19 research outputs found
Particle fusion in localization microscopy
No full textSingle molecule localization microscopy (SMLM) shows promise for quantitative structural analysis of subcellular complexes and organelles with a resolution well below the diffraction limit. This superresolution microscopy technique relies on the blinking events of fluorescent molecules that labeled the structure of interest and are spatiotemporally spread over the entire field of view and time. Once hundred thousands frames of these sparse events are recorded, single molecule positions are localized with nanometer precision to form a 2D/3D point set of coordinates. Therefore, SMLM images are not conventional pixelated images but rather spatial point patterns. Photon scarcity and incomplete labeling of the imaged structure, however, limit the resolution that can possibly be achieved by means of SMLM. Moreover, due to experimental limitations the axial resolution is typically ~2-3 times worse than the lateral resolution in conventional setups. Inspired by single particle analysis (SPA) in cryo-electron microscopy (cryo-EM), proper alignment of repeated structures ("particle fusion") in a 2D/3D SMLM measurement can overcome these limiting factors and so push for isotropic resolution. The existing approaches for particle fusion in SMLM can be classified into customized routines that are borrowed from SPA in EM or methods that use strong prior knowledge about the structure to be reconstructed. While the first approaches are completely ignoring the differences in image formation model between EM and SMLM, the second ones are highly prone to the template-bias problem. In this thesis, a dedicated particle fusion pipeline for 2D/3D SMLM data is proposed. The approach properly considers the pointillistic nature of the SMLM modality and takes into account the localization uncertainties. Furthermore, while it does not require any prior knowledge about the underlying structure of the particles, it can incorporate certain features such as symmetry into the fusion process. Owing to the novel all-to-all registration scheme, the application of the devised pipeline on experimental data with very poor labeling density has been successfully demonstrated. The requirements for successful particle fusion for different SMLM modalities, namely PAINT and STORM, have been characterized through extensive study on 2D and 3D experimental and simulation data. In 2D, an FRC resolution of 3.3 nm on DNA-origami nanostructures has been achieved, and, in 3D, it was demonstrated how the combination of SMLM as a light microscopy technique and a computational approach enables structural analysis of the Nuclear Pore Complex. Future advances of SMLM rely highly on computational routines after data acquisition. Advanced data analysis techniques such as particle fusion can help pushing the boundaries of structural biology using light microscopy.ImPhys/Computational Imagin
Prevalence and subtyping of Blastocystis sp. in ruminants in Southwestern, Iran
No full textAbstract Blastocystis is the most common gastrointestinal protozoan parasite of humans and many vertebrates. This study was carried out to investigate the prevalence and determination subtype (ST) of Blastocystis in domestic ruminants of Shahrekord County, southwestern Iran. In this descriptive cross-sectional study, 330 ruminant fecal samples (107 cows, 115 sheep, and 108 goats) were evaluated by parasitological methods (direct wet mount microscopic examination and formalin-ether concentration), Giemsa staining, In vitro xenic culture (The modified Dobell and Laidlaw culture method), polymerase chain reaction, and sequencing from 2018 to 2019, then data were analyzed using SPSS software version 21. The overall Blastocystis positive in ruminants was 14.2% and the frequency of Blastocystis sp. in cattle, sheep, and goats were 0.93%, 17.4%, and 24.1% respectively. Molecular diagnosis techniques revealed that ruminants were infected with four STs (genotypes) of Blastocystis including ST5(21.3%), ST7(2.1%), ST10(17.1%) and ST14(57.4%). Also, the STs identified in cows were ST10, and the observed STs in sheep were ST5 (40%), ST7 (3%), ST10 (5%), ST14 (45%), and one unknown subspecies. Goats were infected by ST5 (7.7%), ST10 (23.1%), and ST14 (69.2%). In this study, ST14 was identified as the most common subtype of Blastocystis sp. that was not common between humans and livestock, meanwhile, ST5 and ST7 are common between humans and animals accounted 21.3% and 2.1% of the positive cases, respectively, and reinforces the hypothesis that ruminants are reservoirs of blastocystosis in humans
The Rise of Duterte
No full textThis book draws on the extensive literature on populism, democracy, and emerging markets as well as interviews with senior government officials, experts, and journalists in the Philippines and beyond, This book is the first to analyze the significance and implications of the rise of Filipino president Rodrigo Duterte within a rapidly-changing Asia Pacific region. As China\u27s power in the Pacific grows rapidly, nations that have traditionally been US allies, such as the Phillipines, are experiencing political convulsions; Duterte\u27s open willingness to realign towards China (at the expense of America) in exchange for infrastructure investment is one of the clearest indicators of what China\u27s rise might look like for nations around the world. Timely, precise, accessible and fast-paced, this book will be of value to scholars, journalists, policy-makers, and China watchers. © The Editor(s) (if applicable) and The Author(s) 2018. All rights reserved
Esophageal Strictures in Children
No full textIntroduction: To evaluate main aspects of esophageal strictures in children. Materials and Methods:This cross-sectional study was performed on 43 cases of esophageal stenosis ranging from 1 month to 10 years of age who were admitted in Ghaem and Dr. Sheikh Hospitals from 1995 to 2003 in Mashhad, Iran.
Results: Most cases were male (56%). The most common cause of esophageal stricture was anastomotic stricture after esophageal atresia surgery (34.9%) followed by strictures due to gastroesophageal reflux (25.6%), chemical burns (11.6%), and congenital a (11.6%). Proximal esophagus was the most common site of stricture (48.8%). Dilatation and operation had been chosen as the treatment of choice for most of our cases (42%). The majority of our patients recovered after receiving the proper treatment (60.5%).
Conclusion: Anastomotic stricture after surgical repair of esophageal atresia comprised the most common cause of esophageal stricture. Proximal esophagus was the most common site of stricture. Most of the patients recovered with dilatation, surgery, or a combination of the two
Template-free 2D particle fusion in localization microscopy
No full textMethods that fuse multiple localization microscopy images of a single structure can improve signal-to-noise ratio and resolution, but they generally suffer from template bias or sensitivity to registration errors. We present a template-free particle-fusion approach based on an all-to-all registration that provides robustness against individual misregistrations and underlabeling. We achieved 3.3-nm Fourier ring correlation (FRC) image resolution by fusing 383 DNA origami nanostructures with 80% labeling density, and 5.0-nm resolution for structures with 30% labeling density.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.ImPhys/Quantitative ImagingImPhys/Imaging Physic
Joint registration of multiple point clouds for fast particle fusion in localization microscopy
No full textSUMMARY: We present a fast particle fusion method for particles imaged with single-molecule localization microscopy. The state-of-the-art approach based on all-to-all registration has proven to work well but its computational cost scales unfavorably with the number of particles N, namely as N(2). Our method overcomes this problem and achieves a linear scaling of computational cost with N by making use of the Joint Registration of Multiple Point Clouds (JRMPC) method. Straightforward application of JRMPC fails as mostly locally optimal solutions are found. These usually contain several overlapping clusters that each consist of well-aligned particles, but that have different poses. We solve this issue by repeated runs of JRMPC for different initial conditions, followed by a classification step to identify the clusters, and a connection step to link the different clusters obtained for different initializations. In this way a single well-aligned structure is obtained containing the majority of the particles. RESULTS: We achieve reconstructions of experimental DNA-origami datasets consisting of close to 400 particles within only 10 min on a CPU, with an image resolution of 3.2 nm. In addition, we show artifact-free reconstructions of symmetric structures without making any use of the symmetry. We also demonstrate that the method works well for poor data with a low density of labeling and for 3D data. AVAILABILITY AND IMPLEMENTATION: The code is available for download from https://github.com/wexw/Joint-Registration-of-Multiple-Point-Clouds-for-Fast-Particle-Fusion-in-Localization-Microscopy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online
Three Social Work Professors Walk into an Improv Class: How We Applied Performance Art in Social Work Education at a Hispanic Serving Institution
No full textThe first three authors began learning improvisation acting to enhance their teaching. Improvisation (improv) is the art of unscripted and spontaneous acting. Settings and characters are collaboratively created and developed on the spot. The authors illustrate how they used improv exercises in their teaching to energize research and clinical classes. The second author used improv exercises gradually increasing in complexity. The exercises served as ice breakers and to help students critically and actively process the lessons. The third author hired professional improv actors to enhance a lesson on giving family therapy. The actors—a wife and husband—entered the classroom in-character as a family seeking therapy for adjustment to parenting. In this situation, the professor had the flexibility to “pause” the session to facilitate student discussions on the techniques they were using and brainstorm how to proceed, something that would not be possible in work with real clients. These improv exercises are structured to be accessible to those new to theater. The authors conclude that that the exercises are great for developing communication, listening, and cooperative skills that enhance teaching. With this manuscript, the authors aim to pique the reader’s interest in using improvisation acting in teaching
Detecting structural heterogeneity in single-molecule localization microscopy data
No full textParticle fusion for single molecule localization microscopy improves signal-to-noise ratio and overcomes underlabeling, but ignores structural heterogeneity or conformational variability. We present a-priori knowledge-free unsupervised classification of structurally different particles employing the Bhattacharya cost function as dissimilarity metric. We achieve 96% classification accuracy on mixtures of up to four different DNA-origami structures, detect rare classes of origami occuring at 2% rate, and capture variation in ellipticity of nuclear pore complexes
Therapeutic Effects of Topical Tranexamic Acid in Comparison with Hydroquinone in Treatment of Women with Melasma
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