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Academic literature on the topic 'Reference-guided alignment'
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Journal articles on the topic "Reference-guided alignment"
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Godfroid, Maxime, Tal Dagan, and Anne Kupczok. "Recombination Signal in Mycobacterium tuberculosis Stems from Reference-guided Assemblies and Alignment Artefacts." Genome Biology and Evolution 10, no. 8 (2018): 1920–26. http://dx.doi.org/10.1093/gbe/evy143.
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de la Fuente, Rene, Ricardo Fuentes, Jorge Munoz-Gama, et al. "Control-flow analysis of procedural skills competencies in medical training through process mining." Postgraduate Medical Journal 96, no. 1135 (2019): 250–56. http://dx.doi.org/10.1136/postgradmedj-2019-136802.
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BackgroundProcedural skills are key to good clinical results, and training in them involves a significant amount of resources. Control-flow analysis (ie, the order in which a process is performed) can provide new information for those who train and plan procedural training. This study outlines the steps required for control-flow analysis using process mining techniques in training in an ultrasound-guided internal jugular central venous catheter placement using a simulation.MethodsA reference process model was defined through a Delphi study, and execution data (event logs) were collected from video recordings from pretraining (PRE), post-training (POST) and expert (EXP) procedure executions. The analysis was performed to outline differences between the model and executions. We analysed rework (activity repetition), alignment-based fitness (conformance with the ideal model) and trace alignment analysis (visual ordering pattern similarities).ResultsExpert executions do not present repetition of activities (rework). The POST rework is lower than the PRE, concentrated in the steps of the venous puncture and guidewire placement. The adjustment to the ideal model measure as alignment-based fitness, expressed as a median (25th–75th percentile) of PRE 0.74 (0.68–0.78) is less than POST 0.82 (0.76–0.86) and EXP 0.87 (0.82–0.87). There are no significant differences between POST and EXP. The graphic analysis of alignment and executions shows a progressive increase in order from PRE to EXP executions.ConclusionProcess mining analysis is able to pinpoint more difficult steps, assess the concordance between reference mode and executions, and identify control-flow patterns in procedural training courses.
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Wu, Ming-Long, Jong-Chih Chien, Chieh-Tsai Wu, and Jiann-Der Lee. "An Augmented Reality System Using Improved-Iterative Closest Point Algorithm for On-Patient Medical Image Visualization." Sensors 18, no. 8 (2018): 2505. http://dx.doi.org/10.3390/s18082505.
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In many surgery assistance systems, cumbersome equipment or complicated algorithms are often introduced to build the whole system. To build a system without cumbersome equipment or complicated algorithms, and to provide physicians the ability to observe the location of the lesion in the course of surgery, an augmented reality approach using an improved alignment method to image-guided surgery (IGS) is proposed. The system uses RGB-Depth sensor in conjunction with the Point Cloud Library (PCL) to build and establish the patient’s head surface information, and, through the use of the improved alignment algorithm proposed in this study, the preoperative medical imaging information obtained can be placed in the same world-coordinates system as the patient’s head surface information. The traditional alignment method, Iterative Closest Point (ICP), has the disadvantage that an ill-chosen starting position will result only in a locally optimal solution. The proposed improved para-alignment algorithm, named improved-ICP (I-ICP), uses a stochastic perturbation technique to escape from locally optimal solutions and reach the globally optimal solution. After the alignment, the results will be merged and displayed using Microsoft’s HoloLens Head-Mounted Display (HMD), and allows the surgeon to view the patient’s head at the same time as the patient’s medical images. In this study, experiments were performed using spatial reference points with known positions. The experimental results show that the proposed improved alignment algorithm has errors bounded within 3 mm, which is highly accurate.
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Bush, Mary A. A., Chantal Martineau, Janet A. Pronk, and Danielle Brulé. "Eating Well with Canada's Food Guide: “A Tool for the Times”." Canadian Journal of Dietetic Practice and Research 68, no. 2 (2007): 92–96. http://dx.doi.org/10.3148/68.2.2007.92.
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This article outlines the processes undertaken to revise Canada's Food Guide and shares the updated science that underpins the dietary pattern. The Dietary Reference Intakes provide updated nutrient requirement values and better tools for dietary assessment and planning. Alignment with this updated science was an important component of defining and communicating accurate dietary guidance for Canada. Ensuring that stakeholders had access to the updated review of requirements led to the development of the text Dietary Reference Intakes: The Essential Guide to Nutrient Requirements. Equally important was ensuring that stakeholders were provided opportunity to influence the approach taken to giving dietary guidance, both content and the elements of the final package. A combination of research, consultation and expert advice guided the process to the release of Eating Well with Canada's Food Guide(2007).
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Mattelin, Marie-Aline, Jeroen Missinne, Bert De Coensel, and Geert Van Steenberge. "Imprinted Polymer-Based Guided Mode Resonance Grating Strain Sensors." Sensors 20, no. 11 (2020): 3221. http://dx.doi.org/10.3390/s20113221.
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Optical sensors based on guided mode resonance (GMR) realized in polymers are promising candidates for sensitive and cost effective strain sensors. The benefit of GMR grating sensors is the non-contact, easy optical read-out with large working distance, avoiding costly alignment and packaging procedures. The GMR gratings with resonance around 850–900 nm are fabricated using electron beam lithography and replicated using a soft stamp based imprinting technique on 175 μ m-thick foils to make them suitable for optical strain sensing. For the strain measurements, foils are realized with both GMR gratings and waveguides with Bragg gratings. The latter are used as reference sensors and allow extracting the absolute strain sensitivity of the GMR sensor foils. Following this method, it is shown that GMR gratings have an absolute strain sensitivity of 1.02 ± 0.05 pm / μ ε at 870 nm.
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D’haese, Rani, Tom Vrombaut, Geert Hommez, Hugo De Bruyn, and Stefan Vandeweghe. "Accuracy of Guided Implant Surgery in the Edentulous Jaw Using Desktop 3D-Printed Mucosal Supported Guides." Journal of Clinical Medicine 10, no. 3 (2021): 391. http://dx.doi.org/10.3390/jcm10030391.
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Purpose: The aim of this in vitro study is to evaluate the accuracy of implant position using mucosal supported surgical guides, produced by a desktop 3D printer. Methods: Ninety implants (Bone Level Roxolid, 4.1 mm × 10 mm, Straumann, Villerat, Switzerland) were placed in fifteen mandibular casts (Bonemodels, Castellón de la Plana, Spain). A mucosa-supported guide was designed and printed for each of the fifteen casts. After placement of the implants, the location was assessed by scanning the cast and scan bodies with an intra-oral scanner (Primescan®, Dentsply Sirona, York, PA, USA). Two comparisons were performed: one with the mucosa as a reference, and one where only the implants were aligned. Angular, coronal and apical deviations were measured. Results: The mean implant angular deviation for tissue and implant alignment were 3.25° (SD 1.69°) and 2.39° (SD 1.42°) respectively, the coronal deviation 0.82 mm (SD 0.43 mm) and 0.45 mm (SD 0.31 mm) and the apical deviation 0.99 mm (SD 0.45 mm) and 0.71 mm (SD 0.43 mm). All three variables were significantly different between the tissue and implant alignment (p < 0.001). Conclusion: Based on the results of this study, we conclude that guided implant surgery using desktop 3D printed mucosa-supported guides has a clinically acceptable level of accuracy. The resilience of the mucosa has a negative effect on the guide stability and increases the deviation in implant position.
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Peng, Yuan-Chih, Shuyang Chen, Devavrat Jivani, et al. "Sensor-Guided Assembly of Segmented Structures with Industrial Robots." Applied Sciences 11, no. 6 (2021): 2669. http://dx.doi.org/10.3390/app11062669.
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This paper presents a robotic assembly methodology for the manufacturing of large segmented composite structures. The approach addresses three key steps in the assembly process: panel localization and pick-up, panel transport, and panel placement. Multiple stationary and robot-mounted cameras provide information for localization and alignment. A robot wrist-mounted force/torque sensor enables gentle but secure panel pick-up and placement. Human-assisted path planning ensures reliable collision-free motion of the robot with a large load in a tight space. A finite state machine governs the process flow and user interface. It allows process interruption and return to the previous known state in case of error condition or when secondary operations are needed. For performance verification, a high resolution motion capture system provides the ground truth reference. An experimental testbed integrating an industrial robot, vision and force sensors, and representative laminated composite panels demonstrates the feasibility of the proposed assembly process. Experimental results show sub-millimeter placement accuracy with shorter cycle times, lower contact force, and reduced panel oscillation than manual operations. This work demonstrates the versatility of sensor guided robotic assembly operation in a complex end-to-end tasks using the open source Robot Operating System (ROS) software framework.
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Wigginton, Britta, Brianna Fjeldsoe, Allyson Mutch, and Sheleigh Lawler. "Creating Reflexive Health Promotion Practitioners: Our Process of Integrating Reflexivity in the Development of a Health Promotion Course." Pedagogy in Health Promotion 5, no. 1 (2018): 75–78. http://dx.doi.org/10.1177/2373379918766379.
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In response to accreditation of our Master of Public Health program, integration of Indigenous public health competencies, and implementation of the health promotion practitioner accreditation in Australia, we designed a core Master of Public Health promotion course. In this article, we begin by describing the three sets of competencies that informed our course development. Despite consensus that reflexivity is central to effective health promotion practice, there was limited reference to reflexive practice within established competencies. However, given our broader alignment with Freire’s philosophy of “conscientization,” we came to realize that reflexivity was central to our pedagogical framework. In what follows, we describe the conceptualization of reflexivity that guided course development and how reflexivity was integrated into the lecture and assessment content. We highlight how reflection, as part of the assessment, was applied as a means of engaging students in their journey through understanding the inextricably social, political, economic, and cultural nature of health and health promotion practice.
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Shao, Zhenzhou, Yong Guan, and Jindong Tan. "Virtual Reality Aided Positioning of Mobile C-Arms for Image-Guided Surgery." Advances in Mechanical Engineering 6 (January 1, 2014): 943025. http://dx.doi.org/10.1155/2014/943025.
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For the image-guided surgery, the positioning of mobile C-arms is a key technique to take X-ray images in a desired pose for the confirmation of current surgical outcome. Unfortunately, surgeons and patient often suffer the radiation exposure due to the repeated imaging when the X-ray image is of poor quality or not captured at a good projection view. In this paper, a virtual reality (VR) aided positioning method for the mobile C-arm is proposed by the alignment of 3D surface model of region of interest and preoperative anatomy, so that a reference pose of the mobile C-arm with respect to the inside anatomy can be figured out from outside view. It allows a one-time imaging from the outside view to greatly reduce the additional radiation exposure. To control the mobile C-arm to the desired pose, the mobile C-arm is modeled as a robotic arm with a movable base. Experiments were conducted to evaluate the accuracy of appearance model and precision of mobile C-arm positioning. The appearance model was reconstructed with the average error of 2.16 mm. One-time imaging of mobile C-arm was achieved, and new modeling of mobile C-arm with 8 DoFs enlarges the working space in the operating room.
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Matle, Pierneef, Mbatha, Magwedere, and Madoroba. "Genomic Diversity of Common Sequence Types of Listeria monocytogenes Isolated from Ready-to-Eat Products of Animal Origin in South Africa." Genes 10, no. 12 (2019): 1007. http://dx.doi.org/10.3390/genes10121007.
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Listeria monocytogenes is a highly fatal foodborne causative agent that has been implicated in numerous outbreaks and related deaths of listeriosis in the world. In this study, six L. monocytogenes isolated from ready-to-eat (RTE) meat products were analysed using Whole Genome Sequencing (WGS) to identify virulence and resistance genes, prophage sequences, PCR-serogroups, and sequence types (STs). The WGS identified four different STs (ST1, ST121, ST204, and ST876) that belonged to serogroup 4b (lineage I) and 1/2a (lineage II). Core genome, and average nucleotide identity (ANI) phylogenetic analyses showed that the majority of strains from serogroup 4b (lineage I) clustered together. However, two isolates that belong to serogroup 1/2a (lineage II) grouped far from each other and the other strains. Examination of reference-guided scaffolds for the presence of prophages using the PHAge Search Tool Enhanced Release (PHASTER) software identified 24 diverse prophages, which were either intact or incomplete/questionable. The National Center for Biotechnology Information- Nucleotide Basic Local Alignment Search Tool (NCBI-BLASTn) revealed that Listeria monocytogenes strains in this study shared some known major virulence genes that are encoded in Listeria pathogenicity islands 1 and 3. In general, the resistance profiles for all the isolates were similar and encoded for multidrug, heavy metal, antibiotic, and sanitizer resistance genes. All the isolates in this study possessed genes that code for resistance to common food processing antiseptics such as Benzalkonium chloride.
Dissertations / Theses on the topic "Reference-guided alignment"
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Stromberg, Michael Peter. "Enabling high-throughput sequencing data analysis with MOSAIK." Thesis, Boston College, 2010. http://hdl.handle.net/2345/1332.
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Thesis advisor: Gabor T. Marth<br>During the last few years, numerous new sequencing technologies have emerged that require tools that can process large amounts of read data quickly and accurately. Regardless of the downstream methods used, reference-guided aligners are at the heart of all next-generation analysis studies. I have developed a general reference-guided aligner, MOSAIK, to support all current sequencing technologies (Roche 454, Illumina, Applied Biosystems SOLiD, Helicos, and Sanger capillary). The calibrated alignment qualities calculated by MOSAIK allow the user to fine-tune the alignment accuracy for a given study. MOSAIK is a highly configurable and easy-to-use suite of alignment tools that is used in hundreds of labs worldwide. MOSAIK is an integral part of our genetic variant discovery pipeline. From SNP and short-INDEL discovery to structural variation discovery, alignment accuracy is an essential requirement and enables our downstream analyses to provide accurate calls. In this thesis, I present three major studies that were formative during the development of MOSAIK and our analysis pipeline. In addition, I present a novel algorithm that identifies mobile element insertions (non-LTR retrotransposons) in the human genome using split-read alignments in MOSAIK. This algorithm has a low false discovery rate (4.4 %) and enabled our group to be the first to determine the number of mobile elements that differentially occur between any two individuals<br>Thesis (PhD) — Boston College, 2010<br>Submitted to: Boston College. Graduate School of Arts and Sciences<br>Discipline: Biology