116 research outputs found
The Relaxed Complex Method: Accommodating Receptor Flexibility for Drug Design with an Improved Scoring Scheme
No full textAn extension of the new computational methodology for drug design, the " relaxed complex" method (J.-H. Lin, A. L. Perryman, J. R. Schames, and J. A. McCammon, Journal of the American Chemical Society, 2002, vol. 24, pp. 5632-5633), which accommodates receptor flexibility, is described. This relaxed complex method recognizes that ligand may bind to conformations that occur only rarely in the dynamics of the receptor. We have shown that the ligand-enzyme binding modes are very sensitive to the enzyme conformations, and our approach is capable of finding the best ligand enzyme complexes. Rapid docking serves as an efficient initial filtering method to screen a myriad of docking modes to a limited set, and it is then followed by more accurate scoring with the MM/PBSA (Molecular Mechanics/Poisson Boltzmann Surface Area) approach to find the best ligand - receptor complexes. The MM/PBSA scorings consistently indicate that the calculated binding modes that are most similar to those observed in the x- ray crystallographic complexes are the ones with the lowest free energies
Hiv-1 Protease Molecular Dynamics of a Wild-Type and of the V82f/I84v Mutant: Possible Contributions to Drug Resistance and a Potential New Target Site for Drugs
No full textThe protease from type I human immunodeficiency virus (HIV-1 ) is a critical drug target against which many therapeutically useful inhibitors have been developed; however, the set of viral strains in the population has been shifting to become more drug-resistant. Because indirect effects are contributing to drug resistance, an examination of the dynamic structures of a wild-type and a mutant could be insightful. Consequently, this study examined structural properties sampled during 22 nsec, all atom molecular dynamics (MD) simulations (in explicit water) of both a wild - type and the drug-resistant V82F/184V mutant of HIV-1 protease. The V82F/ 184V mutation significantly decreases the binding affinity of all HIV-1 protease inhibitors currently used clinically. Simulations have shown that the curling of the tips of the active site flaps immediately results in flap opening. In the 22-nsec MD simulations presented here, more frequent and more rapid curling of the mutant's active site flap tips was observed. The mutant protease's flaps also opened farther than the wild-type's flaps did and displayed more flexibility. This suggests that the effect of the mutations on the equilibrium between the semiopen and closed conformations could be one aspect of the mechanism of drug resistance for this mutant. In addition, correlated fluctuations in the active site and periphery were noted that point to a possible binding site for allosteric inhibitors
Information behaviors in an online smoking cessation forum
No full textSmoking is a major contributor to morbidity and mortality today, and a focus of attention by primary care practitioners and public health. Few studies take into account the role of community-based information transactions, nor have they examined the information needs of quitting smokers beyond generic patient education pamphlets. A pilot study examines the function and value of information communicated in an online forum dedicated to smoking cessation. Firstly, a Web-based survey was sent to fourteen forum participants known by the author. Twenty questions about medications, decision support sources, the evaluation of those sources, and basic demographic information were asked and the resulting responses were analyzed. Secondly, 371 selected posts from the Web forum were collected to better understand the importance and frequency of specific types of cessation-related information. Several models are discussed in a preliminary attempt to characterize the forum's community-based information behaviors. Survey respondents view the existence of online community-based information resources (in the persons of their community peers) as a major factor in their cessation efforts. Although no attempt was made to generalize findings beyond this initial pilot, gaps were tentatively identified between the support provided by more traditional healthcare practitioners and the information needs experienced by this population. In their provision of a milieu for the exchange of information, online fora may enable support at a depth and quantity unavailable through more immediate channels. Further studies are needed to develop a better understanding of information-related behaviors of this large population
Photogrammetry of blue whales with an unmanned hexacopter
Get PDFAuthor Posting. © Society for Marine Mammalogy, 2016. This article is posted here by permission of Society for Marine Mammalogy for personal use, not for redistribution. The definitive version was published in Marine Mammal Science 32 (2016):1510–1515, doi:10.1111/mms.12328.Baleen whales are the largest animals ever to live on earth, and many populations
were hunted close to extinction in the 20th century (Clapham et al. 1999). Their
recovery is now a key international conservation goal, and they are important in marine
ecosystems as massive consumers that can promote primary production through
nutrient cycling (Roman et al. 2014). However, although abundance has been
assessed to monitor the recovery of some large whale populations (e.g., Barlow et al.
2011, Laake et al. 2012) many populations are wide-ranging and pelagic, and this
inaccessibility has generally impeded quantitative assessments of recovery (Peel et al.
2015). To augment traditional abundance monitoring, we suggest that photogrammetric
measures of individual growth and body condition can also inform about population
status, enabling assessment of individual health as well as population numbers. Photogrammetry
from manned aircraft has used photographs taken from directly above
whales to estimate individual lengths (Gilpatrick and Perryman 2008) and monitor growth trends (Fearnbach et al. 2011), and shape profiles can be measured to assess
body condition to infer reproductive and nutritional status (e.g., Perryman and Lynn
2002, Miller et al. 2012). Recently, Durban et al. (2015) demonstrated the utility of
an unmanned hexacopter for collecting aerial photogrammetry images of killer
whales (Orcinus orca); this provided a noninvasive, cost-effective, and safe platform
that could be deployed from a boat to obtain vertical images of whales. Here we
describe the use of this small, unmanned aerial system (UAS) to measure length and
condition of blue whales (Balaenoptera musculus), the largest of all whales.María Francisca Cortés Solari;
Rafaela Landea Briones;
MERI Foundation;
Woods Hole Oceanographic Institution Acces
Further study is needed to define and measure the use of reflective practice in library and information science
No full textA review of: Grant, Maria J. “The Role of Reflection in the Library and Information Sector: A Systematic Review.” Health Information and Libraries Journal (2007) 24: 155-166.
Objectives - To identify and review the literature of reflective practice in Library and Information Science (LIS) in order to understand its role, particularly with regard to health libraries.
Design - Systematic review
Setting - LIS English-language articles indexed in the Library and Information Science Abstracts (LISA) database and published between 1969 and 2006.
Subjects - 929 citations retrieved from the LISA database.
Methods - The author conducted free text searches in the LISA database for the terms ‘reflective’ or ‘reflection*’ or ‘reflexion*.’ An initial search series was conducted in 2004 in order to retrieve items published between 1969-2003, then in 2007, for articles published between 2004-2006. In all, 929 article citations were retrieved. Exclusion criteria included those articles addressing the facilitation of reflective practices in others, as well as non-English language, and materials predating 1969. After review, 55 articles met the author’s relevance standard. Citation tracking then added 10 articles to the total. From this dataset, full text articles were obtained where possible, if determined on initial scrutiny to be deserving of further examination. Thirteen articles (.013%) were ultimately selected for analysis. These articles were categorized as analytical or non-analytical, with respect to perspective (individual or organizational), and recency of events (retrospective or recent). In addition, a determination was made about whether the articles’ focus was reflection occurring on (in retrospect to) or in (during) practice.
Main results - Of 13 articles, 5 were found to be non-analytical, with the other 6 being analytical. Three of the non-analytical items were the reflections of an individual, while the remaining 2 offered an organizational perspective. The non-analytical accounts were found to be mostly descriptive accounts by an individual, mostly retrospective and offering no consideration of implications for LIS practice. Analytical reflective accounts attempt to systematically appraise events from the recent past, and draw conclusions in order to improve future actions.
Conclusion – A gradual increase in the use of analytical reflective practice is demonstrated over the period from 1969-2006, although insufficient examples of the practice were found in the published literature. Reflective practice is likely to be beneficial to LIS practitioners, especially when time is spent in considering the implications of lessons learned from practice
Tracking theory building and use trends in selected LIS journals: More research is needed
No full textObjective - The authors measure theory incidents occurring in four LIS journals between 1984-2003 in order to examine their number and quality and to analyze them by topic. A third objective, only identified later in the text of the study, was to compare theory development and use between Korean and international journals. Research questions asked include whether LIS has its own theoretical base as a discipline, and what characteristics the theoretical framework has.
Design – Bibliometric study.
Setting – Journal issues selected from four LIS journals for the time span from 1984 - 2003.
Subjects – Two international journals, Journal of the American Society for Information Science and Technology (JASIST) and Library and Information Science Research (LISR) were selected based on their high ranking in the Social Sciences Citation Index (SSCI) impact factors. Two Korean journals, Journal of the Korean Society for Information Management (JKSIM) and Journal of the Korean Society for Library and Information Science (JKSLIS) were selected.
Methods - After having determined a definition of theory, and identifying different levels of theory, the authors set up rules for the identification of theory incidents, which are defined as “events in which the author contributed to the development or the use of theory in his/her own paper” (550).
Content analysis of 1661 research articles was performed to measure theory incidents according to working definitions. Interrater reliability was ensured by conducting independent coding for “subfield classification, identification of theory incidents, and quality measurement” (555), using a sample of 199 articles (random selection not specified), achieving 94-97% interrater reliability. Incidents, once identified, were evaluated for quality using Dubin’s “efficiency of law” criteria, involving measures of relatedness, directionality, co-variation, rate of change, and “profundity,” defined as the depth to which theory is incorporated into the research study.
Main Results - 21.79% (n=362) of the articles contained theory incidents that were analyzed and evaluated. Trend measurement indicated an overall increase, although a slight decrease was shown in the year range 1993-2003. International journals accounted for 61.33% of theory incidents, compared to 38.67% for the Korean journals. T-testing showed that differences in means between Korean and international journals were not statistically significant.
Topical theory areas were ranked by frequency. The top five areas were shown to be nearly identical between Korean and international journals. ANOVA was performed with significant results in the difference between efficiency ratings.
Conclusion – The authors find that the overall proportion of theory incidents including both theory development and use increased through the 20-year time span examined, and that LIS has established its own theoretical framework based upon the frequency of incidents
Does a social network based model of journal metrics improve ranking?
No full textA Review of: Bollen, J., Van de Sompel, H., Smith, J.A., & Luce, R. (2005). Toward alternative metrics of journal impact: A comparison of download and citation data. Information Processing and Management, 41:1419-1440.
Objective: To test a new model for measuring journal impact by using principles of social networking. Research questions are as follows:
Can valid networks of journal relationships be derived from reader article download patterns registered in a digital library’s server logs?
Can social network metrics of journal impact validly be calculated from the structure of such networks?
If so, how do the resulting journal impact rankings relate to the ISI impact factor (IF)?
Design: Bibliometric, social network centrality analysis
Setting: Los Alamos National Laboratory (LANL), New Mexico
Subjects: 40,847 full-text articles downloaded from a large digital library by 1,858 unique users over a 6 month period.
Methods: Full-text article downloads from a large digital library for a six-month period were examined using social networking analysis methods. ISSNs for journals in which the retrieved articles were published were paired based upon the proximity of use by the same user, based on the supposition that proximal downloads are related in some way. Reader-Generated Networks (RGNs) were then tested for small-world characteristics. The resulting RGN data were then compared with Author-Generated Networks (AGNs) for the same journals indexed in the Institute of Scientific Information (ISI) annual impact factor (IF) rankings, in the Journal Citation Reports (JCR) database. Next, a sample of the AGN-derived pairings was examined by a team of 22 scientists, who were asked to rate the strength of relationships between journals on a five-point scale. Centrality ratings were calculated for the AGN and RGN sets of journals, as well as for the ISI IF.
Main results: Closeness and centrality rankings for the ISI IF and the AGN metrics were low, but significant, suggesting that centrality metrics are an acceptable impact metric. Comparison between the RGN and ISI IF data found marked differences, with RGN mirroring local population needs to a much higher degree, and with a non-significant correlation between the ISI IF and RGN ranking, while AGN and RGN centrality rankings show significant centrality and closeness and betweenness correlations. RGN network ranking identified highly localized foci of interest for the LANL, as well as “interest-bridging” subject areas pointing to possible emerging interests among the scientists.
Conclusion: The study results appear to successfully demonstrate an alternative to existing journal impact ranking that can more validly and accurately reflect the practices of a local community. The authors suggest that the social network-derived methodology for identification of impact rankings avoids biases intrinsic to ISI IF as a result of frequentist metrics collected from a global user group. Although the authors resist the idea of generalizability due to the local nature of their data, they suggest that the methodology can be successfully used in other settings, and for a more global community. Finally, the authors propose the automated creation of an open-source RGN whose data could be localized for smaller communities, with potentially large implications for the existing publishing industry
OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery.
No full textThe Zika virus outbreak in the Americas has caused global concern. To help accelerate this fight against Zika, we launched the OpenZika project. OpenZika is an IBM World Community Grid Project that uses distributed computing on millions of computers and Android devices to run docking experiments, in order to dock tens of millions of drug-like compounds against crystal structures and homology models of Zika proteins (and other related flavivirus targets). This will enable the identification of new candidates that can then be tested in vitro, to advance the discovery and development of new antiviral drugs against the Zika virus. The docking data is being made openly accessible so that all members of the global research community can use it to further advance drug discovery studies against Zika and other related flaviviruses
The role of postgraduate students in co-authoring open educational resources to promote social inclusion: a case study at the University of Cape Town
No full textThis is an Accepted Manuscript of an article published by Taylor & Francis in Distance Education on 24 Jul 2012, available online: http://www.tandfonline.com/10.1080/01587919.2012.692052.Like many universities worldwide, the University of Cape Town (UCT) in South Africa has joined the open educational resources (OER) movement, making a selection of teaching and learning materials available through its OER directory, UCT OpenContent. However, persuading and then supporting busy academics to share their teaching materials as OER still remains a challenge. In this article, we report on an empirical study of how UCT postgraduate students have assisted in the process of reworking the academics' teaching materials as OER. Using the concept of contradictions (Engeström, 2001), we endeavor to surface the various disturbances or conflicts with which the postgraduate students had to engage to make OER socially inclusive, as well as Engeström's “layers of causality" (2011, p. 609) to explain postgraduate students' growing sense of agency as they experienced the OER development process as being socially inclusive
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