1,721,013 research outputs found
A Dual-Region Fiber-Optic SPR Biosensor with Self-Referencing Compensation of Bulk Refractive Index and Temperature Effects
No full textDesign and Implementation of a Dual-Region Self-Referencing Fiber-Optic Surface Plasmon Resonance Biosensor
Full text linkThe need for self-referencing is extremely important in the field of biosensing. In this manuscript, we report on the study, design, and validation of a dual-region self-referencing fiber-optic surface plasmon resonance biosensor. One region is intended to measure and monitor the binding events of the biological sample under test, while the other one is designed to be used as a reference channel to compensate for external factors, such as bulk refractive index modifications and temperature oscillations, that can negatively affect the biomolecular interaction measurement. Two different configurations for the biosensor probe are presented and investigated here, both theoretically and experimentally. First, the theoretical performance of the proposed biosensor probes, in terms of surface plasmon resonance wavelength shift, was simulated using a numerical model. Afterward, they were experimentally validated in sucrose-water solutions and showed a response to refractive index and temperature changes with sensitivities up to 2000 nm/RIU and 1.559 nm/°C, respectively. Finally, an aptamer-based bioassay and a high-resolution melting assay were successfully implemented on the two proposed configurations, demonstrating the feasibility of analyzing the binding events and measuring other external signal modifications simultaneously using the same biosensor probe.sponsorship: This work has received funding from European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 955623 (H2020-MSCAITN-CONSENSE). (European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant|955623, European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant|955623)status: Publishe
INNOVATIEVE NUCLEÏNEZUURGEBASEERDE STRATEGIEËN VOOR FIBER OPTIC SURFACE PLASMON RESONANCE BIOSENSORDESIGN
No full textThe diverse information embedded in the specific sequence of DNA molecules has been feeding our understanding and insights in disease heritage, spreading and evolution. Ultrasensitive detection of the DNA molecules themselves is crucial for the early-stage detection of several diseases, as it facilitates the minimization of actual disease burden. Gold standard technologies, such as the polymerase chain reaction (PCR), are mainly restricted to sophisticated laboratory settings, relying on trained personal, bulky equipment and large batches of samples. In order to improve the accessibility of nucleic acid (NA) analysis and provide its valuable information outside these sophisticated settings, alternative biosensors are being developed. These biosensors can offer more user-friendly, robust, fast and cost-effective devices, thereby focusing on the needs of the end-user. In addition, biosensors do not limit themselves to the use of DNA as target molecule. Instead, the unique structure of DNA is also exploited as a building block for smart biosensor design.
Fiber optic surface plasmon resonance (FO-SPR) is a mass-sensitive biosensing technique with some advantageous characteristics, such as its real-time aspect, user-friendliness and fast analysis. While these FO-SPR characteristics match several of the features mentioned above, DNA-based FO-SPR assays are mainly restricted to classical hybridization strategies, limiting the sensitivity to the lower nM range. Ultrasensitive detection of NAs continues to be challenging and alternative FO-SPR designs to generate and amplify this signal have not been fully explored.
Upcoming fields like DNA nanotechnology drive these innovative designs by discovering new functional molecules, such as DNAzymes. These enzyme-like molecules are of great interest in biosensor development due to their easy coupling to existing signal generation systems and their inherent amplification. Because of their NA-based structure, they are more stable, cost-effective, and show superior flexibility compared to their protein counterparts in their design towards different target molecules. However, DNA nanotechnology is not yet mature and surface-based DNAzyme strategies have been concentrating mainly on metal ion detection. NA and protein applications are rare and demand more advanced design and implementation of current DNAzyme-based strategies.
In this framework, the main objective of this dissertation was to design innovative NA-based strategies using a FO-SPR platform for the sensitive and specific detection of NAs. To do so, three different NA-based strategies were presented: (i) a FO-PCR melting assay, (ii) a FO-SPR sensor design sensitive to catalytic DNAzyme activity and (iii) a DNAzyme-based FO-PCR assay.
The first design was based on PCR amplification of the target sequences, which subsequently hybridized to the FO sensor surface and DNA-functionalized gold nanoparticles (AuNPs) for amplification. As a proof-of-concept, the assay was explored for the detection of celery DNA, one of the most important provokers of food allergic reactions. Different concentrations of celery DNA (1 pM - 0.1 fM) were detected and inclusion of a following melting step enabled distinction from closely related sequences, such as carrot DNA. The concept was validated in cleaning water samples and benchmarked against a reference qPCR followed by high resolution melting, which showed excellent agreement (R² = 0.96). This way the FO-PCR melting assay provided a rapid and simple detection method, suitable for one-step quantification and discrimination of single stranded DNA (ssDNA) with great potential in fields such as food quality and safety assurance.
For the second design, first a robust ligation strategy was developed to functionalize the FO-SPR sensing surface with ssDNA, which in turn was labelled with AuNPs, to serve as the DNAzyme substrate. Next, we studied the relation between the change in FO-SPR shift and the DNAzyme cleavage activity, which showed faster cleavage kinetics for higher DNAzyme concentrations. Finally, we translated this real-time cleavage activity into a generic biosensing concept for the detection of ssDNA targets. A DNAzyme-inhibitor complex was designed to release active DNAzymes in a controlled way as function of the target concentration. Reproducible target detection was demonstrated with a theoretical LOD of 1.4 nM. In summary, an innovative DNAzyme-based FO-SPR biosensor was established with great potential to act as universal sensor for promising applications in the medical and agrofood sector.
The final design in this dissertation combined insights from both the first and the second design by boosting the catalytic cleavage activity through PCR-amplification of the DNAzymes. Based on the readout system of the second design, the surface cleavage efficiency of the DNAzyme-extended amplicons (DNAzyme-amps) was first evaluated and confirmed. Next, the PCR and cleavage reaction conditions were fine-tuned to assure compatibility with the FO-SPR system and establish a one-step assay. As a proof-of-concept, the primer pair with the built-in DNAzyme complement was tested for the detection of the antimicrobial resistance gene MCR-2. PCR-amplified DNAzyme-amps generated in the presence of the MCR-2 gene were monitored in real-time, resulting in an experimental LOD of 4 × 10^5 copy numbers or 6.6 fM. In addition, the DNAzyme-based FO-PCR assay was able to discriminate between the MCR-1 and MCR-2 genes, further proving the specificity of this assay. In short, this DNAzyme-based FO-PCR assay provides a universally applicable, real-time system for the detection of virtually any NA target, in a specific and sensitive manner.status: Publishe
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe 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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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