Beyond captions: linking figures with abstract sentences in biomedical articles

Although figures in scientific articles have high information content and concisely communicate many key research findings, they are currently under utilized by literature search and retrieval systems. Many systems ignore figures, and those that do not typically only consider caption text. This study describes and evaluates a fully automated approach for associating figures in the body of a biomedical article with sentences in its abstract. We use supervised methods to learn probabilistic language models, hidden Markov models, and conditional random fields for predicting associations between abstract sentences and figures. Three kinds of evidence are used: text in abstract sentences and figures, relative positions of sentences and figures, and the patterns of sentence/figure associations across an article. Each information source is shown to have predictive value, and models that use all kinds of evidence are more accurate than models that do not. Our most accurate method has an F1-score of 69% on a cross-validation experiment, is competitive with the accuracy of human experts, has significantly better predictive accuracy than state-of-the-art methods and enables users to access figures associated with an abstract sentence with an average of 1.82 fewer mouse clicks. A user evaluation shows that human users find our system beneficial. The system is available at http://FigureItOut.askHERMES.org.     

Full Text and Figure Display Improves Bioscience Literature Search

When reading bioscience journal articles, many researchers focus attention on the figures and their captions. This observation led to the development of the BioText literature search engine [1], a freely available Web-based application that allows biologists to search over the contents of Open Access Journals, and see figures from the articles displayed directly in the search results. This article presents a qualitative assessment of this system in the form of a usability study with 20 biologist participants using and commenting on the system. 19 out of 20 participants expressed a desire to use a bioscience literature search engine that displays articles'' figures alongside the full text search results. 15 out of 20 participants said they would use a caption search and figure display interface either frequently or sometimes, while 4 said rarely and 1 said undecided. 10 out of 20 participants said they would use a tool for searching the text of tables and their captions either frequently or sometimes, while 7 said they would use it rarely if at all, 2 said they would never use it, and 1 was undecided. This study found evidence, supporting results of an earlier study, that bioscience literature search systems such as PubMed should show figures from articles alongside search results. It also found evidence that full text and captions should be searched along with the article title, metadata, and abstract. Finally, for a subset of users and information needs, allowing for explicit search within captions for figures and tables is a useful function, but it is not entirely clear how to cleanly integrate this within a more general literature search interface. Such a facility supports Open Access publishing efforts, as it requires access to full text of documents and the lifting of restrictions in order to show figures in the search interface.     

Suicide and the afterlife: popular religion and the standardisation of 'culture' in Japan

For an overwhelming majority of commentators, including many anthropologists, 'Japanese culture' is still associated with a positive view of suicide. Western-language writings have contributed by feedback loop to perpetuate this stereotype. Besides the local 'samurai ethic', Japanese Buddhism is also said not to prohibit taking one's life. However, the most popular examples of heroic self-sacrifice, from the Edo period to WWII, are fraught with covert contradictions. From ancient times to the present religious practitioners of all sorts have maintained that suicide creates unhappy, resentful spirits who harm the living. This article discusses many examples of a diverse series of narratives, from spirit medium's séances to drama to contemporary films, in which the anguished spirits of suicides are allowed to express themselves directly. After the figures rose alarmingly in the late 1990s various religious organisations have attempted to fight the stigma suffered by bereaved family members and have introduced new interpretations and new rituals.     

Figure summarizer browser extensions for PubMed Central

SUMMARY: Figures in biomedical articles present visual evidence for research facts and help readers understand the article better. However, when figures are taken out of context, it is difficult to understand their content. We developed a summarization algorithm to summarize the content of figures and used it in our figure search engine (http://figuresearch.askhermes.org/). In this article, we report on the development of web browser extensions for Mozilla Firefox, Google Chrome and Apple Safari to display summaries for figures in PubMed Central and NCBI Images. AVAILABILITY: The extensions can be downloaded from http://figuresearch.askhermes.org/articlesearch/extensions.php.     

OSIRIS: a tool for retrieving literature about sequence variants

Sequence variants, in particular single nucleotide polymorphisms (SNPs), are key elements for the identification of genes associated with complex diseases and with particular drug responses. The search for literature about sequence variation is hampered by the large number of allelic variants reported for many genes and by the variability in both gene and sequence variants nomenclatures. We describe OSIRIS, a search tool that integrates different sources of information with the aim to retrieve literature about sequence variation of a gene. In addition, it provides a method to link a dbSNP entry with the articles referring to it. AVAILABILITY: OSIRIS is available for public use at http://ibi.imim.es/     

Figure-Associated Text Summarization and Evaluation

Biomedical literature incorporates millions of figures, which are a rich and important knowledge resource for biomedical researchers. Scientists need access to the figures and the knowledge they represent in order to validate research findings and to generate new hypotheses. By themselves, these figures are nearly always incomprehensible to both humans and machines and their associated texts are therefore essential for full comprehension. The associated text of a figure, however, is scattered throughout its full-text article and contains redundant information content. In this paper, we report the continued development and evaluation of several figure summarization systems, the FigSum+ systems, that automatically identify associated texts, remove redundant information, and generate a text summary for every figure in an article. Using a set of 94 annotated figures selected from 19 different journals, we conducted an intrinsic evaluation of FigSum+. We evaluate the performance by precision, recall, F1, and ROUGE scores. The best FigSum+ system is based on an unsupervised method, achieving F1 score of 0.66 and ROUGE-1 score of 0.97. The annotated data is available at figshare.com (http://figshare.com/articles/Figure_Associated_Text_Summarization_and_Evaluation/858903).     

Automatic figure ranking and user interfacing for intelligent figure search

Background

Figures are important experimental results that are typically reported in full-text bioscience articles. Bioscience researchers need to access figures to validate research facts and to formulate or to test novel research hypotheses. On the other hand, the sheer volume of bioscience literature has made it difficult to access figures. Therefore, we are developing an intelligent figure search engine (http://figuresearch.askhermes.org). Existing research in figure search treats each figure equally, but we introduce a novel concept of “figure ranking”: figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery.

Methodology/Findings

We empirically validated the hypothesis of figure ranking with over 100 bioscience researchers, and then developed unsupervised natural language processing (NLP) approaches to automatically rank figures. Evaluating on a collection of 202 full-text articles in which authors have ranked the figures based on importance, our best system achieved a weighted error rate of 0.2, which is significantly better than several other baseline systems we explored. We further explored a user interfacing application in which we built novel user interfaces (UIs) incorporating figure ranking, allowing bioscience researchers to efficiently access important figures. Our evaluation results show that 92% of the bioscience researchers prefer as the top two choices the user interfaces in which the most important figures are enlarged. With our automatic figure ranking NLP system, bioscience researchers preferred the UIs in which the most important figures were predicted by our NLP system than the UIs in which the most important figures were randomly assigned. In addition, our results show that there was no statistical difference in bioscience researchers'' preference in the UIs generated by automatic figure ranking and UIs by human ranking annotation.

Conclusion/Significance

The evaluation results conclude that automatic figure ranking and user interfacing as we reported in this study can be fully implemented in online publishing. The novel user interface integrated with the automatic figure ranking system provides a more efficient and robust way to access scientific information in the biomedical domain, which will further enhance our existing figure search engine to better facilitate accessing figures of interest for bioscientists.     

Curcumin: A potential therapeutic natural product for adenocarcinomas

Adenocarcinomas comprise a significant class of cancers that occur in several organs (e.g., lung, pancreas, breast, colon, and endometrium). These highly lethal tumor types are predominantly invasive with metastatic tendency. As a pharmacological option for the treatment of adenocarcinomas, curcumin has been widely used in combination with various therapeutic modalities. However, poor stability and low bioavailability of the curcumin has restricted its application in clinic. Therefore, nanoparticle-based curcumin was produced to fortify the pharmacokinetics of curcumin. Enhanced cytotoxicity and bioavailability of curcumin have been obtained by synthesizing new curcumin analogs via chemical modification. This review article aimed to survey recent findings on the role of curcumin in the treatment of adenocarcinomas in several organs and described key players of underlying molecular pathways such as the anti-proliferative, anti-apoptosis, anti-metastasis, anti-inflammatory, and immunomodulatory mechanisms. We also described new approaches to producing curcumin-loaded nanoparticles and combinatorial regimens. A comprehensive literature search has been carried out on PubMed for obtaining the information related to the therapeutic activities of curcumin for adenocarcinomas therapy. The literature search resulted in many in vitro and some in vivo studies that evidenced the effectiveness of curcumin in modulating antitumor signaling pathways to treat adenocarcinomas. In addition, curcumin-loaded nanoplatforms can improve the efficacy against tumor cells. The present review provides a comprehensive view of the therapeutic aspects of curcumin as a treatment for multiple human adenocarcinomas, which warrants further investigation in clinical settings.     

Inpatient insulin therapy

Background: Many diabetic, as well as nondiabetic, hospitalized patients develop hyperglycemia. Numerous studies have demonstrated that critically ill, as well as noncritically ill, hospitalized patients who develop hyperglycemia are at increased risk for morbidity and mortality.Objective: The objective of this article was to review the risks associated with hyperglycemia in hospitalized patients, the biologic rationale for using insulin to prevent increases in glucose levels, and strategies for managing hyperglycemia in the hospital setting.Methods: We conducted a computerized search of biomedical journal literature from MEDLINE, PubMed, and Ovid published from 1994 to March 2008. We reviewed English-language original and review articles found under the subject headings “hospitalization and insulin therapy,” “inpatient diabetes and complications,” and “insulin and inflammation.”Results: More than 200 references were found during the literature search. According to the literature, the adverse outcomes that are associated with hyperglycemia may be attributed to the inflammatory and pro-oxidant effects of elevated glucose levels. The use of insulin, which has anti-inflammatory, vasodilatory, and antioxidant properties as well as the ability to inhibit lipolysis and platelet aggregation, can prevent many of these adverse outcomes.Conclusions: Hospitals should have protocols in place for using insulin to treat and prevent hyperglycemia. Subcutaneous insulin may be used for both purposes in most noncritically ill patients, whereas intravenous infusion of insulin is preferred in critically ill patients.     

GoSurfer

The analysis of complex patterns of gene regulation is central to understanding the biology of cells, tissues and organisms. Patterns of gene regulation pertaining to specific biological processes can be revealed by a variety of experimental strategies, particularly microarrays and other highly parallel methods, which generate large datasets linking many genes. Although methods for detecting gene expression have improved substantially in recent years, understanding the physiological implications of complex patterns in gene expression data is a major challenge. This article presents GoSurfer, an easy-to-use graphical exploration tool with built-in statistical features that allow a rapid assessment of the biological functions represented in large gene sets. GoSurfer takes one or two list(s) of gene identifiers (Affymetrix probe set ID) as input and retrieves all the Gene Ontology (GO) terms associated with the input genes. GoSurfer visualises these GO terms in a hierarchical tree format. With GoSurfer, users can perform statistical tests to search for the GO terms that are enriched in the annotations of the input genes. These GO terms can be highlighted on the GO tree. Users can manipulate the GO tree in various ways and interactively query the genes associated with any GO term. The user-generated graphics can be saved as graphics files, and all the GO information related to the input genes can be exported as text files. AVAILABILITY: GoSurfer is a Windows-based program freely available for noncommercial use and can be downloaded at http://www.gosurfer.org. Datasets used to construct the trees shown in the figures in this article are available at http://www.gosurfer.org/download/GoSurfer.zip.     

A fast GNU method to draw accurate scientific illustrations for taxonomy

Nowadays only digital figures are accepted by the most important journals of taxonomy. These may be produced by scanning conventional drawings, made with high precision technical ink-pens, which normally use capillary cartridge and various line widths. Digital drawing techniques that use vector graphics, have already been described in literature to support scientists in drawing figures and plates for scientific illustrations; these techniques use many different software and hardware devices. The present work gives step-by-step instructions on how to make accurate line drawings with a new procedure that uses bitmap graphics with the GNU Image Manipulation Program (GIMP). This method is noteworthy: it is very accurate, producing detailed lines at the highest resolution; the raster lines appear as realistic ink-made drawings; it is faster than the traditional way of making illustrations; everyone can use this simple technique; this method is completely free as it does not use expensive and licensed software and it can be used with different operating systems. The method has been developed drawing figures of terrestrial isopods and some examples are here given.     

BET proteins: Investigating BRDT as a potential target for male contraception

While many contraception options are available for women, birth control methods for men are limited to condoms and vasectomy. Past research into male contraceptives has focused on hormonal options but the associated side effects have thus far precluded this method from reaching the market. Non-hormonal male contraceptives and vas occlusion have also been explored, but to date no method has progressed past clinical testing. Recent interest in epigenetic research has unveiled a new potential non-hormonal male contraceptive target: the testis-specific bromodomain BRDT. Potent inhibitors for bromodomain-containing proteins are described in the literature, but a BRDT-specific compound has yet to be designed, prepared and tested. The high similarity between bromodomain proteins of the BET family makes development of selective and specific inhibitors both difficult and necessary. Selective inhibition of BRDT by a small molecule is an exciting new target in the search for a new non-hormonal male contraceptive.     

DeTEXT: A Database for Evaluating Text Extraction from Biomedical Literature Figures

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. Since text is a rich source of information in figures, automatically extracting such text may assist in the task of mining figure information. A high-quality ground truth standard can greatly facilitate the development of an automated system. This article describes DeTEXT: A database for evaluating text extraction from biomedical literature figures. It is the first publicly available, human-annotated, high quality, and large-scale figure-text dataset with 288 full-text articles, 500 biomedical figures, and 9308 text regions. This article describes how figures were selected from open-access full-text biomedical articles and how annotation guidelines and annotation tools were developed. We also discuss the inter-annotator agreement and the reliability of the annotations. We summarize the statistics of the DeTEXT data and make available evaluation protocols for DeTEXT. Finally we lay out challenges we observed in the automated detection and recognition of figure text and discuss research directions in this area. DeTEXT is publicly available for downloading at http://prir.ustb.edu.cn/DeTEXT/.     

Umbilical metastases: current viewpoint

BACKGROUND: Umbilical metastases from a malignant neoplasm, also termed Sister Mary Joseph's nodule, are not commonly reported in the English literature, and they have usually been considered as a sign of a poor prognosis for the patient. The present article reports on the current view point on umbilical metastasis besides discussing the epidemiology, clinical presentation, pathophysiology and treatment. METHOD: A search of Pubmed was carried out using the term 'umblic*' and 'metastases' or metastasis' revealed no references. Another search was made using the term "Sister Joseph's nodule" or sister Joseph nodule" that revealed 99 references. Of these there were 14 review articles, however when the search was limited to English language it yielded only 20 articles. Articles selected from these form the basis of this report along with cross references. RESULTS: The primary lesions usually arise from gastrointestinal or genitourinary tract malignancies and may be the presenting symptom or sign of a primary tumour in an unknown site. CONCLUSION: A careful evaluation of all umbilical lesions, including an early biopsy if appropriate, is recommended. Recent studies suggest an aggressive surgical approach combined with chemotherapy for such patients may improve survival.     

Unipolar late-onset depression: A comprehensive review

BACKGROUND: The older population increases all over the world and so also does the number of older psychiatric patients, which manifest certain specific and unique characteristics. The aim of this article is to provide a comprehensive review of the international literature on unipolar depression with onset at old age. METHODS: The authors reviewed several pages and books relevent to the subject but did not search the entire literature because of it's overwhelming size. They chose to review those considered most significant. RESULTS: The prevalence of major depression is estimated to be 2% in the general population over 65 years of age. The clinical picture of geriatric depression differs in many aspects from depression in younger patients. It is not yet clear whether it also varies across cultures and different socio-economic backgrounds. Biological data suggest that it is associated with an increased severity of subcortical vascular disease and greater impairment of cognitive performance. Many authors consider the existence of a somatic disorder to be related to the presence of depression in late life, even constituting a negative prognostic factor for the outcome of depression. Most studies support the opinion that geriatric depression carries a poorer prognosis than depression in younger patients. The therapeutic intervention includes pharmacotherapy, mainly with antidepressants, which is of established value and psychotherapy which is not equally validated. CONCLUSION: A significant number of questions regarding the assessment and treatment of geriatric depression remain unanswered, empirical data are limited, and further research is necessary.     

FigSearch: a figure legend indexing and classification system

FigSearch is a prototype text-mining and classification system for figures from any corpus of full-text biological papers. The system allows users to search for figures that contain genes of interest and illustrate protein interactions. The retrieved figures are ranked by a score representing the likelihood to be of a certain type, in this case, schematic illustrations of protein interactions and signaling events. The system contains a Web interface for search, a module for classification of figures based on vector representations of figure legends and a module for indexing gene names. In a preliminary validation, the FigSearch system showed satisfactory performance according to domain experts in providing the most relevant graphical representations. This strategy may be easily extended to other figure types. Moreover, as more full-text data become available, such a system will find increased usefulness in identifying and presenting compressed biological knowledge. AVAILABILITY: A searchable Web interface, FigSearch, is accessible via http://pubgeneserver.uio.no/figsearch/ for all figures from the available corpus.     

How the slot machine led biologists astray

An extensive search, in the literature, for experiments in which a new enzyme did evolve, produced only two: the first by Campbell et al. in 1973; the second by Hall & Hartl in 1974. Since the experiments provide the only means of gaining a first hand view of how new enzymes evolve, they were scrutinized, minutely, with the objective of ascertaining whether the mutations involved were random or non-random. We report here that they were non-random. Further, with the benefit of hindsight, we highlight the weakness in the insights and the reasoning which produced the belief that new enzymes evolve purely by chance.     

Single molecule measurements and biological motors

Recent technological advances in lasers and optical detectors have enabled a variety of new, single molecule technologies to be developed. Using intense and highly collimated laser light sources in addition to super-sensitive cameras, the fluorescence of single fluorophores can now be imaged in aqueous solution. Also, laser optical tweezers have enabled the piconewton forces produced by pair of interacting biomolecules to be measured directly. However, for a researcher new to the field to begin to use such techniques in their own research might seem a daunting prospect. Most of the equipment that is in use is custom-built. However, most of the equipment is essence fairly simple and the aim of this article is to provide an entry point to the field for a newcomer. It focuses mainly on those practical aspects which are not particularly well covered in the literature, and aims to provide an overview of the field as a whole with references and web links to more detailed sources elsewhere. Indeed, the opportunity to publish an article such as this on the Internet affords many new opportunities (and more space!) for presenting scientific ideas and information. For example, we have illustrated the nature of optical trap data with an interactive Java simulation; provided links to relevant web sites and technical documents, and included a large number of colour figures and plots. Our group’s research focuses on molecular motors, and the bias of this article reflects this. It turns out that molecular motors have been a paradigm (or prototype) for single molecule research and the field has seen a rapid development in the techniques. It is hoped that the methods described here will be broadly applicable to other biological systems.This is an interactive contribution, which can be accessed at:     

Microorganisms and man. Various characteristics of their coexistence at present

Modern data of literature on microbial associations and their role in human health and diseases are presented. As pointed out in this work, the characteristic feature of the XX century is the emergence and the re-emergence of 36 new infections. The emergence of many infections is associated with such factors as the increased migration of the population, ecological environmental disasters, etc. Grounds for a new view on the etiology of a number of chronic somatic diseases are given. The task of preparation development for the immunoprophylaxis of 25-30 infections has been set by WHO as its target for the year 2025. Prospects of new approaches to the development of new generation vaccines against bacterial, viral and parasitic infections, including HIV/AIDS, tuberculosis, virus hepatitides, malaria, etc., are shown.