1,720,979 research outputs found
Nanofluidic electrokinetics in quasi-two-dimensional branched U-turn channels
No full textLab-on-a-Chip (LOC) is a new technology focused on analyzing and controlling flows of fluids, ions, and (bio) particles on the nanometer and micrometer scales, allowing us to shrink a complete fluid-based laboratory into a coin-sized instrumentation. In this thesis, we study a novel fluidic structure with a "branched U-turn" geometry, investigating its potential to perform size-based sorting and characterization on DNA single-molecules. The fluid flow and the DNA molecule motion within the fluidic structure are controlled using electric fields and analyzed with quantitative fluorescence microscopy. The channel depth is less than 1 micrometer, while the channel lengths and widths are in the range of 100 micrometers. Due to these dimensions, the fluidic structure can be simplified as a quasi-two-dimensional system when we perform digital image analysis and numerical simulation. Using these channels, we pose the following research questions: 1. How does the fluid flow behave when various types of electric fields are applied across these channels? 2. How do the pathlines of individual DNA molecules behave inside the confining nanofluidic channels? 3. Can we use these channels as novel devices to sort and characterize single DNA molecules? In Chapter 2, we review the concepts of electrokinetics. Chapter 3 describes the nanofluidic channels studied in this research. In Chapter 4 we studied the first research question by investigating and analyzing the electro-osmotic flow inside the nanofluidic channels. In the experiments, we use distilled water as the liquid in which we add 110 nm diameter fluorescent beads employed as tracer-particles inside 150 nm deep nanofluidic channels. From the results we can characterize the pathlines and velocity distribution of the fluid flow. Due to the complex geometry of the channel, the electro-osmotic flow cannot be calculated analytically. Therefore we use numerical flow simulations to build our model. Comparison between the experimental data and the simulation results give a very good agreement, where the deviation can be explained by the measured Brownian motion of the tracer-particles which was not incorporated in the simulation. The second research question was investigated in Chapter 5. Experiments are performed with two types of dsDNA molecules, λ (48.5 kbp) and T4GT7 (165.6 kbp), using channels with depth of 400 nm. We observe that the electrokinetic pathlines of the DNA molecules depends on the DNA size. We use numerical simulation to calculate the distribution of electrokinetic forces in the channels, which can explain the observed experimental phenomena. The results of Chapter 5 also indicate that, for the first time, size-based separation of DNA molecules can be done in a continuous, sieve-less, manner. This is related to our third research question. By using the nanofluidic channel geometry, we can configure the electric field distribution in the channels and manipulate the electrokinetic forces to influence the pathlines of the DNA molecules. The same results can be expected not only on DNA molecules, but also on any other polarizable biological molecules that can be manipulated using dielectrophoresis.Applied Science
Nuclear Architecture: Image Processing and Analyses
No full textCancer is one of the most well-known groups of diseases that finds its cause in cells having chromosomal aberrations. How and why these aberrations can occur is one of the most important questions asked in modern molecular biology. In the last decades it has become clear that gene regulation in the nucleus, where the chromosomes reside, is strongly correlated with structural organization of nuclear components like the telomeres, centromeres and the chromosomes. With new microscopes, better cameras and new fluorescent labels, the demand for analyses of all the images that can be made is growing. The goal of this thesis is the development of image processing and analyses methods for three dimensional (3D) images acquired by fluorescence microscopy. Several microscopy techniques are described, together with two techniques to visualize the nuclear components (chapter 2). In chapter 3 several deconvolution methods are described. Chapter 4 gives two methods to segment the components in the images. Several analyses can be done after segmentation. In chapter 4 we show, after localization, that telomeres from mouse lymphocytes redistribute into a disk-like structure during G2. In chapter 5 we give a novel method to determine the relative length of telomeres by measuring the integrated intensity in the 3D images. Using this information we can define extremely high signals as telomere aggregates. In chapter 6 we use the segmentation and localization techniques to measure the radial redistributions of components in human mesenchymal stem cells.Applied Science
Midfield microscope: Exploring the extraordinary
No full textIn this thesis the development of the midfield microscope is presented. This is a microscope in which the extraordinary transmission (EOT) through sub-wavelength hole-arrays is applied. Before trying to combine microscopy and EOT, we look at them separately. In chapter 1 an overview is given of the current microscope techniques. The main research questions posed are which qualities, like resolution, the midfield microscope will possess and more importantly whether it will be an addition to the current variety of microscopes. EOT has been subject of research ever since its discovery. A literature study is given in chapter 2, in which both experimental and theoretical results are given. Physical explanations are developed, like surface plasmons and coupled diffracted evanescent waves. For applications, like microscopy or lithography, these explanations are of less importance, as long as the device is working. Because of the lack of a unified theory to predict the transmitted spectra and intensity distribution, we analyze them ourselves. The influence of various parameters, like period or incidence angle, is measured on home-made arrays and is described in chapter 3. We confirmed experimentally that the simple surface plasmon model predicts the transmission spectrum only up to a certain level; experimental verification is an absolute must. Polarization measurements show that the polarization has no influence on the spectrum in 2D, which supports the idea of the array being an active device. The limited angular spread is supported by far-field measurements of the transmission for both Köhler and collimated illumination. Now that we measured the spectra, we should know whether the wavelengths corresponding to the peaks result in an interesting transmission pattern. A theoretical calculation, which is limited to the case of a (two-dimensional) slit-array, is done in chapter 4. The transmission pattern having the best contrast and highly localized spots is not the one corresponding to the peak intensity, but to an interference pattern because the wavelength smaller than the period. Fortunately the intensity is still enhanced (at that wavelength more light is transmitted through a periodic than through a random hole-array, chapter 3). Through an analytical approach was found that for a wavelength smaller than the period the contribution to the pattern is mostly due to the transmission (and not so much the surface waves). The theoretical predictions gave already enough information to formulate the working of the midfield microscope. In chapter 5 it is shown that the microscope is comparable with a confocal one, but instead of two pinholes the hole-array is used in the illumination pathway and a CCD in the imaging pathway. Based on the predicted size of lobes in the intensity pattern the midfield resolution is similar to the confocal one, because the point spread functions have a similar size. The possible use of increased resolution by means of structured illumination in possible combination with nonlinear techniques is discussed. In chapter 6 fluorescence measurements are described. Fluorescent molecules are used as probes for the local intensity. The measurement with continuous fluorescence results in an intensity distribution, similar to the one predicted earlier. This is the first time fluorescence is used to measure the transmitted intensity pattern through a hole-array. Moreover, it is a proof-of-principle that the midfield microscope is able to image a sample, in this case continuously labeled and placed in the transmitted "midfield" intensity distribution. Chapter 7 answers the research questions, conclude this thesis and gives recommendations for further research.Applied Science
Optical microscope and method for obtaining an optical image
No full textThe invention relates to an optical microscope, comprising, at least a light source, a carrier for an object to be examined, a detector for registering the illuminated object, and a light path that during operation runs substantially from the light source to the object and form the object to the detector, wherein a metallic film having a periodic hole array is placed in the light path between the light source and the object, and wherein the carrier of the object is provided with a drive to allow the same to be adjusted in the plane of the carrier, wherein the holes of the metallic thin film have a diameter that is smaller than approximately 250 nm, in that the drive is designed for adjusting the carrier for the object in an orientation perpendicular to the plane of the carrier, and in that a processing device is provided that is connected with the detector for constructing a three-dimensional image of the object.Applied Science
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
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