WorldWideScience

Sample records for level biology pubmed

  1. Enriching PubMed Related Article Search with Sentence Level Co-citations

    Science.gov (United States)

    Tran, Nam; Alves, Pedro; Ma, Shuangge

    2009-01-01

    PubMed related article links identify closely related articles and enhance our ability to navigate the biomedical literature. They are derived by calculating the word similarity between two articles, relating articles with overlapping word content. In this paper, we propose to enrich PubMed with a new type of related article link based on citations within a single sentence (i.e. sentence level co-citations or SLCs). Using different similarity metrics, we demonstrated that articles linked by SLCs are highly related. We also showed that only half of SLCs are found among PubMed related article links. Additionally, we discuss how the citing sentence of an SLC explains the connection between two articles. PMID:20351935

  2. Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS.

    Science.gov (United States)

    Yu, Hwanjo; Kim, Taehoon; Oh, Jinoh; Ko, Ilhwan; Kim, Sungchul; Han, Wook-Shin

    2010-04-16

    Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results. Researchers have applied machine learning techniques to find relevant articles by ranking the articles according to the learned relevance function. However, the process of learning and ranking is usually done offline without integrated with the keyword queries, and the users have to provide a large amount of training documents to get a reasonable learning accuracy. This paper proposes a novel multi-level relevance feedback system for PubMed, called RefMed, which supports both ad-hoc keyword queries and a multi-level relevance feedback in real time on PubMed. RefMed supports a multi-level relevance feedback by using the RankSVM as the learning method, and thus it achieves higher accuracy with less feedback. RefMed "tightly" integrates the RankSVM into RDBMS to support both keyword queries and the multi-level relevance feedback in real time; the tight coupling of the RankSVM and DBMS substantially improves the processing time. An efficient parameter selection method for the RankSVM is also proposed, which tunes the RankSVM parameter without performing validation. Thereby, RefMed achieves a high learning accuracy in real time without performing a validation process. RefMed is accessible at http://dm.postech.ac.kr/refmed. RefMed is the first multi-level relevance feedback system for PubMed, which achieves a high accuracy with less feedback. It effectively learns an accurate relevance function from the user's feedback and efficiently processes the function to return relevant articles in real time.

  3. Content-rich biological network constructed by mining PubMed abstracts

    Directory of Open Access Journals (Sweden)

    Sharp Burt M

    2004-10-01

    Full Text Available Abstract Background The integration of the rapidly expanding corpus of information about the genome, transcriptome, and proteome, engendered by powerful technological advances, such as microarrays, and the availability of genomic sequence from multiple species, challenges the grasp and comprehension of the scientific community. Despite the existence of text-mining methods that identify biological relationships based on the textual co-occurrence of gene/protein terms or similarities in abstract texts, knowledge of the underlying molecular connections on a large scale, which is prerequisite to understanding novel biological processes, lags far behind the accumulation of data. While computationally efficient, the co-occurrence-based approaches fail to characterize (e.g., inhibition or stimulation, directionality biological interactions. Programs with natural language processing (NLP capability have been created to address these limitations, however, they are in general not readily accessible to the public. Results We present a NLP-based text-mining approach, Chilibot, which constructs content-rich relationship networks among biological concepts, genes, proteins, or drugs. Amongst its features, suggestions for new hypotheses can be generated. Lastly, we provide evidence that the connectivity of molecular networks extracted from the biological literature follows the power-law distribution, indicating scale-free topologies consistent with the results of previous experimental analyses. Conclusions Chilibot distills scientific relationships from knowledge available throughout a wide range of biological domains and presents these in a content-rich graphical format, thus integrating general biomedical knowledge with the specialized knowledge and interests of the user. Chilibot http://www.chilibot.net can be accessed free of charge to academic users.

  4. Advancing PubMed?

    DEFF Research Database (Denmark)

    Wildgaard, Lorna Elizabeth; Lund, Haakon

    2016-01-01

    the efficiency of biomedical literature searches. PubMed remains the primary resource for biomedical literature, and as PubMed makes the Medline data and Entrez PubMed Programming utilities freely available, any developer can produce alternative tools to search the database. The authors question if PubMed still...... provides the superior search interface for systematic searches or if the innovativeness of third-party tools provide alternatives worth considering. The paper aims to discuss these issues. Design/methodology/approach In all, 76 third-party tools that build on PubMed content were identified in a PubMed...... search and in published studies known to the authors. Only tools that provided free access to the broad PubMed content and designed specifically to enhance the search were included, reducing the set to 16 tools. The functionality of each tool within the scenario of a systematic search was compared across...

  5. Relative Citation Ratio of Top Twenty Macedonian Biomedical Scientists in PubMed: A New Metric that Uses Citation Rates to Measure Influence at the Article Level.

    Science.gov (United States)

    Spiroski, Mirko

    2016-06-15

    The aim of this study was to analyze relative citation ratio (RCR) of top twenty Macedonian biomedical scientists with a new metric that uses citation rates to measure influence at the article level. Top twenty Macedonian biomedical scientists were identified by GoPubMed on the base of the number of deposited abstracts in PubMed, corrected with the data from previously published paper, and completed with the Macedonian biomedical scientists working in countries outside the Republic of Macedonia, but born or previously worked in the country. iCite was used as a tool to access a dashboard of bibliometrics for papers associated with a portfolio. The biggest number of top twenty Macedonian biomedical scientists has RCR lower than one. Only four Macedonian biomedical scientists have bigger RCR in comparison with those in PubMed. The most prominent RCR of 2.29 has Rosoklija G. RCR of the most influenced individual papers deposited in PubMed has shown the biggest value for the paper of Efremov D (35.19). This paper has the biggest number of authors (860). It is necessary to accept top twenty Macedonian biomedical scientists as an example of new metric that uses citation rates to measure influence at the article level, rather than qualification of the best Macedonian biomedical scientists.

  6. PubMed

    Data.gov (United States)

    U.S. Department of Health & Human Services — PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to...

  7. PubMed

    CERN Document Server

    PubMed is the National Library of Medicine's search service that provides access to over 10 million citations in MEDLINE, PreMEDLINE, and other related databases, with links to participating online journals.

  8. Low level radiation: biological effects

    International Nuclear Information System (INIS)

    Loken, M.K.

    1983-01-01

    It is imperative that physicians and scientists using radiations in health care delivery continue to assess the benefits derived, vs. potential risk, to patients and radiation workers being exposed to radiation in its various forms as part of our health delivery system. Insofar as possible we should assure our patients and ourselves that the benefits outweigh the potential hazards involved. Inferences as to the possible biological effects of low level radiation are generally based on extrapolations from those effects observed and measured following acute exposures to considerably higher doses of radiation. Thus, in order to shed light on the question of the possible biological effects of low level radiation, a wide variety of studies have been carried out using cells in culture and various species of plant and animal life. This manuscript makes reference to some of those studies with indications as to how and why the studies were done and the conclusions that might be drawn there from. In addition reference is made to the handling of this information by scientists, by environmentalists, and by the news media. Unfortunately, in many instances the public has been misled by what has been said and/or written. It is hoped that this presentation will provide an understandable and reasonable perspective on the various appropriate uses of radiation in our lives and how such uses do provide significant improvement in our health and in our quality of life

  9. Analyzing the Biology on the System Level

    OpenAIRE

    Tong, Wei

    2016-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

  10. SNAB: A New Advanced Level Biology Course

    Science.gov (United States)

    Reiss, Michael J.

    2005-01-01

    Of all the sciences, biology has probably made the most rapid progress in recent years and the need for this to be reflected in a new Advanced Level biology course has long been recognised in the UK. After wide-ranging consultation and successful piloting in over 50 schools and colleges in England and Wales, the new Salters-Nuffield Advanced…

  11. Structural Biology for A-Level Students

    Science.gov (United States)

    Philip, Judith

    2013-01-01

    The relationship between the structure and function of proteins is an important area in biochemistry. Pupils studying A-level Biology are introduced to the four levels of protein structure (primary, secondary, tertiary and quaternary) and how these can be used to describe the progressive folding of a chain of amino acid residues to a final,…

  12. Relative Citation Ratio of Top Twenty Macedonian Biomedical Scientists in PubMed: A New Metric that Uses Citation Rates to Measure Influence at the Article Level

    Directory of Open Access Journals (Sweden)

    Mirko Spiroski

    2016-06-01

    Conclusion: It is necessary to accept top twenty Macedonian biomedical scientists as an example of new metric that uses citation rates to measure influence at the article level, rather than qualification of the best Macedonian biomedical scientists.

  13. Hologenomics: Systems-Level Host Biology.

    Science.gov (United States)

    Theis, Kevin R

    2018-01-01

    The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.

  14. Towards PubMed 2.0.

    Science.gov (United States)

    Fiorini, Nicolas; Lipman, David J; Lu, Zhiyong

    2017-10-30

    Staff from the National Center for Biotechnology Information in the US describe recent improvements to the PubMed search engine and outline plans for the future, including a new experimental site called PubMed Labs.

  15. Designing and Implementing a New Advanced Level Biology Course

    Science.gov (United States)

    Hall, Angela; Reiss, Michael J.; Rowell, Cathy; Scott, Anne

    2003-01-01

    Salters-Nuffield Advanced Biology is a new advanced level biology course, piloted from September 2002 in England with around 1200 students. This paper discusses the reasons for developing a new advanced biology course at this time, the philosophy of the project and how the materials are being written and the specification devised. The aim of the…

  16. A theory of biological relativity: no privileged level of causation.

    Science.gov (United States)

    Noble, Denis

    2012-02-06

    Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of 'biological relativity' and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined.

  17. Designing and implementing a new advanced level biology course.

    OpenAIRE

    Hall, Angela; Reiss, Michael; Rowell, Cathy; Scott, C.; Scott, Anne

    2003-01-01

    Salters-Nuffield Advanced Biology is a new advanced level biology course currently being piloted from September 2002 in England with around 1200 students. This paper discusses the reasons for developing a new advanced biology course at this time, the philosophy of the project and how the materials are being written and the specification devised. The aim of the project is to provide an up-to-date course that interests students, is considered appropriate by teachers and other professionals in b...

  18. Plant Systems Biology at the Single-Cell Level.

    Science.gov (United States)

    Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

    2017-11-01

    Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Inter-level relations in computer science, biology, and psychology

    NARCIS (Netherlands)

    Boogerd, F.; Bruggeman, F.; Jonker, C.M.; Looren de Jong, H.; Tamminga, A.; Treur, J.; Westerhoff, H.V.; Wijngaards, W.C.A.

    2002-01-01

    Investigations into inter-level relations in computer science, biology and psychology call for an empirical turn in the philosophy of mind. Rather than concentrate on a priori discussions of inter-level relations between 'completed' sciences, a case is made for the actual study of the way

  20. Inter-level relations in computer science, biology and psychology

    NARCIS (Netherlands)

    Boogerd, F.C.; Bruggeman, F.J.; Jonker, C.M.; Looren De Jong, H.; Tamminga, A.M.; Treur, J.; Westerhoff, H.V.; Wijngaards, W.C.A.

    2002-01-01

    Investigations into inter-level relations in computer science, biology and psychology call for an empirical turn in the philosophy of mind. Rather than concentrate on a priori discussions of inter-level relations between "completed" sciences, a case is made for the actual study of the way

  1. Inter-level relations in computer science, biology, and psychology

    NARCIS (Netherlands)

    Boogerd, Fred; Bruggeman, Frank; Jonker, Catholijn; Looren de Jong, Huib; Tamminga, Allard; Treur, Jan; Westerhoff, Hans; Wijngaards, Wouter

    2002-01-01

    Investigations into inter-level relations in computer science, biology and psychology call for an *empirical* turn in the philosophy of mind. Rather than concentrate on *a priori* discussions of inter-level relations between “completed” sciences, a case is made for the actual study of the way

  2. Predicting clicks of PubMed articles.

    Science.gov (United States)

    Mao, Yuqing; Lu, Zhiyong

    2013-01-01

    Predicting the popularity or access usage of an article has the potential to improve the quality of PubMed searches. We can model the click trend of each article as its access changes over time by mining the PubMed query logs, which contain the previous access history for all articles. In this article, we examine the access patterns produced by PubMed users in two years (July 2009 to July 2011). We explore the time series of accesses for each article in the query logs, model the trends with regression approaches, and subsequently use the models for prediction. We show that the click trends of PubMed articles are best fitted with a log-normal regression model. This model allows the number of accesses an article receives and the time since it first becomes available in PubMed to be related via quadratic and logistic functions, with the model parameters to be estimated via maximum likelihood. Our experiments predicting the number of accesses for an article based on its past usage demonstrate that the mean absolute error and mean absolute percentage error of our model are 4.0% and 8.1% lower than the power-law regression model, respectively. The log-normal distribution is also shown to perform significantly better than a previous prediction method based on a human memory theory in cognitive science. This work warrants further investigation on the utility of such a log-normal regression approach towards improving information access in PubMed.

  3. Multi-level and hybrid modelling approaches for systems biology.

    Science.gov (United States)

    Bardini, R; Politano, G; Benso, A; Di Carlo, S

    2017-01-01

    During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

  4. Biological intrusion of low-level-waste trench covers

    Science.gov (United States)

    Hakonson, T. E.; Gladney, E. S.

    The long-term integrity of low-level waste shallow land burialsites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. The need to consider biological processes as being potentially important in reducing the integrity of waste burial site cover treatment is demonstrated. One approach to limiting biological intrusion through the waste cover is to apply a barrier within the profile to limit root and animal penetration with depth. Experiments in the Los Alamos Experimental Engineered Test Facility were initiated to develop and evaluate biological barriers that are effective in minimizing intrusion into waste trenches. The experiments that are described employ four different candidate barrier materials of geologic origin. Experimental variables that will be evaluated, in addition to barrier type, are barrier depth and sil overburden depth.

  5. Towards Integration of Biological and Physiological Functions at Multiple Levels

    Directory of Open Access Journals (Sweden)

    Taishin eNomura

    2010-12-01

    Full Text Available An aim of systems physiology today can be stated as to establish logical and quantitative bridges between phenomenological attributes of physiological entities such as cells and organs and physical attributes of biological entities, i.e., biological molecules, allowing us to describe and better understand physiological functions in terms of underlying biological functions. This article illustrates possible schema that can be used for promoting systems physiology by integrating quantitative knowledge of biological and physiological functions at multiple levels of time and space with the use of information technology infrastructure. Emphasis will be made for systematic, modular, hierarchical, and standardized descriptions of mathematical models of the functions and advantages for the use of them.

  6. Teaching information literacy skills to sophomore-level biology majors.

    Science.gov (United States)

    Thompson, Leigh; Blankinship, Lisa Ann

    2015-05-01

    Many undergraduate students lack a sound understanding of information literacy. The skills that comprise information literacy are particularly important when combined with scientific writing for biology majors as they are the foundation skills necessary to complete upper-division biology course assignments, better train students for research projects, and prepare students for graduate and professional education. To help undergraduate biology students develop and practice information literacy and scientific writing skills, a series of three one-hour hands-on library sessions, discussions, and homework assignments were developed for Biological Literature, a one-credit, one-hour-per-week, required sophomore-level course. The embedded course librarian developed a learning exercise that reviewed how to conduct database and web searches, the difference between primary and secondary sources, source credibility, and how to access articles through the university's databases. Students used the skills gained in the library training sessions for later writing assignments including a formal lab report and annotated bibliography. By focusing on improving information literacy skills as well as providing practice in scientific writing, Biological Literature students are better able to meet the rigors of upper-division biology courses and communicate research findings in a more professional manner.

  7. Biological intrusion of low-level-waste trench covers

    International Nuclear Information System (INIS)

    Hakonson, T.E.; Gladney, E.S.

    1981-01-01

    The long-term integrity of low-level waste shallow land burial sites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. Past research on low-level waste shallow land burial methods has emphasized physical (i.e., water infiltration, soil erosion) and chemical (radionuclide leaching) processes that can cause waste site failure and subsequent radionuclide transport. The purpose of this paper is to demonstrate the need to consider biological processes as being potentially important in reducing the integrity of waste burial site cover treatments. Plants and animals not only can transport radionuclides to the ground surface via root systems and soil excavated from the cover profile by animal burrowing activities, but they modify physical and chemical processes within the cover profile by changing the water infiltration rates, soil erosion rates and chemical composition of the soil. One approach to limiting biological intrusion through the waste cover is to apply a barrier within the profile to limit root and animal penetration with depth. Experiments in the Los Alamos Experimental Engineered Test Facility were initiated to develop and evaluate biological barriers that are effective in minimizing intrusion into waste trenches. The experiments that are described employ four different candidate barrier materials of geologic origin. Experimental variables that will be evaluated, in addition to barrier type, are barrier depth and soil overburden depth. The rate of biological intrusion through the various barrier materials is being evaluated through the use of activatable stable tracers

  8. Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

    Science.gov (United States)

    Ziegler, Brittany; Montplaisir, Lisa

    2014-01-01

    Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students' perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest…

  9. Acta informatica medica is indexed in pubmed and archived in pubmed central.

    Science.gov (United States)

    Masic, Izet

    2013-03-01

    Acta Informatica Medica journal has been accepted for archiving in PubMed Central from 2011 onward. The journal started in 1993 as the official journal of the Society for Medical Informatics of Bosnia and Herzegovina. During the last 3 years, Acta Informatica Medica has een included in almost all prestigious online databases, including PubMed, Scopus and EMBASE. The 20th volume of the journal is fully international, with papers from 18 countries.

  10. Dose inhomogeneities at various levels of biological organization

    International Nuclear Information System (INIS)

    Bond, V.P.

    1988-01-01

    Dose inhomogeneities in both tumor and normal tissue, inherent to the application of boron neutron capture therapy (BNCT), can be the result not only of ununiform distribution of 10 B at various levels of biological organization, but also of the distribution of the thermal neutrons and of the energy depositions from more energetic neutrons and other radiations comprising the externally-applied beams. The severity of the problems resulting from such inhomogeneities, and approaches to evaluating them, are illustrated by three examples, at the macro, micro and intermediate levels

  11. Levels of biological organization and the origin of novelty.

    Science.gov (United States)

    Hall, Brian K; Kerney, Ryan

    2012-09-01

    The concept of novelty in evolutionary biology pertains to multiple tiers of biological organization from behavioral and morphological changes to changes at the molecular level. Identifying novel features requires assessments of similarity (homology and homoplasy) of relationships (phylogenetic history) and of shared developmental and genetic pathways or networks. After a brief discussion of how novelty is used in recent literature, we discuss whether the evolutionary approach to homology and homoplasy initially formulated by Lankester in the 19th century informs our understanding of novelty today. We then discuss six examples of morphological features described in the recent literature as novelties, and assess the basis upon which they are regarded as novel. The six are: origin of the turtle shell, transition from fish fins to tetrapod limbs, origination of the neural crest and neural crest cells, cement glands in frogs and casquettes in fish, whale bone-eating tubeworms, and the digestion of plant proteins by nematodes. The article concludes with a discussion of means of acquiring novel genetic information that can account for novelty recognized at higher levels. These are co-options of existing genetic circuitry, gene duplication followed by neofunctionalization, gene rearrangements through mobile genetic elements, and lateral gene transfer. We conclude that on the molecular level only the latter category provides novel genetic information, in that there is no homologous precursor. However, novel phenotypes can be generated through both neofunctionalization and gene rearrangements. Therefore, assigning phenotypic or genotypic "novelty" is contingent on the level of biological organization addressed. Copyright © 2011 Wiley Periodicals, Inc.

  12. Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

    OpenAIRE

    Ziegler, Brittany; Montplaisir, Lisa

    2014-01-01

    Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (postte...

  13. Biological monitors for low levels of ionising radiation

    International Nuclear Information System (INIS)

    Mohankumar, M.N.; Jeevanram, R.K.

    1995-01-01

    The biological effects of high doses of ionising radiation are well understood and the methods of measurement of these doses well established. However the effects due to extremely low doses remain by and large uncertain. This is because of the fact that at such low doses no gross symptoms are seen. In fact, at these levels the occurrence of double strand breaks leading to the formation of chromosomal aberrations like dicentrics is rare and chances of mutation due to base damage are negligible. Hence neither chromosomal aberration studies nor mutational assays are useful for detecting doses of the order of a few milligray. Results of exhaustive work done by various laboratories indicate that below 20 mGy the chromosomal aberration technique based on scoring of dicentrics cannot distinguish between a linear or a threshold model. However indirect methods like unscheduled DNA synthesis (UDS) and sister chromatid exchanges (SCEs) appear to be promising for the detection of radiation exposures due to low levels of radiation. This report reviews the available literature on the biological effects of low levels of ionising radiation and highlights the merits and demerits of the various methods employed in the measurement of UDS and SCE. The phenomenon of radio-adaptive response (RAR) and its relation to DNA repair is also discussed. (author)

  14. Biological monitors for low levels of ionising radiation

    Energy Technology Data Exchange (ETDEWEB)

    Mohankumar, M N; Jeevanram, R K [Safety Research and Health Physics Group, Indira Gandhi Centre for Atomic Research, Kalpakkam (India)

    1996-12-31

    The biological effects of high doses of ionising radiation are well understood and the methods of measurement of these doses well established. However the effects due to extremely low doses remain by and large uncertain. This is because of the fact that at such low doses no gross symptoms are seen. In fact, at these levels the occurrence of double strand breaks leading to the formation of chromosomal aberrations like dicentrics is rare and chances of mutation due to base damage are negligible. Hence neither chromosomal aberration studies nor mutational assays are useful for detecting doses of the order of a few milligray. Results of exhaustive work done by various laboratories indicate that below 20 mGy the chromosomal aberration technique based on scoring of dicentrics cannot distinguish between a linear or a threshold model. However indirect methods like unscheduled DNA synthesis (UDS) and sister chromatid exchanges (SCEs) appear to be promising for the detection of radiation exposures due to low levels of radiation. This report reviews the available literature on the biological effects of low levels of ionising radiation and highlights the merits and demerits of the various methods employed in the measurement of UDS and SCE. The phenomenon of radio-adaptive response (RAR) and its relation to DNA repair is also discussed. (author). 98 refs., 11 figs., 4 tabs.

  15. Insights into Monascus biology at the genetic level.

    Science.gov (United States)

    Shao, Yanchun; Lei, Ming; Mao, Zejing; Zhou, Youxiang; Chen, Fusheng

    2014-05-01

    The genus of Monascus was nominated by van Tieghem in 1884, but its fermented product-red mold rice (RMR), namely red yeast rice, has been used as folk medicines, food colorants, and fermentation starters for more than thousands of years in oriental countries. Nowadays, RMR is widely developed as food supplements around the world due to its functional compounds such as monacolin K (MK, also called lovastatin) and γ-aminobutyric acid. But the usage of RMR also incurs controversy resulting from contamination of citrinin (a kind of mycotoxin) produced by some Monascus strains. In the past decade, it has made great progress to Monascus spp. at the genetic level with the application of molecular biology techniques to restrain the citrinin production and increase the yields of MK and pigment in RMR, as well as aid Monascus classification and phylogenesis. Up to now, hundreds of papers about Monascus molecular biology (MMB) have been published in the international primary journals. However, to our knowledge, there is no MMB review issued until now. In this review, current understanding of Monascus spp. from the view of molecular biology will be covered and insights into research areas that need to be further investigated will also be discussed.

  16. Praktische handleiding PubMed : hét boek om snel en doeltreffend te zoeken in PubMed

    NARCIS (Netherlands)

    Etten-Jamaludin, van F.; Deurenberg, H.W.J.

    2010-01-01

    Praktische handleidng PubMed is de eerste Nederlandstalige gids die op overzichtelijke wijze op de uitgebreide mogelijkheden van PubMed ingaat. PubMed (www.pubmed.gov) biedt gratis toegang tot MEDLINE en is de meest gebruikte medische zoekmachine. In deze geheel herziene derde editie van Praktisch

  17. Antibiotic resistance shaping multi-level population biology of bacteria.

    Science.gov (United States)

    Baquero, Fernando; Tedim, Ana P; Coque, Teresa M

    2013-01-01

    Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent "population biologies." Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of "clinical" antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level

  18. Multiple levels of epigenetic control for bone biology and pathology.

    Science.gov (United States)

    Montecino, Martin; Stein, Gary; Stein, Janet; Zaidi, Kaleem; Aguilar, Rodrigo

    2015-12-01

    Multiple dimensions of epigenetic control contribute to regulation of gene expression that governs bone biology and pathology. Once confined to DNA methylation and a limited number of post-translational modifications of histone proteins, the definition of epigenetic mechanisms is expanding to include contributions of non-coding RNAs and mitotic bookmarking, a mechanism for retaining phenotype identity during cell proliferation. Together these different levels of epigenetic control of physiological processes and their perturbations that are associated with compromised gene expression during the onset and progression of disease, have contributed to an unprecedented understanding of the activities (operation) of the genomic landscape. Here, we address general concepts that explain the contribution of epigenetic control to the dynamic regulation of gene expression during eukaryotic transcription. This article is part of a Special Issue entitled Epigenetics and Bone. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Searching PubMed during a pandemic.

    Directory of Open Access Journals (Sweden)

    Ole Norgaard

    Full Text Available BACKGROUND: The 2009 influenza A(H1N1 pandemic has generated thousands of articles and news items. However, finding relevant scientific articles in such rapidly developing health crises is a major challenge which, in turn, can affect decision-makers' ability to utilise up-to-date findings and ultimately shape public health interventions. This study set out to show the impact that the inconsistent naming of the pandemic can have on retrieving relevant scientific articles in PubMed/MEDLINE. METHODOLOGY: We first formulated a PubMed search algorithm covering different names of the influenza pandemic and simulated the results that it would have retrieved from weekly searches for relevant new records during the first 10 weeks of the pandemic. To assess the impact of failing to include every term in this search, we then conducted the same searches but omitted in turn "h1n1," "swine," "influenza" and "flu" from the search string, and compared the results to those for the full string. PRINCIPAL FINDINGS: On average, our core search string identified 44.3 potentially relevant new records at the end of each week. Of these, we determined that an average of 27.8 records were relevant. When we excluded one term from the string, the percentage of records missed out of the total number of relevant records averaged 18.7% for omitting "h1n1," 13.6% for "swine," 17.5% for "influenza," and 20.6% for "flu." CONCLUSIONS: Due to inconsistent naming, while searching for scientific material about rapidly evolving situations such as the influenza A(H1N1 pandemic, there is a risk that one will miss relevant articles. To address this problem, the international scientific community should agree on nomenclature and the specific name to be used earlier, and the National Library of Medicine in the US could index potentially relevant materials faster and allow publishers to add alert tags to such materials.

  20. Quantum Biology at the Cellular Level - elements of the research program

    OpenAIRE

    Bordonaro, Michael; Ogryzko, Vasily

    2013-01-01

    Quantum Biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (Quantum Biology at Cellular Level), a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. Key words. decoherence, macroscopic superpositions, basis-dependence, formal superposition, non-classical correlations,...

  1. Analysis of PubMed User Sessions Using a Full-Day PubMed Query Log: A Comparison of Experienced and Nonexperienced PubMed Users

    Science.gov (United States)

    2015-01-01

    Background PubMed is the largest biomedical bibliographic information source on the Internet. PubMed has been considered one of the most important and reliable sources of up-to-date health care evidence. Previous studies examined the effects of domain expertise/knowledge on search performance using PubMed. However, very little is known about PubMed users’ knowledge of information retrieval (IR) functions and their usage in query formulation. Objective The purpose of this study was to shed light on how experienced/nonexperienced PubMed users perform their search queries by analyzing a full-day query log. Our hypotheses were that (1) experienced PubMed users who use system functions quickly retrieve relevant documents and (2) nonexperienced PubMed users who do not use them have longer search sessions than experienced users. Methods To test these hypotheses, we analyzed PubMed query log data containing nearly 3 million queries. User sessions were divided into two categories: experienced and nonexperienced. We compared experienced and nonexperienced users per number of sessions, and experienced and nonexperienced user sessions per session length, with a focus on how fast they completed their sessions. Results To test our hypotheses, we measured how successful information retrieval was (at retrieving relevant documents), represented as the decrease rates of experienced and nonexperienced users from a session length of 1 to 2, 3, 4, and 5. The decrease rate (from a session length of 1 to 2) of the experienced users was significantly larger than that of the nonexperienced groups. Conclusions Experienced PubMed users retrieve relevant documents more quickly than nonexperienced PubMed users in terms of session length. PMID:26139516

  2. Connecting the dots between PubMed abstracts.

    Directory of Open Access Journals (Sweden)

    M Shahriar Hossain

    Full Text Available BACKGROUND: There are now a multitude of articles published in a diversity of journals providing information about genes, proteins, pathways, and diseases. Each article investigates subsets of a biological process, but to gain insight into the functioning of a system as a whole, we must integrate information from multiple publications. Particularly, unraveling relationships between extra-cellular inputs and downstream molecular response mechanisms requires integrating conclusions from diverse publications. METHODOLOGY: We present an automated approach to biological knowledge discovery from PubMed abstracts, suitable for "connecting the dots" across the literature. We describe a storytelling algorithm that, given a start and end publication, typically with little or no overlap in content, identifies a chain of intermediate publications from one to the other, such that neighboring publications have significant content similarity. The quality of discovered stories is measured using local criteria such as the size of supporting neighborhoods for each link and the strength of individual links connecting publications, as well as global metrics of dispersion. To ensure that the story stays coherent as it meanders from one publication to another, we demonstrate the design of novel coherence and overlap filters for use as post-processing steps. CONCLUSIONS: WE DEMONSTRATE THE APPLICATION OF OUR STORYTELLING ALGORITHM TO THREE CASE STUDIES: i a many-one study exploring relationships between multiple cellular inputs and a molecule responsible for cell-fate decisions, ii a many-many study exploring the relationships between multiple cytokines and multiple downstream transcription factors, and iii a one-to-one study to showcase the ability to recover a cancer related association, viz. the Warburg effect, from past literature. The storytelling pipeline helps narrow down a scientist's focus from several hundreds of thousands of relevant documents to only

  3. Connecting the Dots between PubMed Abstracts

    Science.gov (United States)

    Hossain, M. Shahriar; Gresock, Joseph; Edmonds, Yvette; Helm, Richard; Potts, Malcolm; Ramakrishnan, Naren

    2012-01-01

    Background There are now a multitude of articles published in a diversity of journals providing information about genes, proteins, pathways, and diseases. Each article investigates subsets of a biological process, but to gain insight into the functioning of a system as a whole, we must integrate information from multiple publications. Particularly, unraveling relationships between extra-cellular inputs and downstream molecular response mechanisms requires integrating conclusions from diverse publications. Methodology We present an automated approach to biological knowledge discovery from PubMed abstracts, suitable for “connecting the dots” across the literature. We describe a storytelling algorithm that, given a start and end publication, typically with little or no overlap in content, identifies a chain of intermediate publications from one to the other, such that neighboring publications have significant content similarity. The quality of discovered stories is measured using local criteria such as the size of supporting neighborhoods for each link and the strength of individual links connecting publications, as well as global metrics of dispersion. To ensure that the story stays coherent as it meanders from one publication to another, we demonstrate the design of novel coherence and overlap filters for use as post-processing steps. Conclusions We demonstrate the application of our storytelling algorithm to three case studies: i) a many-one study exploring relationships between multiple cellular inputs and a molecule responsible for cell-fate decisions, ii) a many-many study exploring the relationships between multiple cytokines and multiple downstream transcription factors, and iii) a one-to-one study to showcase the ability to recover a cancer related association, viz. the Warburg effect, from past literature. The storytelling pipeline helps narrow down a scientist's focus from several hundreds of thousands of relevant documents to only around a hundred

  4. Nanotechnology for biology and medicine at the building block level

    CERN Document Server

    Silva, Gabriel A

    2011-01-01

    This text book will bring together a mix of both internationally known and established senior scientists along side up and coming (but already accomplished) junior scientists that have varying expertise in fundamental and applied nanotechnology to biology and medicine.

  5. Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

    Science.gov (United States)

    Montplaisir, Lisa

    2014-01-01

    Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. PMID:26086662

  6. High school and college biology: A multi-level model of the effects of high school biology courses on student academic performance in introductory college biology courses

    Science.gov (United States)

    Loehr, John Francis

    The issue of student preparation for college study in science has been an ongoing concern for both college-bound students and educators of various levels. This study uses a national sample of college students enrolled in introductory biology courses to address the relationship between high school biology preparation and subsequent introductory college biology performance. Multi-Level Modeling was used to investigate the relationship between students' high school science and mathematics experiences and college biology performance. This analysis controls for student demographic and educational background factors along with factors associated with the college or university attended. The results indicated that high school course-taking and science instructional experiences have the largest impact on student achievement in the first introductory college biology course. In particular, enrollment in courses, such as high school Calculus and Advanced Placement (AP) Biology, along with biology course content that focuses on developing a deep understanding of the topics is found to be positively associated with student achievement in introductory college biology. On the other hand, experiencing high numbers of laboratory activities, demonstrations, and independent projects along with higher levels of laboratory freedom are associated with negative achievement. These findings are relevant to high school biology teachers, college students, their parents, and educators looking beyond the goal of high school graduation.

  7. PubMed Medical Publications From Libya | Bakoush | Libyan ...

    African Journals Online (AJOL)

    We also used the same method to obtain data on the PubMed medical publications from Tunisia, Morocco and Yemen. Tunisia had the largest number of PubMed publications among the studied countries: 20.4 publications per million population per year and 7.2 publications per year per one billion US$ GDP. Libya had ...

  8. A systems biology approach for pathway level analysis

    OpenAIRE

    Draghici, Sorin; Khatri, Purvesh; Tarca, Adi Laurentiu; Amin, Kashyap; Done, Arina; Voichita, Calin; Georgescu, Constantin; Romero, Roberto

    2007-01-01

    A common challenge in the analysis of genomics data is trying to understand the underlying phenomenon in the context of all complex interactions taking place on various signaling pathways. A statistical approach using various models is universally used to identify the most relevant pathways in a given experiment. Here, we show that the existing pathway analysis methods fail to take into consideration important biological aspects and may provide incorrect results in certain situations. By usin...

  9. Networks as a Privileged Way to Develop Mesoscopic Level Approaches in Systems Biology

    OpenAIRE

    Alessandro Giuliani

    2014-01-01

    The methodologies advocated in computational biology are in many cases proper system-level approaches. These methodologies are variously connected to the notion of “mesosystem” and thus on the focus on relational structures that are at the basis of biological regulation. Here, I describe how the formalization of biological systems by means of graph theory constitutes an extremely fruitful approach to biology. I suggest the epistemological relevance of the notion of graph resides in its multil...

  10. Improving accuracy for identifying related PubMed queries by an integrated approach.

    Science.gov (United States)

    Lu, Zhiyong; Wilbur, W John

    2009-10-01

    PubMed is the most widely used tool for searching biomedical literature online. As with many other online search tools, a user often types a series of multiple related queries before retrieving satisfactory results to fulfill a single information need. Meanwhile, it is also a common phenomenon to see a user type queries on unrelated topics in a single session. In order to study PubMed users' search strategies, it is necessary to be able to automatically separate unrelated queries and group together related queries. Here, we report a novel approach combining both lexical and contextual analyses for segmenting PubMed query sessions and identifying related queries and compare its performance with the previous approach based solely on concept mapping. We experimented with our integrated approach on sample data consisting of 1539 pairs of consecutive user queries in 351 user sessions. The prediction results of 1396 pairs agreed with the gold-standard annotations, achieving an overall accuracy of 90.7%. This demonstrates that our approach is significantly better than the previously published method. By applying this approach to a one day query log of PubMed, we found that a significant proportion of information needs involved more than one PubMed query, and that most of the consecutive queries for the same information need are lexically related. Finally, the proposed PubMed distance is shown to be an accurate and meaningful measure for determining the contextual similarity between biological terms. The integrated approach can play a critical role in handling real-world PubMed query log data as is demonstrated in our experiments.

  11. Tracking Australian health and medical research expenditure with a PubMed bibliometric method.

    Science.gov (United States)

    Mendis, Kumara; Bailey, Jannine; McLean, Rick

    2015-06-01

    To assess Australian health and medical research (HMR) investment returns by measuring the trends in HMR expenditure and PubMed publications by Australian authors. Bibliometric analysis collating Australian HMR expenditure reported by the Australian Institute of Health and Welfare and Australian HMR publications indexed in PubMed. Similar methods were applied to data from the United Kingdom and New Zealand. From financial year 2000/01 through 2011/12, HMR investment increased by 232% from $1.49 to $4.94 billion (current prices adjusted for inflation), while PubMed publications increased by 123% from 10,696 to 23,818. The average HMR investment required for a single PubMed publication rose by 49% from $139,304 in 2000/01 to $207,364 in 2011/12. Quality analyses showed an increase in systematic reviews, cohort studies and clinical trials, and a decrease in publications in PubMed's core clinical journal collection. Comparisons with New Zealand and the United Kingdom showed that Australia has had the greatest overall percentage increase in gross publication numbers and publications per capita. Our analyses confirm that increased HMR expenditure is associated with an increase in HMR publications in PubMed. Tracking HMR investment outcomes using this method could be useful for future policy and funding decisions at a federal and specific institution level. © 2015 Public Health Association of Australia.

  12. Just the Facts? Introductory Undergraduate Biology Courses Focus on Low-Level Cognitive Skills

    Science.gov (United States)

    Momsen, Jennifer L.; Long, Tammy M.; Wyse, Sara A.; Ebert-May, Diane

    2010-01-01

    Introductory biology courses are widely criticized for overemphasizing details and rote memorization of facts. Data to support such claims, however, are surprisingly scarce. We sought to determine whether this claim was evidence-based. To do so we quantified the cognitive level of learning targeted by faculty in introductory-level biology courses.…

  13. Influence of Inoculation Method and Spawn Level on Biological ...

    African Journals Online (AJOL)

    ADOWIE PERE

    in and layering) and spawn levels (3, 5, 7, 9, 11, and 13%) on the mushroom. The results ... grows faster and has more energy available for fruiting body formation, hence the increased .... The shortest spawn running time obtained when the.

  14. PubMed searches: overview and strategies for clinicians.

    Science.gov (United States)

    Lindsey, Wesley T; Olin, Bernie R

    2013-04-01

    PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search.

  15. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

    Directory of Open Access Journals (Sweden)

    Sorokin Anatoly

    2015-06-01

    Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

  16. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

    Directory of Open Access Journals (Sweden)

    Mi Huaiyu

    2015-06-01

    Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

  17. Nanogold – Biological effects and occupational exposure levels

    Directory of Open Access Journals (Sweden)

    Anna Maria Świdwińska-Gajewska

    2017-08-01

    Full Text Available Nanogold has different properties and biological activity compared to metallic gold. It can be applied in many fields, such as medicine, laboratory diagnostics and electronics. Studies on laboratory animals show that nanogold can be absorbed by inhalation and ingestion. It can penetrate deep into the epidermis and dermis, but there is no evidence that it is absorbed through the skin. Gold nanoobjects accumulate mainly in the liver and spleen, but they can also reach other internal organs. Nanogold can cross the blood–brain and blood–placenta barriers. Toxicokinetics of nanogold depends on the particle size, shape and surface charge. In animals exposure to gold nanoparticles via inhalation induces slight changes in the lungs. Exposure to nanogold by the oral route does not cause adverse health effects in rodents. In animals after injection of gold nanoobjects changes in the liver and lungs were observed. Nanogold induced genotoxic effects in cells, but not in animals. No adverse effects on the fetus or reproduction were found. There are no carcinogenicity studies on gold nanoparticles. The mechanism of toxicity may be related to the interaction of gold nanoobjects with proteins and DNA, and it leads to the induction of oxidative stress and genetic material damage. The impact of nanostructures on human health has not yet been fully understood. The person, who works with nanomaterials should exercise extreme caution and apply existing recommendations on the evaluation of nanoobjects exposure. The risk assessment should be the basis for taking appropriate measures to limit potential exposure to nanometals, including nanogold. Med Pr 2017;68(4:545–556

  18. Evaluating forensic biology results given source level propositions.

    Science.gov (United States)

    Taylor, Duncan; Abarno, Damien; Hicks, Tacha; Champod, Christophe

    2016-03-01

    The evaluation of forensic evidence can occur at any level within the hierarchy of propositions depending on the question being asked and the amount and type of information that is taken into account within the evaluation. Commonly DNA evidence is reported given propositions that deal with the sub-source level in the hierarchy, which deals only with the possibility that a nominated individual is a source of DNA in a trace (or contributor to the DNA in the case of a mixed DNA trace). We explore the use of information obtained from examinations, presumptive and discriminating tests for body fluids, DNA concentrations and some case circumstances within a Bayesian network in order to provide assistance to the Courts that have to consider propositions at source level. We use a scenario in which the presence of blood is of interest as an exemplar and consider how DNA profiling results and the potential for laboratory error can be taken into account. We finish with examples of how the results of these reports could be presented in court using either numerical values or verbal descriptions of the results. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. Comparison of PubMed and Google Scholar literature searches.

    Science.gov (United States)

    Anders, Michael E; Evans, Dennis P

    2010-05-01

    Literature searches are essential to evidence-based respiratory care. To conduct literature searches, respiratory therapists rely on search engines to retrieve information, but there is a dearth of literature on the comparative efficiencies of search engines for researching clinical questions in respiratory care. To compare PubMed and Google Scholar search results for clinical topics in respiratory care to that of a benchmark. We performed literature searches with PubMed and Google Scholar, on 3 clinical topics. In PubMed we used the Clinical Queries search filter. In Google Scholar we used the search filters in the Advanced Scholar Search option. We used the reference list of a related Cochrane Collaboration evidence-based systematic review as the benchmark for each of the search results. We calculated recall (sensitivity) and precision (positive predictive value) with 2 x 2 contingency tables. We compared the results with the chi-square test of independence and Fisher's exact test. PubMed and Google Scholar had similar recall for both overall search results (71% vs 69%) and full-text results (43% vs 51%). PubMed had better precision than Google Scholar for both overall search results (13% vs 0.07%, P PubMed searches with the Clinical Queries filter are more precise than with the Advanced Scholar Search in Google Scholar for respiratory care topics. PubMed appears to be more practical to conduct efficient, valid searches for informing evidence-based patient-care protocols, for guiding the care of individual patients, and for educational purposes.

  20. Interactomes to Biological Phase Space: a call to begin thinking at a new level in computational biology.

    Energy Technology Data Exchange (ETDEWEB)

    Davidson, George S.; Brown, William Michael

    2007-09-01

    Techniques for high throughput determinations of interactomes, together with high resolution protein collocalizations maps within organelles and through membranes will soon create a vast resource. With these data, biological descriptions, akin to the high dimensional phase spaces familiar to physicists, will become possible. These descriptions will capture sufficient information to make possible realistic, system-level models of cells. The descriptions and the computational models they enable will require powerful computing techniques. This report is offered as a call to the computational biology community to begin thinking at this scale and as a challenge to develop the required algorithms and codes to make use of the new data.3

  1. Systems-Level Synthetic Biology for Advanced Biofuel Production

    Energy Technology Data Exchange (ETDEWEB)

    Ruffing, Anne [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Jensen, Travis J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Strickland, Lucas Marshall [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Meserole, Stephen [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Tallant, David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-03-01

    Cyanobacteria have been shown to be capable of producing a variety of advanced biofuels; however, product yields remain well below those necessary for large scale production. New genetic tools and high throughput metabolic engineering techniques are needed to optimize cyanobacterial metabolisms for enhanced biofuel production. Towards this goal, this project advances the development of a multiple promoter replacement technique for systems-level optimization of gene expression in a model cyanobacterial host: Synechococcus sp. PCC 7002. To realize this multiple-target approach, key capabilities were developed, including a high throughput detection method for advanced biofuels, enhanced transformation efficiency, and genetic tools for Synechococcus sp. PCC 7002. Moreover, several additional obstacles were identified for realization of this multiple promoter replacement technique. The techniques and tools developed in this project will help to enable future efforts in the advancement of cyanobacterial biofuels.

  2. The impact of an introductory college-level biology class on biology self-efficacy and attitude towards science

    Science.gov (United States)

    Thomas, Megan Elizabeth

    Self-efficacy theory was first introduced in a seminal article by Albert Bandura in 1977 entitled "Self-efficacy: Toward a unifying theory of behavioral change". Since its original introduction, self-efficacy has been a major focus of academic performance, anxiety, career development, and teacher retention research. Self-efficacy can be defined as the belief an individual possesses about their ability to perform a given task. Bandura proposed that self-efficacy should be measured at the highest level of specificity due to the fact that different people are efficacious in different areas. Interested in students' efficacy toward biology, Ebert-May, Baldwin, & Allred (1997) created and validated a survey to measure students' biology self-efficacy. Their survey was modeled after the guidelines for science literacy, and loaded to three sub-factors; methods of biology, generalization to other science courses, and application of the concepts. As self-efficacy theory has been related to effort expenditure and persistence (Bandura, 1977; 1997), one might think it would have some effect on students' attitudes toward the topic at hand. The current research investigated what changes in biology self-efficacy occurred after an introductory biology course with an inquiry based laboratory learning environment. In addition, changes in students' attitudes towards science were explored and how self-efficacy might affect them.

  3. Gaps in affiliation indexing in Scopus and PubMed.

    Science.gov (United States)

    Schmidt, Cynthia M; Cox, Roxanne; Fial, Alissa V; Hartman, Teresa L; Magee, Martha L

    2016-04-01

    The authors sought to determine whether unexpected gaps existed in Scopus's author affiliation indexing of publications written by the University of Nebraska Medical Center or Nebraska Medicine (UNMC/NM) authors during 2014. First, we compared Scopus affiliation identifier search results to PubMed affiliation keyword search results. Then, we searched Scopus using affiliation keywords (UNMC, etc.) and compared the results to PubMed affiliation keyword and Scopus affiliation identifier searches. We found that Scopus's records for approximately 7% of UNMC/NM authors' publications lacked appropriate UNMC/NM author affiliation identifiers, and many journals' publishers were supplying incomplete author affiliation information to PubMed. Institutions relying on Scopus to track their impact should determine whether Scopus's affiliation identifiers will, in fact, identify all articles published by their authors and investigators.

  4. Just the facts? Introductory undergraduate biology courses focus on low-level cognitive skills.

    Science.gov (United States)

    Momsen, Jennifer L; Long, Tammy M; Wyse, Sara A; Ebert-May, Diane

    2010-01-01

    Introductory biology courses are widely criticized for overemphasizing details and rote memorization of facts. Data to support such claims, however, are surprisingly scarce. We sought to determine whether this claim was evidence-based. To do so we quantified the cognitive level of learning targeted by faculty in introductory-level biology courses. We used Bloom's Taxonomy of Educational Objectives to assign cognitive learning levels to course goals as articulated on syllabi and individual items on high-stakes assessments (i.e., exams and quizzes). Our investigation revealed the following: 1) assessment items overwhelmingly targeted lower cognitive levels, 2) the cognitive level of articulated course goals was not predictive of the cognitive level of assessment items, and 3) there was no influence of course size or institution type on the cognitive levels of assessments. These results support the claim that introductory biology courses emphasize facts more than higher-order thinking.

  5. pubmed.mineR: an R package with text-mining algorithms to analyse PubMed abstracts.

    Science.gov (United States)

    Rani, Jyoti; Shah, A B Rauf; Ramachandran, Srinivasan

    2015-10-01

    The PubMed literature database is a valuable source of information for scientific research. It is rich in biomedical literature with more than 24 million citations. Data-mining of voluminous literature is a challenging task. Although several text-mining algorithms have been developed in recent years with focus on data visualization, they have limitations such as speed, are rigid and are not available in the open source. We have developed an R package, pubmed.mineR, wherein we have combined the advantages of existing algorithms, overcome their limitations, and offer user flexibility and link with other packages in Bioconductor and the Comprehensive R Network (CRAN) in order to expand the user capabilities for executing multifaceted approaches. Three case studies are presented, namely, 'Evolving role of diabetes educators', 'Cancer risk assessment' and 'Dynamic concepts on disease and comorbidity' to illustrate the use of pubmed.mineR. The package generally runs fast with small elapsed times in regular workstations even on large corpus sizes and with compute intensive functions. The pubmed.mineR is available at http://cran.rproject. org/web/packages/pubmed.mineR.

  6. Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.

    Science.gov (United States)

    Beal, Jacob; Lu, Ting; Weiss, Ron

    2011-01-01

    The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks. Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.

  7. PubMed Central Canada: Beyond an Open Access Repository?

    Science.gov (United States)

    Nariani, Rajiv

    2013-01-01

    PubMed Central Canada (PMC Canada) represents a partnership between the Canadian Institutes of Health Research (CIHR), the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), and the National Library of Medicine of the US. The present study was done to gauge faculty awareness about the CIHR Policy on…

  8. How Complementary and Alternative Medicine Practitioners Use PubMed

    Science.gov (United States)

    Quint-Rapoport, Mia

    2007-01-01

    Background PubMed is the largest bibliographic index in the life sciences. It is freely available online and is used by professionals and the public to learn more about medical research. While primarily intended to serve researchers, PubMed provides an array of tools and services that can help a wider readership in the location, comprehension, evaluation, and utilization of medical research. Objective This study sought to establish the potential contributions made by a range of PubMed tools and services to the use of the database by complementary and alternative medicine practitioners. Methods In this study, 10 chiropractors, 7 registered massage therapists, and a homeopath (N = 18), 11 with prior research training and 7 without, were taken through a 2-hour introductory session with PubMed. The 10 PubMed tools and services considered in this study can be divided into three functions: (1) information retrieval (Boolean Search, Limits, Related Articles, Author Links, MeSH), (2) information access (Publisher Link, LinkOut, Bookshelf ), and (3) information management (History, Send To, Email Alert). Participants were introduced to between six and 10 of these tools and services. The participants were asked to provide feedback on the value of each tool or service in terms of their information needs, which was ranked as positive, positive with emphasis, negative, or indifferent. Results The participants in this study expressed an interest in the three types of PubMed tools and services (information retrieval, access, and management), with less well-regarded tools including MeSH Database and Bookshelf. In terms of their comprehension of the research, the tools and services led the participants to reflect on their understanding as well as their critical reading and use of the research. There was universal support among the participants for greater access to complete articles, beyond the approximately 15% that are currently open access. The abstracts provided by PubMed were

  9. Entry to medical schools with 'A' level in mathematics rather than biology.

    Science.gov (United States)

    Spurgin, C B

    1975-09-01

    The majority of British medical schools now accept for their shortest courses students who have mathematics at A level in place of the former requirement of biology A level. Only a small fraction of the entry, less than one-fifth, enters this way, in spite of statements by most medical schools that they make no distinction between those with mathematics and those with biology when making conditional offers of places. There is no evidence that those without biology are at a disadvantage in the courses. If the prospects of entry without A level biology were better publicized medical schools would have a wider field of possibly abler entrants, and pupils entering sixth forms could defer for a year a choice between a medical (or dental) career and one involving physical science, engineering, or other mathematics-based university education.

  10. Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

    Science.gov (United States)

    Moodie, Stuart; Le Novère, Nicolas; Demir, Emek; Mi, Huaiyu; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  11. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

    Science.gov (United States)

    Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  12. Low-level radiation: biological interactions, risks, and benefits. A bibliography

    Energy Technology Data Exchange (ETDEWEB)

    None

    1978-09-01

    The bibliography contains 3294 references that were selected from the Department of Energy's data base (EDB). The subjects covered are lower-level radiation effects on man, environmental radiation, and other biological interactions of radiation that appear to be applicable to the low-level radiation problem.

  13. Low-level radiation: biological interactions, risks, and benefits. A bibliography

    International Nuclear Information System (INIS)

    1978-09-01

    The bibliography contains 3294 references that were selected from the Department of Energy's data base (EDB). The subjects covered are lower-level radiation effects on man, environmental radiation, and other biological interactions of radiation that appear to be applicable to the low-level radiation problem

  14. Levels of organization in biology: on the nature and nomenclature of ecology's fourth level.

    Science.gov (United States)

    Lidicker, William Z

    2008-02-01

    Viewing the universe as being composed of hierarchically arranged systems is widely accepted as a useful model of reality. In ecology, three levels of organization are generally recognized: organisms, populations, and communities (biocoenoses). For half a century increasing numbers of ecologists have concluded that recognition of a fourth level would facilitate increased understanding of ecological phenomena. Sometimes the word "ecosystem" is used for this level, but this is arguably inappropriate. Since 1986, I and others have argued that the term "landscape" would be a suitable term for a level of organization defined as an ecological system containing more than one community type. However, "landscape" and "landscape level" continue to be used extensively by ecologists in the popular sense of a large expanse of space. I therefore now propose that the term "ecoscape" be used instead for this fourth level of organization. A clearly defined fourth level for ecology would focus attention on the emergent properties of this level, and maintain the spatial and temporal scale-free nature inherent in this hierarchy of organizational levels for living entities.

  15. AliBaba: PubMed as a graph.

    Science.gov (United States)

    Plake, Conrad; Schiemann, Torsten; Pankalla, Marcus; Hakenberg, Jörg; Leser, Ulf

    2006-10-01

    The biomedical literature contains a wealth of information on associations between many different types of objects, such as protein-protein interactions, gene-disease associations and subcellular locations of proteins. When searching such information using conventional search engines, e.g. PubMed, users see the data only one-abstract at a time and 'hidden' in natural language text. AliBaba is an interactive tool for graphical summarization of search results. It parses the set of abstracts that fit a PubMed query and presents extracted information on biomedical objects and their relationships as a graphical network. AliBaba extracts associations between cells, diseases, drugs, proteins, species and tissues. Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance. http://alibaba.informatik.hu-berlin.de/

  16. Quantum biology at the cellular level--elements of the research program.

    Science.gov (United States)

    Bordonaro, Michael; Ogryzko, Vasily

    2013-04-01

    Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) - a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the 'basis-dependent' nature of these concepts. We introduce the notion of 'formal superposition' and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular 'decision-making' and adaptation. We stress that the interpretation of the notion of 'formal superposition' should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., 'Basis-Dependent Selection', BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the 'evolvability mechanism' loophole are also discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  17. The Main Biological Hazards in Animal Biosafety Level 2 Facilities and Strategies for Control.

    Science.gov (United States)

    Li, Xiao Yan; Xue, Kang Ning; Jiang, Jin Sheng; Lu, Xuan Cheng

    2016-04-01

    Concern about the biological hazards involved in microbiological research, especially research involving laboratory animals, has increased in recent years. Working in an animal biosafety level 2 facility (ABSL-2), commonly used for research on infectious diseases, poses various biological hazards. Here, the regulations and standards related to laboratory biosafety in China are introduced, the potential biological hazards present in ABSL-2 facilities are analyzed, and a series of strategies to control the hazards are presented. Copyright © 2016 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  18. A dedicated database system for handling multi-level data in systems biology

    OpenAIRE

    Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

    2014-01-01

    Background Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging...

  19. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

    Science.gov (United States)

    Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  20. [Systematic literature search in PubMed : A short introduction].

    Science.gov (United States)

    Blümle, A; Lagrèze, W A; Motschall, E

    2018-03-01

    In order to identify current (and relevant) evidence for a specific clinical question within the unmanageable amount of information available, solid skills in performing a systematic literature search are essential. An efficient approach is to search a biomedical database containing relevant literature citations of study reports. The best known database is MEDLINE, which is searchable for free via the PubMed interface. In this article, we explain step by step how to perform a systematic literature search via PubMed by means of an example research question in the field of ophthalmology. First, we demonstrate how to translate the clinical problem into a well-framed and searchable research question, how to identify relevant search terms and how to conduct a text word search and a search with keywords in medical subject headings (MeSH) terms. We then show how to limit the number of search results if the search yields too many irrelevant hits and how to increase the number in the case of too few citations. Finally, we summarize all essential principles that guide a literature search via PubMed.

  1. Biological/Genetic Regulation of Physical Activity Level: Consensus from GenBioPAC.

    Science.gov (United States)

    Lightfoot, J Timothy; DE Geus, Eco J C; Booth, Frank W; Bray, Molly S; DEN Hoed, Marcel; Kaprio, Jaakko; Kelly, Scott A; Pomp, Daniel; Saul, Michael C; Thomis, Martine A; Garland, Theodore; Bouchard, Claude

    2018-04-01

    Physical activity unquestionably maintains and improves health; however, physical activity levels globally are low and not rising despite all the resources devoted to this goal. Attention in both the research literature and the public policy domain has focused on social-behavioral factors; however, a growing body of literature suggests that biological determinants play a significant role in regulating physical activity levels. For instance, physical activity level, measured in various manners, has a genetic component in both humans and nonhuman animal models. This consensus article, developed as a result of an American College of Sports Medicine-sponsored round table, provides a brief review of the theoretical concepts and existing literature that supports a significant role of genetic and other biological factors in the regulation of physical activity. Future research on physical activity regulation should incorporate genetics and other biological determinants of physical activity instead of a sole reliance on social and other environmental determinants.

  2. Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters.

    Science.gov (United States)

    Lokker, Cynthia; Haynes, R Brian; Wilczynski, Nancy L; McKibbon, K Ann; Walter, Stephen D

    2011-01-01

    Clinical Queries filters were developed to improve the retrieval of high-quality studies in searches on clinical matters. The study objective was to determine the yield of relevant citations and physician satisfaction while searching for diagnostic and treatment studies using the Clinical Queries page of PubMed compared with searching PubMed without these filters. Forty practicing physicians, presented with standardized treatment and diagnosis questions and one question of their choosing, entered search terms which were processed in a random, blinded fashion through PubMed alone and PubMed Clinical Queries. Participants rated search retrievals for applicability to the question at hand and satisfaction. For treatment, the primary outcome of retrieval of relevant articles was not significantly different between the groups, but a higher proportion of articles from the Clinical Queries searches met methodologic criteria (p=0.049), and more articles were published in core internal medicine journals (p=0.056). For diagnosis, the filtered results returned more relevant articles (p=0.031) and fewer irrelevant articles (overall retrieval less, p=0.023); participants needed to screen fewer articles before arriving at the first relevant citation (p<0.05). Relevance was also influenced by content terms used by participants in searching. Participants varied greatly in their search performance. Clinical Queries filtered searches returned more high-quality studies, though the retrieval of relevant articles was only statistically different between the groups for diagnosis questions. Retrieving clinically important research studies from Medline is a challenging task for physicians. Methodological search filters can improve search retrieval.

  3. PubMed and beyond: a survey of web tools for searching biomedical literature

    Science.gov (United States)

    Lu, Zhiyong

    2011-01-01

    The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search PMID:21245076

  4. PubMed and beyond: a survey of web tools for searching biomedical literature.

    Science.gov (United States)

    Lu, Zhiyong

    2011-01-01

    The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search.

  5. Multiweek Cell Culture Project for Use in Upper-Level Biology Laboratories

    Science.gov (United States)

    Marion, Rebecca E.; Gardner, Grant E.; Parks, Lisa D.

    2012-01-01

    This article describes a laboratory protocol for a multiweek project piloted in a new upper-level biology laboratory (BIO 426) using cell culture techniques. Human embryonic kidney-293 cells were used, and several culture media and supplements were identified for students to design their own experiments. Treatments included amino acids, EGF,…

  6. Advanced Level Biology Teachers' Attitudes towards Assessment and Their Engagement in Assessment for Learning

    Science.gov (United States)

    Bramwell-Lalor, Sharon; Rainford, Marcia

    2015-01-01

    This paper reports on a Mixed Methods study involving an investigation into the attitudes of advanced level biology teachers towards assessment and describes the teachers' experiences while being engaged in Assessment for Learning (AfL) practices such as sharing of learning objectives and peer- and self-assessment. Quantitative data were collected…

  7. Turkish students' perceptions of their biology learning environments: the effects of gender and grade level

    NARCIS (Netherlands)

    Telli, S.; Brok, den P.J.; Tekkaya, C.; Cakiroglu, J.

    2009-01-01

    This study investigates the effects of gender and grade level on Turkish secondary school students’ perceptions of their biology learning environment. A total of 1474 high school students completed the What is Happening in This Classroom (WIHIC) questionnaire. The WIHIC maps several important

  8. A dedicated database system for handling multi-level data in systems biology.

    Science.gov (United States)

    Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

    2014-01-01

    Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

  9. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

    Science.gov (United States)

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

  10. Growing trend of CE at the omics level: the frontier of systems biology.

    Science.gov (United States)

    Oh, Eulsik; Hasan, Md Nabiul; Jamshed, Muhammad; Park, Soo Hyun; Hong, Hye-Min; Song, Eun Joo; Yoo, Young Sook

    2010-01-01

    In a novel attempt to comprehend the complexity of life, systems biology has recently emerged as a state-of-the-art approach for biological research in contrast to the reductionist approaches that have been used in molecular cell biology since the 1950s. Because a massive amount of information is required in many systems biology studies of life processes, we have increasingly come to depend on techniques that provide high-throughput omics data. CE and CE coupled to MS have served as powerful analytical tools for providing qualitative and quantitative omics data. Recent systems biology studies have focused strongly on the diagnosis and treatment of diseases. The increasing number of clinical research papers on drug discovery and disease therapies reflects this growing interest among scientists. Since such clinical research reflects one of the ultimate purposes of bioscience, these trends will be sustained for a long time. Thus, this review mainly focuses on the application of CE and CE-MS in diagnosis as well as on the latest CE methods developed. Furthermore, we outline the new challenges that arose in 2008 and later in elucidating the system-level functions of the bioconstituents of living organisms.

  11. Biological ramifications of the subseabed disposal of high-level nuclear waste

    International Nuclear Information System (INIS)

    Gomez, L.S.; Hessler, R.R.; Jackson, D.W.; Marietta, M.G.; Smith, K.L. Jr.; Talbert, D.M.; Yayanos, A.A.

    1980-05-01

    The primary goal of the US Subseabed Disposal Program (SDP) is to assess the technical and environmental feasibility of disposing of high-level nuclear waste in deep-sea sediments. The subseabed biology program is charged with assessing possible ecosystem effects of radionuclides as well as possible health effects to man from radionuclides which may be released in the deep sea and transported to the ocean surface. Current biological investigations are attempting to determine benthic community structure; benthic community metabolism; the biology of deep-sea mobile scavengers; the faunal composition of midwater nekton; rates of microbial processes; and the radiation sensitivity of deep-sea organisms. Existing models of the dispersal of radionuclides in the deep sea have not considered many of the possible biological mechanisms which may influence the movement of radionuclides. Therefore, a multi-compartment foodweb model is being developed which considers both biological and physical influences on radionuclide transport. This model will allow parametric studies to be made of the impact on the ocean environment and on man of potential releases of radionuclides

  12. Biological ramifications of the subseabed disposal of high-level nuclear waste

    International Nuclear Information System (INIS)

    Gomez, L.S.; Hessler, R.R.; Jackson, D.W.; Marietta, M.G.; Smith, K.L. Jr.; Talbert, D.M.; Yayanos, A.A.

    1980-01-01

    The primary goal of the US Subseabed Disposal Program (SDP) is to assess the technical and environmental feasibility of disposing of high-level nuclear waste in deep-sea sediments. The subseabed biology program is charged with assessing possible ecosystem effects of radionuclides as well as possible health effects to man from radionuclides which may be released in the deep sea and transported to the ocean surface. Current biological investigations are attempting to determine benthic community structure; benthic community metabolism; the biology of deep-sea mobile scavengers; the faunal composition of midwater nekton; rates of microbial processes, and the radiation sensitivity of deep-sea organisms. Existing models of the dispersal of radionuclides in the deep sea have not considered many of the possible biological mechanisms which may influence the movement of radionuclides. Therefore, a multi-compartment foodweb model is being developed which considers both biological and physical influences on radionuclide transport. This model will allow parametric studies to be made of the impact on the ocean environment and on man of potential releases of radionuclides

  13. Attempts to develop a new nuclear measurement technique of β-glucuronidase levels in biological samples

    International Nuclear Information System (INIS)

    Unak, T.; Avcibasi, U.; Yildirim, Y.; Cetinkaya, B.

    2003-01-01

    β-Glucuronidase is one of the most important hydrolytic enzymes in living systems and plays an essential role in the detoxification pathway of toxic materials incorporated into the metabolism. Some organs, especially liver and some tumour tissues, have high level of β-glucuronidase activity. As a result the enzymatic activity of some kind of tumour cells, the radiolabelled glucuronide conjugates of cytotoxic, as well as radiotoxic compounds have potentially very valuable diagnostic and therapeutic applications in cancer research. For this reason, a sensitive measurement of β-glucuronidase levels in normal and tumour tissues is a very important step for these kinds of applications. According to the classical measurement method of β-glucuronidase activity, in general, the quantity of phenolphthalein liberated from its glucuronide conjugate, i.e. phenolphthalein-glucuronide, by β-glucuronidase has been measured by use of the spectrophotometric technique. The lower detection limit of phenolphthalein by the spectrophotometric technique is about 1-3 mg. This means that the β-glucuronidase levels could not be detected in biological samples having lower levels of β-glucuronidase activity and therefore the applications of the spectrophotometric technique in cancer research are very seriously limited. Starting from this consideration, we recently attempted to develop a new nuclear technique to measure much lower concentrations of β-glucuronidase in biological samples. To improve the detection limit, phenolphthalein-glucuronide and also phenyl-N-glucuronide were radioiodinated with 131 I and their radioactivity was measured by use of the counting technique. Therefore, the quantity of phenolphthalein or aniline radioiodinated with 131 I and liberated by the deglucuronidation reactivity of β-glucuronidase was used in an attempt to measure levels lower than the spectrophotometric measurement technique. The results obtained clearly verified that 0.01 pg level of

  14. Student selection: are the school-leaving A-level grades in biology and chemistry important?

    Science.gov (United States)

    Green, A; Peters, T J; Webster, D J

    1993-01-01

    This study determined the relationships of grades in A-level biology and chemistry with examination success or failure during the medical course. By inspection of medical student records, A-level grades at entry to medical school and examination performance were obtained for 128 (91%) of the students who sat their final MBBCh examination at the University of Wales College of Medicine in June 1988. The majority, 92 (72%), completed their medical school careers with no professional examination failures; 15 failed examinations just in the period up to 2nd MB; 11 failed examinations in the clinical period only and 10 failed examinations in both periods. Whereas grade achieved in A-level chemistry was not associated with undergraduate examination performance, students with a grade A or B in A-level biology were less likely to have problems than the others (21% compared with 47%; the difference of 26% has a 95% confidence interval of 7% to 44%). Specifically, there appears to be a strong relationship between a low grade in biology and difficulties in the preclinical examinations. Moreover, for those who have difficulties at this stage, this association continues later in the course.

  15. Examining portfolio-based assessment in an upper-level biology course

    Science.gov (United States)

    Ziegler, Brittany Ann

    Historically, students have been viewed as empty vessels and passive participants in the learning process but students actually are active forming their own conceptions. One way student learning is impacted is through assessment. Alternative assessment, which contrasts traditional assessment methods, takes into account how students learn by promoting engagement and construction of knowledge This dissertation explores portfolio-based assessment, a method of alternative assessment, which requires students to compose a purposeful collection of work demonstrating their knowledge in an upper-level biology course. The research objectives include characterizing and contributing to the understanding of portfolio-based assessment in higher education, examining reflection and inquiry portfolio components, determining student knowledge of biological concepts, and investigating student integrative thinking through the transformation of reflections into concept webs One main finding includes the majority of reflections categorized as naive or novice in quality. There was no difference in quality of reflections among biological topic. There was a relatively equal amount of high and low cognitive level questions. Students' knowledge of biological concepts significantly increased from the beginning to end of the course. Student written reflections were transformed into concept webs to allow for examination of student integrative thinking. Concepts, relationships, and interconnections in concept webs showed variation but declined by the end of the semester This study is one of the first examining portfolio-based assessment in an upper-level biology course We do not contend that this method of assessment is the only way to promote student learning but portfolio-based assessment may be a tool that can transform science education but currently the role of portfolio-based assessment in science education remains unclear. Additional research needs to be conducted before we will fully

  16. Effects of low-level radiation on biologic systems: a literature review

    International Nuclear Information System (INIS)

    Best, T.L.; Hoditschek, B.

    1980-12-01

    This review presents an organized survey of scientific literature dealing with the biologic effects of low-level radiation. It includes brief discussions of topics of particular interest, a listing of useful review articles, an extensive bibliography, and listings of sources that can be used to update this document in the future. The topics discussed include experimental studies, the linear hypothesis, medical effects, occupational effects, effects of exposure to naturally occurring radiation, consumer products, and laws and regulations

  17. Cold Spring Harbor symposia on quantitative biology: Volume 49, Recombination at the DNA level

    International Nuclear Information System (INIS)

    1984-01-01

    This volume contains full papers prepared by the participants to the 1984 Cold Springs Harbor Symposia on Quantitative Biology. This year's theme is entitled Recombination at the DNA level. The volume consists of 93 articles grouped into subject areas entitled chromosome mechanics, yeast systems, mammalian homologous recombination, transposons, mu, plant transposons/T4 recombination, topoisomerase, resolvase and gyrase, Escherichia coli general recombination, RecA, repair, leukaryotic enzymes, integration and excision of bacteriophage, site-specific recombination, and recombination in vitro

  18. Chemical and biological attributes of a lowland soil affected by land leveling

    Directory of Open Access Journals (Sweden)

    José Maria Barbat Parfitt

    2013-11-01

    Full Text Available The objective of this work was to evaluate the relationship between soil chemical and biological attributes and the magnitude of cuts and fills after the land leveling process of a lowland soil. Soil samples were collected from the 0 - 0.20 m layer, before and after leveling, on a 100 point grid established in the experimental area, to evaluate chemical attributes and soil microbial biomass carbon (MBC. Leveling operations altered the magnitude of soil chemical and biological attributes. Values of Ca, Mg, S, cation exchange capacity, Mn, P, Zn, and soil organic matter (SOM decreased in the soil profile, whereas Al, K, and MBC increased after leveling. Land leveling decreased in 20% SOM average content in the 0 - 0.20 m layer. The great majority of the chemical attributes did not show relations between their values and the magnitude of cuts and fills. The relation was quadratic for SOM, P, and total N, and was linear for K, showing a positive slope and indicating increase in the magnitude of these attributes in cut areas and stability in fill areas. The relationships between these chemical attributes and the magnitude of cuts and fills indicate that the land leveling map may be a useful tool for degraded soil recuperation through amendments and organic fertilizers.

  19. Impaired global, and compensatory local, biological motion processing in people with high levels of autistic traits.

    Science.gov (United States)

    van Boxtel, Jeroen J A; Lu, Hongjing

    2013-01-01

    People with Autism Spectrum Disorder (ASD) are hypothesized to have poor high-level processing but superior low-level processing, causing impaired social recognition, and a focus on non-social stimulus contingencies. Biological motion perception provides an ideal domain to investigate exactly how ASD modulates the interaction between low and high-level processing, because it involves multiple processing stages, and carries many important social cues. We investigated individual differences among typically developing observers in biological motion processing, and whether such individual differences associate with the number of autistic traits. In Experiment 1, we found that individuals with fewer autistic traits were automatically and involuntarily attracted to global biological motion information, whereas individuals with more autistic traits did not show this pre-attentional distraction. We employed an action adaptation paradigm in the second study to show that individuals with more autistic traits were able to compensate for deficits in global processing with an increased involvement in local processing. Our findings can be interpreted within a predictive coding framework, which characterizes the functional relationship between local and global processing stages, and explains how these stages contribute to the perceptual difficulties associated with ASD.

  20. Next-generation mammalian genetics toward organism-level systems biology.

    Science.gov (United States)

    Susaki, Etsuo A; Ukai, Hideki; Ueda, Hiroki R

    2017-01-01

    Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.

  1. Disclosure Level of CPC 29 Biological Assets: Analysis of Determining Factors in Brazilian companies

    Directory of Open Access Journals (Sweden)

    Daniel Ramos Nogueira

    2017-04-01

    Full Text Available The research question guiding this research is "What are the Determining Factors of CPC 29 Disclosure in Brazilian Companies?". In this aspect, the research objective was to evaluate the main factors that affect the disclosure of information related to biological assets. For this, 5 variables highlighted in the literature were selected as evidence influencers. The sample was composed of Brazilian companies with biological assets in the Balance Sheet. From this list, financial statements, explanatory notes, corporate management level and independent auditing company for the 6 years (2010 to 2015 were collected. With the collected information, the dependent variable (Disclosure level of CPC 29 and the independent variables of each year were verified. At the end (after exclusions, 100 observations were analyzed. The results indicated that the variables Size, Representativeness of Biological Assets and Effectiveness of OCPC 07 positively impacted the level of Disclosure. The first two confirmed the predicted hypothesis and OCPC 07 presented a relation that was different from what was expected, showing an increase and not a reduction in the number of disclosures in the years 2014 and 2015.

  2. Impaired global, and compensatory local, biological motion processing in people with high levels of autistic traits

    Directory of Open Access Journals (Sweden)

    Jeroen J A Van Boxtel

    2013-04-01

    Full Text Available People with Autism Spectrum Disorder (ASD are hypothesized to have poor high-level processing but superior low-level processing, causing impaired social recognition, and a focus on non-social stimulus contingencies. Biological motion perception provides an ideal domain to investigate exactly how ASD modulates the interaction between low and high-level processing, because it involves multiple processing stages, and carries many important social cues. We investigated individual differences among typically developing observers in biological motion processing, and whether such individual differences associate with the number of autistic traits. In Experiment 1, we found that individuals with fewer autistic traits were automatically and involuntarily attracted to global biological motion information, whereas individuals with more autistic traits did not show this pre-attentional distraction. We employed an action adaptation paradigm in the second study to show that individuals with more autistic traits were able to compensate for deficits in global processing with an increased involvement in local processing. Our findings can be interpreted within a predictive coding framework, which characterizes the functional relationship between local and global processing stages, and explains how these stages contribute to the perceptual difficulties associated with ASD.

  3. Selected factors associated with achievement of biology preparatory students and their follow-up to higher level biology courses

    Science.gov (United States)

    Biermann, Carol A.; Sarinsky, Gary B.

    This study was undertaken to determine whether a biology preparatory course given at an urban community college was helping students to develop the proper skills and background necessary for them to successfully complete follow-up courses in biology. A group of students who enrolled in a biology preparatory course, and subsequently, a follow-up anatomy and physiology or general biology course (experimental group) was compared to a group of students who should have registered for the preparatory course, but who enrolled directly into the anatomy and physiology or general biology course (control group). It was shown that there was no significant difference in their anatomy and physiology or general biology grades. Furthermore, only 16% of the initial group of preparatory students enrolled in and passed a follow-up biology course. Examination of the preparatory group using discriminant analysis ascertained that mathematics score was the principle discriminator between pass/fail groups. A stepwise multiple regression analysis of the variables explaining the preparatory grade showed that mathematics score, reading score, and type of high school degree explained 33% of the variance. Of the students who did pass the preparatory course and enrolled in a follow-up biology class, their preparatory grade was a good predictor of their achievement (measured by follow-up course grade), as determined by multiple regression.

  4. The Use of Textbooks for Advanced-Level GCE Courses in Physics, Chemistry and Biology by Sixth-Form Students.

    Science.gov (United States)

    Newton, D. P.

    1984-01-01

    A survey of sixth-form students to determine the level of A-level textbook use in physics, chemistry, and biology in English schools found that texts are used primarily after the lesson, at the student's discretion, and with great variations between students. Biology texts were used most, and physics texts used least. (MBR)

  5. Key Issues Concerning Biolog Use for Aerobic and Anaerobic Freshwater Bacterial Community-Level Physiological Profiling

    Science.gov (United States)

    Christian, Bradley W.; Lind, Owen T.

    2006-06-01

    Bacterial heterotrophy in aquatic ecosystems is important in the overall carbon cycle. Biolog MicroPlates provide information into the metabolic potential of bacteria involved in carbon cycling. Specifically, Biolog EcoPlatesTM were developed with ecologically relevant carbon substrates to allow investigators to measure carbon substrate utilization patterns and develop community-level physiological profiles from natural bacterial assemblages. However, understanding of the functionality of these plates in freshwater research is limited. We explored several issues of EcoPlate use for freshwater bacterial assemblages including inoculum density, incubation temperature, non-bacterial color development, and substrate selectivity. Each of these has various effects on plate interpretation. We offer suggestions and techniques to resolve these interpretation issues. Lastly we propose a technique to allow EcoPlate use in anaerobic freshwater bacterial studies.

  6. The Effects of Urban Sprawl on Birds at Multiple Levels of Biological Organization

    Directory of Open Access Journals (Sweden)

    Robert Blair

    2004-12-01

    Full Text Available Urban sprawl affects the environment in myriad ways and at multiple levels of biological organization. In this paper I explore the effects of sprawl on native bird communities by comparing the occurrence of birds along gradients of urban land use in southwestern Ohio and northern California and by examining patterns at the individual, species, community, landscape, and continental levels. I do this by assessing the distribution and abundance of all bird species occupying sites of differing land-use intensity in Ohio and California. Additionally, I conducted predation experiments using artificial nests, tracked the nest fate of American Robins and Northern Cardinals, and assessed land cover in these sites. At the individual level, predation on artificial nests decreased with urbanization; however, this trend was not reflected in the nesting success of robins and cardinals, which did not increase with urbanization. At the species level, sprawl affected local patterns of extinction and invasion; the density of different species peaked at different levels of urbanization. At the community level, species richness and diversity peaked at moderate levels of urbanization, and the number of low-nesting species and of species with multiple broods increased with urbanization. The community-level results may reflect both the species-level patterns of local extinction and invasion as well as broader landscape-level patterns. At the landscape level, a linear combination of spatial heterogeneity and density of woody patches accurately predicted both species richness and Shannon Diversity. At the continental level, local extinction of endemic species, followed by the invasion of ubiquitous weedy species, leads to faunal homogenization between ecoregions.

  7. TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations.

    Science.gov (United States)

    Alvaro, Nestor; Miyao, Yusuke; Collier, Nigel

    2017-05-03

    Work on pharmacovigilance systems using texts from PubMed and Twitter typically target at different elements and use different annotation guidelines resulting in a scenario where there is no comparable set of documents from both Twitter and PubMed annotated in the same manner. This study aimed to provide a comparable corpus of texts from PubMed and Twitter that can be used to study drug reports from these two sources of information, allowing researchers in the area of pharmacovigilance using natural language processing (NLP) to perform experiments to better understand the similarities and differences between drug reports in Twitter and PubMed. We produced a corpus comprising 1000 tweets and 1000 PubMed sentences selected using the same strategy and annotated at entity level by the same experts (pharmacists) using the same set of guidelines. The resulting corpus, annotated by two pharmacists, comprises semantically correct annotations for a set of drugs, diseases, and symptoms. This corpus contains the annotations for 3144 entities, 2749 relations, and 5003 attributes. We present a corpus that is unique in its characteristics as this is the first corpus for pharmacovigilance curated from Twitter messages and PubMed sentences using the same data selection and annotation strategies. We believe this corpus will be of particular interest for researchers willing to compare results from pharmacovigilance systems (eg, classifiers and named entity recognition systems) when using data from Twitter and from PubMed. We hope that given the comprehensive set of drug names and the annotated entities and relations, this corpus becomes a standard resource to compare results from different pharmacovigilance studies in the area of NLP. ©Nestor Alvaro, Yusuke Miyao, Nigel Collier. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 03.05.2017.

  8. Hearing Tests on Mobile Devices: Evaluation of the Reference Sound Level by Means of Biological Calibration.

    Science.gov (United States)

    Masalski, Marcin; Kipiński, Lech; Grysiński, Tomasz; Kręcicki, Tomasz

    2016-05-30

    Hearing tests carried out in home setting by means of mobile devices require previous calibration of the reference sound level. Mobile devices with bundled headphones create a possibility of applying the predefined level for a particular model as an alternative to calibrating each device separately. The objective of this study was to determine the reference sound level for sets composed of a mobile device and bundled headphones. Reference sound levels for Android-based mobile devices were determined using an open access mobile phone app by means of biological calibration, that is, in relation to the normal-hearing threshold. The examinations were conducted in 2 groups: an uncontrolled and a controlled one. In the uncontrolled group, the fully automated self-measurements were carried out in home conditions by 18- to 35-year-old subjects, without prior hearing problems, recruited online. Calibration was conducted as a preliminary step in preparation for further examination. In the controlled group, audiologist-assisted examinations were performed in a sound booth, on normal-hearing subjects verified through pure-tone audiometry, recruited offline from among the workers and patients of the clinic. In both the groups, the reference sound levels were determined on a subject's mobile device using the Bekesy audiometry. The reference sound levels were compared between the groups. Intramodel and intermodel analyses were carried out as well. In the uncontrolled group, 8988 calibrations were conducted on 8620 different devices representing 2040 models. In the controlled group, 158 calibrations (test and retest) were conducted on 79 devices representing 50 models. Result analysis was performed for 10 most frequently used models in both the groups. The difference in reference sound levels between uncontrolled and controlled groups was 1.50 dB (SD 4.42). The mean SD of the reference sound level determined for devices within the same model was 4.03 dB (95% CI 3

  9. The biological model of postradiation restoration of plants on the organismic and population levels of organization

    International Nuclear Information System (INIS)

    Ivanishvili, N.I.; Gogebashvili, M.E.

    2012-01-01

    Full text : When studying postradiating restoration of plants, the question of working out of biological models for testing of biosystems' reliability has become rather urgent. It is known that each organization level of a live organism is characterized by certain mechanisms of postradiating restoration at the formation of various radiobiological reactions. For example, the basic processes at cellular, tissue and organism levels are reparation and regeneration whereas at cenosis level the leading processes are often the forms of population restoration. Besides, in spite of the fact that the population restoration at cenosis level is continuously inked with restoration at the lower organization levels, at this level the specific forms of restoration characterized for only this level are seen. It is natural that studying of the mechanisms of response to the influence of damaging factors needs new methodological approaches on various forms of population restoration with the use of adequate test systems. For this purpose the species of duckweed was used. It was seen that this test-system is characterized by the two levels of response to radiation influence. The first one - at a rather low level of radiation influence (up to 50Gy) when decrease in intensity of leaf growth as well as in colony formation was observed and the second one - at a high level of radiation influence (up to 200Gy) when a crushing of colonies took place and an increase in quantity of undeveloped plant leaves was seen. Thus, thanks to the step character of response of culture duckweed it becomes possible to definite quantity indicators for the investigated populations, not only at the influence of concrete physical and chemical factors but also at multifactorial influences that is often difficult to be calculated. It can be concluded that at the first level of damage an increase of plant resistance to unfavorable factors takes place that is due to the inhibition of growth processes

  10. Spatial transcriptomics: paving the way for tissue-level systems biology.

    Science.gov (United States)

    Moor, Andreas E; Itzkovitz, Shalev

    2017-08-01

    The tissues in our bodies are complex systems composed of diverse cell types that often interact in highly structured repeating anatomical units. External gradients of morphogens, directional blood flow, as well as the secretion and absorption of materials by cells generate distinct microenvironments at different tissue coordinates. Such spatial heterogeneity enables optimized function through division of labor among cells. Unraveling the design principles that govern this spatial division of labor requires techniques to quantify the entire transcriptomes of cells while accounting for their spatial coordinates. In this review we describe how recent advances in spatial transcriptomics open the way for tissue-level systems biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. The Systems Biology Markup Language (SBML: Language Specification for Level 3 Version 2 Core

    Directory of Open Access Journals (Sweden)

    Hucka Michael

    2018-03-01

    Full Text Available Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language, validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

  12. Systems Biology Markup Language (SBML Level 2 Version 5: Structures and Facilities for Model Definitions

    Directory of Open Access Journals (Sweden)

    Hucka Michael

    2015-06-01

    Full Text Available Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

  13. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

    Science.gov (United States)

    Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

    2015-09-04

    Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org.

  14. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

    Science.gov (United States)

    Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

    2018-03-09

    Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

  15. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

    Science.gov (United States)

    Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

    2015-09-04

    Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

  16. The Systems Biology Markup Language (SBML: Language Specification for Level 3 Version 1 Core

    Directory of Open Access Journals (Sweden)

    Hucka Michael

    2018-04-01

    Full Text Available Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language, validation rules that determine the validity of an SBML document, and examples of models in SBML form. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the format of annotations, the correction of errata and the addition of clarifications. Other materials and software are available from the SBML project website at http://sbml.org/.

  17. Public accessibility of biomedical articles from PubMed Central reduces journal readership--retrospective cohort analysis.

    Science.gov (United States)

    Davis, Philip M

    2013-07-01

    Does PubMed Central--a government-run digital archive of biomedical articles--compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.

  18. Occurrence of 210Po and Biological Effects of Low-Level Exposure: The Need for Research

    Science.gov (United States)

    Wiemels, Joseph L.

    2012-01-01

    Background: Polonium-210 (210Po) concentrations that exceed 1 Bq/L in drinking-water supplies have been reported from four widely separated U.S. states where exposure to it went unnoticed for decades. The radionuclide grandparents of 210Po are common in sediments, and segments of the public may be chronically exposed to low levels of 210Po in drinking water or in food products from animals raised in contaminated areas. Objectives: We summarized information on the environmental behavior, biokinetics, and toxicology of 210Po and identified the need for future research. Methods: Potential linkages between environmental exposure to 210Po and human health effects were identified in a literature review. Discussion: 210Po accumulates in the ovaries where it kills primary oocytes at low doses. Because of its radiosensitivity and tendency to concentrate 210Po, the ovary may be the critical organ in determining the lowest injurious dose for 210Po. 210Po also accumulates in the yolk sac of the embryo and in the fetal and placental tissues. Low-level exposure to 210Po may have subtle, long-term biological effects because of its tropism towards reproductive and embryonic and fetal tissues where exposure to a single alpha particle may kill or damage critical cells. 210Po is present in cigarettes and maternal smoking has several effects that appear consistent with the toxicology of 210Po. Conclusions: Much of the important biological and toxicological research on 210Po is more than four decades old. New research is needed to evaluate environmental exposure to 210Po and the biological effects of low-dose exposure to it so that public health officials can develop appropriate mitigation measures where necessary. PMID:22538346

  19. Evaluation of geologic materials to limit biological intrusion of low-level waste site covers

    International Nuclear Information System (INIS)

    Hakonson, T.E.; White, G.C.; Karlen, E.M.

    1982-01-01

    The long-term integrity of low-level waste shallow land burial sites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. This paper reports the preliminary results of a screening study to-determine the effectiveness of four biobarrier materials to stop plant root and animal penetration into simulated low-level wastes. Experiments employed 288 lysimeters consisting of 25-cm-diam PVC pipe, with four factors tested: plant species (alfalfa, barley, and sweet clover); top soil thickness (30 and 60 cm); biobarrier material (crushed tuff, bentonite clay, cobble, and cobble-gravel); and biobarrier thickness (clay-15, 30, and 45 cm, others 30, 60, and 90 cm). The crushed tuff, a sandy backfill material, offers little resistance to root and animal intrusion through the cover profile, while bentonite clay, cobble, and cobble-gravel combinations do reduce plant root and animal intrusion thorugh cover profiles. However, dessication of the clay barrier by invading plant roots may limit the usefulness of this material as a moisture and/or biological barrier. The cobble-gravel combination appears to be the best candidate for further testing on a larger scale because the gravel helps impede the imgration of soil into the cobble layer - the probable cause of failure of cobble-only biobarriers

  20. Comparison of the biological effects of {sup 18}F at different intracellular levels

    Energy Technology Data Exchange (ETDEWEB)

    Kashino, Genro, E-mail: kashino@oita-u.ac.jp [Advanced Molecular Imaging Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita 879-5593 (Japan); Hayashi, Kazutaka; Douhara, Kazumasa [Advanced Molecular Imaging Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita 879-5593 (Japan); Kobashigawa, Shinko; Mori, Hiromu [Department of Radiology, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita 879-5593 (Japan)

    2014-11-07

    Highlights: • We estimated the inductions of DNA DSB in cell treated with {sup 18}F-FDG. • We found that inductions of DNA DSB are dependent on accumulation of {sup 18}F in cell. • Accumulation of {sup 18}F in cell may be indispensable for risk estimation of PET. - Abstract: We herein examined the biological effects of cells treated with {sup 18}F labeled drugs for positron emission tomography (PET). The relationship between the intracellular distribution of {sup 18}F and levels of damaged DNA has yet to be clarified in detail. We used culture cells (Chinese Hamster Ovary cells) treated with two types of {sup 18}F labeled drugs, fluorodeoxyglucose (FDG) and fluorine ion (HF). FDG efficiently accumulated in cells, whereas HF did not. To examine the induction of DNA double strand breaks (DSB), we measured the number of foci for 53BP1 that formed at the site of DNA DSB. The results revealed that although radioactivity levels were the same, the induction of 53BP1 foci was stronger in cells treated with {sup 18}F-FDG than in those treated with {sup 18}F-HF. The clonogenic survival of cells was significantly lower with {sup 18}F-FDG than with {sup 18}F-HF. We concluded that the efficient accumulation of {sup 18}F in cells led to stronger biological effects due to more severe cellular lethality via the induction of DNA DSB.

  1. Lead levels in some biological samples of auto-mechanics in Abeokuta, Nigeria.

    Science.gov (United States)

    Babalola, O O; Ojo, L O; Aderemi, M O

    2005-12-01

    Lead levels were determined in the blood, scalp hair and fingernails of 38, all male auto-mechanics (aged 18-45 years) from Abeokuta, South-western Nigeria. The subjects were classified into four sub-groups based on the period of exposure namely: 1-5, 6-10, 11-15, and >16 years. Thirty-two occupationally unexposed subjects (mainly office workers) served as the control. The weight, height and body mass indexes of all subjects were noted, in addition to other information obtained through structured questionnaire. The mean values of blood lead (BPb), hair lead (HPb) and fingernail lead (NPb) of the occupationally exposed subjects (n=38) were 48.50 +/- 9.08 microg/dL, 17.75 +/- 5.16 microg/g, and 5.92 +/- 3.30 microg/g respectively, while the corresponding mean values for these parameters in the control subjects (n = 32) were 33.(,5 +/- 10.09 microg/dL, 14.30 +/- 5.90 microg/g and 5.31 +/- 2.77 microg/g respectively. The differences in BPb and HPb levels of the two groups were statistically significant (P <0.05 and P <0.01 respectively), while that of NPb was not significant. The levels of lead in the biological samples appeared to have no relationship with the number of years on the job. From these results, it was obvious that the higher levels of lead in the biological samples of test subjects, compared with those of the controls were from environmental sources.

  2. The inclusion of an online journal in PubMed central - a difficult path.

    Science.gov (United States)

    Grech, Victor

    2016-01-01

    The indexing of a journal in a prominent database (such as PubMed) is an important imprimatur. Journals accepted for inclusion in PubMed Central (PMC) are automatically indexed in PubMed but must provide the entire contents of their publications as XML-tagged (Extensible Markup Language) data files compliant with PubMed's document type definition (DTD). This paper describes the various attempts that the journal Images in Paediatric Cardiology made in its efforts to convert the journal contents (including all of the extant backlog) to PMC-compliant XML for archiving and indexing in PubMed after the journal was accepted for inclusion by the database.

  3. The Effects of Using Concept Mapping for Improving Advanced Level Biology Students' Lower- and Higher-Order Cognitive Skills

    Science.gov (United States)

    Bramwell-Lalor, Sharon; Rainford, Marcia

    2014-01-01

    This paper reports on teachers' use of concept mapping as an alternative assessment strategy in advanced level biology classes and its effects on students' cognitive skills on selected biology concepts. Using a mixed methods approach, the study employed a pre-test/post-test quasi-experimental design involving 156 students and 8 teachers from…

  4. Multiweek cell culture project for use in upper-level biology laboratories.

    Science.gov (United States)

    Marion, Rebecca E; Gardner, Grant E; Parks, Lisa D

    2012-06-01

    This article describes a laboratory protocol for a multiweek project piloted in a new upper-level biology laboratory (BIO 426) using cell culture techniques. Human embryonic kidney-293 cells were used, and several culture media and supplements were identified for students to design their own experiments. Treatments included amino acids, EGF, caffeine, epinephrine, heavy metals, and FBS. Students researched primary literature to determine their experimental variables, made their own solutions, and treated their cells over a period of 2 wk. Before this, a sterile technique laboratory was developed to teach students how to work with the cells and minimize contamination. Students designed their experiments, mixed their solutions, seeded their cells, and treated them with their control and experimental media. Students had the choice of manipulating a number of variables, including incubation times, exposure to treatment media, and temperature. At the end of the experiment, students observed the effects of their treatment, harvested and dyed their cells, counted relative cell numbers in control and treatment flasks, and determined the ratio of living to dead cells using a hemocytometer. At the conclusion of the experiment, students presented their findings in a poster presentation. This laboratory can be expanded or adapted to include additional cell lines and treatments. The ability to design and implement their own experiments has been shown to increase student engagement in the biology-related laboratory activities as well as develop the critical thinking skills needed for independent research.

  5. The pros and cons of ecological risk assessment based on data from different levels of biological organization

    Science.gov (United States)

    Rohr, Jason R.; Salice, Christopher J.; Nisbet, Roger M.

    2016-01-01

    Ecological risk assessment (ERA) is the process used to evaluate the safety of manufactured chemicals to the environment. Here we review the pros and cons of ERA across levels of biological organization, including suborganismal (e.g. biomarkers), individual, population, community, ecosystem, and landscapes levels. Our review revealed that level of biological organization is often related negatively with ease at assessing cause-effect relationships, ease of high-throughput screening of large numbers of chemicals (it is especially easier for suborganismal endpoints), and uncertainty of the ERA because low levels of biological organization tend to have a large distance between their measurement (what is quantified) and assessment endpoints (what is to be protected). In contrast, level of biological organization is often related positively with sensitivity to important negative and positive feedbacks and context dependencies within biological systems, and ease at capturing recovery from adverse contaminant effects. Some endpoints did not show obvious trends across levels of biological organization, such as the use of vertebrate animals in chemical testing and ease at screening large numbers of species, and other factors lacked sufficient data across levels of biological organization, such as repeatability, variability, cost per study, and cost per species of effects assessment, the latter of which might be a more defensible way to compare costs of ERAs than cost per study. To compensate for weaknesses of ERA at any particular level of biological organization, we also review mathematical modeling approaches commonly used to extrapolate effects across levels of organization. Finally, we provide recommendations for next generation ERA, submitting that if there is an ideal level of biological organization to conduct ERA, it will only emerge if ERA is approached simultaneously from the bottom of biological organization up as well as from the top down, all while employing

  6. The pros and cons of ecological risk assessment based on data from different levels of biological organization.

    Science.gov (United States)

    Rohr, Jason R; Salice, Christopher J; Nisbet, Roger M

    2016-10-01

    Ecological risk assessment (ERA) is the process used to evaluate the safety of manufactured chemicals to the environment. Here we review the pros and cons of ERA across levels of biological organization, including suborganismal (e.g., biomarkers), individual, population, community, ecosystem and landscapes levels. Our review revealed that level of biological organization is often related negatively with ease at assessing cause-effect relationships, ease of high-throughput screening of large numbers of chemicals (it is especially easier for suborganismal endpoints), and uncertainty of the ERA because low levels of biological organization tend to have a large distance between their measurement (what is quantified) and assessment endpoints (what is to be protected). In contrast, level of biological organization is often related positively with sensitivity to important negative and positive feedbacks and context dependencies within biological systems, and ease at capturing recovery from adverse contaminant effects. Some endpoints did not show obvious trends across levels of biological organization, such as the use of vertebrate animals in chemical testing and ease at screening large numbers of species, and other factors lacked sufficient data across levels of biological organization, such as repeatability, variability, cost per study and cost per species of effects assessment, the latter of which might be a more defensible way to compare costs of ERAs than cost per study. To compensate for weaknesses of ERA at any particular level of biological organization, we also review mathematical modeling approaches commonly used to extrapolate effects across levels of organization. Finally, we provide recommendations for next generation ERA, submitting that if there is an ideal level of biological organization to conduct ERA, it will only emerge if ERA is approached simultaneously from the bottom of biological organization up as well as from the top down, all while employing

  7. Geochemical and biological research at the NEA dumpsite for low-level radioactive waste

    International Nuclear Information System (INIS)

    Rutgers van der Loeff, M.M.; Lavaleye, M.S.S.

    1984-01-01

    A geochemical and biological study of the sea floor at the NEA dumpsite for low-level radioactive waste is reported. The sea bottom has rather steep hillsides. Slumps are usual phenomena and could be triggered by the dumping operations. The sediment is described in terms of its mineralogical and elemental composition. The variation in CaCO 3 content accounts for most of the variation in the elemental composition and cation exchange capacity. The present depth of the lysocline is shown to be about 4700 m. A description is given of the early diagenetic processes: (1) Mineralization of organic material, (2) Cation exchange, (3) Change in redox conditions and (4) Carbonate dissolution and recrystallization; and discussed in terms of their effects on the redistribution and transport of trace elements and radionuclides within the sediment and between sediment and overlying water. (orig.)

  8. Identifying novel glioma associated pathways based on systems biology level meta-analysis.

    Science.gov (United States)

    Hu, Yangfan; Li, Jinquan; Yan, Wenying; Chen, Jiajia; Li, Yin; Hu, Guang; Shen, Bairong

    2013-01-01

    With recent advances in microarray technology, including genomics, proteomics, and metabolomics, it brings a great challenge for integrating this "-omics" data to analysis complex disease. Glioma is an extremely aggressive and lethal form of brain tumor, and thus the study of the molecule mechanism underlying glioma remains very important. To date, most studies focus on detecting the differentially expressed genes in glioma. However, the meta-analysis for pathway analysis based on multiple microarray datasets has not been systematically pursued. In this study, we therefore developed a systems biology based approach by integrating three types of omics data to identify common pathways in glioma. Firstly, the meta-analysis has been performed to study the overlapping of signatures at different levels based on the microarray gene expression data of glioma. Among these gene expression datasets, 12 pathways were found in GeneGO database that shared by four stages. Then, microRNA expression profiles and ChIP-seq data were integrated for the further pathway enrichment analysis. As a result, we suggest 5 of these pathways could be served as putative pathways in glioma. Among them, the pathway of TGF-beta-dependent induction of EMT via SMAD is of particular importance. Our results demonstrate that the meta-analysis based on systems biology level provide a more useful approach to study the molecule mechanism of complex disease. The integration of different types of omics data, including gene expression microarrays, microRNA and ChIP-seq data, suggest some common pathways correlated with glioma. These findings will offer useful potential candidates for targeted therapeutic intervention of glioma.

  9. The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

    Science.gov (United States)

    Chaouiya, Claudine; Keating, Sarah M; Berenguier, Duncan; Naldi, Aurélien; Thieffry, Denis; van Iersel, Martijn P; Le Novère, Nicolas; Helikar, Tomáš

    2015-09-04

    Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as, for example, gene expression data coming from functional genomic experiments. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding qualitative models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Qualitative Models package for SBML Level 3 adds features so that qualitative models can be directly and explicitly encoded. The approach taken in this package is essentially based on the definition of regulatory or influence graphs. The SBML Qualitative Models package defines the structure and syntax necessary to describe qualitative models that associate discrete levels of activities with entity pools and the transitions between states that describe the processes involved. This is particularly suited to logical models (Boolean or multi-valued) and some classes of Petri net models can be encoded with the approach.

  10. Study of Effects of Sorghum Cultivation on Some Soil Biological Indicators at Different Zinc Levels

    Directory of Open Access Journals (Sweden)

    S. Bagheri

    2015-06-01

    Full Text Available Zinc is an essential element for plant growth which its high concentrations can cause pollution and toxicity in plant. In this study, the effects of sorghum cultivation on some indicators of microbial activity and its association with increased zinc concentrations in two soils with relatively similar physical and chemical properties, but different in concentration of heavy metals were investigated. In both soils zinc levels were added to obtain 250, 375 and 500 mg kg-1 (based on the initial nitric acid extractable content. Using plastic boxes containing 8 kg of soil, growth boxes (Rhizobox were prepared. The box interior was divided into three sections S1 (the rhizosphere, S2 (adjacent to the rhizosphere and S3 (bulk soil using nylon net plates. The results showed that at all levels of zinc in both soil types, BCF were bigger than units, so using this indicator, sorghum can be considered as a plant for accumulation of zinc. Microbial respiration and dehydrogenase activity was reduced in all sections adjacent to root in the polluted soil. It is generally understood that substrates and inhibitors (heavy metals compete in the formation of substrate-enzyme and inhibitor-enzyme complexes, but the effects of sorghum cultivation in increasing biological and enzyme activity indexes in soil 1 (non-polluted was higher than soil 2 (polluted, perhaps due to improvements in microbial activity in the vicinity of the roots, even in concentration higher than stress condition levels for zinc in soil.

  11. Time-dependent migration of citations through PubMed and OvidSP subsets: a study on a series of simultaneous PubMed and OvidSP searches.

    Science.gov (United States)

    Boeker, Martin; Vach, Werner; Motschall, Edith

    2013-01-01

    To quantitatively describe (1) differences between search results derived at consecutive time points with the PubMed and OvidSP literature search interfaces over a five day interval, and (2) the migration of citations through different subsets to estimate the timeliness of OvidSP. PubMed-Identifiers (PMIDs) of the following subsets were retrieved from PubMed and OvidSP simultaneously (within 8 h) at 11 days in March and April 2010 including 5 consecutive days: as supplied by publisher, in process, PubMed not MEDLINE, and OLDMEDLINE. Search results were compared for difference and intersection sets. The migration of citations on individual level was determined by comparison of corresponding sets over several days. The "in process" set was stable with about 446,000 - 452,000 citations; a small fraction of up to 3 % of the total subsets were in PubMed only and OvidSP only subsets. About 96 % of the ca. 10,500 citations in the OvidSP only subset migrated within 2 days out of the "in process" subset. The database of OvidSP is updated within a period of two days.

  12. Using Mathematics and Engineering to Solve Problems in Secondary Level Biology

    Science.gov (United States)

    Cox, Charles; Reynolds, Birdy; Schunn, Christian; Schuchardt, Anita

    2016-01-01

    There are strong classroom ties between mathematics and the sciences of physics and chemistry, but those ties seem weaker between mathematics and biology. Practicing biologists realize both that there are interesting mathematics problems in biology, and that viewing classroom biology in the context of another discipline could support students'…

  13. The Effect of Knowledge Linking Levels in Biology Lessons upon Students' Knowledge Structure

    Science.gov (United States)

    Wadouh, Julia; Liu, Ning; Sandmann, Angela; Neuhaus, Birgit J.

    2014-01-01

    Knowledge structure is an important aspect for defining students' competency in biology learning, but how knowledge structure is influenced by the teaching process in naturalistic biology classroom settings has scarcely been empirically investigated. In this study, 49 biology lessons in the teaching unit "blood and circulatory system" in…

  14. Platelet serotonin level and impulsivity in human self-destructive behavior: A biological and psychological study

    Directory of Open Access Journals (Sweden)

    S Era Dutta

    2017-01-01

    Full Text Available Context: Suicide is a disease and a global public health problem. Suicidology has come to become a topic of study for intervention and research. The serotonin (5-hydroxytryptamine [5HT] system has remained a prime area of investigation. The neurons and platelets display structural and functional similarities. Ninety-nine percent of 5HT is contained in platelets, which shares similar 5HT uptake and release mechanisms with 5HT neurons. Aims: This study aims to study human self-destructive behavior (HSDB. Objectives: Exploring the biological (serotonin levels in platelets and psychological aspects (impulsivity of attempted suicide or HSDB. Settings and Design: Thirty-one patients, above the age of 18 years, with a recent history of HSDB, were studied and given an International Classification of Diseases-10 diagnosis, after a detailed interview. Subjects and Methods: For the platelet 5HT estimation, blood samples were collected, and enzyme immunometric assay carried out. Detailed assessment of the impulsivity was done by the 25-item structured diagnostic interview for borderlines by Zanarini et al. Statistical Analysis Used: We obtained both categorical and continuous data. Chi-square test, Fisher's test, Student's t-test, and Pearson's product moment correlation were used. Results: Female subjects outnumbered males by 2:1. Major depression, adjustment disorder, personality disorder were predominant diagnoses. The mean platelet serotonin concentration for males = 57.3 ng/ml, that of females = 56.05 ng/ml (P > 0.05. Platelet 5HT levels were found to be negatively correlated with impulsivity scores (P < 0.05. Conclusions: Platelet serotonin levels in our study sample were quite low when compared with those reported in published literature. Low serotonin levels were inversely related to impulsivity, but only in males.

  15. The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core.

    Science.gov (United States)

    Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wengler, Katja; Bergmann, Frank Thomas

    2015-09-04

    Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded. The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.

  16. Center of cancer systems biology second annual workshop--tumor metronomics: timing and dose level dynamics.

    Science.gov (United States)

    Hahnfeldt, Philip; Hlatky, Lynn; Klement, Giannoula Lakka

    2013-05-15

    Metronomic chemotherapy, the delivery of doses in a low, regular manner so as to avoid toxic side effects, was introduced over 12 years ago in the face of substantial clinical and preclinical evidence supporting its tumor-suppressive capability. It constituted a marked departure from the classic maximum-tolerated dose (MTD) strategy, which, given its goal of rapid eradication, uses dosing sufficiently intense to require rest periods between cycles to limit toxicity. Even so, upfront tumor eradication is frequently not achieved with MTD, whereupon a de facto goal of longer-term tumor control is often pursued. As metronomic dosing has shown tumor control capability, even for cancers that have become resistant to the same drug delivered under MTD, the question arises whether it may be a preferable alternative dosing approach from the outset. To date, however, our knowledge of the coupled dynamics underlying metronomic dosing is neither sufficiently well developed nor widely enough disseminated to establish its actual potential. Meeting organizers thus felt the time was right, armed with new quantitative approaches, to call a workshop on "Tumor Metronomics: Timing and Dose Level Dynamics" to explore prospects for gaining a deeper, systems-level appreciation of the metronomics concept. The workshop proved to be a forum in which experts from the clinical, biologic, mathematical, and computational realms could work together to clarify the principles and underpinnings of metronomics. Among other things, the need for significant shifts in thinking regarding endpoints to be used as clinical standards of therapeutic progress was recognized. ©2013 AACR.

  17. The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

    Science.gov (United States)

    Olivier, Brett G; Bergmann, Frank T

    2015-09-04

    Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state. The Flux Balance Constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modelling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. The FBC package establishes a base level for the unambiguous exchange of genome-scale, constraint-based models, that can be built upon by the community to meet future needs (e. g. by extending it to cover dynamic FBC models).

  18. Assessment of DDT levels in selected environmental media and biological samples from Mexico and Central America.

    Science.gov (United States)

    Pérez-Maldonado, Iván N; Trejo, Antonio; Ruepert, Clemens; Jovel, Reyna del Carmen; Méndez, Mónica Patricia; Ferrari, Mirtha; Saballos-Sobalvarro, Emilio; Alexander, Carlos; Yáñez-Estrada, Leticia; Lopez, Dania; Henao, Samuel; Pinto, Emilio R; Díaz-Barriga, Fernando

    2010-03-01

    Taking into account the environmental persistence and the toxicity of DDT, the Pan American Health Organization (PAHO) organized a surveillance program in Mesoamerica which included the detection of residual DDT in environmental (soil) and biological samples (fish tissue and children's blood). This program was carried out in communities from Mexico, Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica and Panama. This paper presents the first report of that program. As expected, the results show that the levels for [summation operator] DDT in soil (outdoor or indoor) and fish samples in the majority of the locations studied are below guidelines. However, in some locations, we found children with high concentrations of DDT as in Mexico (mean level 50.2 ng/mL). Furthermore, in some communities and for some matrices, the DDT/DDE quotient is higher than one and this may reflect a recent DDT exposure. Therefore, more efforts are needed to avoid exposure and to prevent the reintroduction of DDT into the region. In this regard it is important to know that under the surveillance of PAHO and with the support of UNEP, a regional program in Mesoamerica for the collection and disposal of DDT and other POPs stockpiles is in progress. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  19. The Systems Biology Markup Language (SBML Level 3 Package: Layout, Version 1 Core

    Directory of Open Access Journals (Sweden)

    Gauges Ralph

    2015-06-01

    Full Text Available Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on. For software tools that also read and write models in SBML (Systems Biology Markup Language format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded.

  20. Evaluating biological transport of radionuclides at low-level waste burial sites

    International Nuclear Information System (INIS)

    Cadwell, L.L.; Kennedy, W.E.; McKenzie, D.H.

    1983-08-01

    The purpose of the work reported here is to develop and demonstrate methods for evaluating the long-term impact of biological processes at low-level waste (LLW) disposal sites. As part of this effort, we developed order-of-magnitude estimates of dose-to-man resulting from animal burrowing activity and plant translocation of radionuclides. Reference low-level waste sites in both arid and humid areas of the United States were examined. The results of our evaluation for generalized arid LLW burial site are presented here. Dose-to-man estimates resulting from biotic transport are compared with doses calculated from human intrusion exposure scenarios. Dose-to-man estimates, as a result of biotic transport, are of the same order of magnitude as those resulting from a more commonly evaluated human intrusion scenario. The reported lack of potential importance of biotic transport at LLW sites in earlier assessment studies is not confirmed by our findings. These results indicate that biotic transport has the long-term potential to mobilize radionuclides. Therefore, biotic transport should be carefully evaluated during burial site assessment

  1. The correlation of arsenic levels in drinking water with the biological samples of skin disorders

    Energy Technology Data Exchange (ETDEWEB)

    Kazi, Tasneem Gul [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: tgkazi@yahoo.com; Arain, Muhammad Balal [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: bilal_ku2004@yahoo.com; Baig, Jameel Ahmed [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: jab_mughal@yahoo.com; Jamali, Muhammad Khan [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: mkhanjamali@yahoo.com; Afridi, Hassan Imran [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: hassanimranafridi@yahoo.com; Jalbani, Nusrat [Pakistan Council for Scientific and Industrial Research, University Road Karachi-75280 (Pakistan)], E-mail: nusratjalbani_21@yahoo.com; Sarfraz, Raja Adil [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: rajaadilsarfraz@gmail.com; Shah, Abdul Qadir [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: aqshah07@yahoo.com; Niaz, Abdul [Center of Excellence in Analytical Chemistry, University of Sindh, Jamshoro 76080 (Pakistan)], E-mail: niazchemist2k6@yahoo.com

    2009-01-15

    Arsenic (As) poisoning has become a worldwide public health concern. The skin is quite sensitive to As and skin lesions are the most common and earliest nonmalignant effects associated to chronic As exposure. In 2005-2007, a survey was carried out on surface and groundwater arsenic contamination and relationships between As exposure via the drinking water and related adverse health effects (melanosis and keratosis) on villagers resides on the banks of Manchar lake, southern part of Sindh, Pakistan. We screened the population from arsenic-affected villages, 61 to 73% population were identified patients suffering from chronic arsenic toxicity. The effects of As toxicity via drinking water were estimated by biological samples (scalp hair and blood) of adults (males and females), have or have not skin problem (n = 187). The referent samples of both genders were also collected from the areas having low level of As (< 10 {mu}g/L) in drinking water (n = 121). Arsenic concentration in drinking water and biological samples were analyzed using electrothermal atomic absorption spectrometry. The range of arsenic concentrations in lake surface water was 35.2-158 {mu}g/L, which is 3-15 folds higher than World Health Organization [WHO, 2004. Guidelines for drinking-water quality third ed., WHO Geneva Switzerland.]. It was observed that As concentration in the scalp hair and blood samples were above the range of permissible values 0.034-0.319 {mu}g As/g for hair and < 0.5-4.2 {mu}g/L for blood. The linear regressions showed good correlations between arsenic concentrations in water versus hair and blood samples of exposed skin diseased subjects (R{sup 2} = 0.852 and 0.718) as compared to non-diseased subjects (R{sup 2} = 0.573 and 0.351), respectively.

  2. Retrieving clinical evidence: a comparison of PubMed and Google Scholar for quick clinical searches.

    Science.gov (United States)

    Shariff, Salimah Z; Bejaimal, Shayna Ad; Sontrop, Jessica M; Iansavichus, Arthur V; Haynes, R Brian; Weir, Matthew A; Garg, Amit X

    2013-08-15

    Physicians frequently search PubMed for information to guide patient care. More recently, Google Scholar has gained popularity as another freely accessible bibliographic database. To compare the performance of searches in PubMed and Google Scholar. We surveyed nephrologists (kidney specialists) and provided each with a unique clinical question derived from 100 renal therapy systematic reviews. Each physician provided the search terms they would type into a bibliographic database to locate evidence to answer the clinical question. We executed each of these searches in PubMed and Google Scholar and compared results for the first 40 records retrieved (equivalent to 2 default search pages in PubMed). We evaluated the recall (proportion of relevant articles found) and precision (ratio of relevant to nonrelevant articles) of the searches performed in PubMed and Google Scholar. Primary studies included in the systematic reviews served as the reference standard for relevant articles. We further documented whether relevant articles were available as free full-texts. Compared with PubMed, the average search in Google Scholar retrieved twice as many relevant articles (PubMed: 11%; Google Scholar: 22%; PGoogle Scholar: 8%; P=.07). Google Scholar provided significantly greater access to free full-text publications (PubMed: 5%; Google Scholar: 14%; PGoogle Scholar returns twice as many relevant articles as PubMed and provides greater access to free full-text articles.

  3. Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students†

    OpenAIRE

    Beach, Dale L.; Alvarez, Consuelo J.

    2015-01-01

    Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniq...

  4. Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology.

    Science.gov (United States)

    MacLeod, Miles; Nersessian, Nancy J

    2015-02-01

    In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding." Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Asian Americans and European Americans' stigma levels in response to biological and social explanations of depression.

    Science.gov (United States)

    Cheng, Zhen Hadassah

    2015-05-01

    Mental illness stigma is prevalent among Asian Americans, and it is a key barrier that prevents them from seeking psychological services. Limited studies have experimentally examined how Asian Americans respond to biological and social explanations of mental illness. Understanding how to educate and communicate about mental illness effectively is crucial in increasing service utilization among Asian Americans. To assess how genetic, neurobiological, and social explanations for the onset of depression affects Asian American and European American's mental illness stigma. 231 Asian Americans and 206 European Americans read about an individual with major depression and were randomly assigned to be informed that the cause was either genetic, neurobiological, social, or unknown. Various stigma outcomes, including social distance, fear, and depression duration were assessed. Consistent with prior research, Asian Americans had higher baseline levels of stigma compared to European Americans. Greater social essentialist beliefs predicted positive stigma outcomes for Asian Americans, such as a greater willingness to be near, help, and hire someone with depression, but genetic essentialist beliefs predicted negative stigma outcomes, such as fear. In addition, a social explanation for the etiology of depression led to lower stigma outcomes for Asian Americans; it decreased their fear of someone with depression and increased the perception that depression is treatable. For European Americans, both genetic and social essentialist beliefs predicted a greater perception of depression treatability. Although genetics do play a role in the development of depression, emphasizing a social explanation for the origin of depression may help reduce stigma for Asian Americans.

  6. The correlation of arsenic levels in drinking water with the biological samples of skin disorders

    International Nuclear Information System (INIS)

    Kazi, Tasneem Gul; Arain, Muhammad Balal; Baig, Jameel Ahmed; Jamali, Muhammad Khan; Afridi, Hassan Imran; Jalbani, Nusrat; Sarfraz, Raja Adil; Shah, Abdul Qadir; Niaz, Abdul

    2009-01-01

    Arsenic (As) poisoning has become a worldwide public health concern. The skin is quite sensitive to As and skin lesions are the most common and earliest nonmalignant effects associated to chronic As exposure. In 2005-2007, a survey was carried out on surface and groundwater arsenic contamination and relationships between As exposure via the drinking water and related adverse health effects (melanosis and keratosis) on villagers resides on the banks of Manchar lake, southern part of Sindh, Pakistan. We screened the population from arsenic-affected villages, 61 to 73% population were identified patients suffering from chronic arsenic toxicity. The effects of As toxicity via drinking water were estimated by biological samples (scalp hair and blood) of adults (males and females), have or have not skin problem (n = 187). The referent samples of both genders were also collected from the areas having low level of As ( 2 = 0.852 and 0.718) as compared to non-diseased subjects (R 2 = 0.573 and 0.351), respectively

  7. Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.

    Science.gov (United States)

    Kafkas, Şenay; Kim, Jee-Hyub; Pi, Xingjun; McEntyre, Johanna R

    2015-01-01

    In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Using text-mining methods to identify and extract a variety of core biological database accession numbers, we found that the supplemental data files contain many more database citations than the body of the article, and that those citations often take the form of a relatively small number of articles citing large collections of accession numbers in text-based files. Moreover, citation of value-added databases derived from submission databases (such as Pfam, UniProt or Ensembl) is common, demonstrating the reuse of these resources as datasets in themselves. All the database accession numbers extracted from the supplementary data are publicly accessible from http://dx.doi.org/10.5281/zenodo.11771. Our study suggests that supplementary data should be considered when linking articles with data, in curation pipelines, and in information retrieval tasks in order to make full use of the entire research article. These observations highlight the need to improve the management of supplemental data in general, in order to make this information more discoverable and useful.

  8. Systematic identification of latent disease-gene associations from PubMed articles.

    Science.gov (United States)

    Zhang, Yuji; Shen, Feichen; Mojarad, Majid Rastegar; Li, Dingcheng; Liu, Sijia; Tao, Cui; Yu, Yue; Liu, Hongfang

    2018-01-01

    Recent scientific advances have accumulated a tremendous amount of biomedical knowledge providing novel insights into the relationship between molecular and cellular processes and diseases. Literature mining is one of the commonly used methods to retrieve and extract information from scientific publications for understanding these associations. However, due to large data volume and complicated associations with noises, the interpretability of such association data for semantic knowledge discovery is challenging. In this study, we describe an integrative computational framework aiming to expedite the discovery of latent disease mechanisms by dissecting 146,245 disease-gene associations from over 25 million of PubMed indexed articles. We take advantage of both Latent Dirichlet Allocation (LDA) modeling and network-based analysis for their capabilities of detecting latent associations and reducing noises for large volume data respectively. Our results demonstrate that (1) the LDA-based modeling is able to group similar diseases into disease topics; (2) the disease-specific association networks follow the scale-free network property; (3) certain subnetwork patterns were enriched in the disease-specific association networks; and (4) genes were enriched in topic-specific biological processes. Our approach offers promising opportunities for latent disease-gene knowledge discovery in biomedical research.

  9. Science Seeker: A New Model for Teaching Information Literacy to Entry-Level Biology Undergraduates

    Science.gov (United States)

    Petzold, Jacquelyn; Winterman, Brian; Montooth, Kristi

    2010-01-01

    In order to integrate library instruction seamlessly into an introductory biology course, two librarians collaborated with a biology faculty member to create a three-part series of instruction sessions known as the Science Seeker. The Science Seeker taught students about the structure of scientific information by tracing the path that discoveries…

  10. Level of Awareness of Biology and Geography Students Related to Recognizing Some Plants

    Science.gov (United States)

    Aladag, Caner; Kaya, Bastürk; Dinç, Muhittin

    2017-01-01

    The aim of this study is to investigate the awareness of the geography and biology students about recognizing some plants which they see frequently around them in accordance with the information they gained during their education process. The sample of the study consists of 37 biology and 40 geography students studying at the Ahmet Kelesoglu…

  11. Analyzing Change in Students' Gene-to-Evolution Models in College-Level Introductory Biology

    Science.gov (United States)

    Dauer, Joseph T.; Momsen, Jennifer L.; Speth, Elena Bray; Makohon-Moore, Sasha C.; Long, Tammy M.

    2013-01-01

    Research in contemporary biology has become increasingly complex and organized around understanding biological processes in the context of systems. To better reflect the ways of thinking required for learning about systems, we developed and implemented a pedagogical approach using box-and-arrow models (similar to concept maps) as a foundational…

  12. Health informatics research in Australia: retrospective analysis using PubMed

    Directory of Open Access Journals (Sweden)

    Kumara Mendis

    2007-01-01

    Discussion Australian HI publications in PubMed increased consistently throughout the period 1970-2005, which is on a par with world trends in HI publications. In Australia, most HI publications are in general medical journals. Lack of consistency in author names and failure to include the country name and even the state are the main obstacles to PubMed bibliometric analysis.

  13. Validation of search filters for identifying pediatric studies in PubMed

    NARCIS (Netherlands)

    Leclercq, Edith; Leeflang, Mariska M. G.; van Dalen, Elvira C.; Kremer, Leontien C. M.

    2013-01-01

    To identify and validate PubMed search filters for retrieving studies including children and to develop a new pediatric search filter for PubMed. We developed 2 different datasets of studies to evaluate the performance of the identified pediatric search filters, expressed in terms of sensitivity,

  14. Growing trend of CE at the omics level: the frontier of systems biology--an update.

    Science.gov (United States)

    Ban, Eunmi; Park, Soo Hyun; Kang, Min-Jung; Lee, Hyun-Jung; Song, Eun Joo; Yoo, Young Sook

    2012-01-01

    Omics is the study of proteins, peptides, genes, and metabolites in living organisms. Systems biology aims to understand the system through the study of the relationship between elements such as genes and proteins in biological system. Recently, systems biology emerged as the result of the advanced development of high-throughput analysis technologies such as DNA sequencers, DNA arrays, and mass spectrometry for omics studies. Among a number of analytical tools and technologies, CE and CE coupled to MS are promising and relatively rapidly developing tools with the potential to provide qualitative and quantitative analyses of biological molecules. With an emphasis on CE for systems biology, this review summarizes the method developments and applications of CE for the genomic, transcriptomic, proteomic, and metabolomic studies focusing on the drug discovery and disease diagnosis and therapies since 2009. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. [THE INCONSISTENCIES OF REGULATION OF METABOLISM IN PHYLOGENESIS AT THREE LEVELS OF "RELATIVE BIOLOGICAL PERFECTION": ETIOLOGY OF METABOLIC PANDEMICS].

    Science.gov (United States)

    Titov, V N

    2015-11-01

    The regulation of metabolism in vivo can be comprehended by considering stages of becoming inphylogenesis of humoral, hormonal, vegetative regulators separately: at the level of cells; in paracrin-regulated cenosises of cells; organs and systems under open blood circulation and closed system of blood flow. The levels of regulations formed at different stages of phylogenesis. Their completion occurred at achievement of "relative biological perfection". Only this way need of cells in functional, structural interaction and forming of multicellular developed. The development of organs and systems of organs also completed at the level of "relative biological perfection". From the same level the third stage of becoming of regulation of metabolism at the level of organism started. When three conditions of "relative biological perfection" achieved consequently at level in vivo are considered in species Homo sapiens using system approach it is detected that "relative biological perfection" in vivo is accompanied by different inconsistencies of regulation of metabolism. They are etiologic factors of "metabolic pandemics ". The inconsistencies (etiological factors) are consider as exemplified by local (at the level of paracrin-regulated cenosises of cells) and system (at the level of organism) regulation of biological reaction metabolism-microcirculation that results in dysfunction of target organs and development of pathogenesis of essential metabolic arterial hypertension. The article describes phylogenetic difference between visceral fatty cells and adpocytes, regulation of metabolism by phylogenetically late insulin, reaction of albumin at increasing of content of unesterified fatty acids in blood plasma, difference of function of resident macrophage and monocytes-macrophages in pathogenesis of atherosclerosis, metabolic syndrome, insulin resistance, obesity, under diabetes mellitus and essential metabolic arterial hypertension.

  16. [Knowledge and power at a molecular level; biological psychiatry in a social context].

    Science.gov (United States)

    Verhoeff, B

    2009-01-01

    How do we acquire our knowledge about psychiatric disorders and how did the current biologically way of thinking in psychiatry originate? With the help of the philosophy of Michel Foucault and Nikolas Rose this essay describes the conditions that made possible today's biological approach in psychiatry. It will become clear that research in the life sciences and the psychiatric knowledge arising from this research are shaped and formed in a complex network of social, economic, political and scientific forces. The biological approach to psychiatric disorders is the product of present-day relationships between scientific developments and commercial corporations.

  17. Ecohydrological role of biological soil crusts across a gradient in levels of development

    Science.gov (United States)

    Whitney, Kristen M.; Vivoni, Enrique R.; Duniway, Michael C.; Bradford, John B.; Reed, Sasha C.; Belnap, Jayne

    2017-01-01

    Though biological soil crusts (biocrusts) form abundant covers in arid and semiarid regions, their competing effects on soil hydrologic conditions are rarely accounted for in models. This study presents the modification of a soil water balance model to account for the presence of biocrusts at different levels of development (LOD) and their impact on one-dimensional hydrologic processes during warm and cold seasons. The model is developed, tested, and applied to study the hydrologic controls of biocrusts in context of a long-term manipulative experiment equipped with meteorological and soil moisture measurements in a Colorado Plateau ecosystem near Moab, Utah. The climate manipulation treatments resulted in distinct biocrust communities, and model performance with respect to soil moisture was assessed in experimental plots with varying LOD as quantified through a field-based roughness index (RI). Model calibration and testing yielded excellent comparisons to observations and smooth variations of biocrust parameters with RI approximated through simple regressions. The model was then used to quantify how LOD affects soil infiltration, evapotranspiration, and runoff under calibrated conditions and in simulation experiments with gradual modifications in biocrust porosity and hydraulic conductivity. Simulation results show that highly developed biocrusts modulate soil moisture nonlinearly with LOD by altering soil infiltration and buffering against evapotranspiration losses, with small impacts on runoff. The nonlinear and threshold variations of the soil water balance in the presence of biocrusts of varying LOD helps explain conflicting outcomes of various field studies and sheds light on the ecohydrological role of biocrusts in arid and semiarid ecosystems.

  18. Evaluation of geologic materials to limit biological intrusion into low-level radioactive waste disposal sites

    International Nuclear Information System (INIS)

    Hakonson, T.E.

    1986-02-01

    This report describes the results of a three-year research program to evaluate the performance of selected soil and rock trench cap designs in limiting biological intrusion into simulated waste. The report is divided into three sections including a discussion of background material on biological interactions with waste site trench caps, a presentation of experimental data from field studies conducted at several scales, and a final section on the interpretation and limitations of the data including implications for the user

  19. Quantity and quality assessment of randomized controlled trials on orthodontic practice in PubMed.

    Science.gov (United States)

    Shimada, Tatsuo; Takayama, Hisako; Nakamura, Yoshiki

    2010-07-01

    To find current high-quality evidence for orthodontic practice within a reasonable time, we tested the performance of a PubMed search. PubMed was searched using publication type randomized controlled trial and medical subject heading term "orthodontics" for articles published between 2003 and 2007. The PubMed search results were compared with those from a hand search of four orthodontic journals to determine the sensitivity of PubMed search. We evaluated the precision of the PubMed search result and assessed the quality of individual randomized controlled trials using the Jadad scale. Sensitivity and precision were 97.46% and 58.12%, respectively. In PubMed, of the 277 articles retrieved, 161 (58.12%) were randomized controlled trials on orthodontic practice, and 115 of the 161 articles (71.42%) were published in four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics. Assessment by the Jadad scale revealed 60 high-quality randomized controlled trials on orthodontic practice, of which 45 (75%) were published in these four journals. PubMed is a highly desirable search engine for evidence-based orthodontic practice. To stay current and get high-quality evidence, it is reasonable to look through four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics.

  20. Leaving the Lecture Behind: Putting PubMed Instruction into the Hands of the Students.

    Science.gov (United States)

    Turner, Rose L; M Ketchum, Andrea; Ratajeski, Melissa A; Wessel, Charles B

    2017-01-01

    This column describes the development of a one-shot PubMed instruction class for medical students at a health sciences library. Background information on the objective is presented and discussed in the context of educational practice literature. The new course design centers on a guided group method of instruction in order to integrate more active learning. Surveyed students reported that the method was an effective way to learn how to search PubMed and that they preferred it to a traditional lecture. Pros and cons of the method are offered for other health sciences libraries interested in presenting PubMed instruction in a similar manner.

  1. Integrative assessment of Evolutionary theory acceptance and knowledge levels of Biology undergraduate students from a Brazilian university

    Science.gov (United States)

    Tavares, Gustavo Medina; Bobrowski, Vera Lucia

    2018-03-01

    The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students' perceptions towards evolution, and studies can help to reveal those factors. We used a conceptual questionnaire, the Measure of Acceptance of the Theory of Evolution (MATE) instrument, and a Knowledge test to assess (1) the level of acceptance and understanding of 23 undergraduate Biology students nearing the end of their course, (2) other factors that could affect these levels, including course structure, and (3) the most difficult topics regarding evolutionary biology. The results of this study showed that the students, on average, had a 'Very High Acceptance' (89.91) and a 'Very Low Knowledge' (59.42%) of Evolutionary theory, and also indicated a moderate positive correlation between the two (r = 0.66, p = .001). The most difficult topics were related to the definition of evolution and dating techniques. We believe that the present study provides evidence for policymakers to reformulate current school and university curricula in order to improve the teachers' acceptance and understanding of evolution and other biological concepts, consequently, helping students reduce their misconceptions related to evolutionary biology.

  2. Co-culture systems and technologies: taking synthetic biology to the next level.

    Science.gov (United States)

    Goers, Lisa; Freemont, Paul; Polizzi, Karen M

    2014-07-06

    Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  3. Atypical biological motion kinematics are represented by complementary lower-level and top-down processes during imitation learning.

    Science.gov (United States)

    Hayes, Spencer J; Dutoy, Chris A; Elliott, Digby; Gowen, Emma; Bennett, Simon J

    2016-01-01

    Learning a novel movement requires a new set of kinematics to be represented by the sensorimotor system. This is often accomplished through imitation learning where lower-level sensorimotor processes are suggested to represent the biological motion kinematics associated with an observed movement. Top-down factors have the potential to influence this process based on the social context, attention and salience, and the goal of the movement. In order to further examine the potential interaction between lower-level and top-down processes in imitation learning, the aim of this study was to systematically control the mediating effects during an imitation of biological motion protocol. In this protocol, we used non-human agent models that displayed different novel atypical biological motion kinematics, as well as a control model that displayed constant velocity. Importantly the three models had the same movement amplitude and movement time. Also, the motion kinematics were displayed in the presence, or absence, of end-state-targets. Kinematic analyses showed atypical biological motion kinematics were imitated, and that this performance was different from the constant velocity control condition. Although the imitation of atypical biological motion kinematics was not modulated by the end-state-targets, movement time was more accurate in the absence, compared to the presence, of an end-state-target. The fact that end-state targets modulated movement time accuracy, but not biological motion kinematics, indicates imitation learning involves top-down attentional, and lower-level sensorimotor systems, which operate as complementary processes mediated by the environmental context. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Microtask crowdsourcing for disease mention annotation in PubMed abstracts.

    Science.gov (United States)

    Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

    2015-01-01

    Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the 'training set' of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402.

  5. [Use of PubMed to improve evidence-based medicine in routine urological practice].

    Science.gov (United States)

    Rink, M; Kluth, L A; Shariat, S F; Chun, F K; Fisch, M; Dahm, P

    2013-03-01

    Applying evidence-based medicine in daily clinical practice is the basis of patient-centered medicine and knowledge of accurate literature acquisition skills is necessary for informed clinical decision-making. PubMed is an easy accessible, free bibliographic database comprising over 21 million citations from the medical field, life-science journals and online books. The article summarizes the effective use of PubMed in routine urological clinical practice based on a common case scenario. This article explains the simple use of PubMed to obtain the best search results with the highest evidence. Accurate knowledge about the use of PubMed in routine clinical practice can improve evidence-based medicine and also patient treatment.

  6. PubMed search filters for the study of putative outdoor air pollution determinants of disease

    OpenAIRE

    Curti, Stefania; Gori, Davide; Di Gregori, Valentina; Farioli, Andrea; Baldasseroni, Alberto; Fantini, Maria Pia; Christiani, David C; Violante, Francesco S; Mattioli, Stefano

    2016-01-01

    Objectives: Several PubMed search filters have been developed in contexts other than environmental. We aimed at identifying efficient PubMed search filters for the study of environmental determinants of diseases related to outdoor air pollution. Methods: We compiled a list of Medical Subject Headings (MeSH) and non-MeSH terms seeming pertinent to outdoor air pollutants exposure as determinants of diseases in the general population. We estimated proportions of potentially pertinent articles to...

  7. PREDICTING LEVELS OF STRESS FROM BIOLOGICAL ASSESSMENT DATA: EMPIRICAL MODELS FROM THE EASTERN CORN BELT PLAINS

    Science.gov (United States)

    Biological assessment is becoming an increasingly popular tool in the evaluation of stream ecosystem integrity. However, little progress has been made to date in developing tools to relate assessment results to specific stressors. This paper continues the investigation of the f...

  8. The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

    NARCIS (Netherlands)

    Olivier, B.G.; Bergmann, F.T.

    2015-01-01

    Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux

  9. Neutron-Activation Analysis of Biological Material with High Radiation Levels

    Energy Technology Data Exchange (ETDEWEB)

    Samsahl, K

    1966-09-15

    A method has been developed for the chemical separation and subsequent gamma-spectrometric analysis of the alkali metals, the alkaline earths, the rare earths, chromium, hafnium, lanthanum, manganese, phosphorus, scandium and silver in neutron-activated biological material. The separation steps, being fully automatic, are based on a combination of ion-exchange and partition chromatography and require 40 min.

  10. Neutron-Activation Analysis of Biological Material with High Radiation Levels

    International Nuclear Information System (INIS)

    Samsahl, K.

    1966-09-01

    A method has been developed for the chemical separation and subsequent gamma-spectrometric analysis of the alkali metals, the alkaline earths, the rare earths, chromium, hafnium, lanthanum, manganese, phosphorus, scandium and silver in neutron-activated biological material. The separation steps, being fully automatic, are based on a combination of ion-exchange and partition chromatography and require 40 min

  11. The Biological Behaviors of Rat Dermal Fibroblasts Can Be Inhibited by High Levels of MMP9

    Directory of Open Access Journals (Sweden)

    Sheng-Neng Xue

    2012-01-01

    Full Text Available Aims. To explore the effects of the high expression of MMP9 on biological behaviors of fibroblasts. Methods. High glucose and hyperhomocysteine were used to induce MMP9 expression in skin fibroblasts. Cell proliferation was detected by flow cytometry and cell viability by CCK-8. ELISA assay was used to detect collagen (hydroxyproline secretion. Scratch test was employed to evaluate horizontal migration of cells and transwell method to evaluate vertical migration of cells. Results. The mRNA and protein expressions of MMP9 and its protease activity were significantly higher in cells treated with high glucose and hyperhomocysteine than those in control group. At the same time, the S-phase cell ratio, proliferation index, cell viability, collagen (hydroxyproline secretion, horizontal migration rate, and the number of vertical migration cells decreased in high-glucose and hyperhomocysteine-treated group. Tissue inhibitor of metalloproteinase 1 (TIMP1, which inhibits the activity of MMP9, recovered the above biological behaviors. Conclusions. High expression of MMP9 in skin fibroblasts could be induced by cultureing in high glucose and hyperhomocysteine medium, which inhibited cell biological behaviors. Inhibitions could be reversed by TIMP1. The findings suggested that MMP9 deters the healing of diabetic foot ulcers by inhibiting the biological behaviors of fibroblasts.

  12. Predicting in vivo effect levels for repeat-dose systemic toxicity using chemical, biological, kinetic and study covariates.

    Science.gov (United States)

    Truong, Lisa; Ouedraogo, Gladys; Pham, LyLy; Clouzeau, Jacques; Loisel-Joubert, Sophie; Blanchet, Delphine; Noçairi, Hicham; Setzer, Woodrow; Judson, Richard; Grulke, Chris; Mansouri, Kamel; Martin, Matthew

    2018-02-01

    In an effort to address a major challenge in chemical safety assessment, alternative approaches for characterizing systemic effect levels, a predictive model was developed. Systemic effect levels were curated from ToxRefDB, HESS-DB and COSMOS-DB from numerous study types totaling 4379 in vivo studies for 1247 chemicals. Observed systemic effects in mammalian models are a complex function of chemical dynamics, kinetics, and inter- and intra-individual variability. To address this complex problem, systemic effect levels were modeled at the study-level by leveraging study covariates (e.g., study type, strain, administration route) in addition to multiple descriptor sets, including chemical (ToxPrint, PaDEL, and Physchem), biological (ToxCast), and kinetic descriptors. Using random forest modeling with cross-validation and external validation procedures, study-level covariates alone accounted for approximately 15% of the variance reducing the root mean squared error (RMSE) from 0.96 log 10 to 0.85 log 10  mg/kg/day, providing a baseline performance metric (lower expectation of model performance). A consensus model developed using a combination of study-level covariates, chemical, biological, and kinetic descriptors explained a total of 43% of the variance with an RMSE of 0.69 log 10  mg/kg/day. A benchmark model (upper expectation of model performance) was also developed with an RMSE of 0.5 log 10  mg/kg/day by incorporating study-level covariates and the mean effect level per chemical. To achieve a representative chemical-level prediction, the minimum study-level predicted and observed effect level per chemical were compared reducing the RMSE from 1.0 to 0.73 log 10  mg/kg/day, equivalent to 87% of predictions falling within an order-of-magnitude of the observed value. Although biological descriptors did not improve model performance, the final model was enriched for biological descriptors that indicated xenobiotic metabolism gene expression, oxidative stress, and

  13. Operationalising Ecologically Sustainable Development at the Micro Level Pareto Optimality and the Preservation of Biologically Crucial Levels.

    NARCIS (Netherlands)

    Bithas, K.; Nijkamp, P.

    2006-01-01

    The concept of Ecologically Sustainable Economic Development (ESED) has led to relentlessly heated debate. Yet, it still remains without a clear operational framework. At the micro level where a multitude of projects and programmes are designed, the absence of operational principles has serious

  14. Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students.

    Science.gov (United States)

    Beach, Dale L; Alvarez, Consuelo J

    2015-12-01

    Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic "parts," students construct a "reporter plasmid" expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a "sensor plasmid," the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses.

  15. GOClonto: an ontological clustering approach for conceptualizing PubMed abstracts.

    Science.gov (United States)

    Zheng, Hai-Tao; Borchert, Charles; Kim, Hong-Gee

    2010-02-01

    Concurrent with progress in biomedical sciences, an overwhelming of textual knowledge is accumulating in the biomedical literature. PubMed is the most comprehensive database collecting and managing biomedical literature. To help researchers easily understand collections of PubMed abstracts, numerous clustering methods have been proposed to group similar abstracts based on their shared features. However, most of these methods do not explore the semantic relationships among groupings of documents, which could help better illuminate the groupings of PubMed abstracts. To address this issue, we proposed an ontological clustering method called GOClonto for conceptualizing PubMed abstracts. GOClonto uses latent semantic analysis (LSA) and gene ontology (GO) to identify key gene-related concepts and their relationships as well as allocate PubMed abstracts based on these key gene-related concepts. Based on two PubMed abstract collections, the experimental results show that GOClonto is able to identify key gene-related concepts and outperforms the STC (suffix tree clustering) algorithm, the Lingo algorithm, the Fuzzy Ants algorithm, and the clustering based TRS (tolerance rough set) algorithm. Moreover, the two ontologies generated by GOClonto show significant informative conceptual structures.

  16. Radiation and cancer in Wales. The biological consequences of low-level radiation

    International Nuclear Information System (INIS)

    Busby, C.C.

    1994-01-01

    recent developments have made necessary the revision of the original booklet. Chapter 1 of this second edition is an updating of the first edition. Chapter 2 covers in more detail the effects of low-level radiation in Wales, including discussion of the increases in bone cancer and the effects of Chernobyl. The second-event theory is reproduced as Chapter 3, which also includes a copy of the original paper to the International Journal of Radiation Biology and some of the responses which have been made to it, both by the referees for this journal and other authorities in the field

  17. Radiation and cancer in Wales. The biological consequences of low-level radiation

    Energy Technology Data Exchange (ETDEWEB)

    Busby, C C

    1994-07-01

    recent developments have made necessary the revision of the original booklet. Chapter 1 of this second edition is an updating of the first edition. Chapter 2 covers in more detail the effects of low-level radiation in Wales, including discussion of the increases in bone cancer and the effects of Chernobyl. The second-event theory is reproduced as Chapter 3, which also includes a copy of the original paper to the International Journal of Radiation Biology and some of the responses which have been made to it, both by the referees for this journal and other authorities in the field.

  18. Net improvement of correct answers to therapy questions after pubmed searches: pre/post comparison.

    Science.gov (United States)

    McKibbon, Kathleen Ann; Lokker, Cynthia; Keepanasseril, Arun; Wilczynski, Nancy L; Haynes, R Brian

    2013-11-08

    Clinicians search PubMed for answers to clinical questions although it is time consuming and not always successful. To determine if PubMed used with its Clinical Queries feature to filter results based on study quality would improve search success (more correct answers to clinical questions related to therapy). We invited 528 primary care physicians to participate, 143 (27.1%) consented, and 111 (21.0% of the total and 77.6% of those who consented) completed the study. Participants answered 14 yes/no therapy questions and were given 4 of these (2 originally answered correctly and 2 originally answered incorrectly) to search using either the PubMed main screen or PubMed Clinical Queries narrow therapy filter via a purpose-built system with identical search screens. Participants also picked 3 of the first 20 retrieved citations that best addressed each question. They were then asked to re-answer the original 14 questions. We found no statistically significant differences in the rates of correct or incorrect answers using the PubMed main screen or PubMed Clinical Queries. The rate of correct answers increased from 50.0% to 61.4% (95% CI 55.0%-67.8%) for the PubMed main screen searches and from 50.0% to 59.1% (95% CI 52.6%-65.6%) for Clinical Queries searches. These net absolute increases of 11.4% and 9.1%, respectively, included previously correct answers changing to incorrect at a rate of 9.5% (95% CI 5.6%-13.4%) for PubMed main screen searches and 9.1% (95% CI 5.3%-12.9%) for Clinical Queries searches, combined with increases in the rate of being correct of 20.5% (95% CI 15.2%-25.8%) for PubMed main screen searches and 17.7% (95% CI 12.7%-22.7%) for Clinical Queries searches. PubMed can assist clinicians answering clinical questions with an approximately 10% absolute rate of improvement in correct answers. This small increase includes more correct answers partially offset by a decrease in previously correct answers.

  19. Integrating phenotypic data from electronic patient records with molecular level systems biology

    DEFF Research Database (Denmark)

    Brunak, Søren

    2011-01-01

    Electronic patient records remain a rather unexplored, but potentially rich data source for discovering correlations between diseases. We describe a general approach for gathering phenotypic descriptions of patients from medical records in a systematic and non-cohort dependent manner. By extracti...... Classification of Disease ontology and is therefore in principle language independent. As a use case we show how records from a Danish psychiatric hospital lead to the identification of disease correlations, which subsequently are mapped to systems biology frameworks....

  20. Biological Signatures of Brain Damage Associated with High Serum Ferritin Levels in Patients with Acute Ischemic Stroke and Thrombolytic Treatment

    Directory of Open Access Journals (Sweden)

    Mónica Millán

    2008-01-01

    Full Text Available Background and purpose: Increased body iron stores have been related to greater oxidative stress and brain injury in clinical and experimental cerebral ischemia and reperfusion. We aimed to investigate the biological signatures of excitotoxicity, inflammation and blood brain barrier disruption potentially associated with high serum ferritin levels-related damage in acute stroke patients treated with i.v. t-PA.

  1. Effect of different humidity levels on the biology of longtailed mealy bug pseudococcus longispinus (targioni and tozzetti) (homoptera: pseudococidae)

    International Nuclear Information System (INIS)

    Gillani, W.A.

    2009-01-01

    On determining the effects of different humidity levels on the biology of mealy bug Pseudococcus longispinus (Targioni and Tozzetti), it was found that the relative humidity (RH) at 35%, 55% and 75% had no effect on pre-adult development, adult longevity, life span and fecundity of P. longispinus. The survival of pre-adult stages was minimal at 35% RH. Sex ratio was male-biased at 35% RH and female-biased at 75% RH. (author)

  2. An exploratory analysis of PubMed's free full-text limit on citation retrieval for clinical questions.

    Science.gov (United States)

    Krieger, Mary M; Richter, Randy R; Austin, Tricia M

    2008-10-01

    The research sought to determine (1) how use of the PubMed free full-text (FFT) limit affects citation retrieval and (2) how use of the FFT limit impacts the types of articles and levels of evidence retrieved. Four clinical questions based on a research agenda for physical therapy were searched in PubMed both with and without the use of the FFT limit. Retrieved citations were examined for relevancy to each question. Abstracts of relevant citations were reviewed to determine the types of articles and levels of evidence. Descriptive analysis was used to compare the total number of citations, number of relevant citations, types of articles, and levels of evidence both with and without the use of the FFT limit. Across all 4 questions, the FFT limit reduced the number of citations to 11.1% of the total number of citations retrieved without the FFT limit. Additionally, high-quality evidence such as systematic reviews and randomized controlled trials were missed when the FFT limit was used. Health sciences librarians play a key role in educating users about the potential impact the FFT limit has on the number of citations, types of articles, and levels of evidence retrieved.

  3. Top-down models in biology: explanation and control of complex living systems above the molecular level.

    Science.gov (United States)

    Pezzulo, Giovanni; Levin, Michael

    2016-11-01

    It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).

  4. Biological effects of radiation and health risks from exposure to low levels of ionizing radiation

    International Nuclear Information System (INIS)

    Kotian, Rahul P.; Kotian, Sahana Rahul; Sukumar, Suresh

    2013-01-01

    The very fact that ionizing radiation produces biological effects is known from many years. The first case of injury reported by Sir Roentgen was reported just after a few months after discovery of X-rays in 1895. As early as 1902, the first case of X-ray induced cancer was reported in the literature. Early human evidence of harmful effects as a result of exposure to radiation in large amounts existed in the 1920s and 1930s, based upon the experience of early radiologists, miners exposed to airborne radioactivity underground, persons working in the radium industry, and other special occupational groups. The long-term biological significance of smaller, repeated doses of radiation, however, was not widely appreciated until relatively recently, and most of our knowledge of the biological effects of radiation has been accumulated since World War II. The mechanisms that lead to adverse health effects after exposure to ionizing radiation are still not fully understood. Ionizing radiation has sufficient energy to change the structure of molecules, including DNA, within the cells of the body. Some of these molecular changes are so complex that it may be difficult for the body's repair mechanisms to mend them correctly. However, the evidence is that only a small fraction of such changes would be expected to result in cancer or other health effects. The most thoroughly studied individuals for the evaluation of health effects of ionizing radiation are the survivors of the Hiroshima and Nagasaki atomic bombings, a large population that includes all ages and both sexes.The Radiation Effects Research Foundation (RERF) in Japan has conducted followup studies on these survivors for more than 50 years. An important finding from these studies is that the occurrence of solid cancers increases in proportion to radiation dose. More than 60% of exposed survivors received a dose of radiation of less than 100 mSv (the definition of low dose used by the BEIR VII report). (author)

  5. A study of the biological effects of rare earth elements at cellular level using nuclear techniques

    International Nuclear Information System (INIS)

    Feng Zhihui; Wang Xi; Zhang Sunxi; An Lizhi; Zhang Jingxia; Yao Huiying

    2001-01-01

    Objective: To investigate the biological effects and the effecting mechanisms of rare earth elements La, Gd and Ce on cultured rat cells. Methods: The biological effects of La 3+ on cultured rat cells and the subcellular distribution of La and Gd and Ce, and the inflow of 45 Ca 2+ into the cells and total cellular calcium were measured by isotopic tracing, Proton Induced X Ray Emission Analysis (PIXE) and the techniques of biochemistry and cellular biology. Results: La 3+ at the concentration of 10- 10( or 10 -9 ) - 10 -6 mol/L significantly increased quantity of incorporation of 3 H-TdR into DNA, total cellular protein and the activity of succinic dehydrogenase of mitochondria. The cell cycle analysis showed that the proportions of cells in S phase were accordingly increased acted by La 3+ at above range of concentration. But these values were significantly decreased when concentration of La 3+ raised to 10 -4 - 10 -3 mol/L. It was further discovered that La, Gd and Ce distributed mostly in the nuclei, and then in membranes. Gd and Ce also promoted the inflow of 45 Ca 2+ into the cells and increased the total calcium content in cells. Conclusions: 1) La 3+ at a wide concentration range of 10 -10 ( or 10 -9 ) - 10 -6 mol/L promotes proliferation of cultured rat cells, but at even higher concentration (10 -4 - 10 -3 mol/L) shows cellular toxicity, and there is a striking dose-effect relationship. 2) La, Gd and Ce can enter the cells and mainly distribute in the nuclei. 3) Gd and Ce can promote the inflow of extracellular Ca 2+ into the cells and increase total cellular calcium

  6. Health effects of low-level ionising radiation: biological basis for risk assessment

    International Nuclear Information System (INIS)

    Upton, A.C.

    1987-01-01

    The biological basis for risk assessment is discussed. The risks of carcinogenic effects, teratogenic effects, and genetic (heritable) effects are estimated to vary in proportion with the dose of radiation in the low-dose domain; however, the risks also appear to vary with the LET of the radiation, age at the time of irradiation, and other variables. Although the data suffice to place the risks in perspective with other hazards of modern life, further research to refine the reliability of the risk assessment is called for. (author)

  7. Building Design Guidelines of Interior Architecture for Bio safety Levels of Biology Laboratories

    International Nuclear Information System (INIS)

    ElDib, A.A.

    2014-01-01

    This paper discusses the pivotal role of the Interior Architecture As one of the scientific disciplines minute to complete the Architectural Sciences, which relied upon the achievement and development of facilities containing scientific research laboratories, in terms of planning and design, particularly those containing biological laboratories using radioactive materials, adding to that, the application of the materials or raw materials commensurate with each discipline of laboratory and its work nature, and by the discussion the processing of design techniques and requirements of interior architecture dealing with Research Laboratory for electronic circuits an their applications with the making of its prototypes

  8. Feasibility of disposal of high-level radioactive waste into the seabed. Volume 6: Deep-sea biology, biological processes and radiobiology

    International Nuclear Information System (INIS)

    Pentreath, R.J.; Hargrave, B.T.; Roe, H.S.J.; Sibuet, M.

    1988-01-01

    One of the options suggested for disposal of high-level radioactive waste resulting from the generation of nuclear power is burial beneath the deep ocean floor in geologically stable sediment formations which have no economic value. The 8-volume series provides an assessment of the technical feasibility and radiological safety of this disposal concept based on the results obtained by ten years of co-operation and information exchange among the Member countries participating in the NEA Seabed Working Group. This report summarizes the biological description of selected sites, the means by which radionuclides could result in human exposure via seafood pathways, and the doses likely to be received by, and effects on, the deep-sea fauna

  9. MET network in PubMed: a text-mined network visualization and curation system.

    Science.gov (United States)

    Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

    2016-01-01

    Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET.Database URL: http://btm.tmu.edu.tw/metastasisway. © The Author(s) 2016. Published by Oxford University Press.

  10. How does undergraduate college biology students' level of understanding, in regard to the role of the seed plant root system, relate to their level of understanding of photosynthesis?

    Science.gov (United States)

    Njeng'ere, James Gicheha

    This research study investigated how undergraduate college biology students' level of understanding of the role of the seed plant root system relates to their level of understanding of photosynthesis. This research was conducted with 65 undergraduate non-majors biology who had completed 1 year of biology at Louisiana State University in Baton Rouge and Southeastern Louisiana University in Hammond. A root probe instrument was developed from some scientifically acceptable propositional statements about the root system, the process of photosynthesis, as well as the holistic nature of the tree. These were derived from research reviews of the science education and the arboriculture literature. This was administered to 65 students selected randomly from class lists of the two institutions. Most of the root probe's items were based on the Live Oak tree. An in-depth, clinical interview-based analysis was conducted with 12 of those tested students. A team of root experts participated by designing, validating and answering the same questions that the students were asked. A "systems" lens as defined by a team of college instructors, root experts (Shigo, 1991), and this researcher was used to interpret the results. A correlational coefficient determining students' level of understanding of the root system and their level of understanding of the process of photosynthesis was established by means of Pearson's r correlation (r = 0.328) using the SAS statistical analysis (SAS, 1987). From this a coefficient of determination (r2 = 0.104) was determined. Students' level of understanding of the Live Oak root system (mean score 5.94) was not statistically different from their level of understanding of the process of photosynthesis (mean score 5.54) as assessed by the root probe, t (129) = 0.137, p > 0.05 one tailed-test. This suggests that, to some degree, level of the root system limits level of understanding of photosynthesis and vice versa. Analysis of quantitative and qualitative

  11. Sea-level Rise Impacts on Oregon Estuaries: Biology and Hydrology

    Science.gov (United States)

    Estuaries are transitional ecosystems located at the margin of the land and ocean and as a result they are particularly sensitive to sea level rise and other climate drivers. In this presentation, we summarize the potential impacts of sea level rise on key estuarine habitats inc...

  12. Sea-level Rise Impacts on Oregon Estuaries: Biology and Hydrology - for posting on website

    Science.gov (United States)

    Estuaries are transitional ecosystems located at the margin of the land and ocean and as a result they are particularly sensitive to sea level rise and other climate drivers. In this presentation, we summarize the potential impacts of sea level rise on key estuarine habitats incl...

  13. Cellular energy allocation in zebra mussels exposed along a pollution gradient: linking cellular effects to higher levels of biological organization

    International Nuclear Information System (INIS)

    Smolders, R.; Bervoets, L.; Coen, W. de; Blust, R.

    2004-01-01

    Organisms exposed to suboptimal environments incur a cost of dealing with stress in terms of metabolic resources. The total amount of energy available for maintenance, growth and reproduction, based on the biochemical analysis of the energy budget, may provide a sensitive measure of stress in an organism. While the concept is clear, linking cellular or biochemical responses to the individual and population or community level remains difficult. The aim of this study was to validate, under field conditions, using cellular energy budgets [i.e. changes in glycogen-, lipid- and protein-content and mitochondrial electron transport system (ETS)] as an ecologically relevant measurement of stress by comparing these responses to physiological and organismal endpoints. Therefore, a 28-day in situ bioassay with zebra mussels (Dreissena polymorpha) was performed in an effluent-dominated stream. Five locations were selected along the pollution gradient and compared with a nearby (reference) site. Cellular Energy Allocation (CEA) served as a biomarker of cellular energetics, while Scope for Growth (SFG) indicated effects on a physiological level and Tissue Condition Index and wet tissue weight/dry tissue weight ratio were used as endpoints of organismal effects. Results indicated that energy budgets at a cellular level of biological organization provided the fastest and most sensitive response and energy budgets are a relevant currency to extrapolate cellular effects to higher levels of biological organization within the exposed mussels. - Exposure of zebra mussels along a pollution gradient has adverse effects on the cellular energy allocation, and results can be linked with higher levels of biological organization

  14. Cellular energy allocation in zebra mussels exposed along a pollution gradient: linking cellular effects to higher levels of biological organization

    Energy Technology Data Exchange (ETDEWEB)

    Smolders, R.; Bervoets, L.; Coen, W. de; Blust, R

    2004-05-01

    Organisms exposed to suboptimal environments incur a cost of dealing with stress in terms of metabolic resources. The total amount of energy available for maintenance, growth and reproduction, based on the biochemical analysis of the energy budget, may provide a sensitive measure of stress in an organism. While the concept is clear, linking cellular or biochemical responses to the individual and population or community level remains difficult. The aim of this study was to validate, under field conditions, using cellular energy budgets [i.e. changes in glycogen-, lipid- and protein-content and mitochondrial electron transport system (ETS)] as an ecologically relevant measurement of stress by comparing these responses to physiological and organismal endpoints. Therefore, a 28-day in situ bioassay with zebra mussels (Dreissena polymorpha) was performed in an effluent-dominated stream. Five locations were selected along the pollution gradient and compared with a nearby (reference) site. Cellular Energy Allocation (CEA) served as a biomarker of cellular energetics, while Scope for Growth (SFG) indicated effects on a physiological level and Tissue Condition Index and wet tissue weight/dry tissue weight ratio were used as endpoints of organismal effects. Results indicated that energy budgets at a cellular level of biological organization provided the fastest and most sensitive response and energy budgets are a relevant currency to extrapolate cellular effects to higher levels of biological organization within the exposed mussels. - Exposure of zebra mussels along a pollution gradient has adverse effects on the cellular energy allocation, and results can be linked with higher levels of biological organization.

  15. A study on PubMed search tag usage pattern: association rule mining of a full-day PubMed query log.

    Science.gov (United States)

    Mosa, Abu Saleh Mohammad; Yoo, Illhoi

    2013-01-09

    The practice of evidence-based medicine requires efficient biomedical literature search such as PubMed/MEDLINE. Retrieval performance relies highly on the efficient use of search field tags. The purpose of this study was to analyze PubMed log data in order to understand the usage pattern of search tags by the end user in PubMed/MEDLINE search. A PubMed query log file was obtained from the National Library of Medicine containing anonymous user identification, timestamp, and query text. Inconsistent records were removed from the dataset and the search tags were extracted from the query texts. A total of 2,917,159 queries were selected for this study issued by a total of 613,061 users. The analysis of frequent co-occurrences and usage patterns of the search tags was conducted using an association mining algorithm. The percentage of search tag usage was low (11.38% of the total queries) and only 2.95% of queries contained two or more tags. Three out of four users used no search tag and about two-third of them issued less than four queries. Among the queries containing at least one tagged search term, the average number of search tags was almost half of the number of total search terms. Navigational search tags are more frequently used than informational search tags. While no strong association was observed between informational and navigational tags, six (out of 19) informational tags and six (out of 29) navigational tags showed strong associations in PubMed searches. The low percentage of search tag usage implies that PubMed/MEDLINE users do not utilize the features of PubMed/MEDLINE widely or they are not aware of such features or solely depend on the high recall focused query translation by the PubMed's Automatic Term Mapping. The users need further education and interactive search application for effective use of the search tags in order to fulfill their biomedical information needs from PubMed/MEDLINE.

  16. Use of scientific social networking to improve the research strategies of PubMed readers.

    Science.gov (United States)

    Evdokimov, Pavel; Kudryavtsev, Alexey; Ilgisonis, Ekaterina; Ponomarenko, Elena; Lisitsa, Andrey

    2016-02-18

    Keeping up with journal articles on a daily basis is an important activity of scientists engaged in biomedical research. Usually, journal articles and papers in the field of biomedicine are accessed through the Medline/PubMed electronic library. In the process of navigating PubMed, researchers unknowingly generate user-specific reading profiles that can be shared within a social networking environment. This paper examines the structure of the social networking environment generated by PubMed users. A web browser plugin was developed to map [in Medical Subject Headings (MeSH) terms] the reading patterns of individual PubMed users. We developed a scientific social network based on the personal research profiles of readers of biomedical articles. A browser plugin is used to record the digital object identifier or PubMed ID of web pages. Recorded items are posted on the activity feed and automatically mapped to PubMed abstract. Within the activity feed a user can trace back previously browsed articles and insert comments. By calculating the frequency with which specific MeSH occur, the research interests of PubMed users can be visually represented with a tag cloud. Finally, research profiles can be searched for matches between network users. A social networking environment was created using MeSH terms to map articles accessed through the Medline/PubMed online library system. In-network social communication is supported by the recommendation of articles and by matching users with similar scientific interests. The system is available at http://bioknol.org/en/.

  17. Relative biological effectiveness of tritiated water on cultured mammalian cells at molecular and cellular level

    International Nuclear Information System (INIS)

    Okada, S.; Sakai, K.; Nakamura, N.

    1986-01-01

    Factors that affect RBE values have been investigated in cultured cells. It was shown that: (1) Different RBE values were obtained with the same tritiated water treated cells depending upon the biological end-point; this may be related to target size. (2) The RBE value for one end-point (e.g. cell killing) in different cell types was often different. In some cells, the RBE value increased with reducing dose; in other cells, the value remained constant. (3) The RBE value for tritiated water seemed to fit a general RBE-LET relationship. These results suggest that although the RBE value might vary from 1 to 2 when cells are exposed to HTO, there are situations where the value becomes higher than 2; these are associated with low dose and low dose rate exposures in some cell types. (author)

  18. PubstractHelper: A Web-based Text-Mining Tool for Marking Sentences in Abstracts from PubMed Using Multiple User-Defined Keywords.

    Science.gov (United States)

    Chen, Chou-Cheng; Ho, Chung-Liang

    2014-01-01

    While a huge amount of information about biological literature can be obtained by searching the PubMed database, reading through all the titles and abstracts resulting from such a search for useful information is inefficient. Text mining makes it possible to increase this efficiency. Some websites use text mining to gather information from the PubMed database; however, they are database-oriented, using pre-defined search keywords while lacking a query interface for user-defined search inputs. We present the PubMed Abstract Reading Helper (PubstractHelper) website which combines text mining and reading assistance for an efficient PubMed search. PubstractHelper can accept a maximum of ten groups of keywords, within each group containing up to ten keywords. The principle behind the text-mining function of PubstractHelper is that keywords contained in the same sentence are likely to be related. PubstractHelper highlights sentences with co-occurring keywords in different colors. The user can download the PMID and the abstracts with color markings to be reviewed later. The PubstractHelper website can help users to identify relevant publications based on the presence of related keywords, which should be a handy tool for their research. http://bio.yungyun.com.tw/ATM/PubstractHelper.aspx and http://holab.med.ncku.edu.tw/ATM/PubstractHelper.aspx.

  19. An automatic method to generate domain-specific investigator networks using PubMed abstracts

    Directory of Open Access Journals (Sweden)

    Gwinn Marta

    2007-06-01

    Full Text Available Abstract Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8% and from 94.2% of HuGE PubMed records (accuracy 87.0. We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit, indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a

  20. Mining PubMed for Biomarker-Disease Associations to Guide Discovery

    OpenAIRE

    Jessen, Walter; Landschulz, Katherine; Turi, Thomas; Reams, Rachel

    2012-01-01

    Biomedical knowledge is growing exponentially; however, meta-knowledge around the data is often lacking. PubMed is a database comprising more than 21 million citations for biomedical literature from MEDLINE and additional life science journals dating back to the 1950s. To explore the use and frequency of biomarkers across human disease, we mined PubMed for biomarker-disease associations. We then ranked the top 100 linked diseases by relevance and mapped them to medical subject headings (MeSH)...

  1. An automatic method to generate domain-specific investigator networks using PubMed abstracts

    Science.gov (United States)

    Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Gwinn, Marta; Khoury, Muin J

    2007-01-01

    Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a web-based prototype

  2. High School and College Biology: A Multi-Level Model of the Effects of High School Courses on Introductory Course Performance

    Science.gov (United States)

    Loehr, John F.; Almarode, John T.; Tai, Robert H.; Sadler, Philip M.

    2012-01-01

    In a climate where increasing numbers of students are encouraged to pursue post-secondary education, the level of preparedness students have for college-level coursework is not far from the minds of all educators, especially high school teachers. Specifically within the biological sciences, introductory biology classes often serve as the…

  3. Exploring the Alignment of the Intended and Implemented Curriculum through Teachers' Interpretation: A Case Study of A-Level Biology Practical Work

    Science.gov (United States)

    Phaeton, Mukaro Joe; Stears, Michèle

    2017-01-01

    The research reported on here is part of a larger study exploring the alignment of the intended, implemented and attained curriculum with regard to practical work in the Zimbabwean A-level Biology curriculum. In this paper we focus on the alignment between the intended and implemented A-Level Biology curriculum through the lens of teachers'…

  4. Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.

    Science.gov (United States)

    Li, Jinyang; Liu, Yi; Kim, Eunkyoung; March, John C; Bentley, William E; Payne, Gregory F

    2017-04-01

    The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O 2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H 2 O 2 ) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this

  5. Abiotic stressors and stress responses: What commonalities appear between species across biological organization levels?

    International Nuclear Information System (INIS)

    Sulmon, Cécile; Baaren, Joan van; Cabello-Hurtado, Francisco; Gouesbet, Gwenola; Hennion, Françoise; Mony, Cendrine; Renault, David; Bormans, Myriam; El Amrani, Abdelhak; Wiegand, Claudia; Gérard, Claudia

    2015-01-01

    Organisms are regularly subjected to abiotic stressors related to increasing anthropogenic activities, including chemicals and climatic changes that induce major stresses. Based on various key taxa involved in ecosystem functioning (photosynthetic microorganisms, plants, invertebrates), we review how organisms respond and adapt to chemical- and temperature-induced stresses from molecular to population level. Using field-realistic studies, our integrative analysis aims to compare i) how molecular and physiological mechanisms related to protection, repair and energy allocation can impact life history traits of stressed organisms, and ii) to what extent trait responses influence individual and population responses. Common response mechanisms are evident at molecular and cellular scales but become rather difficult to define at higher levels due to evolutionary distance and environmental complexity. We provide new insights into the understanding of the impact of molecular and cellular responses on individual and population dynamics and assess the potential related effects on communities and ecosystem functioning. - Highlights: • Responses to chemical and thermal stressors are reviewed across organization levels. • Common responses between taxa are evident at the molecular and cellular scales. • At individual level, energy allocation connects species-specific stress responses. • Commonality decreases at higher levels due to increasing environmental complexity. - The commonality of stress responses to chemical and thermal stressors among taxa is evident at the molecular and cellular scales but remains unclear at higher levels of organization

  6. Cellular energy allocation in zebra mussels exposed along a pollution gradient: linking cellular effects to higher levels of biological organization.

    Science.gov (United States)

    Smolders, R; Bervoets, L; De Coen, W; Blust, R

    2004-05-01

    Organisms exposed to suboptimal environments incur a cost of dealing with stress in terms of metabolic resources. The total amount of energy available for maintenance, growth and reproduction, based on the biochemical analysis of the energy budget, may provide a sensitive measure of stress in an organism. While the concept is clear, linking cellular or biochemical responses to the individual and population or community level remains difficult. The aim of this study was to validate, under field conditions, using cellular energy budgets [i.e. changes in glycogen-, lipid- and protein-content and mitochondrial electron transport system (ETS)] as an ecologically relevant measurement of stress by comparing these responses to physiological and organismal endpoints. Therefore, a 28-day in situ bioassay with zebra mussels (Dreissena polymorpha) was performed in an effluent-dominated stream. Five locations were selected along the pollution gradient and compared with a nearby (reference) site. Cellular Energy Allocation (CEA) served as a biomarker of cellular energetics, while Scope for Growth (SFG) indicated effects on a physiological level and Tissue Condition Index and wet tissue weight/dry tissue weight ratio were used as endpoints of organismal effects. Results indicated that energy budgets at a cellular level of biological organization provided the fastest and most sensitive response and energy budgets are a relevant currency to extrapolate cellular effects to higher levels of biological organization within the exposed mussels.

  7. Biological effects of low-level ionizing and non-ionizing radiation

    International Nuclear Information System (INIS)

    Upton, A.C.

    1986-01-01

    Early in this century it was recognized that large doses of ionizing radiation could injure almost any tissue in the body, but small doses were generally thought to be harmless. By the middle of the century however it came to be suspected that even the smallest doses of ionizing radiation to the gonads might increase the risk of hereditary disease in subsequently-conceived offspring. Since then the hypothesis that carcinogenic and teratogenic effects also have no threshold has been adopted for purposes of radiological protection. It is estimated nevertheless that the risks that may be associated with natural background levels of ionizing irradiation are too small to be detectable. Hence validation of such risk estimates will depend on further elucidation of the dose-effect relationships and mechanisms of the effects in question, through studies at higher dose levels. In contrast to the situation with ionizing radiation, exposure to natural background levels of ultraviolet radiation has been implicated definitively in the etiology of skin cancers in fair-skinned individuals. Persons with inherited effects in DNA repair capacity are particularly susceptible. Non-ionizing radiations of other types can also affect health at high dose levels, but whether they can cause injury at low levels of exposure is not known

  8. Atmospheric ions and probable indirect biological effect of low-level radiation

    International Nuclear Information System (INIS)

    Spurny, Z.

    1984-01-01

    The problem is discussed of the health consequences of low radiation doses (of less than 0.01 Gy). Owing to natural radioactivity and cosmic radiation, ions are formed in the atmosphere which may thus indirectly mediate the effects of ionizing radiation on the organism. The rate of ion formation is approximately 6.1 ion pairs/cm 3 .s and their number will not exceed 10 3 ions/cm 3 . In an environment where artificial radioactive sources are used, the ion concentration may reach up to 10 5 ions/cm 3 . The effect of ions on man may be divided into several types: 1. effect on mental state (behaviour, fatigue, headaches); 2. effect on the cardiovascular system; 3. effect on the bronchial system;and 4. effect on physiological processes, e.g., secretion by endocrine glands. It is not yet known whether the biological effect of small (fast) ions is a function of their electric charge only or of their kinetic energy as well. The view is discussed that low radiation doses through indirect effects have favourable and beneficial influence on the human organism. (M.D.)

  9. Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

    Science.gov (United States)

    D'Souza, Mark; Sulakhe, Dinanath; Wang, Sheng; Xie, Bing; Hashemifar, Somaye; Taylor, Andrew; Dubchak, Inna; Conrad Gilliam, T; Maltsev, Natalia

    2017-01-01

    Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.

  10. Aerated biofilters with multiple-level air injection configurations to enhance biological treatment of methane emissions.

    Science.gov (United States)

    Farrokhzadeh, Hasti; Hettiaratchi, J Patrick A; Jayasinghe, Poornima; Kumar, Sunil

    2017-09-01

    Aiming to improve conventional methane biofilter performance, a multiple-level aeration biofilter design is proposed. Laboratory flow-through column experiments were conducted to evaluate three actively-aerated methane biofilter configurations. Columns were aerated at one, two, and three levels of the bed depth, with air introduced at flow rates calculated from methane oxidation reaction stoichiometry. Inlet methane loading rates were increased in five stages between 6 and 18mL/min. The effects of methane feeding rate, levels of aeration, and residence time on methane oxidation rates were determined. Samples collected after completion of flow-through experiments were used to determine methane oxidation kinetic parameters, V max , K m , and methanotrophic community distribution across biofilter columns. Results obtained from mixed variances analysis and response surfaces, as well as methanotrophic activity data, suggested that, biofilter column with two aeration levels has the most even performance over time, maintaining 85.1% average oxidation efficiency over 95days of experiments. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Translating crustacean biological responses from CO2 bubbling experiments into population-level predictions

    Science.gov (United States)

    Many studies of animal responses to ocean acidification focus on uniformly conditioned age cohorts that lack complexities typically found in wild populations. These studies have become the primary data source for predicting higher level ecological effects, but the roles of intras...

  12. Quantifying levels of biological invasion: towards the objective classification of invaded and invasible ecosystems

    Czech Academy of Sciences Publication Activity Database

    Catford, J.A.; Vesk, P.A.; Richardson, D. M.; Pyšek, Petr

    2012-01-01

    Roč. 18, č. 1 (2012), s. 44-62 ISSN 1354-1013 R&D Projects: GA ČR(CZ) GAP505/11/1112 Institutional research plan: CEZ:AV0Z60050516 Institutional support: RVO:67985939 Keywords : level of invasion * standard metrics * abundance Subject RIV: EF - Botanics Impact factor: 6.910, year: 2012

  13. Determination of the plutonium contamination level in biological samples by liquid scintillation

    International Nuclear Information System (INIS)

    Willemot, J.M.; Verry, M.; Lataillade, G.

    1989-01-01

    Usual radiochemical processes are unable to carry out without delay the very large number of analyses as required in plutonium toxicology studies. Liquid scintillation is the best method to quickly determine plutonium contamination levels in most various samples (bone, organs,...) [fr

  14. Biological/Genetic Regulation of Physical Activity Level : Consensus from GenBioPAC

    NARCIS (Netherlands)

    Lightfoot, J Timothy; De Geus, Eco J C; Booth, Frank W; Bray, Molly S; den Hoed, Marcel; Kaprio, Jaakko; Kelly, Scott A; Pomp, Daniel; Saul, Michael C; Thomis, Martine A; Garland, Theodore; Bouchard, Claude

    2017-01-01

    PURPOSE: Physical activity unquestionably maintains and improves health; however, physical activity levels globally are low and not rising despite all the resources devoted to this goal. Attention in both the research literature and the public policy domain has focused on social-behavioral factors;

  15. Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

    Science.gov (United States)

    Falagas, Matthew E; Pitsouni, Eleni I; Malietzis, George A; Pappas, Georgios

    2008-02-01

    The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.

  16. Information architecture: study and analysis of data Public Medical base (PubMed

    Directory of Open Access Journals (Sweden)

    Odete Máyra Mesquita Sales

    2016-07-01

    Full Text Available Objective. Based on principles proposed by Rosenfeld and Morville (2006, the present study examined the PubMed database interface, since a well-structured information architecture contributes to good usability in any digital environment. Method. The research development occurred through the use of literature techniques and empirical study on the analysis of information architecture based on organization, navigation, recommended labeling and search for Rosenfeld and Morville (2006 for the sake of usability base PubMed. For better understanding and description of these principles, we used the technique of content analysis. Results. The results showed that the database interface meets the criteria established by the elements of Information Architecture, such as organization based on hypertext structure, horizontal menu and local content divided into categories, identifying active links, global navigation , breadcrumb, textual labeling and iconographic and highlight the search engine. Conclusions. This research showed that the PubMed database interface is well structured, friendly and objective, with numerous possibilities of search and information retrieval. However, there is a need to adopt accessibility standards on this website, so that it reaches more efficiently its purpose of facilitating access to information organized and stored in the PubMed database.

  17. pubmed. mineR: An R package with text-mining algorithms to ...

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Three case studies are presented, namely, `Evolving role of diabetes educators', `Cancer risk assessment' and `Dynamic concepts on disease and comorbidity' to illustrate the use of pubmed.mineR. The package generally runs fast with small elapsed times in regular workstations even on large corpus ...

  18. Measuring Medical Student Preference: A Comparison of Classroom Versus Online Instruction for Teaching Pubmed*EC

    Science.gov (United States)

    Schimming, Laura M.

    2008-01-01

    Objective: The research analyzed evaluation data to assess medical student satisfaction with the learning experience when required PubMed training is offered entirely online. Methods: A retrospective study analyzed skills assessment scores and student feedback forms from 455 first-year medical students who completed PubMed training either through classroom sessions or an online tutorial. The class of 2006 (n = 99) attended traditional librarian-led sessions in a computer classroom. The classes of 2007 (n = 120), 2008 (n = 121), and 2009 (n = 115) completed the training entirely online through a self-paced tutorial. PubMed skills assessment scores and student feedback about the training were compared for all groups. Results: As evidenced by open-ended comments about the training, students who took the online tutorial were equally or more satisfied with the learning experience than students who attended classroom sessions, with the classes of 2008 and 2009 reporting greater satisfaction (PPubMed skills assessment (91%) was the same for all groups of students. Conclusions: Student satisfaction improved and PubMed assessment scores did not change when instruction was offered online to first-year medical students. Comments from the students who received online training suggest that the increased control and individual engagement with the web-based content led to their satisfaction with the online tutorial. PMID:18654658

  19. Multi-lingual search engine to access PubMed monolingual subsets: a feasibility study.

    Science.gov (United States)

    Darmoni, Stéfan J; Soualmia, Lina F; Griffon, Nicolas; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse

    2013-01-01

    PubMed contains many articles in languages other than English but it is difficult to find them using the English version of the Medical Subject Headings (MeSH) Thesaurus. The aim of this work is to propose a tool allowing access to a PubMed subset in one language, and to evaluate its performance. Translations of MeSH were enriched and gathered in the information system. PubMed subsets in main European languages were also added in our database, using a dedicated parser. The CISMeF generic semantic search engine was evaluated on the response time for simple queries. MeSH descriptors are currently available in 11 languages in the information system. All the 654,000 PubMed citations in French were integrated into CISMeF database. None of the response times exceed the threshold defined for usability (2 seconds). It is now possible to freely access biomedical literature in French using a tool in French; health professionals and lay people with a low English language may find it useful. It will be expended to several European languages: German, Spanish, Norwegian and Portuguese.

  20. Risk factors for bladder cancer: challenges of conducting a literature search using PubMed.

    Science.gov (United States)

    Joshi, Ashish; Preslan, Elicia

    2011-04-01

    The objective of this study was to assess the risk factors for bladder cancer using PubMed articles from January 2000 to December 2009. The study also aimed to describe the challenges encountered in the methodology of a literature search for bladder cancer risk factors using PubMed. Twenty-six categories of risk factors for bladder cancer were identified using the National Cancer Institute Web site and the Medical Subject Headings (MeSH) Web site. A total of 1,338 PubMed searches were run using the term "urinary bladder cancer" and a risk factor term (e.g., "cigarette smoking") and were screened to identify 260 articles for final analysis. The search strategy had an overall precision of 3.42 percent, relative recall of 12.64 percent, and an F-measure of 5.39 percent. Although search terms derived from MeSH had the highest overall precision and recall, the differences did not reach significance, which indicates that for generalized, free-text searches of the PubMed database, the searchers' own terms are generally as effective as MeSH terms.

  1. PubMed Phrases, an open set of coherent phrases for searching biomedical literature

    Science.gov (United States)

    Kim, Sun; Yeganova, Lana; Comeau, Donald C.; Wilbur, W. John; Lu, Zhiyong

    2018-01-01

    In biomedicine, key concepts are often expressed by multiple words (e.g., ‘zinc finger protein’). Previous work has shown treating a sequence of words as a meaningful unit, where applicable, is not only important for human understanding but also beneficial for automatic information seeking. Here we present a collection of PubMed® Phrases that are beneficial for information retrieval and human comprehension. We define these phrases as coherent chunks that are logically connected. To collect the phrase set, we apply the hypergeometric test to detect segments of consecutive terms that are likely to appear together in PubMed. These text segments are then filtered using the BM25 ranking function to ensure that they are beneficial from an information retrieval perspective. Thus, we obtain a set of 705,915 PubMed Phrases. We evaluate the quality of the set by investigating PubMed user click data and manually annotating a sample of 500 randomly selected noun phrases. We also analyze and discuss the usage of these PubMed Phrases in literature search. PMID:29893755

  2. Searching PubMed for molecular epidemiology studies: the case of chromosome aberrations

    DEFF Research Database (Denmark)

    Ugolini, Donatella; Neri, Monica; Knudsen, Lisbeth E

    2006-01-01

    to environmental pollutants. The search, done on the PubMed/MedLine database, was based on a strategy combining descriptors listed in the PubMed Medical Subject Headings (MeSH) Thesaurus and other available tools (free text or phrase search tools). 178 articles were retrieved by searching the period from January 1...

  3. [Useful tools and methods for literature retrieval in pubmed: step-by-step guide for physicians].

    Science.gov (United States)

    Hevia M, Joaquín; Huete G, Álvaro; Alfaro F, Sandra; Palominos V, Verónica

    2017-12-01

    Developing skills to search the medical literature has potential benefits on patient care and allow physicians to better orient their efforts when answering daily clinical questions. The objective of this paper is to share useful tools for optimizing medical literature retrieval in MEDLINE using PubMed including MeSH terms, filters and connectors.

  4. The acclimation of Chlorella to high-level nitrite for potential application in biological NOx removal from industrial flue gases.

    Science.gov (United States)

    Li, Tianpei; Xu, Gang; Rong, Junfeng; Chen, Hui; He, Chenliu; Giordano, Mario; Wang, Qiang

    2016-05-20

    Nitrogen oxides (NOx) are the components of fossil flue gas that give rise to the greatest environmental concerns. This study evaluated the ability of the green algae Chlorella to acclimate to high level of NOx and the potential utilization of Chlorella strains in biological NOx removal (DeNOx) from industrial flue gases. Fifteen Chlorella strains were subject to high-level of nitrite (HN, 176.5 mmolL(-1) nitrite) to simulate exposure to high NOx. These strains were subsequently divided into four groups with respect to their ability to tolerate nitrite (excellent, good, fair, and poor). One strain from each group was selected to evaluate their photosynthetic response to HN condition, and the nitrite adaptability of the four Chlorella strains were further identified by using chlorophyll fluorescence. The outcome of our experiments shows that, although high concentrations of nitrite overall negatively affect growth and photosynthesis of Chlorella strains, the degree of nitrite tolerance is a strain-specific feature. Some Chlorella strains have an appreciably higher ability to acclimate to high-level of nitrite. Acclimation is achieved through a three-step process of restrict, acclimate, and thriving. Notably, Chlorella sp. C2 was found to have a high tolerance and to rapidly acclimate to high concentrations of nitrite; it is therefore a promising candidate for microalgae-based biological NOx removal. Copyright © 2016 Elsevier GmbH. All rights reserved.

  5. The Relevance of Chromosome Aberration Yields for Biological Dosimetry After Low-Level Occupational Irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Bauchinger, M.; Schmid, E.; Hug, O. [Gesellschaft fuer Strahlenforschung, Institut fuer Biologie, Neuherberg, Federal Republic of Germany (Germany); Strahlenbiologisches Institut der Universitaet Muenchen, Federal Republic of Germany (Germany)

    1971-06-15

    The usefulness of chromosome analysis for biological dosimetry has been tested in two groups of persons occupationally exposed to radiation: (I) in nurses employed in gynaecological radiology, exposed especially when handling radium inserts; and (II) in nuclear industry workers, all of which were exposed to external gamma irradiation and some of them also to internal radiation after incorporation of various radionuclides. The total dose registered with personal dosimeters ranged in Group 1 from 0.1 to 91.1 rem accumulated over working periods of 0.1 to 13 years, and in Group II from 1.0 to 18.2 rem accumulated over 1 to 9 years. Compared with unexposed controls, both groups exhibit a significant increase of cells with chromosome aberrations as well as larger numbers of breaks per cell. Dicentrics and rings could be observed in some cells, providing good evidence for previous radiation exposure, since these types of aberrations are extremely rare events in unexposed individuals. No correlation between the aberration yields and the film badge values could be demonstrated in Group II. Also, in Group I the fluctuations from individual to individual are rather high. Nevertheless, a positive correlation to the ''dose'' was obtained. Even a sub-group of the nurses that had only been exposed to 20 rem showed significantly more aberrations than control persons. From the results obtained, type and frequency of chromosome aberrations may be considered an indicator of radiation exposure even at the low doses. The reasons for lack of correspondence of chromosome aberration yields and the results of personal monitoring procedures are discussed in detail. (author)

  6. Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

    Science.gov (United States)

    Christen, Matthias; Del Medico, Luca; Christen, Heinz; Christen, Beat

    2017-01-01

    Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

  7. Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

    Directory of Open Access Journals (Sweden)

    Matthias Christen

    Full Text Available Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

  8. SYMBIOSIS: development, implementation, and assessment of a model curriculum across biology and mathematics at the introductory level.

    Science.gov (United States)

    Depelteau, Audrey M; Joplin, Karl H; Govett, Aimee; Miller, Hugh A; Seier, Edith

    2010-01-01

    "It takes a lot of courage to release the familiar and seemingly secure, to embrace the new. But there is no real security in what is no longer meaningful. There is more security in the adventurous and exciting, for in movement there is life, and in change there is power." Alan Cohen (Used by permission. All rights reserved. For more information on Alan Cohen's books and programs, see (www.alancohen.com.) With the support of the East Tennessee State University (ETSU) administration and a grant from Howard Hughes Medical Institute, the departments of Biological Sciences, Mathematics and Statistics, and Curriculum and Instruction have developed a biology-math integrated curriculum. An interdisciplinary faculty team, charged with teaching the 18 curriculum modules, designed this three-semester curriculum, known as SYMBIOSIS. This curriculum was piloted to two student cohorts during the developmental stage. The positive feedback and assessment results of this project have given us the foundation to implement the SYMBIOSIS curriculum as a replacement for the standard biology majors curriculum at the introductory level. This article addresses the history and development of the curriculum, previous assessment results and current assessment protocol, and the future of ETSU's approach to implementing the SYMBIOSIS curriculum.

  9. Effect of a care plan based on Roy adaptation model biological dimension on stroke patients' physiologic adaptation level.

    Science.gov (United States)

    Alimohammadi, Nasrollah; Maleki, Bibi; Shahriari, Mohsen; Chitsaz, Ahmad

    2015-01-01

    Stroke is a stressful event with several functional, physical, psychological, social, and economic problems that affect individuals' different living balances. With coping strategies, patients try to control these problems and return to their natural life. The aim of this study is to investigate the effect of a care plan based on Roy adaptation model biological dimension on stroke patients' physiologic adaptation level. This study is a clinical trial in which 50 patients, affected by brain stroke and being admitted in the neurology ward of Kashani and Alzahra hospitals, were randomly assigned to control and study groups in Isfahan in 2013. Roy adaptation model care plan was administered in biological dimension in the form of four sessions and phone call follow-ups for 1 month. The forms related to Roy adaptation model were completed before and after intervention in the two groups. Chi-square test and t-test were used to analyze the data through SPSS 18. There was a significant difference in mean score of adaptation in physiological dimension in the study group after intervention (P adaptation in the patients affected by brain stroke in the study and control groups showed a significant increase in physiological dimension in the study group by 47.30 after intervention (P adaptation model biological dimension care plan can result in an increase in adaptation in patients with stroke in physiological dimension. Nurses can use this model for increasing patients' adaptation.

  10. Validation of search filters for identifying pediatric studies in PubMed.

    Science.gov (United States)

    Leclercq, Edith; Leeflang, Mariska M G; van Dalen, Elvira C; Kremer, Leontien C M

    2013-03-01

    To identify and validate PubMed search filters for retrieving studies including children and to develop a new pediatric search filter for PubMed. We developed 2 different datasets of studies to evaluate the performance of the identified pediatric search filters, expressed in terms of sensitivity, precision, specificity, accuracy, and number needed to read (NNR). An optimal search filter will have a high sensitivity and high precision with a low NNR. In addition to the PubMed Limits: All Child: 0-18 years filter (in May 2012 renamed to PubMed Filter Child: 0-18 years), 6 search filters for identifying studies including children were identified: 3 developed by Kastner et al, 1 developed by BestBets, one by the Child Health Field, and 1 by the Cochrane Childhood Cancer Group. Three search filters (Cochrane Childhood Cancer Group, Child Health Field, and BestBets) had the highest sensitivity (99.3%, 99.5%, and 99.3%, respectively) but a lower precision (64.5%, 68.4%, and 66.6% respectively) compared with the other search filters. Two Kastner search filters had a high precision (93.0% and 93.7%, respectively) but a low sensitivity (58.5% and 44.8%, respectively). They failed to identify many pediatric studies in our datasets. The search terms responsible for false-positive results in the reference dataset were determined. With these data, we developed a new search filter for identifying studies with children in PubMed with an optimal sensitivity (99.5%) and precision (69.0%). Search filters to identify studies including children either have a low sensitivity or a low precision with a high NNR. A new pediatric search filter with a high sensitivity and a low NNR has been developed. Copyright © 2013 Mosby, Inc. All rights reserved.

  11. Impact of PubMed search filters on the retrieval of evidence by physicians.

    Science.gov (United States)

    Shariff, Salimah Z; Sontrop, Jessica M; Haynes, R Brian; Iansavichus, Arthur V; McKibbon, K Ann; Wilczynski, Nancy L; Weir, Matthew A; Speechley, Mark R; Thind, Amardeep; Garg, Amit X

    2012-02-21

    Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles. We investigated whether the use of search filters in PubMed improves searching by physicians. We asked a random sample of Canadian nephrologists to answer unique clinical questions derived from 100 systematic reviews of renal therapy. Physicians provided the search terms that they would type into PubMed to locate articles to answer these questions. We entered the physician-provided search terms into PubMed and applied two types of search filters alone or in combination: a methods-based filter designed to identify high-quality studies about treatment (clinical queries "therapy") and a topic-based filter designed to identify studies with renal content. We evaluated the comprehensiveness (proportion of relevant articles found) and efficiency (ratio of relevant to nonrelevant articles) of the filtered and nonfiltered searches. Primary studies included in the systematic reviews served as the reference standard for relevant articles. The average physician-provided search terms retrieved 46% of the relevant articles, while 6% of the retrieved articles were relevant (corrected) (the ratio of relevant to nonrelevant articles was 1:16). The use of both filters together produced a marked improvement in efficiency, resulting in a ratio of relevant to nonrelevant articles of 1:5 (16 percentage point improvement; 99% confidence interval 9% to 22%; p PubMed search filters improves the efficiency of physician searches. Improved search performance may enhance the transfer of research into practice and improve patient care.

  12. Electron transfer behaviour of biological macromolecules towards the single-molecule level

    DEFF Research Database (Denmark)

    Zhang, Jingdong; Grubb, Mikala; Hansen, Allan Glargaard

    2003-01-01

    is combined with state-of-the-art physical electrochemistry with emphasis on single-crystal, atomically planar electrode surfaces, in situ scanning tunnelling microscopy (STM) and other surface techniques. These approaches have brought bioelectrochemistry important steps forward towards the nanoscale...... and single-molecule levels.We discuss here these advances with reference to two specific redox metalloproteins, the blue single-copper protein Pseudomonas aeruginosa azurin and the single-haem protein Saccharomyces cerevisiae yeast cytochrome c, and a short oligonucleotide. Both proteins can be immobilized...... electron transfer (ET) function retained. In situ STM can also address the microscopic mechanisms for electron tunnelling through the biomolecules and offers novel notions such as coherent multi-ET between the substrate and tip via the molecular redox levels. This differs in important respects from...

  13. Biological effects of tolerable level chronic boron intake on transcription factors.

    Science.gov (United States)

    Orenay Boyacioglu, Seda; Korkmaz, Mehmet; Kahraman, Erkan; Yildirim, Hatice; Bora, Selin; Ataman, Osman Yavuz

    2017-01-01

    The mechanism of boron effect on human transcription and translation has not been fully understood. In the current study it was aimed to reveal the role of boron on the expression of certain transcription factors that play key roles in many cellular pathways on human subjects chronically exposed to low amounts of boron. The boron concentrations in drinking water samples were 1.57±0.06mg/l for boron group while the corresponding value for the control group was 0.016±0.002mg/l. RNA isolation was performed using PAX gene RNA kit on the blood samples from the subjects. The RNA was then reverse transcribed into cDNA and analyzed using the Human Transcription Factors RT 2 Profiler™ PCR Arrays. While the boron amount in urine was detected as 3.56±1.47mg/day in the boron group, it was 0.72±0.30mg/day in the control group. Daily boron intake of the boron and control groups were calculated to be 6.98±3.39 and 1.18±0.41mg/day, respectively. The expression levels of the transcription factor genes were compared between the boron and control groups and no statistically significant difference was detected (P>0.05). The data suggest that boron intake at 6.98±3.39mg/day, which is the dose at which beneficial effects might be seen, does not result in toxicity at molecular level since the expression levels of transcription factors are not changed. Although boron intake over this level will seem to increase RNA synthesis, further examination of the topic is needed using new molecular epidemiological data. Copyright © 2016 Elsevier GmbH. All rights reserved.

  14. Occurrence of 210Po and Biological Effects of Low-Level Exposure: The Need for Research

    OpenAIRE

    Seiler, Ralph L.; Wiemels, Joseph L.

    2012-01-01

    Background: Polonium-210 (210Po) concentrations that exceed 1 Bq/L in drinking-water supplies have been reported from four widely separated U.S. states where exposure to it went unnoticed for decades. The radionuclide grandparents of 210Po are common in sediments, and segments of the public may be chronically exposed to low levels of 210Po in drinking water or in food products from animals raised in contaminated areas. Objectives: We summarized information on the environmental behavior, bioki...

  15. Voyageurs National Park: Water-level regulation and effects on water quality and aquatic biology

    Science.gov (United States)

    Christensen, Victoria G.; Maki, Ryan P.; LeDuc, Jaime F.

    2018-01-01

    Following dam installations in the remote Rainy Lake Basin during the early 1900s, water-level fluctuations were considered extreme (1914–1949) compared to more natural conditions. In 1949, the International Joint Commission (IJC), which sets rules governing dam operation on waters shared by the United States and Canada, established the first rule curves to regulate water levels on these waterbodies. However, rule curves established prior to 2000 were determined to be detrimental to the ecosystem. Therefore, the IJC implemented an order in 2000 to change rule curves and to restore a more natural water regime. After 2000, measured chlorophyll-a concentrations in the two most eutrophic water bodies decreased whereas concentrations in oligotrophic lakes did not show significant water-quality differences. Fish mercury data were inconclusive, due to the variation in water levels and fish mercury concentrations, but can be used by the IJC as part of a long term data set.

  16. Biological effects of low-level laser irradiation on umbilical cord mesenchymal stem cells

    International Nuclear Information System (INIS)

    Chen, Hongli; Wang, Hong; Li, Yingxin; Liu, Weichao; Chen, Zhuying; Wang, Chao

    2016-01-01

    Low-level laser irradiation (LLLI) can enhance stem cell (SC) activity by increasing migration and proliferation. This study investigated the effects of LLLI on proliferation, enzymatic activity, and growth factor production in human umbilical cord mesenchymal SCs (hUC-MSCs) as well as the underlying mechanisms. hUC-MSCs were assigned to a control group (non-irradiation group) and three LLLI treatment groups (635 nm group, 808 nm group, and 635/808 nm group). Laser power density and energy density of 20 mW/cm"2 and 12 J/cm"2, respectively, were used for each experiment. The proliferation rate was higher in the 635 nm as compared to the other groups. LLLI at 808 nm did not induce cell proliferation. ROS levels in cells exposed to 635, 808, and 635/808 nm radiation were increased by 52.81%, 26.89%, and 21.15%, respectively, relative to the control group. CAT, tGPx, and SOD activity was increased. LLLI at 808 nm increased the levels of IL-1, IL-6, and NFκB but not VEGF. LLLI improved hUC-MSCs function and increased antioxidant activity. Dual-wavelength LLLI had more potent effects on hUC-MSCs than single-wavelength treatment. LLLI has potential applications in the preconditioning of hUC-MSCs in vitro prior to transplantation, which could improve the regenerative capacity of cells.

  17. Biological effects of low-level laser irradiation on umbilical cord mesenchymal stem cells

    Science.gov (United States)

    Chen, Hongli; Wang, Hong; Li, Yingxin; Liu, Weichao; Wang, Chao; Chen, Zhuying

    2016-04-01

    Low-level laser irradiation (LLLI) can enhance stem cell (SC) activity by increasing migration and proliferation. This study investigated the effects of LLLI on proliferation, enzymatic activity, and growth factor production in human umbilical cord mesenchymal SCs (hUC-MSCs) as well as the underlying mechanisms. hUC-MSCs were assigned to a control group (non-irradiation group) and three LLLI treatment groups (635 nm group, 808 nm group, and 635/808 nm group). Laser power density and energy density of 20 mW/cm2 and 12 J/cm2, respectively, were used for each experiment. The proliferation rate was higher in the 635 nm as compared to the other groups. LLLI at 808 nm did not induce cell proliferation. ROS levels in cells exposed to 635, 808, and 635/808 nm radiation were increased by 52.81%, 26.89%, and 21.15%, respectively, relative to the control group. CAT, tGPx, and SOD activity was increased. LLLI at 808 nm increased the levels of IL-1, IL-6, and NFκB but not VEGF. LLLI improved hUC-MSCs function and increased antioxidant activity. Dual-wavelength LLLI had more potent effects on hUC-MSCs than single-wavelength treatment. LLLI has potential applications in the preconditioning of hUC-MSCs in vitro prior to transplantation, which could improve the regenerative capacity of cells.

  18. Biological effects of low-level laser irradiation on umbilical cord mesenchymal stem cells

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Hongli; Wang, Hong; Li, Yingxin, E-mail: yingxinli2005@126.com; Liu, Weichao; Chen, Zhuying [Key Laboratory of Laser Medicine of Tianjin, Institute of Biomedical Engineering, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192 (China); Wang, Chao [Biomedical Engineering and Technology College, Tianjin Medical University, Tianjin, 300070 (China)

    2016-04-15

    Low-level laser irradiation (LLLI) can enhance stem cell (SC) activity by increasing migration and proliferation. This study investigated the effects of LLLI on proliferation, enzymatic activity, and growth factor production in human umbilical cord mesenchymal SCs (hUC-MSCs) as well as the underlying mechanisms. hUC-MSCs were assigned to a control group (non-irradiation group) and three LLLI treatment groups (635 nm group, 808 nm group, and 635/808 nm group). Laser power density and energy density of 20 mW/cm{sup 2} and 12 J/cm{sup 2}, respectively, were used for each experiment. The proliferation rate was higher in the 635 nm as compared to the other groups. LLLI at 808 nm did not induce cell proliferation. ROS levels in cells exposed to 635, 808, and 635/808 nm radiation were increased by 52.81%, 26.89%, and 21.15%, respectively, relative to the control group. CAT, tGPx, and SOD activity was increased. LLLI at 808 nm increased the levels of IL-1, IL-6, and NFκB but not VEGF. LLLI improved hUC-MSCs function and increased antioxidant activity. Dual-wavelength LLLI had more potent effects on hUC-MSCs than single-wavelength treatment. LLLI has potential applications in the preconditioning of hUC-MSCs in vitro prior to transplantation, which could improve the regenerative capacity of cells.

  19. Biological effects of high level natural background radiation on human population residing in Kerala coast, South West India

    International Nuclear Information System (INIS)

    Seshadri, M.

    2010-01-01

    The populations residing in Kerala coast are exposed to elevated natural background radiation since many generations. Extensive studies conducted by Bio-Medical group, Bhabha Atomic Research Center have generated wealth of data from this area dealing with epidemiology, monitoring the newborns for malformations, Health Audit Survey, Dosimetry and biological studies using cytogenetic and molecular biology techniques. Our studies on congenital malformations and chromosomal anomalies in children born to parents residing in High Level Natural Radiation Areas in Kerala have not shown any significant difference from normal radiation areas. Screening of over 1,25,000 consecutively born children showed an incidence rate which is comparable in both areas. Other factors such as consanguinity, maternal age and gravida status are more significant contributors than radiation dose to the risk for having malformation in child. Radiation prevalent in the HLNRA is in the dose range of above 1.5 to about 50 mGy per year which translates to doses in the range of nGy per hour. This clearly indicate the number of cells exposed to radiations will be one in few thousand or ten thousands. This throws up challenges in our capability to investigate the effects of radiation on cells. It has become imperative to develop and exploit techniques which will detect responses in single cells and would be able screen large number of cells at a time. Developments in cell biology and molecular biology are now giving us these capabilities. Use of flowcytometer and next generation sequencing would enable us to address many of these questions and provide meaningful approaches to understand the effects of such low dose radiation

  20. Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection.

    Science.gov (United States)

    Labots, Mariette; van der Mijn, Johannes C; Beekhof, Robin; Piersma, Sander R; de Goeij-de Haas, Richard R; Pham, Thang V; Knol, Jaco C; Dekker, Henk; van Grieken, Nicole C T; Verheul, Henk M W; Jiménez, Connie R

    2017-06-06

    Mass spectrometry-based phosphoproteomics of cancer cell and tissue lysates provides insight in aberrantly activated signaling pathways and potential drug targets. For improved understanding of individual patient's tumor biology and to allow selection of tyrosine kinase inhibitors in individual patients, phosphoproteomics of small clinical samples should be feasible and reproducible. We aimed to scale down a pTyr-phosphopeptide enrichment protocol to biopsy-level protein input and assess reproducibility and applicability to tumor needle biopsies. To this end, phosphopeptide immunoprecipitation using anti-phosphotyrosine beads was performed using 10, 5 and 1mg protein input from lysates of colorectal cancer (CRC) cell line HCT116. Multiple needle biopsies from 7 human CRC resection specimens were analyzed at the 1mg-level. The total number of phosphopeptides captured and detected by LC-MS/MS ranged from 681 at 10mg input to 471 at 1mg HCT116 protein. ID-reproducibility ranged from 60.5% at 10mg to 43.9% at 1mg. Per 1mg-level biopsy sample, >200 phosphopeptides were identified with 57% ID-reproducibility between paired tumor biopsies. Unsupervised analysis clustered biopsies from individual patients together and revealed known and potential therapeutic targets. This study demonstrates the feasibility of label-free pTyr-phosphoproteomics at the tumor biopsy level based on reproducible analyses using 1mg of protein input. The considerable number of identified phosphopeptides at this level is attributed to an effective down-scaled immuno-affinity protocol as well as to the application of ID propagation in the data processing and analysis steps. Unsupervised cluster analysis reveals patient-specific profiles. Together, these findings pave the way for clinical trials in which pTyr-phosphoproteomics will be performed on pre- and on-treatment biopsies. Such studies will improve our understanding of individual tumor biology and may enable future p

  1. Student learning style preferences in college-level biology courses: Implications for teaching and academic performance

    Science.gov (United States)

    Sitton, Jennifer Susan

    Education research has focused on defining and identifying student learning style preferences and how to incorporate this knowledge into teaching practices that are effective in engaging student interest and transmitting information. One objective was determining the learning style preferences of undergraduate students in Biology courses at New Mexico State University by using the online VARK Questionnaire and an investigator developed survey (Self Assessed Learning Style Survey, LSS). Categories include visual, aural, read-write, kinesthetic, and multimodal. The courses differed in VARK single modal learning preferences (p = 0.035) but not in the proportions of the number of modes students preferred (p = 0.18). As elsewhere, the majority of students were multimodal. There were similarities and differences between LSS and VARK results and between students planning on attending medical school and those not. Preferences and modalities tended not to match as expected for ratings of helpfulness of images and text. To detect relationships between VARK preferred learning style and academic performance, ANOVAs were performed using modality preferences and normalized learning gains from pre and post tests over material taught in the different modalities, as well as on end of semester laboratory and lecture grades. Overall, preference did not affect the performance for a given modality based activity, quiz, or final lecture or laboratory grades (p > 0.05). This suggests that a student's preference does not predict an improved performance when supplied with material in that modality. It is recommended that methods be developed to aid learning in a variety of modalities, rather than catering to individual learning styles. Another topic that is heavily debated in the field of education is the use of simulations or videos to replace or supplement dissections. These activities were compared using normalized learning gains from pre and post tests, as well as attitude surveys

  2. MEASUREMENT OF TRACE LEVELS OF DEUTERIUM OXIDE IN BIOLOGIC FLUIDS USING INFRARED SPECTROPHOTOMETRY.

    Science.gov (United States)

    Experimental data relevant to the assay of D2O in human serum, urine, and parotid fluid are presented. For serum, with triplicate scans, values of precision...and of accuracy of plus or minus 3% at the 250 p.p.m. D2O level are obtained. By use of parotid fluid the values are narrowed to plus or minus 2% at...aqueous compartments using values for serum water content. Parotid fluid appears to be particularly suitable for biomedical applications due to its ease

  3. A Global Overview of Exposure Levels and Biological Effects of Trace Elements in Penguins.

    Science.gov (United States)

    Espejo, Winfred; Celis, José E; GonzÃlez-Acuña, Daniel; Banegas, Andiranel; Barra, Ricardo; Chiang, Gustavo

    2018-01-01

    Trace elements are chemical contaminants that can be present almost anywhere on the planet. The study of trace elements in biotic matrices is a topic of great relevance for the implications that it can have on wildlife and human health. Penguins are very useful, since they live exclusively in the Southern Hemisphere and represent about 90% of the biomass of birds of the Southern Ocean. The levels of trace elements (dry weight) in different biotic matrices of penguins were reviewed here. Maps of trace element records in penguins were included. Data on exposure and effects of trace elements in penguins were collected from the literature. The most reported trace elements in penguins are aluminum, arsenic, cadmium, lead, mercury, copper, zinc, and manganese. Trace elements have been measured in 11 of the 18 species of penguins. The most studied biotic matrices are feathers and excreta. Most of the studies have been performed in Antarctica and subantarctic Islands. Little is known about the interaction among metals, which could provide better knowledge about certain mechanisms of detoxification in penguins. Future studies of trace elements in penguins must incorporate other metals such as vanadium, cobalt, nickel, and chromium. Data of metals in the species such as Eudyptes pachyrhynchus, Eudyptes moseleyi, Eudyptes sclateri, Eudyptes robustus, Eudyptes schlegeli, Spheniscus demersus, Spheniscus mendiculus, and Megadyptes antipodes are urged. It is important to correlate levels of metals in different biotic matrices with the effects on different species and in different geographic locations.

  4. Occurrence of ²¹⁰Po and biological effects of low-level exposure: the need for research.

    Science.gov (United States)

    Seiler, Ralph L; Wiemels, Joseph L

    2012-09-01

    Polonium-210 (²¹⁰Po) concentrations that exceed 1 Bq/L in drinking-water supplies have been reported from four widely separated U.S. states where exposure to it went unnoticed for decades. The radionuclide grandparents of ²¹⁰Po are common in sediments, and segments of the public may be chronically exposed to low levels of ²¹⁰Po in drinking water or in food products from animals raised in contaminated areas. We summarized information on the environmental behavior, biokinetics, and toxicology of ²¹⁰Po and identified the need for future research. Potential linkages between environmental exposure to ²¹⁰Po and human health effects were identified in a literature review. ²¹⁰Po accumulates in the ovaries where it kills primary oocytes at low doses. Because of its radiosensitivity and tendency to concentrate ²¹⁰Po, the ovary may be the critical organ in determining the lowest injurious dose for ²¹⁰Po. ²¹⁰Po also accumulates in the yolk sac of the embryo and in the fetal and placental tissues. Low-level exposure to ²¹⁰Po may have subtle, long-term biological effects because of its tropism towards reproductive and embryonic and fetal tissues where exposure to a single alpha particle may kill or damage critical cells. ²¹⁰Po is present in cigarettes and maternal smoking has several effects that appear consistent with the toxicology of ²¹⁰Po. Much of the important biological and toxicological research on ²¹⁰Po is more than four decades old. New research is needed to evaluate environmental exposure to ²¹⁰Po and the biological effects of low-dose exposure to it so that public health officials can develop appropriate mitigation measures where necessary.

  5. A sow replacement model using Bayesian updating in a three-level hierarchic Markov process. I. Biological model

    DEFF Research Database (Denmark)

    Kristensen, Anders Ringgaard; Søllested, Thomas Algot

    2004-01-01

    that really uses all these methodological improvements. In this paper, the biological model describing the performance and feed intake of sows is presented. In particular, estimation of herd specific parameters is emphasized. The optimization model is described in a subsequent paper......Several replacement models have been presented in literature. In other applicational areas like dairy cow replacement, various methodological improvements like hierarchical Markov processes and Bayesian updating have been implemented, but not in sow models. Furthermore, there are methodological...... improvements like multi-level hierarchical Markov processes with decisions on multiple time scales, efficient methods for parameter estimations at herd level and standard software that has been hardly implemented at all in any replacement model. The aim of this study is to present a sow replacement model...

  6. Pilot scale evaluation of biological and pressure clarification processes for the removal of high level of iron and manganese

    Energy Technology Data Exchange (ETDEWEB)

    Yannoni, C.C.; Kinsley, B.P. [Fay, Spofford & Thorndike, Inc., Burlington, MA (United States); Marston, T.R. [Connecticut Water Company, Clinton, CT (United States)

    1996-11-01

    Iron and manganese originating from groundwater supplies have a long history of causing consumer complaints in water distribution systems. Although iron and manganese are not public health concerns, they are a major concern from an aesthetic standpoint. The elevated awareness of consumers in regard to the quality of drinking water, an increase in regulations requiring additional treatment and the cost associated with developing new sources of supply, has required many utilities to implement improvements to existing facilities. Historical water quality data collected from the Connecticut Water Company`s (CWC) Westbrook Well revealed an increasing trend in iron and manganese concentrations. As a result, the existing greensand filtration facility located at the well, provides insufficient removal rates and inefficient operating cycles. Variations in operating procedures were not successful in correcting these problems. A water treatment feasibility study recommended evaluation of biological and pressure clarification processes to reduce iron (9 mg/l) and manganese (1.5 mg/l) levels below the secondary maximum contaminant levels of 0.30 and 0.05 mg/l, respectively. Assessment of these processes was accomplished through the construction and operation of a 5 gallon per minute (gpm) capacity pilot plant at the Westbrook Water Treatment Plant. Application of biological treatment for iron removal was then piloted on the existing full-scale treatment facility.

  7. Agronomic efficiency INIAP-17 rice with levels of chemical and biological fertilization in Ecuadorian Coast

    Directory of Open Access Journals (Sweden)

    Eduardo Neptali Colina Navarrete

    2017-05-01

    Full Text Available The investigation was carried out in the experimental farm of the College of Agricultural Sciences of the Technical University of Babahoyo, canton Babahoyo. Ten treatments were evaluated with three repetitions. The objective was to analyze the influence of four organic bioestimulantes on the efficiency of the conventional chemical fertilization in rice (Oryza sativa, to measure the effect on the agronomic behavior of the cultivation. The variety of rice INIAP-17 was sowed in parcels of 20 m2. The treatments were distributed at random in a design of complete blocks. For the evaluation of stockings the test was used from Tukey to significancia 5%. At the end of the cycle of the cultivation was evaluated: height of plants, sprout number for m2, grains for panicles, length and number of panicles m2, days to flowering, days to crop, number of grains for panicles, weight 1000 grains and yield for hectare. The results determined that the application of a program of high fertilization level (140-60-90-30 kg/ha, of N-P-K-S + Azospirillum 3 L/ha, the grain yield increased with increments of 23,44% with relationship to the witness. In the same way applications of Bacilllus and Azotobacter more levels means (120-40-60-20 and first floor (100-30-40-10 of application of N-P-K-S, they don't impact in days to the flowering, tipping, weight of 1000 grains, number of grains for panicles and relationship grain/straw.

  8. A novel bi-level meta-analysis approach: applied to biological pathway analysis.

    Science.gov (United States)

    Nguyen, Tin; Tagett, Rebecca; Donato, Michele; Mitrea, Cristina; Draghici, Sorin

    2016-02-01

    The accumulation of high-throughput data in public repositories creates a pressing need for integrative analysis of multiple datasets from independent experiments. However, study heterogeneity, study bias, outliers and the lack of power of available methods present real challenge in integrating genomic data. One practical drawback of many P-value-based meta-analysis methods, including Fisher's, Stouffer's, minP and maxP, is that they are sensitive to outliers. Another drawback is that, because they perform just one statistical test for each individual experiment, they may not fully exploit the potentially large number of samples within each study. We propose a novel bi-level meta-analysis approach that employs the additive method and the Central Limit Theorem within each individual experiment and also across multiple experiments. We prove that the bi-level framework is robust against bias, less sensitive to outliers than other methods, and more sensitive to small changes in signal. For comparative analysis, we demonstrate that the intra-experiment analysis has more power than the equivalent statistical test performed on a single large experiment. For pathway analysis, we compare the proposed framework versus classical meta-analysis approaches (Fisher's, Stouffer's and the additive method) as well as against a dedicated pathway meta-analysis package (MetaPath), using 1252 samples from 21 datasets related to three human diseases, acute myeloid leukemia (9 datasets), type II diabetes (5 datasets) and Alzheimer's disease (7 datasets). Our framework outperforms its competitors to correctly identify pathways relevant to the phenotypes. The framework is sufficiently general to be applied to any type of statistical meta-analysis. The R scripts are available on demand from the authors. sorin@wayne.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e

  9. Non-Linear Relationships between Aflatoxin B1 Levels and the Biological Response of Monkey Kidney Vero Cells

    Directory of Open Access Journals (Sweden)

    Mendel Friedman

    2013-08-01

    Full Text Available Aflatoxin-producing fungi contaminate food and feed during pre-harvest, storage and processing periods. Once consumed, aflatoxins (AFs accumulate in tissues, causing illnesses in animals and humans. Most human exposure to AF seems to be a result of consumption of contaminated plant and animal products. The policy of blending and dilution of grain containing higher levels of aflatoxins with uncontaminated grains for use in animal feed implicitly assumes that the deleterious effects of low levels of the toxins are linearly correlated to concentration. This assumption may not be justified, since it involves extrapolation of these nontoxic levels in feed, which are not of further concern. To develop a better understanding of the significance of low dose effects, in the present study, we developed quantitative methods for the detection of biologically active aflatoxin B1 (AFB1 in Vero cells by two independent assays: the green fluorescent protein (GFP assay, as a measure of protein synthesis by the cells, and the microculture tetrazolium (MTT assay, as a measure of cell viability. The results demonstrate a non-linear dose-response relationship at the cellular level. AFB1 at low concentrations has an opposite biological effect to higher doses that inhibit protein synthesis. Additional studies showed that heat does not affect the stability of AFB1 in milk and that the Vero cell model can be used to determine the presence of bioactive AFB1 in spiked beef, lamb and turkey meat. The implication of the results for the cumulative effects of low amounts of AFB1 in numerous foods is discussed.

  10. Alcohol intoxication at Swedish football matches: A study using biological sampling to assess blood alcohol concentration levels among spectators.

    Directory of Open Access Journals (Sweden)

    Natalie Durbeej

    Full Text Available Alcohol use and alcohol-related problems, including accidents, vandalism and violence, at sporting events are of increased concern in Sweden and other countries. The relationship between alcohol use and violence has been established and can be explained by the level of intoxication. Given the occurrence of alcohol use and alcohol-related problems at sporting events, research has assessed intoxication levels measured through biological sampling among spectators. This cross-sectional study aimed to assess the level of alcohol intoxication among spectators at football matches in the Swedish Premier Football League. Spectators were randomly selected and invited to participate in the study. Alcohol intoxication was measured with a breath analyser for Blood Alcohol Concentration levels, and data on gender, age, and recent alcohol use were gathered through a face-to-face interview. Blood Alcohol Concentration samples from 4420 spectators were collected. Almost half (46.8% had a positive Blood Alcohol Concentration level, with a mean value of 0.063%, while 8.9% had a Blood Alcohol Concentration level ≥ 0.1%, with a mean value of 0.135%. Factors that predicted a higher Blood Alcohol Concentration level included male gender (p = 0.005, lower age (p < 0.001, attending a local derby (p < 0.001, alcohol use prior to having entered the arena (p < 0.001, attending a weekend match (p < 0.001, and being a spectator at supporter sections (p < 0.001. About half of all spectators at football matches in the Swedish Premier Football League drink alcohol in conjunction with the match. Approximately one tenth have a high level of alcohol intoxication.

  11. Ground-Level Ozone Following Astrophysical Ionizing Radiation Events: An Additional Biological Hazard?

    Science.gov (United States)

    Thomas, Brian C; Goracke, Byron D

    2016-01-01

    Astrophysical ionizing radiation events such as supernovae, gamma-ray bursts, and solar proton events have been recognized as a potential threat to life on Earth, primarily through depletion of stratospheric ozone and subsequent increase in solar UV radiation at Earth's surface and in the upper levels of the ocean. Other work has also considered the potential impact of nitric acid rainout, concluding that no significant threat is likely. Not yet studied to date is the potential impact of ozone produced in the lower atmosphere following an ionizing radiation event. Ozone is a known irritant to organisms on land and in water and therefore may be a significant additional hazard. Using previously completed atmospheric chemistry modeling, we examined the amount of ozone produced in the lower atmosphere for the case of a gamma-ray burst and found that the values are too small to pose a significant additional threat to the biosphere. These results may be extended to other ionizing radiation events, including supernovae and extreme solar proton events.

  12. Radiation and man - evaluation of biological and environmental low level radiation effects

    International Nuclear Information System (INIS)

    Riklis, E.

    1977-01-01

    The harmful effects of acute radiation cannot be resolved by statistical means and require clearer knowledge of mechanisms of action and much wider collection of human experience before any definite sound stand can be taken. Much information has accumulated from animal experiments, and still the interpretations are not always clearcut, but for human experience it is only the occasional accident which can give a direct answer. Some of the phenomena attributed to low dose radiation are summarized. There are regions of radiation exposure about which we have only limited positive knowledge, an all low-dose risk estimates have been based on effects observed at relatively high doses. Much information has been gathered which does not support the severity of former basic principles, especially our knowledge of mechanisms of repair existing in most cells as natural defence against the damages caused by radiation as well as by many chemicals which act as mutagenic and carcinogenic agents. Understanding these mechanism, their scope of action and their availability to a damaged cell and organism will lead towards modification of the acceptable permissible exposures, in some cases towards severity, but in most cases towards leniency and higher values. For the evaluation of the effects of low level low dose-rate radiations, whether external, or from internal deposition of isotopes, only late somatic and genetic effects should be considered. (B.G.)

  13. Biological bases of the maximum permissible exposure levels of the UK laser standard BS 4803: 1983

    International Nuclear Information System (INIS)

    McKinlay, A.F.; Harlen, F.

    1983-10-01

    The use of lasers has increased greatly over the past 15 years or so, to the extent that they are now used routinely in many occupational and public situations. There has been an increasing awareness of the potential hazards presented by lasers and substantial efforts have been made to formulate safety standards. In the UK the relevant Safety Standard is the British Standards Institution Standard BS 4803. This Standard was originally published in 1972 and a revision has recently been published (BS 4803: 1983). The revised standard has been developed using the American National Standards Institute Standard, ANSI Z136.1 (1973 onwards), as a model. In other countries, national standards have been similarly formulated, resulting in a large measure of international agreement through participation in the work of the International Electrotechnical Commission (IEC). The bases of laser safety standards are biophysical data on threshold injury effects, particularly on the retina, and the development of theoretical models of damage mechanisms. This report deals in some detail with the mechanisms of injury from over exposure to optical radiations, in particular with the dependency of the type and degree of damage on wavelength, image size and pulse duration. The maximum permissible exposure levels recommended in BS 4803: 1983 are compared with published data for damage thresholds and the adequacy of the standard is discussed. (author)

  14. Increasing URM Undergraduate Student Success through Assessment-Driven Interventions: A Multiyear Study Using Freshman-Level General Biology as a Model System

    Science.gov (United States)

    Carmichael, Mary C.; St. Clair, Candace; Edwards, Andrea M.; Barrett, Peter; McFerrin, Harris; Davenport, Ian; Awad, Mohamed; Kundu, Anup; Ireland, Shubha Kale

    2016-01-01

    Xavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students. In this multiyear study with ~5500 participants, data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course. The three hour-long exams were common and…

  15. An Evaluation of Teachers' Attitudes and Beliefs Levels on Classroom Control in Terms of Teachers' Sense of Efficacy (The Sample of Biology Teachers in Turkey)

    Science.gov (United States)

    Kurt, Hakan

    2014-01-01

    The aim of this study is to evaluate biology teachers' attitudes and belief levels on classroom control in terms of teachers' sense of efficacy. The screening model was used in the study. The study group was comprised of 135 biology teachers. In this study, Teachers' Sense of Efficacy Scale (TSES) and The Attitudes and Beliefs on Classroom Control…

  16. The Treatment of Low Level Radioactive Liquid Waste Containing Detergent by Biological Activated Sludge Process

    International Nuclear Information System (INIS)

    Zainus Salimin

    2002-01-01

    The treatment of low level radioactive liquid waste containing persil detergent from laundry operation of contaminated clothes by activated sludge process has been done, for alternative process replacing the existing treatment by evaporation. The detergent concentration in water solution from laundry operation is 14.96 g/l. After rinsing operation of clothes and mixing of laundry water solution with another liquid waste, the waste water solution contains about ≤ 1.496 g/l of detergent and 10 -3 Ci/m 3 of Cs-137 activity. The simulation waste having equivalent activity of Cs-137 10 -3 Ci/m 3 , detergent content (X) 1.496, 0.748, 0.374, 0.187, 0.1496 and 0.094 g/l on BOD value respectively 186, 115, 71, 48, 19, and 16 ppm was processed by activated sludge in reactor of 18.6 l capacity on ambient temperature. It is used Super Growth Bacteria (SGB) 102 and SGB 104, nitrogen and phosphor nutrition, and aeration. The result show that bacteria of SGB 102 and SGB 104 were able to degrade the persil detergent for attaining standard quality of water release category B in which BOD values 6 ppm. It was need 30 hours for X ≤ 0.187 g/l, 50 hours for 0.187 < X ≤ 0.374 g/l, 75 hours for 0.374 < X ≤ 0.748, and 100 hours for 0.748 < X ≤ 1.496 g/l. On the initial period the bacteria of SGB 104 interact most quickly to degrade the detergent comparing SGB 102. Biochemical oxidation process decontaminate the solution on the decontamination factor of 350, Cs-137 be concentrate in sludge by complexing with the bacteria wall until the activity of solution be become very low. (author)

  17. What time-lag for a retraction search on PubMed?

    Science.gov (United States)

    Decullier, Evelyne; Huot, Laure; Maisonneuve, Hervé

    2014-06-25

    To investigate fraud and errors, scientists have studied cohorts of retraction notices. These researches have been performed using a PubMed search on publication type "retraction of publication" which retrieves the notices of the retractions. We assessed the stability of the indexation of retraction notices over a 15-month period and what was the time-lag to get stability. A search on notices of retraction issued in 2008 was repeated every 3 months during 15 months from February 2011. The first search resulted in 237 notices of retraction. Throughout the study period, 14 discrepancies with the initial search were observed (6%). We found that the number of retraction notices became stable 35 months after the retraction. The time-lag observed in this study has to be taken into account when performing a PubMed search.

  18. A bibliometric analysis of Australian general practice publications from 1980 to 2007 using PubMed.

    Science.gov (United States)

    Mendis, Kumara; Kidd, Michael R; Schattner, Peter; Canalese, Joseph

    2010-01-01

    We analysed Australian general practice (GP) publications in PubMed from 1980 to 2007 to determine journals, authors, publication types, national health priority areas (NHPA) and compared the results with those from three specialties (public health, cardiology and medical informatics) and two countries (the UK and New Zealand). Australian GP publications were downloaded in MEDLINE format using PubMed queries and were written to a Microsoft Access database using a software application. Search Query Language and online PubMed queries were used for further analysis. There were 4777 publications from 1980 to 2007. Australian Family Physician (38.1%) and the Medical Journal of Australia (17.6%) contributed 55.7% of publications. Reviews (12.7%), letters (6.6%), clinical trials (6.5%) and systematic reviews (5%) were the main PubMed publication types. Thirty five percent of publications addressed National Health Priority Areas with material on mental health (13.7%), neoplasms (6.5%) and cardiovascular conditions (5.9%). The comparable numbers of publications for the three specialties were: public health - 80 911, cardiology - 15 130 and medical informatics - 3338; total country GP comparisons were: UK - 14 658 and New Zealand - 1111. Australian GP publications have shown an impressive growth from 1980 to 2007 with a 15-fold increase. This increase may be due in part to the actions of the Australian government over the past decade to financially support research in primary care, as well as the maturing of academic general practice. This analysis can assist governments, researchers, policy makers and others to target resources so that further developments can be encouraged, supported and monitored.

  19. Use of scientific social networking to improve the research strategies of PubMed readers

    OpenAIRE

    Evdokimov, Pavel; Kudryavtsev, Alexey; Ilgisonis, Ekaterina; Ponomarenko, Elena; Lisitsa, Andrey

    2016-01-01

    Background Keeping up with journal articles on a daily basis is an important activity of scientists engaged in biomedical research. Usually, journal articles and papers in the field of biomedicine are accessed through the Medline/PubMed electronic library. In the process of navigating PubMed, researchers unknowingly generate user-specific reading profiles that can be shared within a social networking environment. This paper examines the structure of the social networking environment generated...

  20. PubMed Interact: an Interactive Search Application for MEDLINE/PubMed

    Science.gov (United States)

    Muin, Michael; Fontelo, Paul; Ackerman, Michael

    2006-01-01

    Online search and retrieval systems are important resources for medical literature research. Progressive Web 2.0 technologies provide opportunities to improve search strategies and user experience. Using PHP, Document Object Model (DOM) manipulation and Asynchronous JavaScript and XML (Ajax), PubMed Interact allows greater functionality so users can refine search parameters with ease and interact with the search results to retrieve and display relevant information and related articles. PMID:17238658

  1. PubMedReco: A Real-Time Recommender System for PubMed Citations.

    Science.gov (United States)

    Samuel, Hamman W; Zaïane, Osmar R

    2017-01-01

    We present a recommender system, PubMedReco, for real-time suggestions of medical articles from PubMed, a database of over 23 million medical citations. PubMedReco can recommend medical article citations while users are conversing in a synchronous communication environment such as a chat room. Normally, users would have to leave their chat interface to open a new web browser window, and formulate an appropriate search query to retrieve relevant results. PubMedReco automatically generates the search query and shows relevant citations within the same integrated user interface. PubMedReco analyzes relevant keywords associated with the conversation and uses them to search for relevant citations using the PubMed E-utilities programming interface. Our contributions include improvements to the user experience for searching PubMed from within health forums and chat rooms, and a machine learning model for identifying relevant keywords. We demonstrate the feasibility of PubMedReco using BMJ's Doc2Doc forum discussions.

  2. Respiratory infections research in afghanistan: bibliometric analysis with the database pubmed

    International Nuclear Information System (INIS)

    Pilsezek, F.H.

    2015-01-01

    Infectious diseases research in a low-income country like Afghanistan is important. Methods: In this study an internet-based database Pubmed was used for bibliometric analysis of infectious diseases research activity. Research publications entries in PubMed were analysed according to number of publications, topic, publication type, and country of investigators. Results: Between 2002-2011, 226 (77.7%) publications with the following research topics were identified: respiratory infections 3 (1.3%); parasites 8 (3.5%); diarrhoea 10 (4.4%); tuberculosis 10 (4.4%); human immunodeficiency virus (HIV) 11(4.9%); multi-drug resistant bacteria (MDR) 18(8.0%); polio 31(13.7%); leishmania 31(13.7%); malaria 46(20.4%). From 2002-2011, 11 (4.9%) publications were basic science laboratory-based research studies. Between 2002-2011, 8 (3.5%) publications from Afghan institutions were identified. Conclusion: In conclusion, the internet-based database Pubmed can be consulted to collect data for guidance of infectious diseases research activity of low-income countries. The presented data suggest that infectious diseases research in Afghanistan is limited for respiratory infections research, has few studies conducted by Afghan institutions, and limited laboratory-based research contributions. (author)

  3. Dialysis search filters for PubMed, Ovid MEDLINE, and Embase databases.

    Science.gov (United States)

    Iansavichus, Arthur V; Haynes, R Brian; Lee, Christopher W C; Wilczynski, Nancy L; McKibbon, Ann; Shariff, Salimah Z; Blake, Peter G; Lindsay, Robert M; Garg, Amit X

    2012-10-01

    Physicians frequently search bibliographic databases, such as MEDLINE via PubMed, for best evidence for patient care. The objective of this study was to develop and test search filters to help physicians efficiently retrieve literature related to dialysis (hemodialysis or peritoneal dialysis) from all other articles indexed in PubMed, Ovid MEDLINE, and Embase. A diagnostic test assessment framework was used to develop and test robust dialysis filters. The reference standard was a manual review of the full texts of 22,992 articles from 39 journals to determine whether each article contained dialysis information. Next, 1,623,728 unique search filters were developed, and their ability to retrieve relevant articles was evaluated. The high-performance dialysis filters consisted of up to 65 search terms in combination. These terms included the words "dialy" (truncated), "uremic," "catheters," and "renal transplant wait list." These filters reached peak sensitivities of 98.6% and specificities of 98.5%. The filters' performance remained robust in an independent validation subset of articles. These empirically derived and validated high-performance search filters should enable physicians to effectively retrieve dialysis information from PubMed, Ovid MEDLINE, and Embase.

  4. RESPIRATORY INFECTIONS RESEARCH IN AFGHANISTAN: BIBLIOMETRIC ANALYSIS WITH THE DATABASE PUBMED.

    Science.gov (United States)

    Pilsczek, Florian H

    2015-01-01

    Infectious diseases research in a low-income country like Afghanistan is important. In this study an internet-based database Pubmed was used for bibliometric analysis of infectious diseases research activity. Research publications entries in PubMed were analysed according to number of publications, topic, publication type, and country of investigators. Between 2002-2011, 226 (77.7%) publications with the following research topics were identified: respiratory infections 3 (1.3%); parasites 8 (3.5%); diarrhoea 10 (4.4%); tuberculosis 10 (4.4%); human immunodeficiency virus (HIV) 11 (4.9%); multi-drug resistant bacteria (MDR) 18 (8.0%); polio 31 (13.7%); leishmania 31 (13.7%); malaria 46 (20.4%). From 2002-2011, 11 (4.9%) publications were basic science laboratory-based research studies. Between 2002-2011, 8 (3.5%) publications from Afghan institutions were identified. In conclusion, the internet-based database Pubmed can be consulted to collect data for guidance of infectious diseases research activity of low-income countries. The presented data suggest that infectious diseases research in Afghanistan is limited for respiratory infections research, has few studies conducted by Afghan institutions, and limited laboratory-based research contributions.

  5. [A statistical analysis and perspective of headache-related papers covered in 2011 PubMed].

    Science.gov (United States)

    Zhang, Ming-jie; Yu, Sheng-yuan; Chu, Bing-qian; Dai, Wei

    2013-01-01

    To investigate the distribution and hot spots of literatures on headache by bibliometric analysis in order to provide reference for further study. Literatures that contained headache or migraine in text words published in 2011 in PubMed databases (www.ncbi.nlm.nih.gov/Pubmed) were searched. Journals, countries and subjects were bibliometrically analysed. There were 3683 papers involved to headache published in PubMed in 2011, of which 1527 papers were on headache research. The number of papers on headache research published by USA was the most followed by Italy and Germany (USA 23.25%, Italy 10.74%, Germany 5.83%). The mainly studied subjects were therapy (29.60%), pathophysiology (18.66%) and etiology (16.31%). 14.86% papers published in Cephalalgia, which is one of the most important journals, reported negative results. The emphasis of headache research was on migraine. Therapy, pathophysiology and etiology were the hot spot. Literatures with negative result attracted authors to give the more attention.

  6. Biological Signatures of Brain Damage Associated with High Serum Ferritin Levels in Patients with Acute Ischemic Stroke and Thrombolytic Treatment

    Science.gov (United States)

    Millán, Mónica; Sobrino, Tomás; Arenillas, Juan Francisco; Rodríguez-Yáñez, Manuel; García, María; Nombela, Florentino; Castellanos, Mar; de la Ossa, Natalia Pérez; Cuadras, Patricia; Serena, Joaquín; Castillo, José; Dávalos, Antoni

    2008-01-01

    Background and purpose: Increased body iron stores have been related to greater oxidative stress and brain injury in clinical and experimental cerebral ischemia and reperfusion. We aimed to investigate the biological signatures of excitotoxicity, inflammation and blood brain barrier disruption potentially associated with high serum ferritin levels-related damage in acute stroke patients treated with i.v. t-PA. Methods: Serum levels of ferritin (as index of increased cellular iron stores), glutamate, interleukin-6, matrix metalloproteinase-9 and cellular fibronectin were determined in 134 patients treated with i.v. t-PA within 3 hours from stroke onset in blood samples obtained before t-PA treatment, at 24 and 72 hours. Results: Serum ferritin levels before t-PA infusion correlated to glutamate (r = 0.59, p < 0.001) and interleukin-6 (r = 0.55, p <0.001) levels at baseline, and with glutamate (r = 0.57,p <0.001), interleukin-6 (r = 0.49,p <0.001), metalloproteinase-9 (r = 0.23, p = 0.007) and cellular fibronectin (r = 0.27, p = 0.002) levels measured at 24 hours and glutamate (r = 0.415, p < 0.001), interleukin-6 (r = 0.359, p < 0.001) and metalloproteinase-9 (r = 0.261, p = 0.004) at 72 hours. The association between ferritin and glutamate levels remained after adjustment for confounding factors in generalized linear models. Conclusions: Brain damage associated with increased iron stores in acute ischemic stroke patients treated with iv. tPA may be mediated by mechanisms linked to excitotoxic damage. The role of inflammation, blood brain barrier disruption and oxidative stress in this condition needs further research. PMID:19096131

  7. Perspective of use of Pinus sylvestris L. as biological indicator of areas with low level radioactive pollution

    International Nuclear Information System (INIS)

    Dragan, G.I.; Dragan, N.V.; Levon, F.M.

    2006-01-01

    Research indicates data about distinct of Pinus sylvestris as biological indicator. Especially important is discovered distinctiveness of reactions of Pinus sylvestris to low level radioactive pollution. To identify radioactive pollution in habitats using biological indicators it is recommended the following complex of markers of functions of vegetative and reproductive systems of Pinus sylvestris: specific changes in architectonic of tree crowns; increase in number of annual cycles of growth to two or three and duration of active vegetation drastic change in morphogenesis of vegetative shoots in secondary (summer) shoots; formation of intermediate structures (combined buds and shoots) with mosaic development of some metamers with regular or affected structure; stimulation of buds (general increase of points of growth and appearance of additional ways of their formation); specific changes in gistogenesis of needles; hollow tar channels filled with sclerenhyma or parenchyma ect.; interruption of morphogenesis of male reproductive shoots; increase in the number of abnormal pollen grains to 70%; abnormal branching of pollen channels. All affects in vegetative system of Pinus sylvestris take place at the age of up to 12-14 (20) years. (authors)

  8. Abstract databases in nuclear medicine; New database for articles not indexed in PubMed

    International Nuclear Information System (INIS)

    Ugrinska, A.; Mustafa, B.

    2004-01-01

    Full text: Abstract databases available on Internet free of charge were searched for nuclear medicine contents. The only comprehensive database found was PubMed. Analysis of nuclear medicine journals included in PubMed was performed. PubMed contains 25 medical journals that contain the phrase 'nuclear medicine' in different languages in their title. Searching the Internet with the search engine 'Google' we have found four more peer-reviewed journals with the phrase 'nuclear medicine' in their title. In addition, we are fully aware that many articles related to nuclear medicine are published in national medical journals devoted to general medicine. For example in year 2000 colleagues from Institute of Pathophysiology and Nuclear Medicine, Skopje, Macedonia have published 10 articles out of which none could be found on PubMed. This suggested that a big amount of research work is not accessible for the people professionally involved in nuclear medicine. Therefore, we have created a database framework for abstracts that couldn't be found in PubMed. The database is organized in user-friendly manner. There are two main sections: 'post an abstract' and 'search for abstracts'. Authors of the articles are expected to submit their work in the section 'post an abstract'. During the submission process authors should fill the separate boxes with the Title in English, Title in original language, Country of origin, Journal name, Volume, Issue and Pages. Authors should choose up to five keywords from a drop-down menu. Authors are encouraged if the abstract is not published in English to translate it. The section 'search for abstract' is searchable according to Author, Keywords, and words and phrases incorporated in the English title. The abstract database currently resides on an MS Access back-end, with a front-end in ASP (Active Server Pages). In the future, we plan to migrate the database on a MS SQL Server, which should provide a faster and more reliable framework for hosting a

  9. Development of a radiochemical neutron activation analysis procedure for determination of rhenium in biological and environmental samples at ultratrace level

    International Nuclear Information System (INIS)

    Kucera, J.; Lucanikova, M.; Czech Technical Univ., Prague

    2006-01-01

    Radiochemical neutron activation procedures using liquid-liquid extraction with tetraphenylarsonium chloride in chloroform from 1M HCl and solid extraction with ALIQUAT 336 incorporated in a polyacrylonitrile binding matrix from 0.1M HCl were developed for accurate determination of rhenium in biological and environmental samples at the sub-ng x g -1 level. Concentrations of Re in the range of 0.1 to 2.4 ng x g -1 were determined in several botanical reference materials (RM), while in a RM of road dust a value of ∼ 10 ng x g -1 was found. Significantly elevated values of Re, up to 90 ng x g -1 were found in seaweed (brown algae). Results for Re in the brown algae Fucus vesiculosus in which elevated 99 Tc values had previously been determined suggested possible competition between Re and Tc in the accumulation process. (author)

  10. ‘PROTEIN SYNTHESIS GAME’: UTILIZING GAME-BASED APPROACH FOR IMPROVING COMMUNICATIVE SKILLS IN A-LEVELS BIOLOGY CLASS

    Directory of Open Access Journals (Sweden)

    Mohd Adlan Ramly

    2017-12-01

    Full Text Available This experimental paper seeks to elucidate the usage of the card game ‘Protein Synthesis Game’ as a student’s learning tool in studying the Biology topic of protein synthesis during an A-Level course. A total of 24 experimental students in 3 induced groups and 24 controlled students in controlled groups were involved in the experiment which began with a pretest on the topic of Protein Synthesis, followed by the experimentation, and ended with a post-test administered after the incubation period. Results indicate that students have better facilitative communicative engagement in learning protein synthesis when playing the game as compared to studying the topic from a book. The data suggests that such communicative engagement may lead to a successful meaningful learning on the students’ part.

  11. PubMed had a higher sensitivity than Ovid-MEDLINE in the search for systematic reviews.

    Science.gov (United States)

    Katchamart, Wanruchada; Faulkner, Amy; Feldman, Brian; Tomlinson, George; Bombardier, Claire

    2011-07-01

    To compare the performance of Ovid-MEDLINE vs. PubMed for identifying randomized controlled trials of methotrexate (MTX) in patients with rheumatoid arthritis (RA). We created search strategies for Ovid-MEDLINE and PubMed for a systematic review of MTX in RA. Their performance was evaluated using sensitivity, precision, and number needed to read (NNR). Comparing searches in Ovid-MEDLINE vs. PubMed, PubMed retrieved more citations overall than Ovid-MEDLINE; however, of the 20 citations that met eligibility criteria for the review, Ovid-MEDLINE retrieved 17 and PubMed 18. The sensitivity was 85% for Ovid-MEDLINE vs. 90% for PubMed, whereas the precision and NNR were comparable (precision: 0.881% for Ovid-MEDLINE vs. 0.884% for PubMed and NNR: 114 for Ovid-MEDLINE vs. 113 for PubMed). In systematic reviews of RA, PubMed has higher sensitivity than Ovid-MEDLINE with comparable precision and NNR. This study highlights the importance of well-designed database-specific search strategies. Copyright © 2010 Elsevier Inc. All rights reserved.

  12. Modern Biology

    OpenAIRE

    ALEKSIC, Branko

    2014-01-01

    The purpose of this course is to learn the philosophy, principles, and techniques of modern biology. The course is particularly designed for those who have not learned biology previously or whose major is other than biology, and who may think that they do not need to know any biology at all. The topics are covered in a rather general, overview manner, but certain level of diligence in grasping concepts and memorizing the terminology is expected.

  13. Using PubMed search strings for efficient retrieval of manual therapy research literature.

    Science.gov (United States)

    Pillastrini, Paolo; Vanti, Carla; Curti, Stefania; Mattioli, Stefano; Ferrari, Silvano; Violante, Francesco Saverio; Guccione, Andrew

    2015-02-01

    The aim of this study was to construct PubMed search strings that could efficiently retrieve studies on manual therapy (MT), especially for time-constrained clinicians. Our experts chose 11 Medical Subject Heading terms describing MT along with 84 additional potential terms. For each term that was able to retrieve more than 100 abstracts, we systematically extracted a sample of abstracts from which we estimated the proportion of studies potentially relevant to MT. We then constructed 2 search strings: 1 narrow (threshold of pertinent articles ≥40%) and 1 expanded (including all terms for which a proportion had been calculated). We tested these search strings against articles on 2 conditions relevant to MT (thoracic and temporomandibular pain). We calculated the number of abstracts needed to read (NNR) to identify 1 potentially pertinent article in the context of these conditions. Finally, we evaluated the efficiency of the proposed PubMed search strings to identify relevant articles included in a systematic review on spinal manipulative therapy for chronic low back pain. Fifty-five search terms were able to extract more than 100 citations. The NNR to find 1 potentially pertinent article using the narrow string was 1.2 for thoracic pain and 1.3 for temporomandibular pain, and the NNR for the expanded string was 1.9 and 1.6, respectively. The narrow search strategy retrieved all the randomized controlled trials included in the systematic review selected for comparison. The proposed PubMed search strings may help health care professionals locate potentially pertinent articles and review a large number of MT studies efficiently to better implement evidence-based practice. Copyright © 2015 National University of Health Sciences. Published by Elsevier Inc. All rights reserved.

  14. The trend of indexed papers in PubMed covering different aspects of self-immolation.

    Science.gov (United States)

    Rezaeian, Mohsen

    2014-01-01

    Self-immolation is a fatal and devastating method of committing suicide used around the world. The chief aim of the present article is to look at the trend of indexed papers in PubMed covering different aspects of self-immolation. PubMed search engine (http://www.ncbi.nlm.nih.gov) was searched by using six keywords i.e. "self-immolation", "self-inflicted burn", "self-burning", "self-incineration", "suicidal burns" and "suicide by burning". These keywords should appear either in the title or the abstract of the articles. The time frame was set as to retrieve papers expanding from early indexing time up to end of the year 2011. Based on the search strategy 132 papers were retrieved from these total numbers; 12 (9%) were categorized as review papers; 24 (18%) as case reports and the rest 96 (73%) were original studies. It seems that the number of papers increased during the years of investigations and the highest indexed papers i.e. 14 (10.6%) belonged to the year 2011. While most journals, published only one article the highest indexed papers i.e. 35 (26.5%) belonged to Burns. There was an increasing trend in the number of self-immolation articles indexed in PubMed since 1965. Three journals i.e. Burns, Journal of Burn Care and Rehabilitation and Journal of Forensic Sciences hosted for more than 37% of all those indexed articles. However, given the increasing trend of self-immolation still more studies are needed to shed light on the diverse aspects of this appalling human behavior.

  15. Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks.

    Science.gov (United States)

    Deeter, Anthony; Dalman, Mark; Haddad, Joseph; Duan, Zhong-Hui

    2017-01-01

    The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS- Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways.

  16. [Google and PubMed for physicians: how to find information without getting lost].

    Science.gov (United States)

    Muñoz Núñez, C F; Sendra Portero, F

    2013-06-01

    Searching on Internet looking for clinically relevant medical information, used as a clinical decision aid tool, for self-learning or for research, is currently a common practice in Radiology. This task has been strengthened by the technological environment where radiologists work with direct access to information sources from the Workstation. The aim of this paper is to review the basic features of information searching tools in order to understand their functions and to optimize medical information searching on Internet. Google, Google Scholar and PubMed are reviewed as models for that purpose. Copyright © 2012 SERAM. Published by Elsevier Espana. All rights reserved.

  17. Beyond PubMed: Searching the "Grey Literature" for Clinical Trial Results.

    Science.gov (United States)

    Citrome, Leslie

    2014-07-01

    Clinical trial results have been traditionally communicated through the publication of scholarly reports and reviews in biomedical journals. However, this dissemination of information can be delayed or incomplete, making it difficult to appraise new treatments, or in the case of missing data, evaluate older interventions. Going beyond the routine search of PubMed, it is possible to discover additional information in the "grey literature." Examples of the grey literature include clinical trial registries, patent databases, company and industrywide repositories, regulatory agency digital archives, abstracts of paper and poster presentations on meeting/congress websites, industry investor reports and press releases, and institutional and personal websites.

  18. "Life-bearing molecules" versus "life-embodying systems": Two contrasting views on the what-is-life (WIL) problem persisting from the early days of molecular biology to the post-genomic cell- and organism-level biology.

    Science.gov (United States)

    Sato, Naoki

    2018-05-01

    "What is life?" is an ultimate biological quest for the principle that makes organisms alive. This 'WIL problem' is not, however, a simple one that we have a straightforward strategy to attack. From the beginning, molecular biology tried to identify molecules that bear the essence of life: the double helical DNA represented replication, and enzymes were micro-actuators of biological activities. A dominating idea behind these mainstream biological studies relies on the identification of life-bearing molecules, which themselves are models of life. Another, prevalent idea emphasizes that life resides in the whole system of an organism, but not in some particular molecules. The behavior of a complex system may be considered to embody the essence of life. The thermodynamic view of life system in the early 20th century was remodeled as physics of complex systems and systems biology. The two views contrast with each other, but they are no longer heritage of the historical dualism in biology, such as mechanism/materialism versus vitalism, or reductionism versus holism. These two views are both materialistic and mechanistic, and act as driving forces of modern biology. In reality, molecules function in a context of systems, whereas systems presuppose functional molecules. A key notion to reconcile this conflict is that subjects of biological studies are given before we start to study them. Cell- or organism-level biology is destined to the dialectic of molecules and systems, but this antagonism can be resolved by dynamic thinking involving biological evolution. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Towards a system level understanding of non-model organisms sampled from the environment: a network biology approach.

    Directory of Open Access Journals (Sweden)

    Tim D Williams

    2011-08-01

    Full Text Available The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations.

  20. Towards a system level understanding of non-model organisms sampled from the environment: a network biology approach.

    Science.gov (United States)

    Williams, Tim D; Turan, Nil; Diab, Amer M; Wu, Huifeng; Mackenzie, Carolynn; Bartie, Katie L; Hrydziuszko, Olga; Lyons, Brett P; Stentiford, Grant D; Herbert, John M; Abraham, Joseph K; Katsiadaki, Ioanna; Leaver, Michael J; Taggart, John B; George, Stephen G; Viant, Mark R; Chipman, Kevin J; Falciani, Francesco

    2011-08-01

    The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations.

  1. The quality of the reported sample size calculations in randomized controlled trials indexed in PubMed.

    Science.gov (United States)

    Lee, Paul H; Tse, Andy C Y

    2017-05-01

    There are limited data on the quality of reporting of information essential for replication of the calculation as well as the accuracy of the sample size calculation. We examine the current quality of reporting of the sample size calculation in randomized controlled trials (RCTs) published in PubMed and to examine the variation in reporting across study design, study characteristics, and journal impact factor. We also reviewed the targeted sample size reported in trial registries. We reviewed and analyzed all RCTs published in December 2014 with journals indexed in PubMed. The 2014 Impact Factors for the journals were used as proxies for their quality. Of the 451 analyzed papers, 58.1% reported an a priori sample size calculation. Nearly all papers provided the level of significance (97.7%) and desired power (96.6%), and most of the papers reported the minimum clinically important effect size (73.3%). The median (inter-quartile range) of the percentage difference of the reported and calculated sample size calculation was 0.0% (IQR -4.6%;3.0%). The accuracy of the reported sample size was better for studies published in journals that endorsed the CONSORT statement and journals with an impact factor. A total of 98 papers had provided targeted sample size on trial registries and about two-third of these papers (n=62) reported sample size calculation, but only 25 (40.3%) had no discrepancy with the reported number in the trial registries. The reporting of the sample size calculation in RCTs published in PubMed-indexed journals and trial registries were poor. The CONSORT statement should be more widely endorsed. Copyright © 2016 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

  2. GeneView: a comprehensive semantic search engine for PubMed.

    Science.gov (United States)

    Thomas, Philippe; Starlinger, Johannes; Vowinkel, Alexander; Arzt, Sebastian; Leser, Ulf

    2012-07-01

    Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. The enormous ambiguity among most names of biomedical objects such as genes, chemicals and diseases often produces too large and unspecific search results. We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. Annotation is performed by a multitude of state-of-the-art text-mining tools for recognizing mentions from 10 entity classes and for identifying protein-protein interactions. GeneView currently contains annotations for >194 million entities from 10 classes for ∼21 million citations with 271,000 full text bodies. GeneView can be searched at http://bc3.informatik.hu-berlin.de/.

  3. Medical literature searches: a comparison of PubMed and Google Scholar.

    Science.gov (United States)

    Nourbakhsh, Eva; Nugent, Rebecca; Wang, Helen; Cevik, Cihan; Nugent, Kenneth

    2012-09-01

    Medical literature searches provide critical information for clinicians. However, the best strategy for identifying relevant high-quality literature is unknown. We compared search results using PubMed and Google Scholar on four clinical questions and analysed these results with respect to article relevance and quality. Abstracts from the first 20 citations for each search were classified into three relevance categories. We used the weighted kappa statistic to analyse reviewer agreement and nonparametric rank tests to compare the number of citations for each article and the corresponding journals' impact factors. Reviewers ranked 67.6% of PubMed articles and 80% of Google Scholar articles as at least possibly relevant (P = 0.116) with high agreement (all kappa P-values PubMed searches and Google Scholar searches often identify different articles. In this study, Google Scholar articles were more likely to be classified as relevant, had higher numbers of citations and were published in higher impact factor journals. The identification of frequently cited articles using Google Scholar for searches probably has value for initial literature searches. © 2012 The authors. Health Information and Libraries Journal © 2012 Health Libraries Group.

  4. Diagnosis checking of statistical analysis in RCTs indexed in PubMed.

    Science.gov (United States)

    Lee, Paul H; Tse, Andy C Y

    2017-11-01

    Statistical analysis is essential for reporting of the results of randomized controlled trials (RCTs), as well as evaluating their effectiveness. However, the validity of a statistical analysis also depends on whether the assumptions of that analysis are valid. To review all RCTs published in journals indexed in PubMed during December 2014 to provide a complete picture of how RCTs handle assumptions of statistical analysis. We reviewed all RCTs published in December 2014 that appeared in journals indexed in PubMed using the Cochrane highly sensitive search strategy. The 2014 impact factors of the journals were used as proxies for their quality. The type of statistical analysis used and whether the assumptions of the analysis were tested were reviewed. In total, 451 papers were included. Of the 278 papers that reported a crude analysis for the primary outcomes, 31 (27·2%) reported whether the outcome was normally distributed. Of the 172 papers that reported an adjusted analysis for the primary outcomes, diagnosis checking was rarely conducted, with only 20%, 8·6% and 7% checked for generalized linear model, Cox proportional hazard model and multilevel model, respectively. Study characteristics (study type, drug trial, funding sources, journal type and endorsement of CONSORT guidelines) were not associated with the reporting of diagnosis checking. The diagnosis of statistical analyses in RCTs published in PubMed-indexed journals was usually absent. Journals should provide guidelines about the reporting of a diagnosis of assumptions. © 2017 Stichting European Society for Clinical Investigation Journal Foundation.

  5. Using data sources beyond PubMed has a modest impact on the results of systematic reviews of therapeutic interventions.

    Science.gov (United States)

    Halladay, Christopher W; Trikalinos, Thomas A; Schmid, Ian T; Schmid, Christopher H; Dahabreh, Issa J

    2015-09-01

    Searching multiple sources when conducting systematic reviews is considered good practice. We aimed to investigate the impact of using sources beyond PubMed in systematic reviews of therapeutic interventions. We randomly selected 50 Cochrane reviews that searched the PubMed (or MEDLINE) and EMBASE databases and included a meta-analysis of ≥10 studies. We checked whether each eligible record in each review (n = 2,700) was retrievable in PubMed and EMBASE. For the first-listed meta-analysis of ≥10 studies in each review, we examined whether excluding studies not found in PubMed affected results. A median of one record per review was indexed in EMBASE but not in PubMed; a median of four records per review was not indexed in PubMed or EMBASE. Meta-analyses included a median of 13.5 studies; a median of zero studies per meta-analysis was indexed in EMBASE but not in PubMed; a median of one study per meta-analysis was not indexed in PubMed or EMBASE. Meta-analysis using only PubMed-indexed vs. all available studies led to a different conclusion in a single case (on the basis of conventional criteria for statistical significance). In meta-regression analyses, effects in PubMed- vs. non-PubMed-indexed studies were statistically significantly different in a single data set. For systematic reviews of the effects of therapeutic interventions, gains from searching sources beyond PubMed, and from searching EMBASE in particular are modest. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Creatine level and lipide analysis in radiosensitive organs of mice after total body irradiation - a contribution to further development of biologic radiodosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Breiter, N; Ungemach, F R; Hegner, D; Beck, G; Mayr, A

    1986-02-01

    The authors intended to test the suitability of creatine level and/or certain criteria of lipide analysis in radiosensitive organs for an individual (i.e. considering biologic variations of radiosensitivity), qualitative and quantitative demonstration of an irradiation damage. It was found that creatine determination and several criteria of lipide peroxydation are not suitable for a biologic radiation dosimetry due to the absence of organ dependent, radiation dose dependent, and time dependent changes. The reasons are discussed.

  7. Creatine level and lipide analysis in radiosensitive organs of mice after total body irradiation - a contribution to further development of biologic radiodosimetry

    International Nuclear Information System (INIS)

    Breiter, N.; Ungemach, F.R.; Hegner, D.; Beck, G.; Mayr, A.

    1986-01-01

    The authors intended to test the suitability of creatine level and/or certain criteria of lipide analysis in radiosensitive organs for an individual (i.e. considering biologic variations of radiosensitivity), qualitative and quantitative demonstration of an irradiation damage. It was found that creatine determination and several criteria of lipide peroxydation are not suitable for a biologic radiation dosimetry due to the absence of organ dependent, radiation dose dependent, and time dependent changes. The reasons are discussed. (orig.) [de

  8. Holography and coherent diffraction with low-energy electrons: A route towards structural biology at the single molecule level.

    Science.gov (United States)

    Latychevskaia, Tatiana; Longchamp, Jean-Nicolas; Escher, Conrad; Fink, Hans-Werner

    2015-12-01

    The current state of the art in structural biology is led by NMR, X-ray crystallography and TEM investigations. These powerful tools however all rely on averaging over a large ensemble of molecules. Here, we present an alternative concept aiming at structural analysis at the single molecule level. We show that by combining electron holography and coherent diffraction imaging estimations concerning the phase of the scattered wave become needless as the phase information is extracted from the data directly and unambiguously. Performed with low-energy electrons the resolution of this lens-less microscope is just limited by the De Broglie wavelength of the electron wave and the numerical aperture, given by detector geometry. In imaging freestanding graphene, a resolution of 2Å has been achieved revealing the 660.000 unit cells of the graphene sheet from a single data set. Once applied to individual biomolecules the method shall ultimately allow for non-destructive imaging and imports the potential to distinguish between different conformations of proteins with atomic resolution. Copyright © 2015. Published by Elsevier B.V.

  9. A Comparison of Two Low-Stakes Methods for Administering a Program-Level Biology Concept Assessment.

    Science.gov (United States)

    Couch, Brian A; Knight, Jennifer K

    2015-12-01

    Concept assessments are used commonly in undergraduate science courses to assess student learning and diagnose areas of student difficulty. While most concept assessments align with the content of individual courses or course topics, some concept assessments have been developed for use at the programmatic level to gauge student progress and achievement over a series of courses or an entire major. The broad scope of a program-level assessment, which exceeds the content of any single course, creates several test administration issues, including finding a suitable time for students to take the assessment and adequately incentivizing student participation. These logistical considerations must also be weighed against test security and the ability of students to use unauthorized resources that could compromise test validity. To understand how potential administration methods affect student outcomes, we administered the Molecular Biology Capstone Assessment (MBCA) to three pairs of matched upper-division courses in two ways: an online assessment taken by students outside of class and a paper-based assessment taken during class. We found that overall test scores were not significantly different and that individual item difficulties were highly correlated between these two administration methods. However, in-class administration resulted in reduced completion rates of items at the end of the assessment. Taken together, these results suggest that an online, outside-of-class administration produces scores that are comparable to a paper-based, in-class format and has the added advantages that instructors do not have to dedicate class time and students are more likely to complete the entire assessment.

  10. Author Disambiguation in PubMed: Evidence on the Precision and Recall of Author-ity among NIH-Funded Scientists.

    Science.gov (United States)

    Lerchenmueller, Marc J; Sorenson, Olav

    2016-01-01

    We examined the usefulness (precision) and completeness (recall) of the Author-ity author disambiguation for PubMed articles by associating articles with scientists funded by the National Institutes of Health (NIH). In doing so, we exploited established unique identifiers-Principal Investigator (PI) IDs-that the NIH assigns to funded scientists. Analyzing a set of 36,987 NIH scientists who received their first R01 grant between 1985 and 2009, we identified 355,921 articles appearing in PubMed that would allow us to evaluate the precision and recall of the Author-ity disambiguation. We found that Author-ity identified the NIH scientists with 99.51% precision across the articles. It had a corresponding recall of 99.64%. Precision and recall, moreover, appeared stable across common and uncommon last names, across ethnic backgrounds, and across levels of scientist productivity.

  11. Visual Literacy Skills of Students in College-Level Biology: Learning Outcomes Following Digital or Hand-Drawing Activities

    Science.gov (United States)

    Bell, Justine C.

    2014-01-01

    To test the claim that digital learning tools enhance the acquisition of visual literacy in this generation of biology students, a learning intervention was carried out with 33 students enrolled in an introductory college biology course. This study compared learning outcomes following two types of learning tools: a traditional drawing activity, or…

  12. SYMBIOSIS: Development, Implementation, and Assessment of a Model Curriculum across Biology and Mathematics at the Introductory Level

    Science.gov (United States)

    Depelteau, Audrey M.; Joplin, Karl H.; Govett, Aimee; Miller, Hugh A., III; Seier, Edith

    2010-01-01

    With the support of the East Tennessee State University (ETSU) administration and a grant from Howard Hughes Medical Institute, the departments of Biological Sciences, Mathematics and Statistics, and Curriculum and Instruction have developed a biology-math integrated curriculum. An interdisciplinary faculty team, charged with teaching the 18…

  13. Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed.

    Science.gov (United States)

    Vellay, S G P; Latimer, N E Miller; Paillard, G

    2009-06-01

    Text mining has become an integral part of all research in the medical field. Many text analysis software platforms support particular use cases and only those. We show an example of a bibliographic tool that can be used to support virtually any use case in an agile manner. Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search results. This will be of interest to any scientist to help identify the most relevant papers in a topical area more quickly and to evaluate the results of query refinement. Links with Entrez databases help both the biologist and the chemist alike. We illustrate this application with Leishmaniasis, a neglected tropical disease, as a case study.

  14. A Case Study on Sepsis Using PubMed and Deep Learning for Ontology Learning.

    Science.gov (United States)

    Arguello Casteleiro, Mercedes; Maseda Fernandez, Diego; Demetriou, George; Read, Warren; Fernandez Prieto, Maria Jesus; Des Diz, Julio; Nenadic, Goran; Keane, John; Stevens, Robert

    2017-01-01

    We investigate the application of distributional semantics models for facilitating unsupervised extraction of biomedical terms from unannotated corpora. Term extraction is used as the first step of an ontology learning process that aims to (semi-)automatic annotation of biomedical concepts and relations from more than 300K PubMed titles and abstracts. We experimented with both traditional distributional semantics methods such as Latent Semantic Analysis (LSA) and Latent Dirichlet Allocation (LDA) as well as the neural language models CBOW and Skip-gram from Deep Learning. The evaluation conducted concentrates on sepsis, a major life-threatening condition, and shows that Deep Learning models outperform LSA and LDA with much higher precision.

  15. Comparative Analysis of the Combined Effects of Different Water and Phosphate Levels on Growth and Biological Nitrogen Fixation of Nine Cowpea Varieties

    OpenAIRE

    Jemo, Martin; Sulieman, Saad; Bekkaoui, Faouzi; Olomide, Oluwatosin A. K.; Hashem, Abeer; Abd_Allah, Elsayed Fathi; Alqarawi, Abdulaziz A.; Tran, Lam-Son Phan

    2017-01-01

    Water deficit and phosphate (Pi) deficiency adversely affect growth and biological nitrogen fixation (BNF) of legume crops. In this study, we examined the impact of interaction between soil water conditions and available soil-Pi levels on growth, nodule development and BNF potential of nine cowpea varieties grown on dry savanna soils. In our experimental design, soils with different available soil-Pi levels, i.e., low, moderate, and high soil-Pi levels, collected from various farming fields w...

  16. The development of PubMed search strategies for patient preferences for treatment outcomes

    Directory of Open Access Journals (Sweden)

    Ralph van Hoorn

    2016-07-01

    Full Text Available Abstract Background The importance of respecting patients’ preferences when making treatment decisions is increasingly recognized. Efficiently retrieving papers from the scientific literature reporting on the presence and nature of such preferences can help to achieve this goal. The objective of this study was to create a search filter for PubMed to help retrieve evidence on patient preferences for treatment outcomes. Methods A total of 27 journals were hand-searched for articles on patient preferences for treatment outcomes published in 2011. Selected articles served as a reference set. To develop optimal search strategies to retrieve this set, all articles in the reference set were randomly split into a development and a validation set. MeSH-terms and keywords retrieved using PubReMiner were tested individually and as combinations in PubMed and evaluated for retrieval performance (e.g. sensitivity (Se and specificity (Sp. Results Of 8238 articles, 22 were considered to report empirical evidence on patient preferences for specific treatment outcomes. The best search filters reached Se of 100 % [95 % CI 100-100] with Sp of 95 % [94–95 %] and Sp of 97 % [97–98 %] with 75 % Se [74–76 %]. In the validation set these queries reached values of Se of 90 % [89–91 %] with Sp 94 % [93–95 %] and Se of 80 % [79–81 %] with Sp of 97 % [96–96 %], respectively. Conclusions Narrow and broad search queries were developed which can help in retrieving literature on patient preferences for treatment outcomes. Identifying such evidence may in turn enhance the incorporation of patient preferences in clinical decision making and health technology assessment.

  17. PubMed search filters for the study of putative outdoor air pollution determinants of disease

    Science.gov (United States)

    Curti, Stefania; Gori, Davide; Di Gregori, Valentina; Farioli, Andrea; Baldasseroni, Alberto; Fantini, Maria Pia; Christiani, David C; Violante, Francesco S; Mattioli, Stefano

    2016-01-01

    Objectives Several PubMed search filters have been developed in contexts other than environmental. We aimed at identifying efficient PubMed search filters for the study of environmental determinants of diseases related to outdoor air pollution. Methods We compiled a list of Medical Subject Headings (MeSH) and non-MeSH terms seeming pertinent to outdoor air pollutants exposure as determinants of diseases in the general population. We estimated proportions of potentially pertinent articles to formulate two filters (one ‘more specific’, one ‘more sensitive’). Their overall performance was evaluated as compared with our gold standard derived from systematic reviews on diseases potentially related to outdoor air pollution. We tested these filters in the study of three diseases potentially associated with outdoor air pollution and calculated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these diseases. Last searches were run in January 2016. Results The ‘more specific’ filter was based on the combination of terms that yielded a threshold of potentially pertinent articles ≥40%. The ‘more sensitive’ filter was based on the combination of all search terms under study. When compared with the gold standard, the ‘more specific’ filter reported the highest specificity (67.4%; with a sensitivity of 82.5%), while the ‘more sensitive’ one reported the highest sensitivity (98.5%; with a specificity of 47.9%). The NNR to find one potentially pertinent article was 1.9 for the ‘more specific’ filter and 3.3 for the ‘more sensitive’ one. Conclusions The proposed search filters could help healthcare professionals investigate environmental determinants of medical conditions that could be potentially related to outdoor air pollution. PMID:28003291

  18. Trend Analysis of Studies on Water Fluoridation Related to Dental Caries in PubMed.

    Science.gov (United States)

    Oh, Hyo-Jung; Choi, Hyeon-Mi; Kim, Chonghyuck; Jeon, Jae-Gyu

    2018-04-04

    Water fluoridation has been cited as one of the top 10 public health achievements of the 20th century. Herein, we analyzed water fluoridation articles related to dental caries published in PubMed between 1950 and 2016 using informetrics and linguistic methods to investigate trends in the studies. To this aim, queries such as "dental caries and (water fluoridation or fluoridated water)," "dental caries and (fluoride or fluoridation)," and "dental caries" were submitted to PubMed to retrieve information about articles on water fluoridation within the area of dental caries and fluoride - their titles, abstracts, publication dates, author affiliations, and publication journals. This article information was then collected by an automatic web crawler and examined through informetrics and linguistic analyses. It was found that the number of articles concerned with water fluoridation and dental caries was 3,381 and declined over time after 1970. The articles were published by 750 journals - most notably, Community Dentistry and Oral Epidemiology and Caries Research. With regard to the geographic distribution of the authors, Europe and North America, especially the USA and UK, accounted for 59.9% of the articles published during the years 1987 to 2015, though there was a sharp increase in the number of authors in Oceania and Asia in recent years. In the titles and abstracts of the articles, "community" and "fluorosis" were mentioned more frequently than the other key terms selected in this study, regardless of the period examined. Our findings may allow one to assess how the research on water fluoridation has evolved over the past several decades. © 2018 S. Karger AG, Basel.

  19. A Bibliometric Analysis of PubMed Literature on Middle East Respiratory Syndrome.

    Science.gov (United States)

    Wang, Zhengting; Chen, Yongdi; Cai, Gaofeng; Jiang, Zhenggang; Liu, Kui; Chen, Bin; Jiang, Jianmin; Gu, Hua

    2016-06-13

    Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, "conronavirus", "case", "transmission" and "detection" were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened.

  20. Developing topic-specific search filters for PubMed with click-through data.

    Science.gov (United States)

    Li, J; Lu, Z

    2013-01-01

    Search filters have been developed and demonstrated for better information access to the immense and ever-growing body of publications in the biomedical domain. However, to date the number of filters remains quite limited because the current filter development methods require significant human efforts in manual document review and filter term selection. In this regard, we aim to investigate automatic methods for generating search filters. We present an automated method to develop topic-specific filters on the basis of users' search logs in PubMed. Specifically, for a given topic, we first detect its relevant user queries and then include their corresponding clicked articles to serve as the topic-relevant document set accordingly. Next, we statistically identify informative terms that best represent the topic-relevant document set using a background set composed of topic irrelevant articles. Lastly, the selected representative terms are combined with Boolean operators and evaluated on benchmark datasets to derive the final filter with the best performance. We applied our method to develop filters for four clinical topics: nephrology, diabetes, pregnancy, and depression. For the nephrology filter, our method obtained performance comparable to the state of the art (sensitivity of 91.3%, specificity of 98.7%, precision of 94.6%, and accuracy of 97.2%). Similarly, high-performing results (over 90% in all measures) were obtained for the other three search filters. Based on PubMed click-through data, we successfully developed a high-performance method for generating topic-specific search filters that is significantly more efficient than existing manual methods. All data sets (topic-relevant and irrelevant document sets) used in this study and a demonstration system are publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/downloads/CQ_filter/

  1. The development of PubMed search strategies for patient preferences for treatment outcomes.

    Science.gov (United States)

    van Hoorn, Ralph; Kievit, Wietske; Booth, Andrew; Mozygemba, Kati; Lysdahl, Kristin Bakke; Refolo, Pietro; Sacchini, Dario; Gerhardus, Ansgar; van der Wilt, Gert Jan; Tummers, Marcia

    2016-07-29

    The importance of respecting patients' preferences when making treatment decisions is increasingly recognized. Efficiently retrieving papers from the scientific literature reporting on the presence and nature of such preferences can help to achieve this goal. The objective of this study was to create a search filter for PubMed to help retrieve evidence on patient preferences for treatment outcomes. A total of 27 journals were hand-searched for articles on patient preferences for treatment outcomes published in 2011. Selected articles served as a reference set. To develop optimal search strategies to retrieve this set, all articles in the reference set were randomly split into a development and a validation set. MeSH-terms and keywords retrieved using PubReMiner were tested individually and as combinations in PubMed and evaluated for retrieval performance (e.g. sensitivity (Se) and specificity (Sp)). Of 8238 articles, 22 were considered to report empirical evidence on patient preferences for specific treatment outcomes. The best search filters reached Se of 100 % [95 % CI 100-100] with Sp of 95 % [94-95 %] and Sp of 97 % [97-98 %] with 75 % Se [74-76 %]. In the validation set these queries reached values of Se of 90 % [89-91 %] with Sp 94 % [93-95 %] and Se of 80 % [79-81 %] with Sp of 97 % [96-96 %], respectively. Narrow and broad search queries were developed which can help in retrieving literature on patient preferences for treatment outcomes. Identifying such evidence may in turn enhance the incorporation of patient preferences in clinical decision making and health technology assessment.

  2. PubMed search filters for the study of putative outdoor air pollution determinants of disease.

    Science.gov (United States)

    Curti, Stefania; Gori, Davide; Di Gregori, Valentina; Farioli, Andrea; Baldasseroni, Alberto; Fantini, Maria Pia; Christiani, David C; Violante, Francesco S; Mattioli, Stefano

    2016-12-21

    Several PubMed search filters have been developed in contexts other than environmental. We aimed at identifying efficient PubMed search filters for the study of environmental determinants of diseases related to outdoor air pollution. We compiled a list of Medical Subject Headings (MeSH) and non-MeSH terms seeming pertinent to outdoor air pollutants exposure as determinants of diseases in the general population. We estimated proportions of potentially pertinent articles to formulate two filters (one 'more specific', one 'more sensitive'). Their overall performance was evaluated as compared with our gold standard derived from systematic reviews on diseases potentially related to outdoor air pollution. We tested these filters in the study of three diseases potentially associated with outdoor air pollution and calculated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these diseases. Last searches were run in January 2016. The 'more specific' filter was based on the combination of terms that yielded a threshold of potentially pertinent articles ≥40%. The 'more sensitive' filter was based on the combination of all search terms under study. When compared with the gold standard, the 'more specific' filter reported the highest specificity (67.4%; with a sensitivity of 82.5%), while the 'more sensitive' one reported the highest sensitivity (98.5%; with a specificity of 47.9%). The NNR to find one potentially pertinent article was 1.9 for the 'more specific' filter and 3.3 for the 'more sensitive' one. The proposed search filters could help healthcare professionals investigate environmental determinants of medical conditions that could be potentially related to outdoor air pollution. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  3. Testing search strategies for systematic reviews in the Medline literature database through PubMed.

    Science.gov (United States)

    Volpato, Enilze S N; Betini, Marluci; El Dib, Regina

    2014-04-01

    A high-quality electronic search is essential in ensuring accuracy and completeness in retrieved records for the conducting of a systematic review. We analysed the available sample of search strategies to identify the best method for searching in Medline through PubMed, considering the use or not of parenthesis, double quotation marks, truncation and use of a simple search or search history. In our cross-sectional study of search strategies, we selected and analysed the available searches performed during evidence-based medicine classes and in systematic reviews conducted in the Botucatu Medical School, UNESP, Brazil. We analysed 120 search strategies. With regard to the use of phrase searches with parenthesis, there was no difference between the results with and without parenthesis and simple searches or search history tools in 100% of the sample analysed (P = 1.0). The number of results retrieved by the searches analysed was smaller using double quotations marks and using truncation compared with the standard strategy (P = 0.04 and P = 0.08, respectively). There is no need to use phrase-searching parenthesis to retrieve studies; however, we recommend the use of double quotation marks when an investigator attempts to retrieve articles in which a term appears to be exactly the same as what was proposed in the search form. Furthermore, we do not recommend the use of truncation in search strategies in the Medline via PubMed. Although the results of simple searches or search history tools were the same, we recommend using the latter.

  4. Information management and complementary alternative medicine: the anatomy of information about CAMs through PubMed.

    Science.gov (United States)

    Corrao, Salvatore; Argano, Christiano; Colomba, Daniela; Ippolito, Calogero; Gargano, Vincenzo; Arcoraci, Vincenzo; Licata, Giuseppe

    2013-10-01

    In recent years, there has been a growing interest about complementary and alternative medicine (CAM), and the use of CAM interventions has become more common among people. For these reasons, health professionals must be able to effectively manage information in this field of knowledge according to an evidence-based point of view. This study assessed the anatomy of the available information about CAMs using PubMed, to give practical instructions to manage information in this field. We also analyzed the anatomy of information according to each alternative medicine branch, narrow and broad search methods, subset filters for indexed-for-Medline and non-indexed citations, and different publication types including randomized controlled trials (RCTs) and meta-analyses. Our results demonstrated that the use of CAMs subset (supplied by PubMed search engine) leads to a great number of citations determining an information overload. Our data reveal that it would be more useful to search for the CAM separately, identifying specific items and study design. Moreover, we found the largest number of randomized clinical trials and meta-analyses related to herbal medicine and acupuncture, neither RCTs nor meta-analyses were available for bach and flower remedies, auriculoacupuncture, iridology, and pranotherapy. For the first time, our study gives a comprehensive view of the anatomy of information regarding CAMs and each branch of them. We suggest a methodological approach to face with searching information about this emerging issue from an evidence-based point of view. Finally, our data pointed out some "grey zones" since neither RCTs nor meta-analyses were available for some CAMs.

  5. Mathematical biology

    CERN Document Server

    Murray, James D

    1993-01-01

    The book is a textbook (with many exercises) giving an in-depth account of the practical use of mathematical modelling in the biomedical sciences. The mathematical level required is generally not high and the emphasis is on what is required to solve the real biological problem. The subject matter is drawn, e.g. from population biology, reaction kinetics, biological oscillators and switches, Belousov-Zhabotinskii reaction, reaction-diffusion theory, biological wave phenomena, central pattern generators, neural models, spread of epidemics, mechanochemical theory of biological pattern formation and importance in evolution. Most of the models are based on real biological problems and the predictions and explanations offered as a direct result of mathematical analysis of the models are important aspects of the book. The aim is to provide a thorough training in practical mathematical biology and to show how exciting and novel mathematical challenges arise from a genuine interdisciplinary involvement with the biosci...

  6. Metal(loid) levels in biological matrices from human populations exposed to mining contamination--Panasqueira Mine (Portugal).

    Science.gov (United States)

    Coelho, Patrícia; Costa, Solange; Silva, Susana; Walter, Alan; Ranville, James; Sousa, Ana C A; Costa, Carla; Coelho, Marta; García-Lestón, Julia; Pastorinho, M Ramiro; Laffon, Blanca; Pásaro, Eduardo; Harrington, Chris; Taylor, Andrew; Teixeira, João Paulo

    2012-01-01

    Mining activities may affect the health of miners and communities living near mining sites, and these health effects may persist even when the mine is abandoned. During mining processes various toxic wastes are produced and released into the surrounding environment, resulting in contamination of air, drinking water, rivers, plants, and soils. In a geochemical sampling campaign undertaken in the Panasqueira Mine area of central Portugal, an anomalous distribution of several metals and arsenic (As) was identified in various environmental media. Several potentially harmful elements, including As, cadmium (Cd), chromium (Cr), manganese (Mn), nickel (Ni), lead (Pb), and selenium (Se), were quantified in blood, urine, hair, and nails (toe and finger) from a group of individuals living near the Panasqueira Mine who were environmentally and occupationally exposed. A group with similar demographic characteristics without known exposure to mining activities was also compared. Genotoxicity was evaluated by means of T-cell receptor (TCR) mutation assay, and percentages of different lymphocyte subsets were selected as immunotoxicity biomarkers. Inductively coupled plasma-mass spectrometry (ICP-MS) and inductively coupled plasma-atomic emission spectrometry (ICP-AES) analysis showed elevated levels of As, Cd, Cr, Mn, and Pb in all biological samples taken from populations living close to the mine compared to controls. Genotoxic and immunotoxic differences were also observed. The results provide evidence of an elevated potential risk to the health of populations, with environmental and occupational exposures resulting from mining activities. Further, the results emphasize the need to implement preventive measures, remediation, and rehabilitation plans for the region.

  7. Clinical and Biological Predictors of Plasma Levels of Soluble RAGE in Critically Ill Patients: Secondary Analysis of a Prospective Multicenter Observational Study

    Directory of Open Access Journals (Sweden)

    Thibaut Pranal

    2018-01-01

    Full Text Available Rationale. Although soluble forms of the receptor for advanced glycation end products (RAGE have been recently proposed as biomarkers in multiple acute or chronic diseases, few studies evaluated the influence of usual clinical and biological parameters, or of patient characteristics and comorbidities, on circulating levels of soluble RAGE in the intensive care unit (ICU setting. Objectives. To determine, among clinical and biological parameters that are usually recorded upon ICU admission, which variables, if any, could be associated with plasma levels of soluble RAGE. Methods. Data for this ancillary study were prospectively obtained from adult patients with at least one ARDS risk factor upon ICU admission enrolled in a large multicenter observational study. At ICU admission, plasma levels of total soluble RAGE (sRAGE and endogenous secretory (esRAGE were measured by duplicate ELISA and baseline patient characteristics, comorbidities, and usual clinical and biological indices were recorded. After univariate analyses, significant variables were used in multivariate, multidimensional analyses. Measurements and Main Results. 294 patients were included in this ancillary study, among whom 62% were admitted for medical reasons, including septic shock (11%, coma (11%, and pneumonia (6%. Although some variables were associated with plasma levels of RAGE soluble forms in univariate analysis, multidimensional analyses showed no significant association between admission parameters and baseline plasma sRAGE or esRAGE. Conclusions. We found no obvious association between circulating levels of soluble RAGE and clinical and biological indices that are usually recorded upon ICU admission. This trial is registered with NCT02070536.

  8. PubMed vs. HighWire Press: a head-to-head comparison of two medical literature search engines.

    Science.gov (United States)

    Vanhecke, Thomas E; Barnes, Michael A; Zimmerman, Janet; Shoichet, Sandor

    2007-09-01

    PubMed and HighWire Press are both useful medical literature search engines available for free to anyone on the internet. We measured retrieval accuracy, number of results generated, retrieval speed, features and search tools on HighWire Press and PubMed using the quick search features of each. We found that using HighWire Press resulted in a higher likelihood of retrieving the desired article and higher number of search results than the same search on PubMed. PubMed was faster than HighWire Press in delivering search results regardless of search settings. There are considerable differences in search features between these two search engines.

  9. Test Results of Level A Suits to Challenge by Chemical and Biological Warfare Agents and Simulants: Summary Report

    National Research Council Canada - National Science Library

    Belmonte, Richard B

    1998-01-01

    ...) terrorism incidents. As part of an effective response, people who are responding to an incident will use personal protective equipment to protect them from exposure to chemical agents or biological agents...

  10. The acclimation of Chlorella to high-level nitrite for potential application in biological NOx removal from industrial flue gases

    Czech Academy of Sciences Publication Activity Database

    Li, T.; Xu, G.; Rong, J.; Chen, H.; He, Ch.; Giordano, Mario; Wang, Q.

    2016-01-01

    Roč. 195, May (2016), s. 73-79 ISSN 0176-1617 Institutional support: RVO:61388971 Keywords : Acclimation * Biological NOx removal * Chlorella Subject RIV: EF - Botanics Impact factor: 3.121, year: 2016

  11. PubMed Informer: Monitoring MEDLINE/PubMed through E-mail Alerts, SMS, PDA downloads and RSS feeds

    Science.gov (United States)

    Muin, Michael; Fontelo, Paul; Ackerman, Michael

    2005-01-01

    Summary PubMed Informer is a Web-based monitoring tool for topics of interest from MEDLINE/PubMed primarily designed for healthcare professionals. Five tracking methods are available: Web access, e-mail, Short Message Service (SMS), PDA downloads and RSS feeds. PubMed Informer delivers focused search updates and specific information to users with varying information-seeking practices. PMID:16779344

  12. Mesoscopic biology

    Indian Academy of Sciences (India)

    In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological ...

  13. Sensitivity and predictive value of 15 PubMed search strategies to answer clinical questions rated against full systematic reviews.

    Science.gov (United States)

    Agoritsas, Thomas; Merglen, Arnaud; Courvoisier, Delphine S; Combescure, Christophe; Garin, Nicolas; Perrier, Arnaud; Perneger, Thomas V

    2012-06-12

    Clinicians perform searches in PubMed daily, but retrieving relevant studies is challenging due to the rapid expansion of medical knowledge. Little is known about the performance of search strategies when they are applied to answer specific clinical questions. To compare the performance of 15 PubMed search strategies in retrieving relevant clinical trials on therapeutic interventions. We used Cochrane systematic reviews to identify relevant trials for 30 clinical questions. Search terms were extracted from the abstract using a predefined procedure based on the population, interventions, comparison, outcomes (PICO) framework and combined into queries. We tested 15 search strategies that varied in their query (PIC or PICO), use of PubMed's Clinical Queries therapeutic filters (broad or narrow), search limits, and PubMed links to related articles. We assessed sensitivity (recall) and positive predictive value (precision) of each strategy on the first 2 PubMed pages (40 articles) and on the complete search output. The performance of the search strategies varied widely according to the clinical question. Unfiltered searches and those using the broad filter of Clinical Queries produced large outputs and retrieved few relevant articles within the first 2 pages, resulting in a median sensitivity of only 10%-25%. In contrast, all searches using the narrow filter performed significantly better, with a median sensitivity of about 50% (all P PubMed pages. These results can help clinicians apply effective strategies to answer their questions at the point of care.

  14. Supplementary searches of PubMed to improve currency of MEDLINE and MEDLINE In-Process searches via Ovid.

    Science.gov (United States)

    Duffy, Steven; de Kock, Shelley; Misso, Kate; Noake, Caro; Ross, Janine; Stirk, Lisa

    2016-10-01

    The research investigated whether conducting a supplementary search of PubMed in addition to the main MEDLINE (Ovid) search for a systematic review is worthwhile and to ascertain whether this PubMed search can be conducted quickly and if it retrieves unique, recently published, and ahead-of-print studies that are subsequently considered for inclusion in the final systematic review. Searches of PubMed were conducted after MEDLINE (Ovid) and MEDLINE In-Process (Ovid) searches had been completed for seven recent reviews. The searches were limited to records not in MEDLINE or MEDLINE In-Process (Ovid). Additional unique records were identified for all of the investigated reviews. Search strategies were adapted quickly to run in PubMed, and reviewer screening of the results was not time consuming. For each of the investigated reviews, studies were ordered for full screening; in six cases, studies retrieved from the supplementary PubMed searches were included in the final systematic review. Supplementary searching of PubMed for studies unavailable elsewhere is worthwhile and improves the currency of the systematic reviews.

  15. Web-Based Learning Enhancements: Video Lectures through Voice-Over PowerPoint in a Majors-Level Biology Course

    Science.gov (United States)

    Lents, Nathan H.; Cifuentes, Oscar E.

    2009-01-01

    This study is an experimental introduction of web-based lecture delivery into a majors-level introductory biology course. Web-based delivery, achieved through the use of prerecorded Voice-Over PowerPoint video lectures, was introduced on a limited basis to an experimental section while a control group, with the same instructor, received standard…

  16. A Western Blot-based Investigation of the Yeast Secretory Pathway Designed for an Intermediate-Level Undergraduate Cell Biology Laboratory

    Science.gov (United States)

    Hood-DeGrenier, Jennifer K.

    2008-01-01

    The movement of newly synthesized proteins through the endomembrane system of eukaryotic cells, often referred to generally as the secretory pathway, is a topic covered in most intermediate-level undergraduate cell biology courses. An article previously published in this journal described a laboratory exercise in which yeast mutants defective in…

  17. Experiences performed at the C:R: Saluggia of ENEA in low-level determination of plutonium in biological and environmental samples

    International Nuclear Information System (INIS)

    Spezzano, Pasquale

    1997-10-01

    This report describes some experiences performed at the Research Center Saluggia of ENEA concerning low-level determination of plutonium in biological and environmental samples, with discussions of practical analytical problems. The main characteristics and properties of plutonium with emphasis to aqueous solutions chemistry and environmental behaviour are also reported

  18. Could the biological robustness of low level laser therapy (Photobiomodulation) impact its use in the management of mucositis in head and neck cancer patients

    NARCIS (Netherlands)

    Sonis, Stephen T.; Hashemi, Sepehr; Epstein, Joel B.; Nair, Raj G.; Raber-Durlacher, Judith E.

    2016-01-01

    Low level laser therapy (LLLT) has been noted to be effective in mitigating the development of oral mucositis among patients being treated with chemoradiation for cancers of the head and neck. To explain the biological basis for this observation we performed a comprehensive literature search. Our

  19. Cupping Therapy May be Harmful for Eczema: A PubMed Search

    Science.gov (United States)

    Hon, Kam Lun E.; Luk, David Chi Kong; Leong, Kin Fon; Leung, Alexander K. C.

    2013-01-01

    Eczema is a common childhood atopic condition and treatment is with emollients, topical corticosteroids, and avoidance of possible triggers. S. aureus colonization is a common complication. As there is no immediate cure, many parents seek alternative therapies that claim unproven therapeutic efficacy. We report a girl with long history of treatment noncompliance. After practicing a long period of dietary avoidance and supplementation, the grandparents took her to an alternative medicine practitioner. Following cupping therapy and acupuncture, the child developed blistering and oozing over her back the next day, which rapidly evolved to two large irregular-edge deep ulcers. She was treated with intravenous antibiotics and received multidisciplinary supportive intervention. Using search words of  “cupping,” “eczema,” and “atopic dermatitis,” only two reports were found on PubMed. Therapeutic efficacy was claimed but not scientifically documented in these reports. Childhood eczema is an eminently treatable atopic disease. Extreme alternative therapy seems not to be efficacious and may even be associated with serious undesirable sequelae. Physicians should be aware of various alternative treatment modalities and be prepared to offer evidence-based advice to the patients with eczema and their families. PMID:24282650

  20. Cupping Therapy May be Harmful for Eczema: A PubMed Search

    Directory of Open Access Journals (Sweden)

    Kam Lun E. Hon

    2013-01-01

    Full Text Available Eczema is a common childhood atopic condition and treatment is with emollients, topical corticosteroids, and avoidance of possible triggers. S. aureus colonization is a common complication. As there is no immediate cure, many parents seek alternative therapies that claim unproven therapeutic efficacy. We report a girl with long history of treatment noncompliance. After practicing a long period of dietary avoidance and supplementation, the grandparents took her to an alternative medicine practitioner. Following cupping therapy and acupuncture, the child developed blistering and oozing over her back the next day, which rapidly evolved to two large irregular-edge deep ulcers. She was treated with intravenous antibiotics and received multidisciplinary supportive intervention. Using search words of  “cupping,” “eczema,” and “atopic dermatitis,” only two reports were found on PubMed. Therapeutic efficacy was claimed but not scientifically documented in these reports. Childhood eczema is an eminently treatable atopic disease. Extreme alternative therapy seems not to be efficacious and may even be associated with serious undesirable sequelae. Physicians should be aware of various alternative treatment modalities and be prepared to offer evidence-based advice to the patients with eczema and their families.

  1. Bibliometrics analysis of the PubMed literatures on low-dose CT

    International Nuclear Information System (INIS)

    Wang Qian; Xia Guanghui; Ma Xiaohong; Zhao Xinming

    2012-01-01

    Objective: The purposes of this study were to evaluate the developmental rule and feature in low-dose CT examinations and to provide useful references for study in the future. Materials and Methods: The journal articles on PubMed from 2002 to 2011 were processed by Thomson Data Analyzer and five aspects were analysed: time, authors, institutions, journals, countries, and keywords. Results: The number of journal articles in low-dose CT examinations were 6 433, 3165 were from US (49.2%), 112 from China (1.4%); 3664 authors (80.42%) published only one article, the famous authors published more than 4 articles; there were 9 core journals in this area. In the last decade, the number and quality of the journal articles in low -dose CT have been dramatically increased. Conclusion: The interest on the low -dose CT examination has been steadily increasing, and world famous research teams have been established. The research in low-dose CT is a multi-discipline involving medicine, medical physics, and mathematics. Cooperation between multiple scientific domains is needed for the future studies. (authors)

  2. A search engine to access PubMed monolingual subsets: proof of concept and evaluation in French.

    Science.gov (United States)

    Griffon, Nicolas; Schuers, Matthieu; Soualmia, Lina Fatima; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse; Darmoni, Stéfan Jacques

    2014-12-01

    PubMed contains numerous articles in languages other than English. However, existing solutions to access these articles in the language in which they were written remain unconvincing. The aim of this study was to propose a practical search engine, called Multilingual PubMed, which will permit access to a PubMed subset in 1 language and to evaluate the precision and coverage for the French version (Multilingual PubMed-French). To create this tool, translations of MeSH were enriched (eg, adding synonyms and translations in French) and integrated into a terminology portal. PubMed subsets in several European languages were also added to our database using a dedicated parser. The response time for the generic semantic search engine was evaluated for simple queries. BabelMeSH, Multilingual PubMed-French, and 3 different PubMed strategies were compared by searching for literature in French. Precision and coverage were measured for 20 randomly selected queries. The results were evaluated as relevant to title and abstract, the evaluator being blind to search strategy. More than 650,000 PubMed citations in French were integrated into the Multilingual PubMed-French information system. The response times were all below the threshold defined for usability (2 seconds). Two search strategies (Multilingual PubMed-French and 1 PubMed strategy) showed high precision (0.93 and 0.97, respectively), but coverage was 4 times higher for Multilingual PubMed-French. It is now possible to freely access biomedical literature using a practical search tool in French. This tool will be of particular interest for health professionals and other end users who do not read or query sufficiently in English. The information system is theoretically well suited to expand the approach to other European languages, such as German, Spanish, Norwegian, and Portuguese.

  3. Development of a radiochemical neutron activation analysis procedure for determination of rhenium in biological and environmental samples at ultratrace level

    Czech Academy of Sciences Publication Activity Database

    Kučera, Jan; Byrne, A. R.; Mizera, Jiří; Lučaníková, M.; Řanda, Zdeněk

    2006-01-01

    Roč. 269, č. 2 (2006), s. 251-257 ISSN 0236-5731 R&D Projects: GA ČR(CZ) GA203/04/0943 Institutional research plan: CEZ:AV0Z10480505 Keywords : radiochemical neutron activation analysis * rhenium * biological and environmental samples Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 0.509, year: 2006

  4. Integrative Assessment of Evolutionary Theory Acceptance and Knowledge Levels of Biology Undergraduate Students from a Brazilian University

    Science.gov (United States)

    Tavares, Gustavo Medina; Bobrowski, Vera Lucia

    2018-01-01

    The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students'…

  5. How Important Is the Assessment of Practical Work? An Opinion Piece on the New Biology A-Level from BERG

    Science.gov (United States)

    Journal of Biological Education, 2014

    2014-01-01

    As education in England emerges from a major curriculum review (DfE 2013), the next few years will see significant changes in what is taught in schools and how this is assessed. As a core subject, under the current proposals, all students, from the beginning of primary school until age 16, will study science in some detail. Biology is an exciting,…

  6. Development of a Semester-Long, Inquiry-Based Laboratory Course in Upper-Level Biochemistry and Molecular Biology

    Science.gov (United States)

    Murthy, Pushpalatha P. N.; Thompson, Martin; Hungwe, Kedmon

    2014-01-01

    A semester-long laboratory course was designed and implemented to familiarize students with modern biochemistry and molecular biology techniques. The designed format involved active student participation, evaluation of data, and critical thinking, and guided students to become independent researchers. The first part of the course focused on…

  7. Population-level compensation impedes biological control of an invasive forb and indirect release of a native grass

    Science.gov (United States)

    Yvette K. Ortega; Dean E. Pearson; Lauren P. Waller; Nancy J. Sturdevant; John L. Maron

    2012-01-01

    The intentional introduction of specialist insect herbivores for biological control of exotic weeds provides ideal but understudied systems for evaluating important ecological concepts related to top-down control, plant compensatory responses, indirect effects, and the influence of environmental context on these processes. Centaurea stoebe (spotted knapweed) is a...

  8. Perceptions of patients with rheumatic diseases treated with subcutaneous biologicals on their level of information: RHEU-LIFE Survey.

    Science.gov (United States)

    de Toro, Javier; Cea-Calvo, Luis; Battle, Enrique; Carmona, Loreto; Arteaga, María J; Fernández, Sabela; González, Carlos M

    2017-12-22

    To investigate, in Spanish patients with rheumatic diseases treated with subcutaneous biological drugs, their sources of information, which sources they consider most relevant, and their satisfaction with the information received in the hospital. Rheumatologists from 50 hospitals handed out an anonymous survey to 20 consecutive patients with rheumatoid arthritis, axial spondyloarthritis or psoriatic arthritis treated with subcutaneous biologicals. The survey was developed ad hoc by 4 rheumatologists and 3 patients, and included questions with closed-ended responses on sources of information and satisfaction. The survey was handed-out to 1,000 patients, 592 of whom completed it (response rate: 59.2%). The rheumatologist was mentioned as the most important source of information (75%), followed by the primary care physician, nurses, and electronic resources; 45.2% received oral and written information about the biological, 46.1% oral only, and 6.0% written only; 8.7% stated that they had not been taught to inject the biological. The percentage of patients satisfied with the information received was high (87.2%), although the satisfaction was lower in relation to safety. If the information came from the rheumatologist, the satisfaction was higher (89.6%) than when coming from other sources (59.6%; P<.001). Satisfaction was also higher if the information was provided orally and written (92.8%) than if provided only orally (86.1%; P=.013); 45.2% reported having sought information from sources outside the hospital. The rheumatologist is key in transmitting satisfactory information on biological treatment to patients. He or she must also act as a guide, since a high percentage of patients seeks information in other different sources. Copyright © 2017. Publicado por Elsevier España, S.L.U.

  9. NEMO: Extraction and normalization of organization names from PubMed affiliations.

    Science.gov (United States)

    Jonnalagadda, Siddhartha Reddy; Topham, Philip

    2010-10-04

    Today, there are more than 18 million articles related to biomedical research indexed in MEDLINE, and information derived from them could be used effectively to save the great amount of time and resources spent by government agencies in understanding the scientific landscape, including key opinion leaders and centers of excellence. Associating biomedical articles with organization names could significantly benefit the pharmaceutical marketing industry, health care funding agencies and public health officials and be useful for other scientists in normalizing author names, automatically creating citations, indexing articles and identifying potential resources or collaborators. Large amount of extracted information helps in disambiguating organization names using machine-learning algorithms. We propose NEMO, a system for extracting organization names in the affiliation and normalizing them to a canonical organization name. Our parsing process involves multi-layered rule matching with multiple dictionaries. The system achieves more than 98% f-score in extracting organization names. Our process of normalization that involves clustering based on local sequence alignment metrics and local learning based on finding connected components. A high precision was also observed in normalization. NEMO is the missing link in associating each biomedical paper and its authors to an organization name in its canonical form and the Geopolitical location of the organization. This research could potentially help in analyzing large social networks of organizations for landscaping a particular topic, improving performance of author disambiguation, adding weak links in the co-author network of authors, augmenting NLM's MARS system for correcting errors in OCR output of affiliation field, and automatically indexing the PubMed citations with the normalized organization name and country. Our system is available as a graphical user interface available for download along with this paper.

  10. Trends and topics in eye disease research in PubMed from 2010 to 2014.

    Science.gov (United States)

    Boudry, Christophe; Denion, Eric; Mortemousque, Bruno; Mouriaux, Fréderic

    2016-01-01

    The purpose of this study is to provide a report on scientific production during the period 2010-2014 in order to identify the major topics as well as the predominant actors (journals, countries, continents) involved in the field of eye disease. A PubMed search was carried out to extract articles related to eye diseases during the period 2010-2014. Data were downloaded and processed through developed PHP scripts for further analysis. A total of 62,123 articles were retrieved. A total of 3,368 different journals were found, and 19 journals were identified as "core journals" according to Braford's law. English was by far the predominant language. A total of 853,182 MeSH terms were found, representing an average of 13.73 (SD = 4.98) MeSH terms per article. Among these 853,182 MeSH terms, 14,689 different MeSH terms were identified. Vision Disorders, Glaucoma, Diabetic Retinopathy, Macular Degeneration, and Cataract were the most frequent five MeSH terms related to eye diseases. The analysis of the total number of publications showed that Europe and Asia were the most productive continents, and the USA and China the most productive countries. Interestingly, using the mean Five-Year Impact Factor, the two most productive continents were North America and Oceania. After adjustment for population, the overall ranking positions changed in favor of smaller countries (i.e. Iceland, Switzerland, Denmark, and New Zealand), while after adjustment for Gross Domestic Product (GDP), the overall ranking positions changed in favor of some developing countries (Malawi, Guatemala, Singapore). Due to the large number of articles included and the numerous parameters analyzed, this study provides a wide view of scientific productivity related to eye diseases during the period 2010-2014 and allows us to better understand this field.

  11. PubMed search strings for the study of agricultural workers' diseases.

    Science.gov (United States)

    Mattioli, Stefano; Gori, Davide; Di Gregori, Valentina; Ricotta, Lara; Baldasseroni, Alberto; Farioli, Andrea; Zanardi, Francesca; Galletti, Stefania; Colosio, Claudio; Curti, Stefania; Violante, Francesco S

    2013-12-01

    Several optimized search strategies have been developed in Medicine, and more recently in Occupational Medicine. The aim of this study was to identify efficient PubMed search strategies to retrieve articles regarding putative occupational determinants of agricultural workers' diseases. We selected the Medical Subjects Heading (MeSH) term agricultural workers' diseases and six MeSH terms describing farm work (agriculture, agrochemicals NOT pesticides, animal husbandry, pesticides, rural health, rural population) alongside 61 other promising terms. We estimated proportions of articles containing potentially pertinent information regarding occupational etiology to formulate two search strategies (one "more specific," one "more sensitive"). We applied these strategies to retrieve information on the possible occupational etiology among agricultural workers of kidney cancer, knee osteoarthritis, and multiple sclerosis. We evaluated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these pathologies. The "more specific" search string was based on the combination of terms that yielded the highest proportion (40%) of potentially pertinent abstracts. The "more sensitive" string was based on use of broader search fields and additional coverage provided by other search terms under study. Using the "more specific" string, the NNR to find one potentially pertinent article were: 1.1 for kidney cancer; 1.4 for knee osteoarthritis; 1.2 for multiple sclerosis. Using the sensitive strategy, the NNR were 1.4, 3.6, and 6.3, respectively. The proposed strings could help health care professionals explore putative occupational etiology for agricultural workers' diseases (even if not generally thought to be work related). © 2013 Wiley Periodicals, Inc.

  12. [An analysis of Chilean biomedical publications in PubMed in the years 2008-2009].

    Science.gov (United States)

    Valdés S, Gloria; Pérez G, Fernanda; Reyes B, Humberto

    2015-08-01

    During the years 2008 and 2009, 1,191 biomedical articles authored by Chilean investigators working in Chile were indexed in PubMed. To evaluate the potential visibility of those articles, according to scientometric indexes of the journals where they were published. Those journals where the articles had been published were identified and each journal’s Impact Factor (JIF), 5-year JIF, SCImago Journal Rank (SJR), SCImago Quartiles (Q) for 2010 and the Source Normalized Impact per Paper (SNIP) for 2008-2009 were identified. Three hundred and twelve articles (26,2%) were dedicated to experimental studies in animals, tissues or cells and they were classified as “Biomedicine”, while 879 (73,8%) were classified as “Clinical Medicine”; in both areas the main type of articles were original reports (90% and 73.6%, respectively). Revista Médica de Chile and Revista Chilena de Infectología concentrated the greater number of publications. Articles classified in Biomedicine were published more frequently in English and in journals with higher scientometric indexes than those classified in Clinical Medicine. Biomedical articles dealing with clinical topics, particularly case reports, were published mostly in national journals or in foreign journals with low scientometric indexes. It can be partly attributable to the authors’ interest in reaching local readers. The evaluation of research productivity should combine several scientometric indexes, selected according to the field of research, the institution's and investigators’ interests, with a qualitative and multifactorial assessment.

  13. Discrepancies among Scopus, Web of Science, and PubMed coverage of funding information in medical journal articles.

    Science.gov (United States)

    Kokol, Peter; Vošner, Helena Blažun

    2018-01-01

    The overall aim of the present study was to compare the coverage of existing research funding information for articles indexed in Scopus, Web of Science, and PubMed databases. The numbers of articles with funding information published in 2015 were identified in the three selected databases and compared using bibliometric analysis of a sample of twenty-eight prestigious medical journals. Frequency analysis of the number of articles with funding information showed statistically significant differences between Scopus, Web of Science, and PubMed databases. The largest proportion of articles with funding information was found in Web of Science (29.0%), followed by PubMed (14.6%) and Scopus (7.7%). The results show that coverage of funding information differs significantly among Scopus, Web of Science, and PubMed databases in a sample of the same medical journals. Moreover, we found that, currently, funding data in PubMed is more difficult to obtain and analyze compared with that in the other two databases.

  14. Enhancing search efficiency by means of a search filter for finding all studies on animal experimentation in PubMed.

    Science.gov (United States)

    Hooijmans, Carlijn R; Tillema, Alice; Leenaars, Marlies; Ritskes-Hoitinga, Merel

    2010-07-01

    Collecting and analysing all available literature before starting an animal experiment is important and it is indispensable when writing a systematic review (SR) of animal research. Writing such review prevents unnecessary duplication of animal studies and thus unnecessary animal use (Reduction). One of the factors currently impeding the production of 'high-quality' SRs in laboratory animal science is the fact that searching for all available literature concerning animal experimentation is rather difficult. In order to diminish these difficulties, we developed a search filter for PubMed to detect all publications concerning animal studies. This filter was compared with the method most frequently used, the PubMed Limit: Animals, and validated further by performing two PubMed topic searches. Our filter performs much better than the PubMed limit: it retrieves, on average, 7% more records. Other important advantages of our filter are that it also finds the most recent records and that it is easy to use. All in all, by using our search filter in PubMed, all available literature concerning animal studies on a specific topic can easily be found and assessed, which will help in increasing the scientific quality and thereby the ethical validity of animal experiments.

  15. The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

    Science.gov (United States)

    Pollard, Thomas D

    2014-12-02

    This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  16. The use of writing assignments to help students synthesize content in upper-level undergraduate biology courses.

    Science.gov (United States)

    Sparks-Thissen, Rebecca L

    2017-02-01

    Biology education is undergoing a transformation toward a more student-centered, inquiry-driven classroom. Many educators have designed engaging assignments that are designed to help undergraduate students gain exposure to the scientific process and data analysis. One of these types of assignments is use of a grant proposal assignment. Many instructors have used these assignments in lecture-based courses to help students process information in the literature and apply that information to a novel problem such as design of an antiviral drug or a vaccine. These assignments have been helpful in engaging students in the scientific process in the absence of an inquiry-driven laboratory. This commentary discusses the application of these grant proposal writing assignments to undergraduate biology courses. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Do language fluency and other socioeconomic factors influence the use of PubMed and MedlinePlus?

    Science.gov (United States)

    Sheets, L; Gavino, A; Callaghan, F; Fontelo, P

    2013-01-01

    Increased usage of MedlinePlus by Spanish-speakers was observed after introduction of MedlinePlus in Spanish. This probably reflects increased usage of MEDLINE and PubMed by those with greater fluency in the language in which it is presented; but this has never been demonstrated in English speakers. Evidence that lack of English fluency deters international healthcare personnel from using PubMed could support the use of multi-language search tools like Babel-MeSH. This study aims to measure the effects of language fluency and other socioeconomic factors on PubMed MEDLINE and MedlinePlus access by international users. We retrospectively reviewed server pageviews of PubMed and MedlinePlus from various periods of time, and analyzed them against country statistics on language fluency, GDP, literacy rate, Internet usage, medical schools, and physicians per capita, to determine whether they were associated. We found fluency in English to be positively associated with pageviews of PubMed and MedlinePlus in countries with high literacy rates. Spanish was generally found to be positively associated with pageviews of MedlinePlus en Español. The other parameters also showed varying degrees of association with pageviews. After adjusting for the other factors investigated in this study, language fluency was a consistently significant predictor of the use of PubMed, MedlinePlus English and MedlinePlus en Español. This study may support the need for multi-language search tools and may increase access of health information resources from non-English speaking countries.

  18. Publication Trends in Acupuncture Research: A 20-Year Bibliometric Analysis Based on PubMed.

    Science.gov (United States)

    Ma, Yan; Dong, Ming; Zhou, Kehua; Mita, Carol; Liu, Jianping; Wayne, Peter M

    2016-01-01

    Acupuncture has become popular and widely practiced in many countries around the world. Despite the large amount of acupuncture-related literature that has been published, broader trends in the prevalence and scope of acupuncture research remain underexplored. The current study quantitatively analyzes trends in acupuncture research publications in the past 20 years. A bibliometric approach was used to search PubMed for all acupuncture-related research articles including clinical and animal studies. Inclusion criteria were articles published between 1995 and 2014 with sufficient information for bibliometric analyses. Rates and patterns of acupuncture publication within the 20 year observational period were estimated, and compared with broader publication rates in biomedicine. Identified eligible publications were further analyzed with respect to study type/design, clinical condition addressed, country of origin, and journal impact factor. A total of 13,320 acupuncture-related publications were identified using our search strategy and eligibility criteria. Regression analyses indicated an exponential growth in publications over the past two decades, with a mean annual growth rate of 10.7%. This compares to a mean annual growth rate of 4.5% in biomedicine. A striking trend was an observed increase in the proportion of randomized clinical trials (RCTs), from 7.4% in 1995 to 20.3% in 2014, exceeding the 4.5% proportional growth of RCTs in biomedicine. Over the 20 year period, pain was consistently the most common focus of acupuncture research (37.9% of publications). Other top rankings with respect to medical focus were arthritis, neoplasms/cancer, pregnancy or labor, mood disorders, stroke, nausea/vomiting, sleep, and paralysis/palsy. Acupuncture research was conducted in 60 countries, with the top 3 contributors being China (47.4%), United States (17.5%), and United Kingdom (8.2%). Retrieved articles were published mostly in complementary and alternative medicine (CAM

  19. Mentoring programs for medical students - a review of the PubMed literature 2000 - 2008

    Directory of Open Access Journals (Sweden)

    Buddeberg-Fischer Barbara

    2010-04-01

    Full Text Available Abstract Background Although mentoring is acknowledged as a key to successful and satisfying careers in medicine, formal mentoring programs for medical students are lacking in most countries. Within the framework of planning a mentoring program for medical students at Zurich University, an investigation was carried out into what types of programs exist, what the objectives pursued by such programs are, and what effects are reported. Methods A PubMed literature search was conducted for 2000 - 2008 using the following keywords or their combinations: mentoring, mentoring program, medical student, mentor, mentee, protégé, mentorship. Although a total of 438 publications were identified, only 25 papers met the selection criteria for structured programs and student mentoring surveys. Results The mentoring programs reported in 14 papers aim to provide career counseling, develop professionalism, increase students' interest in research, and support them in their personal growth. There are both one-to-one and group mentorships, established in the first two years of medical school and continuing through graduation. The personal student-faculty relationship is important in that it helps students to feel that they are benefiting from individual advice and encourages them to give more thought to their career choices. Other benefits are an increase in research productivity and improved medical school performance in general. Mentored students also rate their overall well-being as higher. - The 11 surveys address the requirements for being an effective mentor as well as a successful mentee. A mentor should empower and encourage the mentee, be a role model, build a professional network, and assist in the mentee's personal development. A mentee should set agendas, follow through, accept criticism, and be able to assess performance and the benefits derived from the mentoring relationship. Conclusion Mentoring is obviously an important career advancement tool for

  20. Mentoring programs for medical students - a review of the PubMed literature 2000 - 2008

    Science.gov (United States)

    2010-01-01

    Background Although mentoring is acknowledged as a key to successful and satisfying careers in medicine, formal mentoring programs for medical students are lacking in most countries. Within the framework of planning a mentoring program for medical students at Zurich University, an investigation was carried out into what types of programs exist, what the objectives pursued by such programs are, and what effects are reported. Methods A PubMed literature search was conducted for 2000 - 2008 using the following keywords or their combinations: mentoring, mentoring program, medical student, mentor, mentee, protégé, mentorship. Although a total of 438 publications were identified, only 25 papers met the selection criteria for structured programs and student mentoring surveys. Results The mentoring programs reported in 14 papers aim to provide career counseling, develop professionalism, increase students' interest in research, and support them in their personal growth. There are both one-to-one and group mentorships, established in the first two years of medical school and continuing through graduation. The personal student-faculty relationship is important in that it helps students to feel that they are benefiting from individual advice and encourages them to give more thought to their career choices. Other benefits are an increase in research productivity and improved medical school performance in general. Mentored students also rate their overall well-being as higher. - The 11 surveys address the requirements for being an effective mentor as well as a successful mentee. A mentor should empower and encourage the mentee, be a role model, build a professional network, and assist in the mentee's personal development. A mentee should set agendas, follow through, accept criticism, and be able to assess performance and the benefits derived from the mentoring relationship. Conclusion Mentoring is obviously an important career advancement tool for medical students. In Europe

  1. The photo biological effect of low level laser therapy on serum level of leptin, cholesterol and triglycerides in overweight and obese females

    International Nuclear Information System (INIS)

    Salem, E.S.; Tawfik, M.S.; Youssef, S.S.; Serry, Z.M.; Aboel magd, H.F.

    2013-01-01

    The use of low level laser for body contouring and weight reduction depends on the photochemical non thermal effect of laser light on the adipose tissue. LLLT was reported to liquefy or release stored fat in adipocytes by the opening of specialized yet not identified cell membrane-associated pores after a brief treatment The concentration of leptin in adipose tissue and serum closely parallel the mass of adipose tissue and adipocyte size and triglycerides content. Thus, leptin increases in obesity and falls with weight loss. The current study was conducted to evaluate the effect of the low level laser therapy (LLLT) on leptin hormone, Cholesterol and triglyceride in both overweight and obese females. Twenty women were included in this study. Their ages ranged from 30-40 years. They were divided into two equal groups. Group A (Overweight group): included 10 females with BMI between 25 and 29.9 Kg/m2 -Group B (Obese group): included 10 females with BMI . 30. Both groups received LLL to the abdomen using laser scanner for uniform distribution of the beam above and below the umbilicus. Duration of treatment was 30 minutes, 2 times per week for 8 weeks as a total period of treatment. Serum level of leptin was estimated by radioimmunoassay (RIA). As regards serum cholesterol and triglyceride they were determined by enzymatic colorimetric test. Biochemical assessments were done before and after treatment. Results of the present study showed that in the overweight group laser treatment resulted in highly significant reduction in leptin serum level accompanied by highly significant increase in serum triglycerides level. Meanwhile, the increase in cholesterol level was insignificant. As regards the obese group, alteration in serum leptin level caused by laser treatment was not significant. In this group the increase in triglycerides and cholesterol serum levels after treatment were highly significant

  2. Cardiovascular diseases induced by low level ionizing radiation. Current status and proposal of future directions of the biological studies

    International Nuclear Information System (INIS)

    Iwasaki, Toshiyasu; Nomura, Takaharu; Ishii, Keiichiro

    2013-01-01

    In the publication on tissue reactions of the International Commission on Radiological Protection (ICRP), the risk of cardiovascular diseases (CVD) was calculated based on linear non-threshold model, without taking account of dose-rate effect. To evaluate the validity of this estimation, we analyzed recent epidemiological and biological findings on CVD at low dose or low dose-rate. Though epidemiological data suggested that radiation would have a causal association with CVD by inducing atherosclerosis, it was limited by heterogeneity among studies, and the contribution of other pathways was also suggested. As biological mechanisms, inflammation is considered as the critical factor of radiation induced CVD. However, the inflammatory responses at low dose were inconsistent among studies, and there were few data at low dose-rate. Furthermore, because those responses were transient, it was very difficult to link them to CVD with long latency. We proposed a concept for the analysis of these long latency diseases by focusing the premonitory symptoms of CVD which could be affected by radiation. As the premonitory symptoms recruitment of white blood cells to inflamed blood vessels and/or tissues would have the highest priority to investigate. To elucidate the dose-rate effect and reflect the results on the radiological protection, it would be important to examine the premonitory symptoms after long term exposure mimicking the actual situation, such as chronic exposure or fractionated exposure of very small dose. (author)

  3. Shifting Sands: Science Researchers on Google Scholar, Web of Science, and PubMed, with Implications for Library Collections Budgets

    Science.gov (United States)

    Hightower, Christy; Caldwell, Christy

    2010-01-01

    Science researchers at the University of California Santa Cruz were surveyed about their article database use and preferences in order to inform collection budget choices. Web of Science was the single most used database, selected by 41.6%. Statistically there was no difference between PubMed (21.5%) and Google Scholar (18.7%) as the second most…

  4. Combining PubMed knowledge and EHR data to develop a weighted bayesian network for pancreatic cancer prediction.

    Science.gov (United States)

    Zhao, Di; Weng, Chunhua

    2011-10-01

    In this paper, we propose a novel method that combines PubMed knowledge and Electronic Health Records to develop a weighted Bayesian Network Inference (BNI) model for pancreatic cancer prediction. We selected 20 common risk factors associated with pancreatic cancer and used PubMed knowledge to weigh the risk factors. A keyword-based algorithm was developed to extract and classify PubMed abstracts into three categories that represented positive, negative, or neutral associations between each risk factor and pancreatic cancer. Then we designed a weighted BNI model by adding the normalized weights into a conventional BNI model. We used this model to extract the EHR values for patients with or without pancreatic cancer, which then enabled us to calculate the prior probabilities for the 20 risk factors in the BNI. The software iDiagnosis was designed to use this weighted BNI model for predicting pancreatic cancer. In an evaluation using a case-control dataset, the weighted BNI model significantly outperformed the conventional BNI and two other classifiers (k-Nearest Neighbor and Support Vector Machine). We conclude that the weighted BNI using PubMed knowledge and EHR data shows remarkable accuracy improvement over existing representative methods for pancreatic cancer prediction. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Characterization of the mechanism of drug-drug interactions from PubMed using MeSH terms.

    Science.gov (United States)

    Lu, Yin; Figler, Bryan; Huang, Hong; Tu, Yi-Cheng; Wang, Ju; Cheng, Feng

    2017-01-01

    Identifying drug-drug interaction (DDI) is an important topic for the development of safe pharmaceutical drugs and for the optimization of multidrug regimens for complex diseases such as cancer and HIV. There have been about 150,000 publications on DDIs in PubMed, which is a great resource for DDI studies. In this paper, we introduced an automatic computational method for the systematic analysis of the mechanism of DDIs using MeSH (Medical Subject Headings) terms from PubMed literature. MeSH term is a controlled vocabulary thesaurus developed by the National Library of Medicine for indexing and annotating articles. Our method can effectively identify DDI-relevant MeSH terms such as drugs, proteins and phenomena with high accuracy. The connections among these MeSH terms were investigated by using co-occurrence heatmaps and social network analysis. Our approach can be used to visualize relationships of DDI terms, which has the potential to help users better understand DDIs. As the volume of PubMed records increases, our method for automatic analysis of DDIs from the PubMed database will become more accurate.

  6. Identification of risk conditions for the development of adrenal disorders: how optimized PubMed search strategies makes the difference.

    Science.gov (United States)

    Guaraldi, Federica; Parasiliti-Caprino, Mirko; Goggi, Riccardo; Beccuti, Guglielmo; Grottoli, Silvia; Arvat, Emanuela; Ghizzoni, Lucia; Ghigo, Ezio; Giordano, Roberta; Gori, Davide

    2014-12-01

    The exponential growth of scientific literature available through electronic databases (namely PubMed) has increased the chance of finding interesting articles. At the same time, search has become more complicated, time consuming, and at risk of missing important information. Therefore, optimized strategies have to be adopted to maximize searching impact. The aim of this study was to formulate efficient strings to search PubMed for etiologic associations between adrenal disorders (ADs) and other conditions. A comprehensive list of terms identifying endogenous conditions primarily affecting adrenals was compiled. An ad hoc analysis was performed to find the best way to express each term in order to find the highest number of potentially pertinent articles in PubMed. A predefined number of retrieved abstracts were read to assess their association with ADs' etiology. A more sensitive (providing the largest literature coverage) and a more specific (including only those terms retrieving >40 % of potentially pertinent articles) string were formulated. Various researches were performed to assess strings' ability to identify articles of interest in comparison with non-optimized literature searches. We formulated optimized, ready applicable tools for the identification of the literature assessing etiologic associations in the field of ADs using PubMed, and demonstrated the advantages deriving from their application. Detailed description of the methodological process is also provided, so that this work can easily be translated to other fields of practice.

  7. Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014 : retrospective analysis

    NARCIS (Netherlands)

    Vinkers, Christiaan H|info:eu-repo/dai/nl/304824755; Tijdink, Joeri K; Otte, Willem M

    2015-01-01

    OBJECTIVE: To investigate whether language used in science abstracts can skew towards the use of strikingly positive and negative words over time. DESIGN: Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014. METHODS: The yearly frequencies of positive, negative, and

  8. Characterization of the mechanism of drug-drug interactions from PubMed using MeSH terms.

    Directory of Open Access Journals (Sweden)

    Yin Lu

    Full Text Available Identifying drug-drug interaction (DDI is an important topic for the development of safe pharmaceutical drugs and for the optimization of multidrug regimens for complex diseases such as cancer and HIV. There have been about 150,000 publications on DDIs in PubMed, which is a great resource for DDI studies. In this paper, we introduced an automatic computational method for the systematic analysis of the mechanism of DDIs using MeSH (Medical Subject Headings terms from PubMed literature. MeSH term is a controlled vocabulary thesaurus developed by the National Library of Medicine for indexing and annotating articles. Our method can effectively identify DDI-relevant MeSH terms such as drugs, proteins and phenomena with high accuracy. The connections among these MeSH terms were investigated by using co-occurrence heatmaps and social network analysis. Our approach can be used to visualize relationships of DDI terms, which has the potential to help users better understand DDIs. As the volume of PubMed records increases, our method for automatic analysis of DDIs from the PubMed database will become more accurate.

  9. Using noun phrases for navigating biomedical literature on Pubmed: how many updates are we losing track of?

    Science.gov (United States)

    Srikrishna, Devabhaktuni; Coram, Marc A

    2011-01-01

    Author-supplied citations are a fraction of the related literature for a paper. The "related citations" on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMed "related citations." We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers, 5 search terms are CV-D, and 10 search terms are CV-S, and 6 unique citations validate these searches. Potentially related literature uncovered by citation-validated searches (either CV-S or CV-D) are on the order of ten per paper--many more if the remaining searches that are not citation-validated are taken into account. The significance and relationship of each search result to the paper can only be vetted and explained by a researcher with knowledge of or interest in that paper.

  10. Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device.

    Science.gov (United States)

    Ball, David A; Lux, Matthew W; Graef, Russell R; Peterson, Matthew W; Valenti, Jane D; Dileo, John; Peccoud, Jean

    2010-01-01

    The concept of co-design is common in engineering, where it is necessary, for example, to determine the optimal partitioning between hardware and software of the implementation of a system features. Here we propose to adapt co-design methodologies for synthetic biology. As a test case, we have designed an environmental sensing device that detects the presence of three chemicals, and returns an output only if at least two of the three chemicals are present. We show that the logical operations can be implemented in three different design domains: (1) the transcriptional domain using synthetically designed hybrid promoters, (2) the protein domain using bi-molecular fluorescence complementation, and (3) the fluorescence domain using spectral unmixing and relying on electronic processing. We discuss how these heterogeneous design strategies could be formalized to develop co-design algorithms capable of identifying optimal designs meeting user specifications.

  11. A chemical biology approach to interrogate quorum-sensing regulated behaviors at the molecular and cellular level.

    Science.gov (United States)

    Lowery, Colin A; Matamouros, Susana; Niessen, Sherry; Zhu, Jie; Scolnick, Jonathan; Lively, Jenny M; Cravatt, Benjamin F; Miller, Samuel I; Kaufmann, Gunnar F; Janda, Kim D

    2013-07-25

    Small molecule probes have been used extensively to explore biologic systems and elucidate cellular signaling pathways. In this study, we use an inhibitor of bacterial communication to monitor changes in the proteome of Salmonella enterica serovar Typhimurium with the aim of discovering unrecognized processes regulated by AI-2-based quorum-sensing (QS), a mechanism of bacterial intercellular communication that allows for the coordination of gene expression in a cell density-dependent manner. In S. typhimurium, this system regulates the uptake and catabolism of intercellular signals and has been implicated in pathogenesis, including the invasion of host epithelial cells. We demonstrate that our QS antagonist is capable of selectively inhibiting the expression of known QS-regulated proteins in S. typhimurium, thus attesting that QS inhibitors may be used to confirm proposed and elucidate previously unidentified QS pathways without relying on genetic manipulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. [Accidents with exposure to biological material contaminated with HIV in workers at a third level hospital in Madrid].

    Science.gov (United States)

    García de Codes Ilario, Aurelia; de Juanes Pardo, José Ramón; Arrazola Martínez, M del Pilar; Jaén Herreros, Felisa; Sanz Gallardo, M Inmaculada; Lago López, Emilia

    2004-01-01

    Human Immunodeficiency Virus (HIV) is an occupational hazard among healthcare professionals accidentally contaminated with HIV-positive blood. This study is aimed at describing the characteristics of the accidents involving blood of HIV-positive patients recorded over a sixteen-year period at a general hospital. Epidemiological study of the accidents reported in 2001 involving biological material from an HIV-positive source by the healthcare personnel of a general hospital throughout the 1986-2001 period entailing the presence of biological material from HIV-positive serology individuals. Individual, time and place-related variables, in addition to the initial serologies and those throughout the protocolized follow-up were studied for those individuals involved in these accidents. A total 550 accidents entailing an HIV-positive source were reported. The average number of accidents was 34.4/year. The accidental exposure rate for the period under study was 7.5/1000 workers/year. The professional group showing the highest accident rate was the nursing staff (54.4%). Percutaneous injuries were the most frequent (80.2%). The mean exposure rate was 2.6/100 beds/year. The anatomical areas involved to the greatest degree were the fingers (75.6%). A total 53.4% of those injured completed the serological follow-up without having shown any seroconversion. Throughout the sixteen-year period under study, the annual incidence of accidents involving an HIV-positive source increased from the 27 accidents reported in 1986 to the 60 accidents reported in 1990, there having been a downward trend as of that point in time, to the point of 12 accidents having been recorded in 2001.

  13. Preliminary assessment of geologic materials to minimize biological intrusion of low-level waste trench covers and plans for the future

    International Nuclear Information System (INIS)

    Hakonson, T.E.; White, G.C.; Gladney, E.S.; Muller, M.

    1981-01-01

    The long-term integrity of low-level waste shallow land burial sites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. Past research on low-level waste shallow land burial methods has emphasized physical (i.e., water infiltration, soil erosion) and chemical (radionuclide leaching) processes that can cause radionuclide transport from a waste site. Preliminary results demonstrate that a sandy backfill material offers little resistance to root and animal intrusion through the cover profile. However, bentonite clay, cobble, and cobble-gravel combinations do reduce plant root and animal intrusion through cover profiles compared with sandy backfill soil. However, bentonite clay barrier systems appear to be degraded by plant roots through time. Desiccation of the clay barrier by invading plant roots may limit the usefulness of bentonite clay as a moisture and/or biological carrier unless due consideration is given to this interaction. Future experiments are described that further examine the effect of plant roots on clay barrier systems and that determine the effectiveness of proposed biological barriers on larger scales and under various stress conditions

  14. A Personalized Approach to Biological Therapy Using Prediction of Clinical Response Based on MRP8/14 Serum Complex Levels in Rheumatoid Arthritis Patients.

    Directory of Open Access Journals (Sweden)

    S C Nair

    Full Text Available Measurement of MRP8/14 serum levels has shown potential in predicting clinical response to different biological agents in rheumatoid arthritis (RA. We aimed to develop a treatment algorithm based on a prediction score using MRP8/14 measurements and clinical parameters predictive for response to different biological agents.Baseline serum levels of MRP8/14 were measured in 170 patients starting treatment with infliximab, adalimumab or rituximab. We used logistic regression analysis to develop a predictive score for clinical response at 16 weeks. MRP8/14 levels along with clinical variables at baseline were investigated. We also investigated how the predictive effect of MRP8/14 was modified by drug type. A treatment algorithm was developed based on categorizing the expected response per drug type as high, intermediate or low for each patient and optimal treatment was defined. Finally, we present the utility of using this treatment algorithm in clinical practice.The probability of response increased with higher baseline MRP8/14 complex levels (OR = 1.39, differentially between the TNF-blockers and rituximab (OR of interaction term = 0.78, and also increased with higher DAS28 at baseline (OR = 1.28. Rheumatoid factor positivity, functional disability (a higher HAQ, and previous use of a TNF-inhibitor decreased the probability of response. Based on the treatment algorithm 80 patients would have been recommended for anti-TNF treatment, 8 for rituximab, 13 for another biological treatment (other than TNFi or rituximab and for 69 no recommendation was made. The predicted response rates matched the observed response in the cohort well. On group level the predicted response based on the algorithm resulted in a modest 10% higher response rate in our cohort with much higher differences in response probability in individual patients treated contrary to treatment recommendation.Prediction of response using MRP8/14 levels along with clinical predictors has

  15. 6-sulfatoxymelatonin levels in pregnant women during workplace and nonworkplace stresses: a potential biologic marker of sympathetic activity.

    Science.gov (United States)

    Katz, V L; Ekstrom, R D; Mason, G A; Golden, R N

    1995-07-01

    Melatonin production is regulated by both catecholamines and sympathetic activity. Urine levels of the major metabolite of melatonin, 6-sulfatoxymelatonin, correlate well with serum melatonin levels and have been used to evaluate sympathetic output. We tested the hypothesis that urinary levels of 6-sulfatoxymelatonin would reflect the change in adrenergic activity on working days compared with nonworking days during pregnancy. Twenty-three healthy pregnant women, employed in a variety of occupations, including physicians, nurses, secretaries, salespeople, and laboratory workers were recruited from the clinics of the University of North Carolina School of Medicine. We measured 6-sulfatoxymelatonin levels in first morning voids and for the subsequent 10 hours at 24, 28, 32, and 36 weeks' gestation. Urine was collected in sets during working days and during nonworking days. 6-Sulfatoxymelatonin was measured by radioimmunoassay. In 11 women we also measured urine catecholamines by high-performance liquid chromatography. Levels of 6-sulfatoxymelatonin output did not change across gestation, although they tended to drift down as pregnancy progressed. Median levels at first morning void were 6.3 micrograms on workdays and 4.6 micrograms on nonworkdays. Although all values were skewed toward work being greater than nonwork, there were large interindividual variations. We therefore compared subjects against themselves and compared work levels for each subject to the corresponding gestational age-matched nonwork value. Among the 23 women, median 6-sulfatoxymelatonin levels were 81% greater during work than nonwork (p < 0.0002) when first morning collections were compared. Daytime urinary excretion of 6-sulfatoxymelatonin on workdays was 38% (p < 0.005) greater than during nonworkdays.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. Stairway to heaven: evaluating levels of biological organization correlated with the successful ascent of natural waterfalls in the Hawaiian stream goby Sicyopterus stimpsoni.

    Directory of Open Access Journals (Sweden)

    Heiko L Schoenfuss

    Full Text Available Selective pressures generated by locomotor challenges act at the level of the individual. However, phenotypic variation among individuals that might convey a selective advantage may occur across any of multiple levels of biological organization. In this study, we test for differences in external morphology, muscle mechanical advantage, muscle fiber type and protein expression among individuals of the waterfall climbing Hawaiian fish Sicyopterus stimpsoni collected from sequential pools increasing in elevation within a single freshwater stream. Despite predictions from previous laboratory studies of morphological selection, few directional morphometric changes in body shape were observed at successively higher elevations. Similarly, lever arm ratios associated with the main pelvic sucker, central to climbing ability in this species, did not differ between elevations. However, among climbing muscles, the adductor pelvicus complex (largely responsible for generating pelvic suction during climbing contained a significantly greater red muscle fiber content at upstream sites. A proteomic analysis of the adductor pelvicus revealed two-fold increases in expression levels for two respiratory chain proteins (NADH:ubiquinone reductase and cytochrome b that are essential for aerobic respiration among individuals from successively higher elevations. Assessed collectively, these evaluations reveal phenotypic differences at some, but not all levels of biological organization that are likely the result of selective pressures experienced during climbing.

  17. Stairway to heaven: evaluating levels of biological organization correlated with the successful ascent of natural waterfalls in the Hawaiian stream goby Sicyopterus stimpsoni.

    Science.gov (United States)

    Schoenfuss, Heiko L; Maie, Takashi; Moody, Kristine N; Lesteberg, Kelsey E; Blob, Richard W; Schoenfuss, Tonya C

    2013-01-01

    Selective pressures generated by locomotor challenges act at the level of the individual. However, phenotypic variation among individuals that might convey a selective advantage may occur across any of multiple levels of biological organization. In this study, we test for differences in external morphology, muscle mechanical advantage, muscle fiber type and protein expression among individuals of the waterfall climbing Hawaiian fish Sicyopterus stimpsoni collected from sequential pools increasing in elevation within a single freshwater stream. Despite predictions from previous laboratory studies of morphological selection, few directional morphometric changes in body shape were observed at successively higher elevations. Similarly, lever arm ratios associated with the main pelvic sucker, central to climbing ability in this species, did not differ between elevations. However, among climbing muscles, the adductor pelvicus complex (largely responsible for generating pelvic suction during climbing) contained a significantly greater red muscle fiber content at upstream sites. A proteomic analysis of the adductor pelvicus revealed two-fold increases in expression levels for two respiratory chain proteins (NADH:ubiquinone reductase and cytochrome b) that are essential for aerobic respiration among individuals from successively higher elevations. Assessed collectively, these evaluations reveal phenotypic differences at some, but not all levels of biological organization that are likely the result of selective pressures experienced during climbing.

  18. Environmental regulation of plant gene expression: an RT-qPCR laboratory project for an upper-level undergraduate biochemistry or molecular biology course.

    Science.gov (United States)

    Eickelberg, Garrett J; Fisher, Alison J

    2013-01-01

    We present a novel laboratory project employing "real-time" RT-qPCR to measure the effect of environment on the expression of the FLOWERING LOCUS C gene, a key regulator of floral timing in Arabidopsis thaliana plants. The project requires four 3-hr laboratory sessions and is aimed at upper-level undergraduate students in biochemistry or molecular biology courses. The project provides students with hands-on experience with RT-qPCR, the current "gold standard" for gene expression analysis, including detailed data analysis using the common 2-ΔΔCT method. Moreover, it provides a convenient starting point for many inquiry-driven projects addressing diverse questions concerning ecological biochemistry, naturally occurring genetic variation, developmental biology, and the regulation of gene expression in nature. Copyright © 2013 Wiley Periodicals, Inc.

  19. The Current Status of the Space Station Biological Research Project: a Core Facility Enabling Multi-Generational Studies under Slectable Gravity Levels

    Science.gov (United States)

    Santos, O.

    2002-01-01

    The Space Station Biological Research Project (SSBRP) has developed a new plan which greatly reduces the development costs required to complete the facility. This new plan retains core capabilities while allowing for future growth. The most important piece of equipment required for quality biological research, the 2.5 meter diameter centrifuge capable of accommodating research specimen habitats at simulated gravity levels ranging from microgravity to 2.0 g, is being developed by NASDA, the Japanese space agency, for the SSBRP. This is scheduled for flight to the ISS in 2007. The project is also developing a multi-purpose incubator, an automated cell culture unit, and two microgravity habitat holding racks, currently scheduled for launch in 2005. In addition the Canadian Space Agency is developing for the project an insect habitat, which houses Drosophila melanogaster, and provides an internal centrifuge for 1 g controls. NASDA is also developing for the project a glovebox for the contained manipulation and analysis of biological specimens, scheduled for launch in 2006. This core facility will allow for experimentation on small plants (Arabidopsis species), nematode worms (C. elegans), fruit flies (Drosophila melanogaster), and a variety of microorganisms, bacteria, yeast, and mammalian cells. We propose a plan for early utilization which focuses on surveys of changes in gene expression and protein structure due to the space flight environment. In the future, the project is looking to continue development of a rodent habitat and a plant habitat that can be accommodated on the 2.5 meter centrifuge. By utilizing the early phases of the ISS to broadly answer what changes occur at the genetic and protein level of cells and organisms exposed to the ISS low earth orbit environment, we can generate interest for future experiments when the ISS capabilities allow for direct manipulation and intervention of experiments. The ISS continues to hold promise for high quality, long

  20. A multi-level biological approach to evaluate impacts of a major municipal effluent in wild St. Lawrence River yellow perch (Perca flavescens)

    Energy Technology Data Exchange (ETDEWEB)

    Houde, Magali, E-mail: magali.houde@ec.gc.ca [Centre Saint-Laurent, Environment Canada, 105 McGill Street, Montreal, QC H2Y 2E7 (Canada); Giraudo, Maeva, E-mail: maeva.giraudo@ec.gc.ca [Centre Saint-Laurent, Environment Canada, 105 McGill Street, Montreal, QC H2Y 2E7 (Canada); Douville, Mélanie, E-mail: melanie.douville@ec.gc.ca [Centre Saint-Laurent, Environment Canada, 105 McGill Street, Montreal, QC H2Y 2E7 (Canada); Bougas, Bérénice, E-mail: berenice.bougas.1@ulaval.ca [Institut de biologie intégrative et des systèmes, Université Laval, 1030, avenue de la Médecine, Québec, QC G1V 0A6 (Canada); Institut National de la Recherche Scientifique, Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC G1K 9A9 (Canada); Couture, Patrice, E-mail: patrice.couture@ete.inrs.ca [Institut National de la Recherche Scientifique, Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC G1K 9A9 (Canada); De Silva, Amila O., E-mail: amila.desilva@ec.gc.ca [Canada Centre for Inland Waters, Environment Canada, 867 Lakeshore Road, P.O. Box 5050, Burlington, ON L7R 4A6 (Canada); Spencer, Christine, E-mail: christine.spencer@ec.gc.ca [Canada Centre for Inland Waters, Environment Canada, 867 Lakeshore Road, P.O. Box 5050, Burlington, ON L7R 4A6 (Canada); Lair, Stéphane, E-mail: stephane.lair@umontreal.ca [Centre québécois sur la santé des animaux sauvages, Université de Montréal, C.P. 5000, St-Hyacinthe, QC J2S 7C6 (Canada); and others

    2014-11-01

    The development of integrated ecotoxicological approaches is of great interest in the investigation of global concerns such as impacts of municipal wastewater effluents on aquatic ecosystems. The objective of this study was to investigate the effects of a major wastewater municipal effluent on fish using a multi-level biological approach, from gene transcription and enzyme activities to histological changes. Yellow perch (Perca flavescens) were selected based on their wide distribution, their commercial and recreational importance, and the availability of a customized microarray. Yellow perch were sampled upstream of a major municipal wastewater treatment plant (WWTP) and 4 km and 10 km downstream from its point of discharge in the St. Lawrence River (Quebec, Canada). Concentrations of perfluoroalkyl substances (PFASs), polybrominated diphenyl ethers (PBDEs) and metals/trace elements in whole body homogenates were comparable to those from other industrialized regions of the world. Genomic results indicated that the transcription level of 177 genes was significantly different (p < 0.024) between exposed and non-exposed fish. Among these genes, 38 were found to be differentially transcribed at both downstream sites. Impacted genes were associated with biological processes and molecular functions such as immunity, detoxification, lipid metabolism/energy homeostasis (e.g., peroxisome proliferation), and retinol metabolism suggesting impact of WWTP on these systems. Moreover, antioxidant enzyme activities were more elevated in perch collected at the 4 km site. Biomarkers of lipid metabolism, biosynthetic activity, and aerobic capacities were significantly lower (p < 0.05) in fish residing near the outfall of the effluent. Histological examination of the liver indicated no differences between sites. Correlations between PFAS, PBDE, and metal/trace element tissue concentrations and markers of peroxisomal proliferation, oxidative stress, and retinoid metabolism were found

  1. Socioeconomic status in children is associated with hair cortisol levels as a biological measure of chronic stress.

    Science.gov (United States)

    Vliegenthart, J; Noppe, G; van Rossum, E F C; Koper, J W; Raat, H; van den Akker, E L T

    2016-03-01

    Low socioeconomic status (SES) may be associated with a high risk of lifestyle-related diseases such as cardiovascular diseases. There is a strong association between parental SES, stress and indicators of child health and adult health outcome. The exact mechanisms underlying this association have not yet been fully clarified. Low SES may be associated with chronic stress, which may lead to activation of the hypothalamic-pituitary-adrenal (HPA)-axis, resulting in a higher circulating level of the stress hormone cortisol. Therefore, chronic stress may mediate the association between low SES and elevated cortisol levels and its adverse outcomes. We investigated whether SES was associated with a chronic measure of cortisol exposure in a child population. Cortisol and cortisone were measured in scalp hair in 270 children and adolescents, aged 4-18 years, enrolled through school visits. Neighborhood level SES was based on a score developed by the Netherlands Institute for Social Research using postal codes, and this includes neighborhood measures of income education and unemployment. Maternal and paternal education level were used as indicators of family SES. Neighborhood level socioeconomic status score was significantly associated with hair cortisol (β=-0.103, p=0.007, 95%CI [-0.179, -0.028]) and hair cortisone (β=-0.091, p=0.023, 95%CI [-0.167, -0.015]), adjusted for age and sex. Additionally, hair cortisol was significantly correlated with maternal education level and hair cortisone was significantly correlated with paternal education level. The results of our study suggest that the widely shown association between low family SES and adverse child health outcomes may be mediated by chronic stress, given the chronically higher levels of cortisol in children and adolescents in families with low SES. It is especially notable that the association between SES and cortisol was already found in children of young age as this can have major consequences, such as increased

  2. ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-Level Rule-Based Models in Cell Biology.

    Science.gov (United States)

    Bittig, Arne T; Uhrmacher, Adelinde M

    2017-01-01

    Spatio-temporal dynamics of cellular processes can be simulated at different levels of detail, from (deterministic) partial differential equations via the spatial Stochastic Simulation algorithm to tracking Brownian trajectories of individual particles. We present a spatial simulation approach for multi-level rule-based models, which includes dynamically hierarchically nested cellular compartments and entities. Our approach ML-Space combines discrete compartmental dynamics, stochastic spatial approaches in discrete space, and particles moving in continuous space. The rule-based specification language of ML-Space supports concise and compact descriptions of models and to adapt the spatial resolution of models easily.

  3. Ankylosing Spondylitis Patients Commencing Biologic Therapy Have High Baseline Levels of Comorbidity: A Report from the Australian Rheumatology Association Database

    Directory of Open Access Journals (Sweden)

    John Oldroyd

    2009-01-01

    Full Text Available Aims. To compare the baseline characteristics of a population-based cohort of patients with ankylosing spondylitis (AS commencing biological therapy to the reported characteristics of bDMARD randomised controlled trials (RCTs participants. Methods. Descriptive analysis of AS participants in the Australian Rheumatology Association Database (ARAD who were commencing bDMARD therapy. Results. Up to December 2008, 389 patients with AS were enrolled in ARAD. 354 (91.0% had taken bDMARDs at some time, and 198 (55.9% completed their entry questionnaire prior to or within 6 months of commencing bDMARDs. 131 (66.1% had at least one comorbid condition, and 24 (6.8% had a previous malignancy (15 nonmelanoma skin, 4 melanoma, 2 prostate, 1 breast, cervix, and bowel. Compared with RCT participants, ARAD participants were older, had longer disease duration and higher baseline disease activity. Conclusions. AS patients commencing bDMARDs in routine care are significantly different to RCT participants and have significant baseline comorbidities.

  4. Looking at biological community level to improve ecotoxicological assessment of freshwater sediments: report on a first French-Swiss workshop.

    Science.gov (United States)

    Pesce, Stéphane; Perceval, Olivier; Bonnineau, Chloé; Casado-Martinez, Carmen; Dabrin, Aymeric; Lyautey, Emilie; Naffrechoux, Emmanuel; Ferrari, Benoit J D

    2018-01-01

    The first French-Swiss workshop on ecotoxicology of freshwater sediment communities was co-organized by the French Research Institute of Science and Technology for Environment and Agriculture (Irstea) and the Swiss Centre for Applied Ecotoxicology (Ecotox Centre EAWAG-EPFL) in Villié-Morgon (Beaujolais Region, France) on April 27-28, 2017. The workshop brought together scientists working in different fields of expertise (ecotoxicologists, ecologists, environmental chemists…), environmental stakeholder groups and managers, as well as economic players (start-ups and consultancies) to better connect research needs of potential end-users with research outputs. The objectives of this workshop were (i) to establish the state of the art of research in the characterization of sediment contamination and in the evaluation of the effects on sediment-associated biological communities and ecosystem functioning and (ii) to give an overview of the French and Swiss regulations dealing with the assessment of contaminated sediments in freshwater ecosystems. The ultimate goal was to collectively identify research needs and knowledge gaps, as well as to highlight ways to improve the ecotoxicological assessment of sediments in freshwater environments by further considering the structure and functions of associated microbial and invertebrate communities.

  5. Biological variation in circulating levels of mannan-binding lectin (MBL) and MBL-associated serine protease-2 and the influence of age, gender and physical exercise

    DEFF Research Database (Denmark)

    Ytting, H; Christensen, IJ; Thiel, Steffen

    2007-01-01

    Mannan-binding lectin (MBL) and MBL-associated serine protease 2 (MASP-2) are central components of the MBL pathway of complement activation, and may have potential as clinical biomarkers in colorectal cancer (CRC). Prior to clinical usage, knowledge of the biological variations of the molecules...... is needed. We here investigate variations of MBL and MASP-2 in healthy persons over time and in relation to gender, age and physical activity. MBL and MASP-2 concentrations were determined in serum from healthy adults over a 3-week period and this was repeated 6 months later (n = 32); during a 24-h period...... not affect the levels (P > 0.8). Serum and plasma levels were only marginally different, and were independent of age and gender. Circulating levels of MBL and MASP-2 are stable over time in healthy individuals, which is advantageous for their potential application as biomarkers....

  6. Biological variation in circulating levels of mannan-binding lectin (MBL) and MBL-associated serine protease-2 and the influence of age, gender and physical exercise

    DEFF Research Database (Denmark)

    Ytting, H; Christensen, I J; Thiel, S

    2007-01-01

    Mannan-binding lectin (MBL) and MBL-associated serine protease 2 (MASP-2) are central components of the MBL pathway of complement activation, and may have potential as clinical biomarkers in colorectal cancer (CRC). Prior to clinical usage, knowledge of the biological variations of the molecules...... is needed. We here investigate variations of MBL and MASP-2 in healthy persons over time and in relation to gender, age and physical activity. MBL and MASP-2 concentrations were determined in serum from healthy adults over a 3-week period and this was repeated 6 months later (n = 32); during a 24-h period...... not affect the levels (P > 0.8). Serum and plasma levels were only marginally different, and were independent of age and gender. Circulating levels of MBL and MASP-2 are stable over time in healthy individuals, which is advantageous for their potential application as biomarkers....

  7. Biological Variation in Circulating Levels of Mannan-Binding Lectin (MBL) and MBL-Associated Serine Protease-2 and the Influence of Age, Gender and Physical Exercise

    DEFF Research Database (Denmark)

    Ytting, Henriette; Christensen, Ib Jarle; Thiel, S.

    2007-01-01

    is needed. We here investigate variations of MBL and MASP-2 in healthy persons over time and in relation to gender, age and physical activity. MBL and MASP-2 concentrations were determined in serum from healthy adults over a 3-week period and this was repeated 6 months later (n = 32); during a 24-h period...... not affect the levels (P > 0.8). Serum and plasma levels were only marginally different, and were independent of age and gender. Circulating levels of MBL and MASP-2 are stable over time in healthy individuals, which is advantageous for their potential application as biomarkers.......Mannan-binding lectin (MBL) and MBL-associated serine protease 2 (MASP-2) are central components of the MBL pathway of complement activation, and may have potential as clinical biomarkers in colorectal cancer (CRC). Prior to clinical usage, knowledge of the biological variations of the molecules...

  8. Some Misconceptions in Meiosis Shown by Students Responding to an Advanced Level Practical Examination Question in Biology.

    Science.gov (United States)

    Brown, C. R.

    1990-01-01

    Discussed are problems revealed in student responses to a practical task which formed part of an advanced level examination. The frequencies with which some misconceptions about cell reproduction and genetics occurred are presented. The nature of these misconceptions is analyzed and their implications discussed. (CW)

  9. Establishing the Biological Relevance of Dipentyl Phthalate Reductions in Fetal Rat Testosterone Production and Plasma and Testis Testosterone Levels

    Science.gov (United States)

    Phthalate esters (PEs) constitute a large class of compounds that are used for many consumer product applications. Many of the C2-C7 di-ortho PEs reduce fetal testicular hormone and gene expression levels in rats resulting in adverse effects seen later in life but it appears that...

  10. THE EFFECT OF CIPLUKAN (Physalis angulata L. FRUIT EXTRACT ON SGPT AND SGOT LEVELS AGAINST WHITE MALE MICE (Mus musculus HYPERGLYCEMIA INDUCED BY ALLOXAN AS BIOLOGY LEARNING RESOURCES

    Directory of Open Access Journals (Sweden)

    Nur Lailatul Fitri

    2016-07-01

    Full Text Available Ciplukan (Physalis angulata L. used by the community as an antidiabetic drug. Antidiabetic effects caused ciplukan fruit of this plant contain chemicals flavonoids with the percentage of fruit extract 300 mg / ml was 84%. Flavonoids are antioxidant compounds one that works a treat or neutralize free radicals that are expected with the administration of these antioxidants can be inhibited damage to body cells and can prevent damage to the body and the onset of degenerative diseases. This type of research is True Experimental Research. The research design using The Posttest-Only Control Group Design. The research design used completely randomized design (CRD. This research data is data SGPT and SGOT levels. Analysis of data using one-way analysis of variance at significance level of 0.05 and Duncan 5%. The results showed that different doses of fruit extract ciplukan effect on SGPT and SGOT levels of mice. Duncan test showed that the treatment dose ciplukan fruit extract is the most effective dose of 2 ml / kg. The research results can be used by teachers as information of an alternative to utilize medical plants of hyperglicemia and antiocsidant on Biology subject for X Grade of Senior High School, especially on the concept Maintenance and Utilizing of Biological Diversity in Core Competence 4

  11. Changes in lake levels, salinity and the biological community of Great Salt Lake (Utah, USA), 1847-1987

    Science.gov (United States)

    Stephens, D.W.

    1990-01-01

    Great Salt Lake is the fourth largest terminal lake in the world, with an area of about 6000 square kilometers at its historic high elevation. Since its historic low elevation of 1277.52 meters in 1963, the lake has risen to a new historic high elevation of 1283.77 meters in 1986-1987, a net increase of about 6.25 meters. About 60 percent of this increase, 3.72 meters, has occurred since 1982 in response to greater than average precipitation and less than average evaporation. Variations in salinity have resulted in changes in the composition of the aquatic biological community which consists of bacteria, protozoa, brine shrimp and brine flies. These changes were particularly evident following the completion of a causeway in 1959 which divided the lake. Subsequent salinities in the north part of the lake have ranged from 16 to 29 percent and in the south part from 6 to 28 percent. Accompanying the rise in lake elevation from 1982 to 1987 have been large decreases in salinity of both parts of the lake. This has resulted in changes in the biota from obligate halophiles, such as Dunaliella salina and D. viridis, to opportunistic forms such as a blue-green alga (Nodularia spumigena). The distribution and abundance of brine shrimp (Artemia salina) in the lake also have followed closely the salinity. In 1986, when the salinity of the south part of the lake was about 6 percent, a population of brackish-water killifish (Lucania parva) was observed along the shore near inflow from a spring. ?? 1990 Kluwer Academic Publishers.

  12. Effect of habitat disturbance on pollination biology of the columnar cactus Stenocereus quevedonis at landscape-level in central Mexico.

    Science.gov (United States)

    Rodríguez-Oseguera, A G; Casas, A; Herrerías-Diego, Y; Pérez-Negrón, E

    2013-05-01

    Stenocereus quevedonis ('pitire') is a columnar cactus endemic to central Mexico, grown for its edible fruit. Phenology, pollination biology and behaviour of flower visitors of this species were compared in six conserved and disturbed sites, hypothesising that: (i) pitire pollination is self-incompatible, requiring animal vectors; (ii) higher incidence of radiation on plants in cleared forest may lead to a higher number of flowers per pitire plant and longer blooming season, and disturbing and differential spatial availability of flower resources may determine differential attraction of pollinators to conserved and disturbed areas; (iii) if pitire pollination system is specialised, reproductive success would decrease with pollinator scarcity, or other species may substitute for main pollinators. In all sites, pitire reproduction started in January, flowering peak occurring in April, anthesis duration was 15 h and predominantly nocturnal (9 h), pollen was released at 23:00 h, nectar was produced throughout anthesis, and breeding system was self-incompatible. Flower production per plant was similar in disturbed and conserved sites, but flower availability was higher (because of higher tree density) and longer in disturbed sites. Pollination is nocturnal, the most frequent legitimate pollinator being the bat Leptonycteris yerbabuenae; diurnal pollination is rare but possible, carried out by bee species. Fruit and seed set in control and nocturnal pollination treatments at disturbed sites were higher than in conserved sites. Frequency of L. yerbabuenae visits was similar among site types, but more visits of complementary nocturnal and diurnal pollinators were recorded in disturbed sites, which could explain differences in reproductive success. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  13. The use of Sphagnum recurvum Pal. Beauv. as biological tests for determination of the level of pollution with fluorine compounds and sulphur dioxide in the environment

    Directory of Open Access Journals (Sweden)

    Maria Świeboda

    2014-01-01

    Full Text Available The green parts of the peat moss Sphagnum recurvum Pal. Beauv. were used as a biological test to evaluate the pollution level of the natural environment in the region of the aluminium works "Skawina" (Southern Poland with fluorine compounds and sulphur dioxide. The moss samples were placed in nylon nets and exposed to the polluted air for 6 weeks, then the fluorine and sulphur content in them was determined. The results demonstrated the usefulness of this method for the purpose of establishing the range of influence of the emitted industrial pollution.

  14. Using clickers in nonmajors- and majors-level biology courses: student opinion, learning, and long-term retention of course material.

    Science.gov (United States)

    Crossgrove, Kirsten; Curran, Kristen L

    2008-01-01

    Student response systems (clickers) are viewed positively by students and instructors in numerous studies. Evidence that clickers enhance student learning is more variable. After becoming comfortable with the technology during fall 2005-spring 2006, we compared student opinion and student achievement in two different courses taught with clickers in fall 2006. One course was an introductory biology class for nonmajors, and the other course was a 200 level genetics class for biology majors. Students in both courses had positive opinions of the clickers, although we observed some interesting differences between the two groups of students. Student performance was significantly higher on exam questions covering material taught with clickers, although the differences were more dramatic for the nonmajors biology course than the genetics course. We also compared retention of information 4 mo after the course ended, and we saw increased retention of material taught with clickers for the nonmajors course, but not for the genetics course. We discuss the implications of our results in light of differences in how the two courses were taught and differences between science majors and nonmajors.

  15. Study of the influence of microgravity on the biological cells and molecular level; Seitai saibo bunshi level ni okeru bisho juryoku no eikyo ni kansuru kenkyu

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-03-01

    The shape of osteoblast, gene appearance, gene of rice blast, cellular fusion of plants, gravity acceptance mechanism of unicellular organisms, and physiological and immunity functions of mice were investigated under the microgravity condition. The influence of gravity on the vital reaction and the influence of microgravity on the crystallization of vital substances were also investigated. For the observation of osteoblast, the fluorescence dye reacted with Ca was well taken in the cells. The microgravity affected the stability of rice blast, but hardly affected the protoplast culture of mushroom. The reaction of ciliate against the gravity related to the specific gravity difference between cells and outer liquid. The level of adrenaline in blood of mice increased during the drop. The moving speed of trigger waves of chemical parallel slit formed at the BZ reaction under the microgravity became 60% to 80% of that on the ground. In the case of crystallization at the deposition agent concentration of 1% to 4%, the turbidity showing the degree of crystallization changed complicatedly. Nine processes of crystal growth were recognized. 21 refs., 55 figs., 1 tab.

  16. A biological basis for the linear non-threshold dose-response relationship for low-level carcinogen exposure

    International Nuclear Information System (INIS)

    Albert, R.E.

    1981-01-01

    This chapter examines low-level dose-response relationships in terms of the two-stage mouse tumorigenesis model. Analyzes the feasibility of the linear non-threshold dose-response model which was first adopted for use in the assessment of cancer risks from ionizing radiation and more recently from chemical carcinogens. Finds that both the interaction of B(a)P with epidermal DNA of the mouse skin and the dose-response relationship for the initiation stage of mouse skin tumorigenesis showed a linear non-threshold dose-response relationship. Concludes that low level exposure to environmental carcinogens has a linear non-threshold dose-response relationship with the carcinogen acting as an initiator and the promoting action being supplied by the factors that are responsible for the background cancer rate in the target tissue

  17. Combined effects of temperature changes and metal contamination at different levels of biological organization in yellow perch

    International Nuclear Information System (INIS)

    Grasset, Julie; Ollivier, Élodie; Bougas, Bérénice; Yannic, Glenn; Campbell, Peter G.C.; Bernatchez, Louis; Couture, Patrice

    2016-01-01

    Highlights: • Yellow perch were exposed to a combination of heat and metal (Cd or Ni) stress. • Kidney metal accumulation was greatly enhanced at higher temperatures. • Elevated temperatures negatively affected several indicators of condition and metabolic capacities. • Exposure to Ni stimulated gonad development. • Metal stress modified the normal response of antioxidant capacities and apoptosis to heat stress. - Abstract: In this study, we measured the effects of temperature (9 °C, 20 °C, and 28 °C), metal contamination (cadmium and nickel) and their interaction on yellow perch (Perca flavescens) using liver enzymatic and transcriptomic endpoints and biometric indices. Kidney metal concentrations increased with a rise of temperature. The biometric indices analysed (Fulton condition factor, pyloric cæca, hepatosomatic and gonadosomatic indices) generally decreased with an increase of temperature but not with metal contamination. At the enzymatic level, the activity of superoxide dismutase (SOD), involved in antioxidant response, was affected by both temperature and metal contamination, whereas the activity of glucose-6-phosphate dehydrogenase (G6PDH), involved in energy accumulation but also in antioxidant response, was only affected by metal exposure. The response of perch to the stressors at the transcriptional level differed from the metabolic response. In particular, the transcription level of the cco and g6pdh genes sharply decreased with increasing temperature, while the activities of the corresponding enzymes remained stable. The normal response of the transcription level of the apoptotic gene (diablo) to heat stress was also altered in metal-contaminated fish. The combination of metal and temperature stresses also modified the response of antioxidant metabolism induced by these stressors individually. This study contributes to a better understanding of the influences of natural stressors like temperature on biomarkers commonly used in

  18. Combined effects of temperature changes and metal contamination at different levels of biological organization in yellow perch

    Energy Technology Data Exchange (ETDEWEB)

    Grasset, Julie [Institut National de la Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC G1K 9A9 (Canada); Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6 (Canada); Ollivier, Élodie [Institut National de la Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC G1K 9A9 (Canada); Bougas, Bérénice [Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6 (Canada); Yannic, Glenn [Laboratoire d’Écologie Alpine, UMR CNRS 5553, Université de Savoie Mont Blanc, 73376 Le Bourget-du-lac (France); Campbell, Peter G.C. [Institut National de la Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC G1K 9A9 (Canada); Bernatchez, Louis [Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6 (Canada); Couture, Patrice, E-mail: patrice.couture@ete.inrs.ca [Institut National de la Recherche Scientifique (INRS), Centre Eau Terre Environnement, 490 de la Couronne, Québec, QC G1K 9A9 (Canada)

    2016-08-15

    Highlights: • Yellow perch were exposed to a combination of heat and metal (Cd or Ni) stress. • Kidney metal accumulation was greatly enhanced at higher temperatures. • Elevated temperatures negatively affected several indicators of condition and metabolic capacities. • Exposure to Ni stimulated gonad development. • Metal stress modified the normal response of antioxidant capacities and apoptosis to heat stress. - Abstract: In this study, we measured the effects of temperature (9 °C, 20 °C, and 28 °C), metal contamination (cadmium and nickel) and their interaction on yellow perch (Perca flavescens) using liver enzymatic and transcriptomic endpoints and biometric indices. Kidney metal concentrations increased with a rise of temperature. The biometric indices analysed (Fulton condition factor, pyloric cæca, hepatosomatic and gonadosomatic indices) generally decreased with an increase of temperature but not with metal contamination. At the enzymatic level, the activity of superoxide dismutase (SOD), involved in antioxidant response, was affected by both temperature and metal contamination, whereas the activity of glucose-6-phosphate dehydrogenase (G6PDH), involved in energy accumulation but also in antioxidant response, was only affected by metal exposure. The response of perch to the stressors at the transcriptional level differed from the metabolic response. In particular, the transcription level of the cco and g6pdh genes sharply decreased with increasing temperature, while the activities of the corresponding enzymes remained stable. The normal response of the transcription level of the apoptotic gene (diablo) to heat stress was also altered in metal-contaminated fish. The combination of metal and temperature stresses also modified the response of antioxidant metabolism induced by these stressors individually. This study contributes to a better understanding of the influences of natural stressors like temperature on biomarkers commonly used in

  19. Influence of nutrient levels in Tamarix on Diorhabda sublineata (Coleoptera: Chrysomelidae) survival and fitness with implications for biological control.

    Science.gov (United States)

    Guenther, D A; Gardner, K T; Thompson, D C

    2011-02-01

    Establishment of the saltcedar leaf beetle (Diorhabda spp.) has been unpredictable when caged or released in the field for saltcedar (Tamarix spp.) biocontrol. It has been observed that one caged tree might be voraciously fed upon by beetles while an adjacent tree in the cage is left untouched. We hypothesized that differences in the nutrient content of individual trees may explain this behavior. We evaluated survival, development rate, and egg production of beetles fed in the laboratory on saltcedar foliage from trees that had been grown under a range of fertilizer treatments. Tissue samples from the experimental trees and from the field were analyzed for percent nitrogen, phosphorus, and potassium. There was essentially no survival of beetle larvae fed foliage from saltcedar trees at nitrogen levels below 2.0%. At levels above 2.0% N, beetle larvae had corresponding increased survival rates and shorter development times. Multiple regression analyses indicated that nitrogen and phosphorus are important for larval survival and faster development rates. Higher levels of potassium were important for increased egg cluster production. The plant tissue analysis showed that the percentage of nitrogen in the experimental trees reflected the range of trees in the field and also that there is high variability within trees in the field. Our research indicates that if beetles are released on trees with poor nutrient quality, the larvae will not survive. © 2011 Entomological Society of America

  20. Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014 : retrospective analysis

    OpenAIRE

    Vinkers, Christiaan H; Tijdink, Joeri K; Otte, Willem M

    2015-01-01

    OBJECTIVE: To investigate whether language used in science abstracts can skew towards the use of strikingly positive and negative words over time. DESIGN: Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014. METHODS: The yearly frequencies of positive, negative, and neutral words (25 preselected words in each category), plus 100 randomly selected words were normalised for the total number of abstracts. Subanalyses included pattern quantification of individual wo...

  1. GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

    Directory of Open Access Journals (Sweden)

    Khoury Muin J

    2008-04-01

    Full Text Available Abstract Background Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM, a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. Results The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. Conclusion GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge.

  2. Validation of a search strategy to identify nutrition trials in PubMed using the relative recall method.

    Science.gov (United States)

    Durão, Solange; Kredo, Tamara; Volmink, Jimmy

    2015-06-01

    To develop, assess, and maximize the sensitivity of a search strategy to identify diet and nutrition trials in PubMed using relative recall. We developed a search strategy to identify diet and nutrition trials in PubMed. We then constructed a gold standard reference set to validate the identified trials using the relative recall method. Relative recall was calculated by dividing the number of references from the gold standard our search strategy identified by the total number of references in the gold standard. Our gold standard comprised 298 trials, derived from 16 included systematic reviews. The initial search strategy identified 242 of 298 references, with a relative recall of 81.2% [95% confidence interval (CI): 76.3%, 85.5%]. We analyzed titles and abstracts of the 56 missed references for possible additional terms. We then modified the search strategy accordingly. The relative recall of the final search strategy was 88.6% (95% CI: 84.4%, 91.9%). We developed a search strategy to identify diet and nutrition trials in PubMed with a high relative recall (sensitivity). This could be useful for establishing a nutrition trials register to support the conduct of future research, including systematic reviews. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  3. Marine Biology

    Science.gov (United States)

    Dewees, Christopher M.; Hooper, Jon K.

    1976-01-01

    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  4. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species.

    Science.gov (United States)

    Teeling, Emma C; Vernes, Sonja C; Dávalos, Liliana M; Ray, David A; Gilbert, M Thomas P; Myers, Eugene

    2018-02-15

    Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.

  5. Cork-based activated carbons as supported adsorbent materials for trace level analysis of ibuprofen and clofibric acid in environmental and biological matrices.

    Science.gov (United States)

    Neng, N R; Mestre, A S; Carvalho, A P; Nogueira, J M F

    2011-09-16

    In this contribution, powdered activated carbons (ACs) from cork waste were supported for bar adsorptive micro-extraction (BAμE), as novel adsorbent phases for the analysis of polar compounds. By combining this approach with liquid desorption followed by high performance liquid chromatography with diode array detection (BAμE(AC)-LD/HPLC-DAD), good analytical performance was achieved using clofibric acid (CLOF) and ibuprofen (IBU) model compounds in environmental and biological matrices. Assays performed on 30 mL water samples spiked at the 25.0 μg L(-1) level yielded recoveries around 80% for CLOF and 95% for IBU, under optimized experimental conditions. The ACs textural and surface chemistry properties were correlated with the results obtained. The analytical performance showed good precision (0.9922) from 1.0 to 600.0 μg L(-1). By using the standard addition methodology, the application of the present approach to environmental water and urine matrices allowed remarkable performance at the trace level. The proposed methodology proved to be a viable alternative for acidic pharmaceuticals analysis, showing to be easy to implement, reliable, sensitive and requiring low sample volume to monitor these priority compounds in environmental and biological matrices. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Butter blend containing fish oil improves the level of n-3 fatty acids in biological tissues of hamster

    DEFF Research Database (Denmark)

    Porsgaard, Trine; Overgaard, Jesper; Krogh, Anne Louise

    2007-01-01

    Many studies have shown beneficial effects of long chain n-3 polyunsaturated fatty acids (PUFA) on human health. Regardless of the positive effects of n-3 PUFA, the intake of these fatty acids remains low. An approach to increase the intake of n-3 PUFA in the population is to incorporate fish oil...... Syrian hamsters received hamster feed blended with one of the three butter products. After 6 weeks of feeding, the fatty acid compositions of plasma, erythrocytes, liver, brain, and visceral fat were determined. The intake of butter product with fish oil resulted in a higher level of n-3 PUFA in plasma...... into food. In the present study, fish oil was incorporated into butter blends by enzymatic interesterification. The aim of the study was to investigate the effects of this butter product in comparison with a commercial butter blend and a product produced by interesterification but without fish oil. Golden...

  7. Incineration and monitoring of low-level 3H and 14C wastes at a biological research institution

    International Nuclear Information System (INIS)

    Hamrick, P.E.; Knapp, S.J.; Parker, M.G.; Watson, J.E. Jr.

    1986-01-01

    Low-level radioactive waste containing liquid scintillation fluid and known amounts of 14 C and 3 H has been incinerated in a modified pathological incinerator with the incinerator effluent, refractory surface and ash being monitored. The study relates the activity monitored to that incinerated and discusses how this relation was affected by a modification of the incinerator and monitoring conditions. No significant activity was found to be associated with the ash, particulates or the refractory surface. These data suggest that most of the activity is released as tritiated water vapor and 14 C-labeled carbon dioxide. However, incomplete oxidation may occur for short periods of time depending on the amount of liquid scintillation fluid incinerated, with the possible release of 14 C-labeled carbon monoxide

  8. Simulation to aid in interpreting biological relevance and setting of population-level protection goals for risk assessment of pesticides.

    Science.gov (United States)

    Topping, Christopher John; Luttik, Robert

    2017-10-01

    Specific protection goals (SPGs) comprise an explicit expression of the environmental components that need protection and the maximum impacts that can be tolerated. SPGs are set by risk managers and are typically based on protecting populations or functions. However, the measurable endpoints available to risk managers, at least for vertebrates, are typically laboratory tests. We demonstrate, using the example of eggshell thinning in skylarks, how simulation can be used to place laboratory endpoints in context of population-level effects as an aid to setting the SPGs. We develop explanatory scenarios investigating the impact of different assumptions of eggshell thinning on skylark population size, density and distribution in 10 Danish landscapes, chosen to represent the range of typical Danish agricultural conditions. Landscape and timing of application of the pesticide were found to be the most critical factors to consider in the impact assessment. Consequently, a regulatory scenario of monoculture spring barley with an early spray treatment eliciting the eggshell thinning effect was applied using concentrations eliciting effects of zero to 100% in steps of 5%. Setting the SPGs requires balancing scientific, social and political realities. However, the provision of clear and detailed options such as those from comprehensive simulation results can inform the decision process by improving transparency and by putting the more abstract testing data into the context of real-world impacts. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Multi-level biological responses in Ucides cordatus (Linnaeus, 1763) (Brachyura, Ucididae) as indicators of conservation status in mangrove areas from the western atlantic.

    Science.gov (United States)

    Duarte, Luis Felipe de Almeida; Souza, Caroline Araújo de; Nobre, Caio Rodrigues; Pereira, Camilo Dias Seabra; Pinheiro, Marcelo Antonio Amaro

    2016-11-01

    There is a global lack of knowledge on tropical ecotoxicology, particularly in terms of mangrove areas. These areas often serve as nurseries or homes for several animal species, including Ucides cordatus (the uçá crab). This species is widely distributed, is part of the diet of human coastal communities, and is considered to be a sentinel species due to its sensitivity to toxic xenobiotics in natural environments. Sublethal damages to benthic populations reveal pre-pathological conditions, but discussions of the implications are scarce in the literature. In Brazil, the state of São Paulo offers an interesting scenario for ecotoxicology and population studies: it is easy to distinguish between mangroves that are well preserved and those which are significantly impacted by human activity. The objectives of this study were to provide the normal baseline values for the frequency of Micronucleated cells (MN‰) and for neutral red retention time (NRRT) in U. cordatus at pristine locations, as well to indicate the conservation status of different mangrove areas using a multi-level biological response approach in which these biomarkers and population indicators (condition factor and crab density) are applied in relation to environmental quality indicators (determined via information in the literature and solid waste volume). A mangrove area with no effects of impact (areas of reference or pristine areas) presented a mean value of MN‰120min, values which were assumed as baseline values representing genetic and physiological normality. A significant correlation was found between NRRT and MN, with both showing similar and effective results for distinguishing between different mangrove areas according to conservation status. Furthermore, crab density was lower in more impacted mangrove areas, a finding which also reflects the effects of sublethal damage; this finding was not determined by condition factor measurements. Multi-level biological responses were able to

  10. Ecotoxicity of triphenyltin on the marine copepod Tigriopus japonicus at various biological organisations: from molecular to population-level effects.

    Science.gov (United States)

    Yi, Andy Xianliang; Han, Jeonghoon; Lee, Jae-Seong; Leung, Kenneth M Y

    2014-09-01

    Triphenyltin compounds (TPTs), as effective biocides for different industrial and agricultural purposes, have been detected in coastal marine environments worldwide, in particular in Asian countries. However, little is known about their toxicity to marine organisms. This study comprehensively investigated the molecular, individual and population responses of the marine copepod, Tigriopus japonicus upon waterborne exposure to TPT chloride (TPTCl). Our results indicated that TPTCl was highly toxic to adult T. japonicus, with a 96-h LC50 concentration at 6.3 μg/L. As shown in a chronic full life-cycle test, T. japonicus exposed to 1.0 μg/L TPTCl exhibited a delay in development and a significant reduction of population growth, in terms of the intrinsic rate of increase (r m ). Based on the negative relationship between the r m and exposure concentration, a critical effect concentration was estimated at 1.6 μg/L TPTCl; at or above which population extinction could occur. At 0.1 μg/L TPTCl or above, the sex ratio of the second generation of the copepod was significantly altered and changed to a male-biased population. At molecular level, the inhibition of the transcriptional expression of glutathione S-transferase related genes might lead to dysfunction of detoxification, and the inhibition of retinoid X receptor mRNA expression implied an interruption of the growth and moulting process in T. japonicus. As the only gene that observed up-regulated in this study, the expression of heat shock protein 70 (hsp70) increased in a concentration-dependent manner, indicating its function in protecting the copepod from TPT-mediated oxidative stress. The study advances our understanding on the ecotoxicity of TPT, and provides some initial data on its toxic mechanisms in small crustaceans like copepods.

  11. Computational Systems Chemical Biology

    OpenAIRE

    Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

  12. Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed.

    Science.gov (United States)

    Eisinger, Daniel; Tsatsaronis, George; Bundschus, Markus; Wieneke, Ulrich; Schroeder, Michael

    2013-04-15

    Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms.Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources.

  13. Development of a PubMed Based Search Tool for Identifying Sex and Gender Specific Health Literature.

    Science.gov (United States)

    Song, Michael M; Simonsen, Cheryl K; Wilson, Joanna D; Jenkins, Marjorie R

    2016-02-01

    An effective literature search strategy is critical to achieving the aims of Sex and Gender Specific Health (SGSH): to understand sex and gender differences through research and to effectively incorporate the new knowledge into the clinical decision making process to benefit both male and female patients. The goal of this project was to develop and validate an SGSH literature search tool that is readily and freely available to clinical researchers and practitioners. PubMed, a freely available search engine for the Medline database, was selected as the platform to build the SGSH literature search tool. Combinations of Medical Subject Heading terms, text words, and title words were evaluated for optimal specificity and sensitivity. The search tool was then validated against reference bases compiled for two disease states, diabetes and stroke. Key sex and gender terms and limits were bundled to create a search tool to facilitate PubMed SGSH literature searches. During validation, the search tool retrieved 50 of 94 (53.2%) stroke and 62 of 95 (65.3%) diabetes reference articles selected for validation. A general keyword search of stroke or diabetes combined with sex difference retrieved 33 of 94 (35.1%) stroke and 22 of 95 (23.2%) diabetes reference base articles, with lower sensitivity and specificity for SGSH content. The Texas Tech University Health Sciences Center SGSH PubMed Search Tool provides higher sensitivity and specificity to sex and gender specific health literature. The tool will facilitate research, clinical decision-making, and guideline development relevant to SGSH.

  14. High-performance information search filters for acute kidney injury content in PubMed, Ovid Medline and Embase.

    Science.gov (United States)

    Hildebrand, Ainslie M; Iansavichus, Arthur V; Haynes, R Brian; Wilczynski, Nancy L; Mehta, Ravindra L; Parikh, Chirag R; Garg, Amit X

    2014-04-01

    We frequently fail to identify articles relevant to the subject of acute kidney injury (AKI) when searching the large bibliographic databases such as PubMed, Ovid Medline or Embase. To address this issue, we used computer automation to create information search filters to better identify articles relevant to AKI in these databases. We first manually reviewed a sample of 22 992 full-text articles and used prespecified criteria to determine whether each article contained AKI content or not. In the development phase (two-thirds of the sample), we developed and tested the performance of >1.3-million unique filters. Filters with high sensitivity and high specificity for the identification of AKI articles were then retested in the validation phase (remaining third of the sample). We succeeded in developing and validating high-performance AKI search filters for each bibliographic database with sensitivities and specificities in excess of 90%. Filters optimized for sensitivity reached at least 97.2% sensitivity, and filters optimized for specificity reached at least 99.5% specificity. The filters were complex; for example one PubMed filter included >140 terms used in combination, including 'acute kidney injury', 'tubular necrosis', 'azotemia' and 'ischemic injury'. In proof-of-concept searches, physicians found more articles relevant to topics in AKI with the use of the filters. PubMed, Ovid Medline and Embase can be filtered for articles relevant to AKI in a reliable manner. These high-performance information filters are now available online and can be used to better identify AKI content in large bibliographic databases.

  15. High-performance information search filters for CKD content in PubMed, Ovid MEDLINE, and EMBASE.

    Science.gov (United States)

    Iansavichus, Arthur V; Hildebrand, Ainslie M; Haynes, R Brian; Wilczynski, Nancy L; Levin, Adeera; Hemmelgarn, Brenda R; Tu, Karen; Nesrallah, Gihad E; Nash, Danielle M; Garg, Amit X

    2015-01-01

    Finding relevant articles in large bibliographic databases such as PubMed, Ovid MEDLINE, and EMBASE to inform care and future research is challenging. Articles relevant to chronic kidney disease (CKD) are particularly difficult to find because they are often published under different terminology and are found across a wide range of journal types. We used computer automation within a diagnostic test assessment framework to develop and validate information search filters to identify CKD articles in large bibliographic databases. 22,992 full-text articles in PubMed, Ovid MEDLINE, or EMBASE. 1,374,148 unique search filters. We established the reference standard of article relevance to CKD by manual review of all full-text articles using prespecified criteria to determine whether each article contained CKD content or not. We then assessed filter performance by calculating sensitivity, specificity, and positive predictive value for the retrieval of CKD articles. Filters with high sensitivity and specificity for the identification of CKD articles in the development phase (two-thirds of the sample) were then retested in the validation phase (remaining one-third of the sample). We developed and validated high-performance CKD search filters for each bibliographic database. Filters optimized for sensitivity reached at least 99% sensitivity, and filters optimized for specificity reached at least 97% specificity. The filters were complex; for example, one PubMed filter included more than 89 terms used in combination, including "chronic kidney disease," "renal insufficiency," and "renal fibrosis." In proof-of-concept searches, physicians found more articles relevant to the topic of CKD with the use of these filters. As knowledge of the pathogenesis of CKD grows and definitions change, these filters will need to be updated to incorporate new terminology used to index relevant articles. PubMed, Ovid MEDLINE, and EMBASE can be filtered reliably for articles relevant to CKD. These

  16. PubMed-EX: a web browser extension to enhance PubMed search with text mining features.

    Science.gov (United States)

    Tsai, Richard Tzong-Han; Dai, Hong-Jie; Lai, Po-Ting; Huang, Chi-Hsin

    2009-11-15

    PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources. PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/.

  17. Increasing URM Undergraduate Student Success through Assessment-Driven Interventions: A Multiyear Study Using Freshman-Level General Biology as a Model System

    Science.gov (United States)

    Carmichael, Mary C.; St. Clair, Candace; Edwards, Andrea M.; Barrett, Peter; McFerrin, Harris; Davenport, Ian; Awad, Mohamed; Kundu, Anup; Ireland, Shubha Kale

    2016-01-01

    Xavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students. In this multiyear study with ∼5500 participants, data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course. The three hour-long exams were common and administered concurrently to all students. New exam questions were developed using Bloom’s taxonomy, and exam results were analyzed statistically with validated assessment tools. All but the comprehensive final exam were returned to students for self-evaluation and remediation. Among other approaches, course rigor was monitored by using an identical set of 60 questions on the final exam across 10 semesters. Analysis of the identical sets of 60 final exam questions revealed that overall averages increased from 72.9% (2010) to 83.5% (2015). Regression analysis demonstrated a statistically significant correlation between high-risk students and their averages on the 60 questions. Additional analysis demonstrated statistically significant improvements for at least one letter grade from midterm to final and a 20% increase in the course pass rates over time, also for the high-risk population. These results support the hypothesis that our data-driven interventions and assessment techniques are successful in improving student retention, particularly for our academically at-risk students. PMID:27543637

  18. Differential pulse adsorptive stripping voltammetric determination of nanomolar levels of atorvastatin calcium in pharmaceutical and biological samples using a vertically aligned carbon nanotube/graphene oxide electrode.

    Science.gov (United States)

    Silva, Tiago Almeida; Zanin, Hudson; Vicentini, Fernando Campanhã; Corat, Evaldo José; Fatibello-Filho, Orlando

    2014-06-07

    A novel vertically aligned carbon nanotube/graphene oxide (VACNT-GO) electrode is proposed, and its ability to determine atorvastatin calcium (ATOR) in pharmaceutical and biological samples by differential pulse adsorptive stripping voltammetry (DPAdSV) is evaluated. VACNT films were prepared on a Ti substrate by a microwave plasma chemical vapour deposition method and then treated with oxygen plasma to produce the VACNT-GO electrode. The oxygen plasma treatment exfoliates the carbon nanotube tips exposing graphene foils and inserting oxygen functional groups, these effects improved the VACNT wettability (super-hydrophobic) which is crucial for its electrochemical application. The electrochemical behaviour of ATOR on the VACNT-GO electrode was studied by cyclic voltammetry, which showed that it underwent an irreversible oxidation process at a potential of +1.08 V in pHcond 2.0 (0.2 mol L(-1) buffer phosphate solution). By applying DPAdSV under optimized experimental conditions the analytical curve was found to be linear in the ATOR concentration range of 90 to 3.81 × 10(3) nmol L(-1) with a limit of detection of 9.4 nmol L(-1). The proposed DPAdSV method was successfully applied in the determination of ATOR in pharmaceutical and biological samples, and the results were in close agreement with those obtained by a comparative spectrophotometric method at a confidence level of 95%.

  19. Answers to questions posed during daily patient care are more likely to be answered by UpToDate than PubMed.

    NARCIS (Netherlands)

    Hoogendam, A.; Stalenhoef, A.F.H.; Vries Robbe, P.F. de; Overbeke, A.J.P.M.

    2008-01-01

    BACKGROUND: UpToDate and PubMed are popular sources for medical information. Data regarding the efficiency of PubMed and UpToDate in daily medical care are lacking. OBJECTIVE: The purpose of this observational study was to describe the percentage of answers retrieved by these information sources,

  20. Analysis of queries sent to PubMed at the point of care: observation of search behaviour in a medical teaching hospital.

    NARCIS (Netherlands)

    Hoogendam, A.; Stalenhoef, A.F.H.; Vries Robbe, P.F. de; Overbeke, A.J.P.M.

    2008-01-01

    BACKGROUND: The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted. Knowing what aspects of queries are likely to retrieve relevant articles can increase the effectiveness of PubMed searches.

  1. OvidSP Medline-to-PubMed search filter translation: a methodology for extending search filter range to include PubMed's unique content.

    Science.gov (United States)

    Damarell, Raechel A; Tieman, Jennifer J; Sladek, Ruth M

    2013-07-02

    PubMed translations of OvidSP Medline search filters offer searchers improved ease of access. They may also facilitate access to PubMed's unique content, including citations for the most recently published biomedical evidence. Retrieving this content requires a search strategy comprising natural language terms ('textwords'), rather than Medical Subject Headings (MeSH). We describe a reproducible methodology that uses a validated PubMed search filter translation to create a textword-only strategy to extend retrieval to PubMed's unique heart failure literature. We translated an OvidSP Medline heart failure search filter for PubMed and established version equivalence in terms of indexed literature retrieval. The PubMed version was then run within PubMed to identify citations retrieved by the filter's MeSH terms (Heart failure, Left ventricular dysfunction, and Cardiomyopathy). It was then rerun with the same MeSH terms restricted to searching on title and abstract fields (i.e. as 'textwords'). Citations retrieved by the MeSH search but not the textword search were isolated. Frequency analysis of their titles/abstracts identified natural language alternatives for those MeSH terms that performed less effectively as textwords. These terms were tested in combination to determine the best performing search string for reclaiming this 'lost set'. This string, restricted to searching on PubMed's unique content, was then combined with the validated PubMed translation to extend the filter's performance in this database. The PubMed heart failure filter retrieved 6829 citations. Of these, 834 (12%) failed to be retrieved when MeSH terms were converted to textwords. Frequency analysis of the 834 citations identified five high frequency natural language alternatives that could improve retrieval of this set (cardiac failure, cardiac resynchronization, left ventricular systolic dysfunction, left ventricular diastolic dysfunction, and LV dysfunction). Together these terms reclaimed

  2. Baseline levels of bioaerosols and volatile organic compounds around a municipal waste incinerator prior to the construction of a mechanical-biological treatment plant

    International Nuclear Information System (INIS)

    Vilavert, Lolita; Nadal, Marti; Inza, Isabel; Figueras, Maria J.; Domingo, Jose L.

    2009-01-01

    New waste management programs are currently aimed at developing alternative treatment technologies such as mechanical-biological treatment (MBT) and composting plants. However, there is still a high uncertainty concerning the chemical and microbiological risks for human health, not only for workers of these facilities, but also for the population living in the neighborhood. A new MBT plant is planned to be constructed adjacently to a municipal solid waste incinerator (MSWI) in Tarragona (Catalonia, Spain). In order to evaluate its potential impact and to differentiate the impacts of MSWI from those of the MBT when the latter is operative, a pre-operational survey was initiated by determining the concentrations of 20 volatile organic compounds (VOCs) and bioaerosols (total bacteria, Gram-negative bacteria, fungi and Aspergillus fumigatus) in airborne samples around the MSWI. The results indicated that the current concentrations of bioaerosols (ranges: 382-3882, 18-790, 44-926, and 3 for fungi at 25 deg. C, fungi at 37 deg. C, total bacteria, and Gram-negative bacteria, respectively) and VOCs (ranging from 0.9 to 121.2 μg/m 3 ) are very low in comparison to reported levels in indoor and outdoor air in composting and MBT plants, as well in urban and industrial zones. With the exception of total bacteria, no correlations were observed between the environmental concentrations of biological agents and the direction/distance from the facility. However, total bacteria presented significantly higher levels downwind. Moreover, a non-significant increase of VOCs was detected in sites closer to the incinerator, which means that the MSWI could have a very minor impact on the surrounding environment.

  3. Population growth, trophic level, and reproductive biology of two congeneric archer fishes (Toxotes chatareus, Hamilton 1822 and Toxotes jaculatrix, Pallas 1767) inhabiting Malaysian coastal waters.

    Science.gov (United States)

    Simon, K D; Bakar, Y; Samat, A; Zaidi, C C; Aziz, A; Mazlan, A G

    2009-12-01

    Population growth, trophic level, and some aspects of reproductive biology of two congeneric archer fish species, Toxotes chatareus and Toxotes jaculatrix, collected from Johor coastal waters, Malaysia, were studied. Growth pattern by length-weight relationship (W=aL(b)) for the sexes differed, and exhibited positive allometric growth (male, female and combined sexes of T. chatareus; female and combined sexes of T. jaculatrix) and isometric growth (male samples of T. jaculatrix only). Trophic levels of both species were analyzed based on 128 specimens. The results show that, in both species, crustaceans and insects were the most abundant prey items, and among crustaceans the red clawed crab Sesarma bidens and Formicidae family insects were the most represented taxa. The estimated mean trophic levels for T. chatareus and T. jaculatrix were 3.422+/-0.009 and 3.420+/-0.020, respectively, indicating that they are largely carnivores. Fecundity of T. chatareus ranged from 38 354 to 147 185 eggs for females with total length ranging from 14.5 to 22.5 cm and total body weight from 48.7 to 270.2 g, and T. jaculatrix 25 251 to 150 456 eggs for females with total length ranging from 12.2 to 23.0 cm and total body weight from 25.7 to 275.0 g. Differences in values of gonadosomatic and hepatosomatic indexes calculated for both species in this study may have resulted from uneven sample size ranges.

  4. Temporal variations in the gene expression levels of cyanobacterial anti-oxidant enzymes through geological history: implications for biological evolution during the Great Oxidation Event

    Science.gov (United States)

    Harada, M.; Furukawa, R.; Yokobori, S. I.; Tajika, E.; Yamagishi, A.

    2016-12-01

    expression levels of Fe-SOD occurred in response to the GOE. We propose that this is the first direct evidence of the evolution of cyanobacteria related to the rise of O2, and that the methodologies of ancestral promoter analysis used in this study can be a novel tools to reveal the biological adaptation to such a significant geologic event.

  5. Transparency in ovarian cancer clinical trial results: ClinicalTrials.gov versus PubMed, Embase and Google scholar.

    Science.gov (United States)

    Roberto, Anna; Radrezza, Silvia; Mosconi, Paola

    2018-04-10

    In recent years the question of the lack of transparency in clinical research has been debated by clinicians, researchers, citizens and their representatives, authors and publishers. This is particularly important for infrequent cancers such as ovarian cancer, where treatment still gives disappointing results in the majority of cases. Our aim was to assess the availability to the public of results in ClinicalTrials.gov, and the frequency of non-publication of results in ClinicalTrials.gov and in PubMed, Embase and Google Scholar. We collected all trials on ovarian cancer identified as "completed status" in the ClinicalTrials.gov registry on 17 January 2017. We checked the availability of the results in ClinicalTrials.gov and systematically identified published manuscripts on results. Out of 2725 trials on ovarian cancer identified, 752 were classified as "completed status". In those closed between 2008 and 2015, excluding phase I, the frequency of results in ClinicalTrials.gov was 35%. Of the 752 completed studies the frequency of published results in PubMed, Embase or Google Scholar ranged from 57.9% to 69.7% in the last years. These findings show a lack of transparency and credibility of research. Citizens or patients' representatives, with the medical community, should continuously support initiatives to improve the publication and dissemination of clinical study results.

  6. Performance evaluation of unified medical language system®'s synonyms expansion to query PubMed

    Directory of Open Access Journals (Sweden)

    Griffon Nicolas

    2012-02-01

    Full Text Available Abstract Background PubMed is the main access to medical literature on the Internet. In order to enhance the performance of its information retrieval tools, primarily non-indexed citations, the authors propose a method: expanding users' queries using Unified Medical Language System' (UMLS synonyms i.e. all the terms gathered under one unique Concept Unique Identifier. Methods This method was evaluated using queries constructed to emphasize the differences between this new method and the current PubMed automatic term mapping. Four experts assessed citation relevance. Results Using UMLS, we were able to retrieve new citations in 45.5% of queries, which implies a small increase in recall. The new strategy led to a heterogeneous 23.7% mean increase in non-indexed citation retrieved. Of these, 82% have been published less than 4 months earlier. The overall mean precision was 48.4% but differed according to the evaluators, ranging from 36.7% to 88.1% (Inter rater agreement was poor: kappa = 0.34. Conclusions This study highlights the need for specific search tools for each type of user and use-cases. The proposed strategy may be useful to retrieve recent scientific advancement.

  7. Lost in translation? A multilingual Query Builder improves the quality of PubMed queries: a randomised controlled trial.

    Science.gov (United States)

    Schuers, Matthieu; Joulakian, Mher; Kerdelhué, Gaetan; Segas, Léa; Grosjean, Julien; Darmoni, Stéfan J; Griffon, Nicolas

    2017-07-03

    MEDLINE is the most widely used medical bibliographic database in the world. Most of its citations are in English and this can be an obstacle for some researchers to access the information the database contains. We created a multilingual query builder to facilitate access to the PubMed subset using a language other than English. The aim of our study was to assess the impact of this multilingual query builder on the quality of PubMed queries for non-native English speaking physicians and medical researchers. A randomised controlled study was conducted among French speaking general practice residents. We designed a multi-lingual query builder to facilitate information retrieval, based on available MeSH translations and providing users with both an interface and a controlled vocabulary in their own language. Participating residents were randomly allocated either the French or the English version of the query builder. They were asked to translate 12 short medical questions into MeSH queries. The main outcome was the quality of the query. Two librarians blind to the arm independently evaluated each query, using a modified published classification that differentiated eight types of errors. Twenty residents used the French version of the query builder and 22 used the English version. 492 queries were analysed. There were significantly more perfect queries in the French group vs. the English group (respectively 37.9% vs. 17.9%; p PubMed queries in particular for researchers whose first language is not English.

  8. What is covered by "cancer rehabilitation" in PubMed? A review of randomized controlled trials 1990-2011.

    Science.gov (United States)

    Gudbergsson, Sævar Berg; Dahl, Alv A; Loge, Jon Håvard; Thorsen, Lene; Oldervoll, Line M; Grov, Ellen K

    2015-02-01

    This focused review examines randomized controlled studies included by the term "cancer rehabilitation" in PubMed. The research questions concern the type of interventions performed and their methodological quality. Using the Medical Subject Headings (MeSH) terms: neoplasm AND rehabilitation, all articles with randomized controlled studies that included adult cancer patients, written in English, were extracted from PubMed. Papers covering physical exercise, psychiatric/psychological treatment or social support only were excluded as they had been reviewed recently. Abstracts and papers were assessed by 3 pairs of reviewers, and descriptive information was extracted systematically. Methodological quality was rated on a 10-item index scale, and the cut-off for acceptable quality was set at ≥ 8. A total of 132 (19%) of the 683 identified papers met the eligibility criteria and were assessed in detail. The papers were grouped into 5 thematic categories: 44 physical; 15 art and expressive; 47 psycho-educative; 21 emotionally supportive; and 5 others. Good quality of design was observed in 32 studies, 18 of them uni-dimensional and 14 multi-dimensional. Published randomized controlled studies on cancer rehabilitation are heterogeneous in terms of content and samples, and are mostly characterized by suboptimal design quality. Future studies should be more specific and well-designed with sufficient statistical strength.

  9. Comparison of the efficacy of three PubMed search filters in finding randomized controlled trials to answer clinical questions.

    Science.gov (United States)

    Yousefi-Nooraie, Reza; Irani, Shirin; Mortaz-Hedjri, Soroush; Shakiba, Behnam

    2013-10-01

    The aim of this study was to compare the performance of three search methods in the retrieval of relevant clinical trials from PubMed to answer specific clinical questions. Included studies of a sample of 100 Cochrane reviews which recorded in PubMed were considered as the reference standard. The search queries were formulated based on the systematic review titles. Precision, recall and number of retrieved records for limiting the results to clinical trial publication type, and using sensitive and specific clinical queries filters were compared. The number of keywords, presence of specific names of intervention and syndrome in the search keywords were used in a model to predict the recalls and precisions. The Clinical queries-sensitive search strategy retrieved the largest number of records (33) and had the highest recall (41.6%) and lowest precision (4.8%). The presence of specific intervention name was the only significant predictor of all recalls and precisions (P = 0.016). The recall and precision of combination of simple clinical search queries and methodological search filters to find clinical trials in various subjects were considerably low. The limit field strategy yielded in higher precision and fewer retrieved records and approximately similar recall, compared with the clinical queries-sensitive strategy. Presence of specific intervention name in the search keywords increased both recall and precision. © 2010 John Wiley & Sons Ltd.

  10. Alteration of serum thymus and activation-regulated chemokine level during biologic therapy for psoriasis: Possibility as a marker reflecting favorable response to anti-interleukin-17A agents.

    Science.gov (United States)

    Shibuya, Takashi; Honma, Masaru; Iinuma, Shin; Iwasaki, Takeshi; Takahashi, Hidetoshi; Ishida-Yamamoto, Akemi

    2018-06-01

    Biologics show great efficacy in treating psoriasis, a chronic inflammatory skin disease. The high cost and side-effects of biologics, dose-reduction, elongation of administration interval and suspension are possible options. However, there has been no reliable biomarker we can use when we consider these moderations in therapy. This study was conducted to test the possibility of using serum thymus and activation-regulated chemokine (TARC) level as an indicator for step down of biologic therapy. Serum TARC level was measured in 70 psoriatic patients at Asahikawa Medical University, and a correlation of TARC and severity of skin lesions was analyzed. Referring to serum TARC level, psoriatic patients can be divided into two groups. One is a population in which serum TARC level is positively correlated with severity of skin lesions, and the other is a population with low psoriatic severity and high TARC level. Serum TARC level was higher in the group that achieved PASI-clear with biologics than in the group which did not achieve PASI-clear. Among biologics, the group treated with secukinumab, an anti-interleukin (IL)-17A agent, showed significantly higher TARC level compared with the group treated with anti-tumor necrosis factor agents. In certain populations achieving PASI-clear, serum TARC level may be a potent marker reflecting better response to IL-17A inhibitors, and in this case step down of treatment for psoriasis is possible. © 2018 Japanese Dermatological Association.

  11. pubmed.mineR

    Indian Academy of Sciences (India)

    Network of association between terms of abstracts year wise for the diseases or .... 12. Genewise(): To search the number of abstracts for genes. This function will .... The commonly used English words, punctuation marks and white spaces are ...

  12. How Twitter Is Studied in the Medical Professions: A Classification of Twitter Papers Indexed in PubMed.

    Science.gov (United States)

    Williams, Shirley Ann; Terras, Melissa; Warwick, Claire

    2013-01-01

    Since their inception, Twitter and related microblogging systems have provided a rich source of information for researchers and have attracted interest in their affordances and use. Since 2009 PubMed has included 123 journal articles on medicine and Twitter, but no overview exists as to how the field uses Twitter in research. This paper aims to identify published work relating to Twitter within the fields indexed by PubMed, and then to classify it. This classification will provide a framework in which future researchers will be able to position their work, and to provide an understanding of the current reach of research using Twitter in medical disciplines. Papers on Twitter and related topics were identified and reviewed. The papers were then qualitatively classified based on the paper's title and abstract to determine their focus. The work that was Twitter focused was studied in detail to determine what data, if any, it was based on, and from this a categorization of the data set size used in the studies was developed. Using open coded content analysis additional important categories were also identified, relating to the primary methodology, domain, and aspect. As of 2012, PubMed comprises more than 21 million citations from biomedical literature, and from these a corpus of 134 potentially Twitter related papers were identified, eleven of which were subsequently found not to be relevant. There were no papers prior to 2009 relating to microblogging, a term first used in 2006. Of the remaining 123 papers which mentioned Twitter, thirty were focused on Twitter (the others referring to it tangentially). The early Twitter focused papers introduced the topic and highlighted the potential, not carrying out any form of data analysis. The majority of published papers used analytic techniques to sort through thousands, if not millions, of individual tweets, often depending on automated tools to do so. Our analysis demonstrates that researchers are starting to use knowledge

  13. Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface.

    Science.gov (United States)

    Simon, Michael; Hausner, Elke; Klaus, Susan F; Dunton, Nancy E

    2010-08-23

    The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized terminology (e.g. by consistent use of the

  14. How Twitter Is Studied in the Medical Professions: A Classification of Twitter Papers Indexed in PubMed

    Science.gov (United States)

    2013-01-01

    Background Since their inception, Twitter and related microblogging systems have provided a rich source of information for researchers and have attracted interest in their affordances and use. Since 2009 PubMed has included 123 journal articles on medicine and Twitter, but no overview exists as to how the field uses Twitter in research. Objective This paper aims to identify published work relating to Twitter within the fields indexed by PubMed, and then to classify it. This classification will provide a framework in which future researchers will be able to position their work, and to provide an understanding of the current reach of research using Twitter in medical disciplines. Methods Papers on Twitter and related topics were identified and reviewed. The papers were then qualitatively classified based on the paper’s title and abstract to determine their focus. The work that was Twitter focused was studied in detail to determine what data, if any, it was based on, and from this a categorization of the data set size used in the studies was developed. Using open coded content analysis additional important categories were also identified, relating to the primary methodology, domain, and aspect. Results As of 2012, PubMed comprises more than 21 million citations from biomedical literature, and from these a corpus of 134 potentially Twitter related papers were identified, eleven of which were subsequently found not to be relevant. There were no papers prior to 2009 relating to microblogging, a term first used in 2006. Of the remaining 123 papers which mentioned Twitter, thirty were focused on Twitter (the others referring to it tangentially). The early Twitter focused papers introduced the topic and highlighted the potential, not carrying out any form of data analysis. The majority of published papers used analytic techniques to sort through thousands, if not millions, of individual tweets, often depending on automated tools to do so. Our analysis demonstrates that

  15. Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals.

    Science.gov (United States)

    Susaki, Etsuo A; Ueda, Hiroki R

    2016-01-21

    Organism-level systems biology aims to identify, analyze, control and design cellular circuits in organisms. Many experimental and computational approaches have been developed over the years to allow us to conduct these studies. Some of the most powerful methods are based on using optical imaging in combination with fluorescent labeling, and for those one of the long-standing stumbling blocks has been tissue opacity. Recently, the solutions to this problem have started to emerge based on whole-body and whole-organ clearing techniques that employ innovative tissue-clearing chemistry. Here, we review these advancements and discuss how combining new clearing techniques with high-performing fluorescent proteins or small molecule tags, rapid volume imaging and efficient image informatics is resulting in comprehensive and quantitative organ-wide, single-cell resolution experimental data. These technologies are starting to yield information on connectivity and dynamics in cellular circuits at unprecedented resolution, and bring us closer to system-level understanding of physiology and diseases of complex mammalian systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. To what extend the dam dredging can influence the background level of metals in the Rhine River: using chemical and biological long-term monitoring to answer

    Directory of Open Access Journals (Sweden)

    Lebrun Jérémie D.

    2017-01-01

    Full Text Available Dredging generates remobilisation of sediments contaminated by non-degradable compounds such as metals, to which aquatic organisms can be exposed. This study aims at assessing the environmental impact of sediments remobilised in the Rhine River (France during the dredging of Marckolsheim dam by pumping/dilution in 2013 on metal speciation and organisms' exposure. The monitoring coupling chemical and biological tools was performed 2 years before dredging operation on 2 sampling sites, upstream and downstream from the discharge of pumping/dilution, to acquire data on the natural variability of labile (DGT as passive samplers, dissolved and particulate concentrations of Cd, Co, Cr, Cu, Ni, Mn, Pb and Zn in Rhine during full hydrological cycles. In parallel, size-calibrated zebra mussels were transplanted at both sites to monitor continuously metal bioavailability from particulate and dissolved fractions. This long-term monitoring allowed the establishment of reference baselines of Rhine water and mussels' contamination levels and subsequently, the detection of averred environmental changes due to the dredging. Indeed, Co and Mn accumulations in mussels exposed to the discharge were consistent with increasing labile species in Rhine whereas ones of Cr and Pb were likely due to an enhanced particulate bioavailability. Whatever the exposure route, the mussels recovered their basal metal contents 2 weeks after the end of dredging, suggesting a transient impact of sediment remobilisation on bioaccumulation. This long-term monitoring highlights the interest of coupling chemical and biological time-integrated tools for a better assessment of environmental risks because metallic exchanges between organisms and their media are complex and metal-specific.

  17. Radiation biology. Chapter 20

    Energy Technology Data Exchange (ETDEWEB)

    Wondergem, J. [International Atomic Energy Agency, Vienna (Austria)

    2014-09-15

    Radiation biology (radiobiology) is the study of the action of ionizing radiations on living matter. This chapter gives an overview of the biological effects of ionizing radiation and discusses the physical, chemical and biological variables that affect dose response at the cellular, tissue and whole body levels at doses and dose rates relevant to diagnostic radiology.

  18. Bibliometric analysis of the Korean Journal of Parasitology: measured from SCI, PubMed, Scopus, and Synapse databases.

    Science.gov (United States)

    Lee, Choon Shil

    2009-10-01

    The Korean Journal of Parasitology (KJP) is the official journal of the Korean Society for Parasitology which is celebrating its 50th anniversary in 2009. To assess the contributions and achievements of the KJP, bibliometric analysis was conducted based on the citation data retrieved from 4 major databases; SCI, PubMed, Synapse, and Scopus. It was found that the KJP articles were constantly cited by the articles published in major international journals represented in these databases. More than 60% of 1,370 articles published in the KJP from 1963 to June 2009 were cited at least once by SCI articles. The overall average times cited by SCI articles are 2.6. The rate is almost 3 times higher for the articles published in the last 10 years compared to 1.0 for the articles of the 1960s. The SCI journal impact factor for 2008 is calculated as 0.871. It is increasing and it is expected to increase further with the introduction of the KJP in the database in 2008. The more realistic h-indices were measured from the study data set covering all the citations to the KJP; 17 for SCI, 6 for PubMed, 19 for Synapse, and 17 for Scopus. Synapse extensively picked up the citations to the earlier papers not retrievable from the other 3 databases. It identified many papers published in the 1960s and in the 1980s which have been cited heavily, proving the central role of the KJP in the dissemination of the important research findings over the last 5 decades.

  19. PubMed search strategies for the identification of etiologic associations between hypothalamic-pituitary disorders and other medical conditions.

    Science.gov (United States)

    Guaraldi, Federica; Grottoli, Silvia; Arvat, Emanuela; Mattioli, Stefano; Ghigo, Ezio; Gori, Davide

    2013-12-01

    Biomedical literature has enormously grown in the last decades and become broadly available through online databases. Ad-hoc search methods, created on the basis of research field and goals, are required to enhance the quality of searching. Aim of this study was to formulate efficient, evidence-based PubMed search strategies to retrieve articles assessing etiologic associations between a condition of interest and hypothalamic-pituitary disorders (HPD). Based on expert knowledge, 17 MeSH (Medical Subjects Headings) and 79 free terms related to HPD were identified to search PubMed. Using random samples of abstracts retrieved by each term, we estimated the proportion of articles containing pertinent information and formulated two strings (one more specific, one more sensitive) for the detection of articles focusing on the etiology of HPD, that were then applied to retrieve articles identifying possible etiologic associations between HPD and three diseases (malaria, LHON and celiac disease) considered not associated to HPD, and define the number of abstracts needed to read (NNR) to find one potentially pertinent article. We propose two strings: one sensitive string derived from the combination of articles providing the largest literature coverage in the field and one specific including combined terms retrieving ≥40% of potentially pertinent articles. NNR were 2.1 and 1.6 for malaria, 3.36 and 2.29 for celiac disease, 2.8 and 2.2 for LHON, respectively. For the first time, two reliable, readily applicable strings are proposed for the retrieval of medical literature assessing putative etiologic associations between HPD and other medical conditions of interest.

  20. Overweight and Obesity in Southern Italy: their association with social and life-style characteristics and their effect on levels of biologic markers.

    Science.gov (United States)

    Osella, Alberto R; Díaz, María Del Pilar; Cozzolongo, Rafaelle; Bonfiglio, Caterina; Franco, Isabella; Abrescia, Daniela Isabel; Bianco, Antonella; Giampiero, Elba Silvana; Petruzzi, José; Elsa, Lanzilota; Mario, Correale; Mastrosimni, Anna María; Giocchino, Leandro

    2014-01-01

    In the last decades, overweight and obesity have been transformed from minor public health issues to a major threat to public health affecting the most affluent societies and also the less developed ones. To estimate overweight-obesity prevalence in adults, their association with some social determinants and to assess the effect of these two conditions on levels of biologic and biochemical characteristics, by means of a population-based study. A random sample of the general population of Putignano was drawn. All participants completed a general pre-coded and a Food Frequency questionnaire; anthropometric measures were taken and a venous blood sample was drawn. All subjects underwent liver ultra-sonography. Data description was done by means of tables and then Quantile Regression was performed. Overall prevalence of overweight and obesity were 34.5% and 16.1% respectively. Both overweight and obesity were more frequent among male, married and low socio-economic position subjects. There were increasing frequencies of normal weight with higher levels of education. Overweight and obese subjects had more frequently Nonalcoholic Fatty Liver Disease, Hypertension and altered biochemical markers. Quantile regression showed a statistically significant association of age with overweight and obesity (maximum about 64.8 yo), gender (female) and low levels of education in both overweight and obesity. More than 10 gr/day of wine intake was associated with overweight. The prevention and treatment of overweight/obesity on a population wide basis are needed. Population-based strategies should also improve social and physical environmental contexts for healthful lifestyles.

  1. Artificial neural network modelling of biological oxygen demand in rivers at the national level with input selection based on Monte Carlo simulations.

    Science.gov (United States)

    Šiljić, Aleksandra; Antanasijević, Davor; Perić-Grujić, Aleksandra; Ristić, Mirjana; Pocajt, Viktor

    2015-03-01

    Biological oxygen demand (BOD) is the most significant water quality parameter and indicates water pollution with respect to the present biodegradable organic matter content. European countries are therefore obliged to report annual BOD values to Eurostat; however, BOD data at the national level is only available for 28 of 35 listed European countries for the period prior to 2008, among which 46% of data is missing. This paper describes the development of an artificial neural network model for the forecasting of annual BOD values at the national level, using widely available sustainability and economical/industrial parameters as inputs. The initial general regression neural network (GRNN) model was trained, validated and tested utilizing 20 inputs. The number of inputs was reduced to 15 using the Monte Carlo simulation technique as the input selection method. The best results were achieved with the GRNN model utilizing 25% less inputs than the initial model and a comparison with a multiple linear regression model trained and tested using the same input variables using multiple statistical performance indicators confirmed the advantage of the GRNN model. Sensitivity analysis has shown that inputs with the greatest effect on the GRNN model were (in descending order) precipitation, rural population with access to improved water sources, treatment capacity of wastewater treatment plants (urban) and treatment of municipal waste, with the last two having an equal effect. Finally, it was concluded that the developed GRNN model can be useful as a tool to support the decision-making process on sustainable development at a regional, national and international level.

  2. Effect of startup circuit exercise on derivatives reactive oxygen metabolites, biological antioxidant potential levels and physical fitness of adolescents boys with intellectual disabilities.

    Science.gov (United States)

    Kim, Chang-Gyun; Lee, Jin-Seok

    2016-10-01

    The purpose of this study was to examine the effect of starup circuit exercise program on derivatives reactive oxygen metabolite (d-ROM) and biological antioxidant potential (BAP) levels and physical fitness of adolescents with intellectual disabilities, and to sugesst exercise programs to promote the health and physical development of such adolescents. Twelve students with intellectual disabilities were divided into two groups; circuit exercise group (CE group: n=6; age, 14.83±0.98 years; height, 163.83±5.78 cm; body mass, 67.08±3.32 kg; %Fat, 25.68±2.42), control group (CON group: n=6; age: 15.00±0.63 years; height, 162.33±4.41 cm; body mass, 67.50±3.62 kg; %Fat, 26.96±2.06). The CE group performed the CE program 4 times a week over a 12-week period. The CON group maintained their activities of daily living. The following were measured before and after intervention: physical fitness by before and after the completion of the training programm, and were measured and blood samples were assessed. The results of the study indicate that the 12-week CE program increased significantly physical fitness ( P <0.05). Furthermore, This study proved that the CE program improved physical fitness, and reduced the d-ROM levels, and increased the BAP levels of the adolescents with intellectual disabilities. Therefore, it may enhance the health and physical development of adolescents boys with intellectual disabilities.

  3. A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records.

    Science.gov (United States)

    Jiang, Li; Edwards, Stefan M; Thomsen, Bo; Workman, Christopher T; Guldbrandtsen, Bernt; Sørensen, Peter

    2014-09-24

    Prioritizing genetic variants is a challenge because disease susceptibility loci are often located in genes of unknown function or the relationship with the corresponding phenotype is unclear. A global data-mining exercise on the biomedical literature can establish the phenotypic profile of genes with respect to their connection to disease phenotypes. The importance of protein-protein interaction networks in the genetic heterogeneity of common diseases or complex traits is becoming increasingly recognized. Thus, the development of a network-based approach combined with phenotypic profiling would be useful for disease gene prioritization. We developed a random-set scoring model and implemented it to quantify phenotype relevance in a network-based disease gene-prioritization approach. We validated our approach based on different gene phenotypic profiles, which were generated from PubMed abstracts, OMIM, and GeneRIF records. We also investigated the validity of several vocabulary filters and different likelihood thresholds for predicted protein-protein interactions in terms of their effect on the network-based gene-prioritization approach, which relies on text-mining of the phenotype data. Our method demonstrated good precision and sensitivity compared with those of two alternative complex-based prioritization approaches. We then conducted a global ranking of all human genes according to their relevance to a range of human diseases. The resulting accurate ranking of known causal genes supported the reliability of our approach. Moreover, these data suggest many promising novel candidate genes for human disorders that have a complex mode of inheritance. We have implemented and validated a network-based approach to prioritize genes for human diseases based on their phenotypic profile. We have devised a powerful and transparent tool to identify and rank candidate genes. Our global gene prioritization provides a unique resource for the biological interpretation of data

  4. A Western blot-based investigation of the yeast secretory pathway designed for an intermediate-level undergraduate cell biology laboratory.

    Science.gov (United States)

    Hood-Degrenier, Jennifer K

    2008-01-01

    The movement of newly synthesized proteins through the endomembrane system of eukaryotic cells, often referred to generally as the secretory pathway, is a topic covered in most intermediate-level undergraduate cell biology courses. An article previously published in this journal described a laboratory exercise in which yeast mutants defective in two distinct steps of protein secretion were differentiated using a genetic reporter designed specifically to identify defects in the first step of the pathway, the insertion of proteins into the endoplasmic reticulum (Vallen, 2002). We have developed two versions of a Western blotting assay that serves as a second way of distinguishing the two secretory mutants, which we pair with the genetic assay in a 3-wk laboratory module. A quiz administered before and after students participated in the lab activities revealed significant postlab gains in their understanding of the secretory pathway and experimental techniques used to study it. A second survey administered at the end of the lab module assessed student perceptions of the efficacy of the lab activities; the results of this survey indicated that the experiments were successful in meeting a set of educational goals defined by the instructor.

  5. Comparative Analysis of the Combined Effects of Different Water and Phosphate Levels on Growth and Biological Nitrogen Fixation of Nine Cowpea Varieties.

    Science.gov (United States)

    Jemo, Martin; Sulieman, Saad; Bekkaoui, Faouzi; Olomide, Oluwatosin A K; Hashem, Abeer; Abd Allah, Elsayed Fathi; Alqarawi, Abdulaziz A; Tran, Lam-Son Phan

    2017-01-01

    Water deficit and phosphate (Pi) deficiency adversely affect growth and biological nitrogen fixation (BNF) of legume crops. In this study, we examined the impact of interaction between soil water conditions and available soil-Pi levels on growth, nodule development and BNF potential of nine cowpea varieties grown on dry savanna soils. In our experimental design, soils with different available soil-Pi levels, i.e., low, moderate, and high soil-Pi levels, collected from various farming fields were used to grow nine cowpea varieties under well-watered and water-deficit conditions. Significant and severe water deficit-damaging effects on BNF, nodulation, growth, levels of plant-nitrogen (N) and -phosphorus (P), as well as shoot relative water content and chlorophyll content of cowpea plants were observed. Under well-watered and high available soil-Pi conditions, cowpea varieties IT07K-304-9 and Dan'Ila exhibited significantly higher BNF potential and dry biomass, as well as plant-N and -P contents compared with other tested ones. Significant genotypic variations among the cowpeas were recorded under low available soil-Pi and water-deficit conditions in terms of the BNF potential. Principal component (PC) analysis revealed that varieties IT04K-339-1, IT07K-188-49, IT07K-304-9, and IT04K-405-5 were associated with PC1, which was better explained by performance for nodulation, plant biomass, plant-N, plant-P, and BNF potential under the combined stress of water deficit and Pi deficiency, thereby offering prospects for development of varieties with high growth and BNF traits that are adaptive to such stress conditions in the region. On another hand, variety Dan'Ila was significantly related to PC2 that was highly explained by the plant shoot/root ratio and chlorophyll content, suggesting the existence of physiological and morphological adjustments to cope with water deficit and Pi deficiency for this particular variety. Additionally, increases in soil-Pi availability led

  6. Elevated CO2 enhances biological contributions to elevation change in coastal wetlands by offsetting stressors associated with sea-level rise

    Science.gov (United States)

    Cherry, J.A.; McKee, K.L.; Grace, J.B.

    2009-01-01

    mechanisms contributing to marsh elevation change, including amelioration of salt stress by elevated CO2 and the importance of plant production and shoot-base expansion for elevation gain. Identification of biological processes contributing to elevation change is an important first step in developing comprehensive models that permit more accurate predictions of whether coastal marshes will persist with continued sea-level rise or become submerged. ?? 2008 The Authors.

  7. Comparative Analysis of the Combined Effects of Different Water and Phosphate Levels on Growth and Biological Nitrogen Fixation of Nine Cowpea Varieties

    Science.gov (United States)

    Jemo, Martin; Sulieman, Saad; Bekkaoui, Faouzi; Olomide, Oluwatosin A. K.; Hashem, Abeer; Abd_Allah, Elsayed Fathi; Alqarawi, Abdulaziz A.; Tran, Lam-Son Phan

    2017-01-01

    Water deficit and phosphate (Pi) deficiency adversely affect growth and biological nitrogen fixation (BNF) of legume crops. In this study, we examined the impact of interaction between soil water conditions and available soil-Pi levels on growth, nodule development and BNF potential of nine cowpea varieties grown on dry savanna soils. In our experimental design, soils with different available soil-Pi levels, i.e., low, moderate, and high soil-Pi levels, collected from various farming fields were used to grow nine cowpea varieties under well-watered and water-deficit conditions. Significant and severe water deficit-damaging effects on BNF, nodulation, growth, levels of plant-nitrogen (N) and -phosphorus (P), as well as shoot relative water content and chlorophyll content of cowpea plants were observed. Under well-watered and high available soil-Pi conditions, cowpea varieties IT07K-304-9 and Dan'Ila exhibited significantly higher BNF potential and dry biomass, as well as plant-N and -P contents compared with other tested ones. Significant genotypic variations among the cowpeas were recorded under low available soil-Pi and water-deficit conditions in terms of the BNF potential. Principal component (PC) analysis revealed that varieties IT04K-339-1, IT07K-188-49, IT07K-304-9, and IT04K-405-5 were associated with PC1, which was better explained by performance for nodulation, plant biomass, plant-N, plant-P, and BNF potential under the combined stress of water deficit and Pi deficiency, thereby offering prospects for development of varieties with high growth and BNF traits that are adaptive to such stress conditions in the region. On another hand, variety Dan'Ila was significantly related to PC2 that was highly explained by the plant shoot/root ratio and chlorophyll content, suggesting the existence of physiological and morphological adjustments to cope with water deficit and Pi deficiency for this particular variety. Additionally, increases in soil-Pi availability led

  8. Comparative Analysis of the Combined Effects of Different Water and Phosphate Levels on Growth and Biological Nitrogen Fixation of Nine Cowpea Varieties

    Directory of Open Access Journals (Sweden)

    Martin Jemo

    2017-12-01

    Full Text Available Water deficit and phosphate (Pi deficiency adversely affect growth and biological nitrogen fixation (BNF of legume crops. In this study, we examined the impact of interaction between soil water conditions and available soil-Pi levels on growth, nodule development and BNF potential of nine cowpea varieties grown on dry savanna soils. In our experimental design, soils with different available soil-Pi levels, i.e., low, moderate, and high soil-Pi levels, collected from various farming fields were used to grow nine cowpea varieties under well-watered and water-deficit conditions. Significant and severe water deficit-damaging effects on BNF, nodulation, growth, levels of plant-nitrogen (N and -phosphorus (P, as well as shoot relative water content and chlorophyll content of cowpea plants were observed. Under well-watered and high available soil-Pi conditions, cowpea varieties IT07K-304-9 and Dan'Ila exhibited significantly higher BNF potential and dry biomass, as well as plant-N and -P contents compared with other tested ones. Significant genotypic variations among the cowpeas were recorded under low available soil-Pi and water-deficit conditions in terms of the BNF potential. Principal component (PC analysis revealed that varieties IT04K-339-1, IT07K-188-49, IT07K-304-9, and IT04K-405-5 were associated with PC1, which was better explained by performance for nodulation, plant biomass, plant-N, plant-P, and BNF potential under the combined stress of water deficit and Pi deficiency, thereby offering prospects for development of varieties with high growth and BNF traits that are adaptive to such stress conditions in the region. On another hand, variety Dan'Ila was significantly related to PC2 that was highly explained by the plant shoot/root ratio and chlorophyll content, suggesting the existence of physiological and morphological adjustments to cope with water deficit and Pi deficiency for this particular variety. Additionally, increases in soil

  9. Analysis of queries sent to PubMed at the point of care: Observation of search behaviour in a medical teaching hospital

    Science.gov (United States)

    Hoogendam, Arjen; Stalenhoef, Anton FH; Robbé, Pieter F de Vries; Overbeke, A John PM

    2008-01-01

    Background The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted. Knowing what aspects of queries are likely to retrieve relevant articles can increase the effectiveness of PubMed searches. The objectives of our study were to identify queries that are likely to retrieve relevant articles by relating PubMed search techniques and tools to the number of articles retrieved and the selection of articles for further reading. Methods This was a prospective observational study of queries regarding patient-related problems sent to PubMed by residents and internists in internal medicine working in an Academic Medical Centre. We analyzed queries, search results, query tools (Mesh, Limits, wildcards, operators), selection of abstract and full-text for further reading, using a portal that mimics PubMed. Results PubMed was used to solve 1121 patient-related problems, resulting in 3205 distinct queries. Abstracts were viewed in 999 (31%) of these queries, and in 126 (39%) of 321 queries using query tools. The average term count per query was 2.5. Abstracts were selected in more than 40% of queries using four or five terms, increasing to 63% if the use of four or five terms yielded 2–161 articles. Conclusion Queries sent to PubMed by physicians at our hospital during daily medical care contain fewer than three terms. Queries using four to five terms, retrieving less than 161 article titles, are most likely to result in abstract viewing. PubMed search tools are used infrequently by our population and are less effective than the use of four or five terms. Methods to facilitate the formulation of precise queries, using more relevant terms, should be the focus of education and research. PMID:18816391

  10. Systems Biology and Health Systems Complexity in;

    NARCIS (Netherlands)

    Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

    2016-01-01

    Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

  11. Bibliometric Analysis of Traditional Chinese Medicine Scientific Production between 1982 and 2016 Indexed in PubMed.

    Science.gov (United States)

    Consentino, Ricardo; Santos, Maria João; Matos, Luís Carlos; Machado, Jorge Pereira

    2018-05-03

    Background: Traditional Chinese medicine (TCM) may be understood as a system of sensations and findings designed to establish the functional vegetative state of the body. This state may be treated by several therapeutic methods such as acupuncture, Chinese pharmacotherapy, dietetics, Tuina , and Qigong . Nowadays, as a result of several evidence-based reported beneficial effects over specific pathological conditions, there is an increasing tendency to integrate some of these practices in Western medicine. The main goal of this study was to perform a bibliometric analysis of TCM scientific production between 1982 and 2016 indexed in PubMed, by analyzing several parameters including time and location distribution, publication quality, experimental design, and treatment methods. Methods: The methodology was based on the quantitative inventory of published scientific research indexed in PubMed medical subject headings (MeSH), sorted within the broad term “Traditional Chinese Medicine” and integrating the following criteria as limit filters: “Species: Humans”, “Article Type: Clinical Trial”. In addition, the articles’ triage was ruled by temporal limitations set between 1945 and 2016. Results: The overall analysis of data allowed observation of an average annual growth of approximately 33%, with a productive peak of 122 articles in 2007. The scientific production was distributed in 27 countries, led by China (76.1%), followed by the United States of America (3.0%) and South Korea (2.1%). A significant amount of references were published in Chinese journals: more than 50%; however, these journals had a low impact factor. The most cited treatments in the keywords section of the articles were phytotherapy (55%) and acupuncture (40%). Conclusion: The increasing demand for TCM seems to be due to factors such as lower side effects and greater efficacy in some patients not responding well to conventional therapy. As a result, a considerable amount of TCM science

  12. Biological Agents

    Science.gov (United States)

    ... E-Tools Safety and Health Topics / Biological Agents Biological Agents This page requires that javascript be enabled ... 202) 693-2300 if additional assistance is required. Biological Agents Menu Overview In Focus: Ebola Frederick A. ...

  13. LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.

    Science.gov (United States)

    Allot, Alexis; Peng, Yifan; Wei, Chih-Hsuan; Lee, Kyubum; Phan, Lon; Lu, Zhiyong

    2018-05-14

    The identification and interpretation of genomic variants play a key role in the diagnosis of genetic diseases and related research. These tasks increasingly rely on accessing relevant manually curated information from domain databases (e.g. SwissProt or ClinVar). However, due to the sheer volume of medical literature and high cost of expert curation, curated variant information in existing databases are often incomplete and out-of-date. In addition, the same genetic variant can be mentioned in publications with various names (e.g. 'A146T' versus 'c.436G>A' versus 'rs121913527'). A search in PubMed using only one name usually cannot retrieve all relevant articles for the variant of interest. Hence, to help scientists, healthcare professionals, and database curators find the most up-to-date published variant research, we have developed LitVar for the search and retrieval of standardized variant information. In addition, LitVar uses advanced text mining techniques to compute and extract relationships between variants and other associated entities such as diseases and chemicals/drugs. LitVar is publicly available at https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar.

  14. Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed.

    Science.gov (United States)

    Capuzzi, Stephen J; Thornton, Thomas E; Liu, Kammy; Baker, Nancy; Lam, Wai In; O'Banion, Colin P; Muratov, Eugene N; Pozefsky, Diane; Tropsha, Alexander

    2018-02-26

    Elucidation of the mechanistic relationships between drugs, their targets, and diseases is at the core of modern drug discovery research. Thousands of studies relevant to the drug-target-disease (DTD) triangle have been published and annotated in the Medline/PubMed database. Mining this database affords rapid identification of all published studies that confirm connections between vertices of this triangle or enable new inferences of such connections. To this end, we describe the development of Chemotext, a publicly available Web server that mines the entire compendium of published literature in PubMed annotated by Medline Subject Heading (MeSH) terms. The goal of Chemotext is to identify all known DTD relationships and infer missing links between vertices of the DTD triangle. As a proof-of-concept, we show that Chemotext could be instrumental in generating new drug repurposing hypotheses or annotating clinical outcomes pathways for known drugs. The Chemotext Web server is freely available at http://chemotext.mml.unc.edu .

  15. Gendered discourses of youth sexualities--an exploration of PubMed articles on prevention of sexually transmissible infections.

    Science.gov (United States)

    Johansson, Eva E; Alex, Lena; Christianson, Monica

    2014-10-01

    To explore how gender is addressed in medical articles on the prevention of sexually transmissible infections (STI) among adolescents. Sixtyone articles were retrieved from a PubMed search and scrutinized by qualitative content analysis. Most articles were affiliated with North American research institutions, but there were also reports from Europe, Africa, South America, and Asia. Gender turned up in the following four recurrent discourses: Gendered Receptiveness for Information, Stereotyped Heterosexual Expectations, Power Imbalance in Sexual Relations, and Gendered Prevention Approaches. Young women were described as knowledgeable, communicative, and responsible, but at risk because of feminine ideals and a lack of negotiating power. Men were described as less informed, more reluctant to discuss, and more risk taking due to masculine ideals and power dominance. Prevention approaches concerned how to postpone sex and/or tailor gender-sensitive programs for specific groups of young women and men. Researchers' own gender expectations might have a substantial impact on how sex and sexual health is considered in prevention research. To avoid reconstruction of current inequalities and stereotypes regarding sexual practices of young women and men, the impact of gender, the power structures in intimate relations, and the cultural context should be considered. Medical research on STI prevention could benefit from including a wider array of gender perspectives. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms.

    Science.gov (United States)

    Kim, Sun; Yeganova, Lana; Wilbur, W John

    2016-10-01

    Medical Subject Headings (MeSH(®)) is a controlled vocabulary for indexing and searching biomedical literature. MeSH terms and subheadings are organized in a hierarchical structure and are used to indicate the topics of an article. Biologists can use either MeSH terms as queries or the MeSH interface provided in PubMed(®) for searching PubMed abstracts. However, these are rarely used, and there is no convenient way to link standardized MeSH terms to user queries. Here, we introduce a web interface which allows users to enter queries to find MeSH terms closely related to the queries. Our method relies on co-occurrence of text words and MeSH terms to find keywords that are related to each MeSH term. A query is then matched with the keywords for MeSH terms, and candidate MeSH terms are ranked based on their relatedness to the query. The experimental results show that our method achieves the best performance among several term extraction approaches in terms of topic coherence. Moreover, the interface can be effectively used to find full names of abbreviations and to disambiguate user queries. https://www.ncbi.nlm.nih.gov/IRET/MESHABLE/ CONTACT: sun.kim@nih.gov Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  17. Producción científica española en obesidad a través de PubMed (1988-2007 Spanish scientific production in obesity research published in PubMed (1988-2007

    Directory of Open Access Journals (Sweden)

    Jesús Vioque

    2010-06-01

    Full Text Available Objetivo: Analizar la producción científica española sobre obesidad en PubMed durante dos décadas (1988-2007 y contextualizarla en el marco de la Unión Europea. Métodos: Se realizó un estudio bibliométrico a través de la base de datos MEDLINE en PubMed mediante la búsqueda de «obesity» en MeSH, estimando las tendencias del número de publicaciones anuales mediante análisis de regresión. Resultados: Se recopilaron 50.120 documentos sobre obesidad, y 1.407 (2,8% de la producción mundial eran de autores españoles. España fue el quinto país con más documentos de la Unión Europea (8,1%. El 69,1% (n=932 estaban publicados en inglés. El crecimiento medio anual fue del 15%, pasando de 91 documentos en el primer quinquenio a 702 en el último. La especialidad más frecuente del primer firmante fue endocrinología, con 279 (22,8% documentos, seguida de fisiología-nutrición-bromatología con 203 (16,6% y bioquímica con 161 (13,2%. Medicina Clínica con 83 (6,1%, Obesity Surgery con 79 (5,8%, International Journal of Obesity con 73 (5,3% y Nutrición Hospitalaria con 59 (4,3% fueron las revistas con mayor número de documentos. Las comunidades autónomas más productoras fueron Cataluña (n=338; 24,9%, Madrid (n=286; 20,6% y Navarra (n=159; 11,7%. Las instituciones más productivas fueron los hospitales, con 708 (52,1% documentos, y las universidades, con 521 (38,5% documentos. Conclusiones: La investigación sobre obesidad en España ha crecido en los últimos 20 años y ha supuesto una aportación importante en el conjunto de la Unión Europea. La mitad de las publicaciones españolas se hicieron en revistas extranjeras y procedían predominantemente de hospitales y universidades.Objective: To analyse Spanish scientific research output related to obesity during a 20-year period from 1988 to 2007 into context with the European Union productivity Methods: The bibliometric study was based on research of the MEDLINE database in PubMed

  18. Radiation sensitizations at DNA-level by chemical and biological agents. Coordinated programme on improvement of radiotherapy of cancer using modifiers of radiosensitivity of cells

    International Nuclear Information System (INIS)

    Altmann, H.

    1982-01-01

    Radiation sensitization by chemical agents at DNA level is discussed. Procaine, Halothan and Metronidazole showed no significant effect on unscheduled DNA synthesis (UDS) in mouse spleen cells, investigated by autoradiography and no effect on rejoining of DNA single strand breaks after gamma or UV irradiation. Oxyphenbutazon and prednisolone reduced the replicative DNA synthesis in vitro and in vivo but there was only little effect on DNA repair in the in vivo experiments. These two substances showed also a small reduction in poly(ADP-ribose) synthesis (PAR synthesis). 5-methoxypsoralen (5-MOP) and 8-methoxypsoralen (8-MOP) in combination with UV irradiation showed that 5-MOP was more toxic than mutagen, but induced much less DNA crosslinks than 8-MOP. Autoradiographic studies of radiation sensitization by biological agents showed significant inhibition of UDS in Yoshida tumor cells after acute mycoplasma infection in rats. Nucleoid sedimentation studies showed only in the case of Yoshida tumor cells after mycoplasma infection a dramatic effect in the sedimentation behaviour. Sensitization of cells by changing chromatin structure was also studied. Benzamide, 3-NH 2 -benzamide, 3-Methoxybenzamide, Spermine, Theophyllin and Caffeine were tested in different concentrations on replicative DNA synthesis, UDS after UV irradiation and PAR synthesis Chinese hamster ovary cells. 5-Methoxybenzamide was the strongest sensitizer and inhibitor of the PAR synthesis, and was used in further experiments. Results of KFA Juelich on sensitization of a mamma-adenocarcinoma EO 771 on C57 B1 mice are given. Replicative DNA synthesis, DNA repair and PAR synthesis were compared in spleen cells and adenocarcinoma cells after treatment with 5-Methoxybenzamide. An inhibitory effect on UDS could be shown only in adenocarcinoma cells but not in the mice spleen cells

  19. DMPD: Lysophospholipid receptors: signaling and biology. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 15189145 Lysophospholipid receptors: signaling and biology. Ishii I, Fukushima N, Y...e X, Chun J. Annu Rev Biochem. 2004;73:321-54. (.png) (.svg) (.html) (.csml) Show Lysophospholipid receptors...: signaling and biology. PubmedID 15189145 Title Lysophospholipid receptors: signaling and biology. Authors

  20. Travel and biologic therapy: travel-related infection risk, vaccine response and recommendations.

    Science.gov (United States)

    Hall, Victoria; Johnson, Douglas; Torresi, Joseph

    2018-01-01

    Biologic therapy has revolutionized the management of refractory chronic autoimmune and auto-inflammatory disease, as well as several malignancies, providing rapid symptomatic relief and/or disease remission. Patients receiving biologic therapies have an improved quality of life, facilitating travel to exotic destinations and potentially placing them at risk of a range of infections. For each biologic agent, we review associated travel-related infection risk and expected travel vaccine response and effectiveness. A PUBMED search [vaccination OR vaccine] AND/OR ['specific vaccine'] AND/OR [immunology OR immune response OR response] AND [biologic OR biological OR biologic agent] was performed. A review of the literature was performed in order to develop recommendations on vaccination for patients in receipt of biologic therapy travelling to high-risk travel destinations. There is a paucity of literature in this area, however, it is apparent that travel-related infection risk is increased in patients on biologic therapy and when illness occurs they are at a higher risk of complication and hospitalization. Patients in receipt of biologic agents are deemed as having a high level of immunosuppression-live vaccines, including the yellow fever vaccine, are contraindicated. Inactivated vaccines are considered safe; however, vaccine response can be attenuated by the patient's biologic therapy, thereby resulting in reduced vaccine effectiveness and protection. Best practice requires a collaborative approach between the patient's primary healthcare physician, relevant specialist and travel medicine expert, who should all be familiar with the immunosuppressive and immunomodulatory effects resulting from the biologic therapies. Timing of vaccines should be carefully planned, and if possible, vaccination provided well before established immunosuppression.

  1. MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank.

    Science.gov (United States)

    Mao, Yuqing; Lu, Zhiyong

    2017-04-17

    MeSH indexing is the task of assigning relevant MeSH terms based on a manual reading of scholarly publications by human indexers. The task is highly important for improving literature retrieval and many other scientific investigations in biomedical research. Unfortunately, given its manual nature, the process of MeSH indexing is both time-consuming (new articles are not immediately indexed until 2 or 3 months later) and costly (approximately ten dollars per article). In response, automatic indexing by computers has been previously proposed and attempted but remains challenging. In order to advance the state of the art in automatic MeSH indexing, a community-wide shared task called BioASQ was recently organized. We propose MeSH Now, an integrated approach that first uses multiple strategies to generate a combined list of candidate MeSH terms for a target article. Through a novel learning-to-rank framework, MeSH Now then ranks the list of candidate terms based on their relevance to the target article. Finally, MeSH Now selects the highest-ranked MeSH terms via a post-processing module. We assessed MeSH Now on two separate benchmarking datasets using traditional precision, recall and F 1 -score metrics. In both evaluations, MeSH Now consistently achieved over 0.60 in F-score, ranging from 0.610 to 0.612. Furthermore, additional experiments show that MeSH Now can be optimized by parallel computing in order to process MEDLINE documents on a large scale. We conclude that MeSH Now is a robust approach with state-of-the-art performance for automatic MeSH indexing and that MeSH Now is capable of processing PubMed scale documents within a reasonable time frame. http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/MeSHNow/ .

  2. Searching PubMed for a broad subject area: how effective are palliative care clinicians in finding the evidence in their field?

    Science.gov (United States)

    Damarell, Raechel A; Tieman, Jennifer J

    2016-03-01

    Health professionals must be able to search competently for evidence to support practice. We sought to understand how palliative care clinicians construct searches for palliative care literature in PubMed, to quantify search efficacy in retrieving a set of relevant articles and to compare performance against a Palliative CareSearch Filter (PCSF). Included studies from palliative care systematic reviews formed a test set. Palliative care clinicians (n = 37) completed a search task using PubMed. Individual clinician searches were reconstructed in PubMed and combined with the test set to calculate retrieval sensitivity. PCSF performance in the test set was also determined. Many clinicians struggled to create useful searches. Twelve used a single search term, 17 narrowed the search inappropriately and 8 confused Boolean operators. The mean number of test set citations (n = 663) retrieved was 166 (SD = 188), or 25% although 76% of clinicians believed they would find more than 50% of the articles. Only 8 participants (22%) achieved this. Correlations between retrieval and PubMed confidence (r = 0.13) or frequency of use (r = -0.18) were weak. Many palliative care clinicians search PubMed ineffectively. Targeted skills training and PCSF promotion may improve evidence retrieval. © 2015 Health Libraries Group.

  3. Bibliometric and content analysis of medical articles in the PubMed database published by North Korean authors from 1997 to July 2017

    Directory of Open Access Journals (Sweden)

    Geum Hee Jeong

    2017-08-01

    Full Text Available This study aimed at analyzing the bibliometric characteristics and content of medical articles from North Korea in PubMed and characterizing the patterns of international cooperation of medical researchers in North Korea. We hypothesized that the number of publications from North Korea in PubMed has increased recently as a result of active cooperation with foreign researchers. PubMed was searched on July 19, 2017 using the search term “(North Korea [Affiliation] OR Democratic People’s Republic of Korea [Affiliation] OR DPRK [Affiliation].” The content of medical articles was analyzed and cooperative work with foreign researchers was noted. The number of medical articles in PubMed through July 2017 was 16, of which 2 were by North Korean authors only. From the content of these articles, it was found that researchers in top-notch institutions, including Kim Il Sung University, can access the internet, and that a dental caries prevention program supported by Finland has been in place for more than 10 years. The number of publications from North Korea in PubMed has increased recently, although the amount is still very small. Providing internet access to North Korean researchers will accelerate their submissions to international journals.

  4. A Study of the Association of Attitudes to the Philosophy of Science with Classroom Contexts, Academic Qualification and Professional Training, amongst A-Level Biology Teachers in Harare, Zimbabwe.

    Science.gov (United States)

    Gwimbi, Eric; Monk, Martin

    2003-01-01

    Investigates the association between attitude towards the philosophy of science and academic qualification professional training. Analyzes responses from 33 A-level biology teachers to a questionnaire and reports from teachers in Harare on their school contexts. Suggests that the differential distribution of facilities and resources across school…

  5. A systematic literature review on reviews and meta-analyses of biologically based CAM-practices for cancer patients

    DEFF Research Database (Denmark)

    Paludan-Müller, Christine; Lunde, Anita; Johannessen, Helle

    2010-01-01

    levels of evidence and were excluded from further evaluation. Among the 32 high-quality reviews the most reviewed practices were soy/plant hormones (7), Chinese herbal medicine (7), antioxidants (5) and mistletoe (4). Fifteen of the 32 reviews included data on the efficacy of biologically-based CAM......-practices against cancer, but none of the reviews concluded a positive effect on the cancer. Reviews including data on quality of life (10) and/or reduction of side effects (12) showed promising, but yet insufficient evidence for Chinese herbal medicine against pain  and side effects of chemotherapy, and mistletoe......Purpose To provide an overview and evaluate the evidence of biologically based CAM-practices for cancer patients. Methods Pubmed, Social Science Citation Index, AMED and the Cochrane library were systematically searched for reviews on effects of biologically based CAM-practices, including herbal...

  6. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B

    2016-01-01

    This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

  7. The Study of Microbial Environmental Processes Related to the Natural Attenuation of Uranium at the Rifle Site using Systems-level Biology

    Energy Technology Data Exchange (ETDEWEB)

    Methe, Barbara [J. Craig Venter Inst. (JCVI), Rockville, MD (United States); Lipton, Mary [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mahadevan, Krishna [Univ. of Toronto, ON (Canada)

    2016-08-31

    Microbes exist in communities in the environment where they are fundamental drivers of global carbon, nutrient and metal cycles. In subsurface environments, they possess significant metabolic potential to affect these global cycles including the transformation of radionuclides. This study examined the influence of microbial communities in sediment zones undergoing biogeochemical cycling of carbon, nutrients and metals including natural attenuation of uranium. This study examined the relationship of both the microbiota (taxonomy) and their metabolic capacity (function) in driving carbon, nutrient and metal cycles including uranium reduction at the Department of Energy (DOE) Rifle Integrated Field Research Challenge (RIFRC). Objectives of this project were: 1) to apply systems-level biology through application of ‘metaomics’ approaches (collective analyses of whole microbial community DNA, RNA and protein) to the study of microbial environmental processes and their relationship to C, N and metals including the influence of microbial communities on uranium contaminant mobility in subsurface settings undergoing natural attenuation, 2) improve methodologies for data generation using metaomics (collectively metagenomics, metatranscriptomics and proteomics) technologies and analysis and interpretation of that data and 3) use the data generated from these studies towards microbial community-scale metabolic modeling. The strategy for examining these subsurface microbial communities was to generate sequence reads from microbial community DNA (metagenomics or whole genome shotgun sequencing (WGS)) and RNA (metatranscriptomcs or RNAseq) and protein information using proteomics. Results were analyzed independently and through computational modeling. Overall, the community model generated information on the microbial community structure that was observed using metaomic approaches at RIFRC sites and thus provides an important framework for continued community modeling

  8. Bibliometric assessment of publication output of child and adolescent psychiatric/psychological affiliations between 2005 and 2010 based on the databases PubMed and Scopus.

    Science.gov (United States)

    Albayrak, Ozgür; Föcker, Manuel; Wibker, Katrin; Hebebrand, Johannes

    2012-06-01

    We aimed to determine the quantitative scientific publication output of child and adolescent psychiatric/psychological affiliations during 2005-2010 by country based on both, "PubMed" and "Scopus" and performed a bibliometric qualitative evaluation for 2009 using "PubMed". We performed our search by affiliation related to child and adolescent psychiatric/psychological institutions using "PubMed". For the quantitative analysis for 2005-2010, we counted the number of abstracts. For the qualitative analysis for 2009 we derived the impact factor of each abstract's journal from "Journal Citation Reports". We related total impact factor scores to the gross domestic product (GDP) and population size of each country. Additionally, we used "Scopus" to determine the number of abstracts for each country that was identified via "PubMed" for 2009 and compared the ranking of countries between the two databases. 61 % of the publications between 2005 and 2010 originated from European countries and 26 % from the USA. After adjustment for GDP and population size, the ranking positions changed in favor of smaller European countries with a population size of less than 20 million inhabitants. The ranking of countries for the count of articles in 2009 as derived from "Scopus" was similar to that identified via the "PubMed" search. The performed search revealed only minor differences between "Scopus" and "PubMed" related to the ranking of countries. Our data indicate a sharp difference between countries with a high versus low GDP with regard to scientific publication output in child and adolescent psychiatry/psychology.

  9. The effects on populations of exposure to low levels of ionizing radiation. Report of the Advisory Committee on the Biological Effects of Ionizing Radiations

    International Nuclear Information System (INIS)

    1972-11-01

    In the summer of 1970, the Federal Radiation Council (whose activities have since been transferred to the Radiation Office of the EPA) asked the National Academy of Sciences for information relevant to an evaluation of present radiation protection guides. This report is in response to that request. It presents a summary and analysis, by members of the Advisory Committee on the Biological Effects of Ionizing Radiations and its subcommittees, of current knowledge relating to risks from exposure to ionizing radiation. In many respects, the report is a sequel to the reports of the Committee on the Biological Effects of Atomic Radiation, published by the NAS-NRC from 1956 to 1961

  10. Paramecium aurelia as a cellular model used for studies of the biological effects of natural ionizing radiation or chronic low-level irradiation

    International Nuclear Information System (INIS)

    Planel, H.; Soleilhavoup, J.P.; Tixador, R.; Croute, F.; Richoilley, G.

    1979-01-01

    Paramecium aurelia appears to be a very suitable object for investigating the biological effects of natural ionizing radiation or the influence of low doses of radiation. The biological effects of ionizing radiation on cell proliferation kinetics were tested. It is shown that radio-protection or chronic exposure to very low doses of 60 Co gamma rays induce different changes in cell growth rate. Special experimental techniques can help to obtain more obvious results using cells more sensitive to the stimulating effects of low doses of ionizing radiation. (author)

  11. The effects on populations of exposure to low levels of ionizing radiation. Report of the Advisory Committee on the Biological Effects of Ionizing Radiations

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1972-11-01

    In the summer of 1970, the Federal Radiation Council (whose activities have since been transferred to the Radiation Office of the EPA) asked the National Academy of Sciences for information relevant to an evaluation of present radiation protection guides. This report is in response to that request. It presents a summary and analysis, by members of the Advisory Committee on the Biological Effects of Ionizing Radiations and its subcommittees, of current knowledge relating to risks from exposure to ionizing radiation. In many respects, the report is a sequel to the reports of the Committee on the Biological Effects of Atomic Radiation, published by the NAS-NRC from 1956 to 1961.

  12. Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014: retrospective analysis.

    Science.gov (United States)

    Vinkers, Christiaan H; Tijdink, Joeri K; Otte, Willem M

    2015-12-14

    To investigate whether language used in science abstracts can skew towards the use of strikingly positive and negative words over time. Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014. The yearly frequencies of positive, negative, and neutral words (25 preselected words in each category), plus 100 randomly selected words were normalised for the total number of abstracts. Subanalyses included pattern quantification of individual words, specificity for selected high impact journals, and comparison between author affiliations within or outside countries with English as the official majority language. Frequency patterns were compared with 4% of all books ever printed and digitised by use of Google Books Ngram Viewer. Frequencies of positive and negative words in abstracts compared with frequencies of words with a neutral and random connotation, expressed as relative change since 1980. The absolute frequency of positive words increased from 2.0% (1974-80) to 17.5% (2014), a relative increase of 880% over four decades. All 25 individual positive words contributed to the increase, particularly the words "robust," "novel," "innovative," and "unprecedented," which increased in relative frequency up to 15,000%. Comparable but less pronounced results were obtained when restricting the analysis to selected journals with high impact factors. Authors affiliated to an institute in a non-English speaking country used significantly more positive words. Negative word frequencies increased from 1.3% (1974-80) to 3.2% (2014), a relative increase of 257%. Over the same time period, no apparent increase was found in neutral or random word use, or in the frequency of positive word use in published books. Our lexicographic analysis indicates that scientific abstracts are currently written with more positive and negative words, and provides an insight into the evolution of scientific writing. Apparently scientists look on the bright side of research

  13. Mentoring programs for medical students--a review of the PubMed literature 2000-2008.

    Science.gov (United States)

    Frei, Esther; Stamm, Martina; Buddeberg-Fischer, Barbara

    2010-04-30

    Although mentoring is acknowledged as a key to successful and satisfying careers in medicine, formal mentoring programs for medical students are lacking in most countries. Within the framework of planning a mentoring program for medical students at Zurich University, an investigation was carried out into what types of programs exist, what the objectives pursued by such programs are, and what effects are reported. A PubMed literature search was conducted for 2000 - 2008 using the following keywords or their combinations: mentoring, mentoring program, medical student, mentor, mentee, protégé, mentorship. Although a total of 438 publications were identified, only 25 papers met the selection criteria for structured programs and student mentoring surveys. The mentoring programs reported in 14 papers aim to provide career counseling, develop professionalism, increase students' interest in research, and support them in their personal growth. There are both one-to-one and group mentorships, established in the first two years of medical school and continuing through graduation. The personal student-faculty relationship is important in that it helps students to feel that they are benefiting from individual advice and encourages them to give more thought to their career choices. Other benefits are an increase in research productivity and improved medical school performance in general. Mentored students also rate their overall well-being as higher. - The 11 surveys address the requirements for being an effective mentor as well as a successful mentee. A mentor should empower and encourage the mentee, be a role model, build a professional network, and assist in the mentee's personal development. A mentee should set agendas, follow through, accept criticism, and be able to assess performance and the benefits derived from the mentoring relationship. Mentoring is obviously an important career advancement tool for medical students. In Europe, more mentoring programs should be

  14. Best, Useful and Objective Precisions for Information Retrieval of Three Search Methods in PubMed and iPubMed

    Directory of Open Access Journals (Sweden)

    Somayyeh Nadi Ravandi

    2016-10-01

    Full Text Available MEDLINE is one of the valuable sources of medical information on the Internet. Among the different open access sites of MEDLINE, PubMed is the best-known site. In 2010, iPubMed was established with an interaction-fuzzy search method for MEDLINE access. In the present work, we aimed to compare the precision of the retrieved sources (Best, Useful and Objective precision in the PubMed and iPubMed using two search methods (simple and MeSH search in PubMed and interaction-fuzzy method in iPubmed. During our semi-empirical study period, we held training workshops for 61 students of higher education to teach them Simple Search, MeSH Search, and Fuzzy-Interaction Search methods. Then, the precision of 305 searches for each method prepared by the students was calculated on the basis of Best precision, Useful precision, and Objective precision formulas. Analyses were done in SPSS version 11.5 using the Friedman and Wilcoxon Test, and three precisions obtained with the three precision formulas were studied for the three search methods. The mean precision of the interaction-fuzzy Search method was higher than that of the simple search and MeSH search for all three types of precision, i.e., Best precision, Useful precision, and Objective precision, and the Simple search method was in the next rank, and their mean precisions were significantly different (P < 0.001. The precision of the interaction-fuzzy search method in iPubmed was investigated for the first time. Also for the first time, three types of precision were evaluated in PubMed and iPubmed. The results showed that the Interaction-Fuzzy search method is more precise than using the natural language search (simple search and MeSH search, and users of this method found papers that were more related to their queries; even though search in Pubmed is useful, it is important that users apply new search methods to obtain the best results.

  15. Preparation of Biological Samples Containing Metoprolol and Bisoprolol for Applying Methods for Quantitative Analysis

    Directory of Open Access Journals (Sweden)

    Corina Mahu Ştefania

    2015-12-01

    Full Text Available Arterial hypertension is a complex disease with many serious complications, representing a leading cause of mortality. Selective beta-blockers such as metoprolol and bisoprolol are frequently used in the management of hypertension. Numerous analytical methods have been developed for the determination of these substances in biological fluids, such as liquid chromatography coupled with mass spectrometry, gas chromatography coupled with mass spectrometry, high performance liquid chromatography. Due to the complex composition of biological fluids a biological sample pre-treatment before the use of the method for quantitative determination is required in order to remove proteins and potential interferences. The most commonly used methods for processing biological samples containing metoprolol and bisoprolol were identified through a thorough literature search using PubMed, ScienceDirect, and Willey Journals databases. Articles published between years 2005-2015 were reviewed. Protein precipitation, liquid-liquid extraction and solid phase extraction are the main techniques for the extraction of these drugs from plasma, serum, whole blood and urine samples. In addition, numerous other techniques have been developed for the preparation of biological samples, such as dispersive liquid-liquid microextraction, carrier-mediated liquid phase microextraction, hollow fiber-protected liquid phase microextraction, on-line molecularly imprinted solid phase extraction. The analysis of metoprolol and bisoprolol in human plasma, urine and other biological fluids provides important information in clinical and toxicological trials, thus requiring the application of appropriate extraction techniques for the detection of these antihypertensive substances at nanogram and picogram levels.

  16. An On-Campus Botanical Tour to Promote Student Satisfaction and Learning in a University Level Biodiversity or General Biology Course

    Science.gov (United States)

    Ratnayaka, Harish H.

    2017-01-01

    Outdoor, hands-on and experiential learning, as opposed to instruction-based learning in classroom, increases student satisfaction and motivation leading to a deeper understanding of the subject. However, the use of outdoor exercises in undergraduate biology courses is declining due to a variety of constraints. Thus, the goal of this paper is to…

  17. An Evaluation of Two Different Methods of Assessing Independent Investigations in an Operational Pre-University Level Examination in Biology in England.

    Science.gov (United States)

    Brown, Chris

    1998-01-01

    Explored aspects of assessment of extended investigation ("project") practiced in the operational examinations of The University of Cambridge Local Examinations Syndicate (UCLES) for the perspective of construct validity. Samples of the 1993 (n=333) and 1996 (n=259) biology test results reveal two methods of assessing the project. (MAK)

  18. The effects of insect biological control on a Tamarix invaded ecosystem: ecosystem water and carbon fluxes and plant-level responses

    Science.gov (United States)

    Background / Questions / Methods: Tamarix spp. (saltcedar) has invaded many river systems in the western United States with detrimental impacts to flora and fauna. Traditional methods of invasive plant control have been ineffective or costly. Therefore, insect biological control of Tamarix with Di...

  19. CHRISTMAS 2015 : THE PUBLICATION GAME Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014: retrospective analysis

    NARCIS (Netherlands)

    Vinkers, Christiaan H.; Tijdink, Joeri K.; Otte, Wim

    2015-01-01

    Objective To investigate whether language used in science abstracts can skew towards the use of strikingly positive and negative words over time. Design Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014. Methods The yearly frequencies of positive, negative, and

  20. Worldwide access to evidence-based mental health literature: how useful is PubMed in Anglo-Saxon and non-Anglo-Saxon countries?

    Science.gov (United States)

    Morlino, Massimo; Polese, Daniela; Bruni, Andrea; Renato, Bellinello

    2005-10-01

    The aim of this study was to verify the presence of cultural variety among the psychiatric journals available on PubMed, the major online tool for accessing literature. Data for analysis were taken from a survey of the world psychiatric journals indexed in Index Medicus 1999 (IM), the alphabetical list used by PubMed, and from the mean impact factor (IF) values of the journals. Approximately 80% of international psychiatric literature available on PubMed is published in Anglo-Saxon countries, especially in the USA (59.8% of the total). The widespread use of the English language (94.9% of all the journals) further stresses the dominance of the Anglo-Saxon cultural model, as do the mean IF values of Anglo-Saxon journals compared to non-Anglo-Saxon publications (3.252 vs. 1.693; P=0.0079). The under-representation of non-Anglo-Saxon cultural models on PubMed plays a negative role for bringing about a truly multicultural literature in psychiatry.

  1. Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature.

    Science.gov (United States)

    Sutton, Victoria R; Hauser, Susan E

    2005-01-01

    MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information.

  2. A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records

    DEFF Research Database (Denmark)

    Jiang, Li; Edwards, Stefan M.; Thomsen, Bo

    2014-01-01

    from PubMed abstracts, OMIM, and GeneRIF records. We also investigated the validity of several vocabulary filters and different likelihood thresholds for predicted protein-protein interactions in terms of their effect on the network-based gene-prioritization approach, which relies on text...

  3. The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly "The Emperor of All Maladies"?

    Science.gov (United States)

    Reyes-Aldasoro, Constantino Carlos

    2017-01-01

    In this work, the public database of biomedical literature PubMed was mined using queries with combinations of keywords and year restrictions. It was found that the proportion of Cancer-related entries per year in PubMed has risen from around 6% in 1950 to more than 16% in 2016. This increase is not shared by other conditions such as AIDS, Malaria, Tuberculosis, Diabetes, Cardiovascular, Stroke and Infection some of which have, on the contrary, decreased as a proportion of the total entries per year. Organ-related queries were performed to analyse the variation of some specific cancers. A series of queries related to incidence, funding, and relationship with DNA, Computing and Mathematics, were performed to test correlation between the keywords, with the hope of elucidating the cause behind the rise of Cancer in PubMed. Interestingly, the proportion of Cancer-related entries that contain "DNA", "Computational" or "Mathematical" have increased, which suggests that the impact of these scientific advances on Cancer has been stronger than in other conditions. It is important to highlight that the results obtained with the data mining approach here presented are limited to the presence or absence of the keywords on a single, yet extensive, database. Therefore, results should be observed with caution. All the data used for this work is publicly available through PubMed and the UK's Office for National Statistics. All queries and figures were generated with the software platform Matlab and the files are available as supplementary material.

  4. Searching for observational studies: what does citation tracking add to PubMed? A case study in depression and coronary heart disease

    Directory of Open Access Journals (Sweden)

    Hemingway Harry

    2006-02-01

    Full Text Available Abstract Background PubMed is the most widely used method for searches of the medical literature, but fails to identify many relevant articles. Electronic citation tracking offers an alternative search method. Methods Articles investigating the role of depression in the aetiology and prognosis of coronary heart disease were sought through two methods: a PubMed, and b citation tracking where Science Citation Index was searched for all articles which cited ("forward citation tracking" or were cited by ("backward citation tracking" any of the articles in an index review. The number and quality of eligible articles identified by the two methods were compared. Results 50 articles that were not already included in the index review met our inclusion criteria; 11 were identified through Science Citation Index alone, 8 through PubMed alone, and 31 through both methods. Articles identified by Science Citation Index alone were published in higher impact factor journals, were larger and were less likely to show a positive association. Conclusion Science Citation Index identified more eligible articles than PubMed, and these differed qualitatively. Failing to use citation tracking in a systematic review of observational studies may result in bias.

  5. Using the mixed media according to internet-based on the instructional multimedia for developing students' learning achievements in biology course on foundational cell issue of secondary students at the 10th grade level in Rangsit University demonstration school

    Science.gov (United States)

    Kangloan, Pichet; Chayaburakul, Kanokporn; Santiboon, Toansakul

    2018-01-01

    The aims of this research study were 1) to develop students' learning achievements in biology course on foundational cell issue, 2) to examine students' satisfactions of their learning activities through the mixed media according to internet-based multi-instruction in biology on foundational cell issue at the 10th grade level were used in the first semester in the academic year 2014, which a sample size of 17 students in Rangsit University Demonstration School with cluster random sampling was selected. Students' learning administrations were instructed with the 3-instructional lesson plans according to the 5-Step Ladder Learning Management Plan (LLMP) namely; the maintaining lesson plan on the equilibrium of cell issue, a lesson plan for learning how to communicate between cell and cell division. Students' learning achievements were assessed with the 30-item Assessment of Learning Biology Test (ALBT), students' perceptions of their satisfactions were satisfied with the 20-item Questionnaire on Students Satisfaction (QSS), and students' learning activities were assessed with the Mixed Media Internet-Based Instruction (MMIBI) on foundational cell issue was designed. The results of this research study have found that: statistically significant of students' post-learning achievements were higher than their pre-learning outcomes and indicated that the differences were significant at the .05 level. Students' performances of their satisfaction to their perceptions toward biology class with the mixed media according to internet-based multi instruction in biology on foundational cell issue were the highest level and evidence of average mean score as 4.59.

  6. [Side effects of biologic therapies in psoriasis].

    Science.gov (United States)

    Altenburg, A; Augustin, M; Zouboulis, C C

    2018-04-01

    The introduction of biologics has revolutionized the treatment of moderate to severe plaque psoriasis. Due to the continuous expansion of biological therapies for psoriasis, it is particularly important to acknowledge efficacy and safety of the compounds not only in clinical trials but also in long-term registry-based observational studies. Typical side effects and significant risks of antipsoriatic biologic therapies considering psoriatic control groups are presented. A selective literature search was conducted in PubMed and long-term safety studies of the psoriasis registries PsoBest, PSOLAR and BADBIR were evaluated. To assess the long-term safety of biologics, the evaluation of the course of large patient cohorts in long-term registries is of particular medical importance. Newer biologic drugs seem to exhibit a better safety profile than older ones.

  7. The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews.

    Science.gov (United States)

    Bramer, Wichor M; Giustini, Dean; Kramer, Bianca Mr; Anderson, Pf

    2013-12-23

    The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. GS' overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be

  8. Biological therapeutics

    National Research Council Canada - National Science Library

    Greenstein, Ben; Brook, Daniel A

    2011-01-01

    This introductory textbook covers all the main categories of biological medicines, including vaccines, hormonal preparations, drugs for rheumatoid arthritis and other connective tissue diseases, drugs...

  9. Workshop Introduction: Systems Biology and Biological Models

    Science.gov (United States)

    As we consider the future of toxicity testing, the importance of applying biological models to this problem is clear. Modeling efforts exist along a continuum with respect to the level of organization (e.g. cell, tissue, organism) linked to the resolution of the model. Generally,...

  10. Biological Soil Crust Web Site

    Science.gov (United States)

    www.soilcrust.org Crust 101 Advanced Gallery References CCERS site Links Biological Soil Crusts Textbook Corrections Level of Development Index Biological soil crusts are the community of organisms , mosses, liverworts and lichens. A Field Guide to Biological Soil Crusts of Western U.S. Drylands: Common

  11. Is synthetic biology mechanical biology?

    Science.gov (United States)

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  12. The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly “The Emperor of All Maladies”?

    Science.gov (United States)

    2017-01-01

    In this work, the public database of biomedical literature PubMed was mined using queries with combinations of keywords and year restrictions. It was found that the proportion of Cancer-related entries per year in PubMed has risen from around 6% in 1950 to more than 16% in 2016. This increase is not shared by other conditions such as AIDS, Malaria, Tuberculosis, Diabetes, Cardiovascular, Stroke and Infection some of which have, on the contrary, decreased as a proportion of the total entries per year. Organ-related queries were performed to analyse the variation of some specific cancers. A series of queries related to incidence, funding, and relationship with DNA, Computing and Mathematics, were performed to test correlation between the keywords, with the hope of elucidating the cause behind the rise of Cancer in PubMed. Interestingly, the proportion of Cancer-related entries that contain “DNA”, “Computational” or “Mathematical” have increased, which suggests that the impact of these scientific advances on Cancer has been stronger than in other conditions. It is important to highlight that the results obtained with the data mining approach here presented are limited to the presence or absence of the keywords on a single, yet extensive, database. Therefore, results should be observed with caution. All the data used for this work is publicly available through PubMed and the UK’s Office for National Statistics. All queries and figures were generated with the software platform Matlab and the files are available as supplementary material. PMID:28282418

  13. Computational biology

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2011-01-01

    Computation via biological devices has been the subject of close scrutiny since von Neumann’s early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved t...

  14. Monitoring biodiversity loss with primary species-occurrence data: toward national-level indicators for the 2010 target of the convention on biological diversity.

    Science.gov (United States)

    Soberón, Jorge; Peterson, A Townsend

    2009-02-01

    Development of effective indicators is indispensable for countries and societies to monitor effects of their actions on biodiversity, as is recognized in decision VI/26 of the Convention on Biological Diversity. Good indicators would ideally be scalable, at least for the different scales that characterize biodiversity patterns and process. Existing indicators are mostly global in scope, and often based on secondary information, such as classifications of endangered species, rather than on primary data. We propose a complementary approach, based on the increased availability of raw data about occurrences of species, cutting-edge modeling techniques for estimating distributional areas, and land-use information based on remotely sensed data to allow estimation of rates of range loss for species affected by land-use conversion. This method can be implemented by developing countries, given increasing availability of data and the open and well-documented nature of the techniques required.

  15. To compare PubMed Clinical Queries and UpToDate in teaching information mastery to clinical residents: a crossover randomized controlled trial.

    Science.gov (United States)

    Sayyah Ensan, Ladan; Faghankhani, Masoomeh; Javanbakht, Anna; Ahmadi, Seyed-Foad; Baradaran, Hamid Reza

    2011-01-01

    To compare PubMed Clinical Queries and UpToDate regarding the amount and speed of information retrieval and users' satisfaction. A cross-over randomized trial was conducted in February 2009 in Tehran University of Medical Sciences that included 44 year-one or two residents who participated in an information mastery workshop. A one-hour lecture on the principles of information mastery was organized followed by self learning slide shows before using each database. Subsequently, participants were randomly assigned to answer 2 clinical scenarios using either UpToDate or PubMed Clinical Queries then crossed to use the other database to answer 2 different clinical scenarios. The proportion of relevantly answered clinical scenarios, time to answer retrieval, and users' satisfaction were measured in each database. Based on intention-to-treat analysis, participants retrieved the answer of 67 (76%) questions using UpToDate and 38 (43%) questions using PubMed Clinical Queries (PPubMed Clinical Queries (PPubMed Clinical Queries users (PPubmed Clinical Queries can lead to not only a higher proportion of relevant answer retrieval within a shorter time, but also a higher users' satisfaction. So, addition of tutoring pre-appraised sources such as UpToDate to the information mastery curricula seems to be highly efficient.

  16. A Brief Review of the Biology of Anorexia Nervosa

    DEFF Research Database (Denmark)

    Sjögren, Magnus

    2015-01-01

    PUBMED and the following search terms: “Anorexia Nervosa” and “biomarker” revealed 180 articles (8th of May 2015). Additional searches included the search terms “gene”, “genetic”, “epigenetic”, “appetite”, “hormone”, and a specific search on “biology” and “review”. Furthermore, articles of interest were...... retrieved from the reference lists of the identified articles of the first PUBMED search. Results: In general, there is a shortage of studies on biomarkers and the biology of AN, at least when you compare to similar fields of research in Affective disorders and Schizophrenia. The studies performed reveals...

  17. Clinicians' perceptions of usefulness of the PubMed4Hh mobile device application for clinical decision making at the point of care: a pilot study.

    Science.gov (United States)

    Gartrell, Kyungsook; Brennan, Caitlin W; Wallen, Gwenyth R; Liu, Fang; Smith, Karen G; Fontelo, Paul

    2018-05-08

    Although evidence-based practice in healthcare has been facilitated by Internet access through wireless mobile devices, research on the effectiveness of clinical decision support for clinicians at the point of care is lacking. This study examined how evidence as abstracts and the bottom-line summaries, accessed with PubMed4Hh mobile devices, affected clinicians' decision making at the point of care. Three iterative steps were taken to evaluate the usefulness of PubMed4Hh tools at the NIH Clinical Center. First, feasibility testing was conducted using data collected from a librarian. Next, usability testing was carried out by a postdoctoral research fellow shadowing clinicians during rounds for one month in the inpatient setting. Then, a pilot study was conducted from February, 2016 to January, 2017, with clinicians using a mobile version of PubMed4Hh. Invitations were sent via e-mail lists to clinicians (physicians, physician assistants and nurse practitioners) along with periodic reminders. Participants rated the usefulness of retrieved bottom-line summaries and abstracts and indicated their usefulness on a 7-point Likert scale. They also indicated location of use (office, rounds, etc.). Of the 166 responses collected in the feasibility phase, more than half of questions (57%, n = 94) were answerable by both the librarian using various resources and by the postdoctoral research fellow using PubMed4Hh. Sixty-six questions were collected during usability testing. More than half of questions (60.6%) were related to information about medication or treatment, while 21% were questions regarding diagnosis, and 12% were specific to disease entities. During the pilot study, participants reviewed 34 abstracts and 40 bottom-line summaries. The abstracts' usefulness mean scores were higher (95% CI [6.12, 6.64) than the scores of the bottom-line summaries (95% CI [5.25, 6.10]). The most frequent reason given was that it confirmed current or tentative diagnostic or

  18. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi

    2009-06-01

    Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

  19. Physics and biology

    International Nuclear Information System (INIS)

    Frauenfelder, H.

    1988-01-01

    The author points out that the coupling between physics and biology is becoming closer as time goes on. He tries to show that physical studies on biological systems not only yield insight into biology but also provide results of interest to physics. Biological systems are extremly complex system. Ideally one would like to understand the behavior of such systems in terms of the behavior of its constituent atoms. Since in small organisms this may be 10 20 atoms, it is clear these are not simple many-body systems. He reviews the basic elements of cells and then considers the broader questions of structure, complexity, and function, which must be looked at on levels from the cell to the organism. Despite the vast amount of observational material already in existence, biophysics and biological physics are only at a beginning. We can expect that physics will continue to interact strongly with biology. Actually, the connection also includes chemistry and mathematics. New tools that become available in physics will continue to be applied to biological problems. We can expect that the flow of information will not be one way; biological systems will provide new information on many old and new parts of physics, from reaction theory and transport phenomena to complexity, cooperativity, and nonlinear processes

  20. The effect of level of feeding, genetic merit, body condition score and age on biological parameters of a mammary gland model.

    Science.gov (United States)

    Bryant, J R; Lopez-Villalobos, N; Holmes, C W; Pryce, J E; Pitman, G D; Davis, S R

    2007-03-01

    An evolutionary algorithm was applied to a mechanistic model of the mammary gland to find the parameter values that minimised the difference between predicted and actual lactation curves of milk yields in New Zealand Jersey cattle managed at different feeding levels. The effect of feeding level, genetic merit, body condition score at parturition and age on total lactation yields of milk, fat and protein, days in milk, live weight and evolutionary algorithm derived mammary gland parameters was then determined using a multiple regression model. The mechanistic model of the mammary gland was able to fit lactation curves that corresponded to actual lactation curves with a high degree of accuracy. The senescence rate of quiescent (inactive) alveoli was highest at the very low feeding level. The active alveoli population at peak lactation was highest at very low feeding levels, but lower nutritional status at this feeding level prevented high milk yields from being achieved. Genetic merit had a significant linear effect on the active alveoli population at peak and mid to late lactation, with higher values in animals, which had higher breeding values for milk yields. A type of genetic merit × feeding level scaling effect was observed for total yields of milk and fat, and total number of alveoli produced from conception until the end of lactation with the benefits of increases in genetic merit being greater at high feeding levels. A genetic merit × age scaling effect was observed for total lactation protein yields. Initial rates of differentiation of progenitor cells declined with age. Production levels of alveoli from conception to the end of lactation were lowest in 5- to 8-year-old animals; however, in these older animals, quiescent alveoli were reactivated more frequently. The active alveoli population at peak lactation and rates of active alveoli proceeding to quiescence were highest in animals of intermediate body condition scores of 4.0 to 5.0. The results

  1. Changes in stream chemistry and biology in response to reduced levels of acid deposition during 1987-2003 in the Neversink River Basin, Catskill Mountains

    Science.gov (United States)

    Burns, Douglas A.; Riva-Murray, K.; Bode, R.W.; Passy, S.

    2008-01-01

    Atmospheric acid deposition has decreased in the northeastern United States since the 1970s, resulting in modest increases in pH, acid-neutralizing capacity (ANC), and decreases in inorganic monomeric aluminum (AlIM) concentrations since stream chemistry monitoring began in the 1980s in the acid-sensitive upper Neversink River basin in the Catskill Mountains of New York. Stream pH has increased by 0.01 units/year during 1987-2003 at three sites in the Neversink basin as determined by Seasonal Kendall trend analysis. In light of this observed decrease in stream acidity, we sampled 12 stream sites within the Neversink River watershed for water chemistry, macroinvertebrates, fish, and periphytic diatoms in 2003 to compare with a similar data set collected in 1987. Metrics and indices that reflect sensitivity to stream acidity were developed with these biological data to determine whether changes in stream biota over the intervening 16 years parallel those of stream chemistry. Statistical comparisons of data on stream chemistry and an acid biological assessment profile (Acid BAP) derived from invertebrate data showed no significant differences between the two years. For pH and ANC, however, values in 2003 were generally lower than those in 1987; this difference likely resulted from higher streamflow in summer 2003. Despite these likely flow-induced changes in summer 2003, an ordination and cluster analysis of macroinvertebrate taxa based on the Acid BAP indicated that the most acidic sites in the upstream half of the East Branch Neversink River form a statistically significant separate cluster consistent with less acidic stream conditions. This analysis is consistent with limited recovery of invertebrate species in the most acidic reaches of the river, but will require additional improvement in stream chemistry before a stronger conclusion can be drawn. Data on the fish and periphytic diatom communities in 2003 indicate that slimy sculpin had not extended their habitat

  2. A cohort study evaluating the implications of biology, weight status and socioeconomic level on global self-esteem competence among female African-American adolescents.

    Science.gov (United States)

    Powell-Young, Yolanda M; Zabaleta, Jovanny; Velasco-Gonzalez, Cruz; Sothern, Melinda S

    2013-07-01

    The link between obesity and self-esteem among minority youth has received minimal empirical evaluation. This study aims to describe the magnitude of risk that body mass index, household income, and transitional age have on global self-esteem levels among African-American adolescents. These analyses were conducted on cross-sectional data obtained from 264 urban-dwelling African-American females between 14 and 18 years of age. Survey data on global self-esteem levels, transitory age, and socioeconomic levels were collected using self-administered questionnaires. Measured height and weight values were used to calculate and categorize weight status according to body mass index. Logistic regression models examined the probability of reporting less than average levels of global self-esteem. Adolescent African-American females residing in low-income households were 10 times more likely to report lower global self-esteem scores than those individuals from more affluent households (95% CI: 1.94, 60.19, p self-esteem among participants in this study. Household income appears to be the greatest predictor of global self-esteem levels. Further research in this area is needed to fully elucidate precursors for psychological health vulnerability and facilitate intervention development.

  3. The biologic effects of grounding the human body during sleep as measured by cortisol levels and subjective reporting of sleep, pain, and stress.

    Science.gov (United States)

    Ghaly, Maurice; Teplitz, Dale

    2004-10-01

    Diurnal cortisol secretion levels were measured and circadian cortisol profiles were evaluated in a pilot study conducted to test the hypothesis that grounding the human body to earth during sleep will result in quantifiable changes in cortisol. It was also hypothesized that grounding the human body would result in changes in sleep, pain, and stress (anxiety, depression, irritability), as measured by subjective reporting. Twelve (12) subjects with complaints of sleep dysfunction, pain, and stress were grounded to earth during sleep for 8 weeks in their own beds using a conductive mattress pad. Saliva tests were administered to establish pregrounding baseline cortisol levels. Levels were obtained at 4-hour intervals for a 24-hour period to determine the circadian cortisol profile. Cortisol testing was repeated at week 6. Subjective symptoms of sleep dysfunction, pain, and stress were reported daily throughout the 8-week test period. Measurable improvements in diurnal cortisol profiles were observed, with cortisol levels significantly reduced during night-time sleep. Subjects' 24-hour circadian cortisol profiles showed a trend toward normalization. Subjectively reported symptoms, including sleep dysfunction, pain, and stress, were reduced or eliminated in nearly all subjects. Results indicate that grounding the human body to earth ("earthing") during sleep reduces night-time levels of cortisol and resynchronizes cortisol hormone secretion more in alignment with the natural 24-hour circadian rhythm profile. Changes were most apparent in females. Furthermore, subjective reporting indicates that grounding the human body to earth during sleep improves sleep and reduces pain and stress.

  4. A Cohort Study Evaluating the Implications of Biology, Weight Status and Socioeconomic Level on Global Self-Esteem Competence Among Female African-American Adolescents

    Science.gov (United States)

    Powell-Young, Yolanda M.; Zabaleta, Jovanny; Velasco-Gonzalez, Cruz; Sothern, Melinda S.

    2014-01-01

    The link between obesity and self-esteem among minority youth has received minimal empirical evaluation. This study aims to describe the magnitude of risk that body mass index, household income, and transitional age have on global self-esteem levels among African-American adolescents. These analyses were conducted on cross-sectional data obtained from 264 urban-dwelling African-American females between 14 and 18 years of age. Survey data on global self-esteem levels, transitory age, and socioeconomic levels were collected using self-administered questionnaires. Measured height and weight values were used to calculate and categorize weight status according to body mass index. Logistic regression models examined the probability of reporting less than average levels of global self-esteem. Adolescent African-American females residing in low-income households were 10 times more likely to report lower global self-esteem scores than those individuals from more affluent households (95% CI: 1.94, 60.19, p self-esteem among participants in this study. Household income appears to be the greatest predictor of global self-esteem levels. Further research in this area is needed to fully elucidate precursors for psychological health vulnerability and facilitate intervention development. PMID:24218867

  5. Biological desulfurisation

    Energy Technology Data Exchange (ETDEWEB)

    Arena, B.J. [UOP LLC (United States); Benschop, A.; Janssen, A. [Paques Natural Solutions (Netherlands); Kijlstra, S. [Shell Global Solutions (Netherlands)

    2001-03-01

    This article focuses on the biological THIOPAQ process for removing hydrogen sulphide from refinery gases and recovering elemental sulphur. Details are given of the process which absorbs hydrogen sulphide-containing gas in alkaline solution prior to oxidation of the dissolved sulphur to elemental sulphur in a THIOPAQ aerobic biological reactor, with regeneration of the caustic solution. Sulphur handling options including sulphur wash, the drying of the sulphur cake, and sulphur smelting by pressure liquefaction are described. Agricultural applications of the biologically recovered sulphur, and application of the THIOPAQ process to sulphur recovery are discussed.

  6. Concentration levels of rare-earth elements and thorium on plants from the Morro de Ferro environment as an indicator for the biological availability of transuranium elements

    International Nuclear Information System (INIS)

    Miekeley, N.; Casartelli, E.A.; Dotto, R.M.

    1994-01-01

    Plants and soils from a natural thorium and rare-earth element occurrence (Morro do Ferro, Brazil) were analyzed by alpha spectrometry (Th) and ICP-AES (REE), after pre-concentration of the elements by solvent extraction, co-precipitation and ion exchange procedures. Leaching experiments with humic acid solutions and different soils were performed to estimate the fraction of elements biologically available. High concentrations of the light rare-earth elements (LREE) and of Th, reaching some hundreds of μg/g-ash, were measured in plant leaves from the areas of the highest concentration of these elements in soil and in near-surface waters. Chondrite normalized REE plots of plant leaves and corresponding soils are very similar, suggesting that there is no significant fractionation between the REE during uptake from the soil solution and incorporation into the leaves. However, Ce-depletion was observed for some plant species, increasing for Solanum ciliatum in the sequence: leaves -3 to 10 -2 . Leaching experiments confirmed the importance of humic acid complexation for the bio-uptake of Th and REE and further showed that only a very small fraction of these elements in soil is leachable. The implications of these results on the calculated CR's will be discussed. (author) 26 refs.; 5 figs.; 5 tabs

  7. Using an international p53 mutation database as a foundation for an online laboratory in an upper level undergraduate biology class.

    Science.gov (United States)

    Melloy, Patricia G

    2015-01-01

    A two-part laboratory exercise was developed to enhance classroom instruction on the significance of p53 mutations in cancer development. Students were asked to mine key information from an international database of p53 genetic changes related to cancer, the IARC TP53 database. Using this database, students designed several data mining activities to look at the changes in the p53 gene from a number of perspectives, including potential cancer-causing agents leading to particular changes and the prevalence of certain p53 variations in certain cancers. In addition, students gained a global perspective on cancer prevalence in different parts of the world. Students learned how to use the database in the first part of the exercise, and then used that knowledge to search particular cancers and cancer-causing agents of their choosing in the second part of the exercise. Students also connected the information gathered from the p53 exercise to a previous laboratory exercise looking at risk factors for cancer development. The goal of the experience was to increase student knowledge of the link between p53 genetic variation and cancer. Students also were able to walk a similar path through the website as a cancer researcher using the database to enhance bench work-based experiments with complementary large-scale database p53 variation information. © 2014 The International Union of Biochemistry and Molecular Biology.

  8. Environmental Regulation of Plant Gene Expression: An Rt-qPCR Laboratory Project for an Upper-Level Undergraduate Biochemistry or Molecular Biology Course

    Science.gov (United States)

    Eickelberg, Garrett J.; Fisher, Alison J.

    2013-01-01

    We present a novel laboratory project employing "real-time" RT-qPCR to measure the effect of environment on the expression of the "FLOWERING LOCUS C" gene, a key regulator of floral timing in "Arabidopsis thaliana" plants. The project requires four 3-hr laboratory sessions and is aimed at upper-level undergraduate…

  9. Systems Biology

    Indian Academy of Sciences (India)

    IAS Admin

    study and understand the function of biological systems, particu- larly, the response of such .... understand the organisation and behaviour of prokaryotic sys- tems. ... relationship of the structure of a target molecule to its ability to bind a certain ...

  10. Determination of organically bound tritium background level in biological samples from a wide area in the south-west of France

    International Nuclear Information System (INIS)

    Pointurier, F.; Baglan, N.; Alanic, G.; Chiappini, R.

    2003-01-01

    In this paper, the authors describe a sensitive method for low-level non-exchangeable OBT determination. This methodology combines suitable sample treatment, a combustion apparatus for large-sized samples and low-background liquid scintillation spectrometry, along with precautions that substantially reduce the risks of sample contamination. Great care must be taken in the measurement of non-exchangeable OBT at environmental levels. Many authors have discussed the opportunities for cross-contamination between samples and contamination by exchange with the laboratory atmosphere. The authors also describe an application of the methodology to a large-scale sampling and measurement campaign, aimed at the determination of the environmental non-exchangeable OBT background level in tree leaves and ferns collected on the site and in the vicinity of a research centre located in the south-west of France, not far from Bordeaux. This study constitutes a 'zero level' for the non-exchangeable OBT activity, as, to our knowledge, there is no tritium source within or in the surroundings of the sampled area capable of producing non-exchangeable OBT activities above the natural levels. Our analyses showed that non-exchangeable OBT activities in the collected samples were very low, ranging from below the detection limit (ca 0.7 Bq kg -1 of dry material) to ca 2 Bq kg -1 of dry material. These values are similar to the natural tritium background measured in water samples. No discrepancies can be shown between fern samples and oak tree leaf samples or between samples collected inside and outside the research site

  11. Determination of organically bound tritium background level in biological samples from a wide area in the south-west of France

    Energy Technology Data Exchange (ETDEWEB)

    Pointurier, F. E-mail: fabien.pointurier@cea.fr; Baglan, N.; Alanic, G.; Chiappini, R

    2003-07-01

    In this paper, the authors describe a sensitive method for low-level non-exchangeable OBT determination. This methodology combines suitable sample treatment, a combustion apparatus for large-sized samples and low-background liquid scintillation spectrometry, along with precautions that substantially reduce the risks of sample contamination. Great care must be taken in the measurement of non-exchangeable OBT at environmental levels. Many authors have discussed the opportunities for cross-contamination between samples and contamination by exchange with the laboratory atmosphere. The authors also describe an application of the methodology to a large-scale sampling and measurement campaign, aimed at the determination of the environmental non-exchangeable OBT background level in tree leaves and ferns collected on the site and in the vicinity of a research centre located in the south-west of France, not far from Bordeaux. This study constitutes a 'zero level' for the non-exchangeable OBT activity, as, to our knowledge, there is no tritium source within or in the surroundings of the sampled area capable of producing non-exchangeable OBT activities above the natural levels. Our analyses showed that non-exchangeable OBT activities in the collected samples were very low, ranging from below the detection limit (ca 0.7 Bq kg{sup -1} of dry material) to ca 2 Bq kg{sup -1} of dry material. These values are similar to the natural tritium background measured in water samples. No discrepancies can be shown between fern samples and oak tree leaf samples or between samples collected inside and outside the research site.

  12. Systems Biology-an interdisciplinary approach.

    Science.gov (United States)

    Friboulet, Alain; Thomas, Daniel

    2005-06-15

    System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

  13. Preliminary design of a biological treatment facility for trench water from a low-level radioactive waste disposal area at West Valley, New York

    Energy Technology Data Exchange (ETDEWEB)

    Rosten, R.; Malkumus, D. [Pacific Nuclear, Inc. (United States); Sonntag, T. [New York State Energy Research and Development Authority, NY (United States); Sundquist, J. [Ecology and Environment, Inc. (United States)

    1993-03-01

    The New York State Energy Research and Development Authority (NYSERDA) owns and manages a State-Licensed Low-Level Radioactive Waste Disposal Area (SDA) at West Valley, New York. Water has migrated into the burial trenches at the SDA and collected there, becoming contaminated with radionuclides and organic compounds. The US Environmental Protection Agency issued an order to NYSERDA to reduce the levels of water in the trenches. A treatability study of the contaminated trench water (leachate) was performed and determined the best available technology to treat the leachate and discharge the effluent. This paper describes the preliminary design of the treatment facility that incorporates the bases developed in the leachate treatability study.

  14. Assessments at multiple levels of biological organization allow for an integrative determination of physiological tolerances to turbidity in an endangered fish species

    OpenAIRE

    Hasenbein, Matthias; Fangue, Nann A.; Geist, Juergen; Komoroske, Lisa M.; Truong, Jennifer; McPherson, Rina; Connon, Richard E.

    2016-01-01

    Turbidity can influence trophic levels by altering species composition and can potentially affect fish feeding strategies and predator?prey interactions. The estuarine turbidity maximum, described as an area of increased suspended particles, phytoplankton and zooplankton, generally represents a zone with higher turbidity and enhanced food sources important for successful feeding and growth in many fish species. The delta smelt (Hypomesus transpacificus) is an endangered, pelagic fish species ...

  15. Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology.

    Science.gov (United States)

    Bonham, Kevin S; Stefan, Melanie I

    2017-10-01

    While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance.

  16. Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology.

    Directory of Open Access Journals (Sweden)

    Kevin S Bonham

    2017-10-01

    Full Text Available While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance.

  17. Wishing away Plagiarism in Scientific Publications! Will it work? A situational analysis of Plagiarism policy of journals in PubMed.

    Science.gov (United States)

    Debnath, Jyotindu; Cariappa, M P

    2018-04-01

    Plagiarism remains a scourge for the modern academia. There are inconsistencies in the plagiarism policy scientific journals. The aims of this study was to analyze types of published articles on 'Plagiarism' available on PubMed over last two decades against a backdrop of the plagiarism policy of the journals publishing such articles. A literature search on PubMed (https://www.ncbi.nlm.nih.gov/pubmed) was made using the search term "plagiarism" from 01 January 1997 till 29 March 17. All publications having 'plagiarism' in the title formed the study group. The following were noted: types of articles published, ethical and plagiarism policy of the journal as available in the Instructions to authors and or in the journal home page. A total of 582 publications from 320 journals were studied. Editorials (165, 28.3%) and Letters to the Editor (159, 27.3%) formed the bulk. Research articles (56, 9.6%), Review articles (51, 8.7%) and Commentaries (47, 8%) formed the remainder. Detailed ethical guidelines were present in 221 (69%). Outline ethical guidelines only were present in 15 (4.7%) journals. 49 (15.3%) journals did not have any ethical guidelines. Detailed description of the policy on plagiarism was found in 80 (25%) journals. Only an outline description was found in 29 (9%) journals while a plagiarism policy/statement was totally absent in 176 (55%) journals. There is a need to have a well defined plagiarism policy/statement for all scholarly journals easily visible on their home pages on the internet and also in their Instructions to Authors.

  18. Nursing identity and patient-centredness in scholarly health services research: a computational text analysis of PubMed abstracts 1986-2013.

    Science.gov (United States)

    Bell, Erica; Campbell, Steve; Goldberg, Lynette R

    2015-01-22

    The most important and contested element of nursing identity may be the patient-centredness of nursing, though this concept is not well-treated in the nursing identity literature. More conceptually-based mapping of nursing identity constructs are needed to help nurses shape their identity. The field of computational text analytics offers new opportunities to scrutinise how growing disciplines such as health services research construct nursing identity. This paper maps the conceptual content of scholarly health services research in PubMed as it relates to the patient-centeredness of nursing. Computational text analytics software was used to analyse all health services abstracts in the database PubMed since 1986. Abstracts were treated as indicative of the content of health services research. The database PubMed was searched for all research papers using the term "service" or "services" in the abstract or keywords for the period 01/01/1986 to 30/06/2013. A total of 234,926 abstracts were obtained. Leximancer software was used in 1) mapping of 4,144,458 instances of 107 concepts; 2) analysis of 106 paired concept co-occurrences for the nursing concept; and 3) sentiment analysis of the nursing concept versus patient, family and community concepts, and clinical concepts. Nursing is constructed within quality assurance or service implementation or workforce development concepts. It is relatively disconnected from patient, family or community care concepts. For those who agree that patient-centredness should be a part of nursing identity in practice, this study suggests that there is a need for development of health services research into both the nature of the caring construct in nursing identity and its expression in practice. More fundamentally, the study raises questions about whether health services research cultures even value the politically popular idea of nurses as patient-centred caregivers and whether they should.

  19. Effects of Mine Waste Contamination on Fish and Wildlife Habitat at Multiple Levels of Biological Organization in the Methow River, 2001-2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Peplow, Dan; Edmonds, Robert.

    2002-06-01

    A three-year multidisciplinary study was conducted on the relationship between mine waste contamination and the effects on aquatic and terrestrial habitats in the Methow River below abandoned mines near Twisp in Okanogan County, Washington (U.S.A.). Ore deposits in the area were mined for gold, silver, copper and zinc until the early 1950's. An above-and-below-mine approach was used to study potentially impacted sites. Although the dissolved metal content of water in the Methow River was below the limits of detection, eleven chemicals of potential environmental concern were identified in the tailings, mine effluents, groundwater, streamwater and sediments (Al, As, B, Ba, Cd, Cr, Cu, Mn, Pb, Se and Zn). The potential for ecosystem level impacts was reflected in the risk of contamination in the mine waste to communities and populations that are valued for their functional properties related to energy storage and nutrient cycling. Dissolved and sediment metal contamination changed the benthic insect community structure in a tributary of the Methow River below Alder Mine, and at the population level, caddisfly larval development in the Methow River was delayed. Arsenic accumulation in bear hair and Cd in fish liver suggest top predators are effected. In situ exposure of juvenile triploid trout (Oncorhynchus mykiss) to conditions at the downstream site resulted in reduced growth and increased mortality among exposed individuals. Histopathological studies of their tissues revealed extensive glycogen inclusions suggesting food is being converted into glycogen and stored in the liver but the glycogen is not being converted back normally into glucose for distribution to other tissues in the body. Subcellular observations revealed mitochondrial changes including a decrease in the number and increase in the size of electron-dense metrical granules, the presence of glycogen bodies in the cytoplasm, and glycogen nuclei in exposed trout hepatocytes, which are signs that

  20. Assessments at multiple levels of biological organization allow for an integrative determination of physiological tolerances to turbidity in an endangered fish species.

    Science.gov (United States)

    Hasenbein, Matthias; Fangue, Nann A; Geist, Juergen; Komoroske, Lisa M; Truong, Jennifer; McPherson, Rina; Connon, Richard E

    2016-01-01

    Turbidity can influence trophic levels by altering species composition and can potentially affect fish feeding strategies and predator-prey interactions. The estuarine turbidity maximum, described as an area of increased suspended particles, phytoplankton and zooplankton, generally represents a zone with higher turbidity and enhanced food sources important for successful feeding and growth in many fish species. The delta smelt (Hypomesus transpacificus) is an endangered, pelagic fish species endemic to the San Francisco Estuary and Sacramento-San Joaquin River Delta, USA, where it is associated with turbid waters. Turbidity is known to play an important role for the completion of the species' life cycle; however, turbidity ranges in the Delta are broad, and specific requirements for this fish species are still unknown. To evaluate turbidity requirements for early life stages, late-larval delta smelt were maintained at environmentally relevant turbidity levels ranging from 5 to 250 nephelometric turbidity units (NTU) for 24 h, after which a combination of physiological endpoints (molecular biomarkers and cortisol), behavioural indices (feeding) and whole-organism measures (survival) were determined. All endpoints delivered consistent results and identified turbidities between 25 and 80 NTU as preferential. Delta smelt survival rates were highest between 12 and 80 NTU and feeding rates were highest between 25 and 80 NTU. Cortisol levels indicated minimal stress between 35 and 80 NTU and were elevated at low turbidities (5, 12 and 25 NTU). Expression of stress-related genes indicated significant responses for gst, hsp70 and glut2 in high turbidities (250 NTU), and principal component analysis on all measured genes revealed a clustering of 25, 35, 50 and 80 NTU separating the medium-turbidity treatments from low- and high-turbidity treatments. Taken together, these data demonstrate that turbidity levels that are either too low or too high affect delta