported in those with high to their The third study the of and IBS patients were randomized to a diet or their diet for those randomized to the diet, reported adequate control of their symptoms compared with of the diet Stool did not between stool frequency was in the diet A significant of this study was the of the dietary the of dietary in the of symptoms, or in the of IBS, is being To two and have been addressed in clinical trials, although it is that other (e.g., of and with the may also be relevant to the effects of food or food the that any of the of an diet or of a food in IBS the data provide limited guidance on the of diet in the management of IBS. and but their in the management of IBS need to be Fiber in IBS Fiber symptom in IBS. Quality of but not bran, symptom in IBS. Quality of intake of dietary is frequently to bowel for IBS, for However, insoluble frequently and abdominal In our prior systematic review we identified two additional studies for a of RCTs involving but trials did not IBS by subtype and only two to IBS-C In the study to patients, of were IBS-C and were were randomized to one of three of the soluble psyllium, of the insoluble bran, or of a placebo for the first a of patients psyllium, but not bran, reported adequate symptom for at least compared with placebo psyllium 95% was more than placebo during the third of treatment only 3 months of symptom in the psyllium was by points compared with points in the placebo and points in the No differences were with to quality of was most common in the most because of in IBS. Data on adverse events were only provided by trials These trials evaluated patients, but as of adverse events were small in 5 of the trials, of data was not A of of patients reported adverse events compared with of in the placebo Although its use in the management of IBS is time the status of fiber, in in IBS, is from may symptoms and provide soluble and psyllium, in provide in IBS. These effects to benefits in terms of of 3. Interventions that modify the microbiota: probiotics, prebiotics, and antibiotics The that the be relevant to IBS first from the that a although of individuals who an of on to IBS IBS Although has been linked to and and in the have been described in IBS, the of the to or other symptoms in IBS, is although both small and and in the have also been linked to IBS the of to IBS and findings in to the in patient probiotics, and have been used for on an basis by IBS they have only been to in clinical The of studies in IBS challenging as studies have employed different and in various patient and in Although the suggested that more than of all IBS sufferers studies have, in to such a high prevalence of in IBS These results may to to the test that may provide an of the this provided a for assessing antibiotics in IBS. a has efficacy in clinical trials in and although significant were over placebo in global IBS symptoms as well as in it is important to note that tests for were not in these trials, the of of in IBS (a) and in IBS: There is insufficient evidence to prebiotics or in IBS. Quality of very Probiotics in as a probiotics global symptoms, and in IBS.

BackgroundIn recent years, many studies on vitamin D have been published. We combed these data for hot spot analyses and predicted future research topic trends.Material/MethodsArticles (4625) concerning vitamin D published in the past 3 years were selected as a study sample. Bibliographic Items Co-occurrence Matrix Builder (BICOMB) software was used to screen high-frequency Medical Subject Headings (MeSH) terms and construct a MeSH terms-source article matrix and MeSH terms co-occurrence matrix. Then, Graphical Clustering Toolkit (gCLUTO) software was employed to analyze the matrix by double-clustering and visual analysis to detect the trends on the subject.ResultsNinety high-frequency major MeSH terms were obtained from 4625 articles and divided into 5 clusters, and we generated a visualized matrix and a mountain map. Strategic coordinates were established by the co-occurrence matrix of the MeSH terms based on the above classification, and the 5 clusters described above were further divided into 7 topics. We classified the vitamin D-related diseases into 12 categories and analyzed their distribution.ConclusionsThe analysis of strategic coordinates revealed that the epidemiological study of vitamin D deficiency and vitamin D-related diseases is a hot research topic. The use of vitamin D in the prevention and treatment of some diseases, especially diabetes, was found to have a significant potential future research value.

The creation of innovative techniques of document representation is critical to the development of effective information retrieval (IR) systems. In this paper, we report on the impact of state-of-the-art human indexing techniques, exemplified by MeSH (Medical Subject Headings) terms, in the document representation. We studied queries formulated by four different kinds of information seekers interactively using an experimental IR system: (1) search novices; (2) domain experts; (3) search experts and (4) medical librarians. The 3,442,321 documents came from the TREC 2004 Genomics Track document set. Effectiveness of retrieval was measured using the relevance judgments provided by TREC. Inclusion of MeSH terms in the document representation did not affect the effectiveness of queries with respect to precision and recall. Adding MeSH terms to the index did not have a positive impact on the effectiveness of queries formulated by different kinds of users. These findings contribute to our understanding of the associations between the users' cognitive space and the information objects in light of the principle of polyrepresentation.

Introduction: Performing systematic review searches related to Canadian Indigenous peoples (First Nations, Inuit, and Métis), particularly in areas of public health, is difficult because Medical Subject Headings (MeSH) terms for both Indigenous peoples and geography do not retrieve all relevant articles in Ovid MEDLINE. Text–word searching for Canadian Indigenous peoples presents challenges in the varieties of names, spellings, and languages. A series of Canadian Indigenous peoples filters were designed to retrieve larger numbers of relevant articles. Objectives: The objectives of this work were (i) to create first-generation search filters that retrieve studies from the Ovid MEDLINE database related to Canadian Indigenous peoples, (ii) to determine whether or not the filters retrieve more records than do searches using the MeSH headings alone, and (iii) to determine how many of the additional records are relevant. Methods: Key terms describing both Canadian Indigenous peoples and Canadian geography were identified using government, historical, and ethnographic publications. Name lists included current and historical names in multiple languages, as well as local and settlement names, and names of linguistic groups. Filters, employing both text–word and MeSH terms were created for each province and territory, excluding Prince Edward Island. Search results were reviewed for false recalls related to terms with multiple meanings and groups of people whose lands straddle provincial and territorial borders. Revised searches were refined with additional terminology that implies the presence of Indigenous peoples. Duplicate records were removed from both the MeSH searches and the filter searches. Results from the MeSH searches were then removed from the results of the filter searches. The remaining results were analyzed for relevance. Results: Twelve Ovid MEDLINE filters were created and the challenges involved in creating them were documented. The filters increased recall by 58 articles, 464% over MeSH searches alone. Of the additional articles retrieved, 28 (100%) met the criteria for relevance. Discussion: The lists of challenges identified in the filter creation will assist other searchers in developing similar filters. The filters allow searchers to retrieve substantially more articles than is currently possible with the MeSH terms alone.