130,463 research outputs found
Bacterial chemotaxis in an optical trap
No full textAn optical trapping technique is implemented to investigate the chemotactic behavior of a marine bacterial strain Vibrio alginolyticus. The technique takes the advantage that the bacterium has only a single polar flagellum, which can rotate either in the counter-clock-wise or clock-wise direction. The two rotation states of the motor can be readily and instantaneously resolved in the optical trap, allowing the flagellar motor switching rate S(t)to be measured under different chemical stimulations. In this paper the focus will be on the bacterial response to an impulsive change of chemoattractant serine. Despite different propulsion apparati and motility patterns, cells of V. alginolyticus apparently use a similar response as Escherichia coli to regulate their chemotactic behavior. Specifically, we found that the switching rate S(t) of the bacterial motor exhibits a biphasic behavior, showing a fast initial response followed by a slow relaxation to the steady-state switching rate S0. The measured S(t)can be mimicked by a model that has been recently proposed for chemotaxis in E. coli. The similarity in the response to the brief chemical stimulation in these two different bacteria is striking, suggesting that the biphasic response may be evolutionarily conserved. This study also demonstrated that optical tweezers can be a useful tool for chemotaxis studies and should be applicable to other polarly flagellated bacteria. © 2011 Altindal et al
Determination of Bacterial Chemotaxis Response Functions by Optical Trapping
No full textA two-lobe response function is considered as a manifestation of temporal signal comparison in bacterial chemosensing. The second lobe in the response function appears as a result of adaptive behavior of the underlying signaling network, which allows bacteria to stay sensitive over a wide range of background signal levels. It has been argued that this two-lobe response reflects the dual requirements of the bacteria to taxis along a chemical gradient and to localize once the top of the gradient is reached. Calculations based on the run-tumble motility pattern of Escherichia coli showed that the second lobe improved the bacterium's localization capability. Intrigued by a recently observed run-reverse-flick motility cycle of a marine bacterium Vibrio alginolyticus, we investigate the motility-response relationship in this bacterium. Using a novel optical trapping technique, we measure the response of V. alginolyticus to an impulsive stimulus of chemoattractant serine. By exploiting an asymmetry in the rotation of the polar flagellum, we are able to determine for the first time how the bacterium responds to chemical stimuli while swimming forward or backward. Our measurements suggest that this marine bacterium regulates its forward and backward swimming intervals differently, exhibiting behaviors that is consistent with an exploration-exploitation strategy.
In our measurements, we also find that the cell-body Ω(t) and the flagellar ω(t) rotational angular frequencies oscillate in time and are in synchrony with the forward and backward swimming intervals. Unexpectedly, Ω(t) and ω(t) are found to be anticorrelated in that the cell body rotates slower in the forward direction than in the backward direction, Ωf<Ωb, but the flagellum rotates faster in the forward direction than in the backward direction. The change in the rotational load (~25%) is significantly greater than that predicted by flagellum deformation but can be accounted for by the precession of the flagellum about the body axis during the backward swimming interval. We postulate that as a result of the precession, a kink is generated at the base of the flagellum that is subsequently amplified when the flagellum motor reverses direction, leading to the flick, the direction randomization step in V. alginolyticus' motility pattern
MeSH term explosion and author rank improve expert recommendations
No full textInformation overload is an often-cited phenomenon that reduces the productivity, efficiency and efficacy of scientists. One challenge for scientists is to find appropriate collaborators in their research. The literature describes various solutions to the problem of expertise location, but most current approaches do not appear to be very suitable for expert recommendations in biomedical research. In this study, we present the development and initial evaluation of a vector space model-based algorithm to calculate researcher similarity using four inputs: 1) MeSH terms of publications; 2) MeSH terms and author rank; 3) exploded MeSH terms; and 4) exploded MeSH terms and author rank. We developed and evaluated the algorithm using a data set of 17,525 authors and their 22,542 papers. On average, our algorithms correctly predicted 2.5 of the top 5/10 coauthors of individual scientists. Exploded MeSH and author rank outperformed all other algorithms in accuracy, followed closely by MeSH and author rank. Our results show that the accuracy of MeSH term-based matching can be enhanced with other metadata such as author rank
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
"Closing the R&D Gap, Evaluating the Sources of R&D Spending"
No full textBoth spending and tax policies have been implemented in the United States with the goal of stimulating private sector research and development (R&D). Karier questions whether current R&D policy, especially the research and experimentation tax credit, can contribute to closing the gap between nondefense expenditures on R&D in the United States and such expenditures in other countries, such as Japan and Germany. He also explores possible changes to our current R&D policy to make it more effective.
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Scholarly Communication and Publishing Lunch and Learn Talk #11: The ULS Open Access Author Fee Fund
No full textAt the May 2014 talk, you will learn about the ULS Open Access Author Fee Fund--what it is, why we do it, how it works, and how the program is going so far
The R&D Tax Incentives
No full textThis article sets out some background information and reflections of the author on the R&D tax incentive schemes included in the Common Corporate Tax Base (CCTB) Proposal. In particular the author analyzes the stimulus to private R&D through ad hoc tax incentives included in the CCTB Proposal and dives into the actual provisions included in the Proposal highlighting the most relevant issues connected with their design and interpretation. Moreover, the author explores the interaction between the CCTB Proposal and the granting by Member States of domestic R&D tax incentives
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