A biomedical information source: the National Clearinghouse for Alcohol Information.

The National Clearinghouse for Alcohol Information (NCALI) is an information resource developed by the National Institute on Alcohol Abuse and Alcoholism of the U.S. Department of Health, Education, and Welfare. It provides numerous alcohol-related information services to professionals in a wide spectrum of biomedical and other disciplines, services that are designed to aid information users in the discrimination and selection of useful literature from the volumes of available information. One such service will provide the biomedical professional, working in an alcohol-related field, with announcements of recent information in categories that he selects from 110 possible fields of interest. Another information service is the quality evaluation of technical documents. The quality evaluation system, which is under continuing development and refinement, serves the literature user by providing a literature quality prescreening process designed to aid users in their literature review and monitoring activities. Additional information services provided by the clearinghouse include Grouped Interest Guides, Subject Area Bibliographies, a quarterly magazine and a periodic general interest information service, and a wide range of special publications. Reference services provide a suitable depth of response to information requests through services that range from assemblages of standard information materials, such as pamphlets and similar publications, to automated data base searches for more technically oriented information requests.     

Student-generated instructional videos facilitate learning through positive emotions

The central focus of this study is a learning method in which university students produce instructional videos about the content matter as part of their learning process, combined with other learning assignments. The rationale for this is to promote a more multimodal pedagogy, and to provide students opportunities for a more learner-centred, motivating, active, engaging and productive role in their learning process. As such we designed a ‘video course’ where the students needed to produce an instructional video which could be used for university teaching. In addition to producing the video, the students needed to write a literature review of the topic of the video and a learning journal. At the end of the course the students filled a questionnaire regarding their learning and emotions during the project. Based on the students’ subjective answers, it appeared that producing a video, combined with writing the literature review can be an efficient way of learning. Most students found the project emotionally very positive and regarded it motivating to work on a video which they knew will have use in the future. This research suggests that a multimodal video project in a higher education setting enhances learning through increased motivation and positive emotions.     

Separating equilibria in continuous signalling games

Much of the literature on costly signalling theory concentrates on separating equilibria of continuous signalling games. At such equilibria, every signaller sends a distinct signal, and signal receivers are able to exactly infer the signaller's condition from the signal sent. In this paper, we introduce a vector-field solution method that simplifies the process of solving for separating equilibria. Using this approach, we show that continuous signalling games can have low-cost separating equilibria despite conflicting interests between signaller and receiver. We find that contrary to prior arguments, honesty does not require wasteful signals. Finally, we examine signalling games in which different signallers have different minimal-cost signals, and provide a mathematical justification for the argument that even non-signalling traits will be exaggerated beyond their phenotypic optimum when they are used by other individuals to judge condition or quality.     

Predicting species distributions for conservation decisions

Species distribution models (SDMs) are increasingly proposed to support conservation decision making. However, evidence of SDMs supporting solutions for on‐ground conservation problems is still scarce in the scientific literature. Here, we show that successful examples exist but are still largely hidden in the grey literature, and thus less accessible for analysis and learning. Furthermore, the decision framework within which SDMs are used is rarely made explicit. Using case studies from biological invasions, identification of critical habitats, reserve selection and translocation of endangered species, we propose that SDMs may be tailored to suit a range of decision‐making contexts when used within a structured and transparent decision‐making process. To construct appropriate SDMs to more effectively guide conservation actions, modellers need to better understand the decision process, and decision makers need to provide feedback to modellers regarding the actual use of SDMs to support conservation decisions. This could be facilitated by individuals or institutions playing the role of ‘translators’ between modellers and decision makers. We encourage species distribution modellers to get involved in real decision‐making processes that will benefit from their technical input; this strategy has the potential to better bridge theory and practice, and contribute to improve both scientific knowledge and conservation outcomes.     

Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup

MOTIVATION: The biological literature is a major repository of knowledge. Many biological databases draw much of their content from a careful curation of this literature. However, as the volume of literature increases, the burden of curation increases. Text mining may provide useful tools to assist in the curation process. To date, the lack of standards has made it impossible to determine whether text mining techniques are sufficiently mature to be useful. RESULTS: We report on a Challenge Evaluation task that we created for the Knowledge Discovery and Data Mining (KDD) Challenge Cup. We provided a training corpus of 862 articles consisting of journal articles curated in FlyBase, along with the associated lists of genes and gene products, as well as the relevant data fields from FlyBase. For the test, we provided a corpus of 213 new ('blind') articles; the 18 participating groups provided systems that flagged articles for curation, based on whether the article contained experimental evidence for gene expression products. We report on the evaluation results and describe the techniques used by the top performing groups.     

A survey of EPA/OPP and open literature on selected pesticide chemicals. II. Mutagenicity and carcinogenicity of selected chloroacetanilides and related compounds.

With this effort, we continue our examination of data on selected pesticide chemicals and their related analogues that have been presented to the U.S. Environmental Protection Agency's (USEPA's) Office of Pesticide Programs (OPP). This report focuses on a group of selected chloroacetanilides and a few related compounds. As part of the registration process for pesticidal chemicals, interested parties (registrants) must submit toxicity information to support the registration including both mutagenicity and carcinogenicity data. Although this information is available to the public via Freedom of Information (FOI) requests to the OPP, publication in the scientific literature allows greater dissemination and examination of the data. For this Special Issue, graphic profiles have been prepared of the mutagenicity and carcinogenicity data available in the submissions to OPP. Also, a discussion is presented about how toxicity data are used to help establish tolerances (limits of pesticide residues in foods). The mutagenicity results submitted by registrants are supplemented by data on these chemicals from the open literature to provide a full perspective of their genetic toxicology. The group of chloroacetanilides reviewed here display a consistent pattern of mutagenic activity, probably mediated via metabolites. This mutagenic activity is a mechanistically plausible factor in the development of tumors seen in experimental animals exposed to this class of chemicals.     

Phenotypic plasticity in evolutionary rescue experiments

Population persistence in a new and stressful environment can be influenced by the plastic phenotypic responses of individuals to this environment, and by the genetic evolution of plasticity itself. This process has recently been investigated theoretically, but testing the quantitative predictions in the wild is challenging because (i) there are usually not enough population replicates to deal with the stochasticity of the evolutionary process, (ii) environmental conditions are not controlled, and (iii) measuring selection and the inheritance of traits affecting fitness is difficult in natural populations. As an alternative, predictions from theory can be tested in the laboratory with controlled experiments. To illustrate the feasibility of this approach, we briefly review the literature on the experimental evolution of plasticity, and on evolutionary rescue in the laboratory, paying particular attention to differences and similarities between microbes and multicellular eukaryotes. We then highlight a set of questions that could be addressed using this framework, which would enable testing the robustness of theoretical predictions, and provide new insights into areas that have received little theoretical attention to date.     

Informed consent for controlled human infection studies in low- and middle-income countries: Ethical challenges and proposed solutions

In controlled human infection studies (CHIs), participants are deliberately exposed to infectious agents in order to better understand the mechanism of infection or disease and test therapies or vaccines. While most CHIs have been conducted in high-income countries, CHIs have recently been expanding into low- and middle-income countries (LMICs). One potential ethical concern about this expansion is the challenge of obtaining the voluntary informed consent of participants, especially those who may not be literate or have limited education. In some CHIs in LMICs, researchers have attempted to address this potential concern by limiting access to literate or educated populations. In this paper, we argue that this practice is unjustified, as it does not increase the chances of obtaining valid informed consent and therefore unfairly excludes illiterate populations and populations with lower education. Instead, we recommend that investigators improve the informed consent process by drawing on existing data on obtaining informed consent in these populations and interventions aimed at improving their understanding. Based on a literature review, we provide concrete suggestions for how to follow this recommendation and ensure that populations with lower literacy or education are given a fair opportunity to protect their rights and interests in the informed consent process.     

Product-Oriented Environmental Management: Lessons from Total Quality Management

Environmental management issues are becoming ever more prominent in business, and their focus is broadening from process orientation toward product orientation. Until now, little attention has been paid to an organizational focus on the environmental performance of products. This article therefore considers product-oriented environmental management (POEM), an approach to organizing and operating a firm in such a way that improving the environmental performance of its products and processes becomes an integrated part of operations and strategy. First, the POEM concept is introduced. Because this concept addresses some issues similar to those of quality management, the possibilities of using insights from total quality management (TQM) in developing POEM are investigated. Based on an overview of the literature and conceptual studies of TQM, a coherent set of several elements are described that can contribute to the organization of POEM. These elements are grouped in a framework, the POEM matrix, which can be used to guide research within this emerging area of organizing for the environmental characteristics of products. This matrix could also provide guidance to practitioners by delivering an integrated perspective on the organizational elements that are conducive to organizing POEM. An example from case study research in the chemical industry illustrates such an application of the matrix.     

The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world

The amount of data currently being generated by proteomics laboratories around the world is increasing exponentially, making it ever more critical that scientists are able to exchange, compare and retrieve datasets when re-evaluation of their original conclusions becomes important. Only a fraction of this data is published in the literature and important information is being lost every day as data formats become obsolete. The Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) was tasked with the creation of data standards and interchange formats to allow both the exchange and storage of such data irrespective of the hardware and software from which it was generated. This article will provide an update on the work of this group, the creation and implementation of these standards and the standards-compliant data repositories being established as result of their efforts.     

Recovery of value added products from rice husk ash to explore an economic way for recycle and reuse of agricultural waste

Rice husk ash (RHA) is the major by-product left after the burning of rice husk, which is profusely present throughout the process of the rice milling. The burnt rice husk, as RHA, in turn causes more environmental pollution and its disposal becomes a difficult problem, hence requiring serious attention from the scientific community regarding its disposal and proper reuse if possible. The major economic reason for recycling the ash is the value added products which can be generated from it. The focus is on the use of RHA as adsorbent and subsequent silica production owing to the fact that the ash is mainly composed of carbon and silica. As regards other potential applications of ash, research is still going on and some of the products, which are under development phase, have also been brought to limelight in this review. This literature review provides an effective scheme to utilize RHA and discussed process pathway for economically valuable products to provide a solution to the problem associated with its proper disposal through superior recycle of this agriculture waste.     

Distance sampling surveys: using components of detection and total error to select among approaches

Wildlife population estimators often require formal adjustment for imperfect detection of individuals during surveys. Conventional distance sampling (CDS) and its extensions (mark-recapture distance sampling [MRDS], temporary emigration distance sampling [TEDS]) are popular approaches for producing unbiased estimators of wildlife abundance. However, despite extensive discussion and development of distance sampling theory in the literature, deciding which of these alternatives is most appropriate for a particular scenario can be confusing. Some of this confusion may stem from an incomplete understanding of how each approach addresses the components of the detection process. Here we describe the proper application of CDS, MRDS, and TEDS approaches and use applied examples to help clarify their differing assumptions with respect to the components of the detection process. To further aid the practitioner, we summarize the differences in a decision tree that can be used to identify cases where a more complex alternative (e.g., MRDS or TEDS) may be appropriate for a given survey application. Although the more complex approaches can account for additional sources of bias, in practical applications one also must consider estimator precision. Therefore, we also review the concept of total estimator error in the context of comparing competing methods for a given application to aid in the selection of the most appropriate distance sampling approach. Finally, we detail how the use of more advanced techniques (i.e., informed priors, open-population distance sampling models, and integrated modeling approaches) can further reduce total estimator error by leveraging information from existing and ongoing data collection. By synthesizing the existing literature on CDS, MRDS, TEDS and their extensions, in conjunction with the concepts of total estimator error and the components of the detection process, we provide a comprehensive guide that can be used by the practitioner to more efficiently, effectively, and appropriately apply distance sampling in a variety of settings.     

Mental Ill Health,Recovery and the Family Assemblage

The recovery approach is now among the most influential paradigms shaping mental health policy and practice across the English-speaking world. While recovery is normally presented as a deeply personal process, critics have challenged the individualism underpinning this view. A growing literature on “family recovery” explores the ways in which people, especially parents with mental ill health, can find it impossible to separate their own recovery experiences from the processes of family life. While sympathetic to this literature, we argue that it remains limited by its anthropocentricity, and therefore struggles to account for the varied human and nonhuman entities and forces involved in the creation and maintenance of family life. The current analysis is based on an ethnographic study conducted in Australia, which focused on families in which the father experiences mental ill health. We employ the emerging concept of the “family assemblage” to explore how the material, social, discursive and affective components of family life enabled and impeded these fathers’ recovery trajectories. Viewing families as heterogeneous assemblages allows for novel insights into some of the most basic aspects of recovery, challenging existing conceptions of the roles and significance of emotion, identity and agency in the family recovery process.     

黄酒酒曲微生物及其代谢产物的研究进展

黄酒发酵过程中的微生物主要来源于酒曲的添加,这些微生物的相互作用以及代谢产物对黄酒的品质和风格具有重要作用。本文在检索近年来黄酒酒曲微生物研究相关文献资料的基础上,综述了黄酒酒曲中细菌、真菌的多样性,制曲过程中微生物的动态变化,酒曲中主要微生物的代谢产物对黄酒品质的作用以及微生物代谢产生安全风险类物质的研究现状,并对今后的研究工作进行了展望,旨在为黄酒微生物的深入研究提供参考。     

Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species

Evolutionary biologists have often suggested that ecology is important in speciation, in that natural selection may drive adaptive divergence between lineages that inhabit different environments. I suggest that it is the tendency of lineages to maintain their ancestral ecological niche (phylogenetic niche conservatism) and their failure to adapt to new environments which frequently isolates incipient species and begins the process of speciation. Niche conservatism may be an important and widespread component of allopatric speciation but is largely unstudied. The perspective outlined here suggests roles for key microevolutionary processes (i.e., natural selection, adaptation) that are strikingly different from those proposed in previous literature on ecology and speciation. Yet, this perspective is complementary to the traditional view because it focuses on a different temporal stage of the speciation process.     

A curated census of autophagy-modulating proteins and small molecules: Candidate targets for cancer therapy

Autophagy, a programmed process in which cell contents are delivered to lysosomes for degradation, appears to have both tumor-suppressive and tumor-promoting functions; both stimulation and inhibition of autophagy have been reported to induce cancer cell death, and particular genes and proteins have been associated both positively and negatively with autophagy. To provide a basis for incisive analysis of those complexities and ambiguities and to guide development of new autophagy-targeted treatments for cancer, we have compiled a comprehensive, curated inventory of autophagy modulators by integrating information from published siRNA screens, multiple pathway analysis algorithms, and extensive, manually curated text-mining of the literature. The resulting inventory includes 739 proteins and 385 chemicals (including drugs, small molecules, and metabolites). Because autophagy is still at an early stage of investigation, we provide extensive analysis of our sources of information and their complex relationships with each other. We conclude with a discussion of novel strategies that could potentially be used to target autophagy for cancer therapy.     

Biomedical question answering using semantic relations

Background

The proliferation of the scientific literature in the field of biomedicine makes it difficult to keep abreast of current knowledge, even for domain experts. While general Web search engines and specialized information retrieval (IR) systems have made important strides in recent decades, the problem of accurate knowledge extraction from the biomedical literature is far from solved. Classical IR systems usually return a list of documents that have to be read by the user to extract relevant information. This tedious and time-consuming work can be lessened with automatic Question Answering (QA) systems, which aim to provide users with direct and precise answers to their questions. In this work we propose a novel methodology for QA based on semantic relations extracted from the biomedical literature.

Results

We extracted semantic relations with the SemRep natural language processing system from 122,421,765 sentences, which came from 21,014,382 MEDLINE citations (i.e., the complete MEDLINE distribution up to the end of 2012). A total of 58,879,300 semantic relation instances were extracted and organized in a relational database. The QA process is implemented as a search in this database, which is accessed through a Web-based application, called SemBT (available at http://sembt.mf.uni-lj.si). We conducted an extensive evaluation of the proposed methodology in order to estimate the accuracy of extracting a particular semantic relation from a particular sentence. Evaluation was performed by 80 domain experts. In total 7,510 semantic relation instances belonging to 2,675 distinct relations were evaluated 12,083 times. The instances were evaluated as correct 8,228 times (68%).

Conclusions

In this work we propose an innovative methodology for biomedical QA. The system is implemented as a Web-based application that is able to provide precise answers to a wide range of questions. A typical question is answered within a few seconds. The tool has some extensions that make it especially useful for interpretation of DNA microarray results.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0365-3) contains supplementary material, which is available to authorized users.     

Reducing complexity when studying seed dispersal at community scales: a functional classification of vertebrate seed dispersers in tropical forests

The process of seed dispersal has a profound effect on vegetation structure and diversity in tropical forests. However, our understanding of the process and our ability to predict its outcomes at a community scale are limited by the frequently large number of interactions associated with it. Here, we outline an approach to dealing with this complexity that reduces the number of unique interactions considered by classifying the participants according to their functional similarity. We derived a classification of dispersers based on the nature of the dispersal service they provide to plants. We described the quantities of fruit handled, the quality of handling and the diversity of plants to which the service is provided. We used ten broad disperser traits to group 26 detailed measures for each disperser. We then applied this approach to vertebrate dispersers in Australia’s tropical forests. Using this we also develop a classification that may be more generally applicable. For each disperser, data relating to each trait was obtained either from the field or published literature. First, we identified dispersers whose service outcomes were so distinct that statistical analysis was not required and assigned them to functional groups. The remaining dispersers were assigned to functional groups using cluster analysis. The combined processes created 15 functional groups from 65 vertebrate dispersers in Australian tropical forests. Our approach—grouping dispersers on the basis of the type of dispersal service provided and the fruit types it is provided to—represents a means of reducing the complexity encountered in tropical seed dispersal systems and could be effectively applied in community level studies. It also represents a useful tool for exploring changes in dispersal services when the distribution and abundance of animal populations change due to human impacts. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Menopause and the transmission of women's knowledge: African American and white women's perspectives

Recent menopause literature does not sufficiently explore women's attitudes on the transmission of knowledge about menopause from sources other than biomedical providers. Analysis of 70 interviews with African American and Euro-American women shows that their perceptions of the intergenerational transfer of knowledge about menopause from their mothers shaped their attitudes toward menopause and the health-care technologies surrounding it. African American women who grew up in the segregated South frequently expressed that their mothers provided them with the knowledge and power to negotiate difficulties during the menopausal process, while many middle-class Euro-American women expressed that their mothers did not. Drawing on literature that examines the effects of race, class, and kinship on mother/daughter relationships, this article explores the reasons for this divergence.     

Intrinsic asymmetries of amino acid enantiomers and their peptides: a possible role in the origin of biochirality

L-amino acids and D-carbohydrates were incorporated into the first forms of life over 3.5 billion years ago, presumably from racemic mixtures of organic solutes produced by abiotic synthetic pathways. The process by which this choice occurred has not been established, but a consensus view is that it was a chance event, such that life could equally well have used D-amino acids and L sugars. In this review we will explore a second, less plausible alternative that minute differences in the physical properties of certain enantiomers made it more likely that L-amino acids and D-carbohydrates would be incorporated into early life. By all classical criteria, chiral isomers are perfect mirror image structures and, therefore, are expected to be identical in their macroscopic properties. However, scattered reports in the literature suggest that there may be slight differences in the physical properties of L- and D-amino acids and their polymers, which could lead to a preferred incorporation of L-amino acids into primitive forms of life. Here we present a literature survey of this issue and discuss its possible role in the origin of biochirality.