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Accurately identifying vertebral levels in large datasets [article]

Daniel C. Elton, Veit Sandfort, Perry J. Pickhardt, Ronald M. Summers
2020 arXiv   pre-print
The goal of this work is to develop a system that can accurately and robustly identify the L1 level in large heterogeneous datasets.  ...  , with an average error of 4.5 mm in the craniocaudal level.  ...  This research was supported in part by the Intramural Research Program of the National Institutes of Health Clinical Center.  ... 
arXiv:2001.10503v1 fatcat:xdpqlz7e4bgoje7y7clwgbpnam

Spinal cord segmentation and classification of degenerative disease

Arjun, Kanchana V
2019 International Journal of Research in Pharmaceutical Sciences  
In here we are using MRI image to perform our work In our proposed work, we are finding degenerative disease from spinal cord image.  ...  Medical image processing technique is extensively used in medical field.  ...  She has helped to ind a dataset of spinal cord MRI image. She is the dental doctor of mother and child in Kannur. The dataset will be collected from MIMs international hospital Calicut.  ... 
doi:10.26452/ijrps.v10i3.1490 fatcat:m3ueaef6fvhdxitxxoamiaqgxy

Automated Segmentation of Vertebrae on Lateral Chest Radiography Using Deep Learning [article]

Sanket Badhe, Varun Singh, Joy Li, Paras Lakhani
2020 arXiv   pre-print
The purpose of this study is to develop an automated algorithm for thoracic vertebral segmentation on chest radiography using deep learning. 124 de-identified lateral chest radiographs on unique patients  ...  Deep learning demonstrates promise in the segmentation of vertebrae on lateral chest radiography.  ...  Automated vertebral body height measurements appropriately applied to a large, diverse dataset could stratify mean values and standard deviations of vertebral heights by patient age, height, sex, and other  ... 
arXiv:2001.01277v1 fatcat:gnuqv4x4gzboxn6uugfbucccxi

Application of deep learning algorithm to detect and visualize vertebral fractures on plain frontal radiographs

Hsuan-Yu Chen, Benny Wei-Yun Hsu, Yu-Kai Yin, Feng-Huei Lin, Tsung-Han Yang, Rong-Sen Yang, Chih-Kuo Lee, Vincent S. Tseng, Yan Chai Hum
2021 PLoS ONE  
Identification of vertebral fractures (VFs) is critical for effective secondary fracture prevention owing to their association with the increasing risks of future fractures.  ...  Results Only 46.6% (204/438) of the VFs were diagnosed in the original PARs reports.  ...  Introduction Vertebral fractures (VFs), which are identified as deformities of vertebral bodies based on the imaging of the lateral spine, are a hallmark of osteoporosis.  ... 
doi:10.1371/journal.pone.0245992 pmid:33507982 fatcat:jrzlcdzd2ze57gfxkegbfz2uui

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

Hannah K Long, David Sims, Andreas Heger, Neil P Blackledge, Claudia Kutter, Megan L Wright, Frank Grützner, Duncan T Odom, Roger Patient, Chris P Ponting, Robert J Klose
2013 eLife  
By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters  ...  In cold-blooded vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates.  ...  Datasets generated in this study are available from GEO under accession GSE43512.  ... 
doi:10.7554/elife.00348 pmid:23467541 pmcid:PMC3583005 fatcat:owpedgj4vnckzonltkdnrqouim

SAINT: automatic taxonomy embedding and categorization by Siamese triplet network [article]

Yang Young Lu, Yiwen Wang, Fang Zhang, Jiaxing Bai, Ying Wang
2021 bioRxiv   pre-print
Conventional approaches to sequence analysis are based on sequence alignment, which is neither scalable to large-scale datasets due to computational inefficiency nor adaptive to next-generation sequencing  ...  Understanding the phylogenetic relationship among organisms is the key in contemporary evolutionary study and sequence analysis is the workhorse towards this goal.  ...  vertebrate dataset.  ... 
doi:10.1101/2021.01.20.426920 fatcat:fdlpt5pkqzg5xeryfwpbau4xvy

Vertebral Tumor Detection and Segmentation Using Analytical Transform Assisted Statistical Characteristic Decomposition Model

Abdulmonem Alsiddiky, Hassan Fouad, Ahmed M. Soliman, Amir Altinawi, Nourelhoda M. Mahmoud
2020 IEEE Access  
In this analysis, the unmarked datasets for pretraining are used for the extraction of high-level features and for fine tuning the identified data.  ...  Further, the segmentation of vertebral datasets has been analyzed using ROC, since it shows the changes in the bias level.  ... 
doi:10.1109/access.2020.3012719 fatcat:qmaguixnlbesfdriatqjwk3cuu

Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity [article]

Nicholas D Youngblut, Jacobo de la Cuesta-Zuluaga, Georg H Reischer, Silke Dauser, Nathalie Schuster, Chris Walzer, Gabrielle Stalder, Andreas Farnleitner, Ruth E Ley
2020 bioRxiv   pre-print
Combined with existing datasets, we produced 5596 non-redundant, quality MAGs and 1522 species-level genome bins (SGBs).  ...  Most SGBs were novel at the species, genus, or family levels, and the majority were enriched in host versus environment metagenomes.  ...  for the gut microbiomes of most vertebrates in our dataset (Figure 389 1).  ... 
doi:10.1101/2020.06.05.135962 fatcat:2uxhnvktbvamrjtepup3ytixki

Orthology prediction methods: A quality assessment using curated protein families

Kalliopi Trachana, Tomas A. Larsson, Sean Powell, Wei-Hua Chen, Tobias Doerks, Jean Muller, Peer Bork
2011 Bioessays  
We used 70 manually curated families to analyze the performance of five public methods in Metazoa.  ...  Generally, most methods did well in assigning orthologous group but they failed to assign the exact number of genes for half of the groups.  ...  Acknowledgments We would like to thank the OrthoDB team for providing us with a customized dataset.  ... 
doi:10.1002/bies.201100062 pmid:21853451 pmcid:PMC3193375 fatcat:5hkwdtl77nehrjs72vlm2fxpnu

A Robust Scheme of Vertebrae Segmentation for Medical Diagnosis

Faisal Rehman, Syed Irtiza Ali Shah, Naveed Riaz, Syed Omer Gilani
2019 IEEE Access  
It assists the radiologists and doctors in identifying various pathologies in the vertebrae with better visualizations.  ...  Precise and reliable segmentation of vertebral column is crucial for accurate computer aided diagnostic system (CADx).  ...  Faiza, POF's Hospital Pakistan (Rawalpindi District) in helping us in dataset collection and providing us expert opinions and corrections on annotated data.  ... 
doi:10.1109/access.2019.2936492 fatcat:rrjlahql25bjxbnyznbizt4tmu

Model-Independent 3D Descriptors of Vertebral Cancellous Bone Architecture

Ian H. Parkinson, Danielle Forbes, Peter Sutton-Smith, Nicola L. Fazzalari
2010 Journal of Osteoporosis  
Twenty-eight vertebral bodies were obtained from four embalmed male cadavers.  ...  From 3D voxel-based datasets, bone volume density, trabecular thickness, and trabecular separation were measured.  ...  enable accurate reconstruction of the specimen as a voxel-based dataset.  ... 
doi:10.4061/2010/641578 pmid:20975775 pmcid:PMC2957160 fatcat:uk5tgdq4mbhiblzujyxuq74tyu

DeepSPINE: Automated Lumbar Vertebral Segmentation, Disc-level Designation, and Spinal Stenosis Grading Using Deep Learning [article]

Jen-Tang Lu, Stefano Pedemonte, Bernardo Bizzo, Sean Doyle, Katherine P. Andriole, Mark H. Michalski, R. Gilberto Gonzalez, Stuart R. Pomerantz
2018 arXiv   pre-print
This study uses a large dataset of 22796 disc-levels extracted from 4075 patients.  ...  of spinal stenosis (2) accurate vertebral segmentation and disc-level localization using a U-Net architecture combined with a spine-curve fitting method, and (3) a multi-input, multi-task, and multi-class  ...  (b) Stenosis grading distribution of the dataset (22796 disc-levels in total; some of them might contain only one or two labels).  ... 
arXiv:1807.10215v1 fatcat:qq2y4fuht5fnjhn3mh2ahegz6m

Automation of Spine Curve Assessment in Frontal Radiographs Using Deep Learning of Vertebral-tilt Vector

Kang Cheol Kim, Hye Sun Yun, Sungjun Kim, Jin Keun Seo
2020 IEEE Access  
an accurate and robust manner, (2) vertebral-tilt field is used to estimate the slope of an individual vertebra, and (3) the Cobb angle is determined by combining the vertebral centroids with the previously  ...  This paper addresses this need through the development of a hierarchical method which consisting of three major parts. (1) A confidence map is used to selectively localize and identify all vertebrae in  ...  QUANTITATIVE EVALUATION ON THE EXTERNAL DATASET In the previous section, we demonstrated that the proposed method provides accurate and robust Cobb angle estimation on the internal testing dataset.  ... 
doi:10.1109/access.2020.2992081 fatcat:ygb6opum4bhhxiwqyymteuifbq

Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans

Misty M. Attwood, Arunkumar Krishnan, Markus Sällman Almén, Helgi B. Schiöth
2017 Scientific Reports  
We identify 123,014 membrane proteins in these 24 eukaryotic species and classify 86% of the dataset.  ...  The data show that enzymes are more highly represented in the LHCA and expand less than threefold throughout metazoan species; in contrast to receptors that are relatively few in the LHCA but expand nearly  ...  large-scale expansions at the origins of metazoans, in species specific inflations, as well as in vertebrates.  ... 
doi:10.1038/s41598-017-11543-z pmid:28959054 pmcid:PMC5620054 fatcat:7m7ye674inewvh6nyivbkwaj74

Automated Pipeline to Generate Anatomically Accurate Patient-Specific Biomechanical Models of Healthy and Pathological FSUs

Sebastiano Caprara, Fabio Carrillo, Jess G. Snedeker, Mazda Farshad, Marco Senteler
2021 Frontiers in Bioengineering and Biotechnology  
representation of vertebral joints.  ...  The major intent of this work is to automate the creation of anatomically accurate patient-specific models by a single pipeline allowing functional modeling of spinal motion in healthy and pathological  ...  The vertebral meshes were divided based on the spinal level and multiple training datasets were created consisting of 100 meshes pro lumbar level.  ... 
doi:10.3389/fbioe.2021.636953 pmid:33585436 pmcid:PMC7876284 fatcat:lfvxm7cdifhifdmxicxzpl6jg4
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