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Journal articles on the topic 'Reference-guided alignment'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

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 v

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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 al

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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 impor

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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 g

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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 com

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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 proce

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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 phi

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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

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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 a

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Ahmed, Iftekhar, and Esther Ruth Charlesworth. "An evaluation framework for assessing resilience of post-disaster housing." International Journal of Disaster Resilience in the Built Environment 6, no. 3 (2015): 300–312. http://dx.doi.org/10.1108/ijdrbe-11-2013-0042.

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Purpose – The purpose of this paper is to discuss the utility of a tool for assessing resilience of housing. After disasters, maximum resources are often allocated for housing reconstruction, and most initiatives on disaster resilient housing have arisen after disasters. With widespread claims by agencies of having “built back better”, it is important to establish an evaluation framework that allows understanding to what extent resilience has been successfully achieved in such housing projects. This paper discusses such a tool developed by the authors. Design/methodology/approach – In a study

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Walsh, Fiona, and Josie Douglas. "No bush foods without people: the essential human dimension to the sustainability of trade in native plant products from desert Australia." Rangeland Journal 33, no. 4 (2011): 395. http://dx.doi.org/10.1071/rj11028.

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Improvement in Aboriginal people’s livelihoods and economic opportunities has been a major aim of increased research and development on bush foods over the past decade. But worldwide the development of trade in non-timber forest products from natural populations has raised questions about the ecological sustainability of harvest. Trade-offs and tensions between commercialisation and cultural values have also been found. We investigated the sustainability of the small-scale commercial harvest and trade in native plant products sourced from central Australian rangelands (including Solanum centra

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Wang, Q., M. Hou, and S. Lyu. "VIRTUAL RESTORATION OF MISSING PAINT LOSS OF MURAL BASED ON GENERATIVE ADVERSARIAL NETWORK." International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLVI-M-1-2021 (August 28, 2021): 807–11. http://dx.doi.org/10.5194/isprs-archives-xlvi-m-1-2021-807-2021.

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Abstract. Mural painting is one of the important cultural heritage reflecting the historical migration of the nation. In order to inherit these precious historical and cultural heritage, how to non - destructively and digitally protect and restore the existing murals has become an urgent task. The use of computer - assisted restoration of murals can not only save manpower and material resources, but also avoid secondary damage to the murals.However, most of the existing computer-assisted mural restoration algorithms use similar blocks with priority calculations and matching blocks in adjacent

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Giese, Sven H., Franziska Zickmann, and Bernhard Y. Renard. "Specificity control for read alignments using an artificial reference genome-guided false discovery rate." Bioinformatics 30, no. 1 (2013): 9–16. http://dx.doi.org/10.1093/bioinformatics/btt255.

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15

Coombe, Lauren, Vladimir Nikolić, Justin Chu, Inanc Birol, and René L. Warren. "ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs." Bioinformatics 36, no. 12 (2020): 3885–87. http://dx.doi.org/10.1093/bioinformatics/btaa253.

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Abstract Summary The ability to generate high-quality genome sequences is cornerstone to modern biological research. Even with recent advancements in sequencing technologies, many genome assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between a draft assembly and reference sequence(s) to contiguate and correct the former with respect to the latter. Instead of alignments, ntJoin uses a lightweight mapping approach based on a graph data structure generated from ordered minimizer sketches. The tool can be used in a variety of

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Moshiri, Niema. "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." Bioinformatics, August 19, 2020. http://dx.doi.org/10.1093/bioinformatics/btaa743.

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Abstract Motivation In molecular epidemiology, the identification of clusters of transmissions typically requires the alignment of viral genomic sequence data. However, existing methods of multiple sequence alignment (MSA) scale poorly with respect to the number of sequences. Results ViralMSA is a user-friendly reference-guided MSA tool that leverages the algorithmic techniques of read mappers to enable the MSA of ultra-large viral genome datasets. It scales linearly with the number of sequences, and it is able to align tens of thousands of full viral genomes in seconds. However, alignments pr

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Ranjard, Louis, Thomas K. F. Wong, and Allen G. Rodrigo. "Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage." BMC Bioinformatics 20, no. 1 (2019). http://dx.doi.org/10.1186/s12859-019-3287-2.

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Abstract Background In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the reads can be difficult because of the occurrence of uncovered gaps. Reference guided assembly can then improve these assemblies. However, when the available reference is phylogenetically distant from the sequencing reads, the mapping rate of the reads can be extremely low. Some recent improvements in read mapping approaches aim at modifying the

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Lloret-Villas, Audald, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries, and Hubert Pausch. "Investigating the impact of reference assembly choice on genomic analyses in a cattle breed." BMC Genomics 22, no. 1 (2021). http://dx.doi.org/10.1186/s12864-021-07554-w.

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Abstract Background Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine reference genome. Haplotype-resolved genomes that exceed the current bovine reference genome in quality and continuity have been assembled for different breeds of cattle. Using whole genome sequencing data of 161 Brown Swiss cattle, we compared the accuracy of read mapping and sequence variant genotyping as well as downstream genomic analyses between t

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Malan, Leon, Richard D. Pitcher, Michelle da Silva, Sharlene Breuninger, and Wilhelm Groenewald. "Diagnostic reference levels for fluoroscopically guided procedures in a South African tertiary hospital." Acta Radiologica, July 8, 2020, 028418512093837. http://dx.doi.org/10.1177/0284185120938371.

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Background The burgeoning usage and complexity of fluoroscopically guided procedures (FGPs) contribute to extended examination times and increased risk of adverse radiation effects. Diagnostic reference levels (DRLs) play a pivotal role in dose optimization. There are limited DRL data for FGPs in low- and middle-income countries (LMICs). Purpose To determine local DRLs (LDRLs) for common FGPs in the South African (SA) context and compare these with published international data. Material and Methods A three-year, retrospective study of the 15 most frequently performed FGPs at a SA institution.

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Scott, Joseph J., Susan Hill, Donna Barwood, and Dawn Penney. "Physical literacy and policy alignment in sport and education in Australia." European Physical Education Review, September 1, 2020, 1356336X2094743. http://dx.doi.org/10.1177/1356336x20947434.

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Sport Australia released the Australian Physical Literacy Framework (APLF) in 2019 to advance a national agenda for physical literacy (PL) and specifically, clarify and promote the development of PL in Australian sport and education sectors. For teachers, this policy initiative followed a period of curriculum development guided by the Australian Curriculum for Health and Physical Education (AC: HPE). The AC: HPE makes no explicit reference to PL, but nevertheless seeks to support young people to lead active healthy lives. This study acknowledged that HPE teachers are now challenged to navigate

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Grisi, Patrícia Umeda, Marieta Caixeta Dorneles, Marli Aparecida Ranal, Ana Paula de Oliveira, Clesnan Mendes-Rodrigues, and Denise Garcia de Santana. "Ex situ initial seedling development of Hymenaea courbaril L. (Fabaceae): a crucial phase to preserve the species." Hoehnea 46, no. 2 (2019). http://dx.doi.org/10.1590/2236-8906-74/2018.

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ABSTRACT Hymenaea courbaril L. is an important Neotropical species, with low population density, restricted to fragments of semideciduous forests, with low mortality and low recruitment. Thus, some questions guided the goals of this paper including the capacity of stored seeds to form normal seedlings. Seeds collected from ten mother plants in the Brazilian Cerrado region and stored during three years were mechanically scarified, sown and analyzed during 43 days. Intraspecific variability was observed for water content, seed biometry, and emergence process. The seedling emergence varied from 1

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Kuo, Richard I., Yuanyuan Cheng, Runxuan Zhang, et al. "Illuminating the dark side of the human transcriptome with long read transcript sequencing." BMC Genomics 21, no. 1 (2020). http://dx.doi.org/10.1186/s12864-020-07123-7.

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Abstract Background The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate high-throughput long read transcript sequencing can now provide additional evidence for rare transcripts and genes such as mono-exonic and non-coding genes that were previously either undetectable or impossible to differentiate from sequencing noise. Results We developed the Transcriptome Annotation by Modular Algorithms (TAMA) software to leverage t

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Kovaka, Sam, Aleksey V. Zimin, Geo M. Pertea, Roham Razaghi, Steven L. Salzberg, and Mihaela Pertea. "Transcriptome assembly from long-read RNA-seq alignments with StringTie2." Genome Biology 20, no. 1 (2019). http://dx.doi.org/10.1186/s13059-019-1910-1.

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AbstractRNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2, a reference-guided transcriptome assembler that works with both short and long reads. StringTie2 includes new methods to handle the high error rate of long reads and offers the ability to work with full-length super-reads assembled from short reads, which further improves the quality of short-read assemblies. StringTie2 is more accurate

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Hertzman, Rebecca J., Pooja Deshpande, Shay Leary, et al. "Visual Genomics Analysis Studio as a Tool to Analyze Multiomic Data." Frontiers in Genetics 12 (June 17, 2021). http://dx.doi.org/10.3389/fgene.2021.642012.

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Type B adverse drug reactions (ADRs) are iatrogenic immune-mediated syndromes with mechanistic etiologies that remain incompletely understood. Some of the most severe ADRs, including delayed drug hypersensitivity reactions, are T-cell mediated, restricted by specific human leukocyte antigen risk alleles and sometimes by public or oligoclonal T-cell receptors (TCRs), central to the immunopathogenesis of tissue-damaging response. However, the specific cellular signatures of effector, regulatory, and accessory immune populations that mediate disease, define reaction phenotype, and determine sever

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Cho, Sunghye, Naomi Nevler, Natalia Parjane, et al. "Automated Analysis of Digitized Letter Fluency Data." Frontiers in Psychology 12 (July 29, 2021). http://dx.doi.org/10.3389/fpsyg.2021.654214.

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The letter-guided naming fluency task is a measure of an individual’s executive function and working memory. This study employed a novel, automated, quantifiable, and reproducible method to investigate how language characteristics of words produced during a fluency task are related to fluency performance, inter-word response time (RT), and over task duration using digitized F-letter-guided fluency recordings produced by 76 young healthy participants. Our automated algorithm counted the number of correct responses from the transcripts of the F-letter fluency data, and individual words were rate

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Chapman, Owen. "The Affect of Selection in Digital Sound Art." M/C Journal 8, no. 3 (2005). http://dx.doi.org/10.5204/mcj.2357.

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   A variety of digital technologies exist that can transform sound waves into binary code. Any sound can be ‘sampled’ in this way: drum beats, field recordings, even full-length instrumental or vocal tracks. Copies are then ready to be duplicated, cut, spliced, pitch-shifted, equalised, turned backwards, and/or passed through a myriad of different effects processors before being sequenced and layered into a final stereo mix.   Once obtained, this mix is itself eminently copy-able without loss in audio quality. Moreover, affordable digital reproduction media aboun

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Radywyl, Natalia. "A Moment's Daydreaming." M/C Journal 12, no. 1 (2009). http://dx.doi.org/10.5204/mcj.118.

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Drift: An IntroductionEntering into Drift is akin to entering—or becoming ensnared by—a hum. Projected across one wall, the work uses abstract visual forms to draw visitors into its meditational folds. Quadraphonic sound circulates in smooth, heavy pulses, like the steady rumble of a train running over deep-set tracks. A succession of vibrating lines occupy the screen, much like the horizontal static of a poorly-tuned television. Gradually, the ambient timbre darkens, the hum becomes more persistent and atmospheric undulations more frequent, until room and body expand with intensity. Throbbing

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