1,720,952 research outputs found
Editorial: Next-Generation Genetically-Encoded Fluorescent Sensors
No full textImPhys/Microscopy Instrumentation & Technique
Optical tools towards the improvement of optogenetic stimulation
No full textOptogenetics is a powerful addition to the spectrum of techniques available in neuroscience to investigate neurophysiology and unravel how neural circuit structure is related to circuit function. This technique relies on introducing lightsensitive proteins or molecules as actuators to transduce an optical signal into a physiological perturbation of a living cell in vitro or in a living animal. To date, optogenetics has allowed remote control of neural activity in living and awake animals at different scales from single cells to complex networks of neurons to the investigation of animal behaviours. This wide range of experimental scales has been accomplished through joint progress on engineering the biological sensors and the optical design of instruments capable of manipulating with cellular spatial precision and millisecond temporal resolution.ImPhys/Microscopy Instrumentation & Technique
Distance metrology using optical frequency comb a step closer to industrial applications
No full textLength is one of the fundamental physical quantities and its precise measurement is very important for science and technology. Laser-based distance metrology technique is a powerful tool, which is widely applied in geodetic monitoring, environmental monitoring and precision measurement engineering including in space applications. Since the invention of the optical frequency comb (OFC) at the beginning of this century, it has been used as a versatile tool for many applications, such as frequency metrology, spectroscopy, etc. OFC has played an important role in distance metrology enabling the developed techniques to achieve high accuracy in long distance measurement. In the time domain, OFC is a pulse train, which can measure distance with time of flight method or correlation detection method. In the frequency domain, spectrum of OFC consists of a series of discrete lines with equal frequency difference. Methods of dispersive interferometry, multi-heterodyne interferometry, and multi-wavelength interferometry are the techniques proposed and demonstrated in spectral domain distance metrology. Though distance metrology techniques based on OFC have been developed for tens of years, there are still challenges that need to be overcome. In most applications the measurements are completed in the air, where the results are influenced by refractive index of air. As the OFC is a multi-wavelength laser source, refractive index of air is difficult to determine. The other challenge is complexity and high cost of measurement system. Untilnow, to my knowledge, there is no commercial rangefinder which is based on OFC. The large size, complex configuration and high price are the bottlenecks restricting OFC’s entrance into industrial applications
Explaining the FLASH Effect: Investigating the Oxygen Hypothesis of the Proton FLASH Effect in Zebrafish
No full textThis thesis investigates the tissue sparing effect of FLASH (>40 Gy/s) radiation, as opposed to CONV (conventional, dose rates typically between 0.010.1 Gy/s) radiation. We irradiated zebrafish embryos (4 days past fertilisation) with 116 MeV protons. The aim was (1) to measure the effect, and (2) if the effect were significant, see whether it depended on the oxygen concentration in the tissue, as the oxygen depletion hypothesis (a popular theory on the underlying mechanics of the FLASH effect) predicts. We irradiated embryos with either FLASH or CONV, where a possible FLASH effect would reduce toxicity of the FLASH radiation. We did the same for zebrafish which were deliberately put in a hypoxic condition prior to irradiation. In that case, the depletion hypothesis would predict that the difference between FLASH and CONV disappears. Our biomarkers for radiobiological damage were the survival rate and γH2AX foci formation. In our experimental conditions, the radiation effect on the survival rate waseclipsed by other factors which could not be isolated. We did confirm the possibility of using γH2AX foci formation as a marker for radiobiological damage in fullbody irradiated zebrafish embryos. There were individual samples that showed clear and localised specific γH2AX signal, but these were tooscarce and the signal was too inconsistent across samples to gather meaningful statistics. This was most often caused by limited antibody penetration in the embryo. We were therefore unable to draw conclusions about the FLASH effect. Better and more consistent antibody penetration, e.g. by longer digestion in collagenase before antibody staining, could change this in the future. We further custombuilt and validated a hypoxic aquarium to produce hypoxic zebrafish tissue, as well as a computational model of the irradiation setup to simulate the dose distribution in the zebrafish container. We found the dose distribution to be sufficiently homogeneous for our experiment, at least 91.47% uniform for CONV and 90.72% uniform for FLASH.Applied Physic
Zebrafish irradiation: The effects of high dose-rate radiation on zebrafish embryos
No full textFinding a favorable cure for cancer has been one of the main clinical challenges today. Nowadays the majority of the patients is treated with radiotherapy. Recently research in to a new paradigm of radiotherapy, so called FLASH radiotherapy, has opened up a new insight in to reducing negative side effects. FLASH dose rates (>40 Gy/s) have the ability to reduce the prevalence of negative side effects in patients without sacrificing tumor control. This study focuses on whether dose rate affects the degree of damage to healthy tissues caused by ionizing radiation. Understanding the biological mechanisms that influence the response to radiotherapy and specifically FLASH radiotherapy is therefore key knowledge in the development of new therapeutic protocols.This study evaluates dose-rate effects using zebrafish embryos as a small model organism. To study dose-rate effects the zebrafish are irradiated at 24 hours post fertilization and biomarkers are researched to asses dose-rate effects. They are irradiated using a Co60 irradiator providing a dose-rate of 0.015 Gy/s and a second one providing a dose-rate of 0.211 Gy/s. Several biomarkers for radiation damage are identified, including rate of embryonic development (hatching), DNA breaks and apoptosis. The DNA breaks are measured using a TUNEL assay and apoptosis through a caspase-3 assay. The results of the assay's are measured using confocal microscopy.Monte Carlo simulations of the experimental setup were performed to assess the uniformity of radiation and effective dose. They show a homogeneous dose throughout the sample, they show a 37% lower dose in water in the sample compared to air.The hatching biomarker shows that the hatching rates are 0.24 +-0.03 for non irradiated samples and 0.37 +- 0.31 and 0.43 +- 0.20 for samples that have been irradiated with respectively 0.008 Gy/s and 0.015 Gy/s with a total dose of 10 Gy. It shows that the hatching rates decreases for the irradiated embryos compared to the non irradiated samples however no significant difference can be found for different dose-rates. The sub-cellular biomarkers, the TUNEL assay and the caspase-3 assay, seem more promising in detecting dose-rate differences but more research is needed to find the dose-rate effects on DNA damage and apoptosis. In order to gain a fuller picture into the biological mechanisms of FLASH dose-rate radiation a greater variety of biomarkers and more research in to DNA damage and apoptotic biomarkers is needed
Image Analysis for All-Optical Electrophysiology
No full textThe study of the electrophysiological properties of neurons has reached a new level thanks to recent techniques that combine knowledge from different fields of science. For a method such as all-optical electrophysiology, the quality of cell segmentation in the image has one of the critical roles since the accuracy of illumination and perturbation of cells depends on it. The task becomes challenging because neurons have a complex morphology, and therefore traditional image analysis methods cannot perform accurate segmentation.This project focuses on building two AI-based models for neuron soma detection and mask prediction, as well as such an essential aspect of the experiment as the quality of the image recordings. Developed models demonstrate high performance and are ready to be applied to the images of cells with or without fluorescent labels, although expanding the training dataset is recommended for improving segmentation accuracy. In addition, the signal-to-noise ratio was measured for recordings with different parameters such as camera readout speed, illumination intensity, and frequency of laser switching. The project can be extended to detect and segment dendritic trees and spines to gain new insights into the subtle process of intercellular communication.Applied Sciences | Nanobiolog
Integrated Array Tomography: Development and Applications of a Workflow for 3D Correlative Light and Electron Microscopy
No full textMulti-modal imaging techniques have become essential for better understanding fundamental questions in cell biology such as disease progression. While individual microscopy methods have rapidly advanced in recent years, the information content of any one imaging technique is limited to the type of contrast that particular technique is sensitive to. By tagging particular biomolecules with a fluorescent protein, fluorescence microscopy (FM), for example, can relay dynamic information about the distribution of these biomolecules in their cellular environment. It struggles, however, to convey information regarding the structure of the organelles that might contain these biomolecules or the surroundings of their cellular environment. Electron microscopy (EM), on the other hand, can provide detailed layouts of cellular structure by staining membranes with heavy metals. Thus, by correlating these modalities (correlative light and electron microscopy, CLEM), a more holistic understanding of the relationship between structure and function at the (sub-)cellular level can be achieved. Array tomography (AT) is a technique combining FM and EM for volumetric imaging, first introduced in 2007 for studying brain tissue. The technique has since expanded, but the approach has largely remained the same. Biological material is cut into a series of ultrathin (∼100 nm) sections (an array) and prepared for sequential FM and EM imaging by applying a series of immunofluorescence and heavy metal stains. Correlative images of the serial sections are then computationally aligned to reconstruct the 3D structure (tomography). Compared to other volumetric imaging techniques in the life sciences, AT offers the ability to correlate structure and function at high resolution across large fields of view. Moreover, it enables high axial resolutionfor both EM and FM as determined by the section thickness...ImPhys/Microscopy Instrumentation & Technique
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
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