Access and use of the GUDMAP database of genitourinary development.

PubMed

Davies, Jamie A; Little, Melissa H; Aronow, Bruce; Armstrong, Jane; Brennan, Jane; Lloyd-MacGilp, Sue; Armit, Chris; Harding, Simon; Piu, Xinjun; Roochun, Yogmatee; Haggarty, Bernard; Houghton, Derek; Davidson, Duncan; Baldock, Richard

2012-01-01

The Genitourinary Development Molecular Atlas Project (GUDMAP) aims to document gene expression across time and space in the developing urogenital system of the mouse, and to provide access to a variety of relevant practical and educational resources. Data come from microarray gene expression profiling (from laser-dissected and FACS-sorted samples) and in situ hybridization at both low (whole-mount) and high (section) resolutions. Data are annotated to a published, high-resolution anatomical ontology and can be accessed using a variety of search interfaces. Here, we explain how to run typical queries on the database, by gene or anatomical location, how to view data, how to perform complex queries, and how to submit data.

Monte Carlo calculations for reporting patient organ doses from interventional radiology

NASA Astrophysics Data System (ADS)

Huo, Wanli; Feng, Mang; Pi, Yifei; Chen, Zhi; Gao, Yiming; Xu, X. George

2017-09-01

This paper describes a project to generate organ dose data for the purposes of extending VirtualDose software from CT imaging to interventional radiology (IR) applications. A library of 23 mesh-based anthropometric patient phantoms were involved in Monte Carlo simulations for database calculations. Organ doses and effective doses of IR procedures with specific beam projection, filed of view (FOV) and beam quality for all parts of body were obtained. Comparing organ doses for different beam qualities, beam projections, patients' ages and patient's body mass indexes (BMIs) which generated by VirtualDose-IR, significant discrepancies were observed. For relatively long time exposure, IR doses depend on beam quality, beam direction and patient size. Therefore, VirtualDose-IR, which is based on the latest anatomically realistic patient phantoms, can generate accurate doses for IR treatment. It is suitable to apply this software in clinical IR dose management as an effective tool to estimate patient doses and optimize IR treatment plans.

Photorealistic virtual anatomy based on Chinese Visible Human data.

PubMed

Heng, P A; Zhang, S X; Xie, Y M; Wong, T T; Chui, Y P; Cheng, C Y

2006-04-01

Virtual reality based learning of human anatomy is feasible when a database of 3D organ models is available for the learner to explore, visualize, and dissect in virtual space interactively. In this article, we present our latest work on photorealistic virtual anatomy applications based on the Chinese Visible Human (CVH) data. We have focused on the development of state-of-the-art virtual environments that feature interactive photo-realistic visualization and dissection of virtual anatomical models constructed from ultra-high resolution CVH datasets. We also outline our latest progress in applying these highly accurate virtual and functional organ models to generate realistic look and feel to advanced surgical simulators. (c) 2006 Wiley-Liss, Inc.

Fast vessel segmentation in retinal images using multi-scale enhancement and second-order local entropy

NASA Astrophysics Data System (ADS)

Yu, H.; Barriga, S.; Agurto, C.; Zamora, G.; Bauman, W.; Soliz, P.

2012-03-01

Retinal vasculature is one of the most important anatomical structures in digital retinal photographs. Accurate segmentation of retinal blood vessels is an essential task in automated analysis of retinopathy. This paper presents a new and effective vessel segmentation algorithm that features computational simplicity and fast implementation. This method uses morphological pre-processing to decrease the disturbance of bright structures and lesions before vessel extraction. Next, a vessel probability map is generated by computing the eigenvalues of the second derivatives of Gaussian filtered image at multiple scales. Then, the second order local entropy thresholding is applied to segment the vessel map. Lastly, a rule-based decision step, which measures the geometric shape difference between vessels and lesions is applied to reduce false positives. The algorithm is evaluated on the low-resolution DRIVE and STARE databases and the publicly available high-resolution image database from Friedrich-Alexander University Erlangen-Nuremberg, Germany). The proposed method achieved comparable performance to state of the art unsupervised vessel segmentation methods with a competitive faster speed on the DRIVE and STARE databases. For the high resolution fundus image database, the proposed algorithm outperforms an existing approach both on performance and speed. The efficiency and robustness make the blood vessel segmentation method described here suitable for broad application in automated analysis of retinal images.

Soft Tissue Structure Modelling for Use in Orthopaedic Applications and Musculoskeletal Biomechanics

NASA Astrophysics Data System (ADS)

Audenaert, E. A.; Mahieu, P.; van Hoof, T.; Pattyn, C.

2009-12-01

We present our methodology for the three-dimensional anatomical and geometrical description of soft tissues, relevant for orthopaedic surgical applications and musculoskeletal biomechanics. The technique involves the segmentation and geometrical description of muscles and neurovascular structures from high-resolution computer tomography scanning for the reconstruction of generic anatomical models. These models can be used for quantitative interpretation of anatomical and biomechanical aspects of different soft tissue structures. This approach should allow the use of these data in other application fields, such as musculoskeletal modelling, simulations for radiation therapy, and databases for use in minimally invasive, navigated and robotic surgery.

Design, development and clinical validation of computer-aided surgical simulation system for streamlined orthognathic surgical planning.

PubMed

Yuan, Peng; Mai, Huaming; Li, Jianfu; Ho, Dennis Chun-Yu; Lai, Yingying; Liu, Siting; Kim, Daeseung; Xiong, Zixiang; Alfi, David M; Teichgraeber, John F; Gateno, Jaime; Xia, James J

2017-12-01

There are many proven problems associated with traditional surgical planning methods for orthognathic surgery. To address these problems, we developed a computer-aided surgical simulation (CASS) system, the AnatomicAligner, to plan orthognathic surgery following our streamlined clinical protocol. The system includes six modules: image segmentation and three-dimensional (3D) reconstruction, registration and reorientation of models to neutral head posture, 3D cephalometric analysis, virtual osteotomy, surgical simulation, and surgical splint generation. The accuracy of the system was validated in a stepwise fashion: first to evaluate the accuracy of AnatomicAligner using 30 sets of patient data, then to evaluate the fitting of splints generated by AnatomicAligner using 10 sets of patient data. The industrial gold standard system, Mimics, was used as the reference. When comparing the results of segmentation, virtual osteotomy and transformation achieved with AnatomicAligner to the ones achieved with Mimics, the absolute deviation between the two systems was clinically insignificant. The average surface deviation between the two models after 3D model reconstruction in AnatomicAligner and Mimics was 0.3 mm with a standard deviation (SD) of 0.03 mm. All the average surface deviations between the two models after virtual osteotomy and transformations were smaller than 0.01 mm with a SD of 0.01 mm. In addition, the fitting of splints generated by AnatomicAligner was at least as good as the ones generated by Mimics. We successfully developed a CASS system, the AnatomicAligner, for planning orthognathic surgery following the streamlined planning protocol. The system has been proven accurate. AnatomicAligner will soon be available freely to the boarder clinical and research communities.

Design, development and clinical validation of computer-aided surgical simulation system for streamlined orthognathic surgical planning

PubMed Central

Yuan, Peng; Mai, Huaming; Li, Jianfu; Ho, Dennis Chun-Yu; Lai, Yingying; Liu, Siting; Kim, Daeseung; Xiong, Zixiang; Alfi, David M.; Teichgraeber, John F.; Gateno, Jaime

2017-01-01

Purpose There are many proven problems associated with traditional surgical planning methods for orthognathic surgery. To address these problems, we developed a computer-aided surgical simulation (CASS) system, the AnatomicAligner, to plan orthognathic surgery following our streamlined clinical protocol. Methods The system includes six modules: image segmentation and three-dimensional (3D) reconstruction, registration and reorientation of models to neutral head posture, 3D cephalometric analysis, virtual osteotomy, surgical simulation, and surgical splint generation. The accuracy of the system was validated in a stepwise fashion: first to evaluate the accuracy of AnatomicAligner using 30 sets of patient data, then to evaluate the fitting of splints generated by AnatomicAligner using 10 sets of patient data. The industrial gold standard system, Mimics, was used as the reference. Result When comparing the results of segmentation, virtual osteotomy and transformation achieved with AnatomicAligner to the ones achieved with Mimics, the absolute deviation between the two systems was clinically insignificant. The average surface deviation between the two models after 3D model reconstruction in AnatomicAligner and Mimics was 0.3 mm with a standard deviation (SD) of 0.03 mm. All the average surface deviations between the two models after virtual osteotomy and transformations were smaller than 0.01 mm with a SD of 0.01 mm. In addition, the fitting of splints generated by AnatomicAligner was at least as good as the ones generated by Mimics. Conclusion We successfully developed a CASS system, the AnatomicAligner, for planning orthognathic surgery following the streamlined planning protocol. The system has been proven accurate. AnatomicAligner will soon be available freely to the boarder clinical and research communities. PMID:28432489

A model based method for recognizing psoas major muscles in torso CT images

NASA Astrophysics Data System (ADS)

Kamiya, Naoki; Zhou, Xiangrong; Chen, Huayue; Hara, Takeshi; Yokoyama, Ryujiro; Kanematsu, Masayuki; Hoshi, Hiroaki; Fujita, Hiroshi

2010-03-01

In aging societies, it is important to analyze age-related hypokinesia. A psoas major muscle has many important functional capabilities such as capacity of balance and posture control. These functions can be measured by its cross sectional area (CSA), volume, and thickness. However, these values are calculated manually in the clinical situation. The purpose of our study is to propose an automated recognition method of psoas major muscles in X-ray torso CT images. The proposed recognition process involves three steps: 1) determination of anatomical points such as the origin and insertion of the psoas major muscle, 2) generation of a shape model for the psoas major muscle, and 3) recognition of the psoas major muscles by use of the shape model. The model was built using quadratic function, and was fit to the anatomical center line of psoas major muscle. The shape model was generated using 20 CT cases and tested by 20 other CT cases. The applied database consisted of 12 male and 8 female cases from the ages of 40's to 80's. The average value of Jaccard similarity coefficient (JSC) values employed in the evaluation was 0.7. Our experimental results indicated that the proposed method was effective for a volumetric analysis and could be possible to be used for a quantitative measurement of psoas major muscles in CT images.

Parcellation of the Healthy Neonatal Brain into 107 Regions Using Atlas Propagation through Intermediate Time Points in Childhood.

PubMed

Blesa, Manuel; Serag, Ahmed; Wilkinson, Alastair G; Anblagan, Devasuda; Telford, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Macnaught, Gillian; Semple, Scott I; Bastin, Mark E; Boardman, James P

2016-01-01

Neuroimage analysis pipelines rely on parcellated atlases generated from healthy individuals to provide anatomic context to structural and diffusion MRI data. Atlases constructed using adult data introduce bias into studies of early brain development. We aimed to create a neonatal brain atlas of healthy subjects that can be applied to multi-modal MRI data. Structural and diffusion 3T MRI scans were acquired soon after birth from 33 typically developing neonates born at term (mean postmenstrual age at birth 39(+5) weeks, range 37(+2)-41(+6)). An adult brain atlas (SRI24/TZO) was propagated to the neonatal data using temporal registration via childhood templates with dense temporal samples (NIH Pediatric Database), with the final atlas (Edinburgh Neonatal Atlas, ENA33) constructed using the Symmetric Group Normalization (SyGN) method. After this step, the computed final transformations were applied to T2-weighted data, and fractional anisotropy, mean diffusivity, and tissue segmentations to provide a multi-modal atlas with 107 anatomical regions; a symmetric version was also created to facilitate studies of laterality. Volumes of each region of interest were measured to provide reference data from normal subjects. Because this atlas is generated from step-wise propagation of adult labels through intermediate time points in childhood, it may serve as a useful starting point for modeling brain growth during development.

A reusable anatomically segmented digital mannequin for public health communication.

PubMed

Fujieda, Kaori; Okubo, Kosaku

2016-01-01

The ongoing development of world wide web technologies has facilitated a change in health communication, which has now become bi-directional and encompasses people with diverse backgrounds. To enable an even greater role for medical illustrations, a data set, BodyParts3D, has been generated and its data set can be used by anyone to create and exchange customised three-dimensional (3D) anatomical images. BP3D comprises more than 3000 3D object files created by segmenting a digital mannequin in accordance with anatomical naming conventions. This paper describes the methodologies and features used to generate an anatomically correct male mannequin.

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information.

PubMed

Knowlton, Michelle N; Li, Tongbin; Ren, Yongliang; Bill, Brent R; Ellis, Lynda Bm; Ekker, Stephen C

2008-01-07

The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer trapping and forward genetic screening using transposon insertional mutagenesis. We have created a database to facilitate web-based distribution of data from such genetic studies. The MOrpholino DataBase is a MySQL relational database with an online, PHP interface. Multiple quality control levels allow differential access to data in raw and finished formats. MODBv1 includes sequence information relating to almost 800 morpholinos and their targets and phenotypic data regarding the dose effect of each morpholino (mortality, toxicity and defects). To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and defect produced. This also allows comparison between species utilizing Phenotypic Attribute Trait Ontology (PATO) designated terminology. MODB is also cross-linked with ZFIN, allowing full searches between the two databases. MODB offers users the ability to retrieve morpholino data by sequence of morpholino or target, name of target, anatomical structure affected and defect produced. MODB data can be used for functional genomic analysis of morpholino design to maximize efficacy and minimize toxicity. MODB also serves as a template for future sequence-based functional genetic screen databases, and it is currently being used as a model for the creation of a mutagenic insertional transposon database.

Development of a new generation of high-resolution anatomical models for medical device evaluation: the Virtual Population 3.0

NASA Astrophysics Data System (ADS)

Gosselin, Marie-Christine; Neufeld, Esra; Moser, Heidi; Huber, Eveline; Farcito, Silvia; Gerber, Livia; Jedensjö, Maria; Hilber, Isabel; Di Gennaro, Fabienne; Lloyd, Bryn; Cherubini, Emilio; Szczerba, Dominik; Kainz, Wolfgang; Kuster, Niels

2014-09-01

The Virtual Family computational whole-body anatomical human models were originally developed for electromagnetic (EM) exposure evaluations, in particular to study how absorption of radiofrequency radiation from external sources depends on anatomy. However, the models immediately garnered much broader interest and are now applied by over 300 research groups, many from medical applications research fields. In a first step, the Virtual Family was expanded to the Virtual Population to provide considerably broader population coverage with the inclusion of models of both sexes ranging in age from 5 to 84 years old. Although these models have proven to be invaluable for EM dosimetry, it became evident that significantly enhanced models are needed for reliable effectiveness and safety evaluations of diagnostic and therapeutic applications, including medical implants safety. This paper describes the research and development performed to obtain anatomical models that meet the requirements necessary for medical implant safety assessment applications. These include implementation of quality control procedures, re-segmentation at higher resolution, more-consistent tissue assignments, enhanced surface processing and numerous anatomical refinements. Several tools were developed to enhance the functionality of the models, including discretization tools, posing tools to expand the posture space covered, and multiple morphing tools, e.g., to develop pathological models or variations of existing ones. A comprehensive tissue properties database was compiled to complement the library of models. The results are a set of anatomically independent, accurate, and detailed models with smooth, yet feature-rich and topologically conforming surfaces. The models are therefore suited for the creation of unstructured meshes, and the possible applications of the models are extended to a wider range of solvers and physics. The impact of these improvements is shown for the MRI exposure of an adult woman with an orthopedic spinal implant. Future developments include the functionalization of the models for specific physical and physiological modeling tasks.

Volumetric Nephrogram Represents Renal Function and Complements Aortic Anatomic Severity Grade in Predicting EVAR Outcomes.

PubMed

Balceniuk, Mark D; Trakimas, Lauren; Aghaie, Claudia; Mix, Doran; Rasheed, Khurram; Seaman, Matthew; Ellis, Jennifer; Glocker, Roan; Doyle, Adam; Stoner, Michael C

2018-07-01

Chronic kidney disease (CKD) is a predictor of poor outcomes for patients undergoing endovascular aortic aneurysm repair (EVAR). Anatomic severity grade (ASG) represents a quantitative mechanism for assessing anatomical suitability for endovascular aortic repair. Anatomic severity grade has been correlated with repair outcomes and resource utilization. The purpose of this study was to identify a novel renal perfusion metric as a way to assist ASG with predicting EVAR outcomes. Retrospective review of a prospectively maintained database identified elective infrarenal aortic aneurysm repair cases. Anatomic grading was undertaken by independent reviewers. Using volumetric software, kidney volume, and a novel measure of kidney functional volume, the volumetric nephrogram (VN) was recorded. Systematic evaluation of the relationship of kidney volume and VN to CKD and ASG was undertaken using linear regression and receiver-operator statistical tools. A total of 386 cases with patient and anatomic data were identified and graded. Mean age was 72.9 ± 0.4 years. Renal volume <281 mL correlated with CKD (area under the curve [AUC] = .708; P ≤ .0001). Volumetric nephrogram <22.5 HU·L correlated with CKD (AUC = 0.764; P ≤ .0001). High (≥15) ASG scores correlated with both renal volume (AUC = .628; P ≤ .0001) and VN (AUC = .628; P ≤ .0001). Regression analysis demonstrated a strong, inverse relationship between ASG and VN ( R 2 = .95). These data demonstrate that VN is a strong predictor of CKD in a large database of patients undergoing elective aneurysm repair. We demonstrate an inverse relationship between renal function and ASG that has not been previously described in the literature. Additionally, we have shown that VN complements ASG as a model of overall cardiovascular health and atherosclerotic burden. Outcomes in patients with poor renal function may be related to anatomical issues in addition to well-described systemic ramifications.

Computed Tomographic Analysis of Ventral Atlantoaxial Optimal Safe Implantation Corridors in 27 Dogs.

PubMed

Leblond, Guillaume; Gaitero, Luis; Moens, Noel M M; Zur Linden, Alex; James, Fiona M K; Monteith, Gabrielle J; Runciman, John

2017-11-01

Objectives  Ventral atlantoaxial stabilization techniques are challenging surgical procedures in dogs. Available surgical guidelines are based upon subjective anatomical landmarks, and limited radiographic and computed tomographic data. The aims of this study were (1) to provide detailed anatomical descriptions of atlantoaxial optimal safe implantation corridors to generate objective recommendations for optimal implant placements and (2) to compare anatomical data obtained in non-affected Toy breed dogs, affected Toy breed dogs suffering from atlantoaxial instability and non-affected Beagle dogs. Methods  Anatomical data were collected from a prospectively recruited population of 27 dogs using a previously validated method of optimal safe implantation corridor analysis using computed tomographic images. Results  Optimal implant positions and three-dimensional numerical data were generated successfully in all cases. Anatomical landmarks could be used to generate objective definitions of optimal insertion points which were applicable across all three groups. Overall the geometrical distribution of all implant sites was similar in all three groups with a few exceptions. Clinical Significance  This study provides extensive anatomical data available to facilitate surgical planning of implant placement for atlantoaxial stabilization. Our data suggest that non-affected Toy breed dogs and non-affected Beagle dogs constitute reasonable research models to study atlantoaxial stabilization constructs. Schattauer GmbH Stuttgart.

Nonrigid mammogram registration using mutual information

NASA Astrophysics Data System (ADS)

Wirth, Michael A.; Narhan, Jay; Gray, Derek W. S.

2002-05-01

Of the papers dealing with the task of mammogram registration, the majority deal with the task by matching corresponding control-points derived from anatomical landmark points. One of the caveats encountered when using pure point-matching techniques is their reliance on accurately extracted anatomical features-points. This paper proposes an innovative approach to matching mammograms which combines the use of a similarity-measure and a point-based spatial transformation. Mutual information is a cost-function used to determine the degree of similarity between the two mammograms. An initial rigid registration is performed to remove global differences and bring the mammograms into approximate alignment. The mammograms are then subdivided into smaller regions and each of the corresponding subimages is matched independently using mutual information. The centroids of each of the matched subimages are then used as corresponding control-point pairs in association with the Thin-Plate Spline radial basis function. The resulting spatial transformation generates a nonrigid match of the mammograms. The technique is illustrated by matching mammograms from the MIAS mammogram database. An experimental comparison is made between mutual information incorporating purely rigid behavior, and that incorporating a more nonrigid behavior. The effectiveness of the registration process is evaluated using image differences.

Multiple brain atlas database and atlas-based neuroimaging system.

PubMed

Nowinski, W L; Fang, A; Nguyen, B T; Raphel, J K; Jagannathan, L; Raghavan, R; Bryan, R N; Miller, G A

1997-01-01

For the purpose of developing multiple, complementary, fully labeled electronic brain atlases and an atlas-based neuroimaging system for analysis, quantification, and real-time manipulation of cerebral structures in two and three dimensions, we have digitized, enhanced, segmented, and labeled the following print brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach and Tournoux, Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren, Referentially Oriented Cerebral MRI Anatomy by Talairach and Tournoux, and Atlas of the Cerebral Sulci by Ono, Kubik, and Abernathey. Three-dimensional extensions of these atlases have been developed as well. All two- and three-dimensional atlases are mutually preregistered and may be interactively registered with an actual patient's data. An atlas-based neuroimaging system has been developed that provides support for reformatting, registration, visualization, navigation, image processing, and quantification of clinical data. The anatomical index contains about 1,000 structures and over 400 sulcal patterns. Several new applications of the brain atlas database also have been developed, supported by various technologies such as virtual reality, the Internet, and electronic publishing. Fusion of information from multiple atlases assists the user in comprehensively understanding brain structures and identifying and quantifying anatomical regions in clinical data. The multiple brain atlas database and atlas-based neuroimaging system have substantial potential impact in stereotactic neurosurgery and radiotherapy by assisting in visualization and real-time manipulation in three dimensions of anatomical structures, in quantitative neuroradiology by allowing interactive analysis of clinical data, in three-dimensional neuroeducation, and in brain function studies.

Automated construction of arterial and venous trees in retinal images.

PubMed

Hu, Qiao; Abràmoff, Michael D; Garvin, Mona K

2015-10-01

While many approaches exist to segment retinal vessels in fundus photographs, only a limited number focus on the construction and disambiguation of arterial and venous trees. Previous approaches are local and/or greedy in nature, making them susceptible to errors or limiting their applicability to large vessels. We propose a more global framework to generate arteriovenous trees in retinal images, given a vessel segmentation. In particular, our approach consists of three stages. The first stage is to generate an overconnected vessel network, named the vessel potential connectivity map (VPCM), consisting of vessel segments and the potential connectivity between them. The second stage is to disambiguate the VPCM into multiple anatomical trees, using a graph-based metaheuristic algorithm. The third stage is to classify these trees into arterial or venous (A/V) trees. We evaluated our approach with a ground truth built based on a public database, showing a pixel-wise classification accuracy of 88.15% using a manual vessel segmentation as input, and 86.11% using an automatic vessel segmentation as input.

A novel medical image data-based multi-physics simulation platform for computational life sciences.

PubMed

Neufeld, Esra; Szczerba, Dominik; Chavannes, Nicolas; Kuster, Niels

2013-04-06

Simulating and modelling complex biological systems in computational life sciences requires specialized software tools that can perform medical image data-based modelling, jointly visualize the data and computational results, and handle large, complex, realistic and often noisy anatomical models. The required novel solvers must provide the power to model the physics, biology and physiology of living tissue within the full complexity of the human anatomy (e.g. neuronal activity, perfusion and ultrasound propagation). A multi-physics simulation platform satisfying these requirements has been developed for applications including device development and optimization, safety assessment, basic research, and treatment planning. This simulation platform consists of detailed, parametrized anatomical models, a segmentation and meshing tool, a wide range of solvers and optimizers, a framework for the rapid development of specialized and parallelized finite element method solvers, a visualization toolkit-based visualization engine, a Python scripting interface for customized applications, a coupling framework, and more. Core components are cross-platform compatible and use open formats. Several examples of applications are presented: hyperthermia cancer treatment planning, tumour growth modelling, evaluating the magneto-haemodynamic effect as a biomarker and physics-based morphing of anatomical models.

Anatomic Mesenchymal Stem Cell-Based Engineered Cartilage Constructs for Biologic Total Joint Replacement

PubMed Central

Saxena, Vishal; Kim, Minwook; Keah, Niobra M.; Neuwirth, Alexander L.; Stoeckl, Brendan D.; Bickard, Kevin; Restle, David J.; Salowe, Rebecca; Wang, Margaret Ye; Steinberg, David R.

2016-01-01

Cartilage has a poor healing response, and few viable options exist for repair of extensive damage. Hyaluronic acid (HA) hydrogels seeded with mesenchymal stem cells (MSCs) polymerized through UV crosslinking can generate functional tissue, but this crosslinking is not compatible with indirect rapid prototyping utilizing opaque anatomic molds. Methacrylate-modified polymers can also be chemically crosslinked in a cytocompatible manner using ammonium persulfate (APS) and N,N,N′,N′-tetramethylethylenediamine (TEMED). The objectives of this study were to (1) compare APS/TEMED crosslinking with UV crosslinking in terms of functional maturation of MSC-seeded HA hydrogels; (2) generate an anatomic mold of a complex joint surface through rapid prototyping; and (3) grow anatomic MSC-seeded HA hydrogel constructs using this alternative crosslinking method. Juvenile bovine MSCs were suspended in methacrylated HA (MeHA) and crosslinked either through UV polymerization or chemically with APS/TEMED to generate cylindrical constructs. Minipig porcine femoral heads were imaged using microCT, and anatomic negative molds were generated by three-dimensional printing using fused deposition modeling. Molded HA constructs were produced using the APS/TEMED method. All constructs were cultured for up to 12 weeks in a chemically defined medium supplemented with TGF-β3 and characterized by mechanical testing, biochemical assays, and histologic analysis. Both UV- and APS/TEMED-polymerized constructs showed increasing mechanical properties and robust proteoglycan and collagen deposition over time. At 12 weeks, APS/TEMED-polymerized constructs had higher equilibrium and dynamic moduli than UV-polymerized constructs, with no differences in proteoglycan or collagen content. Molded HA constructs retained their hemispherical shape in culture and demonstrated increasing mechanical properties and proteoglycan and collagen deposition, especially at the edges compared to the center of these larger constructs. Immunohistochemistry showed abundant collagen type II staining and little collagen type I staining. APS/TEMED crosslinking can be used to produce MSC-seeded HA-based neocartilage and can be used in combination with rapid prototyping techniques to generate anatomic MSC-seeded HA constructs for use in filling large and anatomically complex chondral defects or for biologic joint replacement. PMID:26871863

EMAP and EMAGE: a framework for understanding spatially organized data.

PubMed

Baldock, Richard A; Bard, Jonathan B L; Burger, Albert; Burton, Nicolas; Christiansen, Jeff; Feng, Guanjie; Hill, Bill; Houghton, Derek; Kaufman, Matthew; Rao, Jianguo; Sharpe, James; Ross, Allyson; Stevenson, Peter; Venkataraman, Shanmugasundaram; Waterhouse, Andrew; Yang, Yiya; Davidson, Duncan R

2003-01-01

The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.

[3D modeling of the female pelvis by Computer-Assisted Anatomical Dissection: Applications and perspectives].

PubMed

Balaya, V; Uhl, J-F; Lanore, A; Salachas, C; Samoyeau, T; Ngo, C; Bensaid, C; Cornou, C; Rossi, L; Douard, R; Bats, A-S; Lecuru, F; Delmas, V

2016-05-01

To achieve a 3D vectorial model of a female pelvis by Computer-Assisted Anatomical Dissection and to assess educationnal and surgical applications. From the database of "visible female" of Visible Human Project(®) (VHP) of the "national library of medicine" NLM (United States), we used 739 transverse anatomical slices of 0.33mm thickness going from L4 to the trochanters. The manual segmentation of each anatomical structures was done with Winsurf(®) software version 4.3. Each anatomical element was built as a separate vectorial object. The whole colored-rendered vectorial model with realistic textures was exported in 3Dpdf format to allow a real time interactive manipulation with Acrobat(®) pro version 11 software. Each element can be handled separately at any transparency, which allows an anatomical learning by systems: skeleton, pelvic organs, urogenital system, arterial and venous vascularization. This 3D anatomical model can be used as data bank to teach of the fundamental anatomy. This 3D vectorial model, realistic and interactive constitutes an efficient educational tool for the teaching of the anatomy of the pelvis. 3D printing of the pelvis is possible with the new printers. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Standards to support information systems integration in anatomic pathology.

PubMed

Daniel, Christel; García Rojo, Marcial; Bourquard, Karima; Henin, Dominique; Schrader, Thomas; Della Mea, Vincenzo; Gilbertson, John; Beckwith, Bruce A

2009-11-01

Integrating anatomic pathology information- text and images-into electronic health care records is a key challenge for enhancing clinical information exchange between anatomic pathologists and clinicians. The aim of the Integrating the Healthcare Enterprise (IHE) international initiative is precisely to ensure interoperability of clinical information systems by using existing widespread industry standards such as Digital Imaging and Communication in Medicine (DICOM) and Health Level Seven (HL7). To define standard-based informatics transactions to integrate anatomic pathology information to the Healthcare Enterprise. We used the methodology of the IHE initiative. Working groups from IHE, HL7, and DICOM, with special interest in anatomic pathology, defined consensual technical solutions to provide end-users with improved access to consistent information across multiple information systems. The IHE anatomic pathology technical framework describes a first integration profile, "Anatomic Pathology Workflow," dedicated to the diagnostic process including basic image acquisition and reporting solutions. This integration profile relies on 10 transactions based on HL7 or DICOM standards. A common specimen model was defined to consistently identify and describe specimens in both HL7 and DICOM transactions. The IHE anatomic pathology working group has defined standard-based informatics transactions to support the basic diagnostic workflow in anatomic pathology laboratories. In further stages, the technical framework will be completed to manage whole-slide images and semantically rich structured reports in the diagnostic workflow and to integrate systems used for patient care and those used for research activities (such as tissue bank databases or tissue microarrayers).

Anatomic and functional leg-length inequality: A review and recommendation for clinical decision-making. Part II, the functional or unloaded leg-length asymmetry

PubMed Central

Knutson, Gary A

2005-01-01

Background Part II of this review examines the functional "short leg" or unloaded leg length alignment asymmetry, including the relationship between an anatomic and functional leg-length inequality. Based on the reviewed evidence, an outline for clinical decision making regarding functional and anatomic leg-length inequality will be provided. Methods Online databases: Medline, CINAHL and Mantis. Plus library searches for the time frame of 1970–2005 were done using the term "leg-length inequality". Results and Discussion The evidence suggests that an unloaded leg-length asymmetry is a different phenomenon than an anatomic leg-length inequality, and may be due to suprapelvic muscle hypertonicity. Anatomic leg-length inequality and unloaded functional or leg-length alignment asymmetry may interact in a loaded (standing) posture, but not in an unloaded (prone/supine) posture. Conclusion The unloaded, functional leg-length alignment asymmetry is a likely phenomenon, although more research regarding reliability of the measurement procedure and validity relative to spinal dysfunction is needed. Functional leg-length alignment asymmetry should be eliminated before any necessary treatment of anatomic LLI. PMID:16080787

Description of the MHS Health Level 7 Chemistry Laboratory for Public Health Surveillance

DTIC Science & Technology

2012-09-01

document provides a history of the HL7 chemistry database and its contents, explains the creation of chemistry/serology records, describes the pathway...in health surveillance activities. This technical document discusses the chemistry database by providing a history of the dataset and its contents...source for its usefulness in public health surveillance. While HL7 data also includes radiology, anatomic pathology reports and pharmacy transactions

Learning-based stochastic object models for use in optimizing imaging systems

NASA Astrophysics Data System (ADS)

Dolly, Steven R.; Anastasio, Mark A.; Yu, Lifeng; Li, Hua

2017-03-01

It is widely known that the optimization of imaging systems based on objective, or task-based, measures of image quality via computer-simulation requires use of a stochastic object model (SOM). However, the development of computationally tractable SOMs that can accurately model the statistical variations in anatomy within a specified ensemble of patients remains a challenging task. Because they are established by use of image data corresponding a single patient, previously reported numerical anatomical models lack of the ability to accurately model inter- patient variations in anatomy. In certain applications, however, databases of high-quality volumetric images are available that can facilitate this task. In this work, a novel and tractable methodology for learning a SOM from a set of volumetric training images is developed. The proposed method is based upon geometric attribute distribution (GAD) models, which characterize the inter-structural centroid variations and the intra-structural shape variations of each individual anatomical structure. The GAD models are scalable and deformable, and constrained by their respective principal attribute variations learned from training data. By use of the GAD models, random organ shapes and positions can be generated and integrated to form an anatomical phantom. The randomness in organ shape and position will reflect the variability of anatomy present in the training data. To demonstrate the methodology, a SOM corresponding to the pelvis of an adult male was computed and a corresponding ensemble of phantoms was created. Additionally, computer-simulated X-ray projection images corresponding to the phantoms were computed, from which tomographic images were reconstructed.

Visualization of Stereoscopic Anatomic Models of the Paranasal Sinuses and Cervical Vertebrae from the Surgical and Procedural Perspective

ERIC Educational Resources Information Center

Chen, Jian; Smith, Andrew D.; Khan, Majid A.; Sinning, Allan R.; Conway, Marianne L.; Cui, Dongmei

2017-01-01

Recent improvements in three-dimensional (3D) virtual modeling software allows anatomists to generate high-resolution, visually appealing, colored, anatomical 3D models from computed tomography (CT) images. In this study, high-resolution CT images of a cadaver were used to develop clinically relevant anatomic models including facial skull, nasal…

MEPD: a Medaka gene expression pattern database

PubMed Central

Henrich, Thorsten; Ramialison, Mirana; Quiring, Rebecca; Wittbrodt, Beate; Furutani-Seiki, Makoto; Wittbrodt, Joachim; Kondoh, Hisato

2003-01-01

The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensity, category and comments and through a comprehensive, hierarchically organized dictionary of anatomical terms. Sequences of the ESTs are available and searchable through BLAST. ESTs in the database are clustered upon entry and have been blasted against public data-bases. The BLAST results are updated regularly, stored within the database and searchable. The MEPD is a project within the Medaka Genome Initiative (MGI) and entries will be interconnected to integrated genomic map databases. MEPD is accessible through the WWW at http://medaka.dsp.jst.go.jp/MEPD. PMID:12519950

Conserved and Divergent Features of Human and Mouse Kidney Organogenesis.

PubMed

Lindström, Nils O; McMahon, Jill A; Guo, Jinjin; Tran, Tracy; Guo, Qiuyu; Rutledge, Elisabeth; Parvez, Riana K; Saribekyan, Gohar; Schuler, Robert E; Liao, Christopher; Kim, Albert D; Abdelhalim, Ahmed; Ruffins, Seth W; Thornton, Matthew E; Basking, Laurence; Grubbs, Brendan; Kesselman, Carl; McMahon, Andrew P

2018-03-01

Human kidney function is underpinned by approximately 1,000,000 nephrons, although the number varies substantially, and low nephron number is linked to disease. Human kidney development initiates around 4 weeks of gestation and ends around 34-37 weeks of gestation. Over this period, a reiterative inductive process establishes the nephron complement. Studies have provided insightful anatomic descriptions of human kidney development, but the limited histologic views are not readily accessible to a broad audience. In this first paper in a series providing comprehensive insight into human kidney formation, we examined human kidney development in 135 anonymously donated human kidney specimens. We documented kidney development at a macroscopic and cellular level through histologic analysis, RNA in situ hybridization, immunofluorescence studies, and transcriptional profiling, contrasting human development (4-23 weeks) with mouse development at selected stages (embryonic day 15.5 and postnatal day 2). The high-resolution histologic interactive atlas of human kidney organogenesis generated can be viewed at the GUDMAP database (www.gudmap.org) together with three-dimensional reconstructions of key components of the data herein. At the anatomic level, human and mouse kidney development differ in timing, scale, and global features such as lobe formation and progenitor niche organization. The data also highlight differences in molecular and cellular features, including the expression and cellular distribution of anchor gene markers used to identify key cell types in mouse kidney studies. These data will facilitate and inform in vitro efforts to generate human kidney structures and comparative functional analyses across mammalian species. Copyright © 2018 by the American Society of Nephrology.

Statistical analysis of whole-body absorption depending on anatomical human characteristics at a frequency of 2.1 GHz.

PubMed

Habachi, A El; Conil, E; Hadjem, A; Vazquez, E; Wong, M F; Gati, A; Fleury, G; Wiart, J

2010-04-07

In this paper, we propose identification of the morphological factors that may impact the whole-body averaged specific absorption rate (WBSAR). This study is conducted for the case of exposure to a front plane wave at a 2100 MHz frequency carrier. This study is based on the development of different regression models for estimating the WBSAR as a function of morphological factors. For this purpose, a database of 12 anatomical human models (phantoms) has been considered. Also, 18 supplementary phantoms obtained using the morphing technique were generated to build the required relation. This paper presents three models based on external morphological factors such as the body surface area, the body mass index or the body mass. These models show good results in estimating the WBSAR (<10%) for families obtained by the morphing technique, but these are still less accurate (30%) when applied to different original phantoms. This study stresses the importance of the internal morphological factors such as muscle and fat proportions in characterization of the WBSAR. The regression models are then improved using internal morphological factors with an estimation error of approximately 10% on the WBSAR. Finally, this study is suitable for establishing the statistical distribution of the WBSAR for a given population characterized by its morphology.

Statistical analysis of whole-body absorption depending on anatomical human characteristics at a frequency of 2.1 GHz

NASA Astrophysics Data System (ADS)

El Habachi, A.; Conil, E.; Hadjem, A.; Vazquez, E.; Wong, M. F.; Gati, A.; Fleury, G.; Wiart, J.

2010-04-01

In this paper, we propose identification of the morphological factors that may impact the whole-body averaged specific absorption rate (WBSAR). This study is conducted for the case of exposure to a front plane wave at a 2100 MHz frequency carrier. This study is based on the development of different regression models for estimating the WBSAR as a function of morphological factors. For this purpose, a database of 12 anatomical human models (phantoms) has been considered. Also, 18 supplementary phantoms obtained using the morphing technique were generated to build the required relation. This paper presents three models based on external morphological factors such as the body surface area, the body mass index or the body mass. These models show good results in estimating the WBSAR (<10%) for families obtained by the morphing technique, but these are still less accurate (30%) when applied to different original phantoms. This study stresses the importance of the internal morphological factors such as muscle and fat proportions in characterization of the WBSAR. The regression models are then improved using internal morphological factors with an estimation error of approximately 10% on the WBSAR. Finally, this study is suitable for establishing the statistical distribution of the WBSAR for a given population characterized by its morphology.

Characterization of Capsicum species using anatomical and molecular data.

PubMed

Dias, G B; Gomes, V M; Moraes, T M S; Zottich, U P; Rabelo, G R; Carvalho, A O; Moulin, M; Gonçalves, L S A; Rodrigues, R; Da Cunha, M

2013-02-28

Capsicum species are frequently described in terms of genetic divergence, considering morphological, agronomic, and molecular databases. However, descriptions of genetic differences based on anatomical characters are rare. We examined the anatomy and the micromorphology of vegetative and reproductive organs of several Capsicum species. Four Capsicum accessions representing the species C. annuum var. annuum, C. baccatum var. pendulum, C. chinense, and C. frutescens were cultivated in a greenhouse; leaves, fruits and seeds were sampled and their organ structure analyzed by light and scanning electronic microscopy. Molecular accession characterization was made using ISSR markers. Polymorphism was observed among tector trichomes and also in fruit color and shape. High variability among accessions was detected by ISSR markers. Despite the species studied present a wide morphological and molecular variability that was not reflected by anatomical features.

The Main Anatomical Variations of the Pancreatic Duct System: Review of the Literature and Its Importance in Surgical Practice.

PubMed

Dimitriou, Ioannis; Katsourakis, Anastasios; Nikolaidou, Eirini; Noussios, George

2018-05-01

Anatomical variations or anomalies of the pancreatic ducts are important in the planning and performance of endoscopic retrograde cholangiopancreatography (ERCP) and surgical procedures of the pancreas. Normal pancreatic duct anatomy occurs in approximately 94.3% of cases, and multiple variations have been described for the remaining 5.7%. The purpose of this study was to review the literature on the pancreatic duct anatomy and to underline its importance in daily invasive endoscopic and surgical practice. Two main databases were searched for suitable articles published from 2000 to 2017, and results concerning more than 8,200 patients were included in the review. The most common anatomical variation was that of pancreas divisum, which appeared in approximately 4.5% of cases.

Anatomy of the sural nerve: cadaver study and literature review.

PubMed

Riedl, Otto; Frey, Manfred

2013-04-01

The sural nerve is commonly used as donor for nerve grafting. Contrary to its constant retromalleolar position, formation and course of the proximal sural nerve show great variability. The coexistence of different and deceptive terminologies contributes to the complexity, and reviewing the international literature is confusing. Because detailed anatomical knowledge is essential for efficient and safe sural nerve harvesting, this study aims to bring clarity. Previous sural nerve reports listed in the PubMed database and established anatomical textbooks were reviewed. Different terminologies were compared and adjusted. Anatomical details and variations were noted. Subtle prospective anatomical dissections and comparison with actual data followed. Two hundred twenty-one relevant reports were identified and worked up going back to the nineteenth century. Fourteen established German and English language anatomical textbooks were reviewed. Thirty lower limbs were dissected. In total, this study pools the information of more than 2500 sural nerves. This study covers all information about the sural nerve anatomy published internationally. The coexistence of different and confusing terminologies is pinpointed and adjusted to allow comparison of previous reports and to gain a coordinated data pool of more than 2500 investigated sural nerves. Detailed features are clearly described and summarized, findings from the authors' own prospective dissections complete these data, and the prior existing anatomical confusion is resolved. Finally, clinical implications are described.

Patient specific anatomy: the new area of anatomy based on computer science illustrated on liver.

PubMed

Soler, Luc; Mutter, Didier; Pessaux, Patrick; Marescaux, Jacques

2015-01-01

Over the past century, medical imaging has brought a new revolution: internal anatomy of a patient could be seen without any invasive technique. This revolution has highlighted the two main limits of current anatomy: the anatomical description is physician dependent, and the average anatomy is more and more frequently insufficient to describe anatomical variations. These drawbacks can sometimes be so important that they create mistakes but they can be overcome through the use of 3D patient-specific surgical anatomy. In this article, we propose to illustrate such improvement of standard anatomy on liver. We first propose a general scheme allowing to easily compare the four main liver anatomical descriptions by Takasaki, Goldsmith and Woodburne, Bismuth and Couinaud. From this general scheme we propose four rules to apply in order to correct these initial anatomical definitions. Application of these rules allows to correct usual vascular topological mistakes of standard anatomy. We finally validate such correction on a database of 20 clinical cases compared to the 111 clinical cases of a Couinaud article. Out of the 20 images of the database, we note a revealing difference in 14 cases (70%) on at least one important branch of the portal network. Only six cases (30%) do not present a revealing difference between both labellings. We also show that the right portal fissure location on our 20 cases defined between segment V and VI of our anatomical definition is well correlated with the real position described by Couinaud on 111 cases, knowing that the theoretical position was only found in 46 cases out of 111, i.e., 41.44% of cases with the non-corrected Couinaud definition. We have proposed a new anatomical segmentation of the liver based on four main rules to apply in order to correct topological errors of the four main standard segmentations. Our validation clearly illustrates that this new definition corrects the large amount of mistakes created by the current standard definitions, increased by physician interpretation that can vary from one case to another.

Patient specific anatomy: the new area of anatomy based on computer science illustrated on liver

PubMed Central

Mutter, Didier; Pessaux, Patrick; Marescaux, Jacques

2015-01-01

Background Over the past century, medical imaging has brought a new revolution: internal anatomy of a patient could be seen without any invasive technique. This revolution has highlighted the two main limits of current anatomy: the anatomical description is physician dependent, and the average anatomy is more and more frequently insufficient to describe anatomical variations. These drawbacks can sometimes be so important that they create mistakes but they can be overcome through the use of 3D patient-specific surgical anatomy. Methods In this article, we propose to illustrate such improvement of standard anatomy on liver. We first propose a general scheme allowing to easily compare the four main liver anatomical descriptions by Takasaki, Goldsmith and Woodburne, Bismuth and Couinaud. From this general scheme we propose four rules to apply in order to correct these initial anatomical definitions. Application of these rules allows to correct usual vascular topological mistakes of standard anatomy. We finally validate such correction on a database of 20 clinical cases compared to the 111 clinical cases of a Couinaud article. Results Out of the 20 images of the database, we note a revealing difference in 14 cases (70%) on at least one important branch of the portal network. Only six cases (30%) do not present a revealing difference between both labellings. We also show that the right portal fissure location on our 20 cases defined between segment V and VI of our anatomical definition is well correlated with the real position described by Couinaud on 111 cases, knowing that the theoretical position was only found in 46 cases out of 111, i.e., 41.44% of cases with the non-corrected Couinaud definition. Conclusions We have proposed a new anatomical segmentation of the liver based on four main rules to apply in order to correct topological errors of the four main standard segmentations. Our validation clearly illustrates that this new definition corrects the large amount of mistakes created by the current standard definitions, increased by physician interpretation that can vary from one case to another. PMID:29075611

Exploring the anatomical encoding of voice with a mathematical model of the vocal system.

PubMed

Assaneo, M Florencia; Sitt, Jacobo; Varoquaux, Gael; Sigman, Mariano; Cohen, Laurent; Trevisan, Marcos A

2016-11-01

The faculty of language depends on the interplay between the production and perception of speech sounds. A relevant open question is whether the dimensions that organize voice perception in the brain are acoustical or depend on properties of the vocal system that produced it. One of the main empirical difficulties in answering this question is to generate sounds that vary along a continuum according to the anatomical properties the vocal apparatus that produced them. Here we use a mathematical model that offers the unique possibility of synthesizing vocal sounds by controlling a small set of anatomically based parameters. In a first stage the quality of the synthetic voice was evaluated. Using specific time traces for sub-glottal pressure and tension of the vocal folds, the synthetic voices generated perceptual responses, which are indistinguishable from those of real speech. The synthesizer was then used to investigate how the auditory cortex responds to the perception of voice depending on the anatomy of the vocal apparatus. Our fMRI results show that sounds are perceived as human vocalizations when produced by a vocal system that follows a simple relationship between the size of the vocal folds and the vocal tract. We found that these anatomical parameters encode the perceptual vocal identity (male, female, child) and show that the brain areas that respond to human speech also encode vocal identity. On the basis of these results, we propose that this low-dimensional model of the vocal system is capable of generating realistic voices and represents a novel tool to explore the voice perception with a precise control of the anatomical variables that generate speech. Furthermore, the model provides an explanation of how auditory cortices encode voices in terms of the anatomical parameters of the vocal system. Copyright © 2016 Elsevier Inc. All rights reserved.

Using 3D modeling techniques to enhance teaching of difficult anatomical concepts

PubMed Central

Pujol, Sonia; Baldwin, Michael; Nassiri, Joshua; Kikinis, Ron; Shaffer, Kitt

2016-01-01

Rationale and Objectives Anatomy is an essential component of medical education as it is critical for the accurate diagnosis in organs and human systems. The mental representation of the shape and organization of different anatomical structures is a crucial step in the learning process. The purpose of this pilot study is to demonstrate the feasibility and benefits of developing innovative teaching modules for anatomy education of first-year medical students based on 3D reconstructions from actual patient data. Materials and Methods A total of 196 models of anatomical structures from 16 anonymized CT datasets were generated using the 3D Slicer open-source software platform. The models focused on three anatomical areas: the mediastinum, the upper abdomen and the pelvis. Online optional quizzes were offered to first-year medical students to assess their comprehension in the areas of interest. Specific tasks were designed for students to complete using the 3D models. Results Scores of the quizzes confirmed a lack of understanding of 3D spatial relationships of anatomical structures despite standard instruction including dissection. Written task material and qualitative review by students suggested that interaction with 3D models led to a better understanding of the shape and spatial relationships among structures, and helped illustrate anatomical variations from one body to another. Conclusion The study demonstrates the feasibility of one possible approach to the generation of 3D models of the anatomy from actual patient data. The educational materials developed have the potential to supplement the teaching of complex anatomical regions and help demonstrate the anatomic variation among patients. PMID:26897601

Incomplete Hippocampal Inversion: A Comprehensive MRI Study of Over 2000 Subjects.

PubMed

Cury, Claire; Toro, Roberto; Cohen, Fanny; Fischer, Clara; Mhaya, Amel; Samper-González, Jorge; Hasboun, Dominique; Mangin, Jean-François; Banaschewski, Tobias; Bokde, Arun L W; Bromberg, Uli; Buechel, Christian; Cattrell, Anna; Conrod, Patricia; Flor, Herta; Gallinat, Juergen; Garavan, Hugh; Gowland, Penny; Heinz, Andreas; Ittermann, Bernd; Lemaitre, Hervé; Martinot, Jean-Luc; Nees, Frauke; Paillère Martinot, Marie-Laure; Orfanos, Dimitri P; Paus, Tomas; Poustka, Luise; Smolka, Michael N; Walter, Henrik; Whelan, Robert; Frouin, Vincent; Schumann, Gunter; Glaunès, Joan A; Colliot, Olivier

2015-01-01

The incomplete-hippocampal-inversion (IHI), also known as malrotation, is an atypical anatomical pattern of the hippocampus, which has been reported in healthy subjects in different studies. However, extensive characterization of IHI in a large sample has not yet been performed. Furthermore, it is unclear whether IHI are restricted to the medial-temporal lobe or are associated with more extensive anatomical changes. Here, we studied the characteristics of IHI in a community-based sample of 2008 subjects of the IMAGEN database and their association with extra-hippocampal anatomical variations. The presence of IHI was assessed on T1-weighted anatomical magnetic resonance imaging (MRI) using visual criteria. We assessed the association of IHI with other anatomical changes throughout the brain using automatic morphometry of cortical sulci. We found that IHI were much more frequent in the left hippocampus (left: 17%, right: 6%, χ(2)-test, p < 10(-28)). Compared to subjects without IHI, subjects with IHI displayed morphological changes in several sulci located mainly in the limbic lobe. Our results demonstrate that IHI are a common left-sided phenomenon in normal subjects and that they are associated with morphological changes outside the medial temporal lobe.

Incomplete Hippocampal Inversion: A Comprehensive MRI Study of Over 2000 Subjects

PubMed Central

Cury, Claire; Toro, Roberto; Cohen, Fanny; Fischer, Clara; Mhaya, Amel; Samper-González, Jorge; Hasboun, Dominique; Mangin, Jean-François; Banaschewski, Tobias; Bokde, Arun L. W.; Bromberg, Uli; Buechel, Christian; Cattrell, Anna; Conrod, Patricia; Flor, Herta; Gallinat, Juergen; Garavan, Hugh; Gowland, Penny; Heinz, Andreas; Ittermann, Bernd; Lemaitre, Hervé; Martinot, Jean-Luc; Nees, Frauke; Paillère Martinot, Marie-Laure; Orfanos, Dimitri P.; Paus, Tomas; Poustka, Luise; Smolka, Michael N.; Walter, Henrik; Whelan, Robert; Frouin, Vincent; Schumann, Gunter; Glaunès, Joan A.; Colliot, Olivier

2015-01-01

The incomplete-hippocampal-inversion (IHI), also known as malrotation, is an atypical anatomical pattern of the hippocampus, which has been reported in healthy subjects in different studies. However, extensive characterization of IHI in a large sample has not yet been performed. Furthermore, it is unclear whether IHI are restricted to the medial-temporal lobe or are associated with more extensive anatomical changes. Here, we studied the characteristics of IHI in a community-based sample of 2008 subjects of the IMAGEN database and their association with extra-hippocampal anatomical variations. The presence of IHI was assessed on T1-weighted anatomical magnetic resonance imaging (MRI) using visual criteria. We assessed the association of IHI with other anatomical changes throughout the brain using automatic morphometry of cortical sulci. We found that IHI were much more frequent in the left hippocampus (left: 17%, right: 6%, χ2−test, p < 10−28). Compared to subjects without IHI, subjects with IHI displayed morphological changes in several sulci located mainly in the limbic lobe. Our results demonstrate that IHI are a common left-sided phenomenon in normal subjects and that they are associated with morphological changes outside the medial temporal lobe. PMID:26733822

AnatomicalTerms.info: heading for an online solution to the anatomical synonym problem hurdles in data-reuse from the Terminologia Anatomica and the foundational model of anatomy and potentials for future development.

PubMed

Gobée, O Paul; Jansma, Daniël; DeRuiter, Marco C

2011-10-01

The many synonyms for anatomical structures confuse medical students and complicate medical communication. Easily accessible translations would alleviate this problem. None of the presently available resources-Terminologia Anatomica (TA), digital terminologies such as the Foundational Model of Anatomy (FMA), and websites-are fully satisfactory to this aim. Internet technologies offer new possibilities to solve the problem. Several authors have called for an online TA. An online translation resource should be easily accessible, user-friendly, comprehensive, expandable, and its quality determinable. As first step towards this goal, we built a translation website that we named www.AnatomicalTerms.info, based on the database of the FMA. It translates between English, Latin, eponyms, and to a lesser extent other languages, and presently contains over 31,000 terms for 7,250 structures, covering 95% of TA. In addition, it automatically presents searches for images, documents and anatomical variations regarding the sought structure. Several terminological and conceptual issues were encountered in transferring data from TA and FMA into AnatomicalTerms.info, resultant from these resources' different set-ups (paper versus digital) and targets (machine versus human-user). To the best of our knowledge, AnatomicalTerms.info is unique in its combination of user-friendliness and comprehensiveness. As next step, wiki-like expandability will be added to enable open contribution of clinical synonyms and terms in different languages. Specific quality measures will be taken to strike a balance between open contribution and quality assurance. AnatomicalTerms.info's mechanism that "translates" terms to structures furthermore may enhance targeted searching by linking images, descriptions, and other anatomical resources to the structures. Copyright © 2011 Wiley-Liss, Inc.

Evaluation of sexual history-based screening of anatomic sites for chlamydia trachomatis and neisseria gonorrhoeae infection in men having sex with men in routine practice.

PubMed

Peters, Remco P H; Verweij, Stephan P; Nijsten, Noëmi; Ouburg, Sander; Mutsaers, Johan; Jansen, Casper L; van Leeuwen, A Petra; Morré, Servaas A

2011-07-26

Sexually transmitted infection (STI) screening programmes are implemented in many countries to decrease burden of STI and to improve sexual health. Screening for Chlamydia trachomatis and Neisseria gonorrhoeae has a prominent role in these protocols. Most of the screening programmes concerning men having sex with men (MSM) are based on opportunistic urethral testing. In The Netherlands, a history-based approach is used. The aim of this study is to evaluate the protocol of screening anatomic sites for C. trachomatis and N. gonorrhoeae infection based on sexual history in MSM in routine practice in The Netherlands. All MSM visiting the clinic for STI in The Hague are routinely asked about their sexual practice during consulting. As per protocol, tests for urogenital, oropharyngeal and anorectal infection are obtained based on reported site(s) of sexual contact. All consultations are entered into a database as part of the national STI monitoring system. Data of an 18 months period were retrieved from this database and analysed. A total of 1455 consultations in MSM were registered during the study period. The prevalence of C. trachomatis and N. gonorrhoeae per anatomic site was: urethral infection 4.0% respectively and 2.8%, oropharynx 1.5% and 4.2%, and anorectum 8.2% and 6.0%. The majority of chlamydia cases (72%) involved a single anatomic site, which was especially manifest for anorectal infections (79%), while 42% of gonorrhoea cases were single site. Twenty-six percent of MSM with anorectal chlamydia and 17% with anorectal gonorrhoea reported symptoms of proctitis; none of the oropharyngeal infections were symptomatic. Most cases of anorectal infection (83%) and oropharyngeal infection (100%) would have remained undiagnosed with a symptom-based protocol. The current strategy of sexual-history based screening of multiple anatomic sites for chlamydia and gonorrhoea in MSM is a useful and valid guideline which is to be preferred over a symptom-based screening protocol.

Computer aided three-dimensional reconstruction and modeling of the pelvis, by using plastinated cross sections, as a powerful tool for morphological investigations.

PubMed

Sora, Mircea-Constantin; Jilavu, Radu; Matusz, Petru

2012-10-01

The aim of this study was to describe a method of developing a computerized model of the human female pelvis using plastinated slices. Computerized reconstruction of anatomical structures is becoming very useful for developing anatomical teaching, research modules and animations. Although databases consisting of serial sections derived from frozen cadaver material exist, plastination represents an alternative method for developing anatomical data useful for computerized reconstruction. A slice anatomy study, using plastinated transparent pelvis cross sections, was performed to obtain a 3D reconstruction. One female human pelvis used for this study, first plastinated as a block, then sliced into thin slices and in the end subjected to 3D computerized reconstruction using WinSURF modeling system (SURFdriver Software). To facilitate the understanding of the complex pelvic floor anatomy on sectional images obtained through MR imaging, and to make the representation more vivid, a female pelvis computer-aided 3D model was created. Qualitative observations revealed that the morphological features of the model were consistent with those displayed by typical cadaveric specimens. The quality of the reconstructed images appeared distinct, especially the spatial positions and complicated relationships of contiguous structures of the female pelvis. All reconstructed structures can be displayed in groups or as a whole and interactively rotated in 3D space. The utilization of plastinates for generating tissue sections is useful for 3D computerized modeling. The 3D model of the female pelvis presented in this paper provides a stereoscopic view to study the adjacent relationship and arrangement of respective pelvis sections. A better understanding of the pelvic floor anatomy is relevant to gynaecologists, radiologists, surgeons, urologists, physical therapists and all professionals who take care of women with pelvic floor dysfunction.

Enhancing radiological volumes with symbolic anatomy using image fusion and collaborative virtual reality.

PubMed

Silverstein, Jonathan C; Dech, Fred; Kouchoukos, Philip L

2004-01-01

Radiological volumes are typically reviewed by surgeons using cross-sections and iso-surface reconstructions. Applications that combine collaborative stereo volume visualization with symbolic anatomic information and data fusions would expand surgeons' capabilities in interpretation of data and in planning treatment. Such an application has not been seen clinically. We are developing methods to systematically combine symbolic anatomy (term hierarchies and iso-surface atlases) with patient data using data fusion. We describe our progress toward integrating these methods into our collaborative virtual reality application. The fully combined application will be a feature-rich stereo collaborative volume visualization environment for use by surgeons in which DICOM datasets will self-report underlying anatomy with visual feedback. Using hierarchical navigation of SNOMED-CT anatomic terms integrated with our existing Tele-immersive DICOM-based volumetric rendering application, we will display polygonal representations of anatomic systems on the fly from menus that query a database. The methods and tools involved in this application development are SNOMED-CT, DICOM, VISIBLE HUMAN, volumetric fusion and C++ on a Tele-immersive platform. This application will allow us to identify structures and display polygonal representations from atlas data overlaid with the volume rendering. First, atlas data is automatically translated, rotated, and scaled to the patient data during loading using a public domain volumetric fusion algorithm. This generates a modified symbolic representation of the underlying canonical anatomy. Then, through the use of collision detection or intersection testing of various transparent polygonal representations, the polygonal structures are highlighted into the volumetric representation while the SNOMED names are displayed. Thus, structural names and polygonal models are associated with the visualized DICOM data. This novel juxtaposition of information promises to expand surgeons' abilities to interpret images and plan treatment.

Pathology economic model tool: a novel approach to workflow and budget cost analysis in an anatomic pathology laboratory.

PubMed

Muirhead, David; Aoun, Patricia; Powell, Michael; Juncker, Flemming; Mollerup, Jens

2010-08-01

The need for higher efficiency, maximum quality, and faster turnaround time is a continuous focus for anatomic pathology laboratories and drives changes in work scheduling, instrumentation, and management control systems. To determine the costs of generating routine, special, and immunohistochemical microscopic slides in a large, academic anatomic pathology laboratory using a top-down approach. The Pathology Economic Model Tool was used to analyze workflow processes at The Nebraska Medical Center's anatomic pathology laboratory. Data from the analysis were used to generate complete cost estimates, which included not only materials, consumables, and instrumentation but also specific labor and overhead components for each of the laboratory's subareas. The cost data generated by the Pathology Economic Model Tool were compared with the cost estimates generated using relative value units. Despite the use of automated systems for different processes, the workflow in the laboratory was found to be relatively labor intensive. The effect of labor and overhead on per-slide costs was significantly underestimated by traditional relative-value unit calculations when compared with the Pathology Economic Model Tool. Specific workflow defects with significant contributions to the cost per slide were identified. The cost of providing routine, special, and immunohistochemical slides may be significantly underestimated by traditional methods that rely on relative value units. Furthermore, a comprehensive analysis may identify specific workflow processes requiring improvement.

An eFTD-VP framework for efficiently generating patient-specific anatomically detailed facial soft tissue FE mesh for craniomaxillofacial surgery simulation

PubMed Central

Zhang, Xiaoyan; Kim, Daeseung; Shen, Shunyao; Yuan, Peng; Liu, Siting; Tang, Zhen; Zhang, Guangming; Zhou, Xiaobo; Gateno, Jaime

2017-01-01

Accurate surgical planning and prediction of craniomaxillofacial surgery outcome requires simulation of soft tissue changes following osteotomy. This can only be achieved by using an anatomically detailed facial soft tissue model. The current state-of-the-art of model generation is not appropriate to clinical applications due to the time-intensive nature of manual segmentation and volumetric mesh generation. The conventional patient-specific finite element (FE) mesh generation methods are to deform a template FE mesh to match the shape of a patient based on registration. However, these methods commonly produce element distortion. Additionally, the mesh density for patients depends on that of the template model. It could not be adjusted to conduct mesh density sensitivity analysis. In this study, we propose a new framework of patient-specific facial soft tissue FE mesh generation. The goal of the developed method is to efficiently generate a high-quality patient-specific hexahedral FE mesh with adjustable mesh density while preserving the accuracy in anatomical structure correspondence. Our FE mesh is generated by eFace template deformation followed by volumetric parametrization. First, the patient-specific anatomically detailed facial soft tissue model (including skin, mucosa, and muscles) is generated by deforming an eFace template model. The adaptation of the eFace template model is achieved by using a hybrid landmark-based morphing and dense surface fitting approach followed by a thin-plate spline interpolation. Then, high-quality hexahedral mesh is constructed by using volumetric parameterization. The user can control the resolution of hexahedron mesh to best reflect clinicians’ need. Our approach was validated using 30 patient models and 4 visible human datasets. The generated patient-specific FE mesh showed high surface matching accuracy, element quality, and internal structure matching accuracy. They can be directly and effectively used for clinical simulation of facial soft tissue change. PMID:29027022

An eFTD-VP framework for efficiently generating patient-specific anatomically detailed facial soft tissue FE mesh for craniomaxillofacial surgery simulation.

PubMed

Zhang, Xiaoyan; Kim, Daeseung; Shen, Shunyao; Yuan, Peng; Liu, Siting; Tang, Zhen; Zhang, Guangming; Zhou, Xiaobo; Gateno, Jaime; Liebschner, Michael A K; Xia, James J

2018-04-01

Accurate surgical planning and prediction of craniomaxillofacial surgery outcome requires simulation of soft tissue changes following osteotomy. This can only be achieved by using an anatomically detailed facial soft tissue model. The current state-of-the-art of model generation is not appropriate to clinical applications due to the time-intensive nature of manual segmentation and volumetric mesh generation. The conventional patient-specific finite element (FE) mesh generation methods are to deform a template FE mesh to match the shape of a patient based on registration. However, these methods commonly produce element distortion. Additionally, the mesh density for patients depends on that of the template model. It could not be adjusted to conduct mesh density sensitivity analysis. In this study, we propose a new framework of patient-specific facial soft tissue FE mesh generation. The goal of the developed method is to efficiently generate a high-quality patient-specific hexahedral FE mesh with adjustable mesh density while preserving the accuracy in anatomical structure correspondence. Our FE mesh is generated by eFace template deformation followed by volumetric parametrization. First, the patient-specific anatomically detailed facial soft tissue model (including skin, mucosa, and muscles) is generated by deforming an eFace template model. The adaptation of the eFace template model is achieved by using a hybrid landmark-based morphing and dense surface fitting approach followed by a thin-plate spline interpolation. Then, high-quality hexahedral mesh is constructed by using volumetric parameterization. The user can control the resolution of hexahedron mesh to best reflect clinicians' need. Our approach was validated using 30 patient models and 4 visible human datasets. The generated patient-specific FE mesh showed high surface matching accuracy, element quality, and internal structure matching accuracy. They can be directly and effectively used for clinical simulation of facial soft tissue change.

How small could a pup sound? The physical bases of signaling body size in harbor seals

PubMed Central

Gross, Stephanie; Garcia, Maxime; Rubio-Garcia, Ana; de Boer, Bart

2017-01-01

Abstract Vocal communication is a crucial aspect of animal behavior. The mechanism which most mammals use to vocalize relies on three anatomical components. First, air overpressure is generated inside the lower vocal tract. Second, as the airstream goes through the glottis, sound is produced via vocal fold vibration. Third, this sound is further filtered by the geometry and length of the upper vocal tract. Evidence from mammalian anatomy and bioacoustics suggests that some of these three components may covary with an animal’s body size. The framework provided by acoustic allometry suggests that, because vocal tract length (VTL) is more strongly constrained by the growth of the body than vocal fold length (VFL), VTL generates more reliable acoustic cues to an animal’s size. This hypothesis is often tested acoustically but rarely anatomically, especially in pinnipeds. Here, we test the anatomical bases of the acoustic allometry hypothesis in harbor seal pups Phoca vitulina. We dissected and measured vocal tract, vocal folds, and other anatomical features of 15 harbor seals post-mortem. We found that, while VTL correlates with body size, VFL does not. This suggests that, while body growth puts anatomical constraints on how vocalizations are filtered by harbor seals’ vocal tract, no such constraints appear to exist on vocal folds, at least during puppyhood. It is particularly interesting to find anatomical constraints on harbor seals’ vocal tracts, the same anatomical region partially enabling pups to produce individually distinctive vocalizations. PMID:29492005

Automated construction of arterial and venous trees in retinal images

PubMed Central

Hu, Qiao; Abràmoff, Michael D.; Garvin, Mona K.

2015-01-01

Abstract. While many approaches exist to segment retinal vessels in fundus photographs, only a limited number focus on the construction and disambiguation of arterial and venous trees. Previous approaches are local and/or greedy in nature, making them susceptible to errors or limiting their applicability to large vessels. We propose a more global framework to generate arteriovenous trees in retinal images, given a vessel segmentation. In particular, our approach consists of three stages. The first stage is to generate an overconnected vessel network, named the vessel potential connectivity map (VPCM), consisting of vessel segments and the potential connectivity between them. The second stage is to disambiguate the VPCM into multiple anatomical trees, using a graph-based metaheuristic algorithm. The third stage is to classify these trees into arterial or venous (A/V) trees. We evaluated our approach with a ground truth built based on a public database, showing a pixel-wise classification accuracy of 88.15% using a manual vessel segmentation as input, and 86.11% using an automatic vessel segmentation as input. PMID:26636114

Terminology of the tonsils.

PubMed

Casteleyn, C; Simoens, P; Van den Broeck, W

2011-06-01

Many terms used for referring to tonsillar structures are applied in immunological research. However, in many cases, the use of these terms is not in compliance with official veterinary anatomical nomenclature. This is partly attributable to ambiguous descriptions present in conventional anatomical textbooks. This study gives an overview of pertaining controversial terms and promotes the official anatomical terminology applicable to the tonsils, to enhance the unequivocal transfer of knowledge generated during immunological research. © 2011 Blackwell Verlag GmbH.

A novel approach for determining three-dimensional acetabular orientation: results from two hundred subjects.

PubMed

Higgins, Sean W; Spratley, E Meade; Boe, Richard A; Hayes, Curtis W; Jiranek, William A; Wayne, Jennifer S

2014-11-05

The inherently complex three-dimensional morphology of both the pelvis and acetabulum create difficulties in accurately determining acetabular orientation. Our objectives were to develop a reliable and accurate methodology for determining three-dimensional acetabular orientation and to utilize it to describe relevant characteristics of a large population of subjects without apparent hip pathology. High-resolution computed tomography studies of 200 patients previously receiving pelvic scans for indications not related to orthopaedic conditions were selected from our institution's database. Three-dimensional models of each osseous pelvis were generated to extract specific anatomical data sets. A novel computational method was developed to determine standard measures of three-dimensional acetabular orientation within an automatically identified anterior pelvic plane reference frame. Automatically selected points on the osseous ridge of the acetabulum were used to generate a best-fit plane for describing acetabular orientation. Our method showed excellent interobserver and intraobserver agreement (an intraclass correlation coefficient [ICC] of >0.999) and achieved high levels of accuracy. A significant difference between males and females in both anteversion (average, 3.5°; 95% confidence interval [CI], 1.9° to 5.1° across all angular definitions; p < 0.0001) and inclination (1.4°; 95% CI, 0.6° to 2.3° for anatomic angular definition; p < 0.002) was observed. Intrapatient asymmetry in anatomic measures showed bilateral differences in anteversion (maximum, 12.1°) and in inclination (maximum, 10.9°). Significant differences in acetabular orientation between the sexes can be detected only with accurate measurements that account for the entire acetabulum. While a wide range of interpatient acetabular orientations was observed, the majority of subjects had acetabula that were relatively symmetrical in both inclination and anteversion. A highly accurate and reproducible method for determining the orientation of the acetabulum's aperture will benefit both surgeons and patients, by further refining the distinctions between normal and abnormal hip characteristics. Enhanced understanding of the acetabulum could be useful in the diagnostic, planning, and execution stages for surgical procedures of the hip or in advancing the design of new implant systems. Copyright © 2014 by The Journal of Bone and Joint Surgery, Incorporated.

Multimodality medical image database for temporal lobe epilepsy

NASA Astrophysics Data System (ADS)

Siadat, Mohammad-Reza; Soltanian-Zadeh, Hamid; Fotouhi, Farshad A.; Elisevich, Kost

2003-05-01

This paper presents the development of a human brain multi-modality database for surgical candidacy determination in temporal lobe epilepsy. The focus of the paper is on content-based image management, navigation and retrieval. Several medical image-processing methods including our newly developed segmentation method are utilized for information extraction/correlation and indexing. The input data includes T1-, T2-Weighted and FLAIR MRI and ictal/interictal SPECT modalities with associated clinical data and EEG data analysis. The database can answer queries regarding issues such as the correlation between the attribute X of the entity Y and the outcome of a temporal lobe epilepsy surgery. The entity Y can be a brain anatomical structure such as the hippocampus. The attribute X can be either a functionality feature of the anatomical structure Y, calculated with SPECT modalities, such as signal average, or a volumetric/morphological feature of the entity Y such as volume or average curvature. The outcome of the surgery can be any surgery assessment such as non-verbal Wechsler memory quotient. A determination is made regarding surgical candidacy by analysis of both textual and image data. The current database system suggests a surgical determination for the cases with relatively small hippocampus and high signal intensity average on FLAIR images within the hippocampus. This indication matches the neurosurgeons expectations/observations. Moreover, as the database gets more populated with patient profiles and individual surgical outcomes, using data mining methods one may discover partially invisible correlations between the contents of different modalities of data and the outcome of the surgery.

Multimedia human brain database system for surgical candidacy determination in temporal lobe epilepsy with content-based image retrieval

NASA Astrophysics Data System (ADS)

Siadat, Mohammad-Reza; Soltanian-Zadeh, Hamid; Fotouhi, Farshad A.; Elisevich, Kost

2003-01-01

This paper presents the development of a human brain multimedia database for surgical candidacy determination in temporal lobe epilepsy. The focus of the paper is on content-based image management, navigation and retrieval. Several medical image-processing methods including our newly developed segmentation method are utilized for information extraction/correlation and indexing. The input data includes T1-, T2-Weighted MRI and FLAIR MRI and ictal and interictal SPECT modalities with associated clinical data and EEG data analysis. The database can answer queries regarding issues such as the correlation between the attribute X of the entity Y and the outcome of a temporal lobe epilepsy surgery. The entity Y can be a brain anatomical structure such as the hippocampus. The attribute X can be either a functionality feature of the anatomical structure Y, calculated with SPECT modalities, such as signal average, or a volumetric/morphological feature of the entity Y such as volume or average curvature. The outcome of the surgery can be any surgery assessment such as memory quotient. A determination is made regarding surgical candidacy by analysis of both textual and image data. The current database system suggests a surgical determination for the cases with relatively small hippocampus and high signal intensity average on FLAIR images within the hippocampus. This indication pretty much fits with the surgeons" expectations/observations. Moreover, as the database gets more populated with patient profiles and individual surgical outcomes, using data mining methods one may discover partially invisible correlations between the contents of different modalities of data and the outcome of the surgery.

A practical workflow for making anatomical atlases for biological research.

PubMed

Wan, Yong; Lewis, A Kelsey; Colasanto, Mary; van Langeveld, Mark; Kardon, Gabrielle; Hansen, Charles

2012-01-01

The anatomical atlas has been at the intersection of science and art for centuries. These atlases are essential to biological research, but high-quality atlases are often scarce. Recent advances in imaging technology have made high-quality 3D atlases possible. However, until now there has been a lack of practical workflows using standard tools to generate atlases from images of biological samples. With certain adaptations, CG artists' workflow and tools, traditionally used in the film industry, are practical for building high-quality biological atlases. Researchers have developed a workflow for generating a 3D anatomical atlas using accessible artists' tools. They used this workflow to build a mouse limb atlas for studying the musculoskeletal system's development. This research aims to raise the awareness of using artists' tools in scientific research and promote interdisciplinary collaborations between artists and scientists. This video (http://youtu.be/g61C-nia9ms) demonstrates a workflow for creating an anatomical atlas.

Stemless shoulder arthroplasty: a literature review

PubMed Central

PETRICCIOLI, DARIO; BERTONE, CELESTE; MARCHI, GIACOMO

2015-01-01

The design of humeral implants for shoulder arthroplasty has evolved over the years. The new-generation modular shoulder prostheses have an anatomical humeral stem that replicates the three-dimensional parameters of the proximal humerus. An anatomical reconstruction is the best way to restore stability and mobility of the prosthetic shoulder and improve implant durability. However, a perfect anatomical match is not always possible in, for example, patients with post-traumatic osteoarthritis of the shoulder and deformities in the metaphyseal region. To avoid stem-related complications while retaining the advantages of the fourth generation of shoulder implants, different stemless implants have been developed. The stemless shoulder prosthesis is a new concept in shoulder arthroplasty. The authors review the indications, surgical technique, clinical and radiological midterm results, and complications of these humeral implants. PMID:26151038

Hereditary Angioedema Attacks: Local Swelling at Multiple Sites.

PubMed

Hofman, Zonne L M; Relan, Anurag; Hack, C Erik

2016-02-01

Hereditary angioedema (HAE) patients experience recurrent local swelling in various parts of the body including painful swelling of the intestine and life-threatening laryngeal oedema. Most HAE literature is about attacks located in one anatomical site, though it is mentioned that HAE attacks may also involve multiple anatomical sites simultaneously. A detailed description of such multi-location attacks is currently lacking. This study investigated the occurrence, severity and clinical course of HAE attacks with multiple anatomical locations. HAE patients included in a clinical database of recombinant human C1-inhibitor (rhC1INH) studies were evaluated. Visual analog scale scores filled out by the patients for various symptoms at various locations and investigator symptoms scores during the attack were analysed. Data of 219 eligible attacks in 119 patients was analysed. Thirty-three patients (28%) had symptoms at multiple locations in anatomically unrelated regions at the same time during their first attack. Up to five simultaneously affected locations were reported. The observation that severe HAE attacks often affect multiple sites in the body suggests that HAE symptoms result from a systemic rather than from a local process as is currently believed.

Preliminary Study on Appearance-Based Detection of Anatomical Point Landmarks in Body Trunk CT Images

NASA Astrophysics Data System (ADS)

Nemoto, Mitsutaka; Nomura, Yukihiro; Hanaoka, Shohei; Masutani, Yoshitaka; Yoshikawa, Takeharu; Hayashi, Naoto; Yoshioka, Naoki; Ohtomo, Kuni

Anatomical point landmarks as most primitive anatomical knowledge are useful for medical image understanding. In this study, we propose a detection method for anatomical point landmark based on appearance models, which include gray-level statistical variations at point landmarks and their surrounding area. The models are built based on results of Principal Component Analysis (PCA) of sample data sets. In addition, we employed generative learning method by transforming ROI of sample data. In this study, we evaluated our method with 24 data sets of body trunk CT images and obtained 95.8 ± 7.3 % of the average sensitivity in 28 landmarks.

COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies

PubMed Central

2017-01-01

COMICS is an interactive and open-access web platform for integration and visualization of molecular expression data in anatomograms of zebrafish, carp, and mouse model systems. Anatomical ontologies are used to map omics data across experiments and between an experiment and a particular visualization in a data-dependent manner. COMICS is built on top of several existing resources. Zebrafish and mouse anatomical ontologies with their controlled vocabulary (CV) and defined hierarchy are used with the ontoCAT R package to aggregate data for comparison and visualization. Libraries from the QGIS geographical information system are used with the R packages “maps” and “maptools” to visualize and interact with molecular expression data in anatomical drawings of the model systems. COMICS allows users to upload their own data from omics experiments, using any gene or protein nomenclature they wish, as long as CV terms are used to define anatomical regions or developmental stages. Common nomenclatures such as the ZFIN gene names and UniProt accessions are provided additional support. COMICS can be used to generate publication-quality visualizations of gene and protein expression across experiments. Unlike previous tools that have used anatomical ontologies to interpret imaging data in several animal models, including zebrafish, COMICS is designed to take spatially resolved data generated by dissection or fractionation and display this data in visually clear anatomical representations rather than large data tables. COMICS is optimized for ease-of-use, with a minimalistic web interface and automatic selection of the appropriate visual representation depending on the input data. PMID:29083911

COMICS: Cartoon Visualization of Omics Data in Spatial Context Using Anatomical Ontologies.

PubMed

Travin, Dmitrii; Popov, Iaroslav; Guler, Arzu Tugce; Medvedev, Dmitry; van der Plas-Duivesteijn, Suzanne; Varela, Monica; Kolder, Iris C R M; Meijer, Annemarie H; Spaink, Herman P; Palmblad, Magnus

2018-01-05

COMICS is an interactive and open-access web platform for integration and visualization of molecular expression data in anatomograms of zebrafish, carp, and mouse model systems. Anatomical ontologies are used to map omics data across experiments and between an experiment and a particular visualization in a data-dependent manner. COMICS is built on top of several existing resources. Zebrafish and mouse anatomical ontologies with their controlled vocabulary (CV) and defined hierarchy are used with the ontoCAT R package to aggregate data for comparison and visualization. Libraries from the QGIS geographical information system are used with the R packages "maps" and "maptools" to visualize and interact with molecular expression data in anatomical drawings of the model systems. COMICS allows users to upload their own data from omics experiments, using any gene or protein nomenclature they wish, as long as CV terms are used to define anatomical regions or developmental stages. Common nomenclatures such as the ZFIN gene names and UniProt accessions are provided additional support. COMICS can be used to generate publication-quality visualizations of gene and protein expression across experiments. Unlike previous tools that have used anatomical ontologies to interpret imaging data in several animal models, including zebrafish, COMICS is designed to take spatially resolved data generated by dissection or fractionation and display this data in visually clear anatomical representations rather than large data tables. COMICS is optimized for ease-of-use, with a minimalistic web interface and automatic selection of the appropriate visual representation depending on the input data.

Anatomical shape analysis of the mandible in Caucasian and Chinese for the production of preformed mandible reconstruction plates.

PubMed

Metzger, Marc C; Vogel, Mathias; Hohlweg-Majert, Bettina; Mast, Hansjörg; Fan, Xianqun; Rüdell, Alexandra; Schlager, Stefan

2011-09-01

The purpose of this study was to evaluate and analyze statistical shapes of the outer mandible contour of Caucasian and Chinese people, offering data for the production of preformed mandible reconstruction plates. A CT-database of 925 Caucasians (male: n=463, female: n=462) and 960 Chinese (male: n=469, female: n=491) including scans of unaffected mandibles were used and imported into the 3D modeling software Voxim (IVS-Solutions, Chemnitz, Germany). Anatomical landmarks (n=22 points for both sides) were set using the 3D view along the outer contour of the mandible at the area where reconstruction plates are commonly located. We used morphometric methods for statistical shape analysis. We found statistical relevant differences between populations including a distinct discrimination given by the landmarks at the mandible. After generating a metric model this shape information which separated the populations appeared to be of no clinical relevance. The metric size information given by ramus length however provided a profound base for the production of standard reconstruction plates. Clustering by ramus length into three sizes and calculating means of these size-clusters seem to be a good solution for constructing preformed reconstruction plates that will fit a vast majority. Copyright © 2010 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Subject-specific longitudinal shape analysis by coupling spatiotemporal shape modeling with medial analysis

NASA Astrophysics Data System (ADS)

Hong, Sungmin; Fishbaugh, James; Rezanejad, Morteza; Siddiqi, Kaleem; Johnson, Hans; Paulsen, Jane; Kim, Eun Young; Gerig, Guido

2017-02-01

Modeling subject-specific shape change is one of the most important challenges in longitudinal shape analysis of disease progression. Whereas anatomical change over time can be a function of normal aging, anatomy can also be impacted by disease related degeneration. Anatomical shape change may also be affected by structural changes from neighboring shapes, which may cause non-linear variations in pose. In this paper, we propose a framework to analyze disease related shape changes by coupling extrinsic modeling of the ambient anatomical space via spatiotemporal deformations with intrinsic shape properties from medial surface analysis. We compare intrinsic shape properties of a subject-specific shape trajectory to a normative 4D shape atlas representing normal aging to isolate shape changes related to disease. The spatiotemporal shape modeling establishes inter/intra subject anatomical correspondence, which in turn enables comparisons between subjects and the 4D shape atlas, and also quantitative analysis of disease related shape change. The medial surface analysis captures intrinsic shape properties related to local patterns of deformation. The proposed framework jointly models extrinsic longitudinal shape changes in the ambient anatomical space, as well as intrinsic shape properties to give localized measurements of degeneration. Six high risk subjects and six controls are randomly sampled from a Huntington's disease image database for qualitative and quantitative comparison.

Anatomical entity mention recognition at literature scale

PubMed Central

Pyysalo, Sampo; Ananiadou, Sophia

2014-01-01

Motivation: Anatomical entities ranging from subcellular structures to organ systems are central to biomedical science, and mentions of these entities are essential to understanding the scientific literature. Despite extensive efforts to automatically analyze various aspects of biomedical text, there have been only few studies focusing on anatomical entities, and no dedicated methods for learning to automatically recognize anatomical entity mentions in free-form text have been introduced. Results: We present AnatomyTagger, a machine learning-based system for anatomical entity mention recognition. The system incorporates a broad array of approaches proposed to benefit tagging, including the use of Unified Medical Language System (UMLS)- and Open Biomedical Ontologies (OBO)-based lexical resources, word representations induced from unlabeled text, statistical truecasing and non-local features. We train and evaluate the system on a newly introduced corpus that substantially extends on previously available resources, and apply the resulting tagger to automatically annotate the entire open access scientific domain literature. The resulting analyses have been applied to extend services provided by the Europe PubMed Central literature database. Availability and implementation: All tools and resources introduced in this work are available from http://nactem.ac.uk/anatomytagger. Contact: sophia.ananiadou@manchester.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:24162468

Relationship between peripheral insertion site and catheter-related phlebitis in adult hospitalized patients: a systematic review.

PubMed

Comparcini, Dania; Simonetti, Valentina; Blot, Stijn; Tomietto, Marco; Cicolini, Giancarlo

2017-01-01

To explore the relationship between the anatomical site of peripheral venous catheterization and risk of catheter-related phlebitis. Peripheral venous catheterization is frequently associated with phlebitis. Recent guidelines, recommend the use of an upper-extremity site for catheter insertion but no univocal consensus exists on the anatomical site with lower risk of phlebitis. Systematic review. We searched Medline (PubMed) and CINAHL (EBSCOhost) databases until the end of January 2017. We also reviewed the reference lists of retrieved articles and gray literature was excluded. Searches were limited to articles published in English with no restriction imposed to date of publication. The primary outcome was the incidence of phlebitis associated with anatomical site of peripheral catheterization. We included randomized controlled trials and observational studies on adult patients who required a peripheral catheter for the administration of medi- cation, intermittent or continuous fluid infusion. Antecubital fossa veins are associated with lower phlebitis rates, while hands veins are the most risky sites to develop phlebitis. There is no consensus regarding vein in forearm. Choosing the right anatomical site to insert a peripheral venous catheter is important to decrease phlebitis rate. Further studies should compare indwelling time in different anatomical sites with phlebitis rate. A more standardized approach in defining and assessing phlebitis among studies is recommended.

Population of anatomically variable 4D XCAT adult phantoms for imaging research and optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Segars, W. P.; Bond, Jason; Frush, Jack

2013-04-15

Purpose: The authors previously developed the 4D extended cardiac-torso (XCAT) phantom for multimodality imaging research. The XCAT consisted of highly detailed whole-body models for the standard male and female adult, including the cardiac and respiratory motions. In this work, the authors extend the XCAT beyond these reference anatomies by developing a series of anatomically variable 4D XCAT adult phantoms for imaging research, the first library of 4D computational phantoms. Methods: The initial anatomy of each phantom was based on chest-abdomen-pelvis computed tomography data from normal patients obtained from the Duke University database. The major organs and structures for each phantommore » were segmented from the corresponding data and defined using nonuniform rational B-spline surfaces. To complete the body, the authors manually added on the head, arms, and legs using the original XCAT adult male and female anatomies. The structures were scaled to best match the age and anatomy of the patient. A multichannel large deformation diffeomorphic metric mapping algorithm was then used to calculate the transform from the template XCAT phantom (male or female) to the target patient model. The transform was applied to the template XCAT to fill in any unsegmented structures within the target phantom and to implement the 4D cardiac and respiratory models in the new anatomy. Each new phantom was refined by checking for anatomical accuracy via inspection of the models. Results: Using these methods, the authors created a series of computerized phantoms with thousands of anatomical structures and modeling cardiac and respiratory motions. The database consists of 58 (35 male and 23 female) anatomically variable phantoms in total. Like the original XCAT, these phantoms can be combined with existing simulation packages to simulate realistic imaging data. Each new phantom contains parameterized models for the anatomy and the cardiac and respiratory motions and can, therefore, serve as a jumping point from which to create an unlimited number of 3D and 4D variations for imaging research. Conclusions: A population of phantoms that includes a range of anatomical variations representative of the public at large is needed to more closely mimic a clinical study or trial. The series of anatomically variable phantoms developed in this work provide a valuable resource for investigating 3D and 4D imaging devices and the effects of anatomy and motion in imaging. Combined with Monte Carlo simulation programs, the phantoms also provide a valuable tool to investigate patient-specific dose and image quality, and optimization for adults undergoing imaging procedures.« less

Phenotip - a web-based instrument to help diagnosing fetal syndromes antenatally.

PubMed

Porat, Shay; de Rham, Maud; Giamboni, Davide; Van Mieghem, Tim; Baud, David

2014-12-10

Prenatal ultrasound can often reliably distinguish fetal anatomic anomalies, particularly in the hands of an experienced ultrasonographer. Given the large number of existing syndromes and the significant overlap in prenatal findings, antenatal differentiation for syndrome diagnosis is difficult. We constructed a hierarchic tree of 1140 sonographic markers and submarkers, organized per organ system. Subsequently, a database of prenatally diagnosable syndromes was built. An internet-based search engine was then designed to search the syndrome database based on a single or multiple sonographic markers. Future developments will include a database with magnetic resonance imaging findings as well as further refinements in the search engine to allow prioritization based on incidence of syndromes and markers.

Can virtual reality improve anatomy education? A randomised controlled study of a computer-generated three-dimensional anatomical ear model.

PubMed

Nicholson, Daren T; Chalk, Colin; Funnell, W Robert J; Daniel, Sam J

2006-11-01

The use of computer-generated 3-dimensional (3-D) anatomical models to teach anatomy has proliferated. However, there is little evidence that these models are educationally effective. The purpose of this study was to test the educational effectiveness of a computer-generated 3-D model of the middle and inner ear. We reconstructed a fully interactive model of the middle and inner ear from a magnetic resonance imaging scan of a human cadaver ear. To test the model's educational usefulness, we conducted a randomised controlled study in which 28 medical students completed a Web-based tutorial on ear anatomy that included the interactive model, while a control group of 29 students took the tutorial without exposure to the model. At the end of the tutorials, both groups were asked a series of 15 quiz questions to evaluate their knowledge of 3-D relationships within the ear. The intervention group's mean score on the quiz was 83%, while that of the control group was 65%. This difference in means was highly significant (P < 0.001). Our findings stand in contrast to the handful of previous randomised controlled trials that evaluated the effects of computer-generated 3-D anatomical models on learning. The equivocal and negative results of these previous studies may be due to the limitations of these studies (such as small sample size) as well as the limitations of the models that were studied (such as a lack of full interactivity). Given our positive results, we believe that further research is warranted concerning the educational effectiveness of computer-generated anatomical models.

Generation of an Atlas of the Proximal Femur and Its Application to Trabecular Bone Analysis

PubMed Central

Carballido-Gamio, Julio; Folkesson, Jenny; Karampinos, Dimitrios C.; Baum, Thomas; Link, Thomas M.; Majumdar, Sharmila; Krug, Roland

2013-01-01

Automatic placement of anatomically corresponding volumes of interest and comparison of parameters against a standard of reference are essential components in studies of trabecular bone. Only recently, in vivo MR images of the proximal femur, an important fracture site, could be acquired with high-spatial resolution. The purpose of this MRI trabecular bone study was two-fold: (1) to generate an atlas of the proximal femur to automatically place anatomically corresponding volumes of interest in a population study and (2) to demonstrate how mean models of geodesic topological analysis parameters can be generated to be used as potential standard of reference. Ten females were used to generate the atlas and geodesic topological analysis models, and 10 females were used to demonstrate the atlas-based trabecular bone analysis. All alignments were based on three-dimensional (3D) multiresolution affine transformations followed by 3D multiresolution free-form deformations. Mean distances less than 1 mm between aligned femora, and sharp edges in the atlas and in fused gray-level images of registered femora indicated that the anatomical variability was well accommodated and explained by the free-form deformations. PMID:21432904

Total Hip Intraoperative Femur Fracture: Do the Design Enhancements of a Second-Generation Tapered-Wedge Stem Reduce the Incidence?

PubMed

Colacchio, Nicholas D; Robbins, Claire E; Aghazadeh, Mehran S; Talmo, Carl T; Bono, James V

2017-10-01

Intraoperative femur fracture (IFF) is a well-known complication in primary uncemented total hip arthroplasty (THA). Variations in implant instrumentation design and operative technique may influence the risk of IFF. This study investigates IFF between a standard uncemented tapered-wedge femoral stem and its second-generation successor with the following design changes: size-specific medial curvature, proportional incremental stem growth, modest reduction in stem length, and distal lateral relief. A single experienced surgeon's patient database was retrospectively queried for IFF occurring during primary uncemented THA using a standard tapered-wedge femoral stem system or a second-generation stem. All procedures were performed using soft tissue preserving anatomic capsule repair and posterior approach. The primary outcome measure was IFF. A z-test of proportions was performed to determine significant difference between the 2 stems with respect to IFF. Patient demographics, Dorr classification, and implant characteristics were also examined. Forty-one of 1510 patients (2.72%) who received a standard tapered-wedge femoral stem sustained an IFF, whereas 5 of 800 patients (0.63%) using the second-generation stem incurred an IFF. No other significant associations were found. A standard tapered-wedge femoral stem instrumentation system resulted in greater than 4 times higher incidence of IFF than its second-generation successor used for primary uncemented THA. Identifying risk factors for IFF is necessary to facilitate implant system improvements and thus maximize patient outcomes. Copyright © 2017. Published by Elsevier Inc.

Contextual cueing of tactile search is coded in an anatomical reference frame.

PubMed

Assumpção, Leonardo; Shi, Zhuanghua; Zang, Xuelian; Müller, Hermann J; Geyer, Thomas

2018-04-01

This work investigates the reference frame(s) underlying tactile context memory, a form of statistical learning in a tactile (finger) search task. In this task, if a searched-for target object is repeatedly encountered within a stable spatial arrangement of task-irrelevant distractors, detecting the target becomes more efficient over time (relative to nonrepeated arrangements), as learned target-distractor spatial associations come to guide tactile search, thus cueing attention to the target location. Since tactile search displays can be represented in several reference frames, including multiple external and an anatomical frame, in Experiment 1 we asked whether repeated search displays are represented in tactile memory with reference to an environment-centered or anatomical reference frame. In Experiment 2, we went on examining a hand-centered versus anatomical reference frame of tactile context memory. Observers performed a tactile search task, divided into a learning and test session. At the transition between the two sessions, we introduced postural manipulations of the hands (crossed ↔ uncrossed in Expt. 1; palm-up ↔ palm-down in Expt. 2) to determine the reference frame of tactile contextual cueing. In both experiments, target-distractor associations acquired during learning transferred to the test session when the placement of the target and distractors was held constant in anatomical, but not external, coordinates. In the latter, RTs were even slower for repeated displays. We conclude that tactile contextual learning is coded in an anatomical reference frame. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Uniportal video-assisted thoracoscopic surgery: safety, efficacy and learning curve during the first 250 cases in Quebec, Canada.

PubMed

Drevet, Gabrielle; Ugalde Figueroa, Paula

2016-03-01

Video-assisted thoracoscopic surgery (VATS) using a single incision (uniportal) may result in better pain control, earlier mobilization and shorter hospital stays. Here, we review the safety and efficiency of our initial experience with uniportal VATS and evaluate our learning curve. We conducted a retrospective review of uniportal VATS using a prospectively maintained departmental database and analyzed patients who had undergone a lung anatomic resection separately from patients who underwent other resections. To assess the learning curve, we compared the first 10 months of the study period with the second 10 months. From January 2014 to August 2015, 250 patients underwent intended uniportal VATS, including 180 lung anatomic resections (72%) and 70 other resections (28%). Lung anatomic resection was successfully completed using uniportal VATS in 153 patients (85%), which comprised all the anatomic segmentectomies (29 patients), 80% (4 of 5) of the pneumonectomies and 82% (120 of 146) of the lobectomies attempted. The majority of lung anatomic resections that required conversion to thoracotomy occurred in the first half of our study period. Seventy patients underwent other uniportal VATS resections. Wedge resections were the most common of these procedures (25 patients, 35.7%). Although 24 of the 70 patients (34%) required the placement of additional ports, none required conversion to thoracotomy. Uniportal VATS was safe and feasible for both standard and complex pulmonary resections. However, when used for pulmonary anatomic resections, uniportal VATS entails a steep learning curve.

Anatomical influences on internally coupled ears in reptiles.

PubMed

Young, Bruce A

2016-10-01

Many reptiles, and other vertebrates, have internally coupled ears in which a patent anatomical connection allows pressure waves generated by the displacement of one tympanic membrane to propagate (internally) through the head and, ultimately, influence the displacement of the contralateral tympanic membrane. The pattern of tympanic displacement caused by this internal coupling can give rise to novel sensory cues. The auditory mechanics of reptiles exhibit more anatomical variation than in any other vertebrate group. This variation includes structural features such as diverticula and septa, as well as coverings of the tympanic membrane. Many of these anatomical features would likely influence the functional significance of the internal coupling between the tympanic membranes. Several of the anatomical components of the reptilian internally coupled ear are under active motor control, suggesting that in some reptiles the auditory system may be more dynamic than previously recognized.

Visual Systems for Interactive Exploration and Mining of Large-Scale Neuroimaging Data Archives

PubMed Central

Bowman, Ian; Joshi, Shantanu H.; Van Horn, John D.

2012-01-01

While technological advancements in neuroimaging scanner engineering have improved the efficiency of data acquisition, electronic data capture methods will likewise significantly expedite the populating of large-scale neuroimaging databases. As they do and these archives grow in size, a particular challenge lies in examining and interacting with the information that these resources contain through the development of compelling, user-driven approaches for data exploration and mining. In this article, we introduce the informatics visualization for neuroimaging (INVIZIAN) framework for the graphical rendering of, and dynamic interaction with the contents of large-scale neuroimaging data sets. We describe the rationale behind INVIZIAN, detail its development, and demonstrate its usage in examining a collection of over 900 T1-anatomical magnetic resonance imaging (MRI) image volumes from across a diverse set of clinical neuroimaging studies drawn from a leading neuroimaging database. Using a collection of cortical surface metrics and means for examining brain similarity, INVIZIAN graphically displays brain surfaces as points in a coordinate space and enables classification of clusters of neuroanatomically similar MRI images and data mining. As an initial step toward addressing the need for such user-friendly tools, INVIZIAN provides a highly unique means to interact with large quantities of electronic brain imaging archives in ways suitable for hypothesis generation and data mining. PMID:22536181

Stroke and Episodic Memory Disorders

ERIC Educational Resources Information Center

Lim, Chun; Alexander, Michael P.

2009-01-01

Memory impairments are common after stroke, and the anatomical basis for impairments may be quite variable. To determine the range of stroke-related memory impairment, we identified all case reports and group studies through the Medline database and the Science Citation Index. There is no hypothesis about memory that is unique to stroke, but there…

State of the art and trends for digital pathology.

PubMed

García Rojo, Marcial

2012-01-01

Anatomic pathology is a medical specialty where both information management systems and digital images systems paly a most important role. Digital pathology is a new concept that considers all uses of this information, including diagnosis, biomedical research and education. Virtual microscopy or whole slide imaging, resulting in digital slides, is an outreaching technology in anatomic pathology. Limiting factors in the expansion of virtual microscopy are formidable storage dimension, scanning speed, quality of image and cultural change. Anatomic pathology data and images should be an important part of the patient electronic health records as well as of clinical data warehouse, epidemiological or biomedical research databases, and platforms dedicated to translational medicine. Integrating anatomic pathology to the "healthcare enterprise" can only be achieved using existing and emerging medical informatics standards like Digital Imaging and Communications in Medicine (DICOM®¹), Health Level Seven (HL7®), and Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT®), following the recommendations of Integrating the Healthcare Enterprise (IHE®). The consequences of the full digitalization of pathology departments are hard to foresee, but short term issues have arisen that imply interesting challenges for health care standards bodies.

Anatomical landmark asymmetry assessment in the lumbar spine and pelvis: a review of reliability.

PubMed

Stovall, Bradley Alan; Kumar, Shrawan

2010-01-01

The purpose of this article is to review current research investigating the reliability of bony anatomical landmark positional asymmetry assessment in the lumbar spine and pelvis, to determine the agreement on findings between authors, and to explore future directions in the area to address the significant issues. The databases MEDLINE, CINAHL, AMED, MANTIS, Academic Search Complete, and Web of Knowledge were searched. A total of 23 articles were identified and reviewed, 10 of which met the inclusion criteria. For these 10 articles, the average interexaminer reliability for bony anatomical landmark positional asymmetry assessment was slightly above chance for all landmarks except medial malleolus, which had fair reliability. Interexaminer reliability on average was less than intraexaminer reliability (anterior superior iliac spine, k = 0.128/0.414; posterior superior iliac spine, k = 0.092/0.371). All interexaminer reliability averages were below values of clinical significance. From the current literature review, bony anatomical landmark positional asymmetry assessment in the lumbar spine and pelvis has not been demonstrated to be a reliable assessment method. However, there are unexplored factors that, after standardization, may improve reliability and further the understanding of musculoskeletal palpatory examination.

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

PubMed

Druzinsky, Robert E; Balhoff, James P; Crompton, Alfred W; Done, James; German, Rebecca Z; Haendel, Melissa A; Herrel, Anthony; Herring, Susan W; Lapp, Hilmar; Mabee, Paula M; Muller, Hans-Michael; Mungall, Christopher J; Sternberg, Paul W; Van Auken, Kimberly; Vinyard, Christopher J; Williams, Susan H; Wall, Christine E

2016-01-01

In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.

Estimate of Space Radiation-Induced Cancer Risks for International Space Station Orbits

NASA Technical Reports Server (NTRS)

Wu, Honglu; Atwell, William; Cucinotta, Francis A.; Yang, Chui-hsu

1996-01-01

Excess cancer risks from exposures to space radiation are estimated for various orbits of the International Space Station (ISS). Organ exposures are computed with the transport codes, BRYNTRN and HZETRN, and the computerized anatomical male and computerized anatomical female models. Cancer risk coefficients in the National Council on Radiation Protection and Measurements report No. 98 are used to generate lifetime excess cancer incidence and cancer mortality after a one-month mission to ISS. The generated data are tabulated to serve as a quick reference for assessment of radiation risk to astronauts on ISS missions.

Divergent hydraulic strategies to cope with freezing in co-occurring temperate tree species with special reference to root and stem pressure generation.

PubMed

Yin, Xiao-Han; Sterck, Frank; Hao, Guang-You

2018-04-23

Some temperate tree species mitigate the negative impacts of frost-induced xylem cavitation by restoring impaired hydraulic function via positive pressures, and may therefore be more resistant to frost fatigue (the phenomenon that post-freezing xylem becomes more susceptible to hydraulic dysfunction) than nonpressure-generating species. We test this hypothesis and investigate underlying anatomical/physiological mechanisms. Using a common garden experiment, we studied key hydraulic traits and detailed xylem anatomical characteristics of 18 sympatric tree species. These species belong to three functional groups, that is, one generating both root and stem pressures (RSP), one generating only root pressure (RP), and one unable to generate such pressures (NP). The three functional groups diverged substantially in hydraulic efficiency, resistance to drought-induced cavitation, and frost fatigue resistance. Most notably, RSP and RP were more resistant to frost fatigue than NP, but this was at the cost of reduced hydraulic conductivity for RSP and reduced resistance to drought-induced cavitation for RP. Our results show that, in environments with strong frost stress: these groups diverge in hydraulic functioning following multiple trade-offs between hydraulic efficiency, resistance to drought and resistance to frost fatigue; and how differences in anatomical characteristics drive such divergence across species. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Semiautomated head-and-neck IMRT planning using dose warping and scaling to robustly adapt plans in a knowledge database containing potentially suboptimal plans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmidt, Matthew, E-mail: matthew.schmidt@varian.com; Grzetic, Shelby; Lo, Joseph Y.

Purpose: Prior work by the authors and other groups has studied the creation of automated intensity modulated radiotherapy (IMRT) plans of equivalent quality to those in a patient database of manually created clinical plans; those database plans provided guidance on the achievable sparing to organs-at-risk (OARs). However, in certain sites, such as head-and-neck, the clinical plans may not be sufficiently optimized because of anatomical complexity and clinical time constraints. This could lead to automated plans that suboptimally exploit OAR sparing. This work investigates a novel dose warping and scaling scheme that attempts to reduce effects of suboptimal sparing in clinicalmore » database plans, thus improving the quality of semiautomated head-and-neck cancer (HNC) plans. Methods: Knowledge-based radiotherapy (KBRT) plans for each of ten “query” patients were semiautomatically generated by identifying the most similar “match” patient in a database of 103 clinical manually created patient plans. The match patient’s plans were adapted to the query case by: (1) deforming the match beam fluences to suit the query target volume and (2) warping the match primary/boost dose distribution to suit the query geometry and using the warped distribution to generate query primary/boost optimization dose-volume constraints. Item (2) included a distance scaling factor to improve query OAR dose sparing with respect to the possibly suboptimal clinical match plan. To further compensate for a component plan of the match case (primary/boost) not optimally sparing OARs, the query dose volume constraints were reduced using a dose scaling factor to be the minimum from either (a) the warped component plan (primary or boost) dose distribution or (b) the warped total plan dose distribution (primary + boost) scaled in proportion to the ratio of component prescription dose to total prescription dose. The dose-volume constraints were used to plan the query case with no human intervention to adjust constraints during plan optimization. Results: KBRT and original clinical plans were dosimetrically equivalent for parotid glands (mean/median doses), spinal cord, and brainstem (maximum doses). KBRT plans significantly reduced larynx median doses (21.5 ± 6.6 Gy to 17.9 ± 3.9 Gy), and oral cavity mean (32.3 ± 6.2 Gy to 28.9 ± 5.4 Gy) and median (28.7 ± 5.7 Gy to 23.2 ± 5.3 Gy) doses. Doses to ipsilateral parotid gland, larynx, oral cavity, and brainstem were lower or equivalent in the KBRT plans for the majority of cases. By contrast, KBRT plans generated without the dose warping and dose scaling steps were not significantly different from the clinical plans. Conclusions: Fast, semiautomatically generated HNC IMRT plans adapted from existing plans in a clinical database can be of equivalent or better quality than manually created plans. The reductions in OAR doses in the semiautomated plans, compared to the clinical plans, indicate that the proposed dose warping and scaling method shows promise in mitigating the impact of suboptimal clinical plans.« less

Nucleus accumbens GABAergic inhibition generates intense eating and fear that resists environmental retuning and needs no dopamine

PubMed Central

Richard, Jocelyn M.; Plawecki, Andrea M.; Berridge, Kent C.

2013-01-01

Intense fearful behavior and/or intense appetitive eating behavior can be generated by localized amino acid inhibitions along a rostrocaudal anatomical gradient within medial shell of nucleus accumbens of the rat. This can be produced by microinjections in medial shell of either the GABAA agonist muscimol (mimicking intrinsic GABAergic inputs) or the AMPA antagonist DNQX (disrupting corticolimbic glutamate inputs). At rostral sites in medial shell, each drug robustly stimulates appetitive eating and food intake, whereas at more caudal sites the same drugs instead produce increasingly fearful behaviors such as escape, distress vocalizations, and defensive treading (an antipredator behavior rodents emit to snakes and scorpions). Previously we showed that intense motivated behaviors generated by glutamate blockade require local endogenous dopamine and can be modulated in valence by environmental ambience. Here we investigated whether GABAergic generation of intense appetitive and fearful motivations similarly depends on local dopamine signals, and whether the valence of motivations generated by GABAergic inhibition can also be retuned by changes in environmental ambience. We report that the answer to both questions is ‘no’. Eating and fear generated by GABAergic inhibition of accumbens shell does not need endogenous dopamine. Also, the appetitive/fearful valence generated by GABAergic muscimol microinjections resists environmental retuning and is determined almost purely by rostrocaudal anatomical placement. These results suggest that NAc GABAergic release of fear and eating are relatively independent of modulatory dopamine signals, and more anatomically pre-determined in valence balance than release of the same intense behaviors by glutamate disruptions. PMID:23551138

Feature-Based Morphometry: Discovering Group-related Anatomical Patterns

PubMed Central

Toews, Matthew; Wells, William; Collins, D. Louis; Arbel, Tal

2015-01-01

This paper presents feature-based morphometry (FBM), a new, fully data-driven technique for discovering patterns of group-related anatomical structure in volumetric imagery. In contrast to most morphometry methods which assume one-to-one correspondence between subjects, FBM explicitly aims to identify distinctive anatomical patterns that may only be present in subsets of subjects, due to disease or anatomical variability. The image is modeled as a collage of generic, localized image features that need not be present in all subjects. Scale-space theory is applied to analyze image features at the characteristic scale of underlying anatomical structures, instead of at arbitrary scales such as global or voxel-level. A probabilistic model describes features in terms of their appearance, geometry, and relationship to subject groups, and is automatically learned from a set of subject images and group labels. Features resulting from learning correspond to group-related anatomical structures that can potentially be used as image biomarkers of disease or as a basis for computer-aided diagnosis. The relationship between features and groups is quantified by the likelihood of feature occurrence within a specific group vs. the rest of the population, and feature significance is quantified in terms of the false discovery rate. Experiments validate FBM clinically in the analysis of normal (NC) and Alzheimer's (AD) brain images using the freely available OASIS database. FBM automatically identifies known structural differences between NC and AD subjects in a fully data-driven fashion, and an equal error classification rate of 0.80 is achieved for subjects aged 60-80 years exhibiting mild AD (CDR=1). PMID:19853047

The concept of individualized anatomic anterior cruciate ligament (ACL) reconstruction.

PubMed

Hofbauer, M; Muller, B; Murawski, C D; van Eck, C F; Fu, F H

2014-05-01

To describe the concept of individualized anatomic anterior cruciate ligament (ACL) reconstruction. The PubMed/Medline database was searched using keywords pertaining to ACL reconstruction. Relevant articles were reviewed in order to summarize important concepts of individualized surgery in ACL reconstruction. Surgical experiences with case examples are also highlighted. Individualized ACL surgery allows for the customization of surgery to each individual patient. Accounting for graft selection and other characteristics such as anatomy, lifestyle and activity preferences may provide the patient with the best potential for a successful outcome. The surgeon should be comfortable with a variety of graft harvests and surgical techniques when practicing individualized surgery. Individualized anatomic ACL reconstruction is founded on the objective evaluation of functional anatomy and individual characteristics, thereby restoring the ACL as closely as possible to the native anatomy and function. The adoption and subsequent use of individualized surgery may facilitate improved clinical as well as objective outcomes, particularly in the long term. V.

Anatomical Entity Recognition with a Hierarchical Framework Augmented by External Resources

PubMed Central

Xu, Yan; Hua, Ji; Ni, Zhaoheng; Chen, Qinlang; Fan, Yubo; Ananiadou, Sophia; Chang, Eric I-Chao; Tsujii, Junichi

2014-01-01

References to anatomical entities in medical records consist not only of explicit references to anatomical locations, but also other diverse types of expressions, such as specific diseases, clinical tests, clinical treatments, which constitute implicit references to anatomical entities. In order to identify these implicit anatomical entities, we propose a hierarchical framework, in which two layers of named entity recognizers (NERs) work in a cooperative manner. Each of the NERs is implemented using the Conditional Random Fields (CRF) model, which use a range of external resources to generate features. We constructed a dictionary of anatomical entity expressions by exploiting four existing resources, i.e., UMLS, MeSH, RadLex and BodyPart3D, and supplemented information from two external knowledge bases, i.e., Wikipedia and WordNet, to improve inference of anatomical entities from implicit expressions. Experiments conducted on 300 discharge summaries showed a micro-averaged performance of 0.8509 Precision, 0.7796 Recall and 0.8137 F1 for explicit anatomical entity recognition, and 0.8695 Precision, 0.6893 Recall and 0.7690 F1 for implicit anatomical entity recognition. The use of the hierarchical framework, which combines the recognition of named entities of various types (diseases, clinical tests, treatments) with information embedded in external knowledge bases, resulted in a 5.08% increment in F1. The resources constructed for this research will be made publicly available. PMID:25343498

"Crosstalk" technique: A comparison between two generations of cryoballoon catheter.

PubMed

Yang, Jian-du; Sun, Qi; Guo, Xiao-Gang; Zhou, Gong-Bu; Liu, Xu; Luo, Bin; Wei, Hui-Qiang; Liang, Jackson J; Ma, Jian

2018-03-30

The "Crosstalk" technique: if pulmonary vein isolation (PVI) of the superior one is not achieved due to a gap in the inferior part, it could be done during inferior vein cryoablation. This maneuver minimizes the total energy delivery time and number of lesions. We aimed to correlate the likelihood of crosstalk phenomenon with certain anatomic characteristics. A total of 676 patients undergoing a first ablation procedure for paroxysmal or persistent atrial fibrillation (470 first-generation cryoballoon [CB] and 206 second-generation CB) between June 2014 and December 2016 were included. "Crosstalk" phenomenon occurred in 32 patients (18 first-generation CB, 14 second-generation CB). Compared to 54 control patients without crosstalk, the angle between left superior pulmonary vein (LSPV) and left atrial (LA) roof-plane, left pulmonary common ostia were significant parameters associated with crosstalk (odds ratio [OR] = 1.20, ±95% confidence interval [CI]: 1.11-1.31, P < 0.001; OR = 5.67, ±95% CI: 1.08-28.69, P = 0.04). As for angle between LSPV and LA roof-plane, the cut-off value was 28.68° with a sensitivity of 72.22%, a specificity of 81.25%, and an area under the receiver operating characteristic curve of 0.87 to predict the possibility of crosstalk technique application to get isolated in LSPV. Among the crosstalk group, there was no statistical difference between first-generation CB and second-generation CB in pulmonary anatomic characteristics. Crosstalk technique can be effective in patients with AF undergoing CB ablation using with both first and second-generation CBs. Anatomic characteristics predictive of crosstalk include a left common ostia and smaller angle between the LSPV and LA roof-plane. © 2018 Wiley Periodicals, Inc.

Skeletal Muscle Fascicle Arrangements Can Be Reconstructed Using a Laplacian Vector Field Simulation

PubMed Central

Choi, Hon Fai; Blemker, Silvia S.

2013-01-01

Skeletal muscles are characterized by a large diversity in anatomical architecture and function. Muscle force and contraction are generated by contractile fiber cells grouped in fascicle bundles, which transmit the mechanical action between origin and insertion attachments of the muscle. Therefore, an adequate representation of fascicle arrangements in computational models of skeletal muscles is important, especially when investigating three-dimensional muscle deformations in finite element models. However, obtaining high resolution in vivo measurements of fascicle arrangements in skeletal muscles is currently still challenging. This motivated the development of methods in previous studies to generate numerical representations of fascicle trajectories using interpolation templates. Here, we present an alternative approach based on the hypothesis of a rotation and divergence free (Laplacian) vector field behavior which reflects observed physical characteristics of fascicle trajectories. To obtain this representation, the Laplace equation was solved in anatomical reconstructions of skeletal muscle shapes based on medical images using a uniform flux boundary condition on the attachment areas. Fascicle tracts were generated through a robust flux based tracing algorithm. The concept of this approach was demonstrated in two-dimensional synthetic examples of typical skeletal muscle architectures. A detailed evaluation was performed in an example of the anatomical human tibialis anterior muscle which showed an overall agreement with measurements from the literature. The utility and capability of the proposed method was further demonstrated in other anatomical examples of human skeletal muscles with a wide range of muscle shapes and attachment morphologies. PMID:24204878

Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication.

PubMed

Metzger, Julia; Tonda, Raul; Beltran, Sergi; Agueda, Lídia; Gut, Marta; Distl, Ottmar

2014-07-04

Domestication has shaped the horse and lead to a group of many different types. Some have been under strong human selection while others developed in close relationship with nature. The aim of our study was to perform next generation sequencing of breed and non-breed horses to provide an insight into genetic influences on selective forces. Whole genome sequencing of five horses of four different populations revealed 10,193,421 single nucleotide polymorphisms (SNPs) and 1,361,948 insertion/deletion polymorphisms (indels). In comparison to horse variant databases and previous reports, we were able to identify 3,394,883 novel SNPs and 868,525 novel indels. We analyzed the distribution of individual variants and found significant enrichment of private mutations in coding regions of genes involved in primary metabolic processes, anatomical structures, morphogenesis and cellular components in non-breed horses and in contrast to that private mutations in genes affecting cell communication, lipid metabolic process, neurological system process, muscle contraction, ion transport, developmental processes of the nervous system and ectoderm in breed horses. Our next generation sequencing data constitute an important first step for the characterization of non-breed in comparison to breed horses and provide a large number of novel variants for future analyses. Functional annotations suggest specific variants that could play a role for the characterization of breed or non-breed horses.

Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition

PubMed Central

Jones, Michael N.

2017-01-01

A central goal of cognitive neuroscience is to decode human brain activity—that is, to infer mental processes from observed patterns of whole-brain activation. Previous decoding efforts have focused on classifying brain activity into a small set of discrete cognitive states. To attain maximal utility, a decoding framework must be open-ended, systematic, and context-sensitive—that is, capable of interpreting numerous brain states, presented in arbitrary combinations, in light of prior information. Here we take steps towards this objective by introducing a probabilistic decoding framework based on a novel topic model—Generalized Correspondence Latent Dirichlet Allocation—that learns latent topics from a database of over 11,000 published fMRI studies. The model produces highly interpretable, spatially-circumscribed topics that enable flexible decoding of whole-brain images. Importantly, the Bayesian nature of the model allows one to “seed” decoder priors with arbitrary images and text—enabling researchers, for the first time, to generate quantitative, context-sensitive interpretations of whole-brain patterns of brain activity. PMID:29059185

An anatomic transcriptional atlas of human glioblastoma.

PubMed

Puchalski, Ralph B; Shah, Nameeta; Miller, Jeremy; Dalley, Rachel; Nomura, Steve R; Yoon, Jae-Guen; Smith, Kimberly A; Lankerovich, Michael; Bertagnolli, Darren; Bickley, Kris; Boe, Andrew F; Brouner, Krissy; Butler, Stephanie; Caldejon, Shiella; Chapin, Mike; Datta, Suvro; Dee, Nick; Desta, Tsega; Dolbeare, Tim; Dotson, Nadezhda; Ebbert, Amanda; Feng, David; Feng, Xu; Fisher, Michael; Gee, Garrett; Goldy, Jeff; Gourley, Lindsey; Gregor, Benjamin W; Gu, Guangyu; Hejazinia, Nika; Hohmann, John; Hothi, Parvinder; Howard, Robert; Joines, Kevin; Kriedberg, Ali; Kuan, Leonard; Lau, Chris; Lee, Felix; Lee, Hwahyung; Lemon, Tracy; Long, Fuhui; Mastan, Naveed; Mott, Erika; Murthy, Chantal; Ngo, Kiet; Olson, Eric; Reding, Melissa; Riley, Zack; Rosen, David; Sandman, David; Shapovalova, Nadiya; Slaughterbeck, Clifford R; Sodt, Andrew; Stockdale, Graham; Szafer, Aaron; Wakeman, Wayne; Wohnoutka, Paul E; White, Steven J; Marsh, Don; Rostomily, Robert C; Ng, Lydia; Dang, Chinh; Jones, Allan; Keogh, Bart; Gittleman, Haley R; Barnholtz-Sloan, Jill S; Cimino, Patrick J; Uppin, Megha S; Keene, C Dirk; Farrokhi, Farrokh R; Lathia, Justin D; Berens, Michael E; Iavarone, Antonio; Bernard, Amy; Lein, Ed; Phillips, John W; Rostad, Steven W; Cobbs, Charles; Hawrylycz, Michael J; Foltz, Greg D

2018-05-11

Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

The Main Anatomic Variations of the Hepatic Artery and Their Importance in Surgical Practice: Review of the Literature.

PubMed

Noussios, George; Dimitriou, Ioannis; Chatzis, Iosif; Katsourakis, Anastasios

2017-04-01

Anatomical variations of the hepatic artery are important in the planning and performance of abdominal surgical procedures. Normal hepatic anatomy occurs in approximately 80% of cases, for the remaining 20% multiple variations have been described. The purpose of this study was to review the existing literature on the hepatic anatomy and to stress out its importance in surgical practice. Two main databases were searched for eligible articles during the period 2000 - 2015, and results concerning more than 19,000 patients were included in the study. The most common variation was the replaced right hepatic artery (type III according to Michels classification) which is the chief source of blood supply to the bile duct.

Monitoring the Use of Anatomical Teaching Material Using a Low-Cost Radio Frequency Identification System: A Comprehensive Assessment

ERIC Educational Resources Information Center

Noël, Geoffroy P. J. C.; Connolly, Ciaran C.

2016-01-01

The correct tracking and monitoring of anatomical specimens is not only imperative in any modern body donation programs but also in any universities for which teaching the next generation of health care professionals is the primary mission. This has long been an arduous process for anatomy institutions across the world, and the recent focus of new…

A diagnostic approach in Alzheimer`s disease using three-dimensional stereotactic surface projections of Fluorine-18-FDG PET

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minoshima, S.; Frey, K.A.; Koeppe, R.A.

1995-07-01

To improve the diagnostic performance of PET as an aid in evaluating patients suspected of having Alzheimer`s disease, the authors developed a fully automated method which generates comprehensive image presentations and objective diagnostic indices. Fluorine-18-fluorodeoxyglucose PET image sets were collected from 37 patients with probable Alzheimer`s disease (including questionable and mild dementia), 22 normal subjects and 5 patients with cerebrovascular disease. Following stereotactic anatomic standardization, metabolic activity on an individual`s PET image set was extracted to a set of predefined surface pixels (three-dimensional stereotactic surface projection, 3D-SSP), which was used in the subsequent analysis. A normal database was created bymore » averaging extracted datasets of the normal subjects. Patients` datasets were compared individually with the normal database by calculating a Z-score on a pixel-by-pixel basis and were displayed in 3D-SSP views for visual inspections. Diagnostic indices were then generated based on averaged Z-scores for the association cortices. Patterns and severities of metabolic reduction in patients with probable Alzheimer`s disease were seen in the standard 3D-SSP views of extracted raw data and statistical Z-scores. When discriminating patients with probable Alzheimer`s disease from normal subjects, diagnostic indices of the parietal association cortex and unilaterally averaged parietal-temporal-frontal cortex showed sensitivities of 95% and 97%, respectively, with a specificity of 100%. Neither index yielded false-positive results for cerebrovascular disease. 3D-SSP enables quantitative data extraction and reliable localization of metabolic abnormalities by means of stereotactic coordinates. The proposed method is a promising approach for interpreting functional brain PET scans. 45 refs., 5 figs.« less

An automatic dose verification system for adaptive radiotherapy for helical tomotherapy

NASA Astrophysics Data System (ADS)

Mo, Xiaohu; Chen, Mingli; Parnell, Donald; Olivera, Gustavo; Galmarini, Daniel; Lu, Weiguo

2014-03-01

Purpose: During a typical 5-7 week treatment of external beam radiotherapy, there are potential differences between planned patient's anatomy and positioning, such as patient weight loss, or treatment setup. The discrepancies between planned and delivered doses resulting from these differences could be significant, especially in IMRT where dose distributions tightly conforms to target volumes while avoiding organs-at-risk. We developed an automatic system to monitor delivered dose using daily imaging. Methods: For each treatment, a merged image is generated by registering the daily pre-treatment setup image and planning CT using treatment position information extracted from the Tomotherapy archive. The treatment dose is then computed on this merged image using our in-house convolution-superposition based dose calculator implemented on GPU. The deformation field between merged and planning CT is computed using the Morphon algorithm. The planning structures and treatment doses are subsequently warped for analysis and dose accumulation. All results are saved in DICOM format with private tags and organized in a database. Due to the overwhelming amount of information generated, a customizable tolerance system is used to flag potential treatment errors or significant anatomical changes. A web-based system and a DICOM-RT viewer were developed for reporting and reviewing the results. Results: More than 30 patients were analysed retrospectively. Our in-house dose calculator passed 97% gamma test evaluated with 2% dose difference and 2mm distance-to-agreement compared with Tomotherapy calculated dose, which is considered sufficient for adaptive radiotherapy purposes. Evaluation of the deformable registration through visual inspection showed acceptable and consistent results, except for cases with large or unrealistic deformation. Our automatic flagging system was able to catch significant patient setup errors or anatomical changes. Conclusions: We developed an automatic dose verification system that quantifies treatment doses, and provides necessary information for adaptive planning without impeding clinical workflows.

Evidence-based anatomical review areas derived from systematic analysis of cases from a radiological departmental discrepancy meeting.

PubMed

Chin, S C; Weir-McCall, J R; Yeap, P M; White, R D; Budak, M J; Duncan, G; Oliver, T B; Zealley, I A

2017-10-01

To produce short checklists of specific anatomical review sites for different regions of the body based on the frequency of radiological errors reviewed at radiology discrepancy meetings, thereby creating "evidence-based" review areas for radiology reporting. A single centre discrepancy database was retrospectively reviewed from a 5-year period. All errors were classified by type, modality, body system, and specific anatomical location. Errors were assigned to one of four body regions: chest, abdominopelvic, central nervous system (CNS), and musculoskeletal (MSK). Frequencies of errors in anatomical locations were then analysed. There were 561 errors in 477 examinations; 290 (46%) errors occurred in the abdomen/pelvis, 99 (15.7%) in the chest, 117 (18.5%) in the CNS, and 125 (19.9%) in the MSK system. In each body system, the five most common location were chest: lung bases on computed tomography (CT), apices on radiography, pulmonary vasculature, bones, and mediastinum; abdominopelvic: vasculature, colon, kidneys, liver, and pancreas; CNS: intracranial vasculature, peripheral cerebral grey matter, bone, parafalcine, and the frontotemporal lobes surrounding the Sylvian fissure; and MSK: calvarium, sacrum, pelvis, chest, and spine. The five listed locations accounted for >50% of all perceptual errors suggesting an avenue for focused review at the end of reporting. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Image-guided tissue engineering of anatomically shaped implants via MRI and micro-CT using injection molding.

PubMed

Ballyns, Jeffery J; Gleghorn, Jason P; Niebrzydowski, Vicki; Rawlinson, Jeremy J; Potter, Hollis G; Maher, Suzanne A; Wright, Timothy M; Bonassar, Lawrence J

2008-07-01

This study demonstrates for the first time the development of engineered tissues based on anatomic geometries derived from widely used medical imaging modalities such as computed tomography (CT) and magnetic resonance imaging (MRI). Computer-aided design and tissue injection molding techniques have demonstrated the ability to generate living implants of complex geometry. Due to its complex geometry, the meniscus of the knee was used as an example of this technique's capabilities. MRI and microcomputed tomography (microCT) were used to design custom-printed molds that enabled the generation of anatomically shaped constructs that retained shape throughout 8 weeks of culture. Engineered constructs showed progressive tissue formation indicated by increases in extracellular matrix content and mechanical properties. The paradigm of interfacing tissue injection molding technology can be applied to other medical imaging techniques that render 3D models of anatomy, demonstrating the potential to apply the current technique to engineering of many tissues and organs.

The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.

PubMed

Tassy, Olivier; Dauga, Delphine; Daian, Fabrice; Sobral, Daniel; Robin, François; Khoueiry, Pierre; Salgado, David; Fox, Vanessa; Caillol, Danièle; Schiappa, Renaud; Laporte, Baptiste; Rios, Anne; Luxardi, Guillaume; Kusakabe, Takehiro; Joly, Jean-Stéphane; Darras, Sébastien; Christiaen, Lionel; Contensin, Magali; Auger, Hélène; Lamy, Clément; Hudson, Clare; Rothbächer, Ute; Gilchrist, Michael J; Makabe, Kazuhiro W; Hotta, Kohji; Fujiwara, Shigeki; Satoh, Nori; Satou, Yutaka; Lemaire, Patrick

2010-10-01

Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks to recent progress in genomics and imaging technologies, systemic approaches are now used in parallel with small-scale studies to establish links between genomic information and phenotypes, often described at the subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets at different scales into a global view of the developmental program. Here, we present a novel, generic digital system, NISEED, and its implementation, ANISEED, to ascidians, which are invertebrate chordates suitable for developmental systems biology approaches. ANISEED hosts an unprecedented combination of anatomical and molecular data on ascidian development. This includes the first detailed anatomical ontologies for these embryos, and quantitative geometrical descriptions of developing cells obtained from reconstructed three-dimensional (3D) embryos up to the gastrula stages. Fully annotated gene model sets are linked to 30,000 high-resolution spatial gene expression patterns in wild-type and experimentally manipulated conditions and to 528 experimentally validated cis-regulatory regions imported from specialized databases or extracted from 160 literature articles. This highly structured data set can be explored via a Developmental Browser, a Genome Browser, and a 3D Virtual Embryo module. We show how integration of heterogeneous data in ANISEED can provide a system-level understanding of the developmental program through the automatic inference of gene regulatory interactions, the identification of inducing signals, and the discovery and explanation of novel asymmetric divisions.

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

PubMed Central

Tassy, Olivier; Dauga, Delphine; Daian, Fabrice; Sobral, Daniel; Robin, François; Khoueiry, Pierre; Salgado, David; Fox, Vanessa; Caillol, Danièle; Schiappa, Renaud; Laporte, Baptiste; Rios, Anne; Luxardi, Guillaume; Kusakabe, Takehiro; Joly, Jean-Stéphane; Darras, Sébastien; Christiaen, Lionel; Contensin, Magali; Auger, Hélène; Lamy, Clément; Hudson, Clare; Rothbächer, Ute; Gilchrist, Michael J.; Makabe, Kazuhiro W.; Hotta, Kohji; Fujiwara, Shigeki; Satoh, Nori; Satou, Yutaka; Lemaire, Patrick

2010-01-01

Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks to recent progress in genomics and imaging technologies, systemic approaches are now used in parallel with small-scale studies to establish links between genomic information and phenotypes, often described at the subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets at different scales into a global view of the developmental program. Here, we present a novel, generic digital system, NISEED, and its implementation, ANISEED, to ascidians, which are invertebrate chordates suitable for developmental systems biology approaches. ANISEED hosts an unprecedented combination of anatomical and molecular data on ascidian development. This includes the first detailed anatomical ontologies for these embryos, and quantitative geometrical descriptions of developing cells obtained from reconstructed three-dimensional (3D) embryos up to the gastrula stages. Fully annotated gene model sets are linked to 30,000 high-resolution spatial gene expression patterns in wild-type and experimentally manipulated conditions and to 528 experimentally validated cis-regulatory regions imported from specialized databases or extracted from 160 literature articles. This highly structured data set can be explored via a Developmental Browser, a Genome Browser, and a 3D Virtual Embryo module. We show how integration of heterogeneous data in ANISEED can provide a system-level understanding of the developmental program through the automatic inference of gene regulatory interactions, the identification of inducing signals, and the discovery and explanation of novel asymmetric divisions. PMID:20647237

Laboratory Information Systems.

PubMed

Henricks, Walter H

2015-06-01

Laboratory information systems (LISs) supply mission-critical capabilities for the vast array of information-processing needs of modern laboratories. LIS architectures include mainframe, client-server, and thin client configurations. The LIS database software manages a laboratory's data. LIS dictionaries are database tables that a laboratory uses to tailor an LIS to the unique needs of that laboratory. Anatomic pathology LIS (APLIS) functions play key roles throughout the pathology workflow, and laboratories rely on LIS management reports to monitor operations. This article describes the structure and functions of APLISs, with emphasis on their roles in laboratory operations and their relevance to pathologists. Copyright © 2015 Elsevier Inc. All rights reserved.

Melanoma of the Skin in the Danish Cancer Registry and the Danish Melanoma Database: A Validation Study.

PubMed

Pedersen, Sidsel Arnspang; Schmidt, Sigrun Alba Johannesdottir; Klausen, Siri; Pottegård, Anton; Friis, Søren; Hölmich, Lisbet Rosenkrantz; Gaist, David

2018-05-01

The nationwide Danish Cancer Registry and the Danish Melanoma Database both record data on melanoma for purposes of monitoring, quality assurance, and research. However, the data quality of the Cancer Registry and the Melanoma Database has not been formally evaluated. We estimated the positive predictive value (PPV) of melanoma diagnosis for random samples of 200 patients from the Cancer Registry (n = 200) and the Melanoma Database (n = 200) during 2004-2014, using the Danish Pathology Registry as "gold standard" reference. We further validated tumor characteristics in the Cancer Registry and the Melanoma Database. Additionally, we estimated the PPV of in situ melanoma diagnoses in the Melanoma Database, and the sensitivity of melanoma diagnoses in 2004-2014. The PPVs of melanoma in the Cancer Registry and the Melanoma Database were 97% (95% CI = 94, 99) and 100%. The sensitivity was 90% in the Cancer Registry and 77% in the Melanoma Database. The PPV of in situ melanomas in the Melanoma Database was 97% and the sensitivity was 56%. In the Melanoma Database, we observed PPVs of ulceration of 75% and Breslow thickness of 96%. The PPV of histologic subtypes varied between 87% and 100% in the Cancer Registry and 93% and 100% in the Melanoma Database. The PPVs for anatomical localization were 83%-95% in the Cancer Registry and 93%-100% in the Melanoma Database. The data quality in both the Cancer Registry and the Melanoma Database is high, supporting their use in epidemiologic studies.

Investigation on location dependent detectability in cone beam CT images with uniform and anatomical backgrounds

NASA Astrophysics Data System (ADS)

Han, Minah; Baek, Jongduk

2017-03-01

We investigate location dependent lesion detectability of cone beam computed tomography images for different background types (i.e., uniform and anatomical), image planes (i.e., transverse and longitudinal) and slice thicknesses. Anatomical backgrounds are generated using a power law spectrum of breast anatomy, 1/f3. Spherical object with a 5mm diameter is used as a signal. CT projection data are acquired by the forward projection of uniform and anatomical backgrounds with and without the signal. Then, projection data are reconstructed using the FDK algorithm. Detectability is evaluated by a channelized Hotelling observer with dense difference-of-Gaussian channels. For uniform background, off-centered images yield higher detectability than iso-centered images for the transverse plane, while for the longitudinal plane, detectability of iso-centered and off-centered images are similar. For anatomical background, off-centered images yield higher detectability for the transverse plane, while iso-centered images yield higher detectability for the longitudinal plane, when the slice thickness is smaller than 1.9mm. The optimal slice thickness is 3.8mm for all tasks, and the transverse plane at the off-center (iso-center and off-center) produces the highest detectability for uniform (anatomical) background.

Synthesis of image sequences for Korean sign language using 3D shape model

NASA Astrophysics Data System (ADS)

Hong, Mun-Ho; Choi, Chang-Seok; Kim, Chang-Seok; Jeon, Joon-Hyeon

1995-05-01

This paper proposes a method for offering information and realizing communication to the deaf-mute. The deaf-mute communicates with another person by means of sign language, but most people are unfamiliar with it. This method enables to convert text data into the corresponding image sequences for Korean sign language (KSL). Using a general 3D shape model of the upper body leads to generating the 3D motions of KSL. It is necessary to construct the general 3D shape model considering the anatomical structure of the human body. To obtain a personal 3D shape model, this general model is to adjust to the personal base images. Image synthesis for KSL consists of deforming a personal 3D shape model and texture-mapping the personal images onto the deformed model. The 3D motions for KSL have the facial expressions and the 3D movements of the head, trunk, arms and hands and are parameterized for easily deforming the model. These motion parameters of the upper body are extracted from a skilled signer's motion for each KSL and are stored to the database. Editing the parameters according to the inputs of text data yields to generate the image sequences of 3D motions.

A topological multilayer model of the human body.

PubMed

Barbeito, Antonio; Painho, Marco; Cabral, Pedro; O'Neill, João

2015-11-04

Geographical information systems deal with spatial databases in which topological models are described with alphanumeric information. Its graphical interfaces implement the multilayer concept and provide powerful interaction tools. In this study, we apply these concepts to the human body creating a representation that would allow an interactive, precise, and detailed anatomical study. A vector surface component of the human body is built using a three-dimensional (3-D) reconstruction methodology. This multilayer concept is implemented by associating raster components with the corresponding vector surfaces, which include neighbourhood topology enabling spatial analysis. A root mean square error of 0.18 mm validated the three-dimensional reconstruction technique of internal anatomical structures. The expansion of the identification and the development of a neighbourhood analysis function are the new tools provided in this model.

The visible human project®: From body to bits.

PubMed

Ackerman, Michael J

2016-08-01

In the middle 1990's the U.S. National Library sponsored the acquisition and development of the Visible Human Project® data base. This image database contains anatomical cross-sectional images which allow the reconstruction of three dimensional male and female anatomy to an accuracy of less than 1.0 mm. The male anatomy is contained in a 15 gigabyte database, the female in a 39 gigabyte database. This talk will describe why and how this project was accomplished and demonstrate some of the products which the Visible Human dataset has made possible. I will conclude by describing how the Visible Human Project, completed over 20 years ago, has led the National Library of Medicine to a series of image research projects including an open source image processing toolkit which is included in several commercial products.

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

PubMed Central

Druzinsky, Robert E.; Balhoff, James P.; Crompton, Alfred W.; Done, James; German, Rebecca Z.; Haendel, Melissa A.; Herrel, Anthony; Herring, Susan W.; Lapp, Hilmar; Mabee, Paula M.; Muller, Hans-Michael; Mungall, Christopher J.; Sternberg, Paul W.; Van Auken, Kimberly; Vinyard, Christopher J.; Williams, Susan H.; Wall, Christine E.

2016-01-01

Background In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. Development and Testing of the Ontology Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. Results and Significance Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities. PMID:26870952

Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data

PubMed Central

2013-01-01

Abstract We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability. PMID:24723752

Keratoconus: The ABCD Grading System.

PubMed

Belin, M W; Duncan, J K

2016-06-01

To propose a new keratoconus classification/staging system that utilises current tomographic data and better reflects the anatomical and functional changes seen in keratoconus. A previously published normative database was reanalysed to generate both anterior and posterior average radii of curvature (ARC and PRC) taken from a 3.0 mm optical zone centred on the thinnest point of the cornea. Mean and standard deviations were recorded and anterior data were compared to the existing Amsler-Krumeich (AK) Classification. ARC, PRC, thinnest pachymetry and distance visual acuity were then used to construct a keratoconus classification. 672 eyes of 336 patients were analysed. Anterior and posterior values were 7.65 ± 0.236 mm and 6.26 ± 0.214 mm, respectively, and thinnest pachymetry values were 534.2 ± 30.36 µm. The ARC values were 2.63, 5.47 and 6.44 standard deviations from the mean values of stages 1-3 in the AK classification, respectively. PRC staging uses the same standard deviation gates. The pachymetric values differed by 4.42 and 7.72 standard deviations for stages 2 and 3, respectively. A new keratoconus staging incorporates anterior and posterior curvature, thinnest pachymetric values, and distance visual acuity and consists of stages 0-4 (5 stages). The proposed system closely matches the existing AK classification stages 1-4 on anterior curvature. As it incorporates posterior curvature and thickness measurements based on the thinnest point, rather than apical measurements, the new staging system better reflects the anatomical changes seen in keratoconus. Georg Thieme Verlag KG Stuttgart · New York.

System, method and apparatus for generating phrases from a database

NASA Technical Reports Server (NTRS)

McGreevy, Michael W. (Inventor)

2004-01-01

A phrase generation is a method of generating sequences of terms, such as phrases, that may occur within a database of subsets containing sequences of terms, such as text. A database is provided and a relational model of the database is created. A query is then input. The query includes a term or a sequence of terms or multiple individual terms or multiple sequences of terms or combinations thereof. Next, several sequences of terms that are contextually related to the query are assembled from contextual relations in the model of the database. The sequences of terms are then sorted and output. Phrase generation can also be an iterative process used to produce sequences of terms from a relational model of a database.

Bone morphology of the hind limbs in two caviomorph rodents.

PubMed

de Araújo, F A P; Sesoko, N F; Rahal, S C; Teixeira, C R; Müller, T R; Machado, M R F

2013-04-01

In order to evaluate the hind limbs of caviomorph rodents a descriptive analysis of the Cuniculus paca (Linnaeus, 1766) and Hydrochoerus hydrochaeris (Linnaeus, 1766) was performed using anatomical specimens, radiography, computed tomography (CT) and full-coloured prototype models to generate bone anatomy data. The appendicular skeleton of the two largest rodents of Neotropical America was compared with the previously reported anatomical features of Rattus norvegicus (Berkenhout, 1769) and domestic Cavia porcellus (Linnaeus, 1758). The structures were analyzed macroscopically and particular findings of each species reported. Features including the presence of articular fibular projection and lunulae were observed in the stifle joint of all rodents. Imaging aided in anatomical description and, specifically in the identification of bone structures in Cuniculus paca and Hydrochoerus hydrochaeris. The imaging findings were correlated with the anatomical structures observed. The data may be used in future studies comparing these animals to other rodents and mammalian species. © 2012 Blackwell Verlag GmbH.

Investigation of adverse events associated with an off-label use of arterial stents and CE-marked iliac vein stents in the iliac vein: insights into developing a better iliac vein stent.

PubMed

Shida, Takuya; Umezu, Mitsuo; Iwasaki, Kiyotaka

2018-06-01

We analyzed the adverse events associated with an off-label use of arterial stents and CE-marked iliac vein stents for the treatment of iliac venous thromboembolism and investigated their relationships with the anatomical features of the iliac vein, to gain insights into the development of a better iliac vein stent. Reports of adverse events following the use of stents in the iliac vein were retrieved from the Manufacturer and User Facility Device Experience (MAUDE) database that contain suspected device-associated complications reported to the Food and Drug Administration. Data from 2006 to 2016 were investigated. The literature analysis was also conducted using PubMed, Cochrane Library, EMBASE, and Web of Science focusing on English articles published up to 4 October 2016. The analysis of 88 adverse events from the MAUDE database and 182 articles from the literature revealed that a higher number of adverse events had been reported following the use of arterial stents in the iliac vein compared to CE-marked iliac vein stents. While stent migration and shortening were reported only for the arterial stents, stent fracture and compression occurred regardless of the stent type, even though a vein does not pulsate. A study of the anatomical features of the iliac vein implies that bending, compression, and kink loads are applied to the iliac vein stents in vivo. For designing, developing, and pre-clinical testing of stents intended for use in the iliac vein, the above mechanical load environments induced by the anatomical features should be considered.

A systematic review of variations of the recurrent laryngeal nerve.

PubMed

Ling, Xing Yao; Smoll, Nicolas Roydon

2016-01-01

With thyroid cancer fast becoming one of the most common endocrine cancers, the frequency of thyroid surgery has increased. A common and debilitating concern with thyroid surgery is recurrent laryngeal nerve (RLN) paralysis leading to glottal obstruction and airway compromise. A systematic review regarding the anatomical variation of the recurrent laryngeal nerve was performed to determine the position of anatomical variants of the RLN in relation to the inferior thyroid artery (ITA) as well as the prevalence of nonrecurrent laryngeal nerve (NRLN). MEDLINE, Web of Science, MEDITEXT, AMED, CINAHL, Cochrane, ProQuest, Pubmed, and ScienceDirect. Databases were searched using the search terms "inferior thyroid artery," "recurrent laryngeal nerve," "nonrecurrent laryngeal nerve," and "anatomical variation." The reference sections of the articles found were searched for additional reports. The references of all articles were searched to find articles missed in the database search. A total of 8,655 RLN sides were included in this study. One thousand eight hundred and thirteen (20.95%; 95% confidence interval (CI) 20.09, 2,182) showed a Type A configuration of RLN in relation to the ITA, 2,432 (28.10%; 95% CI 27.15, 29.06) showed a Type B configuration and 4,410 (50.95%; 95% CI 49.89, 52.01) showed a Type C configuration between the RLN and the ITA. The second search returned with 38,568 recurrent laryngeal sides and only 221 (0.57%; 95%CI 0.5, 0.65) NRLN documented. The RLN is most commonly found in the posterior position, relative to the ITA. The incidence of the NRLN is low, only occurring in 0.57% of people. © 2015 Wiley Periodicals, Inc.

Automatic detection of anatomical regions in frontal x-ray images: comparing convolutional neural networks to random forest

NASA Astrophysics Data System (ADS)

Olory Agomma, R.; Vázquez, C.; Cresson, T.; De Guise, J.

2018-02-01

Most algorithms to detect and identify anatomical structures in medical images require either to be initialized close to the target structure, or to know that the structure is present in the image, or to be trained on a homogeneous database (e.g. all full body or all lower limbs). Detecting these structures when there is no guarantee that the structure is present in the image, or when the image database is heterogeneous (mixed configurations), is a challenge for automatic algorithms. In this work we compared two state-of-the-art machine learning techniques in order to determine which one is the most appropriate for predicting targets locations based on image patches. By knowing the position of thirteen landmarks points, labelled by an expert in EOS frontal radiography, we learn the displacement between salient points detected in the image and these thirteen landmarks. The learning step is carried out with a machine learning approach by exploring two methods: Convolutional Neural Network (CNN) and Random Forest (RF). The automatic detection of the thirteen landmarks points in a new image is then obtained by averaging the positions of each one of these thirteen landmarks estimated from all the salient points in the new image. We respectively obtain for CNN and RF, an average prediction error (both mean and standard deviation in mm) of 29 +/-18 and 30 +/- 21 for the thirteen landmarks points, indicating the approximate location of anatomical regions. On the other hand, the learning time is 9 days for CNN versus 80 minutes for RF. We provide a comparison of the results between the two machine learning approaches.

A Three-Dimensional Statistical Average Skull: Application of Biometric Morphing in Generating Missing Anatomy.

PubMed

Teshima, Tara Lynn; Patel, Vaibhav; Mainprize, James G; Edwards, Glenn; Antonyshyn, Oleh M

2015-07-01

The utilization of three-dimensional modeling technology in craniomaxillofacial surgery has grown exponentially during the last decade. Future development, however, is hindered by the lack of a normative three-dimensional anatomic dataset and a statistical mean three-dimensional virtual model. The purpose of this study is to develop and validate a protocol to generate a statistical three-dimensional virtual model based on a normative dataset of adult skulls. Two hundred adult skull CT images were reviewed. The average three-dimensional skull was computed by processing each CT image in the series using thin-plate spline geometric morphometric protocol. Our statistical average three-dimensional skull was validated by reconstructing patient-specific topography in cranial defects. The experiment was repeated 4 times. In each case, computer-generated cranioplasties were compared directly to the original intact skull. The errors describing the difference between the prediction and the original were calculated. A normative database of 33 adult human skulls was collected. Using 21 anthropometric landmark points, a protocol for three-dimensional skull landmarking and data reduction was developed and a statistical average three-dimensional skull was generated. Our results show the root mean square error (RMSE) for restoration of a known defect using the native best match skull, our statistical average skull, and worst match skull was 0.58, 0.74, and 4.4  mm, respectively. The ability to statistically average craniofacial surface topography will be a valuable instrument for deriving missing anatomy in complex craniofacial defects and deficiencies as well as in evaluating morphologic results of surgery.

Flight Mechanics Project

NASA Technical Reports Server (NTRS)

Steck, Daniel

2009-01-01

This report documents the generation of an outbound Earth to Moon transfer preliminary database consisting of four cases calculated twice a day for a 19 year period. The database was desired as the first step in order for NASA to rapidly generate Earth to Moon trajectories for the Constellation Program using the Mission Assessment Post Processor. The completed database was created running a flight trajectory and optimization program, called Copernicus, in batch mode with the use of newly created Matlab functions. The database is accurate and has high data resolution. The techniques and scripts developed to generate the trajectory information will also be directly used in generating a comprehensive database.

Acoustic analysis of normal Saudi adult voices.

PubMed

Malki, Khalid H; Al-Habib, Salman F; Hagr, Abulrahman A; Farahat, Mohamed M

2009-08-01

To determine the acoustic differences between Saudi adult male and female voices, and to compare the acoustic variables of the Multidimensional Voice Program (MDVP) obtained from North American adults to a group of Saudi males and females. A cross-sectional survey of normal adult male and female voices was conducted at King Abdulaziz University Hospital, Riyadh, Kingdom of Saudi Arabia between March 2007 and December 2008. Ninety-five Saudi subjects sustained the vowel /a/ 6 times, and the steady state portion of 3 samples was analyzed and compared with the samples of the KayPentax normative voice database. Significant differences were found between Saudi and North American KayPentax database groups. In the male subjects, 15 of 33 MDVP variables, and 10 of 33 variables in the female subjects were found to be significantly different from the KayPentax database. We conclude that the acoustical differences may reflect laryngeal anatomical or tissue differences between the Saudi and the KayPentax database.

Anatomical robust optimization to account for nasal cavity filling variation during intensity-modulated proton therapy: a comparison with conventional and adaptive planning strategies

NASA Astrophysics Data System (ADS)

van de Water, Steven; Albertini, Francesca; Weber, Damien C.; Heijmen, Ben J. M.; Hoogeman, Mischa S.; Lomax, Antony J.

2018-01-01

The aim of this study is to develop an anatomical robust optimization method for intensity-modulated proton therapy (IMPT) that accounts for interfraction variations in nasal cavity filling, and to compare it with conventional single-field uniform dose (SFUD) optimization and online plan adaptation. We included CT data of five patients with tumors in the sinonasal region. Using the planning CT, we generated for each patient 25 ‘synthetic’ CTs with varying nasal cavity filling. The robust optimization method available in our treatment planning system ‘Erasmus-iCycle’ was extended to also account for anatomical uncertainties by including (synthetic) CTs with varying patient anatomy as error scenarios in the inverse optimization. For each patient, we generated treatment plans using anatomical robust optimization and, for benchmarking, using SFUD optimization and online plan adaptation. Clinical target volume (CTV) and organ-at-risk (OAR) doses were assessed by recalculating the treatment plans on the synthetic CTs, evaluating dose distributions individually and accumulated over an entire fractionated 50 GyRBE treatment, assuming each synthetic CT to correspond to a 2 GyRBE fraction. Treatment plans were also evaluated using actual repeat CTs. Anatomical robust optimization resulted in adequate CTV doses (V95%  ⩾  98% and V107%  ⩽  2%) if at least three synthetic CTs were included in addition to the planning CT. These CTV requirements were also fulfilled for online plan adaptation, but not for the SFUD approach, even when applying a margin of 5 mm. Compared with anatomical robust optimization, OAR dose parameters for the accumulated dose distributions were on average 5.9 GyRBE (20%) higher when using SFUD optimization and on average 3.6 GyRBE (18%) lower for online plan adaptation. In conclusion, anatomical robust optimization effectively accounted for changes in nasal cavity filling during IMPT, providing substantially improved CTV and OAR doses compared with conventional SFUD optimization. OAR doses can be further reduced by using online plan adaptation.

PylotDB - A Database Management, Graphing, and Analysis Tool Written in Python

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnette, Daniel W.

2012-01-04

PylotDB, written completely in Python, provides a user interface (UI) with which to interact with, analyze, graph data from, and manage open source databases such as MySQL. The UI mitigates the user having to know in-depth knowledge of the database application programming interface (API). PylotDB allows the user to generate various kinds of plots from user-selected data; generate statistical information on text as well as numerical fields; backup and restore databases; compare database tables across different databases as well as across different servers; extract information from any field to create new fields; generate, edit, and delete databases, tables, and fields;more » generate or read into a table CSV data; and similar operations. Since much of the database information is brought under control of the Python computer language, PylotDB is not intended for huge databases for which MySQL and Oracle, for example, are better suited. PylotDB is better suited for smaller databases that might be typically needed in a small research group situation. PylotDB can also be used as a learning tool for database applications in general.« less

Building a high-resolution T2-weighted MR-based probabilistic model of tumor occurrence in the prostate.

PubMed

Nagarajan, Mahesh B; Raman, Steven S; Lo, Pechin; Lin, Wei-Chan; Khoshnoodi, Pooria; Sayre, James W; Ramakrishna, Bharath; Ahuja, Preeti; Huang, Jiaoti; Margolis, Daniel J A; Lu, David S K; Reiter, Robert E; Goldin, Jonathan G; Brown, Matthew S; Enzmann, Dieter R

2018-02-19

We present a method for generating a T2 MR-based probabilistic model of tumor occurrence in the prostate to guide the selection of anatomical sites for targeted biopsies and serve as a diagnostic tool to aid radiological evaluation of prostate cancer. In our study, the prostate and any radiological findings within were segmented retrospectively on 3D T2-weighted MR images of 266 subjects who underwent radical prostatectomy. Subsequent histopathological analysis determined both the ground truth and the Gleason grade of the tumors. A randomly chosen subset of 19 subjects was used to generate a multi-subject-derived prostate template. Subsequently, a cascading registration algorithm involving both affine and non-rigid B-spline transforms was used to register the prostate of every subject to the template. Corresponding transformation of radiological findings yielded a population-based probabilistic model of tumor occurrence. The quality of our probabilistic model building approach was statistically evaluated by measuring the proportion of correct placements of tumors in the prostate template, i.e., the number of tumors that maintained their anatomical location within the prostate after their transformation into the prostate template space. Probabilistic model built with tumors deemed clinically significant demonstrated a heterogeneous distribution of tumors, with higher likelihood of tumor occurrence at the mid-gland anterior transition zone and the base-to-mid-gland posterior peripheral zones. Of 250 MR lesions analyzed, 248 maintained their original anatomical location with respect to the prostate zones after transformation to the prostate. We present a robust method for generating a probabilistic model of tumor occurrence in the prostate that could aid clinical decision making, such as selection of anatomical sites for MR-guided prostate biopsies.

Knowledge modeling in image-guided neurosurgery: application in understanding intraoperative brain shift

NASA Astrophysics Data System (ADS)

Cohen-Adad, Julien; Paul, Perrine; Morandi, Xavier; Jannin, Pierre

2006-03-01

During an image-guided neurosurgery procedure, the neuronavigation system is subject to inaccuracy because of anatomical deformations which induce a gap between the preoperative images and their anatomical reality. Thus, the objective of many research teams is to succeed in quantifying these deformations in order to update preoperative images. Anatomical intraoperative deformations correspond to a complex spatio-temporal phenomenon. Our objective is to identify the parameters implicated in these deformations and to use these parameters as constrains for systems dedicated to updating preoperative images. In order to identify these parameters of deformation we followed the iterative methodology used for cognitive system conception: identification, conceptualization, formalization, implementation and validation. A state of the art about cortical deformations has been established in order to identify relevant parameters probably involved in the deformations. As a first step, 30 parameters have been identified and described following an ontological approach. They were formalized into a Unified Modeling Language (UML) class diagram. We implemented that model into a web-based application in order to fill a database. Two surgical cases have been studied at this moment. After having entered enough surgical cases for data mining purposes, we expect to identify the most relevant and influential parameters and to gain a better ability to understand the deformation phenomenon. This original approach is part of a global system aiming at quantifying and correcting anatomical deformations.

A review of simulation platforms in surgery of the temporal bone.

PubMed

Bhutta, M F

2016-10-01

Surgery of the temporal bone is a high-risk activity in an anatomically complex area. Simulation enables rehearsal of such surgery. The traditional simulation platform is the cadaveric temporal bone, but in recent years other simulation platforms have been created, including plastic and virtual reality platforms. To undertake a review of simulation platforms for temporal bone surgery, specifically assessing their educational value in terms of validity and in enabling transition to surgery. Systematic qualitative review. Search of the Pubmed, CINAHL, BEI and ERIC databases. Assessment of reported outcomes in terms of educational value. A total of 49 articles were included, covering cadaveric, animal, plastic and virtual simulation platforms. Cadaveric simulation is highly rated as an educational tool, but there may be a ceiling effect on educational outcomes after drilling 8-10 temporal bones. Animal models show significant anatomical variation from man. Plastic temporal bone models offer much potential, but at present lack sufficient anatomical or haptic validity. Similarly, virtual reality platforms lack sufficient anatomical or haptic validity, but with technological improvements they are advancing rapidly. At present, cadaveric simulation remains the best platform for training in temporal bone surgery. Technological advances enabling improved materials or modelling mean that in the future plastic or virtual platforms may become comparable to cadaveric platforms, and also offer additional functionality including patient-specific simulation from CT data. © 2015 John Wiley & Sons Ltd.

Unraveling Pancreatic Segmentation.

PubMed

Renard, Yohann; de Mestier, Louis; Perez, Manuela; Avisse, Claude; Lévy, Philippe; Kianmanesh, Reza

2018-04-01

Limited pancreatic resections are increasingly performed, but the rate of postoperative fistula is higher than after classical resections. Pancreatic segmentation, anatomically and radiologically identifiable, may theoretically help the surgeon removing selected anatomical portions with their own segmental pancreatic duct and thus might decrease the postoperative fistula rate. We aimed at systematically and comprehensively reviewing the previously proposed pancreatic segmentations and discuss their relevance and limitations. PubMed database was searched for articles investigating pancreatic segmentation, including human or animal anatomy, and cadaveric or surgical studies. Overall, 47/99 articles were selected and grouped into 4 main hypotheses of pancreatic segmentation methodology: anatomic, vascular, embryologic and lymphatic. The head, body and tail segments are gross description without distinct borders. The arterial territories defined vascular segments and isolate an isthmic paucivascular area. The embryological theory relied on the fusion plans of the embryological buds. The lymphatic drainage pathways defined the lymphatic segmentation. These theories had differences, but converged toward separating the head and body/tail parts, and the anterior from posterior and inferior parts of the pancreatic head. The rate of postoperative fistula was not decreased when surgical resection was performed following any of these segmentation theories; hence, none of them appeared relevant enough to guide pancreatic transections. Current pancreatic segmentation theories do not enable defining anatomical-surgical pancreatic segments. Other approaches should be explored, in particular focusing on pancreatic ducts, through pancreatic ducts reconstructions and embryologic 3D modelization.

Reliability of intracerebral hemorrhage classification systems: A systematic review.

PubMed

Rannikmäe, Kristiina; Woodfield, Rebecca; Anderson, Craig S; Charidimou, Andreas; Chiewvit, Pipat; Greenberg, Steven M; Jeng, Jiann-Shing; Meretoja, Atte; Palm, Frederic; Putaala, Jukka; Rinkel, Gabriel Je; Rosand, Jonathan; Rost, Natalia S; Strbian, Daniel; Tatlisumak, Turgut; Tsai, Chung-Fen; Wermer, Marieke Jh; Werring, David; Yeh, Shin-Joe; Al-Shahi Salman, Rustam; Sudlow, Cathie Lm

2016-08-01

Accurately distinguishing non-traumatic intracerebral hemorrhage (ICH) subtypes is important since they may have different risk factors, causal pathways, management, and prognosis. We systematically assessed the inter- and intra-rater reliability of ICH classification systems. We sought all available reliability assessments of anatomical and mechanistic ICH classification systems from electronic databases and personal contacts until October 2014. We assessed included studies' characteristics, reporting quality and potential for bias; summarized reliability with kappa value forest plots; and performed meta-analyses of the proportion of cases classified into each subtype. We included 8 of 2152 studies identified. Inter- and intra-rater reliabilities were substantial to perfect for anatomical and mechanistic systems (inter-rater kappa values: anatomical 0.78-0.97 [six studies, 518 cases], mechanistic 0.89-0.93 [three studies, 510 cases]; intra-rater kappas: anatomical 0.80-1 [three studies, 137 cases], mechanistic 0.92-0.93 [two studies, 368 cases]). Reporting quality varied but no study fulfilled all criteria and none was free from potential bias. All reliability studies were performed with experienced raters in specialist centers. Proportions of ICH subtypes were largely consistent with previous reports suggesting that included studies are appropriately representative. Reliability of existing classification systems appears excellent but is unknown outside specialist centers with experienced raters. Future reliability comparisons should be facilitated by studies following recently published reporting guidelines. © 2016 World Stroke Organization.

Emission & Generation Resource Integrated Database (eGRID)

EPA Pesticide Factsheets

The Emissions & Generation Resource Integrated Database (eGRID) is an integrated source of data on environmental characteristics of electric power generation. Twelve federal databases are represented by eGRID, which provides air emission and resource mix information for thousands of power plants and generating companies. eGRID allows direct comparison of the environmental attributes of electricity from different plants, companies, States, or regions of the power grid.

Elementary software for the hand lens identification of some common iranian woods

Treesearch

Vahidreza Safdari; Margaret S. Devall

2009-01-01

A computer program, “Hyrcania”, has been developed for identifying some common woods (26 hardwoods and 6 softwoods) from the Hyrcanian forest type of Iran. The program has been written in JavaScript and is usable with computers as well as mobile phones. The databases use anatomical characteristics (visible with a hand lens) and wood colour, and can be searched in...

Real-time database drawn from an electronic health record for a thoracic surgery unit: high-quality clinical data saving time and human resources.

PubMed

Salati, Michele; Pompili, Cecilia; Refai, Majed; Xiumè, Francesco; Sabbatini, Armando; Brunelli, Alessandro

2014-06-01

The aim of the present study was to verify whether the implementation of an electronic health record (EHR) in our thoracic surgery unit allows creation of a high-quality clinical database saving time and costs. Before August 2011, multiple individuals compiled the on-paper documents/records and a single data manager inputted selected data into the database (traditional database, tDB). Since the adoption of an EHR in August 2011, multiple individuals have been responsible for compiling the EHR, which automatically generates a real-time database (EHR-based database, eDB), without the need for a data manager. During the initial period of implementation of the EHR, periodic meetings were held with all physicians involved in the use of the EHR in order to monitor and standardize the data registration process. Data quality of the first 100 anatomical lung resections recorded in the eDB was assessed by measuring the total number of missing values (MVs: existing non-reported value) and inaccurate values (wrong data) occurring in 95 core variables. The average MV of the eDB was compared with the one occurring in the same variables of the last 100 records registered in the tDB. A learning curve was constructed by plotting the number of MVs in the electronic database and tDB with the patients arranged by the date of registration. The tDB and eDB had similar MVs (0.74 vs 1, P = 0.13). The learning curve showed an initial phase including about 35 records, where MV in the eDB was higher than that in the tDB (1.9 vs 0.74, P = 0.03), and a subsequent phase, where the MV was similar in the two databases (0.7 vs 0.74, P = 0.6). The inaccuracy rate of these two phases in the eDB was stable (0.5 vs 0.3, P = 0.3). Using EHR saved an average of 9 min per patient, totalling 15 h saved for obtaining a dataset of 100 patients with respect to the tDB. The implementation of EHR allowed streamlining the process of clinical data recording. It saved time and human resource costs, without compromising the quality of data. © The Author 2014. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Evolution of illustrations in anatomy: a study from the classical period in Europe to modern times.

PubMed

Ghosh, Sanjib Kumar

2015-01-01

Illustrations constitute an essential element of learning anatomy in modern times. However it required a significant evolutionary process spread over centuries, for illustrations to achieve the present status in the subject of anatomy. This review article attempts to outline the evolutionary process by highlighting on the works of esteemed anatomists in a chronological manner. Available literature suggests that illustrations were not used in anatomy during the classical period when the subject was dominated by the descriptive text of Galen. Guido da Vigevano was first to use illustrations in anatomy during the Late Middle Ages and this concept developed further during the Renaissance period when Andreas Vesalius pioneered in illustrations becoming an indispensable tool in conveying anatomical details. Toward later stages of the Renaissance period, Fabricius ab Aquapendente endeavored to restrict dramatization of anatomical illustrations which was a prevalent trend in early Renaissance. During the 18th century, anatomical artwork was characterized by the individual styles of prominent anatomists leading to suppression of anatomical details. In the 19th century, Henry Gray used illustrations in his anatomical masterpiece that focused on depicting anatomical structures and were free from any artistic style. From early part of the 20th century medical images and photographs started to complement traditional handmade anatomical illustrations. Computer technology and advanced software systems played a key role in the evolution of anatomical illustrations during the late 20th century resulting in new generation 3D image datasets that are being used in the 21st century in innovative formats for teaching and learning anatomy. © 2014 American Association of Anatomists.

Accelerating Pathology Image Data Cross-Comparison on CPU-GPU Hybrid Systems

PubMed Central

Wang, Kaibo; Huai, Yin; Lee, Rubao; Wang, Fusheng; Zhang, Xiaodong; Saltz, Joel H.

2012-01-01

As an important application of spatial databases in pathology imaging analysis, cross-comparing the spatial boundaries of a huge amount of segmented micro-anatomic objects demands extremely data- and compute-intensive operations, requiring high throughput at an affordable cost. However, the performance of spatial database systems has not been satisfactory since their implementations of spatial operations cannot fully utilize the power of modern parallel hardware. In this paper, we provide a customized software solution that exploits GPUs and multi-core CPUs to accelerate spatial cross-comparison in a cost-effective way. Our solution consists of an efficient GPU algorithm and a pipelined system framework with task migration support. Extensive experiments with real-world data sets demonstrate the effectiveness of our solution, which improves the performance of spatial cross-comparison by over 18 times compared with a parallelized spatial database approach. PMID:23355955

Dictionary learning-based CT detection of pulmonary nodules

NASA Astrophysics Data System (ADS)

Wu, Panpan; Xia, Kewen; Zhang, Yanbo; Qian, Xiaohua; Wang, Ge; Yu, Hengyong

2016-10-01

Segmentation of lung features is one of the most important steps for computer-aided detection (CAD) of pulmonary nodules with computed tomography (CT). However, irregular shapes, complicated anatomical background and poor pulmonary nodule contrast make CAD a very challenging problem. Here, we propose a novel scheme for feature extraction and classification of pulmonary nodules through dictionary learning from training CT images, which does not require accurately segmented pulmonary nodules. Specifically, two classification-oriented dictionaries and one background dictionary are learnt to solve a two-category problem. In terms of the classification-oriented dictionaries, we calculate sparse coefficient matrices to extract intrinsic features for pulmonary nodule classification. The support vector machine (SVM) classifier is then designed to optimize the performance. Our proposed methodology is evaluated with the lung image database consortium and image database resource initiative (LIDC-IDRI) database, and the results demonstrate that the proposed strategy is promising.

A review of the surface and internal anatomy of the caudal canal in children.

PubMed

Lees, David; Frawley, Geoff; Taghavi, Kiarash; Mirjalili, Seyed Ali

2014-08-01

The anatomy of the sacral hiatus and caudal canal is prone to significant variation, yet studies assessing this in the pediatric population remain limited. Awareness of the possible anatomical variations is critical to the safety and success of caudal epidural blocks, particularly when image guidance is not employed. This systematic review analyzes the available evidence on the clinical anatomy of the caudal canal in pediatric patients, emphasizing surface anatomy and internal anatomical variations. A literature search using three electronic databases and standard pediatric and anatomy reference texts was conducted yielding 24 primary and seven secondary English-language sources. Appreciating that our current landmark-guided approaches to the caudal canal are not well studied in the pediatric population is important for both clinicians and researchers. © 2014 John Wiley & Sons Ltd.

A methodology for generating normal and pathological brain perfusion SPECT images for evaluation of MRI/SPECT fusion methods: application in epilepsy

NASA Astrophysics Data System (ADS)

Grova, C.; Jannin, P.; Biraben, A.; Buvat, I.; Benali, H.; Bernard, A. M.; Scarabin, J. M.; Gibaud, B.

2003-12-01

Quantitative evaluation of brain MRI/SPECT fusion methods for normal and in particular pathological datasets is difficult, due to the frequent lack of relevant ground truth. We propose a methodology to generate MRI and SPECT datasets dedicated to the evaluation of MRI/SPECT fusion methods and illustrate the method when dealing with ictal SPECT. The method consists in generating normal or pathological SPECT data perfectly aligned with a high-resolution 3D T1-weighted MRI using realistic Monte Carlo simulations that closely reproduce the response of a SPECT imaging system. Anatomical input data for the SPECT simulations are obtained from this 3D T1-weighted MRI, while functional input data result from an inter-individual analysis of anatomically standardized SPECT data. The method makes it possible to control the 'brain perfusion' function by proposing a theoretical model of brain perfusion from measurements performed on real SPECT images. Our method provides an absolute gold standard for assessing MRI/SPECT registration method accuracy since, by construction, the SPECT data are perfectly registered with the MRI data. The proposed methodology has been applied to create a theoretical model of normal brain perfusion and ictal brain perfusion characteristic of mesial temporal lobe epilepsy. To approach realistic and unbiased perfusion models, real SPECT data were corrected for uniform attenuation, scatter and partial volume effect. An anatomic standardization was used to account for anatomic variability between subjects. Realistic simulations of normal and ictal SPECT deduced from these perfusion models are presented. The comparison of real and simulated SPECT images showed relative differences in regional activity concentration of less than 20% in most anatomical structures, for both normal and ictal data, suggesting realistic models of perfusion distributions for evaluation purposes. Inter-hemispheric asymmetry coefficients measured on simulated data were found within the range of asymmetry coefficients measured on corresponding real data. The features of the proposed approach are compared with those of other methods previously described to obtain datasets appropriate for the assessment of fusion methods.

Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases

NASA Astrophysics Data System (ADS)

Hoehndorf, Robert; Schofield, Paul N.; Gkoutos, Georgios V.

2015-06-01

Phenotypes are the observable characteristics of an organism arising from its response to the environment. Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases such as OMIM and Orphanet. Exploiting these resources, several computational methods have been developed for integration and analysis of phenotype data to identify the genetic etiology of diseases or suggest plausible interventions. A similar resource would be highly useful not only for rare and Mendelian diseases, but also for common, complex and infectious diseases. We apply a semantic text-mining approach to identify the phenotypes (signs and symptoms) associated with over 6,000 diseases. We evaluate our text-mined phenotypes by demonstrating that they can correctly identify known disease-associated genes in mice and humans with high accuracy. Using a phenotypic similarity measure, we generate a human disease network in which diseases that have similar signs and symptoms cluster together, and we use this network to identify closely related diseases based on common etiological, anatomical as well as physiological underpinnings.

Increased revision rate with posterior tibial tunnel placement after using the 70-degree tibial guide in ACL reconstruction.

PubMed

Inderhaug, Eivind; Raknes, Sveinung; Østvold, Thomas; Solheim, Eirik; Strand, Torbjørn

2017-01-01

To map knee morphology radiographically in a population with a torn ACL and to investigate whether anatomic factors could be related to outcomes after ACL reconstruction at mid- to long-term follow-up. Further, we wanted to assess tibial tunnel placement after using the 70-degree "anti-impingement" tibial tunnel guide and investigate any relation between tunnel placement and revision surgery. Patients undergoing ACL reconstruction involving the 70-degree tibial guide from 2003 to 2008 were included. Two independent investigators analysed pre- and post-operative radiographs. Demographic data and information on revision surgery were collected from an internal database. Anatomic factors and post-operative tibial tunnel placements were investigated as predictors of revision. Three-hundred and seventy-seven patients were included in the study. A large anatomic variation with significant differences between men and women was seen. None of the anatomic factors could be related to a significant increase in revision rate. Patients with a posterior tibial tunnel placement, defined as 50 % or more posterior on the Amis and Jakob line, did, however, have a higher risk of revision surgery compared to patients with an anterior tunnel placement (P = 0.03). Use of the 70-degree tibial guide did result in a high incidence (47 %) of posterior tibial tunnel placements associated with an increased rate of revision surgery. The current study was, however, not able to identify any anatomic variation that could be related to a higher risk of revision surgery. Avoiding graft impingement from the femoral roof in anterior tibial tunnel placements is important, but the insight that overly posterior tunnel placement can lead to inferior outcome should also be kept in mind when performing ACL surgery. IV.

Diagnostic accuracy of magnetic resonance imaging techniques for treatment response evaluation in patients with high-grade glioma, a systematic review and meta-analysis.

PubMed

van Dijken, Bart R J; van Laar, Peter Jan; Holtman, Gea A; van der Hoorn, Anouk

2017-10-01

Treatment response assessment in high-grade gliomas uses contrast enhanced T1-weighted MRI, but is unreliable. Novel advanced MRI techniques have been studied, but the accuracy is not well known. Therefore, we performed a systematic meta-analysis to assess the diagnostic accuracy of anatomical and advanced MRI for treatment response in high-grade gliomas. Databases were searched systematically. Study selection and data extraction were done by two authors independently. Meta-analysis was performed using a bivariate random effects model when ≥5 studies were included. Anatomical MRI (five studies, 166 patients) showed a pooled sensitivity and specificity of 68% (95%CI 51-81) and 77% (45-93), respectively. Pooled apparent diffusion coefficients (seven studies, 204 patients) demonstrated a sensitivity of 71% (60-80) and specificity of 87% (77-93). DSC-perfusion (18 studies, 708 patients) sensitivity was 87% (82-91) with a specificity of 86% (77-91). DCE-perfusion (five studies, 207 patients) sensitivity was 92% (73-98) and specificity was 85% (76-92). The sensitivity of spectroscopy (nine studies, 203 patients) was 91% (79-97) and specificity was 95% (65-99). Advanced techniques showed higher diagnostic accuracy than anatomical MRI, the highest for spectroscopy, supporting the use in treatment response assessment in high-grade gliomas. • Treatment response assessment in high-grade gliomas with anatomical MRI is unreliable • Novel advanced MRI techniques have been studied, but diagnostic accuracy is unknown • Meta-analysis demonstrates that advanced MRI showed higher diagnostic accuracy than anatomical MRI • Highest diagnostic accuracy for spectroscopy and perfusion MRI • Supports the incorporation of advanced MRI in high-grade glioma treatment response assessment.

Feature-based Morphometry

PubMed Central

Toews, Matthew; Wells, William M.; Collins, Louis; Arbel, Tal

2013-01-01

This paper presents feature-based morphometry (FBM), a new, fully data-driven technique for identifying group-related differences in volumetric imagery. In contrast to most morphometry methods which assume one-to-one correspondence between all subjects, FBM models images as a collage of distinct, localized image features which may not be present in all subjects. FBM thus explicitly accounts for the case where the same anatomical tissue cannot be reliably identified in all subjects due to disease or anatomical variability. A probabilistic model describes features in terms of their appearance, geometry, and relationship to sub-groups of a population, and is automatically learned from a set of subject images and group labels. Features identified indicate group-related anatomical structure that can potentially be used as disease biomarkers or as a basis for computer-aided diagnosis. Scale-invariant image features are used, which reflect generic, salient patterns in the image. Experiments validate FBM clinically in the analysis of normal (NC) and Alzheimer’s (AD) brain images using the freely available OASIS database. FBM automatically identifies known structural differences between NC and AD subjects in a fully data-driven fashion, and obtains an equal error classification rate of 0.78 on new subjects. PMID:20426102

Anatomical variations of mandibular canal detected by panoramic radiography and CT: a systematic review and meta-analysis

PubMed Central

Dutra, Kamile; Porporatti, André Luís; Mezzomo, Luis A; De Luca Canto, Graziela; Flores-Mir, Carlos; Corrêa, Márcio

2016-01-01

Objectives: To investigate the anatomical variations of the mandibular canal through assessment in situ, panoramic radiography, CT or CBCT and assess their frequency. Methods: Articles were selected from databases (Cochrane Library, LILACS, ProQuest, PubMed, Scopus, Web of Science and Google Scholar), articles without limitations of language, in which the main objective was to evaluate the frequency of bifurcation of the mandibular canal through assessment in situ, panoramic radiography, CT or CBCT were selected. A meta-analysis of prevalence using random effects was performed. Results: Using a selection process in two phases, 15 articles were identified, and a meta-analysis was conducted. The results from these meta-analyses showed that the overall prevalence of anatomical variations for in situ studies was 6.46%, and through assessment of panoramic radiography and CT or CBCT the overall prevalence shown was 4.20% and 16.25%, respectively. Conclusions: There are two types of variations of the mandibular canal: the retromolar canal and bifid mandibular canal. The frequency variations through assessing in situ, panoramic radiography and CT or CBCT were 6.46%, 4.20% and 16.25%, respectively. PMID:26576624

Adverse cardiac events in 56,000 orthopaedic trauma patients: Does anatomic area make a difference?

PubMed

Lee, Adam K; Dodd, Ashley C; Lakomkin, Nikita; Yarlagadda, Mahesh; Jahangir, A Alex; Collinge, Cory A; Sethi, Manish K

2016-08-01

Postoperative cardiac events in orthopaedic trauma patients constitute severe morbidity and mortality. It is therefore increasingly important to determine patient risk factors that are predictive of postoperative myocardial infarctions and cardiac arrests. This study sought to assess if there is an association between anatomic area and cardiac complications in the orthopaedic trauma patient. From 2006-2013, a total of 361,402 orthopaedic patients were identified in the NSQIP database using Current Procedural Terminology (CPT) codes. Of these, 56,336 (15.6%) patients were identified as orthopaedic trauma patients broken down by anatomic region: 11,905 (21.1%) upper extremity patients (UE), 29,009 (51.5%) hip/pelvis patients (HP), and 15,422 (27.4%) lower extremity patients (LE) using CPT codes. Patients were defined as having adverse cardiac events if they developed myocardial infarctions or cardiac arrests within 30days after surgery. Chi-squared analysis was used to determine if there was an association between anatomic area and rates of cardiac events. Multivariate logistical analysis was used with over 40 patient characteristics including age, gender, history of cardiac disease, and anatomic region as independent predictors to determine whether anatomic area significantly predicted the development of cardiac complications. There were significant differences in baseline demographics among the three groups: HP patients had the greatest average age (77.6 years) compared to 54.8 years for UE patients and 54.1 years in LE patients (p<0.001). HP patients also had the highest average ASA score (3.0) (p<0.001). There was a significant difference in adverse cardiac events based on anatomic area: 0.27% (32/11,905) UE patients developed cardiac complications compared to 2.15% (623/29,009) HP patients and 0.61% (94/15,422) LE patients. After multivariate analysis, HP patients were significantly more likely to develop cardiac complications compared to both UE patients (OR: 6.377, p=0.014) and LE patients (OR: 2.766, p=0.009). There is a significant difference in adverse cardiac events following orthopaedic trauma based on anatomic region. Hip/Pelvis surgery appeared to be a significant risk factor in developing an adverse cardiac event. Further studies should investigate why hip/pelvic patients are at a higher risk of adverse cardiac events. Copyright © 2016 Elsevier Ltd. All rights reserved.

KISTI at TREC 2014 Clinical Decision Support Track: Concept-based Document Re-ranking to Biomedical Information Retrieval

DTIC Science & Technology

2014-11-01

sematic type. Injury or Poisoning inpo T037 Anatomical Abnormality anab T190 Given a document D, a concept vector = {1, 2, … , ...integrating biomedical terminology . Nucleic acids research 32, Database issue (2004), 267–270. 5. Chapman, W.W., Hillert, D., Velupillai, S., et...Conference (TREC), (2011). 9. Koopman, B. and Zuccon, G. Understanding negation and family history to improve clinical information retrieval. Proceedings

Application of Deconvolution Algorithm of Point Spread Function in Improving Image Quality: An Observer Preference Study on Chest Radiography.

PubMed

Chae, Kum Ju; Goo, Jin Mo; Ahn, Su Yeon; Yoo, Jin Young; Yoon, Soon Ho

2018-01-01

To evaluate the preference of observers for image quality of chest radiography using the deconvolution algorithm of point spread function (PSF) (TRUVIEW ART algorithm, DRTECH Corp.) compared with that of original chest radiography for visualization of anatomic regions of the chest. Prospectively enrolled 50 pairs of posteroanterior chest radiographs collected with standard protocol and with additional TRUVIEW ART algorithm were compared by four chest radiologists. This algorithm corrects scattered signals generated by a scintillator. Readers independently evaluated the visibility of 10 anatomical regions and overall image quality with a 5-point scale of preference. The significance of the differences in reader's preference was tested with a Wilcoxon's signed rank test. All four readers preferred the images applied with the algorithm to those without algorithm for all 10 anatomical regions (mean, 3.6; range, 3.2-4.0; p < 0.001) and for the overall image quality (mean, 3.8; range, 3.3-4.0; p < 0.001). The most preferred anatomical regions were the azygoesophageal recess, thoracic spine, and unobscured lung. The visibility of chest anatomical structures applied with the deconvolution algorithm of PSF was superior to the original chest radiography.

Scaled Anatomical Model Creation of Biomedical Tomographic Imaging Data and Associated Labels for Subsequent Sub-surface Laser Engraving (SSLE) of Glass Crystals.

PubMed

Betts, Aislinn M; McGoldrick, Matthew T; Dethlefs, Christopher R; Piotrowicz, Justin; Van Avermaete, Tony; Maki, Jeff; Gerstler, Steve; Leevy, W M

2017-04-25

Biomedical imaging modalities like computed tomography (CT) and magnetic resonance (MR) provide excellent platforms for collecting three-dimensional data sets of patient or specimen anatomy in clinical or preclinical settings. However, the use of a virtual, on-screen display limits the ability of these tomographic images to fully convey the anatomical information embedded within. One solution is to interface a biomedical imaging data set with 3D printing technology to generate a physical replica. Here we detail a complementary method to visualize tomographic imaging data with a hand-held model: Sub Surface Laser Engraving (SSLE) of crystal glass. SSLE offers several unique benefits including: the facile ability to include anatomical labels, as well as a scale bar; streamlined multipart assembly of complex structures in one medium; high resolution in the X, Y, and Z planes; and semi-transparent shells for visualization of internal anatomical substructures. Here we demonstrate the process of SSLE with CT data sets derived from pre-clinical and clinical sources. This protocol will serve as a powerful and inexpensive new tool with which to visualize complex anatomical structures for scientists and students in a number of educational and research settings.

Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development.

PubMed

Rebeiz, Mark; Patel, Nipam H; Hinman, Veronica F

2015-01-01

The molecular and genetic basis for the evolution of anatomical diversity is a major question that has inspired evolutionary and developmental biologists for decades. Because morphology takes form during development, a true comprehension of how anatomical structures evolve requires an understanding of the evolutionary events that alter developmental genetic programs. Vast gene regulatory networks (GRNs) that connect transcription factors to their target regulatory sequences control gene expression in time and space and therefore determine the tissue-specific genetic programs that shape morphological structures. In recent years, many new examples have greatly advanced our understanding of the genetic alterations that modify GRNs to generate newly evolved morphologies. Here, we review several aspects of GRN evolution, including their deep preservation, their mechanisms of alteration, and how they originate to generate novel developmental programs.

NUCFRG2: An evaluation of the semiempirical nuclear fragmentation database

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Tripathi, R. K.; Cucinotta, F. A.; Shinn, J. L.; Badavi, F. F.; Chun, S. Y.; Norbury, J. W.; Zeitlin, C. J.; Heilbronn, L.; Miller, J.

1995-01-01

A semiempirical abrasion-ablation model has been successful in generating a large nuclear database for the study of high charge and energy (HZE) ion beams, radiation physics, and galactic cosmic ray shielding. The cross sections that are generated are compared with measured HZE fragmentation data from various experimental groups. A research program for improvement of the database generator is also discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van de Velde, Joris, E-mail: joris.vandevelde@ugent.be; Department of Radiotherapy, Ghent University, Ghent; Audenaert, Emmanuel

Purpose: To develop contouring guidelines for the brachial plexus (BP) using anatomically validated cadaver datasets. Magnetic resonance imaging (MRI) and computed tomography (CT) were used to obtain detailed visualizations of the BP region, with the goal of achieving maximal inclusion of the actual BP in a small contoured volume while also accommodating for anatomic variations. Methods and Materials: CT and MRI were obtained for 8 cadavers positioned for intensity modulated radiation therapy. 3-dimensional reconstructions of soft tissue (from MRI) and bone (from CT) were combined to create 8 separate enhanced CT project files. Dissection of the corresponding cadavers anatomically validatedmore » the reconstructions created. Seven enhanced CT project files were then automatically fitted, separately in different regions, to obtain a single dataset of superimposed BP regions that incorporated anatomic variations. From this dataset, improved BP contouring guidelines were developed. These guidelines were then applied to the 7 original CT project files and also to 1 additional file, left out from the superimposing procedure. The percentage of BP inclusion was compared with the published guidelines. Results: The anatomic validation procedure showed a high level of conformity for the BP regions examined between the 3-dimensional reconstructions generated and the dissected counterparts. Accurate and detailed BP contouring guidelines were developed, which provided corresponding guidance for each level in a clinical dataset. An average margin of 4.7 mm around the anatomically validated BP contour is sufficient to accommodate for anatomic variations. Using the new guidelines, 100% inclusion of the BP was achieved, compared with a mean inclusion of 37.75% when published guidelines were applied. Conclusion: Improved guidelines for BP delineation were developed using combined MRI and CT imaging with validation by anatomic dissection.« less

Pathology data integration with eXtensible Markup Language.

PubMed

Berman, Jules J

2005-02-01

It is impossible to overstate the importance of XML (eXtensible Markup Language) as a data organization tool. With XML, pathologists can annotate all of their data (clinical and anatomic) in a format that can transform every pathology report into a database, without compromising narrative structure. The purpose of this manuscript is to provide an overview of XML for pathologists. Examples will demonstrate how pathologists can use XML to annotate individual data elements and to structure reports in a common format that can be merged with other XML files or queried using standard XML tools. This manuscript gives pathologists a glimpse into how XML allows pathology data to be linked to other types of biomedical data and reduces our dependence on centralized proprietary databases.

Semi-Automated Trajectory Analysis of Deep Ballistic Penetrating Brain Injury

PubMed Central

Folio, Les; Solomon, Jeffrey; Biassou, Nadia; Fischer, Tatjana; Dworzak, Jenny; Raymont, Vanessa; Sinaii, Ninet; Wassermann, Eric M.; Grafman, Jordan

2016-01-01

Background Penetrating head injuries (PHIs) are common in combat operations and most have visible wound paths on computed tomography (CT). Objective We assess agreement between an automated trajectory analysis-based assessment of brain injury and manual tracings of encephalomalacia on CT. Methods We analyzed 80 head CTs with ballistic PHI from the Institutional Review Board approved Vietnam head injury registry. Anatomic reports were generated from spatial coordinates of projectile entrance and terminal fragment location. These were compared to manual tracings of the regions of encephalomalacia. Dice’s similarity coefficients, kappa, sensitivities, and specificities were calculated to assess agreement. Times required for case analysis were also compared. Results Results show high specificity of anatomic regions identified on CT with semiautomated anatomical estimates and manual tracings of tissue damage. Radiologist’s and medical students’ anatomic region reports were similar (Kappa 0.8, t-test p < 0.001). Region of probable injury modeling of involved brain structures was sensitive (0.7) and specific (0.9) compared with manually traced structures. Semiautomated analysis was 9-fold faster than manual tracings. Conclusion Our region of probable injury spatial model approximates anatomical regions of encephalomalacia from ballistic PHI with time-saving over manual methods. Results show potential for automated anatomical reporting as an adjunct to current practice of radiologist/neurosurgical review of brain injury by penetrating projectiles. PMID:23707123

Anatomical Regional Targeted (ART) BOTOX Injection Technique: A Novel Paradigm for Migraines and Chronic Headaches

PubMed Central

Sanniec, Kyle; Pezeshk, Ronnie; Chung, Michael

2016-01-01

Summary: Migraine headaches are a debilitating disease that causes significant socioeconomic problems. One of the speculated etiologies of the generation of migraines is peripheral nerve irritation at different trigger points. The use of Onabotulinum toxin A (BOTOX), although initially a novel approach, has now been determined to be a valid treatment for chronic headaches and migraines as described in the Phase III Research Evaluating Migraine Prophylaxis Therapy trials that prompted the approval by the Food and Drug Administration for treatment of chronic migraines. The injection paradigm established by this trial was one of a broad injection pattern across large muscle groups that did not always correspond to the anatomical locations of nerves. The senior author developed the Anatomical Regional Targeted BOTOX injection paradigm as an alternative to the current injection model. This technique targets both the anatomical location of nerves known to have causal effects with migraines and the region where the pain localizes, to provide relief across a wide distribution of the peripheral nerve. This article serves as a guide to the Anatomical Regional Targeted injection technique, which, to our knowledge, is the first comprehensive BOTOX injection paradigm described in the literature for treatment of migraines that targets nerves and nerve areas rather than purely muscle groups. This technique is based on the most up-to-date anatomical and scientific studies and large-volume migraine surgery experience. PMID:28293532

Technique of semiautomatic surface reconstruction of the visible Korean human data using commercial software.

PubMed

Park, Jin Seo; Shin, Dong Sun; Chung, Min Suk; Hwang, Sung Bae; Chung, Jinoh

2007-11-01

This article describes the technique of semiautomatic surface reconstruction of anatomic structures using widely available commercial software. This technique would enable researchers to promptly and objectively perform surface reconstruction, creating three-dimensional anatomic images without any assistance from computer engineers. To develop the technique, we used data from the Visible Korean Human project, which produced digitalized photographic serial images of an entire cadaver. We selected 114 anatomic structures (skin [1], bones [32], knee joint structures [7], muscles [60], arteries [7], and nerves [7]) from the 976 anatomic images which were generated from the left lower limb of the cadaver. Using Adobe Photoshop, the selected anatomic structures in each serial image were outlined, creating a segmented image. The Photoshop files were then converted into Adobe Illustrator files to prepare isolated segmented images, so that the contours of the structure could be viewed independent of the surrounding anatomy. Using Alias Maya, these isolated segmented images were then stacked to construct a contour image. Gaps between the contour lines were filled with surfaces, and three-dimensional surface reconstruction could be visualized with Rhinoceros. Surface imperfections were then corrected to complete the three-dimensional images in Alias Maya. We believe that the three-dimensional anatomic images created by these methods will have widespread application in both medical education and research. 2007 Wiley-Liss, Inc

BrainMap VBM: An environment for structural meta-analysis.

PubMed

Vanasse, Thomas J; Fox, P Mickle; Barron, Daniel S; Robertson, Michaela; Eickhoff, Simon B; Lancaster, Jack L; Fox, Peter T

2018-05-02

The BrainMap database is a community resource that curates peer-reviewed, coordinate-based human neuroimaging literature. By pairing the results of neuroimaging studies with their relevant meta-data, BrainMap facilitates coordinate-based meta-analysis (CBMA) of the neuroimaging literature en masse or at the level of experimental paradigm, clinical disease, or anatomic location. Initially dedicated to the functional, task-activation literature, BrainMap is now expanding to include voxel-based morphometry (VBM) studies in a separate sector, titled: BrainMap VBM. VBM is a whole-brain, voxel-wise method that measures significant structural differences between or within groups which are reported as standardized, peak x-y-z coordinates. Here we describe BrainMap VBM, including the meta-data structure, current data volume, and automated reverse inference functions (region-to-disease profile) of this new community resource. CBMA offers a robust methodology for retaining true-positive and excluding false-positive findings across studies in the VBM literature. As with BrainMap's functional database, BrainMap VBM may be synthesized en masse or at the level of clinical disease or anatomic location. As a use-case scenario for BrainMap VBM, we illustrate a trans-diagnostic data-mining procedure wherein we explore the underlying network structure of 2,002 experiments representing over 53,000 subjects through independent components analysis (ICA). To reduce data-redundancy effects inherent to any database, we demonstrate two data-filtering approaches that proved helpful to ICA. Finally, we apply hierarchical clustering analysis (HCA) to measure network- and disease-specificity. This procedure distinguished psychiatric from neurological diseases. We invite the neuroscientific community to further exploit BrainMap VBM with other modeling approaches. © 2018 Wiley Periodicals, Inc.

Pacemaker implantation rate after transcatheter aortic valve implantation with early and new-generation devices: a systematic review.

PubMed

van Rosendael, Philippe J; Delgado, Victoria; Bax, Jeroen J

2018-06-01

The incidence of new-onset conduction abnormalities requiring permanent pacemaker implantation (PPI) after transcatheter aortic valve implantation (TAVI) with new-generation prostheses remains debated. This systematic review analyses the incidence of PPI after TAVI with new-generation devices and evaluates the electrical, anatomical, and procedural factors associated with PPI. In addition, the incidence of PPI after TAVI with early generation prostheses was reviewed for comparison. According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses checklist, this systematic review screened original articles published between October 2010 and October 2017, reporting on the incidence of PPI after implantation of early and new-generation TAVI prostheses. Of the 1406 original articles identified in the first search for new-generation TAVI devices, 348 articles were examined for full text, and finally, 40 studies (n = 17 139) were included. The incidence of a PPI after the use of a new-generation TAVI prosthesis ranged between 2.3% and 36.1%. For balloon-expandable prostheses, the PPI rate remained low when using an early generation SAPIEN device (ranging between 2.3% and 28.2%), and with the new-generation SAPIEN 3 device, the PPI rate was between 4.0% and 24.0%. For self-expandable prostheses, the PPI rates were higher with the early generation CoreValve device (16.3-37.7%), and despite a reduction in PPI rates with the new Evolut R, the rates remained relatively higher (14.7-26.7%). When dividing the studies according to the highest (>26.0%) and the lowest (<12.1%) quintile of PPI rate, patients within the highest quintile were more frequently women when compared with the lowest quintile group (50.9% vs. 46.3%, P < 0.001). Pre-existent conduction abnormalities (electrical factor), calcification of the left ventricular outflow tract (anatomical factor), and balloon valvuloplasty and depth of implantation (procedural factors) were associated with increased risk of PPI. The rate of PPI after TAVI with new-generation devices is highly variable. Specific recommendations for implantation of each prosthesis, taking into consideration the presence of pre-existent conduction abnormalities and anatomical factors, may be needed to reduce the risk of PPI.

A population MRI brain template and analysis tools for the macaque.

PubMed

Seidlitz, Jakob; Sponheim, Caleb; Glen, Daniel; Ye, Frank Q; Saleem, Kadharbatcha S; Leopold, David A; Ungerleider, Leslie; Messinger, Adam

2018-04-15

The use of standard anatomical templates is common in human neuroimaging, as it facilitates data analysis and comparison across subjects and studies. For non-human primates, previous in vivo templates have lacked sufficient contrast to reliably validate known anatomical brain regions and have not provided tools for automated single-subject processing. Here we present the "National Institute of Mental Health Macaque Template", or NMT for short. The NMT is a high-resolution in vivo MRI template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, we generated maps of tissue segmentation and cortical thickness. Surface reconstructions and transformations to previously published digital brain atlases are also provided. We further provide an analysis pipeline using the NMT that automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies. Copyright © 2017 ElsevierCompany. All rights reserved.

Endodontic treatment of a maxillary first molar with seven root canals confirmed with cone beam computer tomography - case report.

PubMed

Martins, Jorge N R

2014-06-01

The most common configuration of the maxillary first molar is the presence of three roots and four root canals, although the presence of several other configurations have already been reported. The objective of this work is to present a rare anatomic configuration with seven root canals diagnosed during an endodontic therapy. Endodontic treatment was performed using a dental operating microscope. Exploring the grooves surrounding the main canals with ultrasonic troughing was able expose unexpected root canals. Instrumentation with files of smaller sizes and tapers was performed to prevent root physical weakness. The anatomic configuration was confirmed with a Cone Beam Computer Tomography image analysis which was able to clearly show the presence of seven root canals. An electronic database search was conducted to identify all the published similar cases and the best techniques to approach them are discussed.

Low-Dimensional Statistics of Anatomical Variability via Compact Representation of Image Deformations.

PubMed

Zhang, Miaomiao; Wells, William M; Golland, Polina

2016-10-01

Using image-based descriptors to investigate clinical hypotheses and therapeutic implications is challenging due to the notorious "curse of dimensionality" coupled with a small sample size. In this paper, we present a low-dimensional analysis of anatomical shape variability in the space of diffeomorphisms and demonstrate its benefits for clinical studies. To combat the high dimensionality of the deformation descriptors, we develop a probabilistic model of principal geodesic analysis in a bandlimited low-dimensional space that still captures the underlying variability of image data. We demonstrate the performance of our model on a set of 3D brain MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Our model yields a more compact representation of group variation at substantially lower computational cost than models based on the high-dimensional state-of-the-art approaches such as tangent space PCA (TPCA) and probabilistic principal geodesic analysis (PPGA).

The braingraph.org database of high resolution structural connectomes and the brain graph tools.

PubMed

Kerepesi, Csaba; Szalkai, Balázs; Varga, Bálint; Grolmusz, Vince

2017-10-01

Based on the data of the NIH-funded Human Connectome Project, we have computed structural connectomes of 426 human subjects in five different resolutions of 83, 129, 234, 463 and 1015 nodes and several edge weights. The graphs are given in anatomically annotated GraphML format that facilitates better further processing and visualization. For 96 subjects, the anatomically classified sub-graphs can also be accessed, formed from the vertices corresponding to distinct lobes or even smaller regions of interests of the brain. For example, one can easily download and study the connectomes, restricted to the frontal lobes or just to the left precuneus of 96 subjects using the data. Partially directed connectomes of 423 subjects are also available for download. We also present a GitHub-deposited set of tools, called the Brain Graph Tools, for several processing tasks of the connectomes on the site http://braingraph.org.

Comparing surgical infections in National Surgical Quality Improvement Project and an Institutional Database.

PubMed

Selby, Luke V; Sjoberg, Daniel D; Cassella, Danielle; Sovel, Mindy; Weiser, Martin R; Sepkowitz, Kent; Jones, David R; Strong, Vivian E

2015-06-15

Surgical quality improvement requires accurate tracking and benchmarking of postoperative adverse events. We track surgical site infections (SSIs) with two systems; our in-house surgical secondary events (SSE) database and the National Surgical Quality Improvement Project (NSQIP). The SSE database, a modification of the Clavien-Dindo classification, categorizes SSIs by their anatomic site, whereas NSQIP categorizes by their level. Our aim was to directly compare these different definitions. NSQIP and the SSE database entries for all surgeries performed in 2011 and 2012 were compared. To match NSQIP definitions, and while blinded to NSQIP results, entries in the SSE database were categorized as either incisional (superficial or deep) or organ space infections. These categorizations were compared with NSQIP records; agreement was assessed with Cohen kappa. The 5028 patients in our cohort had a 6.5% SSI in the SSE database and a 4% rate in NSQIP, with an overall agreement of 95% (kappa = 0.48, P < 0.0001). The rates of categorized infections were similarly well matched; incisional rates of 4.1% and 2.7% for the SSE database and NSQIP and organ space rates of 2.6% and 1.5%. Overall agreements were 96% (kappa = 0.36, P < 0.0001) and 98% (kappa = 0.55, P < 0.0001), respectively. Over 80% of cases recorded by the SSE database but not NSQIP did not meet NSQIP criteria. The SSE database is an accurate, real-time record of postoperative SSIs. Institutional databases that capture all surgical cases can be used in conjunction with NSQIP with excellent concordance. Copyright © 2015 Elsevier Inc. All rights reserved.

Generation of signature databases with fast codes

NASA Astrophysics Data System (ADS)

Bradford, Robert A.; Woodling, Arthur E.; Brazzell, James S.

1990-09-01

Using the FASTSIG signature code to generate optical signature databases for the Ground-based Surveillance and Traking System (GSTS) Program has improved the efficiency of the database generation process. The goal of the current GSTS database is to provide standardized, threat representative target signatures that can easily be used for acquisition and trk studies, discrimination algorithm development, and system simulations. Large databases, with as many as eight interpolalion parameters, are required to maintain the fidelity demands of discrimination and to generalize their application to other strateg systems. As the need increases for quick availability of long wave infrared (LWIR) target signatures for an evolving design4o-threat, FASTSIG has become a database generation alternative to using the industry standard OptiCal Signatures Code (OSC). FASTSIG, developed in 1985 to meet the unique strategic systems demands imposed by the discrimination function, has the significant advantage of being a faster running signature code than the OSC, typically requiring two percent of the cpu time. It uses analytical approximations to model axisymmetric targets, with the fidelity required for discrimination analysis. Access of the signature database is accomplished through use of the waveband integration and interpolation software, INTEG and SIGNAT. This paper gives details of this procedure as well as sample interpolated signatures and also covers sample verification by comparison to the OSC, in order to establish the fidelity of the FASTSIG generated database.

Low-contrast lesion detection in tomosynthetic breast imaging using a realistic breast phantom

NASA Astrophysics Data System (ADS)

Zhou, Lili; Oldan, Jorge; Fisher, Paul; Gindi, Gene

2006-03-01

Tomosynthesis mammography is a potentially valuable technique for detection of breast cancer. In this simulation study, we investigate the efficacy of three different tomographic reconstruction methods, EM, SART and Backprojection, in the context of an especially difficult mammographic detection task. The task is the detection of a very low-contrast mass embedded in very dense fibro-glandular tissue - a clinically useful task for which tomosynthesis may be well suited. The project uses an anatomically realistic 3D digital breast phantom whose normal anatomic variability limits lesion conspicuity. In order to capture anatomical object variability, we generate an ensemble of phantoms, each of which comprises random instances of various breast structures. We construct medium-sized 3D breast phantoms which model random instances of ductal structures, fibrous connective tissue, Cooper's ligaments and power law structural noise for small scale object variability. Random instances of 7-8 mm irregular masses are generated by a 3D random walk algorithm and placed in very dense fibro-glandular tissue. Several other components of the breast phantom are held fixed, i.e. not randomly generated. These include the fixed breast shape and size, nipple structure, fixed lesion location, and a pectoralis muscle. We collect low-dose data using an isocentric tomosynthetic geometry at 11 angles over 50 degrees and add Poisson noise. The data is reconstructed using the three algorithms. Reconstructed slices through the center of the lesion are presented to human observers in a 2AFC (two-alternative-forced-choice) test that measures detectability by computing AUC (area under the ROC curve). The data collected in each simulation includes two sources of variability, that due to the anatomical variability of the phantom and that due to the Poisson data noise. We found that for this difficult task that the AUC value for EM (0.89) was greater than that for SART (0.83) and Backprojection (0.66).

A case for bone canaliculi as the anatomical site of strain generated potentials

NASA Technical Reports Server (NTRS)

Cowin, S. C.; Weinbaum, S.; Zeng, Y.

1995-01-01

We address the question of determining the anatomical site that is the source of the experimentally observed strain generated potentials (SGPs) in bone tissue. There are two candidates for the anatomical site that is the SGP source, the collagen-hydroxyapatite porosity and the larger size lacunar-canalicular porosity. In the past it has been argued, on the basis of experimental data and a reasonable model, that the site of the SGPs in bone is the collagen-hydroxyapatite porosity. The theoretically predicted pore radius necessary for the SGPs to reside in this porosity is 16 nm, which is somewhat larger than the pore radii estimated from gas adsorption data where the preponderance of the pores were estimated to be in the range 5-12.5 nm. However, this pore size is significantly larger than the 2 nm size of the small tracer, microperoxidase, which appears to be excluded from the mineralized matrix. In this work a similar model, but one in which the effects of fluid dynamic drag of the cell surface matrix in the bone canaliculi are included, is used to show that it is possible for the generation of SGPs to be associated with the larger size lacunar-canalicular porosity when the hydraulic drag and electrokinetic contribution of the bone fluid passage through the cell coat (glycocalyx) is considered. The consistency of the SGP data with this model is demonstrated. A general boundary condition is introduced to allow for current leakage at the bone surface. The results suggest that the current leakage is small for the in vitro studies in which the strain generated potentials have been measured.

A reference dataset for deformable image registration spatial accuracy evaluation using the COPDgene study archive

NASA Astrophysics Data System (ADS)

Castillo, Richard; Castillo, Edward; Fuentes, David; Ahmad, Moiz; Wood, Abbie M.; Ludwig, Michelle S.; Guerrero, Thomas

2013-05-01

Landmark point-pairs provide a strategy to assess deformable image registration (DIR) accuracy in terms of the spatial registration of the underlying anatomy depicted in medical images. In this study, we propose to augment a publicly available database (www.dir-lab.com) of medical images with large sets of manually identified anatomic feature pairs between breath-hold computed tomography (BH-CT) images for DIR spatial accuracy evaluation. Ten BH-CT image pairs were randomly selected from the COPDgene study cases. Each patient had received CT imaging of the entire thorax in the supine position at one-fourth dose normal expiration and maximum effort full dose inspiration. Using dedicated in-house software, an imaging expert manually identified large sets of anatomic feature pairs between images. Estimates of inter- and intra-observer spatial variation in feature localization were determined by repeat measurements of multiple observers over subsets of randomly selected features. 7298 anatomic landmark features were manually paired between the 10 sets of images. Quantity of feature pairs per case ranged from 447 to 1172. Average 3D Euclidean landmark displacements varied substantially among cases, ranging from 12.29 (SD: 6.39) to 30.90 (SD: 14.05) mm. Repeat registration of uniformly sampled subsets of 150 landmarks for each case yielded estimates of observer localization error, which ranged in average from 0.58 (SD: 0.87) to 1.06 (SD: 2.38) mm for each case. The additions to the online web database (www.dir-lab.com) described in this work will broaden the applicability of the reference data, providing a freely available common dataset for targeted critical evaluation of DIR spatial accuracy performance in multiple clinical settings. Estimates of observer variance in feature localization suggest consistent spatial accuracy for all observers across both four-dimensional CT and COPDgene patient cohorts.

Scaled Anatomical Model Creation of Biomedical Tomographic Imaging Data and Associated Labels for Subsequent Sub-surface Laser Engraving (SSLE) of Glass Crystals

PubMed Central

Dethlefs, Christopher R.; Piotrowicz, Justin; Van Avermaete, Tony; Maki, Jeff; Gerstler, Steve; Leevy, W. M.

2017-01-01

Biomedical imaging modalities like computed tomography (CT) and magnetic resonance (MR) provide excellent platforms for collecting three-dimensional data sets of patient or specimen anatomy in clinical or preclinical settings. However, the use of a virtual, on-screen display limits the ability of these tomographic images to fully convey the anatomical information embedded within. One solution is to interface a biomedical imaging data set with 3D printing technology to generate a physical replica. Here we detail a complementary method to visualize tomographic imaging data with a hand-held model: Sub Surface Laser Engraving (SSLE) of crystal glass. SSLE offers several unique benefits including: the facile ability to include anatomical labels, as well as a scale bar; streamlined multipart assembly of complex structures in one medium; high resolution in the X, Y, and Z planes; and semi-transparent shells for visualization of internal anatomical substructures. Here we demonstrate the process of SSLE with CT data sets derived from pre-clinical and clinical sources. This protocol will serve as a powerful and inexpensive new tool with which to visualize complex anatomical structures for scientists and students in a number of educational and research settings. PMID:28518066

A Proposed Set of Metrics to Reduce Patient Safety Risk From Within the Anatomic Pathology Laboratory

PubMed Central

Banks, Peter; Brown, Richard; Laslowski, Alex; Daniels, Yvonne; Branton, Phil; Carpenter, John; Zarbo, Richard; Forsyth, Ramses; Liu, Yan-hui; Kohl, Shane; Diebold, Joachim; Masuda, Shinobu; Plummer, Tim

2017-01-01

Background: Anatomic pathology laboratory workflow consists of 3 major specimen handling processes. Among the workflow are preanalytic, analytic, and postanalytic phases that contain multistep subprocesses with great impact on patient care. A worldwide representation of experts came together to create a system of metrics, as a basis for laboratories worldwide, to help them evaluate and improve specimen handling to reduce patient safety risk. Method: Members of the Initiative for Anatomic Pathology Laboratory Patient Safety (IAPLPS) pooled their extensive expertise to generate a list of metrics highlighting processes with high and low risk for adverse patient outcomes. Results: Our group developed a universal, comprehensive list of 47 metrics for patient specimen handling in the anatomic pathology laboratory. Steps within the specimen workflow sequence are categorized as high or low risk. In general, steps associated with the potential for specimen misidentification correspond to the high-risk grouping and merit greater focus within quality management systems. Primarily workflow measures related to operational efficiency can be considered low risk. Conclusion: Our group intends to advance the widespread use of these metrics in anatomic pathology laboratories to reduce patient safety risk and improve patient care with development of best practices and interlaboratory error reporting programs. PMID:28340232

A Proposed Set of Metrics to Reduce Patient Safety Risk From Within the Anatomic Pathology Laboratory.

PubMed

Banks, Peter; Brown, Richard; Laslowski, Alex; Daniels, Yvonne; Branton, Phil; Carpenter, John; Zarbo, Richard; Forsyth, Ramses; Liu, Yan-Hui; Kohl, Shane; Diebold, Joachim; Masuda, Shinobu; Plummer, Tim; Dennis, Eslie

2017-05-01

Anatomic pathology laboratory workflow consists of 3 major specimen handling processes. Among the workflow are preanalytic, analytic, and postanalytic phases that contain multistep subprocesses with great impact on patient care. A worldwide representation of experts came together to create a system of metrics, as a basis for laboratories worldwide, to help them evaluate and improve specimen handling to reduce patient safety risk. Members of the Initiative for Anatomic Pathology Laboratory Patient Safety (IAPLPS) pooled their extensive expertise to generate a list of metrics highlighting processes with high and low risk for adverse patient outcomes. : Our group developed a universal, comprehensive list of 47 metrics for patient specimen handling in the anatomic pathology laboratory. Steps within the specimen workflow sequence are categorized as high or low risk. In general, steps associated with the potential for specimen misidentification correspond to the high-risk grouping and merit greater focus within quality management systems. Primarily workflow measures related to operational efficiency can be considered low risk. Our group intends to advance the widespread use of these metrics in anatomic pathology laboratories to reduce patient safety risk and improve patient care with development of best practices and interlaboratory error reporting programs. © American Society for Clinical Pathology 2017.

Validation and detection of vessel landmarks by using anatomical knowledge

NASA Astrophysics Data System (ADS)

Beck, Thomas; Bernhardt, Dominik; Biermann, Christina; Dillmann, Rüdiger

2010-03-01

The detection of anatomical landmarks is an important prerequisite to analyze medical images fully automatically. Several machine learning approaches have been proposed to parse 3D CT datasets and to determine the location of landmarks with associated uncertainty. However, it is a challenging task to incorporate high-level anatomical knowledge to improve these classification results. We propose a new approach to validate candidates for vessel bifurcation landmarks which is also applied to systematically search missed and to validate ambiguous landmarks. A knowledge base is trained providing human-readable geometric information of the vascular system, mainly vessel lengths, radii and curvature information, for validation of landmarks and to guide the search process. To analyze the bifurcation area surrounding a vessel landmark of interest, a new approach is proposed which is based on Fast Marching and incorporates anatomical information from the knowledge base. Using the proposed algorithms, an anatomical knowledge base has been generated based on 90 manually annotated CT images containing different parts of the body. To evaluate the landmark validation a set of 50 carotid datasets has been tested in combination with a state of the art landmark detector with excellent results. Beside the carotid bifurcation the algorithm is designed to handle a wide range of vascular landmarks, e.g. celiac, superior mesenteric, renal, aortic, iliac and femoral bifurcation.

Lifelike Vascular Reperfusion of a Thiel-Embalmed Pig Model and Evaluation as a Surgical Training Tool.

PubMed

Willaert, Wouter; Tozzi, Francesca; Van Hoof, Tom; Ceelen, Wim; Pattyn, Piet; D''Herde, Katharina

2016-01-01

Vascular reperfusion of Thiel cadavers can aid surgical and anatomical instruction. This study investigated whether ideal embalming circumstances provide lifelike vascular flow, enabling surgical practice and enhancing anatomical reality. Pressure-controlled pump-driven administration of blue embalming solution was assessed directly postmortem in a pig model (n = 4). Investigation of subsequent pump-driven vascular injection of red paraffinum perliquidum (PP) included assessment of flow parameters, intracorporeal distribution, anatomical alterations, and feasibility for surgical training. The microscopic distribution of PP was analyzed in pump-embalmed pig and gravity-embalmed human small intestines. Embalming lasted 50-105 min, and maximum arterial pressure was 65 mm Hg. During embalming, the following consecutive alterations were observed: arterial filling, organ coloration, venous perfusion, and further tissue coloration during the next weeks. Most organs were adequately preserved. PP generated low arterial pressures (<30 mm Hg) and drained through the venous cannula. Generally, realistic reperfusion and preservation of original anatomy were observed, but leakage in the pleural, abdominal, and retroperitoneal cavities occurred, and computed tomography showed edematous spleen and liver. Reduction of arterial flow rates after venous drainage is a prerequisite to prevent anatomical deformation, allowing simulation of various surgeries. In pump-embalmed pig small intestines, PP flowed from artery to vein through the capillaries without extravasation. In contrast, arterioles were blocked in gravity-embalmed human tissues. In a pig model, immediate postmortem pressure-controlled pump embalming generates ideal circumstances for (micro)vascular reperfusion with PP, permitting lifelike anatomy instruction and surgical training. © 2016 S. Karger AG, Basel.

[Functional anatomy of the male continence mechanism].

PubMed

Schwalenberg, T; Neuhaus, J; Dartsch, M; Weissenfels, P; Löffler, S; Stolzenburg, J-U

2010-04-01

The basic structures and organs contributing to continence in men are far less well investigated than in women. This concerns anatomical and functional aspects as well. Especially the cooperation of single components and the dynamic anchoring in the pelvic floor require further investigation. An improved anatomical-functional interpretation is needed to generate therapeutic concepts orientated at the physiology of the bladder neck.Therefore, the focus of anatomical investigations should be on the external sphincter which is the main muscle responsible for urethral closure as well as on the connective tissue, smooth muscular and neuronal structures in the pelvis. The smooth muscular structures involved are the internal sphincter, the inner parts of the external sphincter, the urethral longitudinal musculature, and parts of the centrum perinei and of the ventral suspension apparatus which fixes the position of the bladder neck and seems to be vital for continence and initiation of micturition. These new findings imply an integral concept for men as was developed for women. A first step in this regard would be a consistent and updated anatomical nomenclature.

Improved characterization of combat injury.

PubMed

Champion, Howard R; Holcomb, John B; Lawnick, Mary M; Kelliher, Timothy; Spott, Mary Ann; Galarneau, Michael R; Jenkins, Donald H; West, Susan A; Dye, Judy; Wade, Charles E; Eastridge, Brian J; Blackbourne, Lorne H; Shair, Ellen Kalin

2010-05-01

Combat injury patterns differ from civilian trauma in that the former are largely explosion-related, comprising multiple mechanistic and fragment injuries and high-kinetic-energy bullets. Further, unlike civilians, U.S. armed forces combatants are usually heavily protected with helmets and Kevlar body armor with ceramic plate inserts. Searchable databases providing actionable, statistically valid knowledge of body surface entry wounds and resulting organ injury severity are essential to understanding combat trauma. Two tools were developed to address these unique aspects of combat injury: (1) the Surface Wound Mapping (SWM) database and Surface Wound Analysis Tool (SWAT) software that were developed to generate 3D density maps of point-of-surface wound entry and resultant anatomic injury severity; and (2) the Abbreviated Injury Scale (AIS) 2005-Military that was developed by a panel of military trauma surgeons to account for multiple injury etiology from explosions and other high-kinetic- energy weapons. Combined data from the Joint Theater Trauma Registry, Navy/Marine Combat Trauma Registry, and the Armed Forces Medical Examiner System Mortality Trauma Registry were coded in AIS 2005-Military, entered into the SWM database, and analyzed for entrance site and wounding path. When data on 1,151 patients, who had a total of 3,500 surface wounds and 12,889 injuries, were entered into SWM, surface wounds averaged 3.0 per casualty and injuries averaged 11.2 per casualty. Of the 3,500 surface wounds, 2,496 (71%) were entrance wounds with 6,631 (51%) associated internal injuries, with 2.2 entrance wounds and 5.8 associated injuries per casualty (some details cannot be given because of operational security). Crude deaths rates were calculated using Maximum AIS-Military. These new tools have been successfully implemented to describe combat injury, mortality, and distribution of wounds and associated injuries. AIS 2005-Military is a more precise assignment of severity to military injuries. SWM has brought data from all three combat registries together into one analyzable database. SWM and SWAT allow visualization of wounds and associated injuries by region on a 3D model of the body.

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

PubMed

Guhlin, Joseph; Silverstein, Kevin A T; Zhou, Peng; Tiffin, Peter; Young, Nevin D

2017-08-10

Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data. The Omics Database Generator (ODG) allows users to create customized databases that utilize published genomics data integrated with experimental data which can be queried using a flexible graph database. When provided with omics and experimental data, ODG will create a comparative, multi-dimensional graph database. ODG can import definitions and annotations from other sources such as InterProScan, the Gene Ontology, ENZYME, UniPathway, and others. This annotation data can be especially useful for studying new or understudied species for which transcripts have only been predicted, and rapidly give additional layers of annotation to predicted genes. In better studied species, ODG can perform syntenic annotation translations or rapidly identify characteristics of a set of genes or nucleotide locations, such as hits from an association study. ODG provides a web-based user-interface for configuring the data import and for querying the database. Queries can also be run from the command-line and the database can be queried directly through programming language hooks available for most languages. ODG supports most common genomic formats as well as generic, easy to use tab-separated value format for user-provided annotations. ODG is a user-friendly database generation and query tool that adapts to the supplied data to produce a comparative genomic database or multi-layered annotation database. ODG provides rapid comparative genomic annotation and is therefore particularly useful for non-model or understudied species. For species for which more data are available, ODG can be used to conduct complex multi-omics, pattern-matching queries.

The anatomical relationship between the roots of mandibular second molars and the inferior alveolar nerve.

PubMed

Chong, B S; Quinn, A; Pawar, R R; Makdissi, J; Sidhu, S K

2015-06-01

To evaluate the anatomical relationship between the roots of mandibular second molars and the inferior alveolar nerve (IAN) in relation to the risk of potential nerve injury during root canal treatment. Cone-beam computed tomography (CBCT) images from the patient record database at a dental hospital were selected. The anonymized CBCT images were reconstructed and examined in three planes (coronal, axial and sagittal) using 3D viewing software. The relationship between each root apex of mandibular second molars and the IAN was evaluated by measuring the horizontal and vertical distances from coronal CBCT sections, and the actual distance was then calculated mathematically using Pythagoras' theorem. In 55% of the 272 mandibular second molar roots evaluated, from a total of 134 scans, the distance between the anatomical root apex and the IAN was ≤3 mm. In over 50% of the cases evaluated, there was an intimate relationship between the roots of mandibular second molars and the inferior alveolar nerve (IAN). Therefore, root canal treatment of mandibular second molars may pose a more significant potential risk of IAN injury; necessary precautions should be exercised, and the prudent use of CBCT should be considered if an intimate relationship is suspected. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Simplified three-dimensional model provides anatomical insights in lizards' caudal autotomy as printed illustration.

PubMed

De Amorim, Joana D C G; Travnik, Isadora; De Sousa, Bernadete M

2015-03-01

Lizards' caudal autotomy is a complex and vastly employed antipredator mechanism, with thorough anatomic adaptations involved. Due to its diminished size and intricate structures, vertebral anatomy is hard to be clearly conveyed to students and researchers of other areas. Three-dimensional models are prodigious tools in unveiling anatomical nuances. Some of the techniques used to create them can produce irregular and complicated forms, which despite being very accurate, lack didactical uniformity and simplicity. Since both are considered fundamental characteristics for comprehension, a simplified model could be the key to improve learning. The model here presented depicts the caudal osteology of Tropidurus itambere, and was designed to be concise, in order to be easily assimilated, yet complete, not to compromise the informative aspect. The creation process requires only basic skills in manipulating polygons in 3D modeling softwares, in addition to the appropriate knowledge of the structure to be modeled. As reference for the modeling, we used microscopic observation and a photograph database of the caudal structures. This way, no advanced laboratory equipment was needed and all biological materials were preserved for future research. Therefore, we propose a wider usage of simplified 3D models both in the classroom and as illustrations for scientific publications.

Variability sensitivity of dynamic texture based recognition in clinical CT data

NASA Astrophysics Data System (ADS)

Kwitt, Roland; Razzaque, Sharif; Lowell, Jeffrey; Aylward, Stephen

2014-03-01

Dynamic texture recognition using a database of template models has recently shown promising results for the task of localizing anatomical structures in Ultrasound video. In order to understand its clinical value, it is imperative to study the sensitivity with respect to inter-patient variability as well as sensitivity to acquisition parameters such as Ultrasound probe angle. Fully addressing patient and acquisition variability issues, however, would require a large database of clinical Ultrasound from many patients, acquired in a multitude of controlled conditions, e.g., using a tracked transducer. Since such data is not readily attainable, we advocate an alternative evaluation strategy using abdominal CT data as a surrogate. In this paper, we describe how to replicate Ultrasound variabilities by extracting subvolumes from CT and interpreting the image material as an ordered sequence of video frames. Utilizing this technique, and based on a database of abdominal CT from 45 patients, we report recognition results on an organ (kidney) recognition task, where we try to discriminate kidney subvolumes/videos from a collection of randomly sampled negative instances. We demonstrate that (1) dynamic texture recognition is relatively insensitive to inter-patient variation while (2) viewing angle variability needs to be accounted for in the template database. Since naively extending the template database to counteract variability issues can lead to impractical database sizes, we propose an alternative strategy based on automated identification of a small set of representative models.

An interactive three-dimensional virtual body structures system for anatomical training over the internet.

PubMed

Temkin, Bharti; Acosta, Eric; Malvankar, Ameya; Vaidyanath, Sreeram

2006-04-01

The Visible Human digital datasets make it possible to develop computer-based anatomical training systems that use virtual anatomical models (virtual body structures-VBS). Medical schools are combining these virtual training systems and classical anatomy teaching methods that use labeled images and cadaver dissection. In this paper we present a customizable web-based three-dimensional anatomy training system, W3D-VBS. W3D-VBS uses National Library of Medicine's (NLM) Visible Human Male datasets to interactively locate, explore, select, extract, highlight, label, and visualize, realistic 2D (using axial, coronal, and sagittal views) and 3D virtual structures. A real-time self-guided virtual tour of the entire body is designed to provide detailed anatomical information about structures, substructures, and proximal structures. The system thus facilitates learning of visuospatial relationships at a level of detail that may not be possible by any other means. The use of volumetric structures allows for repeated real-time virtual dissections, from any angle, at the convenience of the user. Volumetric (3D) virtual dissections are performed by adding, removing, highlighting, and labeling individual structures (and/or entire anatomical systems). The resultant virtual explorations (consisting of anatomical 2D/3D illustrations and animations), with user selected highlighting colors and label positions, can be saved and used for generating lesson plans and evaluation systems. Tracking users' progress using the evaluation system helps customize the curriculum, making W3D-VBS a powerful learning tool. Our plan is to incorporate other Visible Human segmented datasets, especially datasets with higher resolutions, that make it possible to include finer anatomical structures such as nerves and small vessels. (c) 2006 Wiley-Liss, Inc.

User`s and reference guide to the INEL RML/analytical radiochemistry sample tracking database version 1.00

DOE Office of Scientific and Technical Information (OSTI.GOV)

Femec, D.A.

This report discusses the sample tracking database in use at the Idaho National Engineering Laboratory (INEL) by the Radiation Measurements Laboratory (RML) and Analytical Radiochemistry. The database was designed in-house to meet the specific needs of the RML and Analytical Radiochemistry. The report consists of two parts, a user`s guide and a reference guide. The user`s guide presents some of the fundamentals needed by anyone who will be using the database via its user interface. The reference guide describes the design of both the database and the user interface. Briefly mentioned in the reference guide are the code-generating tools, CREATE-SCHEMAmore » and BUILD-SCREEN, written to automatically generate code for the database and its user interface. The appendices contain the input files used by the these tools to create code for the sample tracking database. The output files generated by these tools are also included in the appendices.« less

Algorithms and methodology used in constructing high-resolution terrain databases

NASA Astrophysics Data System (ADS)

Williams, Bryan L.; Wilkosz, Aaron

1998-07-01

This paper presents a top-level description of methods used to generate high-resolution 3D IR digital terrain databases using soft photogrammetry. The 3D IR database is derived from aerial photography and is made up of digital ground plane elevation map, vegetation height elevation map, material classification map, object data (tanks, buildings, etc.), and temperature radiance map. Steps required to generate some of these elements are outlined. The use of metric photogrammetry is discussed in the context of elevation map development; and methods employed to generate the material classification maps are given. The developed databases are used by the US Army Aviation and Missile Command to evaluate the performance of various missile systems. A discussion is also presented on database certification which consists of validation, verification, and accreditation procedures followed to certify that the developed databases give a true representation of the area of interest, and are fully compatible with the targeted digital simulators.

Generation of anatomically realistic numerical phantoms for photoacoustic and ultrasonic breast imaging

NASA Astrophysics Data System (ADS)

Lou, Yang; Zhou, Weimin; Matthews, Thomas P.; Appleton, Catherine M.; Anastasio, Mark A.

2017-04-01

Photoacoustic computed tomography (PACT) and ultrasound computed tomography (USCT) are emerging modalities for breast imaging. As in all emerging imaging technologies, computer-simulation studies play a critically important role in developing and optimizing the designs of hardware and image reconstruction methods for PACT and USCT. Using computer-simulations, the parameters of an imaging system can be systematically and comprehensively explored in a way that is generally not possible through experimentation. When conducting such studies, numerical phantoms are employed to represent the physical properties of the patient or object to-be-imaged that influence the measured image data. It is highly desirable to utilize numerical phantoms that are realistic, especially when task-based measures of image quality are to be utilized to guide system design. However, most reported computer-simulation studies of PACT and USCT breast imaging employ simple numerical phantoms that oversimplify the complex anatomical structures in the human female breast. We develop and implement a methodology for generating anatomically realistic numerical breast phantoms from clinical contrast-enhanced magnetic resonance imaging data. The phantoms will depict vascular structures and the volumetric distribution of different tissue types in the breast. By assigning optical and acoustic parameters to different tissue structures, both optical and acoustic breast phantoms will be established for use in PACT and USCT studies.

Two-Phase and Graph-Based Clustering Methods for Accurate and Efficient Segmentation of Large Mass Spectrometry Images.

PubMed

Dexter, Alex; Race, Alan M; Steven, Rory T; Barnes, Jennifer R; Hulme, Heather; Goodwin, Richard J A; Styles, Iain B; Bunch, Josephine

2017-11-07

Clustering is widely used in MSI to segment anatomical features and differentiate tissue types, but existing approaches are both CPU and memory-intensive, limiting their application to small, single data sets. We propose a new approach that uses a graph-based algorithm with a two-phase sampling method that overcomes this limitation. We demonstrate the algorithm on a range of sample types and show that it can segment anatomical features that are not identified using commonly employed algorithms in MSI, and we validate our results on synthetic MSI data. We show that the algorithm is robust to fluctuations in data quality by successfully clustering data with a designed-in variance using data acquired with varying laser fluence. Finally, we show that this method is capable of generating accurate segmentations of large MSI data sets acquired on the newest generation of MSI instruments and evaluate these results by comparison with histopathology.

Getting in touch--3D printing in forensic imaging.

PubMed

Ebert, Lars Chr; Thali, Michael J; Ross, Steffen

2011-09-10

With the increasing use of medical imaging in forensics, as well as the technological advances in rapid prototyping, we suggest combining these techniques to generate displays of forensic findings. We used computed tomography (CT), CT angiography, magnetic resonance imaging (MRI) and surface scanning with photogrammetry in conjunction with segmentation techniques to generate 3D polygon meshes. Based on these data sets, a 3D printer created colored models of the anatomical structures. Using this technique, we could create models of bone fractures, vessels, cardiac infarctions, ruptured organs as well as bitemark wounds. The final models are anatomically accurate, fully colored representations of bones, vessels and soft tissue, and they demonstrate radiologically visible pathologies. The models are more easily understood by laypersons than volume rendering or 2D reconstructions. Therefore, they are suitable for presentations in courtrooms and for educational purposes. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Diffeomorphometry and geodesic positioning systems for human anatomy.

PubMed

Miller, Michael I; Younes, Laurent; Trouvé, Alain

2014-03-01

The Computational Anatomy project has largely been a study of large deformations within a Riemannian framework as an efficient point of view for generating metrics between anatomical configurations. This approach turns D'Arcy Thompson's comparative morphology of human biological shape and form into a metrizable space. Since the metric is constructed based on the geodesic length of the flows of diffeomorphisms connecting the forms, we call it diffeomorphometry . Just as importantly, since the flows describe algebraic group action on anatomical submanifolds and associated functional measurements, they become the basis for positioning information, which we term geodesic positioning . As well the geodesic connections provide Riemannian coordinates for locating forms in the anatomical orbit, which we call geodesic coordinates . These three components taken together - the metric, geodesic positioning of information, and geodesic coordinates - we term the geodesic positioning system . We illustrate via several examples in human and biological coordinate systems and machine learning of the statistical representation of shape and form.

The Anatomical Society core regional anatomy syllabus for undergraduate medicine.

PubMed

Smith, C F; Finn, G M; Stewart, J; Atkinson, M A; Davies, D C; Dyball, R; Morris, J; Ockleford, C; Parkin, I; Standring, S; Whiten, S; Wilton, J; McHanwell, S

2016-01-01

The Anatomical Society's core syllabus for anatomy (2003 and later refined in 2007) set out a series of learning outcomes that an individual medical student should achieve on graduation. The core syllabus, with 182 learning outcomes grouped in body regions, referenced in the General Medical Council's Teaching Tomorrow's Doctors, was open to criticism on the grounds that the learning outcomes were generated by a relatively small group of anatomists, albeit some of whom were clinically qualified. We have therefore used a modified Delphi technique to seek a wider consensus. A Delphi panel was constructed involving 'experts' (n = 39). The revised core syllabus of 156 learning outcomes presented here is applicable to all medical programmes and may be used by curriculum planners, teachers and students alike in addressing the perennial question: 'What do I need to know ?' © 2015 Anatomical Society.

Comparative Vibration Levels Perceived Among Species in a Laboratory Animal Facility

PubMed Central

Norton, John N; Kinard, Will L; Reynolds, Randall P

2011-01-01

The current study was performed to determine the vibration levels that were generated in cages on a ventilated rack by common construction equipment in frequency ranges likely to be perceived by humans, rats, and mice. Vibration generated by the ventilated rack blower caused small but significant increases in some of the abdominal, thoracic, and head resonance frequency ranges (RFR) and sensitivity frequency ranges (SFR) in which each species is most likely to be affected by and perceive vibration, respectively. Vibration caused by various items of construction equipment at 3 ft from the cage were evaluated relative to the RFR and SFR of humans, rats, and mice in 3 anatomic locations. In addition, the vibration levels in the RFR and SFR that resulted from the use of a large jackhammer and were measured at various locations and distances in the facility and evaluated in terms of humans, rats, and mice in 3 anatomic locations. Taken together, the data indicate that a given vibration source generates vibration in frequency ranges that are more likely to affect rats and mice as compared with humans. PMID:22330711

Autologous temporomandibular joint reconstruction independent of exogenous additives: a proof-of-concept study for guided self-generation.

PubMed

Wei, Jiao; Herrler, Tanja; Han, Dong; Liu, Kai; Huang, Rulin; Guba, Markus; Dai, Chuanchang; Li, Qingfeng

2016-11-28

Joint defects are complex and difficult to reconstruct. By exploiting the body's own regenerative capacity, we aimed to individually generate anatomically precise neo-tissue constructs for autologous joint reconstruction without using any exogenous additives. In a goat model, CT scans of the mandibular condyle including articular surface and a large portion of the ascending ramus were processed using computer-aided design and manufacturing. A corresponding hydroxylapatite negative mold was printed in 3D and temporarily embedded into the transition zone of costal periosteum and perichondrium. A demineralized bone matrix scaffold implanted on the contralateral side served as control. Neo-tissue constructs obtained by guided self-generation exhibited accurate configuration, robust vascularization, biomechanical stability, and function. After autologous replacement surgery, the constructs showed stable results with similar anatomical, histological, and functional findings compared to native controls. Further studies are required to assess long-term outcome and possible extensions to other further applications. The absence of exogenous cells, growth factors, and scaffolds may facilitate clinical translation of this approach.

Autologous temporomandibular joint reconstruction independent of exogenous additives: a proof-of-concept study for guided self-generation

PubMed Central

Wei, Jiao; Herrler, Tanja; Han, Dong; Liu, Kai; Huang, Rulin; Guba, Markus; Dai, Chuanchang; Li, Qingfeng

2016-01-01

Joint defects are complex and difficult to reconstruct. By exploiting the body’s own regenerative capacity, we aimed to individually generate anatomically precise neo-tissue constructs for autologous joint reconstruction without using any exogenous additives. In a goat model, CT scans of the mandibular condyle including articular surface and a large portion of the ascending ramus were processed using computer-aided design and manufacturing. A corresponding hydroxylapatite negative mold was printed in 3D and temporarily embedded into the transition zone of costal periosteum and perichondrium. A demineralized bone matrix scaffold implanted on the contralateral side served as control. Neo-tissue constructs obtained by guided self-generation exhibited accurate configuration, robust vascularization, biomechanical stability, and function. After autologous replacement surgery, the constructs showed stable results with similar anatomical, histological, and functional findings compared to native controls. Further studies are required to assess long-term outcome and possible extensions to other further applications. The absence of exogenous cells, growth factors, and scaffolds may facilitate clinical translation of this approach. PMID:27892493

Zero ischemia anatomical partial nephrectomy: a novel approach.

PubMed

Gill, Inderbir S; Patil, Mukul B; Abreu, Andre Luis de Castro; Ng, Casey; Cai, Jie; Berger, Andre; Eisenberg, Manuel S; Nakamoto, Masahiko; Ukimura, Osamu; Goh, Alvin C; Thangathurai, Duraiyah; Aron, Monish; Desai, Mihir M

2012-03-01

We present a novel concept of zero ischemia anatomical robotic and laparoscopic partial nephrectomy. Our technique primarily involves anatomical vascular microdissection and preemptive control of tumor specific, tertiary or higher order renal arterial branch(es) using neurosurgical aneurysm micro-bulldog clamps. In 58 consecutive patients the majority (70%) had anatomically complex tumors including central (67%), hilar (26%), completely intrarenal (23%), pT1b (18%) and solitary kidney (7%). Data were prospectively collected and analyzed from an institutional review board approved database. Of 58 cases undergoing zero ischemia robotic (15) or laparoscopic (43) partial nephrectomy, 57 (98%) were completed without hilar clamping. Mean tumor size was 3.2 cm, mean ± SD R.E.N.A.L. score 7.0 ± 1.9, C-index 2.9 ± 2.4, operative time 4.4 hours, blood loss 206 cc and hospital stay 3.9 days. There were no intraoperative complications. Postoperative complications (22.8%) were low grade (Clavien grade 1 to 2) in 19.3% and high grade (Clavien grade 3 to 5) in 3.5%. All patients had negative cancer surgical margins (100%). Mean absolute and percent change in preoperative vs 4-month postoperative serum creatinine (0.2 mg/dl, 18%), estimated glomerular filtration rate (-11.4 ml/minute/1.73 m(2), 13%), and ipsilateral kidney function on radionuclide scanning at 6 months (-10%) correlated with mean percent kidney excised intraoperatively (18%). Although 21% of patients received a perioperative blood transfusion, no patient had acute or delayed renal hemorrhage, or lost a kidney. The concept of zero ischemia robotic and laparoscopic partial nephrectomy is presented. This anatomical vascular microdissection of the artery first and then tumor allows even complex tumors to be excised without hilar clamping. Global surgical renal ischemia is unnecessary for the majority of patients undergoing robotic and laparoscopic partial nephrectomy at our institution. Copyright © 2012 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Reconfigurable Image Generator

NASA Technical Reports Server (NTRS)

Archdeacon, John L. (Inventor); Iwai, Nelson H. (Inventor); Kato, Kenji H. (Inventor); Sweet, Barbara T. (Inventor)

2017-01-01

A RiG may simulate visual conditions of a real world environment, and generate the necessary amount of pixels in a visual simulation at rates up to 120 frames per second. RiG may also include a database generation system capable of producing visual databases suitable to drive the visual fidelity required by the RiG.

Generators of the brainstem auditory evoked potential in cat. I. An experimental approach to their identification.

PubMed

Melcher, J R; Knudson, I M; Fullerton, B C; Guinan, J J; Norris, B E; Kiang, N Y

1996-04-01

This paper is the first in a series aimed at identifying the cellular generators of the brainstem auditory evoked potential (BAEP) in cats. The approach involves (1) developing experimental procedures for making small selective lesions and determining the corresponding changes in BAEP waveforms, (2) identifying brainstem regions involved in BAEP generation by examining the effects of lesions on the BAEP and (3) identifying specific cell populations involved by combining the lesion results with electrophysiological and anatomical information from other kinds of studies. We created lesions in the lower brainstem by injecting kainic acid which is generally toxic for neuronal cell bodies but not for axons and terminals. This first paper describes the justifications for using kainic acid, explains the associated problems, and develops a methodology that addresses the main difficulties. The issues and aspects of the specific methods are generally applicable to physiological and anatomical studies using any neurotoxin, as well as to the present BAEP study. The methods chosen involved (1) measuring the BAEP at regular intervals until it reached a post-injection steady state and perfusing the animals with fixative shortly after the last BAEP recordings were made, (2) using objective criteria to distinguish injection-related BAEP changes from unrelated ones, (3) making control injections to identify effects not due to kainic acid toxicity, (4) verifying the anatomical and functional integrity of axons in lesioned regions, and (5) examining injected brainstems microscopically for cell loss and cellular abnormalities indicating dysfunction. This combination of methods enabled us to identify BAEP changes which are clearly correlated with lesion locations.

Opioid hedonic hotspot in nucleus accumbens shell: mu, delta, and kappa maps for enhancement of sweetness "liking" and "wanting".

PubMed

Castro, Daniel C; Berridge, Kent C

2014-03-19

A specialized cubic-millimeter hotspot in the rostrodorsal quadrant of medial shell in nucleus accumbens (NAc) of rats may mediate opioid enhancement of gustatory hedonic impact or "liking". Here, we selectively stimulated the three major subtypes of opioid receptors via agonist microinjections [mu (DAMGO), delta (DPDPE), or kappa (U50488H)] and constructed anatomical maps for functional localizations of consequent changes in hedonic "liking" (assessed by affective orofacial reactions to sucrose taste) versus "wanting" (assessed by changes in food intake). Results indicated that the NAc rostrodorsal quadrant contains a shared opioid hedonic hotspot that similarly mediates enhancements of sucrose "liking" for mu, delta, and kappa stimulations. Within the rostrodorsal hotspot boundaries each type of stimulation generated at least a doubling or higher enhancement of hedonic reactions, with comparable intensities for all three types of opioid stimulation. By contrast, a negative hedonic coldspot was mapped in the caudal half of medial shell, where all three types of opioid stimulation suppressed "liking" reactions to approximately one-half normal levels. Different anatomical patterns were produced for stimulation of food "wanting", reflected in food intake. Altogether, these results indicate that the rostrodorsal hotspot in medial shell is unique for generating opioid-induced hedonic enhancement, and add delta and kappa signals to mu as hedonic generators within the hotspot. Also, the identification of a separable NAc caudal coldspot for hedonic suppression, and separate NAc opioid mechanisms for controlling food "liking" versus "wanting" further highlights NAc anatomical heterogeneity and localizations of function within subregions of medial shell.

Localization of Broca's Area Using Functional MR Imaging: Quantitative Evaluation of Paradigms.

PubMed

Kim, Chi Heon; Kim, Jae-Hun; Chung, Chun Kee; Kim, June Sic; Lee, Jong-Min; Lee, Sang Kun

2009-04-01

Functional magnetic resonance imaging (fMRI) is frequently used to localize language areas in a non-invasive manner. Various paradigms for presurgical localization of language areas have been developed, but a systematic quantitative evaluation of the efficiency of those paradigms has not been performed. In the present study, the authors analyzed different language paradigms to see which paradigm is most efficient in localizing frontal language areas. Five men and five women with no neurological deficits participated (mean age, 24 years) in this study. All volunteers were right-handed. Each subject performed 4 tasks, including fixation (Fix), sentence reading (SR), pseudoword reading (PR), and word generation (WG). Fixation and pseudoword reading were used as contrasts. The functional area was defined as the area(s) with a t-value of more than 3.92 in fMRI with different tasks. To apply an anatomical constraint, we used a brain atlas mapping system, which is available in AFNI, to define the anatomical frontal language area. The numbers of voxels in overlapped area between anatomical and functional area were individually counted in the frontal expressive language area. Of the various combinations, the word generation task was most effective in delineating the frontal expressive language area when fixation was used as a contrast (p<0.05). The sensitivity of this test for localizing Broca's area was 81% and specificity was 70%. Word generation versus fixation could effectively and reliably delineate the frontal language area. A customized effective paradigm should be analyzed in order to evaluate various language functions.

Version 1.00 programmer`s tools used in constructing the INEL RML/analytical radiochemistry sample tracking database and its user interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Femec, D.A.

This report describes two code-generating tools used to speed design and implementation of relational databases and user interfaces: CREATE-SCHEMA and BUILD-SCREEN. CREATE-SCHEMA produces the SQL commands that actually create and define the database. BUILD-SCREEN takes templates for data entry screens and generates the screen management system routine calls to display the desired screen. Both tools also generate the related FORTRAN declaration statements and precompiled SQL calls. Included with this report is the source code for a number of FORTRAN routines and functions used by the user interface. This code is broadly applicable to a number of different databases.

Automated segmentation and recognition of the bone structure in non-contrast torso CT images using implicit anatomical knowledge

NASA Astrophysics Data System (ADS)

Zhou, X.; Hayashi, T.; Han, M.; Chen, H.; Hara, T.; Fujita, H.; Yokoyama, R.; Kanematsu, M.; Hoshi, H.

2009-02-01

X-ray CT images have been widely used in clinical diagnosis in recent years. A modern CT scanner can generate about 1000 CT slices to show the details of all the human organs within 30 seconds. However, CT image interpretations (viewing 500-1000 slices of CT images manually in front of a screen or films for each patient) require a lot of time and energy. Therefore, computer-aided diagnosis (CAD) systems that can support CT image interpretations are strongly anticipated. Automated recognition of the anatomical structures in CT images is a basic pre-processing of the CAD system. The bone structure is a part of anatomical structures and very useful to act as the landmarks for predictions of the other different organ positions. However, the automated recognition of the bone structure is still a challenging issue. This research proposes an automated scheme for segmenting the bone regions and recognizing the bone structure in noncontrast torso CT images. The proposed scheme was applied to 48 torso CT cases and a subjective evaluation for the experimental results was carried out by an anatomical expert following the anatomical definition. The experimental results showed that the bone structure in 90% CT cases have been recognized correctly. For quantitative evaluation, automated recognition results were compared to manual inputs of bones of lower limb created by an anatomical expert on 10 randomly selected CT cases. The error (maximum distance in 3D) between the recognition results and manual inputs distributed from 3-8 mm in different parts of the bone regions.

Development of a femoral template for computer-assisted tunnel placement in anatomical double-bundle ACL reconstruction.

PubMed

Luites, J W H; Wymenga, A B; Blankevoort, L; Kooloos, J M G; Verdonschot, N

2011-01-01

Femoral graft placement is an important factor in the success of anterior cruciate ligament (ACL) reconstruction. In addition to improving the accuracy of femoral tunnel placement, Computer Assisted Surgery (CAS) can be used to determine the anatomic location. This is achieved by using a 3D femoral template which indicates the position of the anatomical ACL center based on endoscopically measurable landmarks. This study describes the development and application of this method. The template is generated through statistical shape analysis of the ACL insertion, with respect to the anteromedial (AM) and posterolateral (PL) bundles. The ligament insertion data, together with the osteocartilage edge on the lateral notch, were mapped onto a cylinder fitted to the intercondylar notch surface (n = 33). Anatomic variation, in terms of standard variation of the positions of the ligament centers in the template, was within 2.2 mm. The resulting template was programmed in a computer-assisted navigation system for ACL replacement and its accuracy and precision were determined on 31 femora. It was found that with the navigation system the AM and PL tunnels could be positioned with an accuracy of 2.5 mm relative to the anatomic insertion centers; the precision was 2.4 mm. This system consists of a template that can easily be implemented in 3D computer navigation software. Requiring no preoperative images and planning, the system provides adequate accuracy and precision to position the entrance of the femoral tunnels for anatomical single- or double-bundle ACL reconstruction.

Altered gray matter organization in children and adolescents with ADHD: a structural covariance connectome study

PubMed Central

Griffiths, K R; Grieve, S M; Kohn, M R; Clarke, S; Williams, L M; Korgaonkar, M S

2016-01-01

Although multiple studies have reported structural deficits in multiple brain regions in attention-deficit hyperactivity disorder (ADHD), we do not yet know if these deficits reflect a more systematic disruption to the anatomical organization of large-scale brain networks. Here we used a graph theoretical approach to quantify anatomical organization in children and adolescents with ADHD. We generated anatomical networks based on covariance of gray matter volumes from 92 regions across the brain in children and adolescents with ADHD (n=34) and age- and sex-matched healthy controls (n=28). Using graph theory, we computed metrics that characterize both the global organization of anatomical networks (interconnectivity (clustering), integration (path length) and balance of global integration and localized segregation (small-worldness)) and their local nodal measures (participation (degree) and interaction (betweenness) within a network). Relative to Controls, ADHD participants exhibited altered global organization reflected in more clustering or network segregation. Locally, nodal degree and betweenness were increased in the subcortical amygdalae in ADHD, but reduced in cortical nodes in the anterior cingulate, posterior cingulate, mid temporal pole and rolandic operculum. In ADHD, anatomical networks were disrupted and reflected an emphasis on subcortical local connections centered around the amygdala, at the expense of cortical organization. Brains of children and adolescents with ADHD may be anatomically configured to respond impulsively to the automatic significance of stimulus input without having the neural organization to regulate and inhibit these responses. These findings provide a novel addition to our current understanding of the ADHD connectome. PMID:27824356

A “loop” shape descriptor and its application to automated segmentation of airways from CT scans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pu, Jiantao; Jin, Chenwang, E-mail: jcw76@163.com; Yu, Nan

2015-06-15

Purpose: A novel shape descriptor is presented to aid an automated identification of the airways depicted on computed tomography (CT) images. Methods: Instead of simplifying the tubular characteristic of the airways as an ideal mathematical cylindrical or circular shape, the proposed “loop” shape descriptor exploits the fact that the cross sections of any tubular structure (regardless of its regularity) always appear as a loop. In implementation, the authors first reconstruct the anatomical structures in volumetric CT as a three-dimensional surface model using the classical marching cubes algorithm. Then, the loop descriptor is applied to locate the airways with a concavemore » loop cross section. To deal with the variation of the airway walls in density as depicted on CT images, a multiple threshold strategy is proposed. A publicly available chest CT database consisting of 20 CT scans, which was designed specifically for evaluating an airway segmentation algorithm, was used for quantitative performance assessment. Measures, including length, branch count, and generations, were computed under the aid of a skeletonization operation. Results: For the test dataset, the airway length ranged from 64.6 to 429.8 cm, the generation ranged from 7 to 11, and the branch number ranged from 48 to 312. These results were comparable to the performance of the state-of-the-art algorithms validated on the same dataset. Conclusions: The authors’ quantitative experiment demonstrated the feasibility and reliability of the developed shape descriptor in identifying lung airways.« less

The new vestibular stimuli: sound and vibration-anatomical, physiological and clinical evidence.

PubMed

Curthoys, Ian S

2017-04-01

The classical view of the otoliths-as flat plates of fairly uniform receptors activated by linear acceleration dragging on otoconia and so deflecting the receptor hair bundles-has been replaced by new anatomical and physiological evidence which shows that the maculae are much more complex. There is anatomical spatial differentiation across the macula in terms of receptor types, hair bundle heights, stiffness and attachment to the overlying otolithic membrane. This anatomical spatial differentiation corresponds to the neural spatial differentiation of response dynamics from the receptors and afferents from different regions of the otolithic maculae. Specifically, receptors in a specialized band of cells, the striola, are predominantly type I receptors, with short, stiff hair bundles and looser attachment to the overlying otoconial membrane than extrastriolar receptors. At the striola the hair bundles project into holes in the otolithic membrane, allowing for fluid displacement to deflect the hair bundles and activate the cell. This review shows the anatomical and physiological evidence supporting the hypothesis that fluid displacement, generated by sound or vibration, deflects the short stiff hair bundles of type I receptors at the striola, resulting in neural activation of the irregular afferents innervating them. So these afferents are activated by sound or vibration and show phase-locking to individual cycles of the sound or vibration stimulus up to frequencies above 2000 Hz, underpinning the use of sound and vibration for clinical tests of vestibular function.

Patient feature based dosimetric Pareto front prediction in esophageal cancer radiotherapy.

PubMed

Wang, Jiazhou; Jin, Xiance; Zhao, Kuaike; Peng, Jiayuan; Xie, Jiang; Chen, Junchao; Zhang, Zhen; Studenski, Matthew; Hu, Weigang

2015-02-01

To investigate the feasibility of the dosimetric Pareto front (PF) prediction based on patient's anatomic and dosimetric parameters for esophageal cancer patients. Eighty esophagus patients in the authors' institution were enrolled in this study. A total of 2928 intensity-modulated radiotherapy plans were obtained and used to generate PF for each patient. On average, each patient had 36.6 plans. The anatomic and dosimetric features were extracted from these plans. The mean lung dose (MLD), mean heart dose (MHD), spinal cord max dose, and PTV homogeneity index were recorded for each plan. Principal component analysis was used to extract overlap volume histogram (OVH) features between PTV and other organs at risk. The full dataset was separated into two parts; a training dataset and a validation dataset. The prediction outcomes were the MHD and MLD. The spearman's rank correlation coefficient was used to evaluate the correlation between the anatomical features and dosimetric features. The stepwise multiple regression method was used to fit the PF. The cross validation method was used to evaluate the model. With 1000 repetitions, the mean prediction error of the MHD was 469 cGy. The most correlated factor was the first principal components of the OVH between heart and PTV and the overlap between heart and PTV in Z-axis. The mean prediction error of the MLD was 284 cGy. The most correlated factors were the first principal components of the OVH between heart and PTV and the overlap between lung and PTV in Z-axis. It is feasible to use patients' anatomic and dosimetric features to generate a predicted Pareto front. Additional samples and further studies are required improve the prediction model.

TU-C-17A-10: Patient Features Based Dosimetric Pareto Front Prediction In Esophagus Cancer Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, J; Zhao, K; Peng, J

2014-06-15

Purpose: The purpose of this study is to study the feasibility of the dosimetric pareto front (PF) prediction based on patient anatomic and dosimetric parameters for esophagus cancer patients. Methods: Sixty esophagus patients in our institution were enrolled in this study. A total 2920 IMRT plans were created to generated PF for each patient. On average, each patient had 48 plans. The anatomic and dosimetric features were extracted from those plans. The mean lung dose (MLD), mean heart dose (MHD), spinal cord max dose and PTV homogeneous index (PTVHI) were recorded for each plan. The principal component analysis (PCA) wasmore » used to extract overlap volume histogram (OVH) features between PTV and other critical organs. The full dataset was separated into two parts include the training dataset and the validation dataset. The prediction outcomes were the MHD and MLD for the current study. The spearman rank correlation coefficient was used to evaluate the correlation between the anatomical features and dosimetric features. The PF was fit by the the stepwise multiple regression method. The cross-validation method was used to evaluation the model. Results: The mean prediction error of the MHD was 465 cGy with 100 repetitions. The most correlated factors were the first principal components of the OVH between heart and PTV, and the overlap between heart and PTV in Z-axis. The mean prediction error of the MLD was 195 cGy. The most correlated factors were the first principal components of the OVH between lung and PTV, and the overlap between lung and PTV in Z-axis. Conclusion: It is feasible to use patients anatomic and dosimetric features to generate a predicted PF. Additional samples and further studies were required to get a better prediction model.« less

Patient feature based dosimetric Pareto front prediction in esophageal cancer radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jiazhou; Zhao, Kuaike; Peng, Jiayuan

2015-02-15

Purpose: To investigate the feasibility of the dosimetric Pareto front (PF) prediction based on patient’s anatomic and dosimetric parameters for esophageal cancer patients. Methods: Eighty esophagus patients in the authors’ institution were enrolled in this study. A total of 2928 intensity-modulated radiotherapy plans were obtained and used to generate PF for each patient. On average, each patient had 36.6 plans. The anatomic and dosimetric features were extracted from these plans. The mean lung dose (MLD), mean heart dose (MHD), spinal cord max dose, and PTV homogeneity index were recorded for each plan. Principal component analysis was used to extract overlapmore » volume histogram (OVH) features between PTV and other organs at risk. The full dataset was separated into two parts; a training dataset and a validation dataset. The prediction outcomes were the MHD and MLD. The spearman’s rank correlation coefficient was used to evaluate the correlation between the anatomical features and dosimetric features. The stepwise multiple regression method was used to fit the PF. The cross validation method was used to evaluate the model. Results: With 1000 repetitions, the mean prediction error of the MHD was 469 cGy. The most correlated factor was the first principal components of the OVH between heart and PTV and the overlap between heart and PTV in Z-axis. The mean prediction error of the MLD was 284 cGy. The most correlated factors were the first principal components of the OVH between heart and PTV and the overlap between lung and PTV in Z-axis. Conclusions: It is feasible to use patients’ anatomic and dosimetric features to generate a predicted Pareto front. Additional samples and further studies are required improve the prediction model.« less

Comprehensive BRL-CAD Primitive Database

DTIC Science & Technology

2015-03-01

are not to be construed as an official Department of the Army position unless so designated by other authorized documents. Citation of...database provides the target describers of BRL–CAD with a representative example of each primitive’s shape and its properties. In addition to the...database was completed, a tool was created to generate primitive shapes automatically. This provides target describers—CAD experts who generate

A universal algorithm for an improved finite element mesh generation Mesh quality assessment in comparison to former automated mesh-generators and an analytic model.

PubMed

Kaminsky, Jan; Rodt, Thomas; Gharabaghi, Alireza; Forster, Jan; Brand, Gerd; Samii, Madjid

2005-06-01

The FE-modeling of complex anatomical structures is not solved satisfyingly so far. Voxel-based as opposed to contour-based algorithms allow an automated mesh generation based on the image data. Nonetheless their geometric precision is limited. We developed an automated mesh-generator that combines the advantages of voxel-based generation with improved representation of the geometry by displacement of nodes on the object-surface. Models of an artificial 3D-pipe-section and a skullbase were generated with different mesh-densities using the newly developed geometric, unsmoothed and smoothed voxel generators. Compared to the analytic calculation of the 3D-pipe-section model the normalized RMS error of the surface stress was 0.173-0.647 for the unsmoothed voxel models, 0.111-0.616 for the smoothed voxel models with small volume error and 0.126-0.273 for the geometric models. The highest element-energy error as a criterion for the mesh quality was 2.61x10(-2) N mm, 2.46x10(-2) N mm and 1.81x10(-2) N mm for unsmoothed, smoothed and geometric voxel models, respectively. The geometric model of the 3D-skullbase resulted in the lowest element-energy error and volume error. This algorithm also allowed the best representation of anatomical details. The presented geometric mesh-generator is universally applicable and allows an automated and accurate modeling by combining the advantages of the voxel-technique and of improved surface-modeling.

Characterisation of seven Inocybe ectomycorrhizal morphotypes from a semiarid woody steppe.

PubMed

Seress, Diána; Dima, Bálint; Kovács, Gábor M

2016-04-01

Ectomycorrhizas (ECM) of Inocybe species (Inocybaceae, Basidiomycota) formed by three host plant species (Populus alba, Salix rosmarinifolia and Pinus nigra) in a semiarid woody steppe of Hungary were studied. To identify the fungal partners, we performed phylogenetic analyses of nucleotide sequences for the internal transcribed spacer region of nuclear DNA (nrDNA ITS) together with sequences gained from public databases. Seven Inocybe ectomycorrhiza morphotypes were morpho-anatomically characterised. Five morphotypes were identified (I. phaeoleuca, I. psammophila, I. semifulva, I. splendens and I. subporospora), whereas two morphotypes represented unidentified Inocybe species. Differences were discernible among the morphotypes, and they showed general anatomical characteristics of Inocybe ECM, such as the slightly organised plectenchymatic mantle (types A, B and E and the gelatinous C). The ECM of I. subporospora and I. phaeoleuca were detected from the introduced Pinus nigra. These two fungi are probably native to the area but capable of forming a novel ectomycorrhizal association with the invasive host.

The Manchester Uveitis Clinic: the first 3000 patients--epidemiology and casemix.

PubMed

Jones, Nicholas P

2015-04-01

To demonstrate the demography, anatomical, and diagnostic classification of patients with uveitis attending the Manchester Uveitis Clinic (MUC), a specialist uveitis clinic in the northwest of England, UK. Retrospective retrieval of data on a computerized database incorporating all new referrals to MUC from 1991 to 2013. A total of 3000 new patients with uveitis were seen during a 22-year period. The anatomical types seen were anterior 46%; intermediate 11.1%; posterior 21.8%; and panuveitis 21.1%. The most common diagnoses were Fuchs heterochromic uveitis (11.5% of total), sarcoidosis-related uveitis (9.7%), idiopathic intermediate uveitis (7.9%), idiopathic acute anterior uveitis (7.0%), and toxoplasmosis (6.9%). Syphilis and tuberculosis-associated uveitis increased markedly in frequency during the study period. The uveitis casemix in this region reflects a predominantly white Caucasian population in a temperate country, but with changing characteristics owing to increasing immigration, enhanced diagnostic techniques, changes in referral pattern, and some real changes in disease incidence.

Probabilistic modeling of anatomical variability using a low dimensional parameterization of diffeomorphisms.

PubMed

Zhang, Miaomiao; Wells, William M; Golland, Polina

2017-10-01

We present an efficient probabilistic model of anatomical variability in a linear space of initial velocities of diffeomorphic transformations and demonstrate its benefits in clinical studies of brain anatomy. To overcome the computational challenges of the high dimensional deformation-based descriptors, we develop a latent variable model for principal geodesic analysis (PGA) based on a low dimensional shape descriptor that effectively captures the intrinsic variability in a population. We define a novel shape prior that explicitly represents principal modes as a multivariate complex Gaussian distribution on the initial velocities in a bandlimited space. We demonstrate the performance of our model on a set of 3D brain MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Our model yields a more compact representation of group variation at substantially lower computational cost than the state-of-the-art method such as tangent space PCA (TPCA) and probabilistic principal geodesic analysis (PPGA) that operate in the high dimensional image space. Copyright © 2017 Elsevier B.V. All rights reserved.

Combining deep learning with anatomical analysis for segmentation of the portal vein for liver SBRT planning

NASA Astrophysics Data System (ADS)

Ibragimov, Bulat; Toesca, Diego; Chang, Daniel; Koong, Albert; Xing, Lei

2017-12-01

Automated segmentation of the portal vein (PV) for liver radiotherapy planning is a challenging task due to potentially low vasculature contrast, complex PV anatomy and image artifacts originated from fiducial markers and vasculature stents. In this paper, we propose a novel framework for automated segmentation of the PV from computed tomography (CT) images. We apply convolutional neural networks (CNNs) to learn the consistent appearance patterns of the PV using a training set of CT images with reference annotations and then enhance the PV in previously unseen CT images. Markov random fields (MRFs) were further used to smooth the results of the enhancement of the CNN enhancement and remove isolated mis-segmented regions. Finally, CNN-MRF-based enhancement was augmented with PV centerline detection that relied on PV anatomical properties such as tubularity and branch composition. The framework was validated on a clinical database with 72 CT images of patients scheduled for liver stereotactic body radiation therapy. The obtained accuracy of the segmentation was DSC= 0.83 and \

Anatomical placement of the human eyeball in the orbit--validation using CT scans of living adults and prediction for facial approximation.

PubMed

Guyomarc'h, Pierre; Dutailly, Bruno; Couture, Christine; Coqueugniot, Hélène

2012-09-01

Accuracy of forensic facial approximation and superimposition techniques relies on the knowledge of anatomical correlations between soft and hard tissues. Recent studies by Stephan and collaborators (6,8,10) reviewed traditional guidelines leading to a wrong placement of the eyeball in the orbit. As those statements are based on a small cadaver sample, we propose a validation of these findings on a large database (n = 375) of living people. Computed tomography scans of known age and sex subjects were used to collect landmarks on three-dimensional surfaces and DICOM with TIVMI. Results confirmed a more superior and lateral position of the eyeball relatively to the orbital rims. Orbital height and breadth were used to compute regression formulae and proportional placement using percentages to find the most probable position of the eyeball in the orbit. A size-related sexual dimorphism was present but did not impact on the prediction accuracy. © 2012 American Academy of Forensic Sciences.

Domain Regeneration for Cross-Database Micro-Expression Recognition

NASA Astrophysics Data System (ADS)

Zong, Yuan; Zheng, Wenming; Huang, Xiaohua; Shi, Jingang; Cui, Zhen; Zhao, Guoying

2018-05-01

In this paper, we investigate the cross-database micro-expression recognition problem, where the training and testing samples are from two different micro-expression databases. Under this setting, the training and testing samples would have different feature distributions and hence the performance of most existing micro-expression recognition methods may decrease greatly. To solve this problem, we propose a simple yet effective method called Target Sample Re-Generator (TSRG) in this paper. By using TSRG, we are able to re-generate the samples from target micro-expression database and the re-generated target samples would share same or similar feature distributions with the original source samples. For this reason, we can then use the classifier learned based on the labeled source samples to accurately predict the micro-expression categories of the unlabeled target samples. To evaluate the performance of the proposed TSRG method, extensive cross-database micro-expression recognition experiments designed based on SMIC and CASME II databases are conducted. Compared with recent state-of-the-art cross-database emotion recognition methods, the proposed TSRG achieves more promising results.

Key features for ATA / ATR database design in missile systems

NASA Astrophysics Data System (ADS)

Özertem, Kemal Arda

2017-05-01

Automatic target acquisition (ATA) and automatic target recognition (ATR) are two vital tasks for missile systems, and having a robust detection and recognition algorithm is crucial for overall system performance. In order to have a robust target detection and recognition algorithm, an extensive image database is required. Automatic target recognition algorithms use the database of images in training and testing steps of algorithm. This directly affects the recognition performance, since the training accuracy is driven by the quality of the image database. In addition, the performance of an automatic target detection algorithm can be measured effectively by using an image database. There are two main ways for designing an ATA / ATR database. The first and easy way is by using a scene generator. A scene generator can model the objects by considering its material information, the atmospheric conditions, detector type and the territory. Designing image database by using a scene generator is inexpensive and it allows creating many different scenarios quickly and easily. However the major drawback of using a scene generator is its low fidelity, since the images are created virtually. The second and difficult way is designing it using real-world images. Designing image database with real-world images is a lot more costly and time consuming; however it offers high fidelity, which is critical for missile algorithms. In this paper, critical concepts in ATA / ATR database design with real-world images are discussed. Each concept is discussed in the perspective of ATA and ATR separately. For the implementation stage, some possible solutions and trade-offs for creating the database are proposed, and all proposed approaches are compared to each other with regards to their pros and cons.

Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses.

PubMed

Guillerme, Thomas; Cooper, Natalie

2016-05-01

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies. © 2016 The Authors.

Anatomical recommendations for safe botulinum toxin injection into temporalis muscle: a simplified reproducible approach.

PubMed

Lee, Won-Kang; Bae, Jung-Hee; Hu, Kyung-Seok; Kato, Takafumi; Kim, Seong-Taek

2017-03-01

The objective of this study was to simplify the anatomically safe and reproducible approach for BoNT injection and to generate a detailed topographic map of the important anatomical structures of the temporal region by dividing the temporalis into nine equally sized compartments. Nineteen sides of temporalis muscle were used. The topographies of the superficial temporal artery, middle temporal vein, temporalis tendon, and the temporalis muscle were evaluated. Also evaluated was the postural relations among the foregoing anatomical structures in the temporalis muscle, pivoted upon a total of nine compartments. The temporalis above the zygomatic arch exhibited an oblique quadrangular shape with rounded upper right and left corners. The distance between the anterior and posterior margins of the temporalis muscle was equal to the width of the temporalis rectangle, and the distance between the reference line and the superior temporalis margin was equal to its height. The mean ratio of width to height was 5:4. We recommend compartments Am, Mu, and Pm (coordinates of the rectangular outline) as areas in the temporal region for BoNT injection, because using these sites will avoid large blood vessels and tendons, thus improving the safety and reproducibility of the injection.

Anatomical Study of the Clavicles in a Chinese Population

PubMed Central

Qiu, Xu-sheng; Wang, Xiao-bo; Zhang, Yan; Zhu, Yan-Cheng; Guo, Xia; Chen, Yi-xin

2016-01-01

Background. A reemergence of interest in clavicle anatomy was prompted because of the advocacy for operative treatment of midshaft clavicle fractures. Several anatomical studies of the clavicle have been performed in western population. However, there was no anatomical study of clavicle in Chinese population. Patients and Methods. 52 patients were included in the present study. Three-dimensional reconstructions of the clavicles were generated. The length of the clavicle, the widths and thicknesses of the clavicle, curvatures of the clavicle, the areas of the intramedullary canal, and sectional areas of the clavicle were measured. All the measurements were compared between genders and two sides. Results. The mean length of the clavicles was 144.2 ± 12.0 mm. Clavicles in males were longer, wider, and thicker than in females; also males have different curvatures in both planes compared with females. The men's intramedullary canals and sectional areas of the clavicle were larger than those of women. No significant difference between the sides was found for all the measurements. Conclusion. This study provided an anatomical data of the clavicle in a Chinese population. These clavicle dimensions can be applied to the modifications of the contemporary clavicle plate or a new development for the Chinese population. PMID:27088088

Simulating video-assisted thoracoscopic lobectomy: a virtual reality cognitive task simulation.

PubMed

Solomon, Brian; Bizekis, Costas; Dellis, Sophia L; Donington, Jessica S; Oliker, Aaron; Balsam, Leora B; Zervos, Michael; Galloway, Aubrey C; Pass, Harvey; Grossi, Eugene A

2011-01-01

Current video-assisted thoracoscopic surgery training models rely on animals or mannequins to teach procedural skills. These approaches lack inherent teaching/testing capability and are limited by cost, anatomic variations, and single use. In response, we hypothesized that video-assisted thoracoscopic surgery right upper lobe resection could be simulated in a virtual reality environment with commercial software. An anatomy explorer (Maya [Autodesk Inc, San Rafael, Calif] models of the chest and hilar structures) and simulation engine were adapted. Design goals included freedom of port placement, incorporation of well-known anatomic variants, teaching and testing modes, haptic feedback for the dissection, ability to perform the anatomic divisions, and a portable platform. Preexisting commercial models did not provide sufficient surgical detail, and extensive modeling modifications were required. Video-assisted thoracoscopic surgery right upper lobe resection simulation is initiated with a random vein and artery variation. The trainee proceeds in a teaching or testing mode. A knowledge database currently includes 13 anatomic identifications and 20 high-yield lung cancer learning points. The "patient" is presented in the left lateral decubitus position. After initial camera port placement, the endoscopic view is displayed and the thoracoscope is manipulated via the haptic device. The thoracoscope port can be relocated; additional ports are placed using an external "operating room" view. Unrestricted endoscopic exploration of the thorax is allowed. An endo-dissector tool allows for hilar dissection, and a virtual stapling device divides structures. The trainee's performance is reported. A virtual reality cognitive task simulation can overcome the deficiencies of existing training models. Performance scoring is being validated as we assess this simulator for cognitive and technical surgical education. Copyright © 2011. Published by Mosby, Inc.

Artificial Neural Networks as Decision Support Tools in Cytopathology: Past, Present, and Future.

PubMed

Pouliakis, Abraham; Karakitsou, Efrossyni; Margari, Niki; Bountris, Panagiotis; Haritou, Maria; Panayiotides, John; Koutsouris, Dimitrios; Karakitsos, Petros

2016-01-01

This study aims to analyze the role of artificial neural networks (ANNs) in cytopathology. More specifically, it aims to highlight the importance of employing ANNs in existing and future applications and in identifying unexplored or poorly explored research topics. A systematic search was conducted in scientific databases for articles related to cytopathology and ANNs with respect to anatomical places of the human body where cytopathology is performed. For each anatomic system/organ, the major outcomes described in the scientific literature are presented and the most important aspects are highlighted. The vast majority of ANN applications are related to cervical cytopathology, specifically for the ANN-based, semiautomated commercial diagnostic system PAPNET. For cervical cytopathology, there is a plethora of studies relevant to the diagnostic accuracy; in addition, there are also efforts evaluating cost-effectiveness and applications on primary, secondary, or hybrid screening. For the rest of the anatomical sites, such as the gastrointestinal system, thyroid gland, urinary tract, and breast, there are significantly less efforts relevant to the application of ANNs. Additionally, there are still anatomical systems for which ANNs have never been applied on their cytological material. Cytopathology is an ideal discipline to apply ANNs. In general, diagnosis is performed by experts via the light microscope. However, this approach introduces subjectivity, because this is not a universal and objective measurement process. This has resulted in the existence of a gray zone between normal and pathological cases. From the analysis of related articles, it is obvious that there is a need to perform more thorough analyses, using extensive number of cases and particularly for the nonexplored organs. Efforts to apply such systems within the laboratory test environment are required for their future uptake.

Artificial Neural Networks as Decision Support Tools in Cytopathology: Past, Present, and Future

PubMed Central

Pouliakis, Abraham; Karakitsou, Efrossyni; Margari, Niki; Bountris, Panagiotis; Haritou, Maria; Panayiotides, John; Koutsouris, Dimitrios; Karakitsos, Petros

2016-01-01

OBJECTIVE This study aims to analyze the role of artificial neural networks (ANNs) in cytopathology. More specifically, it aims to highlight the importance of employing ANNs in existing and future applications and in identifying unexplored or poorly explored research topics. STUDY DESIGN A systematic search was conducted in scientific databases for articles related to cytopathology and ANNs with respect to anatomical places of the human body where cytopathology is performed. For each anatomic system/organ, the major outcomes described in the scientific literature are presented and the most important aspects are highlighted. RESULTS The vast majority of ANN applications are related to cervical cytopathology, specifically for the ANN-based, semiautomated commercial diagnostic system PAPNET. For cervical cytopathology, there is a plethora of studies relevant to the diagnostic accuracy; in addition, there are also efforts evaluating cost-effectiveness and applications on primary, secondary, or hybrid screening. For the rest of the anatomical sites, such as the gastrointestinal system, thyroid gland, urinary tract, and breast, there are significantly less efforts relevant to the application of ANNs. Additionally, there are still anatomical systems for which ANNs have never been applied on their cytological material. CONCLUSIONS Cytopathology is an ideal discipline to apply ANNs. In general, diagnosis is performed by experts via the light microscope. However, this approach introduces subjectivity, because this is not a universal and objective measurement process. This has resulted in the existence of a gray zone between normal and pathological cases. From the analysis of related articles, it is obvious that there is a need to perform more thorough analyses, using extensive number of cases and particularly for the nonexplored organs. Efforts to apply such systems within the laboratory test environment are required for their future uptake. PMID:26917984

A systematic review of single- versus double-bundle ACL reconstruction using the anatomic anterior cruciate ligament reconstruction scoring checklist.

PubMed

Desai, Neel; Alentorn-Geli, Eduard; van Eck, Carola F; Musahl, Volker; Fu, Freddie H; Karlsson, Jón; Samuelsson, Kristian

2016-03-01

The aim of this systematic review was to apply the anatomic ACL reconstruction scoring checklist (AARSC) and to evaluate the degree to which clinical studies comparing single-bundle (SB) and double-bundle (DB) ACL reconstructions are anatomic. A systematic electronic search was performed using the databases PubMed (MEDLINE), EMBASE and Cochrane Library. Studies published from January 1995 to January 2014 comparing SB and DB ACL reconstructions with clinical outcome measurements were included. The items from the AARSC were recorded for both the SB and DB groups in each study. Eight-thousand nine-hundred and ninety-four studies were analysed, 77 were included. Randomized clinical trials (29; 38%) and prospective comparative studies (29; 38%) were the most frequent study type. Most studies were published in 2011 (19; 25%). The most commonly reported items for both SB and DB groups were as follows: graft type (152; 99%), femoral and tibial fixation method (149; 97% respectively), knee flexion angle during graft tensioning (124; 8%) and placement of the tibial tunnel at the ACL insertion site (101; 66%). The highest level of documentation used for ACL tunnel position for both groups was often one dimensional, e.g. drawing, operative notes or o'clock reference. The DB reconstruction was in general more thoroughly reported. The means for the AARSC were 6.9 ± 2.8 for the SB group and 8.3 ± 2.8 for the DB group. Both means were below a proposed required minimum score of 10 for anatomic ACL reconstruction. There was substantial underreporting of surgical data for both the SB and DB groups in clinical studies. This underreporting creates difficulties when analysing, comparing and pooling results of scientific studies on this subject.

[Deep infiltrating endometriosis surgical management and pelvic nerves injury].

PubMed

Fermaut, M; Nyangoh Timoh, K; Lebacle, C; Moszkowicz, D; Benoit, G; Bessede, T

2016-05-01

Deep pelvic endometriosis surgery may need substantial excisions, which in turn expose to risks of injury to the pelvic nerves. To limit functional complications, nerve-sparing surgical techniques have been developed but should be adapted to the specific multifocal character of endometriotic lesions. The objective was to identify the anatomical areas where the pelvic nerves are most at risk of injury during endometriotic excisions. The Medline and Embase databases have been searched for available literature using the keywords "hypogastric nerve or hypogastric plexus [Mesh] or autonomic pathway [Mesh], anatomy, endometriosis, surgery [Mesh]". All relevant French and English publications, selected based on their available abstracts, have been reviewed. Five female adult fresh cadavers have been dissected to localize the key anatomical areas where the pelvic nerves are most at risk of injury. Six anatomical areas of high risk for pelvic nerves have been identified, analysed and described. Pelvic nerves can be damaged during the dissection of retrorectal space and the anterolateral rectal excision. Furthermore, before an uterosacral ligament excision, a parametrial excision, a colpectomy or a dissection of the vesico-uterine ligament, the hypogastric nerves, splanchnic nerves, inferior hypogastric plexus and its efferent pathways must be mapped out to avoid injury. The distance between the deep uterin vein and the pelvic splanchnic nerves were measured on four cadavers and varied from 2.5cm to 4cm. Six key anatomical pitfalls must be known in order to limit the functional complications of the endometriotic surgical excision. Applying nerve-sparing surgical techniques for endometriosis would lead to less urinary functional complications and a better short-term postoperative satisfaction. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Surgical Techniques for the Reconstruction of Medial Collateral Ligament and Posteromedial Corner Injuries of the Knee: A Systematic Review.

PubMed

DeLong, Jeffrey M; Waterman, Brian R

2015-11-01

To systematically review reconstruction techniques of the medial collateral ligament (MCL) and associated medial structures of the knee (e.g., posterior oblique ligament). A systematic review of Medline/PubMed Database (1966 to November 2013), reference list scanning and citation searches of included articles, and manual searches of high-impact journals (2000 to July 2013) and conference proceedings (2009 to July 2013) were performed to identify publications describing MCL reconstruction techniques of the knee. Exclusion criteria included (1) MCL primary repair techniques or advancement procedures, (2) lack of clear description of MCL reconstruction technique, (3) animal models, (4) nonrelevant study design, (5) and foreign language articles without available translation. After review of 4,600 references, 25 publications with 359 of 388 patients (92.5%) were isolated for analysis, including 18 single-bundle MCL and 10 double-bundle reconstruction techniques. Only 2 techniques were classified as anatomic reconstructions, and clinical and objective outcomes (n = 28; 100% <3 mm side-to-side difference [SSD]) were superior to those with nonanatomic reconstruction (n = 182; 79.1% <3 mm SSD) and tendon transfer techniques (n = 114; 52.6% <3 mm SSD). This systematic review demonstrated that numerous medial reconstruction techniques have been used in the treatment of isolated and combined medial knee injuries in the existent literature. Many variations exist among reconstruction techniques and may differ by graft choices, method of fixation, number of bundles, tensioning protocol, and degree of anatomic restoration of medial and posteromedial corner knee restraints. Further studies are required to better ascertain the comparative clinical outcomes with anatomic, non-anatomic, and tendon transfer techniques for medial knee reconstruction. Level IV, systematic review of level IV studies and surgical techniques. Published by Elsevier Inc.

Creating Your Own Database.

ERIC Educational Resources Information Center

Blair, John C., Jr.

1982-01-01

Outlines the important factors to be considered in selecting a database management system for use with a microcomputer and presents a series of guidelines for developing a database. General procedures, report generation, data manipulation, information storage, word processing, data entry, database indexes, and relational databases are among the…

Central pattern generator for vocalization: is there a vertebrate morphotype?

PubMed

Bass, Andrew H

2014-10-01

Animals that generate acoustic signals for social communication are faced with two essential tasks: generate a temporally precise signal and inform the auditory system about the occurrence of one's own sonic signal. Recent studies of sound producing fishes delineate a hindbrain network comprised of anatomically distinct compartments coding equally distinct neurophysiological properties that allow an organism to meet these behavioral demands. A set of neural characters comprising a vocal-sonic central pattern generator (CPG) morphotype is proposed for fishes and tetrapods that shares evolutionary developmental origins with pectoral appendage motor systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Central pattern generator for vocalization: Is there a vertebrate morphotype?

PubMed Central

Bass, Andrew H.

2014-01-01

Animals that generate acoustic signals for social communication are faced with two essential tasks: generate a temporally precise signal and inform the auditory system about the occurrence of one’s own sonic signal. Recent studies of sound producing fishes delineate a hindbrain network comprised of anatomically distinct compartments coding equally distinct neurophysiological properties that allow an organism to meet these behavioral demands. A set of neural characters comprising a vocal-sonic central pattern generator (CPG) morphotype is proposed for fishes and tetrapods that shares evolutionary developmental origins with pectoral appendage motor systems. PMID:25050813

Assessment of anatomical knowledge: Approaches taken by higher education institutions.

PubMed

Choudhury, Bipasha; Freemont, Anthony

2017-04-01

Assessment serves the primary function of determining a student's competence in a subject. Several different assessment formats are available for assessing anatomical skills, knowledge and understanding and, as assessment can drive learning, a careful selection of assessments can help to engender the correct deep learning facility required of the safe clinical practitioner. The aim of this review was to survey the published literature to see whether higher education institutions are taking an andragogical approach to assessment. Five databases (EMBASE, ERIC, Medline, PubMed, and Web of Knowledge) were searched using standardized search terms with two limits applied (English language, and 2000 to the present). Among the 2,094 papers found, 32 were deemed suitable for this review. Current literature on assessment can be categorized into the following themes: assessment driven learning, types of assessments, frequency of assessments, and use of images in assessments. The consensus is to use a variety of methods, written and practical, to assess anatomical knowledge and skill in different domains. Institutions aim for different levels of Bloom's taxonomy for students at similar stages of their medical degree. Formative assessments are used widely, in differing formats, with mostly good effects on the final examination grade. In conclusion, a wide variety of assessments, each aimed at a different level of Bloom's taxonomy, are used by different institutions. Clin. Anat. 30:290-299, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Automatic segmentation of brain MRIs and mapping neuroanatomy across the human lifespan

NASA Astrophysics Data System (ADS)

Keihaninejad, Shiva; Heckemann, Rolf A.; Gousias, Ioannis S.; Rueckert, Daniel; Aljabar, Paul; Hajnal, Joseph V.; Hammers, Alexander

2009-02-01

A robust model for the automatic segmentation of human brain images into anatomically defined regions across the human lifespan would be highly desirable, but such structural segmentations of brain MRI are challenging due to age-related changes. We have developed a new method, based on established algorithms for automatic segmentation of young adults' brains. We used prior information from 30 anatomical atlases, which had been manually segmented into 83 anatomical structures. Target MRIs came from 80 subjects (~12 individuals/decade) from 20 to 90 years, with equal numbers of men, women; data from two different scanners (1.5T, 3T), using the IXI database. Each of the adult atlases was registered to each target MR image. By using additional information from segmentation into tissue classes (GM, WM and CSF) to initialise the warping based on label consistency similarity before feeding this into the previous normalised mutual information non-rigid registration, the registration became robust enough to accommodate atrophy and ventricular enlargement with age. The final segmentation was obtained by combination of the 30 propagated atlases using decision fusion. Kernel smoothing was used for modelling the structural volume changes with aging. Example linear correlation coefficients with age were, for lateral ventricular volume, rmale=0.76, rfemale=0.58 and, for hippocampal volume, rmale=-0.6, rfemale=-0.4 (allρ<0.01).

Mandibular Third Molar Impaction: Review of Literature and a Proposal of a Classification

PubMed Central

Daugela, Povilas

2013-01-01

ABSTRACT Objectives The purpose of present article was to review impacted mandibular third molar aetiology, clinical anatomy, radiologic examination, surgical treatment and possible complications, as well as to create new mandibular third molar impaction and extraction difficulty degree classification based on anatomical and radiologic findings and literature review results. Material and Methods Literature was selected through a search of PubMed, Embase and Cochrane electronic databases. The keywords used for search were mandibular third molar, impacted mandibular third molar, inferior alveolar nerve injury third molar, lingual nerve injury third molar. The search was restricted to English language articles, published from 1976 to April 2013. Additionally, a manual search in the major anatomy and oral surgery journals and books was performed. The publications there selected by including clinical and human anatomy studies. Results In total 75 literature sources were obtained and reviewed. Impacted mandibular third molar aetiology, clinical anatomy, radiographic examination, surgical extraction of and possible complications, classifications and risk factors were discussed. New mandibular third molar impaction and extraction difficulty degree classification based on anatomical and radiologic findings and literature review results was proposed. Conclusions The classification proposed here based on anatomical and radiological impacted mandibular third molar features is promising to be a helpful tool for impacted tooth assessment as well as for planning for surgical operation. Further clinical studies should be conducted for new classification validation and reliability evaluation. PMID:24422029

Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated by LC/TOF-MS.

PubMed

Sana, Theodore R; Roark, Joseph C; Li, Xiangdong; Waddell, Keith; Fischer, Steven M

2008-09-01

In an effort to simplify and streamline compound identification from metabolomics data generated by liquid chromatography time-of-flight mass spectrometry, we have created software for constructing Personalized Metabolite Databases with content from over 15,000 compounds pulled from the public METLIN database (http://metlin.scripps.edu/). Moreover, we have added extra functionalities to the database that (a) permit the addition of user-defined retention times as an orthogonal searchable parameter to complement accurate mass data; and (b) allow interfacing to separate software, a Molecular Formula Generator (MFG), that facilitates reliable interpretation of any database matches from the accurate mass spectral data. To test the utility of this identification strategy, we added retention times to a subset of masses in this database, representing a mixture of 78 synthetic urine standards. The synthetic mixture was analyzed and screened against this METLIN urine database, resulting in 46 accurate mass and retention time matches. Human urine samples were subsequently analyzed under the same analytical conditions and screened against this database. A total of 1387 ions were detected in human urine; 16 of these ions matched both accurate mass and retention time parameters for the 78 urine standards in the database. Another 374 had only an accurate mass match to the database, with 163 of those masses also having the highest MFG score. Furthermore, MFG calculated a formula for a further 849 ions that had no match to the database. Taken together, these results suggest that the METLIN Personal Metabolite database and MFG software offer a robust strategy for confirming the formula of database matches. In the event of no database match, it also suggests possible formulas that may be helpful in interpreting the experimental results.

The Cambridge MRI database for animal models of Huntington disease.

PubMed

Sawiak, Stephen J; Morton, A Jennifer

2016-01-01

We describe the Cambridge animal brain magnetic resonance imaging repository comprising 400 datasets to date from mouse models of Huntington disease. The data include raw images as well as segmented grey and white matter images with maps of cortical thickness. All images and phenotypic data for each subject are freely-available without restriction from (http://www.dspace.cam.ac.uk/handle/1810/243361/). Software and anatomical population templates optimised for animal brain analysis with MRI are also available from this site. Copyright © 2015. Published by Elsevier Inc.

Anatomic Sites and Associated Clinical Factors for Deep Dyspareunia.

PubMed

Yong, Paul J; Williams, Christina; Yosef, Ali; Wong, Fontayne; Bedaiwy, Mohamed A; Lisonkova, Sarka; Allaire, Catherine

2017-09-01

Deep dyspareunia negatively affects women's sexual function. There is a known association between deep dyspareunia and endometriosis of the cul-de-sac or uterosacral ligaments in reproductive-age women; however, other factors are less clear in this population. To identify anatomic sites and associated clinical factors for deep dyspareunia in reproductive-age women at a referral center. This study involved the analysis of cross-sectional baseline data from a prospective database of 548 women (87% consent rate) recruited from December 2013 through April 2015 at a tertiary referral center for endometriosis and/or pelvic pain. Exclusion criteria included menopausal status, age at least 50 years, previous hysterectomy or oophorectomy, and not sexually active. We performed a standardized endovaginal ultrasound-assisted pelvic examination to palpate anatomic structures for tenderness and reproduce deep dyspareunia. Multivariable regression was used to determine which tender anatomic structures were independently associated with deep dyspareunia severity and to identify clinical factors independently associated with each tender anatomic site. Severity of deep dyspareunia on a numeric pain rating scale of 0 to 10. Severity of deep dyspareunia (scale = 0-10) was independently associated with tenderness of the bladder (b = 0.88, P = .018), pelvic floor (levator ani) (b = 0.66, P = .038), cervix and uterus (b = 0.88, P = .008), and cul-de-sac or uterosacral ligaments (b = 1.39, P < .001), but not with the adnexa (b = -0.16, P = 0.87). The number of tender anatomic sites was significantly correlated with more severe deep dyspareunia (Spearman r = 0.34, P < .001). For associated clinical factors, greater depression symptom severity was specifically associated with tenderness of the bladder (b = 1.05, P = .008) and pelvic floor (b = 1.07, P < .001). A history of miscarriage was specifically associated with tenderness of the cervix and uterus (b = 2.24, P = .001). Endometriosis was specifically associated with tenderness of the cul-de-sac or uterosacral ligaments (b = 3.54, P < .001). In reproductive-age women at a tertiary referral center, deep dyspareunia was independently associated not only with tenderness of the cul-de-sac and uterosacral ligaments but also with tenderness of the bladder, pelvic floor, and cervix and uterus. Yong PJ, Williams C, Yosef A, et al. Anatomic Sites and Associated Clinical Factors for Deep Dyspareunia. Sex Med 2017;5:e184-e195. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Vesalius on the anatomy and function of the recurrent laryngeal nerves: medical illustration and reintroduction of a physiological demonstration from Galen.

PubMed

Lanska, Douglas J

2014-01-01

The purpose of this article is to review the anatomical illustrations and physiological demonstrations of sixteenth-century Flemish-born anatomist and physician Andreas Vesalius concerning the recurrent laryngeal nerves. Although Vesalius was primarily an anatomist, he also used vivisection as a pedagogical device to help his students understand the function of structures within the fabric of the body that they had previously studied in anatomical detail. Vesalius's masterwork, De humani corporis fabrica or simply the Fabrica (1543, 1555), was ostensibly an anatomy text, but Vesalius included textual and figural references to his use of vivisection to explicate the function of specific structures. Even as he began to criticize the errors in Galen's anatomical works, Vesalius nevertheless adopted some of Galen's classic physiological demonstrations, in particular the ligation (and subsequent release) of the recurrent laryngeal nerves of a pig to demonstrate their role in generating the pig's squeal. Vesalius's illustrations concerning the recurrent laryngeal nerve in the Fabrica were of two types: elegant anatomical woodcut plates-unsurpassed for their clarity, accuracy, and detail - and the distinctly inelegant historiated initial Q, depicting a throng of putti busily engaged in vivisecting a pig. Vesalius' anatomical plates were heavily plagiarized while the historiated initials, showing the rough work of an anatomist or surgeon, were largely ignored and remain little recognized today. While Vesalius' anatomical illustrations of the recurrent laryngeal nerves contained some errors, they were a dramatic departure from prior meager efforts at medical illustration and indeed far surpassed all contemporary published illustrations by others. Vesalius was also influential in reviving Galen's approach to vivisection, at least for pedagogical purposes, if not really then yet as a full-fledged investigative technique.

From chalkboard, slides, and paper to e-learning: How computing technologies have transformed anatomical sciences education.

PubMed

Trelease, Robert B

2016-11-01

Until the late-twentieth century, primary anatomical sciences education was relatively unenhanced by advanced technology and dependent on the mainstays of printed textbooks, chalkboard- and photographic projection-based classroom lectures, and cadaver dissection laboratories. But over the past three decades, diffusion of innovations in computer technology transformed the practices of anatomical education and research, along with other aspects of work and daily life. Increasing adoption of first-generation personal computers (PCs) in the 1980s paved the way for the first practical educational applications, and visionary anatomists foresaw the usefulness of computers for teaching. While early computers lacked high-resolution graphics capabilities and interactive user interfaces, applications with video discs demonstrated the practicality of programming digital multimedia linking descriptive text with anatomical imaging. Desktop publishing established that computers could be used for producing enhanced lecture notes, and commercial presentation software made it possible to give lectures using anatomical and medical imaging, as well as animations. Concurrently, computer processing supported the deployment of medical imaging modalities, including computed tomography, magnetic resonance imaging, and ultrasound, that were subsequently integrated into anatomy instruction. Following its public birth in the mid-1990s, the World Wide Web became the ubiquitous multimedia networking technology underlying the conduct of contemporary education and research. Digital video, structural simulations, and mobile devices have been more recently applied to education. Progressive implementation of computer-based learning methods interacted with waves of ongoing curricular change, and such technologies have been deemed crucial for continuing medical education reforms, providing new challenges and opportunities for anatomical sciences educators. Anat Sci Educ 9: 583-602. © 2016 American Association of Anatomists. © 2016 American Association of Anatomists.

Optogenetic manipulation of anatomical re-entry by light-guided generation of a reversible local conduction block.

PubMed

Watanabe, Masaya; Feola, Iolanda; Majumder, Rupamanjari; Jangsangthong, Wanchana; Teplenin, Alexander S; Ypey, Dirk L; Schalij, Martin J; Zeppenfeld, Katja; de Vries, Antoine A F; Pijnappels, Daniël A

2017-03-01

Anatomical re-entry is an important mechanism of ventricular tachycardia, characterized by circular electrical propagation in a fixed pathway. It's current investigative and therapeutic approaches are non-biological, rather unspecific (drugs), traumatizing (electrical shocks), or irreversible (ablation). Optogenetics is a new biological technique that allows reversible modulation of electrical function with unmatched spatiotemporal precision using light-gated ion channels. We therefore investigated optogenetic manipulation of anatomical re-entry in ventricular cardiac tissue. Transverse, 150-μm-thick ventricular slices, obtained from neonatal rat hearts, were genetically modified with lentiviral vectors encoding Ca2+-translocating channelrhodopsin (CatCh), a light-gated depolarizing ion channel, or enhanced yellow fluorescent protein (eYFP) as control. Stable anatomical re-entry was induced in both experimental groups. Activation of CatCh was precisely controlled by 470-nm patterned illumination, while the effects on anatomical re-entry were studied by optical voltage mapping. Regional illumination in the pathway of anatomical re-entry resulted in termination of arrhythmic activity only in CatCh-expressing slices by establishing a local and reversible, depolarization-induced conduction block in the illuminated area. Systematic adjustment of the size of the light-exposed area in the re-entrant pathway revealed that re-entry could be terminated by either wave collision or extinction, depending on the depth (transmurality) of illumination. In silico studies implicated source-sink mismatches at the site of subtransmural conduction block as an important factor in re-entry termination. Anatomical re-entry in ventricular tissue can be manipulated by optogenetic induction of a local and reversible conduction block in the re-entrant pathway, allowing effective re-entry termination. These results provide distinctively new mechanistic insight into re-entry termination and a novel perspective for cardiac arrhythmia management. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For permissions, please email: journals.permissions@oup.com.

Generation of a Database of Laboratory Laser-Induced Breakdown Spectroscopy (LIBS) Spectra and Associated Analysis Software

NASA Astrophysics Data System (ADS)

Anderson, R. B.; Clegg, S. M.; Graff, T.; Morris, R. V.; Laura, J.

2015-06-01

We describe plans to generate a database of LIBS spectra of planetary analog materials and develop free, open-source software to enable the planetary community to analyze LIBS (and other spectral) data.

Partial automation of database processing of simulation outputs from L-systems models of plant morphogenesis.

PubMed

Chen, Yi- Ping Phoebe; Hanan, Jim

2002-01-01

Models of plant architecture allow us to explore how genotype environment interactions effect the development of plant phenotypes. Such models generate masses of data organised in complex hierarchies. This paper presents a generic system for creating and automatically populating a relational database from data generated by the widely used L-system approach to modelling plant morphogenesis. Techniques from compiler technology are applied to generate attributes (new fields) in the database, to simplify query development for the recursively-structured branching relationship. Use of biological terminology in an interactive query builder contributes towards making the system biologist-friendly.

The importance of data quality for generating reliable distribution models for rare, elusive, and cryptic species

Treesearch

Keith B. Aubry; Catherine M. Raley; Kevin S. McKelvey

2017-01-01

The availability of spatially referenced environmental data and species occurrence records in online databases enable practitioners to easily generate species distribution models (SDMs) for a broad array of taxa. Such databases often include occurrence records of unknown reliability, yet little information is available on the influence of data quality on SDMs generated...

Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data

PubMed Central

Burns, Gully APC; Cheng, Wei-Cheng

2006-01-01

Background Knowledge bases that summarize the published literature provide useful online references for specific areas of systems-level biology that are not otherwise supported by large-scale databases. In the field of neuroanatomy, groups of small focused teams have constructed medium size knowledge bases to summarize the literature describing tract-tracing experiments in several species. Despite years of collation and curation, these databases only provide partial coverage of the available published literature. Given that the scientists reading these papers must all generate the interpretations that would normally be entered into such a system, we attempt here to provide general-purpose annotation tools to make it easy for members of the community to contribute to the task of data collation. Results In this paper, we describe an open-source, freely available knowledge management system called 'NeuroScholar' that allows straightforward structured markup of the PDF files according to a well-designed schema to capture the essential details of this class of experiment. Although, the example worked through in this paper is quite specific to neuroanatomical connectivity, the design is freely extensible and could conceivably be used to construct local knowledge bases for other experiment types. Knowledge representations of the experiment are also directly linked to the contributing textual fragments from the original research article. Through the use of this system, not only could members of the community contribute to the collation task, but input data can be gathered for automated approaches to permit knowledge acquisition through the use of Natural Language Processing (NLP). Conclusion We present a functional, working tool to permit users to populate knowledge bases for neuroanatomical connectivity data from the literature through the use of structured questionnaires. This system is open-source, fully functional and available for download from [1]. PMID:16895608

Manipulating neural activity in physiologically classified neurons: triumphs and challenges

PubMed Central

Gore, Felicity; Schwartz, Edmund C.; Salzman, C. Daniel

2015-01-01

Understanding brain function requires knowing both how neural activity encodes information and how this activity generates appropriate responses. Electrophysiological, imaging and immediate early gene immunostaining studies have been instrumental in identifying and characterizing neurons that respond to different sensory stimuli, events and motor actions. Here we highlight approaches that have manipulated the activity of physiologically classified neurons to determine their role in the generation of behavioural responses. Previous experiments have often exploited the functional architecture observed in many cortical areas, where clusters of neurons share response properties. However, many brain structures do not exhibit such functional architecture. Instead, neurons with different response properties are anatomically intermingled. Emerging genetic approaches have enabled the identification and manipulation of neurons that respond to specific stimuli despite the lack of discernable anatomical organization. These approaches have advanced understanding of the circuits mediating sensory perception, learning and memory, and the generation of behavioural responses by providing causal evidence linking neural response properties to appropriate behavioural output. However, significant challenges remain for understanding cognitive processes that are probably mediated by neurons with more complex physiological response properties. Currently available strategies may prove inadequate for determining how activity in these neurons is causally related to cognitive behaviour. PMID:26240431

bioDBnet - Biological Database Network

Cancer.gov

bioDBnet is a comprehensive resource of most of the biological databases available from different sites like NCBI, Uniprot, EMBL, Ensembl, Affymetrix. It provides a queryable interface to all the databases available, converts identifiers from one database into another and generates comprehensive reports.

An SQL query generator for CLIPS

NASA Technical Reports Server (NTRS)

Snyder, James; Chirica, Laurian

1990-01-01

As expert systems become more widely used, their access to large amounts of external information becomes increasingly important. This information exists in several forms such as statistical, tabular data, knowledge gained by experts and large databases of information maintained by companies. Because many expert systems, including CLIPS, do not provide access to this external information, much of the usefulness of expert systems is left untapped. The scope of this paper is to describe a database extension for the CLIPS expert system shell. The current industry standard database language is SQL. Due to SQL standardization, large amounts of information stored on various computers, potentially at different locations, will be more easily accessible. Expert systems should be able to directly access these existing databases rather than requiring information to be re-entered into the expert system environment. The ORACLE relational database management system (RDBMS) was used to provide a database connection within the CLIPS environment. To facilitate relational database access a query generation system was developed as a CLIPS user function. The queries are entered in a CLlPS-like syntax and are passed to the query generator, which constructs and submits for execution, an SQL query to the ORACLE RDBMS. The query results are asserted as CLIPS facts. The query generator was developed primarily for use within the ICADS project (Intelligent Computer Aided Design System) currently being developed by the CAD Research Unit in the California Polytechnic State University (Cal Poly). In ICADS, there are several parallel or distributed expert systems accessing a common knowledge base of facts. Expert system has a narrow domain of interest and therefore needs only certain portions of the information. The query generator provides a common method of accessing this information and allows the expert system to specify what data is needed without specifying how to retrieve it.

Generation of an Aerothermal Data Base for the X33 Spacecraft

NASA Technical Reports Server (NTRS)

Roberts, Cathy; Huynh, Loc

1998-01-01

The X-33 experimental program is a cooperative program between industry and NASA, managed by Lockheed-Martin Skunk Works to develop an experimental vehicle to demonstrate new technologies for a single-stage-to-orbit, fully reusable launch vehicle (RLV). One of the new technologies to be demonstrated is an advanced Thermal Protection System (TPS) being designed by BF Goodrich (formerly Rohr, Inc.) with support from NASA. The calculation of an aerothermal database is crucial to identifying the critical design environment data for the TPS. The NASA Ames X-33 team has generated such a database using Computational Fluid Dynamics (CFD) analyses, engineering analysis methods and various programs to compare and interpolate the results from the CFD and the engineering analyses. This database, along with a program used to query the database, is used extensively by several X-33 team members to help them in designing the X-33. This paper will describe the methods used to generate this database, the program used to query the database, and will show some of the aerothermal analysis results for the X-33 aircraft.

Development and characterization of a 3D high-resolution terrain database

NASA Astrophysics Data System (ADS)

Wilkosz, Aaron; Williams, Bryan L.; Motz, Steve

2000-07-01

A top-level description of methods used to generate elements of a high resolution 3D characterization database is presented. The database elements are defined as ground plane elevation map, vegetation height elevation map, material classification map, discrete man-made object map, and temperature radiance map. The paper will cover data collection by means of aerial photography, techniques of soft photogrammetry used to derive the elevation data, and the methodology followed to generate the material classification map. The discussion will feature the development of the database elements covering Fort Greely, Alaska. The developed databases are used by the US Army Aviation and Missile Command to evaluate the performance of various missile systems.

Visualization of stereoscopic anatomic models of the paranasal sinuses and cervical vertebrae from the surgical and procedural perspective.

PubMed

Chen, Jian; Smith, Andrew D; Khan, Majid A; Sinning, Allan R; Conway, Marianne L; Cui, Dongmei

2017-11-01

Recent improvements in three-dimensional (3D) virtual modeling software allows anatomists to generate high-resolution, visually appealing, colored, anatomical 3D models from computed tomography (CT) images. In this study, high-resolution CT images of a cadaver were used to develop clinically relevant anatomic models including facial skull, nasal cavity, septum, turbinates, paranasal sinuses, optic nerve, pituitary gland, carotid artery, cervical vertebrae, atlanto-axial joint, cervical spinal cord, cervical nerve root, and vertebral artery that can be used to teach clinical trainees (students, residents, and fellows) approaches for trans-sphenoidal pituitary surgery and cervical spine injection procedure. Volume, surface rendering and a new rendering technique, semi-auto-combined, were applied in the study. These models enable visualization, manipulation, and interaction on a computer and can be presented in a stereoscopic 3D virtual environment, which makes users feel as if they are inside the model. Anat Sci Educ 10: 598-606. © 2017 American Association of Anatomists. © 2017 American Association of Anatomists.

Musculoskeletal Simulation Model Generation from MRI Data Sets and Motion Capture Data

NASA Astrophysics Data System (ADS)

Schmid, Jérôme; Sandholm, Anders; Chung, François; Thalmann, Daniel; Delingette, Hervé; Magnenat-Thalmann, Nadia

Today computer models and computer simulations of the musculoskeletal system are widely used to study the mechanisms behind human gait and its disorders. The common way of creating musculoskeletal models is to use a generic musculoskeletal model based on data derived from anatomical and biomechanical studies of cadaverous specimens. To adapt this generic model to a specific subject, the usual approach is to scale it. This scaling has been reported to introduce several errors because it does not always account for subject-specific anatomical differences. As a result, a novel semi-automatic workflow is proposed that creates subject-specific musculoskeletal models from magnetic resonance imaging (MRI) data sets and motion capture data. Based on subject-specific medical data and a model-based automatic segmentation approach, an accurate modeling of the anatomy can be produced while avoiding the scaling operation. This anatomical model coupled with motion capture data, joint kinematics information, and muscle-tendon actuators is finally used to create a subject-specific musculoskeletal model.

Anatomic Optical Coherence Tomography of Upper Airways

NASA Astrophysics Data System (ADS)

Chin Loy, Anthony; Jing, Joseph; Zhang, Jun; Wang, Yong; Elghobashi, Said; Chen, Zhongping; Wong, Brian J. F.

The upper airway is a complex and intricate system responsible for respiration, phonation, and deglutition. Obstruction of the upper airways afflicts an estimated 12-18 million Americans. Pharyngeal size and shape are important factors in the pathogenesis of airway obstructions. In addition, nocturnal loss in pharyngeal muscular tone combined with high pharyngeal resistance can lead to collapse of the airway and periodic partial or complete upper airway obstruction. Anatomical optical coherence tomography (OCT) has the potential to provide high-speed three-dimensional tomographic images of the airway lumen without the use of ionizing radiation. In this chapter we describe the methods behind endoscopic OCT imaging and processing to generate full three dimensional anatomical models of the human airway which can be used in conjunction with numerical simulation methods to assess areas of airway obstruction. Combining this structural information with flow dynamic simulations, we can better estimate the site and causes of airway obstruction and better select and design surgery for patients with obstructive sleep apnea.

Web based aphasia test using service oriented architecture (SOA)

NASA Astrophysics Data System (ADS)

Voos, J. A.; Vigliecca, N. S.; Gonzalez, E. A.

2007-11-01

Based on an aphasia test for Spanish speakers which analyze the patient's basic resources of verbal communication, a web-enabled software was developed to automate its execution. A clinical database was designed as a complement, in order to evaluate the antecedents (risk factors, pharmacological and medical backgrounds, neurological or psychiatric symptoms, brain injury -anatomical and physiological characteristics, etc) which are necessary to carry out a multi-factor statistical analysis in different samples of patients. The automated test was developed following service oriented architecture and implemented in a web site which contains a tests suite, which would allow both integrating the aphasia test with other neuropsychological instruments and increasing the available site information for scientific research. The test design, the database and the study of its psychometric properties (validity, reliability and objectivity) were made in conjunction with neuropsychological researchers, who participate actively in the software design, based on the patients or other subjects of investigation feedback.

Supplier Management System

NASA Technical Reports Server (NTRS)

Ramirez, Eric; Gutheinz, Sandy; Brison, James; Ho, Anita; Allen, James; Ceritelli, Olga; Tobar, Claudia; Nguyen, Thuykien; Crenshaw, Harrel; Santos, Roxann

2008-01-01

Supplier Management System (SMS) allows for a consistent, agency-wide performance rating system for suppliers used by NASA. This version (2.0) combines separate databases into one central database that allows for the sharing of supplier data. Information extracted from the NBS/Oracle database can be used to generate ratings. Also, supplier ratings can now be generated in the areas of cost, product quality, delivery, and audit data. Supplier data can be charted based on real-time user input. Based on these individual ratings, an overall rating can be generated. Data that normally would be stored in multiple databases, each requiring its own log-in, is now readily available and easily accessible with only one log-in required. Additionally, the database can accommodate the storage and display of quality-related data that can be analyzed and used in the supplier procurement decision-making process. Moreover, the software allows for a Closed-Loop System (supplier feedback), as well as the capability to communicate with other federal agencies.

Ontology to relational database transformation for web application development and maintenance

NASA Astrophysics Data System (ADS)

Mahmudi, Kamal; Inggriani Liem, M. M.; Akbar, Saiful

2018-03-01

Ontology is used as knowledge representation while database is used as facts recorder in a KMS (Knowledge Management System). In most applications, data are managed in a database system and updated through the application and then they are transformed to knowledge as needed. Once a domain conceptor defines the knowledge in the ontology, application and database can be generated from the ontology. Most existing frameworks generate application from its database. In this research, ontology is used for generating the application. As the data are updated through the application, a mechanism is designed to trigger an update to the ontology so that the application can be rebuilt based on the newest ontology. By this approach, a knowledge engineer has a full flexibility to renew the application based on the latest ontology without dependency to a software developer. In many cases, the concept needs to be updated when the data changed. The framework is built and tested in a spring java environment. A case study was conducted to proof the concepts.

Impact of correction factors in human brain lesion-behavior inference.

PubMed

Sperber, Christoph; Karnath, Hans-Otto

2017-03-01

Statistical voxel-based lesion-behavior mapping (VLBM) in neurological patients with brain lesions is frequently used to examine the relationship between structure and function of the healthy human brain. Only recently, two simulation studies noted reduced anatomical validity of this method, observing the results of VLBM to be systematically misplaced by about 16 mm. However, both simulation studies differed from VLBM analyses of real data in that they lacked the proper use of two correction factors: lesion size and "sufficient lesion affection." In simulation experiments on a sample of 274 real stroke patients, we found that the use of these two correction factors reduced misplacement markedly compared to uncorrected VLBM. Apparently, the misplacement is due to physiological effects of brain lesion anatomy. Voxel-wise topographies of collateral damage in the real data were generated and used to compute a metric for the inter-voxel relation of brain damage. "Anatomical bias" vectors that were solely calculated from these inter-voxel relations in the patients' real anatomical data, successfully predicted the VLBM misplacement. The latter has the potential to help in the development of new VLBM methods that provide even higher anatomical validity than currently available by the proper use of correction factors. Hum Brain Mapp 38:1692-1701, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The anatomical problem posed by brain complexity and size: a potential solution.

PubMed

DeFelipe, Javier

2015-01-01

Over the years the field of neuroanatomy has evolved considerably but unraveling the extraordinary structural and functional complexity of the brain seems to be an unattainable goal, partly due to the fact that it is only possible to obtain an imprecise connection matrix of the brain. The reasons why reaching such a goal appears almost impossible to date is discussed here, together with suggestions of how we could overcome this anatomical problem by establishing new methodologies to study the brain and by promoting interdisciplinary collaboration. Generating a realistic computational model seems to be the solution rather than attempting to fully reconstruct the whole brain or a particular brain region.

Design and Validation of 3D Printed Complex Bone Models with Internal Anatomic Fidelity for Surgical Training and Rehearsal.

PubMed

Unger, Bertram J; Kraut, Jay; Rhodes, Charlotte; Hochman, Jordan

2014-01-01

Physical models of complex bony structures can be used for surgical skills training. Current models focus on surface rendering but suffer from a lack of internal accuracy due to limitations in the manufacturing process. We describe a technique for generating internally accurate rapid-prototyped anatomical models with solid and hollow structures from clinical and microCT data using a 3D printer. In a face validation experiment, otolaryngology residents drilled a cadaveric bone and its corresponding printed model. The printed bone models were deemed highly realistic representations across all measured parameters and the educational value of the models was strongly appreciated.

Midwest Generation, Waukegan Generating Station; Order Partially Denying And Partially Granting Petition For Objection To Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Protein Bioinformatics Databases and Resources

PubMed Central

Chen, Chuming; Huang, Hongzhan; Wu, Cathy H.

2017-01-01

Many publicly available data repositories and resources have been developed to support protein related information management, data-driven hypothesis generation and biological knowledge discovery. To help researchers quickly find the appropriate protein related informatics resources, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases in this chapter. We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era. PMID:28150231

Distinct rhythm generators for inspiration and expiration in the juvenile rat

PubMed Central

Janczewski, Wiktor A; Feldman, Jack L

2006-01-01

Inspiration and active expiration are commonly viewed as antagonistic phases of a unitary oscillator that generates respiratory rhythm. This view conflicts with observations we report here in juvenile rats, where by administration of fentanyl, a selective μ-opiate agonist, and induction of lung reflexes, we separately manipulated the frequency of inspirations and expirations. Moreover, completely transecting the brainstem at the caudal end of the facial nucleus abolished active expirations, while rhythmic inspirations continued. We hypothesize that inspiration and expiration are generated by coupled, anatomically separate rhythm generators, one generating active expiration located close to the facial nucleus in the region of the retrotrapezoid nucleus/parafacial respiratory group, the other generating inspiration located more caudally in the preBötzinger Complex. PMID:16293645

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

PubMed Central

2013-01-01

Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

Thermal Protection System Imagery Inspection Management System -TIIMS

NASA Technical Reports Server (NTRS)

Goza, Sharon; Melendrez, David L.; Henningan, Marsha; LaBasse, Daniel; Smith, Daniel J.

2011-01-01

TIIMS is used during the inspection phases of every mission to provide quick visual feedback, detailed inspection data, and determination to the mission management team. This system consists of a visual Web page interface, an SQL database, and a graphical image generator. These combine to allow a user to ascertain quickly the status of the inspection process, and current determination of any problem zones. The TIIMS system allows inspection engineers to enter their determinations into a database and to link pertinent images and video to those database entries. The database then assigns criteria to each zone and tile, and via query, sends the information to a graphical image generation program. Using the official TIPS database tile positions and sizes, the graphical image generation program creates images of the current status of the orbiter, coloring zones, and tiles based on a predefined key code. These images are then displayed on a Web page using customized JAVA scripts to display the appropriate zone of the orbiter based on the location of the user's cursor. The close-up graphic and database entry for that particular zone can then be seen by selecting the zone. This page contains links into the database to access the images used by the inspection engineer when they make the determination entered into the database. Status for the inspection zones changes as determinations are refined and shown by the appropriate color code.

Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.

PubMed

Akune, Yukie; Lin, Chi-Hung; Abrahams, Jodie L; Zhang, Jingyu; Packer, Nicolle H; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P

2016-08-05

Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database. Copyright © 2016 Elsevier Ltd. All rights reserved.

Large-scale subject-specific cerebral arterial tree modeling using automated parametric mesh generation for blood flow simulation.

PubMed

Ghaffari, Mahsa; Tangen, Kevin; Alaraj, Ali; Du, Xinjian; Charbel, Fady T; Linninger, Andreas A

2017-12-01

In this paper, we present a novel technique for automatic parametric mesh generation of subject-specific cerebral arterial trees. This technique generates high-quality and anatomically accurate computational meshes for fast blood flow simulations extending the scope of 3D vascular modeling to a large portion of cerebral arterial trees. For this purpose, a parametric meshing procedure was developed to automatically decompose the vascular skeleton, extract geometric features and generate hexahedral meshes using a body-fitted coordinate system that optimally follows the vascular network topology. To validate the anatomical accuracy of the reconstructed vasculature, we performed statistical analysis to quantify the alignment between parametric meshes and raw vascular images using receiver operating characteristic curve. Geometric accuracy evaluation showed an agreement with area under the curves value of 0.87 between the constructed mesh and raw MRA data sets. Parametric meshing yielded on-average, 36.6% and 21.7% orthogonal and equiangular skew quality improvement over the unstructured tetrahedral meshes. The parametric meshing and processing pipeline constitutes an automated technique to reconstruct and simulate blood flow throughout a large portion of the cerebral arterial tree down to the level of pial vessels. This study is the first step towards fast large-scale subject-specific hemodynamic analysis for clinical applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ioss IO Subsystem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sjaardema, Gregory; Bauer, David; Erik, & Illescas

2017-01-06

The Ioss is a database-independent package for providing an object-oriented, abstract interface to IO capabilities for a finite element application; and concrete database interfaces which provided input and/or output to exodusII, xdmf, generated, and heartbeat database formats. The Ioss provides an object-oriented C++-based IO interface for a finite element application code. The application code can perform all IO operations through the Ioss interface which is typically at a higher abstraction level than the concrete database formats. The Ioss then performs the needed operations to translate the finite element data to the specific format required by the concrete database implementations. Themore » Ioss currently supports interfaces to exodusII, xdmf, generated, and heartbeat formats, but additional formats can be easily added.« less

A novel approach for incremental uncertainty rule generation from databases with missing values handling: application to dynamic medical databases.

PubMed

Konias, Sokratis; Chouvarda, Ioanna; Vlahavas, Ioannis; Maglaveras, Nicos

2005-09-01

Current approaches for mining association rules usually assume that the mining is performed in a static database, where the problem of missing attribute values does not practically exist. However, these assumptions are not preserved in some medical databases, like in a home care system. In this paper, a novel uncertainty rule algorithm is illustrated, namely URG-2 (Uncertainty Rule Generator), which addresses the problem of mining dynamic databases containing missing values. This algorithm requires only one pass from the initial dataset in order to generate the item set, while new metrics corresponding to the notion of Support and Confidence are used. URG-2 was evaluated over two medical databases, introducing randomly multiple missing values for each record's attribute (rate: 5-20% by 5% increments) in the initial dataset. Compared with the classical approach (records with missing values are ignored), the proposed algorithm was more robust in mining rules from datasets containing missing values. In all cases, the difference in preserving the initial rules ranged between 30% and 60% in favour of URG-2. Moreover, due to its incremental nature, URG-2 saved over 90% of the time required for thorough re-mining. Thus, the proposed algorithm can offer a preferable solution for mining in dynamic relational databases.

CycADS: an annotation database system to ease the development and update of BioCyc databases

PubMed Central

Vellozo, Augusto F.; Véron, Amélie S.; Baa-Puyoulet, Patrice; Huerta-Cepas, Jaime; Cottret, Ludovic; Febvay, Gérard; Calevro, Federica; Rahbé, Yvan; Douglas, Angela E.; Gabaldón, Toni; Sagot, Marie-France; Charles, Hubert; Colella, Stefano

2011-01-01

In recent years, genomes from an increasing number of organisms have been sequenced, but their annotation remains a time-consuming process. The BioCyc databases offer a framework for the integrated analysis of metabolic networks. The Pathway tool software suite allows the automated construction of a database starting from an annotated genome, but it requires prior integration of all annotations into a specific summary file or into a GenBank file. To allow the easy creation and update of a BioCyc database starting from the multiple genome annotation resources available over time, we have developed an ad hoc data management system that we called Cyc Annotation Database System (CycADS). CycADS is centred on a specific database model and on a set of Java programs to import, filter and export relevant information. Data from GenBank and other annotation sources (including for example: KAAS, PRIAM, Blast2GO and PhylomeDB) are collected into a database to be subsequently filtered and extracted to generate a complete annotation file. This file is then used to build an enriched BioCyc database using the PathoLogic program of Pathway Tools. The CycADS pipeline for annotation management was used to build the AcypiCyc database for the pea aphid (Acyrthosiphon pisum) whose genome was recently sequenced. The AcypiCyc database webpage includes also, for comparative analyses, two other metabolic reconstruction BioCyc databases generated using CycADS: TricaCyc for Tribolium castaneum and DromeCyc for Drosophila melanogaster. Linked to its flexible design, CycADS offers a powerful software tool for the generation and regular updating of enriched BioCyc databases. The CycADS system is particularly suited for metabolic gene annotation and network reconstruction in newly sequenced genomes. Because of the uniform annotation used for metabolic network reconstruction, CycADS is particularly useful for comparative analysis of the metabolism of different organisms. Database URL: http://www.cycadsys.org PMID:21474551

BDVC (Bimodal Database of Violent Content): A database of violent audio and video

NASA Astrophysics Data System (ADS)

Rivera Martínez, Jose Luis; Mijes Cruz, Mario Humberto; Rodríguez Vázqu, Manuel Antonio; Rodríguez Espejo, Luis; Montoya Obeso, Abraham; García Vázquez, Mireya Saraí; Ramírez Acosta, Alejandro Álvaro

2017-09-01

Nowadays there is a trend towards the use of unimodal databases for multimedia content description, organization and retrieval applications of a single type of content like text, voice and images, instead bimodal databases allow to associate semantically two different types of content like audio-video, image-text, among others. The generation of a bimodal database of audio-video implies the creation of a connection between the multimedia content through the semantic relation that associates the actions of both types of information. This paper describes in detail the used characteristics and methodology for the creation of the bimodal database of violent content; the semantic relationship is stablished by the proposed concepts that describe the audiovisual information. The use of bimodal databases in applications related to the audiovisual content processing allows an increase in the semantic performance only and only if these applications process both type of content. This bimodal database counts with 580 audiovisual annotated segments, with a duration of 28 minutes, divided in 41 classes. Bimodal databases are a tool in the generation of applications for the semantic web.

Low dose CT image restoration using a database of image patches

NASA Astrophysics Data System (ADS)

Ha, Sungsoo; Mueller, Klaus

2015-01-01

Reducing the radiation dose in CT imaging has become an active research topic and many solutions have been proposed to remove the significant noise and streak artifacts in the reconstructed images. Most of these methods operate within the domain of the image that is subject to restoration. This, however, poses limitations on the extent of filtering possible. We advocate to take into consideration the vast body of external knowledge that exists in the domain of already acquired medical CT images, since after all, this is what radiologists do when they examine these low quality images. We can incorporate this knowledge by creating a database of prior scans, either of the same patient or a diverse corpus of different patients, to assist in the restoration process. Our paper follows up on our previous work that used a database of images. Using images, however, is challenging since it requires tedious and error prone registration and alignment. Our new method eliminates these problems by storing a diverse set of small image patches in conjunction with a localized similarity matching scheme. We also empirically show that it is sufficient to store these patches without anatomical tags since their statistics are sufficiently strong to yield good similarity matches from the database and as a direct effect, produce image restorations of high quality. A final experiment demonstrates that our global database approach can recover image features that are difficult to preserve with conventional denoising approaches.

Segmentation and feature extraction of cervical spine x-ray images

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Thoma, George R.

1999-05-01

As part of an R&D project in mixed text/image database design, the National Library of Medicine has archived a collection of 17,000 digitized x-ray images of the cervical and lumbar spine which were collected as part of the second National Health and Nutrition Examination Survey (NHANES II). To make this image data available and usable to a wide audience, we are investigating techniques for indexing the image content by automated or semi-automated means. Indexing of the images by features of interest to researchers in spine disease and structure requires effective segmentation of the vertebral anatomy. This paper describes work in progress toward this segmentation of the cervical spine images into anatomical components of interest, including anatomical landmarks for vertebral location, and segmentation and identification of individual vertebrae. Our work includes developing a reliable method for automatically fixing an anatomy-based coordinate system in the images, and work to adaptively threshold the images, using methods previously applied by researchers in cardioangiography. We describe the motivation for our work and present our current results in both areas.

Database Administrator

ERIC Educational Resources Information Center

Moore, Pam

2010-01-01

The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

How useful is YouTube in learning heart anatomy?

PubMed

Raikos, Athanasios; Waidyasekara, Pasan

2014-01-01

Nowadays more and more modern medical degree programs focus on self-directed and problem-based learning. That requires students to search for high quality and easy to retrieve online resources. YouTube is an emerging platform for learning human anatomy due to easy access and being a free service. The purpose of this study is to make a quantitative and qualitative analysis of the available human heart anatomy videos on YouTube. Using the search engine of the platform we searched for relevant videos using various keywords. Videos with irrelevant content, animal tissue, non-English language, no sound, duplicates, and physiology focused were excluded from further elaboration. The initial search retrieved 55,525 videos, whereas only 294 qualified for further analysis. A unique scoring system was used to assess the anatomical quality and details, general quality, and the general data for each video. Our results indicate that the human heart anatomy videos available on YouTube conveyed our anatomical criteria poorly, whereas the general quality scoring found borderline. Students should be selective when looking up on public video databases as it can prove challenging, time consuming, and the anatomical information may be misleading due to absence of content review. Anatomists and institutions are encouraged to prepare and endorse good quality material and make them available online for the students. The scoring rubric used in the study comprises a valuable tool to faculty members for quality evaluation of heart anatomy videos available on social media platforms. Copyright © 2013 American Association of Anatomists.

Anatomical landmarks of radical prostatecomy.

PubMed

Stolzenburg, Jens-Uwe; Schwalenberg, Thilo; Horn, Lars-Christian; Neuhaus, Jochen; Constantinides, Costantinos; Liatsikos, Evangelos N

2007-03-01

In the present study, we review current literature and based on our experience, we present the anatomical landmarks of open and laparoscopic/endoscopic radical prostatectomy. A thorough literature search was performed with the Medline database on the anatomy and the nomenclature of the structures surrounding the prostate gland. The correct handling of puboprostatic ligaments, external urethral sphincter, prostatic fascias and neurovascular bundle is necessary for avoiding malfunction of the urogenital system after radical prostatectomy. When evaluating new prostatectomy techniques, we should always take into account both clinical and final oncological outcomes. The present review adds further knowledge to the existing "postprostatectomy anatomical hazard" debate. It emphasizes upon the role of the puboprostatic ligaments and the course of the external urethral sphincter for urinary continence. When performing an intrafascial nerve sparing prostatectomy most urologists tend to approach as close to the prostatic capsula as possible, even though there is no concurrence regarding the nomenclature of the surrounding fascias and the course of the actual neurovascular bundles. After completion of an intrafascial technique the specimen does not contain any periprostatic tissue and thus the detection of pT3a disease is not feasible. This especially becomes problematic if the tumour reaches the resection margin. Nerve sparing open and laparoscopic radical prostatectomy should aim in maintaining sexual function, recuperating early continence after surgery, without hindering the final oncological outcome to the procedure. Despite the different approaches for radical prostatectomy the key for better results is the understanding of the anatomy of the bladder neck and the urethra.

Quantitative assessment of anatomical change using a virtual proton depth radiograph for adaptive head and neck proton therapy.

PubMed

Wang, Peng; Yin, Lingshu; Zhang, Yawei; Kirk, Maura; Song, Gang; Ahn, Peter H; Lin, Alexander; Gee, James; Dolney, Derek; Solberg, Timothy D; Maughan, Richard; McDonough, James; Teo, Boon-Keng Kevin

2016-03-08

The aim of this work is to demonstrate the feasibility of using water-equivalent thickness (WET) and virtual proton depth radiographs (PDRs) of intensity corrected cone-beam computed tomography (CBCT) to detect anatomical change and patient setup error to trigger adaptive head and neck proton therapy. The planning CT (pCT) and linear accelerator (linac) equipped CBCTs acquired weekly during treatment of a head and neck patient were used in this study. Deformable image registration (DIR) was used to register each CBCT with the pCT and map Hounsfield units (HUs) from the planning CT (pCT) onto the daily CBCT. The deformed pCT is referred as the corrected CBCT (cCBCT). Two dimensional virtual lateral PDRs were generated using a ray-tracing technique to project the cumulative WET from a virtual source through the cCBCT and the pCT onto a virtual plane. The PDRs were used to identify anatomic regions with large variations in the proton range between the cCBCT and pCT using a threshold of 3 mm relative difference of WET and 3 mm search radius criteria. The relationship between PDR differences and dose distribution is established. Due to weight change and tumor response during treatment, large variations in WETs were observed in the relative PDRs which corresponded spatially with an increase in the number of failing points within the GTV, especially in the pharynx area. Failing points were also evident near the posterior neck due to setup variations. Differences in PDRs correlated spatially to differences in the distal dose distribution in the beam's eye view. Virtual PDRs generated from volumetric data, such as pCTs or CBCTs, are potentially a useful quantitative tool in proton therapy. PDRs and WET analysis may be used to detect anatomical change from baseline during treatment and trigger further analysis in adaptive proton therapy.

SU-F-R-41: Regularized PCA Can Model Treatment-Related Changes in Head and Neck Patients Using Daily CBCTs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chetvertkov, M; Henry Ford Health System, Detroit, MI; Siddiqui, F

2016-06-15

Purpose: To use daily cone beam CTs (CBCTs) to develop regularized principal component analysis (PCA) models of anatomical changes in head and neck (H&N) patients, to guide replanning decisions in adaptive radiation therapy (ART). Methods: Known deformations were applied to planning CT (pCT) images of 10 H&N patients to model several different systematic anatomical changes. A Pinnacle plugin was used to interpolate systematic changes over 35 fractions, generating a set of 35 synthetic CTs for each patient. Deformation vector fields (DVFs) were acquired between the pCT and synthetic CTs and random fraction-to-fraction changes were superimposed on the DVFs. Standard non-regularizedmore » and regularized patient-specific PCA models were built using the DVFs. The ability of PCA to extract the known deformations was quantified. PCA models were also generated from clinical CBCTs, for which the deformations and DVFs were not known. It was hypothesized that resulting eigenvectors/eigenfunctions with largest eigenvalues represent the major anatomical deformations during the course of treatment. Results: As demonstrated with quantitative results in the supporting document regularized PCA is more successful than standard PCA at capturing systematic changes early in the treatment. Regularized PCA is able to detect smaller systematic changes against the background of random fraction-to-fraction changes. To be successful at guiding ART, regularized PCA should be coupled with models of when anatomical changes occur: early, late or throughout the treatment course. Conclusion: The leading eigenvector/eigenfunction from the both PCA approaches can tentatively be identified as a major systematic change during radiotherapy course when systematic changes are large enough with respect to random fraction-to-fraction changes. In all cases the regularized PCA approach appears to be more reliable at capturing systematic changes, enabling dosimetric consequences to be projected once trends are established early in the treatment course. This work is supported in part by a grant from Varian Medical Systems, Palo Alto, CA.« less

Automated extraction of knowledge for model-based diagnostics

NASA Technical Reports Server (NTRS)

Gonzalez, Avelino J.; Myler, Harley R.; Towhidnejad, Massood; Mckenzie, Frederic D.; Kladke, Robin R.

1990-01-01

The concept of accessing computer aided design (CAD) design databases and extracting a process model automatically is investigated as a possible source for the generation of knowledge bases for model-based reasoning systems. The resulting system, referred to as automated knowledge generation (AKG), uses an object-oriented programming structure and constraint techniques as well as internal database of component descriptions to generate a frame-based structure that describes the model. The procedure has been designed to be general enough to be easily coupled to CAD systems that feature a database capable of providing label and connectivity data from the drawn system. The AKG system is capable of defining knowledge bases in formats required by various model-based reasoning tools.

MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.

PubMed

Gacesa, Ranko; Zucko, Jurica; Petursdottir, Solveig K; Gudmundsdottir, Elisabet Eik; Fridjonsson, Olafur H; Diminic, Janko; Long, Paul F; Cullum, John; Hranueli, Daslav; Hreggvidsson, Gudmundur O; Starcevic, Antonio

2017-06-01

The MEGGASENSE platform constructs relational databases of DNA or protein sequences. The default functional analysis uses 14 106 hidden Markov model (HMM) profiles based on sequences in the KEGG database. The Solr search engine allows sophisticated queries and a BLAST search function is also incorporated. These standard capabilities were used to generate the SCATT database from the predicted proteome of Streptomyces cattleya . The implementation of a specialised metagenome database (AMYLOMICS) for bioprospecting of carbohydrate-modifying enzymes is described. In addition to standard assembly of reads, a novel 'functional' assembly was developed, in which screening of reads with the HMM profiles occurs before the assembly. The AMYLOMICS database incorporates additional HMM profiles for carbohydrate-modifying enzymes and it is illustrated how the combination of HMM and BLAST analyses helps identify interesting genes. A variety of different proteome and metagenome databases have been generated by MEGGASENSE.

Definition and maintenance of a telemetry database dictionary

NASA Technical Reports Server (NTRS)

Knopf, William P. (Inventor)

2007-01-01

A telemetry dictionary database includes a component for receiving spreadsheet workbooks of telemetry data over a web-based interface from other computer devices. Another component routes the spreadsheet workbooks to a specified directory on the host processing device. A process then checks the received spreadsheet workbooks for errors, and if no errors are detected the spreadsheet workbooks are routed to another directory to await initiation of a remote database loading process. The loading process first converts the spreadsheet workbooks to comma separated value (CSV) files. Next, a network connection with the computer system that hosts the telemetry dictionary database is established and the CSV files are ported to the computer system that hosts the telemetry dictionary database. This is followed by a remote initiation of a database loading program. Upon completion of loading a flatfile generation program is manually initiated to generate a flatfile to be used in a mission operations environment by the core ground system.

Expanding the Range of Plant Functional Diversity Represented in Global Vegetation Models: Towards Lineage-based Plant Functional Types

NASA Astrophysics Data System (ADS)

Still, C. J.; Griffith, D.; Edwards, E.; Forrestel, E.; Lehmann, C.; Anderson, M.; Craine, J.; Pau, S.; Osborne, C.

2014-12-01

Variation in plant species traits, such as photosynthetic and hydraulic properties, can indicate vulnerability or resilience to climate change, and feed back to broad-scale spatial and temporal patterns in biogeochemistry, demographics, and biogeography. Yet, predicting how vegetation will respond to future environmental changes is severely limited by the inability of our models to represent species-level trait variation in processes and properties, as current generation process-based models are mostly based on the generalized and abstracted concept of plant functional types (PFTs) which were originally developed for hydrological modeling. For example, there are close to 11,000 grass species, but most vegetation models have only a single C4 grass and one or two C3 grass PFTs. However, while species trait databases are expanding rapidly, they have been produced mostly from unstructured research, with a focus on easily researched traits that are not necessarily the most important for determining plant function. Additionally, implementing realistic species-level trait variation in models is challenging. Combining related and ecologically similar species in these models might ameliorate this limitation. Here we argue for an intermediate, lineage-based approach to PFTs, which draws upon recent advances in gene sequencing and phylogenetic modeling, and where trait complex variations and anatomical features are constrained by a shared evolutionary history. We provide an example of this approach with grass lineages that vary in photosynthetic pathway (C3 or C4) and other functional and structural traits. We use machine learning approaches and geospatial databases to infer the most important environmental controls and climate niche variation for the distribution of grass lineages, and utilize a rapidly expanding grass trait database to demonstrate examples of lineage-based grass PFTs. For example, grasses in the Andropogoneae are typically tall species that dominate wet and seasonally burned ecosystems, whereas Chloridoideae grasses are associated with semi-arid regions. These two C4 lineages are expected to respond quite differently to climate change, but are often modelled as a single PFT.

Space Object Radiometric Modeling for Hardbody Optical Signature Database Generation

DTIC Science & Technology

2009-09-01

Introduction This presentation summarizes recent activity in monitoring spacecraft health status using passive remote optical nonimaging ...Approved for public release; distribution is unlimited. Space Object Radiometric Modeling for Hardbody Optical Signature Database Generation...It is beneficial to the observer/analyst to understand the fundamental optical signature variability associated with these detection and

Vascular knowledge in medieval times was the turning point for the humanistic trend.

PubMed

Ducasse, E; Speziale, F; Baste, J C; Midy, D

2006-06-01

Knowledge of the history of our surgical specialty may broaden our viewpoint for everyday practice. We illustrate the scientific progress made in medieval times relevant to the vascular system and blood circulation, progress made despite prevailing religious and philosophical dogma. We located all articles concerning vascular knowledge and historical reviews in databases such as MEDLINE, EMBASE and the database of abstracts of reviews (DARE). We also explored the database of the register from the French National Library, the French Medical Inter-University (BIUM), the Italian National Library and the French and Italian Libraries in the Vatican. All data were collected and analysed in chronological order. Medieval vascular knowledge was inherited from Greek via Byzantine and Arabic writings, the first controversies against the recognized vascular schema emanating from an Arabian physician in the 13th century. Dissection was forbidden and clerical rules instilled a fear of blood. Major contributions to scientific progress in the vascular field in medieval times came from Ibn-al-Nafis and Harvey. Vascular specialists today may feel proud to recall that once religious dogma declined in early medieval times, vascular anatomic and physiological discoveries led the way to scientific progress.

Dynamic publication model for neurophysiology databases.

PubMed

Gardner, D; Abato, M; Knuth, K H; DeBellis, R; Erde, S M

2001-08-29

We have implemented a pair of database projects, one serving cortical electrophysiology and the other invertebrate neurones and recordings. The design for each combines aspects of two proven schemes for information interchange. The journal article metaphor determined the type, scope, organization and quantity of data to comprise each submission. Sequence databases encouraged intuitive tools for data viewing, capture, and direct submission by authors. Neurophysiology required transcending these models with new datatypes. Time-series, histogram and bivariate datatypes, including illustration-like wrappers, were selected by their utility to the community of investigators. As interpretation of neurophysiological recordings depends on context supplied by metadata attributes, searches are via visual interfaces to sets of controlled-vocabulary metadata trees. Neurones, for example, can be specified by metadata describing functional and anatomical characteristics. Permanence is advanced by data model and data formats largely independent of contemporary technology or implementation, including Java and the XML standard. All user tools, including dynamic data viewers that serve as a virtual oscilloscope, are Java-based, free, multiplatform, and distributed by our application servers to any contemporary networked computer. Copyright is retained by submitters; viewer displays are dynamic and do not violate copyright of related journal figures. Panels of neurophysiologists view and test schemas and tools, enhancing community support.

The development of a population of 4D pediatric XCAT phantoms for imaging research and optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Segars, W. P., E-mail: paul.segars@duke.edu; Norris, Hannah; Sturgeon, Gregory M.

Purpose: We previously developed a set of highly detailed 4D reference pediatric extended cardiac-torso (XCAT) phantoms at ages of newborn, 1, 5, 10, and 15 yr with organ and tissue masses matched to ICRP Publication 89 values. In this work, we extended this reference set to a series of 64 pediatric phantoms of varying age and height and body mass percentiles representative of the public at large. The models will provide a library of pediatric phantoms for optimizing pediatric imaging protocols. Methods: High resolution positron emission tomography-computed tomography data obtained from the Duke University database were reviewed by a practicingmore » experienced radiologist for anatomic regularity. The CT portion of the data was then segmented with manual and semiautomatic methods to form a target model defined using nonuniform rational B-spline surfaces. A multichannel large deformation diffeomorphic metric mapping algorithm was used to calculate the transform from the best age matching pediatric XCAT reference phantom to the patient target. The transform was used to complete the target, filling in the nonsegmented structures and defining models for the cardiac and respiratory motions. The complete phantoms, consisting of thousands of structures, were then manually inspected for anatomical accuracy. The mass for each major tissue was calculated and compared to linearly interpolated ICRP values for different ages. Results: Sixty four new pediatric phantoms were created in this manner. Each model contains the same level of detail as the original XCAT reference phantoms and also includes parameterized models for the cardiac and respiratory motions. For the phantoms that were 10 yr old and younger, we included both sets of reproductive organs. This gave them the capability to simulate both male and female anatomy. With this, the population can be expanded to 92. Wide anatomical variation was clearly seen amongst the phantom models, both in organ shape and size, even for models of the same age and sex. The phantoms can be combined with existing simulation packages to generate realistic pediatric imaging data from different modalities. Conclusions: This work provides a large cohort of highly detailed pediatric phantoms with 4D capabilities of varying age, height, and body mass. The population of phantoms will provide a vital tool with which to optimize 3D and 4D pediatric imaging devices and techniques in terms of image quality and radiation-absorbed dose.« less

Generation And Understanding Of Natural Language Using Information In A Frame Structure

NASA Astrophysics Data System (ADS)

Perkins, Walton A.

1989-03-01

Many expert systems and relational database systems store factual information in the form of attributes values of objects. Problems arise in transforming from that attribute (frame) database representation into English surface structure and in transforming the English surface structure into a representation that references information in the frame database. In this paper we consider mainly the generation process, as it is this area in which we have made the most significant progress. In its interaction with the user, the expert system must generate questions, declarations, and uncertain declarations. Attributes such as COLOR, LENGTH, and ILLUMINATION can be referenced using the template: " of " for both questions and declarations. However, many other attributes, such as RATTLES, in "What is RATTLES of the light bulb?", and HAS_STREP_THROAT in, "HAS_STREP_THROAT of Dan is true." do not fit this template. We examined over 300 attributes from several knowledge bases and have grouped them into 16 classes. For each class there is one "question" template, one "declaration" template, and one "uncertain declaration" template for generating English surface structure. The internal databases identifiers (e.g., HAS_STREP_THROAT and DISEASE_35) must also be replaced by output synonyms. Classifying each attribute in combination with synonym translation remarkably improved the English surface structure that the system generated. In the area of understanding, synonym translation and knowledge of the attribute properties, such as legal values, has resulted in a robust database query capability.

Tissue Engineering Whole Bones Through Endochondral Ossification: Regenerating the Distal Phalanx.

PubMed

Sheehy, Eamon J; Mesallati, Tariq; Kelly, Lara; Vinardell, Tatiana; Buckley, Conor T; Kelly, Daniel J

2015-01-01

Novel strategies are urgently required to facilitate regeneration of entire bones lost due to trauma or disease. In this study, we present a novel framework for the regeneration of whole bones by tissue engineering anatomically shaped hypertrophic cartilaginous grafts in vitro that subsequently drive endochondral bone formation in vivo. To realize this, we first fabricated molds from digitized images to generate mesenchymal stem cell-laden alginate hydrogels in the shape of different bones (the temporomandibular joint [TMJ] condyle and the distal phalanx). These constructs could be stimulated in vitro to generate anatomically shaped hypertrophic cartilaginous tissues that had begun to calcify around their periphery. Constructs were then formed into the shape of the distal phalanx to create the hypertrophic precursor of the osseous component of an engineered long bone. A layer of cartilage engineered through self-assembly of chondrocytes served as the articular surface of these constructs. Following chondrogenic priming and subcutaneous implantation, the hypertrophic phase of the engineered phalanx underwent endochondral ossification, leading to the generation of a vascularized bone integrated with a covering layer of stable articular cartilage. Furthermore, spatial bone deposition within the construct could be modulated by altering the architecture of the osseous component before implantation. These findings open up new horizons to whole limb regeneration by recapitulating key aspects of normal bone development.

Sagace: A web-based search engine for biomedical databases in Japan

PubMed Central

2012-01-01

Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816

Implementation of a data management software system for SSME test history data

NASA Technical Reports Server (NTRS)

Abernethy, Kenneth

1986-01-01

The implementation of a software system for managing Space Shuttle Main Engine (SSME) test/flight historical data is presented. The software system uses the database management system RIM7 for primary data storage and routine data management, but includes several FORTRAN programs, described here, which provide customized access to the RIM7 database. The consolidation, modification, and transfer of data from the database THIST, to the RIM7 database THISRM is discussed. The RIM7 utility modules for generating some standard reports from THISRM and performing some routine updating and maintenance are briefly described. The FORTRAN accessing programs described include programs for initial loading of large data sets into the database, capturing data from files for database inclusion, and producing specialized statistical reports which cannot be provided by the RIM7 report generator utility. An expert system tutorial, constructed using the expert system shell product INSIGHT2, is described. Finally, a potential expert system, which would analyze data in the database, is outlined. This system could use INSIGHT2 as well and would take advantage of RIM7's compatibility with the microcomputer database system RBase 5000.

The Mouse Heart Attack Research Tool (mHART) 1.0 Database.

PubMed

DeLeon-Pennell, Kristine Y; Iyer, Rugmani Padmanabhan; Ma, Yonggang; Yabluchanskiy, Andriy; Zamilpa, Rogelio; Chiao, Ying Ann; Cannon, Presley; Cates, Courtney; Flynn, Elizabeth R; Halade, Ganesh V; de Castro Bras, Lisandra E; Lindsey, Merry L

2018-05-18

The generation of Big Data has enabled systems-level dissections into the mechanisms of cardiovascular pathology. Integration of genetic, proteomic, and pathophysiological variables across platforms and laboratories fosters discoveries through multidisciplinary investigations and minimizes unnecessary redundancy in research efforts. The Mouse Heart Attack Research Tool (mHART) consolidates a large dataset of over 10 years of experiments from a single laboratory for cardiovascular investigators to generate novel hypotheses and identify new predictive markers of progressive left ventricular remodeling following myocardial infarction (MI) in mice. We designed the mHART REDCap database using our own data to integrate cardiovascular community participation. We generated physiological, biochemical, cellular, and proteomic outputs from plasma and left ventricles obtained from post-MI and no MI (naïve) control groups. We included both male and female mice ranging in age from 3 to 36 months old. After variable collection, data underwent quality assessment for data curation (e.g. eliminate technical errors, check for completeness, remove duplicates, and define terms). Currently, mHART 1.0 contains >888,000 data points and includes results from >2,100 unique mice. Database performance was tested and an example provided to illustrate database utility. This report explains how the first version of the mHART database was established and provides researchers with a standard framework to aid in the integration of their data into our database or in the development of a similar database.

An automated database case definition for serious bleeding related to oral anticoagulant use.

PubMed

Cunningham, Andrew; Stein, C Michael; Chung, Cecilia P; Daugherty, James R; Smalley, Walter E; Ray, Wayne A

2011-06-01

Bleeding complications are a serious adverse effect of medications that prevent abnormal blood clotting. To facilitate epidemiologic investigations of bleeding complications, we developed and validated an automated database case definition for bleeding-related hospitalizations. The case definition utilized information from an in-progress retrospective cohort study of warfarin-related bleeding in Tennessee Medicaid enrollees 30 years of age or older. It identified inpatient stays during the study period of January 1990 to December 2005 with diagnoses and/or procedures that indicated a current episode of bleeding. The definition was validated by medical record review for a sample of 236 hospitalizations. We reviewed 186 hospitalizations that had medical records with sufficient information for adjudication. Of these, 165 (89%, 95%CI: 83-92%) were clinically confirmed bleeding-related hospitalizations. An additional 19 hospitalizations (10%, 7-15%) were adjudicated as possibly bleeding-related. Of the 165 clinically confirmed bleeding-related hospitalizations, the automated database and clinical definitions had concordant anatomical sites (gastrointestinal, cerebral, genitourinary, other) for 163 (99%, 96-100%). For those hospitalizations with sufficient information to distinguish between upper/lower gastrointestinal bleeding, the concordance was 89% (76-96%) for upper gastrointestinal sites and 91% (77-97%) for lower gastrointestinal sites. A case definition for bleeding-related hospitalizations suitable for automated databases had a positive predictive value of between 89% and 99% and could distinguish specific bleeding sites. Copyright © 2011 John Wiley & Sons, Ltd.

Electrophysiological and Morphological Evidence for Synchronized GnRH Pulse Generator Activity Among Kisspeptin/Neurokinin B/Dynorphin A (KNDy) Neurons in Goats

PubMed Central

WAKABAYASHI, Yoshihiro; YAMAMURA, Takashi; SAKAMOTO, Kohei; MORI, Yuji; OKAMURA, Hiroaki

2012-01-01

Abstract Neurons in the arcuate nucleus (ARC) that concomitantly express kisspeptin, neurokinin B (NKB) and dynorphin A are termed KNDy neurons and are likely candidates for the intrinsic gonadotropin-releasing hormone (GnRH) pulse generator. Our hypothesis is that KNDy neurons are functionally and anatomically interconnected to generate discrete neural signals that govern pulsatile GnRH secretion. Our goal was to address this hypothesis using electrophysiological and anatomical experiments in goats. Bilateral electrodes targeting KNDy neurons were implanted into ovariectomized goats, and GnRH pulse generator activity, represented by characteristic increases in multiple-unit activity (MUA volleys), was measured. Spontaneous and pheromone- or senktide (an NKB receptor agonist)-induced MUA volleys were simultaneously recorded from both sides of the ARC. An anterograde tracer, biotinylated dextran amine (BDA), was also injected unilaterally into the ARC of castrated male goats, and the distribution of fibers containing both BDA and NKB was examined using dual-labeling histochemistry. The results showed that MUA volleys, regardless of origin (spontaneous or experimentally induced), occur simultaneously between the right and left sides of the ARC. Tract tracing indicated that axons projecting from NKB neurons in the ARC were directly apposed to other NKB neuronal cells located bilaterally in the ARC. These results demonstrate that GnRH pulse generator activity occurs synchronously between both sides of the ARC in goats and that KNDy neurons are bilaterally interconnected in the ARC via NKB-containing fibers. Taken together, the results suggest that KNDy neurons form a neuronal circuit to synchronize burst activity among KNDy neurons and thereby generate discrete neural signals that govern pulsatile GnRH secretion. PMID:23080371

Expert Consensus Contouring Guidelines for Intensity Modulated Radiation Therapy in Esophageal and Gastroesophageal Junction Cancer.

PubMed

Wu, Abraham J; Bosch, Walter R; Chang, Daniel T; Hong, Theodore S; Jabbour, Salma K; Kleinberg, Lawrence R; Mamon, Harvey J; Thomas, Charles R; Goodman, Karyn A

2015-07-15

Current guidelines for esophageal cancer contouring are derived from traditional 2-dimensional fields based on bony landmarks, and they do not provide sufficient anatomic detail to ensure consistent contouring for more conformal radiation therapy techniques such as intensity modulated radiation therapy (IMRT). Therefore, we convened an expert panel with the specific aim to derive contouring guidelines and generate an atlas for the clinical target volume (CTV) in esophageal or gastroesophageal junction (GEJ) cancer. Eight expert academically based gastrointestinal radiation oncologists participated. Three sample cases were chosen: a GEJ cancer, a distal esophageal cancer, and a mid-upper esophageal cancer. Uniform computed tomographic (CT) simulation datasets and accompanying diagnostic positron emission tomographic/CT images were distributed to each expert, and the expert was instructed to generate gross tumor volume (GTV) and CTV contours for each case. All contours were aggregated and subjected to quantitative analysis to assess the degree of concordance between experts and to generate draft consensus contours. The panel then refined these contours to generate the contouring atlas. The κ statistics indicated substantial agreement between panelists for each of the 3 test cases. A consensus CTV atlas was generated for the 3 test cases, each representing common anatomic presentations of esophageal cancer. The panel agreed on guidelines and principles to facilitate the generalizability of the atlas to individual cases. This expert panel successfully reached agreement on contouring guidelines for esophageal and GEJ IMRT and generated a reference CTV atlas. This atlas will serve as a reference for IMRT contours for clinical practice and prospective trial design. Subsequent patterns of failure analyses of clinical datasets using these guidelines may require modification in the future. Copyright © 2015 Elsevier Inc. All rights reserved.

Expert consensus contouring guidelines for IMRT in esophageal and gastroesophageal junction cancer

PubMed Central

Wu, Abraham J.; Bosch, Walter R.; Chang, Daniel T.; Hong, Theodore S.; Jabbour, Salma K.; Kleinberg, Lawrence R.; Mamon, Harvey J.; Thomas, Charles R.; Goodman, Karyn A.

2015-01-01

Purpose/Objective(s) Current guidelines for esophageal cancer contouring are derived from traditional two-dimensional fields based on bony landmarks, and do not provide sufficient anatomical detail to ensure consistent contouring for more conformal radiotherapy techniques such as intensity-modulated radiation therapy (IMRT). Therefore, we convened an expert panel with the specific aim to derive contouring guidelines and generate an atlas for the clinical target volume (CTV) in esophageal or gastroesophageal junction (GEJ) cancer. Methods and Materials Eight expert academically-based gastrointestinal radiation oncologists participated. Three sample cases were chosen: a GEJ cancer, a distal esophageal cancer, and a mid-upper esophageal cancer. Uniform CT simulation datasets and an accompanying diagnostic PET-CT were distributed to each expert, and he/she was instructed to generate gross tumor volume (GTV) and CTV contours for each case. All contours were aggregated and subjected to quantitative analysis to assess the degree of concordance between experts and generate draft consensus contours. The panel then refined these contours to generate the contouring atlas. Results Kappa statistics indicated substantial agreement between panelists for each of the three test cases. A consensus CTV atlas was generated for the three test cases, each representing common anatomic presentations of esophageal cancer. The panel agreed on guidelines and principles to facilitate the generalizability of the atlas to individual cases. Conclusions This expert panel successfully reached agreement on contouring guidelines for esophageal and GEJ IMRT and generated a reference CTV atlas. This atlas will serve as a reference for IMRT contours for clinical practice and prospective trial design. Subsequent patterns of failure analyses of clinical datasets utilizing these guidelines may require modification in the future. PMID:26104943

Expert Consensus Contouring Guidelines for Intensity Modulated Radiation Therapy in Esophageal and Gastroesophageal Junction Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Abraham J., E-mail: wua@mskcc.org; Bosch, Walter R.; Chang, Daniel T.

Purpose/Objective(s): Current guidelines for esophageal cancer contouring are derived from traditional 2-dimensional fields based on bony landmarks, and they do not provide sufficient anatomic detail to ensure consistent contouring for more conformal radiation therapy techniques such as intensity modulated radiation therapy (IMRT). Therefore, we convened an expert panel with the specific aim to derive contouring guidelines and generate an atlas for the clinical target volume (CTV) in esophageal or gastroesophageal junction (GEJ) cancer. Methods and Materials: Eight expert academically based gastrointestinal radiation oncologists participated. Three sample cases were chosen: a GEJ cancer, a distal esophageal cancer, and a mid-upper esophagealmore » cancer. Uniform computed tomographic (CT) simulation datasets and accompanying diagnostic positron emission tomographic/CT images were distributed to each expert, and the expert was instructed to generate gross tumor volume (GTV) and CTV contours for each case. All contours were aggregated and subjected to quantitative analysis to assess the degree of concordance between experts and to generate draft consensus contours. The panel then refined these contours to generate the contouring atlas. Results: The κ statistics indicated substantial agreement between panelists for each of the 3 test cases. A consensus CTV atlas was generated for the 3 test cases, each representing common anatomic presentations of esophageal cancer. The panel agreed on guidelines and principles to facilitate the generalizability of the atlas to individual cases. Conclusions: This expert panel successfully reached agreement on contouring guidelines for esophageal and GEJ IMRT and generated a reference CTV atlas. This atlas will serve as a reference for IMRT contours for clinical practice and prospective trial design. Subsequent patterns of failure analyses of clinical datasets using these guidelines may require modification in the future.« less

Energy dynamics of the intraventricular vortex after mitral valve surgery.

PubMed

Nakashima, Kouki; Itatani, Keiichi; Kitamura, Tadashi; Oka, Norihiko; Horai, Tetsuya; Miyazaki, Shohei; Nie, Masaki; Miyaji, Kagami

2017-09-01

Mitral valve morphology after mitral valve surgery affects postoperative intraventricular flow patterns and long-term cardiac performance. We visualized ventricular flow by echocardiography vector flow mapping (VFM) to reveal the impact of different mitral valve procedures. Eleven cases of mechanical mitral valve replacement (nine in the anti-anatomical and two in the anatomical position), three bioprosthetic mitral valve replacements, and four mitral valve repairs were evaluated. The mean age at the procedure was 57.4 ± 17.8 year, and the echocardiography VFM in the apical long-axis view was performed 119.9 ± 126.7 months later. Flow energy loss (EL), kinetic pressure (KP), and the flow energy efficiency ratio (EL/KP) were measured. The cases with MVR in the anatomical position and with valve repair had normal vortex directionality ("Clockwise"; N = 6), whereas those with MVR in the anti-anatomical position and with a bioprosthetic mitral valve had the vortex in the opposite direction ("Counterclockwise"; N = 12). During diastole, vortex direction had no effect on EL ("Clockwise": 0.080 ± 0.025 W/m; "Counterclockwise": 0.083 ± 0.048 W/m; P = 0.31) or KP ("Clockwise": 0.117 ± 0.021 N; "Counterclockwise": 0.099 ± 0.057 N; P = 0.023). However, during systole, the EL/KP ratio was significantly higher in the "Counterclockwise" vortex than that in the "Clockwise" vortex (1.056 ± 0.463 vs. 0.617 ± 0.158; P = 0.009). MVP and MVR with a mechanical valve in the anatomical position preserve the physiological vortex, whereas MVR with a mechanical valve in the anti-anatomical position and a bioprosthetic mitral valve generate inefficient vortex flow patterns, resulting in a potential increase in excessive cardiac workload.

Use of regularized principal component analysis to model anatomical changes during head and neck radiation therapy for treatment adaptation and response assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chetvertkov, Mikhail A., E-mail: chetvertkov@wayne

2016-10-15

Purpose: To develop standard (SPCA) and regularized (RPCA) principal component analysis models of anatomical changes from daily cone beam CTs (CBCTs) of head and neck (H&N) patients and assess their potential use in adaptive radiation therapy, and for extracting quantitative information for treatment response assessment. Methods: Planning CT images of ten H&N patients were artificially deformed to create “digital phantom” images, which modeled systematic anatomical changes during radiation therapy. Artificial deformations closely mirrored patients’ actual deformations and were interpolated to generate 35 synthetic CBCTs, representing evolving anatomy over 35 fractions. Deformation vector fields (DVFs) were acquired between pCT and syntheticmore » CBCTs (i.e., digital phantoms) and between pCT and clinical CBCTs. Patient-specific SPCA and RPCA models were built from these synthetic and clinical DVF sets. EigenDVFs (EDVFs) having the largest eigenvalues were hypothesized to capture the major anatomical deformations during treatment. Results: Principal component analysis (PCA) models achieve variable results, depending on the size and location of anatomical change. Random changes prevent or degrade PCA’s ability to detect underlying systematic change. RPCA is able to detect smaller systematic changes against the background of random fraction-to-fraction changes and is therefore more successful than SPCA at capturing systematic changes early in treatment. SPCA models were less successful at modeling systematic changes in clinical patient images, which contain a wider range of random motion than synthetic CBCTs, while the regularized approach was able to extract major modes of motion. Conclusions: Leading EDVFs from the both PCA approaches have the potential to capture systematic anatomical change during H&N radiotherapy when systematic changes are large enough with respect to random fraction-to-fraction changes. In all cases the RPCA approach appears to be more reliable at capturing systematic changes, enabling dosimetric consequences to be projected once trends are established early in a treatment course, or based on population models.« less

Generating Facial Expressions Using an Anatomically Accurate Biomechanical Model.

PubMed

Wu, Tim; Hung, Alice; Mithraratne, Kumar

2014-11-01

This paper presents a computational framework for modelling the biomechanics of human facial expressions. A detailed high-order (Cubic-Hermite) finite element model of the human head was constructed using anatomical data segmented from magnetic resonance images. The model includes a superficial soft-tissue continuum consisting of skin, the subcutaneous layer and the superficial Musculo-Aponeurotic system. Embedded within this continuum mesh, are 20 pairs of facial muscles which drive facial expressions. These muscles were treated as transversely-isotropic and their anatomical geometries and fibre orientations were accurately depicted. In order to capture the relative composition of muscles and fat, material heterogeneity was also introduced into the model. Complex contact interactions between the lips, eyelids, and between superficial soft tissue continuum and deep rigid skeletal bones were also computed. In addition, this paper investigates the impact of incorporating material heterogeneity and contact interactions, which are often neglected in similar studies. Four facial expressions were simulated using the developed model and the results were compared with surface data obtained from a 3D structured-light scanner. Predicted expressions showed good agreement with the experimental data.

Use of laser 3D surface digitizer in data collection and 3D modeling of anatomical structures

NASA Astrophysics Data System (ADS)

Tse, Kelly; Van Der Wall, Hans; Vu, Dzung H.

2006-02-01

A laser digitizer (Konica-Minolta Vivid 910) is used to obtain 3-dimensional surface scans of anatomical structures with a maximum resolution of 0.1mm. Placing the specimen on a turntable allows multiple scans allaround because the scanner only captures data from the portion facing its lens. A computer model is generated using 3D modeling software such as Geomagic. The 3D model can be manipulated on screen for repeated analysis of anatomical features, a useful capability when the specimens are rare or inaccessible (museum collection, fossils, imprints in rock formation.). As accurate measurements can be performed on the computer model, instead of taking measurements on actual specimens only at the archeological excavation site e.g., a variety of quantitative data can be later obtained on the computer model in the laboratory as new ideas come to mind. Our group had used a mechanical contact digitizer (Microscribe) for this purpose, but with the surface digitizer, we have been obtaining data sets more accurately and more quickly.

A Procedure for Calculating the Vertical Space Height of the Sacrum When Determining Skeletal Height for Use in the Anatomical Method of Adult Stature Estimation.

PubMed

Hayashi, Atsuko; Emanovsky, Paul D; Pietrusewsky, Michael; Holland, Thomas D

2016-03-01

Estimating stature from skeletonized remains is one of the essential parameters in the development of a biological profile. A new procedure for determining skeletal height (SKH) incorporating the vertical space height (VSH) from the anterior margin of the sacral promontory to the superior margins of the acetabulae for use in the anatomical method of stature estimation is introduced. Regression equations for stature estimation were generated from measurements of 38 American males of European ancestry from the William M. Bass Donated Skeletal Collection. The modification to the procedure results in a SKH that is highly correlated with stature (r = 0.925-0.948). Stature estimates have low standard errors of the estimate ranging from 21.79 to 25.95 mm, biases from to 0.50 to 0.94 mm, and accuracy rates from 17.71 mm to 19.45 mm. The procedure for determining the VSH, which replaces "S1 height" in traditional anatomical method models, is a key improvement to the method. © 2016 American Academy of Forensic Sciences.

Transmission line based thermoacoustic imaging of small animals

NASA Astrophysics Data System (ADS)

Omar, Murad; Kellnberger, Stephan; Sergiadis, George; Razansky, Daniel; Ntziachristos, Vasilis

2013-06-01

We have generated high resolution images of RF-Contrast in small animals using nearfield thermoacoustic system. This enables us to see some anatomical features of a mouse such as the heart, the spine and the boundary. OCIS codes: (000.0000) General; (000.0000) General [8-pt. type. For codes, see www.opticsinfobase.org/submit/ocis.

Tongue-Pressure and Hyoid Movement Timing in Healthy Liquid Swallowing

ERIC Educational Resources Information Center

Steele, Catriona; Sasse, Caroline; Bressmann, Tim

2012-01-01

It was hypothesized that tongue-palate pressure generation might directly facilitate hyoid movement in swallowing through the anatomical connections of the extrinsic tongue muscles. If true, non-invasive measures of tongue-palate pressure timing might serve as a proxy measure of hyoid excursion. The timing relationships between events in the…

Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC).

PubMed

Cockrell, Robert Chase; Christley, Scott; Chang, Eugene; An, Gary

2015-01-01

Perhaps the greatest challenge currently facing the biomedical research community is the ability to integrate highly detailed cellular and molecular mechanisms to represent clinical disease states as a pathway to engineer effective therapeutics. This is particularly evident in the representation of organ-level pathophysiology in terms of abnormal tissue structure, which, through histology, remains a mainstay in disease diagnosis and staging. As such, being able to generate anatomic scale simulations is a highly desirable goal. While computational limitations have previously constrained the size and scope of multi-scale computational models, advances in the capacity and availability of high-performance computing (HPC) resources have greatly expanded the ability of computational models of biological systems to achieve anatomic, clinically relevant scale. Diseases of the intestinal tract are exemplary examples of pathophysiological processes that manifest at multiple scales of spatial resolution, with structural abnormalities present at the microscopic, macroscopic and organ-levels. In this paper, we describe a novel, massively parallel computational model of the gut, the Spatially Explicitly General-purpose Model of Enteric Tissue_HPC (SEGMEnT_HPC), which extends an existing model of the gut epithelium, SEGMEnT, in order to create cell-for-cell anatomic scale simulations. We present an example implementation of SEGMEnT_HPC that simulates the pathogenesis of ileal pouchitis, and important clinical entity that affects patients following remedial surgery for ulcerative colitis.

Image deblurring using a joint entropy prior in x-ray luminescence computed tomography

NASA Astrophysics Data System (ADS)

Su, Chang; Dutta, Joyita; Zhang, Hui; El Fakhri, Georges; Li, Quanzheng

2017-03-01

X-ray luminescence computed tomography (XLCT) is an emerging hybrid imaging modality that can provide functional and anatomical images at the same time. Traditional narrow beam XLCT can achieve high spatial resolution as well as high sensitivity. However, by treating the CCD camera as a single pixel detector, this kind of scheme resembles the first generation of CT scanner which results in a long scanning time and a high radiation dose. Although cone beam or fan beam XLCT has the ability to mitigate this problem with an optical propagation model introduced, image quality is affected because the inverse problem is ill-conditioned. Much effort has been done to improve the image quality through hardware improvements or by developing new reconstruction techniques for XLCT. The objective of this work is to further enhance the already reconstructed image by introducing anatomical information through retrospective processing. The deblurring process used a spatially variant point spread function (PSF) model and a joint entropy based anatomical prior derived from a CT image acquired using the same XLCT system. A numerical experiment was conducted with a real mouse CT image from the Digimouse phantom used as the anatomical prior. The resultant images of bone and lung regions showed sharp edges and good consistency with the CT image. Activity error was reduced by 52.3% even for nanophosphor lesion size as small as 0.8mm.

A review of the anatomy of the hip abductor muscles, gluteus medius, gluteus minimus, and tensor fascia lata.

PubMed

Flack, Natasha Amy May Sparks; Nicholson, Helen D; Woodley, Stephanie Jane

2012-09-01

The hip abductor muscles have the capability to contribute to numerous actions, including pelvic stabilization during gait, and abduction and rotation at the hip joint. To fully understand the role of these muscles, as well as their involvement in hip joint dysfunction, knowledge of their anatomical structure is essential. The clinical literature suggests anatomical diversity within these muscles, and that gluteus medius (GMed) and gluteus minimus (GMin), in particular, may be comprised of compartments. This systematic review of the English literature focuses on the gross anatomy of GMed, GMin, and tensor fascia lata (TFL) muscles. Although studies of this muscle group have generated useful descriptions, comparison of results is hindered by methodological limitations. Furthermore, there is no single comprehensive anatomical investigation of all three muscles. Several aspects of the morphology of attachment sites are unknown or unclear. There is little data on fascicle orientation, the interface between fascicles and tendons, and the specific patterning of the superior gluteal nerve. Consequently, the existence of anatomical compartmentalization within the hip abductor muscles is difficult to assess. Further research of the architecture and innervation of the hip abductor muscle group is required; a better understanding of the precise anatomy of these muscles should improve our understanding of their specific functions and their contribution to the pathogenesis of disorders affecting the hip joint. Copyright © 2011 Wiley Periodicals, Inc.

Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms: VISCERAL Anatomy Benchmarks.

PubMed

Jimenez-Del-Toro, Oscar; Muller, Henning; Krenn, Markus; Gruenberg, Katharina; Taha, Abdel Aziz; Winterstein, Marianne; Eggel, Ivan; Foncubierta-Rodriguez, Antonio; Goksel, Orcun; Jakab, Andras; Kontokotsios, Georgios; Langs, Georg; Menze, Bjoern H; Salas Fernandez, Tomas; Schaer, Roger; Walleyo, Anna; Weber, Marc-Andre; Dicente Cid, Yashin; Gass, Tobias; Heinrich, Mattias; Jia, Fucang; Kahl, Fredrik; Kechichian, Razmig; Mai, Dominic; Spanier, Assaf B; Vincent, Graham; Wang, Chunliang; Wyeth, Daniel; Hanbury, Allan

2016-11-01

Variations in the shape and appearance of anatomical structures in medical images are often relevant radiological signs of disease. Automatic tools can help automate parts of this manual process. A cloud-based evaluation framework is presented in this paper including results of benchmarking current state-of-the-art medical imaging algorithms for anatomical structure segmentation and landmark detection: the VISCERAL Anatomy benchmarks. The algorithms are implemented in virtual machines in the cloud where participants can only access the training data and can be run privately by the benchmark administrators to objectively compare their performance in an unseen common test set. Overall, 120 computed tomography and magnetic resonance patient volumes were manually annotated to create a standard Gold Corpus containing a total of 1295 structures and 1760 landmarks. Ten participants contributed with automatic algorithms for the organ segmentation task, and three for the landmark localization task. Different algorithms obtained the best scores in the four available imaging modalities and for subsets of anatomical structures. The annotation framework, resulting data set, evaluation setup, results and performance analysis from the three VISCERAL Anatomy benchmarks are presented in this article. Both the VISCERAL data set and Silver Corpus generated with the fusion of the participant algorithms on a larger set of non-manually-annotated medical images are available to the research community.

Tissue-Engineered Autologous Grafts for Facial Bone Reconstruction

PubMed Central

Bhumiratana, Sarindr; Bernhard, Jonathan C.; Alfi, David M.; Yeager, Keith; Eton, Ryan E.; Bova, Jonathan; Shah, Forum; Gimble, Jeffrey M.; Lopez, Mandi J.; Eisig, Sidney B.; Vunjak-Novakovic, Gordana

2016-01-01

Facial deformities require precise reconstruction of the appearance and function of the original tissue. The current standard of care—the use of bone harvested from another region in the body—has major limitations, including pain and comorbidities associated with surgery. We have engineered one of the most geometrically complex facial bones by using autologous stromal/stem cells, without bone morphogenic proteins, using native bovine bone matrix and a perfusion bioreactor for the growth and transport of living grafts. The ramus-condyle unit (RCU), the most eminent load-bearing bone in the skull, was reconstructed using an image-guided personalized approach in skeletally mature Yucatan minipigs (human-scale preclinical model). We used clinically approved decellularized bovine trabecular bone as a scaffolding material, and crafted it into an anatomically correct shape using image-guided micromilling, to fit the defect. Autologous adipose-derived stromal/stem cells were seeded into the scaffold and cultured in perfusion for 3 weeks in a specialized bioreactor to form immature bone tissue. Six months after implantation, the engineered grafts maintained their anatomical structure, integrated with native tissues, and generated greater volume of new bone and greater vascular infiltration than either non-seeded anatomical scaffolds or untreated defects. This translational study demonstrates feasibility of facial bone reconstruction using autologous, anatomically shaped, living grafts formed in vitro, and presents a platform for personalized bone tissue engineering. PMID:27306665

Deformable templates guided discriminative models for robust 3D brain MRI segmentation.

PubMed

Liu, Cheng-Yi; Iglesias, Juan Eugenio; Tu, Zhuowen

2013-10-01

Automatically segmenting anatomical structures from 3D brain MRI images is an important task in neuroimaging. One major challenge is to design and learn effective image models accounting for the large variability in anatomy and data acquisition protocols. A deformable template is a type of generative model that attempts to explicitly match an input image with a template (atlas), and thus, they are robust against global intensity changes. On the other hand, discriminative models combine local image features to capture complex image patterns. In this paper, we propose a robust brain image segmentation algorithm that fuses together deformable templates and informative features. It takes advantage of the adaptation capability of the generative model and the classification power of the discriminative models. The proposed algorithm achieves both robustness and efficiency, and can be used to segment brain MRI images with large anatomical variations. We perform an extensive experimental study on four datasets of T1-weighted brain MRI data from different sources (1,082 MRI scans in total) and observe consistent improvement over the state-of-the-art systems.

Posterolateral Corner Reconstruction using the Anatomical Two-Tailed Graft Technique: Clinical Outcomes in the Multiligament Injured Knee.

PubMed

Woodmass, Jarret M; Sanders, Thomas L; Johnson, Nick R; Wu, Isabella T; Krych, Aaron J; Stuart, Michael J; Levy, Bruce A

2018-02-14

Injury to the posterolateral corner (PLC) of the knee can lead to both varus and rotational instability. Multiple PLC reconstruction techniques have been described, including one-tailed graft (fibula-based constructs) or two-tailed graft (combined fibula- and tibia-based constructs). The purpose of our study was to evaluate the clinical outcomes of anatomical two-tailed graft reconstruction of the PLC in the setting of multiligament knee injuries (MKLIs) with grade III varus instability. Patients were identified through a prospective MLKI database between 2004 and 2013. Patients who received fibular collateral ligament and PLC reconstructions using a two-tailed graft and had a minimum follow-up of 2 years were included. Patients were assessed for clinical laxity grade, range of motion, and functional outcomes using Lysholm and International Knee Documentation Committee (IKDC) scores. Twenty patients (16 male, 4 female) with a mean age of 30.7 (range: 16-52) and a mean follow-up of 52.2 months (range: 24-93 months) were included. Knee dislocation (KD) grades included: 4 KD-1, 10 KD 3-L, 5 KD-4, and 1 KD-5. No patients had isolated PLC injuries. Mean IKDC and Lysholm score were 73.1 ± 25.8 and 78 ± 26, respectively. Mean range of motion was -1.1 to 122.8. In full extension, two patients (10%) had grade 1 laxity to varus stress. In 30 degrees of knee flexion, five (25%) patients had grade 1 laxity, and two (10%) had grade 2 laxity. Anatomical two-tailed PLC reconstruction can reliably restore varus stability when performed on patients with MLKIs and type C posterolateral instability with hyperextension external rotation recurvatum deformity. Satisfactory functional outcome scores were achieved in the majority of patients. This study supports the use of an anatomical two-tailed PLC reconstruction in the multiligament injured knee. The level of evidence is IV, case series. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Assessing the response to targeted therapies in renal cell carcinoma: technical insights and practical considerations.

PubMed

Bex, Axel; Fournier, Laure; Lassau, Nathalie; Mulders, Peter; Nathan, Paul; Oyen, Wim J G; Powles, Thomas

2014-04-01

The introduction of targeted agents for the treatment of renal cell carcinoma (RCC) has resulted in new challenges for assessing response to therapy, and conventional response criteria using computed tomography (CT) are limited. It is widely recognised that targeted therapies may lead to significant necrosis without significant reduction in tumour size. In addition, the vascular effects of antiangiogenic therapy may occur long before there is any reduction in tumour size. To perform a systematic review of conventional and novel imaging methods for the assessment of response to targeted agents in RCC and to discuss their use from a clinical perspective. Relevant databases covering the period January 2006 to April 2013 were searched for studies reporting on the use of anatomic and functional imaging techniques to predict response to targeted therapy in RCC. Inclusion criteria were randomised trials, nonrandomised controlled studies, retrospective case series, and cohort studies. Reviews, animal and preclinical studies, case reports, and commentaries were excluded. A narrative synthesis of the evidence is presented. A total of 331 abstracts and 76 full-text articles were assessed; 34 studies met the inclusion criteria. Current methods of response assessment in RCC include anatomic methods--based on various criteria including Choi, size and attenuation CT, and morphology, attenuation, size, and structure--and functional techniques including dynamic contrast-enhanced (DCE) CT, DCE-magnetic resonance imaging, DCE-ultrasonography, positron emission tomography, and approaches utilising radiolabelled monoclonal antibodies. Functional imaging techniques are promising surrogate biomarkers of response in RCC and may be more appropriate than anatomic CT-based methods. By enabling quantification of tumour vascularisation, functional techniques can directly and rapidly detect the biologic effects of antiangiogenic therapies compared with the indirect detection of belated effects on tumour size by anatomic methods. However, larger prospective studies are needed to validate early results and standardise techniques. Copyright © 2013 European Association of Urology. All rights reserved.

Evaluation of cost-effectiveness from the funding body's point of view of ultrasound-guided central venous catheter insertion compared with the conventional technique.

PubMed

Noritomi, Danilo Teixeira; Zigaib, Rogério; Ranzani, Otavio T; Teich, Vanessa

2016-01-01

To evaluate the cost-effectiveness, from the funding body's point of view, of real-time ultrasound-guided central venous catheter insertion compared to the traditional method, which is based on the external anatomical landmark technique. A theoretical simulation based on international literature data was applied to the Brazilian context, i.e., the Unified Health System (Sistema Único de Saúde - SUS). A decision tree was constructed that showed the two central venous catheter insertion techniques: real-time ultrasonography versus external anatomical landmarks. The probabilities of failure and complications were extracted from a search on the PubMed and Embase databases, and values associated with the procedure and with complications were taken from market research and the Department of Information Technology of the Unified Health System (DATASUS). Each central venous catheter insertion alternative had a cost that could be calculated by following each of the possible paths on the decision tree. The incremental cost-effectiveness ratio was calculated by dividing the mean incremental cost of real-time ultrasound compared to the external anatomical landmark technique by the mean incremental benefit, in terms of avoided complications. When considering the incorporation of real-time ultrasound and the concomitant lower cost due to the reduced number of complications, the decision tree revealed a final mean cost for the external anatomical landmark technique of 262.27 Brazilian reals (R$) and for real-time ultrasound of R$187.94. The final incremental cost of the real-time ultrasound-guided technique was -R$74.33 per central venous catheter. The incremental cost-effectiveness ratio was -R$2,494.34 due to the pneumothorax avoided. Real-time ultrasound-guided central venous catheter insertion was associated with decreased failure and complication rates and hypothetically reduced costs from the view of the funding body, which in this case was the SUS.

Petition to Object to Midwest Generation, Romeoville Generating Station Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition to Object to Midwest Generation, Joliet Generating Station Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Midwest Generation Waukegan Generating Station, Order Denying Petition for Objection to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Scaling of human body composition to stature: new insights into body mass index.

PubMed

Heymsfield, Steven B; Gallagher, Dympna; Mayer, Laurel; Beetsch, Joel; Pietrobelli, Angelo

2007-07-01

Although Quetelet first reported in 1835 that adult weight scales to the square of stature, limited or no information is available on how anatomical body compartments, including adipose tissue (AT), scale to height. We examined the critical underlying assumptions of adiposity-body mass index (BMI) relations and extended these analyses to major anatomical compartments: skeletal muscle (SM), bone, residual mass, weight (AT+SM+bone), AT-free mass, and organs (liver, brain). This was a cross-sectional analysis of 2 body-composition databases: one including magnetic resonance imaging and dual-energy X-ray absorptiometry (DXA) estimates of evaluated components in adults (total n=411; organs=76) and the other a larger DXA database (n=1346) that included related estimates of fat, fat-free mass, and bone mineral mass. Weight, primary lean components (SM, residual mass, AT-free mass, and fat-free mass), and liver scaled to height with powers of approximately 2 (all P<0.001); bone and bone mineral mass scaled to height with powers >2 (2.31-2.48), and the fraction of weight as bone mineral mass was significantly (P<0.001) correlated with height in women. AT scaled weakly to height with powers of approximately 2, and adiposity was independent of height. Brain mass scaled to height with a power of 0.83 (P=0.04) in men and nonsignificantly in women; the fraction of weight as brain was inversely related to height in women (P=0.002). These observations suggest that short and tall subjects with equivalent BMIs have similar but not identical body composition, provide new insights into earlier BMI-related observations and thus establish a foundation for height-normalized indexes, and create an analytic framework for future studies.

Doctoral theses in diagnostic imaging: a study of Spanish production between 1976 and 2011.

PubMed

Machan, K; Sendra Portero, F

2018-05-15

To analyze the production of doctoral theses in diagnostic imaging in Spain in the period comprising 1976 through 2011 with the aim of a) determining the number of theses and their distribution over time, b) describing the production in terms of universities and directors, and c) analyzing the content of the theses according to the imaging technique, anatomic site, and type of research used. The TESEO database was searched for "radiología" and/or "diagnóstico por imagen" and for terms related to diagnostic imaging in the title of the thesis. A total of 1036 theses related to diagnostic imaging were produced in 37 Spanish universities (mean, 29.6 theses/year; range, 4-59). A total of 963 thesis directors were identified; 10 of these supervised 10 or more theses. Most candidates and directors were men, although since the 2000-2001 academic year the number of male and female candidates has been similar. The anatomic regions most often included in diagnostic imaging theses were the abdomen (22.5%), musculoskeletal system (21.8%), central nervous system (16.4%), and neck and face (15.6%). The imaging techniques most often included were ultrasonography in the entire period (25.5%) and magnetic resonance imaging in the last 5 years. Most theses (63.8%) were related to clinical research. Despite certain limitations, the TESEO database makes it possible to analyze the production of doctoral theses in Spain effectively. The annual mean production of theses in diagnostic imaging is higher than in other medical specialties. This analysis reflects the historic evolution of imaging techniques and research in radiology as well as the development of Spanish universities. Copyright © 2018 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

Scaling of human body composition to stature: new insights into body mass index 123

PubMed Central

Heymsfield, Steven B; Gallagher, Dympna; Mayer, Laurel; Beetsch, Joel; Pietrobelli, Angelo

2009-01-01

Background Although Quetelet first reported in 1835 that adult weight scales to the square of stature, limited or no information is available on how anatomical body compartments, including adipose tissue (AT), scale to height. Objective We examined the critical underlying assumptions of adiposity–body mass index (BMI) relations and extended these analyses to major anatomical compartments: skeletal muscle (SM), bone, residual mass, weight (AT+SM+bone), AT-free mass, and organs (liver, brain). Design This was a cross-sectional analysis of 2 body-composition databases: one including magnetic resonance imaging and dual-energy X-ray absorptiometry (DXA) estimates of evaluated components in adults (total n = 411; organs = 76) and the other a larger DXA database (n = 1346) that included related estimates of fat, fat-free mass, and bone mineral mass. Results Weight, primary lean components (SM, residual mass, AT-free mass, and fat-free mass), and liver scaled to height with powers of ≈2 (all P < 0.001); bone and bone mineral mass scaled to height with powers > 2 (2.31–2.48), and the fraction of weight as bone mineral mass was significantly (P < 0.001) correlated with height in women. AT scaled weakly to height with powers of ≈2, and adiposity was independent of height. Brain mass scaled to height with a power of 0.83 (P = 0.04) in men and nonsignificantly in women; the fraction of weight as brain was inversely related to height in women (P = 0.002). Conclusions These observations suggest that short and tall subjects with equivalent BMIs have similar but not identical body composition, provide new insights into earlier BMI-related observations and thus establish a foundation for height-normalized indexes, and create an analytic framework for future studies. PMID:17616766

EOSCUBE: A Constraint Database System for High-Level Specification and Efficient Generation of EOSDIS Products. Phase 1; Proof-of-Concept

NASA Technical Reports Server (NTRS)

Brodsky, Alexander; Segal, Victor E.

1999-01-01

The EOSCUBE constraint database system is designed to be a software productivity tool for high-level specification and efficient generation of EOSDIS and other scientific products. These products are typically derived from large volumes of multidimensional data which are collected via a range of scientific instruments.

[Selected aspects of computer-assisted literature management].

PubMed

Reiss, M; Reiss, G

1998-01-01

We want to report about our own experiences with a database manager. Bibliography database managers are used to manage information resources: specifically, to maintain a database to references and create bibliographies and reference lists for written works. A database manager allows to enter summary information (record) for articles, book sections, books, dissertations, conference proceedings, and so on. Other features that may be included in a database manager include the ability to import references from different sources, such as MEDLINE. The word processing components allow to generate reference list and bibliographies in a variety of different styles, generates a reference list from a word processor manuscript. The function and the use of the software package EndNote 2 for Windows are described. Its advantages in fulfilling different requirements for the citation style and the sort order of reference lists are emphasized.

Fermilab Security Site Access Request Database

Science.gov Websites

Fermilab Security Site Access Request Database Use of the online version of the Fermilab Security Site Access Request Database requires that you login into the ESH&Q Web Site. Note: Only Fermilab generated from the ESH&Q Section's Oracle database on May 27, 2018 05:48 AM. If you have a question

Anatomy guided automated SPECT renal seed point estimation

NASA Astrophysics Data System (ADS)

Dwivedi, Shekhar; Kumar, Sailendra

2010-04-01

Quantification of SPECT(Single Photon Emission Computed Tomography) images can be more accurate if correct segmentation of region of interest (ROI) is achieved. Segmenting ROI from SPECT images is challenging due to poor image resolution. SPECT is utilized to study the kidney function, though the challenge involved is to accurately locate the kidneys and bladder for analysis. This paper presents an automated method for generating seed point location of both kidneys using anatomical location of kidneys and bladder. The motivation for this work is based on the premise that the anatomical location of the bladder relative to the kidneys will not differ much. A model is generated based on manual segmentation of the bladder and both the kidneys on 10 patient datasets (including sum and max images). Centroid is estimated for manually segmented bladder and kidneys. Relatively easier bladder segmentation is followed by feeding bladder centroid coordinates into the model to generate seed point for kidneys. Percentage error observed in centroid coordinates of organs from ground truth to estimated values from our approach are acceptable. Percentage error of approximately 1%, 6% and 2% is observed in X coordinates and approximately 2%, 5% and 8% is observed in Y coordinates of bladder, left kidney and right kidney respectively. Using a regression model and the location of the bladder, the ROI generation for kidneys is facilitated. The model based seed point estimation will enhance the robustness of kidney ROI estimation for noisy cases.

Efficient Privacy-Enhancing Techniques for Medical Databases

NASA Astrophysics Data System (ADS)

Schartner, Peter; Schaffer, Martin

In this paper, we introduce an alternative for using linkable unique health identifiers: locally generated system-wide unique digital pseudonyms. The presented techniques are based on a novel technique called collision-free number generation which is discussed in the introductory part of the article. Afterwards, attention is payed onto two specific variants of collision-free number generation: one based on the RSA-Problem and the other one based on the Elliptic Curve Discrete Logarithm Problem. Finally, two applications are sketched: centralized medical records and anonymous medical databases.

Oscillatory activity reflects differential use of spatial reference frames by sighted and blind individuals in tactile attention.

PubMed

Schubert, Jonathan T W; Buchholz, Verena N; Föcker, Julia; Engel, Andreas K; Röder, Brigitte; Heed, Tobias

2015-08-15

Touch can be localized either on the skin in anatomical coordinates, or, after integration with posture, in external space. Sighted individuals are thought to encode touch in both coordinate systems concurrently, whereas congenitally blind individuals exhibit a strong bias for using anatomical coordinates. We investigated the neural correlates of this differential dominance in the use of anatomical and external reference frames by assessing oscillatory brain activity during a tactile spatial attention task. The EEG was recorded while sighted and congenitally blind adults received tactile stimulation to uncrossed and crossed hands while detecting rare tactile targets at one cued hand only. In the sighted group, oscillatory alpha-band activity (8-12Hz) in the cue-target interval was reduced contralaterally and enhanced ipsilaterally with uncrossed hands. Hand crossing attenuated the degree of posterior parietal alpha-band lateralization, indicating that attention deployment was affected by external spatial coordinates. Beamforming suggested that this posture effect originated in the posterior parietal cortex. In contrast, cue-related lateralization of central alpha-band as well as of beta-band activity (16-24Hz) were unaffected by hand crossing, suggesting that these oscillations exclusively encode anatomical coordinates. In the blind group, central alpha-band activity was lateralized, but did not change across postures. The pattern of beta-band activity was indistinguishable between groups. Because the neural mechanisms for posterior alpha-band generation seem to be linked to developmental vision, we speculate that the lack of this neural mechanism in blind individuals is related to their preferred use of anatomical over external spatial codes in sensory processing. Copyright © 2015 Elsevier Inc. All rights reserved.

An in vitro comparison of subjective image quality of panoramic views acquired via 2D or 3D imaging.

PubMed

Pittayapat, P; Galiti, D; Huang, Y; Dreesen, K; Schreurs, M; Souza, P Couto; Rubira-Bullen, I R F; Westphalen, F H; Pauwels, R; Kalema, G; Willems, G; Jacobs, R

2013-01-01

The objective of this study is to compare subjective image quality and diagnostic validity of cone-beam CT (CBCT) panoramic reformatting with digital panoramic radiographs. Four dry human skulls and two formalin-fixed human heads were scanned using nine different CBCTs, one multi-slice CT (MSCT) and one standard digital panoramic device. Panoramic views were generated from CBCTs in four slice thicknesses. Seven observers scored image quality and visibility of 14 anatomical structures. Four observers repeated the observation after 4 weeks. Digital panoramic radiographs showed significantly better visualization of anatomical structures except for the condyle. Statistical analysis of image quality showed that the 3D imaging modalities (CBCTs and MSCT) were 7.3 times more likely to receive poor scores than the 2D modality. Yet, image quality from NewTom VGi® and 3D Accuitomo 170® was almost equivalent to that of digital panoramic radiographs with respective odds ratio estimates of 1.2 and 1.6 at 95% Wald confidence limits. A substantial overall agreement amongst observers was found. Intra-observer agreement was moderate to substantial. While 2D-panoramic images are significantly better for subjective diagnosis, 2/3 of the 3D-reformatted panoramic images are moderate or good for diagnostic purposes. Panoramic reformattings from particular CBCTs are comparable to digital panoramic images concerning the overall image quality and visualization of anatomical structures. This clinically implies that a 3D-derived panoramic view can be generated for diagnosis with a recommended 20-mm slice thickness, if CBCT data is a priori available for other purposes.

Intelligent communication assistant for databases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jakobson, G.; Shaked, V.; Rowley, S.

1983-01-01

An intelligent communication assistant for databases, called FRED (front end for databases) is explored. FRED is designed to facilitate access to database systems by users of varying levels of experience. FRED is a second generation of natural language front-ends for databases and intends to solve two critical interface problems existing between end-users and databases: connectivity and communication problems. The authors report their experiences in developing software for natural language query processing, dialog control, and knowledge representation, as well as the direction of future work. 10 references.

Building An Integrated Neurodegenerative Disease Database At An Academic Health Center

PubMed Central

Xie, Sharon X.; Baek, Young; Grossman, Murray; Arnold, Steven E.; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M.-Y.; Trojanowski, John Q.

2010-01-01

Background It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). These comparative studies rely on powerful database tools to quickly generate data sets which match diverse and complementary criteria set by the studies. Methods In this paper, we present a novel Integrated NeuroDegenerative Disease (INDD) database developed at the University of Pennsylvania (Penn) through a consortium of Penn investigators. Since these investigators work on AD, PD, ALS and FTLD, this allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used Microsoft SQL Server as the platform with built-in “backwards” functionality to provide Access as a front-end client to interface with the database. We used PHP hypertext Preprocessor to create the “front end” web interface and then integrated individual neurodegenerative disease databases using a master lookup table. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Results We compare the results of a biomarker study using the INDD database to those using an alternative approach by querying individual database separately. Conclusions We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies across several neurodegenerative diseases. PMID:21784346

Index of prolonged air leak score validation in case of video-assisted thoracoscopic surgery anatomical lung resection: results of a nationwide study based on the French national thoracic database, EPITHOR.

PubMed

Orsini, Bastien; Baste, Jean Marc; Gossot, Dominique; Berthet, Jean Philippe; Assouad, Jalal; Dahan, Marcel; Bernard, Alain; Thomas, Pascal Alexandre

2015-10-01

The incidence rate of prolonged air leak (PAL) after lobectomy, defined as any air leak prolonged beyond 7 days, can be estimated to be in between 6 and 15%. In 2011, the Epithor group elaborated an accurate predictive score for PAL after open lung resections, so-called IPAL (index of prolonged air leak), from a nation-based surgical cohort constituted between 2004 and 2008. Since 2008, video-assisted thoracic surgery (VATS) has become popular in France among the thoracic surgical community, reaching almost 14% of lobectomies performed with this method in 2012. This minimally invasive approach was reported as a means to reduce the duration of chest tube drainage. The aim of our study was thus to validate the IPAL scoring system in patients having received VATS anatomical lung resections. We collected all anatomical VATS lung resections (lobectomy and segmentectomy) registered in the French national general thoracic surgery database (EPITHOR) between 2009 and 2012. The area under the receiver operating characteristic (ROC) curve estimated the discriminating value of the IPAL score. The slope value described the relation between the predicted and observed incidences of PALs. The Hosmer-Lemeshow test was also used to estimate the quality of adequacy between predicted and observed values. A total of 1233 patients were included: 1037 (84%) lobectomies and 196 (16%) segmentectomies. In 1099 cases (89.1%), the resection was performed for a malignant disease. Ninety-six patients (7.7%) presented with a PAL. The IPAL score provided a satisfactory predictive value with an area under the ROC curve of 0.72 (0.67-0.77). The value of the slope, 1.25 (0.9-1.58), and the Hosmer-Lemeshow test (χ(2) = 11, P = 0.35) showed that predicted and observed values were adequate. The IPAL score is valid for the estimation of the predictive risk of PAL after VATS lung resections. It may thus a priori be used to characterize any surgical population submitted to potential preventive measures. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Genome-wide identification of lineage-specific genes in Arabidopsis, Oryza and Populus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiaohan; Jawdy, Sara; Tschaplinski, Timothy J

2009-01-01

Protein sequences were compared among Arabidopsis, Oryza and Populus to identify differential gene (DG) sets that are in one but not the other two genomes. The DG sets were screened against a plant transcript database, the NR protein database and six newly-sequenced genomes (Carica, Glycine, Medicago, Sorghum, Vitis and Zea) to identify a set of species-specific genes (SS). Gene expression, protein motif and intron number were examined. 192, 641 and 109 SS genes were identified in Arabidopsis, Oryza and Populus, respectively. Some SS genes were preferentially expressed in flowers, roots, xylem and cambium or up-regulated by stress. Six conserved motifsmore » in Arabidopsis and Oryza SS proteins were found in other distant lineages. The SS gene sets were enriched with intronless genes. The results reflect functional and/or anatomical differences between monocots and eudicots or between herbaceous and woody plants. The Populus-specific genes are candidates for carbon sequestration and biofuel research.« less

METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters.

PubMed

Geffers, Lars; Tetzlaff, Benjamin; Cui, Xiao; Yan, Jun; Eichele, Gregor

2013-01-01

METscout (http://metscout.mpg.de) brings together metabolism and gene expression landscapes. It is a MySQL relational database linking biochemical pathway information with 3D patterns of gene expression determined by robotic in situ hybridization in the E14.5 mouse embryo. The sites of expression of ∼1500 metabolic enzymes and of ∼350 solute carriers (SLCs) were included and are accessible as single cell resolution images and in the form of semi-quantitative image abstractions. METscout provides several graphical web-interfaces allowing navigation through complex anatomical and metabolic information. Specifically, the database shows where in the organism each of the many metabolic reactions take place and where SLCs transport metabolites. To link enzymatic reactions and transport, the KEGG metabolic reaction network was extended to include metabolite transport. This network in conjunction with spatial expression pattern of the network genes allows for a tracing of metabolic reactions and transport processes across the entire body of the embryo.

Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications

PubMed Central

Hegedűs, Tamás; Chaubey, Pururawa Mayank; Várady, György; Szabó, Edit; Sarankó, Hajnalka; Hofstetter, Lia; Roschitzki, Bernd; Sarkadi, Balázs

2015-01-01

Based on recent results, the determination of the easily accessible red blood cell (RBC) membrane proteins may provide new diagnostic possibilities for assessing mutations, polymorphisms or regulatory alterations in diseases. However, the analysis of the current mass spectrometry-based proteomics datasets and other major databases indicates inconsistencies—the results show large scattering and only a limited overlap for the identified RBC membrane proteins. Here, we applied membrane-specific proteomics studies in human RBC, compared these results with the data in the literature, and generated a comprehensive and expandable database using all available data sources. The integrated web database now refers to proteomic, genetic and medical databases as well, and contains an unexpected large number of validated membrane proteins previously thought to be specific for other tissues and/or related to major human diseases. Since the determination of protein expression in RBC provides a method to indicate pathological alterations, our database should facilitate the development of RBC membrane biomarker platforms and provide a unique resource to aid related further research and diagnostics. Database URL: http://rbcc.hegelab.org PMID:26078478

Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches.

PubMed

Tran, Trung T; Bollineni, Ravi C; Strozynski, Margarita; Koehler, Christian J; Thiede, Bernd

2017-07-07

Alternative splicing is a mechanism in eukaryotes by which different forms of mRNAs are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database that contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to splice variant-specific peptide sequences that match to MS data. Furthermore, we combined this database without alternative splice variant-1-specific peptides with human Swiss-Prot. This combined database can be used as a general database for searching of LC-MS data. LC-MS data derived from in-solution digests of two different cell lines (LNCaP, HeLa) and phosphoproteomics studies were analyzed using these two databases. Several nonalternative splice variant-1-specific peptides were found in both cell lines, and some of them seemed to be cell-line-specific. Control and apoptotic phosphoproteomes from Jurkat T cells revealed several nonalternative splice variant-1-specific peptides, and some of them showed clear quantitative differences between the two states.

Evaluation of relational and NoSQL database architectures to manage genomic annotations.

PubMed

Schulz, Wade L; Nelson, Brent G; Felker, Donn K; Durant, Thomas J S; Torres, Richard

2016-12-01

While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architectures may provide significant advantages in storage and query efficiency, thereby reducing the cost of data management. But their relative advantage when applied to biomedical data sets, such as genetic data, has not been characterized. To this end, we compared the storage, indexing, and query efficiency of a common relational database (MySQL), a document-oriented NoSQL database (MongoDB), and a relational database with NoSQL support (PostgreSQL). When used to store genomic annotations from the dbSNP database, we found the NoSQL architectures to outperform traditional, relational models for speed of data storage, indexing, and query retrieval in nearly every operation. These findings strongly support the use of novel database technologies to improve the efficiency of data management within the biological sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

Component, Context and Manufacturing Model Library (C2M2L)

DTIC Science & Technology

2013-03-01

Penn State team were stored in a relational database for easy access, storage and maintainability. The relational database consisted of a PostGres ...file into a format that can be imported into the PostGres database. This same custom application was used to generate Microsoft Excel templates...Press Break Forming Equipment 4.14 Manufacturing Model Library Database Structure The data storage mechanism for the ARL PSU MML was a PostGres database

Use of large healthcare databases for rheumatology clinical research.

PubMed

Desai, Rishi J; Solomon, Daniel H

2017-03-01

Large healthcare databases, which contain data collected during routinely delivered healthcare to patients, can serve as a valuable resource for generating actionable evidence to assist medical and healthcare policy decision-making. In this review, we summarize use of large healthcare databases in rheumatology clinical research. Large healthcare data are critical to evaluate medication safety and effectiveness in patients with rheumatologic conditions. Three major sources of large healthcare data are: first, electronic medical records, second, health insurance claims, and third, patient registries. Each of these sources offers unique advantages, but also has some inherent limitations. To address some of these limitations and maximize the utility of these data sources for evidence generation, recent efforts have focused on linking different data sources. Innovations such as randomized registry trials, which aim to facilitate design of low-cost randomized controlled trials built on existing infrastructure provided by large healthcare databases, are likely to make clinical research more efficient in coming years. Harnessing the power of information contained in large healthcare databases, while paying close attention to their inherent limitations, is critical to generate a rigorous evidence-base for medical decision-making and ultimately enhancing patient care.

Salvage Holmium laser enucleation of prostate to treat residual benign prostatic hyperplasia.

PubMed

Oh, Jin Kyu; Bae, Jungbum; Jeong, Chang Wook; Paick, Jae-Seung; Oh, Seung-June

2014-03-01

The Holmium laser enucleation of the prostate (HoLEP) technique to remove residual adenoma has not been reported. Salvage HoLEP enables anatomical enucleation of residual adenoma in patients who have previously undergone surgical treatment. We describe not only anatomical insights into the frequent location of adenoma recurrence, but also the feasibility of the salvage HoLEP technique. We retrospectively reviewed a database containing HoLEP video records for 35 patients out of a total of 535 individuals on whom HoLEP was performed by 2 surgeons (SJO & JSP) between July 2008 and June 2011. Group 1 consisted of patients who underwent salvage HoLEP due to recurring adenoma and Group 2 of patients who underwent HoLEP as an initially surgical management to treat benign prostate hyperplasia (BPH). We compared the dataset of pre-, intra- and postoperative parameters between Groups 1 and 2. In the analysis of the video records of Group 1 (n = 35), there was significant remnant tissue around the verumontanum and the lateral lobes were also incompletely removed by previous conventional procedures. When we compared pre-, intra- and postoperative parameters between the 2 groups, there were no significant differences, including operation time, duration of hospital stay. However, the duration of the catheterization of Group 1 was shorter than that of Group 2 (1.38 ± 0.55 vs. 1.90 ± 1.81 days, p < 0.001). Even for cases of residual BPH, salvage HoLEP is a feasible and effective procedure for treating residual adenoma along the anatomical plane.

An anatomically based patient-specific finite element model of patella articulation: towards a diagnostic tool.

PubMed

Fernandez, J W; Hunter, P J

2005-08-01

A 3D anatomically based patient-specific finite element (FE) model of patello-femoral (PF) articulation is presented to analyse the main features of patella biomechanics, namely, patella tracking (kinematics), quadriceps extensor forces, surface contact and internal patella stresses. The generic geometries are a subset from the model database of the International Union of Physiological Sciences (IUPS) (http://www.physiome.org.nz) Physiome Project with soft tissue derived from the widely used visible human dataset, and the bones digitised from an anatomically accurate physical model with muscle attachment information. The models are customised to patient magnetic resonance images using a variant of free-form deformation, called 'host-mesh' fitting. The continuum was solved using the governing equation of finite elasticity, with the multibody problem coupled through contact mechanics. Additional constraints such as tissue incompressibility are also imposed. Passive material properties are taken from the literature and implemented for deformable tissue with a non-linear micro-structurally based constitutive law. Bone and cartilage are implemented using a 'St-Venant Kirchoff' model suitable for rigid body rotations. The surface fibre directions have been estimated from anatomy images of cadaver muscle dissections and active muscle contraction was based on a steady-state calcium-tension relation. The 3D continuum model of muscle, tendon and bone is compared with experimental results from the literature, and surgical simulations performed to illustrate its clinical assessment capabilities (a Maquet procedure for reducing patella stresses and a vastus lateralis release for a bipartite patella). Finally, the model limitations, issues and future improvements are discussed.

Reliability of bony anatomic landmark asymmetry assessment in the lumbopelvic region: application to osteopathic medical education.

PubMed

Stovall, Bradley A; Kumar, Shrawan

2010-11-01

The objective of this review is to establish the current state of knowledge on the reliability of clinical assessment of asymmetry in the lumbar spine and pelvis. To search the literature, the authors consulted the databases of MEDLINE, CINAHL, AMED, MANTIS, Academic Search Complete, and Web of Knowledge using different combinations of the following keywords: palpation, asymmetry, inter or intraexaminer reliability, tissue texture, assessment, and anatomic landmark. Of the 23 studies identified, 14 did not meet the inclusion criteria and were excluded. The quality and methods of studies investigating the reliability of bony anatomic landmark asymmetry assessment are variable. The κ statistic ranges without training for interexaminer reliability were as follows: anterior superior iliac spine (ASIS), -0.01 to 0.19; posterior superior iliac spine (PSIS), 0.04 to 0.15; inferior lateral angle, transverse plane (ILA-A/P), -0.03 to 0.11; inferior lateral angles, coronal plane (ILA-S/I), -0.01 to 0.08; sacral sulcus (SS), -0.4 to 0.37; lumbar spine transverse processes L1 through L5, 0.04 to 0.17. The corresponding ranges for intraexaminer reliability were higher for all associated landmarks: ASIS, 0.19 to 0.4; PSIS, 0.13 to 0.49; ILA-A/P, 0.1 to 0.2; ILA-S/I, 0.03 to 0.21; SS, 0.24 to 0.28; lumbar spine transverse processes L1 through L5, not applicable. Further research is needed to better understand the reliability of asymmetry assessment methods in manipulative medicine.

Reliability of Bony Anatomic Landmark Asymmetry Assessment in the Lumbopelvic Region: Application to Osteopathic Medical Education

PubMed Central

Stovall, Bradley A.; Kumar, Shrawan

2011-01-01

The objective of this review is to establish the current state of knowledge on the reliability of clinical assessment of asymmetry in the lumbar spine and pelvis. To search the literature, the authors consulted the databases of MEDLINE, CINAHL, AMED, MANTIS, Academic Search Complete, and Web of Knowledge using different combinations of the following keywords: palpation, asymmetry, inter- or intraex-aminer reliability, tissue texture, assessment, and anatomic landmark. Of the 23 studies identified, 14 did not meet the inclusion criteria and were excluded. The quality and methods of studies investigating the reliability of bony anatomic landmark asymmetry assessment are variable. The κ statistic ranges without training for interexaminer reliability were as follows: anterior superior iliac spine (ASIS), −0.01 to 0.19; posterior superior iliac spine (PSIS), 0.04 to 0.15; inferior lateral angle, transverse plane (ILA-A/P), −0.03 to 0.11; inferior lateral angles, coronal plane (ILA-S/I), −0.01 to 0.08; sacral sulcus (SS), −0.4 to 0.37; lumbar spine transverse processes L1 through L5, 0.04 to 0.17. The corresponding ranges for intraexaminer reliability were higher for all associated landmarks: ASIS, 0.19 to 0.4; PSIS, 0.13 to 0.49; ILA-A/P, 0.1 to 0.2; ILA-S/I, 0.03 to 0.21; SS, 0.24 to 0.28; lumbar spine transverse processes L1 through L5, not applicable. Further research is needed to better understand the reliability of asymmetry assessment methods in manipulative medicine. PMID:21135198

VirtualDose: a software for reporting organ doses from CT for adult and pediatric patients.

PubMed

Ding, Aiping; Gao, Yiming; Liu, Haikuan; Caracappa, Peter F; Long, Daniel J; Bolch, Wesley E; Liu, Bob; Xu, X George

2015-07-21

This paper describes the development and testing of VirtualDose--a software for reporting organ doses for adult and pediatric patients who undergo x-ray computed tomography (CT) examinations. The software is based on a comprehensive database of organ doses derived from Monte Carlo (MC) simulations involving a library of 25 anatomically realistic phantoms that represent patients of different ages, body sizes, body masses, and pregnant stages. Models of GE Lightspeed Pro 16 and Siemens SOMATOM Sensation 16 scanners were carefully validated for use in MC dose calculations. The software framework is designed with the 'software as a service (SaaS)' delivery concept under which multiple clients can access the web-based interface simultaneously from any computer without having to install software locally. The RESTful web service API also allows a third-party picture archiving and communication system software package to seamlessly integrate with VirtualDose's functions. Software testing showed that VirtualDose was compatible with numerous operating systems including Windows, Linux, Apple OS X, and mobile and portable devices. The organ doses from VirtualDose were compared against those reported by CT-Expo and ImPACT-two dosimetry tools that were based on the stylized pediatric and adult patient models that were known to be anatomically simple. The organ doses reported by VirtualDose differed from those reported by CT-Expo and ImPACT by as much as 300% in some of the patient models. These results confirm the conclusion from past studies that differences in anatomical realism offered by stylized and voxel phantoms have caused significant discrepancies in CT dose estimations.

Computer systems and methods for the query and visualization multidimensional databases

DOEpatents

Stolte, Chris; Tang, Diane L.; Hanrahan, Patrick

2017-04-25

A method of generating a data visualization is performed at a computer having a display, one or more processors, and memory. The memory stores one or more programs for execution by the one or more processors. The process receives user specification of a plurality of characteristics of a data visualization. The data visualization is based on data from a multidimensional database. The characteristics specify at least x-position and y-position of data marks corresponding to tuples of data retrieved from the database. The process generates a data visualization according to the specified plurality of characteristics. The data visualization has an x-axis defined based on data for one or more first fields from the database that specify x-position of the data marks and the data visualization has a y-axis defined based on data for one or more second fields from the database that specify y-position of the data marks.

Characteristics and development of necrophylatic periderms in mature bark of American beech

Treesearch

William D. Ostrofsky; Robert O. Blanchard

1983-01-01

Investigations were made of necrophylactic peridems which were found to delimit natural and experimentally induced cankers in American beech. Anatomical evidence is presented which supports the hypothesis that the necrophylactic periderm is generated from recent derivatives of the vascular cambium as well as from living cells of the bark tissues present at the time of...

Unveiling the morphology of the acetabulum in octopus suckers and its role in attachment

PubMed Central

Tramacere, Francesca; Pugno, Nicola M.; Kuba, Michael J.; Mazzolai, Barbara

2015-01-01

In recent years, the attachment mechanism of the octopus sucker has attracted the interest of scientists from different research areas, including biology, engineering, medicine and robotics. From a technological perspective, the main goal is to identify the underlying mechanisms involved in sucker attachment for use in the development of new generations of artificial devices and materials. Recently, the understanding of the morphology of the sucker has been significantly improved; however, the mechanisms that allow attachment remain largely unknown. In this work, we present new anatomical findings: specifically, a protuberance in the acetabular roof in five different octopus species; previously, this protuberance was identified by the authors in Octopus vulgaris. Moreover, we discuss the role of the protuberance and other anatomical structures in attachment with minimal energy consumption. PMID:25657834

When saliva meets acid: chemical warfare at the oesophagogastric junction

PubMed Central

McColl, K E L

2005-01-01

In the Western world at least, most upper gastrointestinal cancers now arise from the mucosa near to the oesophagogastric junction. Research into the mechanism of the development of adenocarcinoma at the oesophagogastric junction has mainly focused on the noxious effects of acid and bile. There is however an alternative concept for explaining the location of adenocarcinomas: the cancers are occurring at the anatomical site where saliva encounters acidic gastric juice and their interaction generates reactive nitrogen species which are potentially mutagenic and carcinogenic. At present, it is unclear whether the active nitrite chemistry is exerting detrimental effects on the surrounding tissue but it is important to investigate this possibility as it could reveal new ways of preventing and treating the high prevalence of disease occurring at this anatomical site PMID:15591495

Midwest Generation Joliet and Will County Generating Stations, Order Denying Petition for Objection to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

January 22, 2004 Petition Requesting the Administrator Object to Operating Permit for Midwest Generation's Crawford Generating Station

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

January 22, 2004 Petition Requesting the Administrator Object to Operating Permit for Midwest Generation's Fisk Generating Station

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Order Responding to January 22, 2004 Request that the Administrator Object to Operating Permit for Midwest Generation's Fisk Generating Station

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Order Responding to January 22, 2004 Request that the Administrator Object to Operating Permit for Midwest Generation's Crawford Generating Station

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Midwest Generation, LLC, Romeoville Generating Station - Order Responding to Petitioner's Request that the Administrator Object to Issuance of a State Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Midwest Generation, LLC, Joliet Generating Station - Order Responding to Petitioner's Request that the Administrator Object to Issuance of a State Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Midwest Generation Fisk and Crawford Generating Stations, Order Denying Petition for Objection to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Order Denying Petition for Objection to Operating Permit for Luminant Generation Company's Sandow 5 Generating Plant

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Simulation of realistic abnormal SPECT brain perfusion images: application in semi-quantitative analysis

NASA Astrophysics Data System (ADS)

Ward, T.; Fleming, J. S.; Hoffmann, S. M. A.; Kemp, P. M.

2005-11-01

Simulation is useful in the validation of functional image analysis methods, particularly when considering the number of analysis techniques currently available lacking thorough validation. Problems exist with current simulation methods due to long run times or unrealistic results making it problematic to generate complete datasets. A method is presented for simulating known abnormalities within normal brain SPECT images using a measured point spread function (PSF), and incorporating a stereotactic atlas of the brain for anatomical positioning. This allows for the simulation of realistic images through the use of prior information regarding disease progression. SPECT images of cerebral perfusion have been generated consisting of a control database and a group of simulated abnormal subjects that are to be used in a UK audit of analysis methods. The abnormality is defined in the stereotactic space, then transformed to the individual subject space, convolved with a measured PSF and removed from the normal subject image. The dataset was analysed using SPM99 (Wellcome Department of Imaging Neuroscience, University College, London) and the MarsBaR volume of interest (VOI) analysis toolbox. The results were evaluated by comparison with the known ground truth. The analysis showed improvement when using a smoothing kernel equal to system resolution over the slightly larger kernel used routinely. Significant correlation was found between effective volume of a simulated abnormality and the detected size using SPM99. Improvements in VOI analysis sensitivity were found when using the region median over the region mean. The method and dataset provide an efficient methodology for use in the comparison and cross validation of semi-quantitative analysis methods in brain SPECT, and allow the optimization of analysis parameters.

Emotion and the prefrontal cortex: An integrative review.

PubMed

Dixon, Matthew L; Thiruchselvam, Ravi; Todd, Rebecca; Christoff, Kalina

2017-10-01

The prefrontal cortex (PFC) plays a critical role in the generation and regulation of emotion. However, we lack an integrative framework for understanding how different emotion-related functions are organized across the entire expanse of the PFC, as prior reviews have generally focused on specific emotional processes (e.g., decision making) or specific anatomical regions (e.g., orbitofrontal cortex). Additionally, psychological theories and neuroscientific investigations have proceeded largely independently because of the lack of a common framework. Here, we provide a comprehensive review of functional neuroimaging, electrophysiological, lesion, and structural connectivity studies on the emotion-related functions of 8 subregions spanning the entire PFC. We introduce the appraisal-by-content model, which provides a new framework for integrating the diverse range of empirical findings. Within this framework, appraisal serves as a unifying principle for understanding the PFC's role in emotion, while relative content-specialization serves as a differentiating principle for understanding the role of each subregion. A synthesis of data from affective, social, and cognitive neuroscience studies suggests that different PFC subregions are preferentially involved in assigning value to specific types of inputs: exteroceptive sensations, episodic memories and imagined future events, viscero-sensory signals, viscero-motor signals, actions, others' mental states (e.g., intentions), self-related information, and ongoing emotions. We discuss the implications of this integrative framework for understanding emotion regulation, value-based decision making, emotional salience, and refining theoretical models of emotion. This framework provides a unified understanding of how emotional processes are organized across PFC subregions and generates new hypotheses about the mechanisms underlying adaptive and maladaptive emotional functioning. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Nonlinear aspects of acoustic radiation force in biomedical applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ostrovsky, Lev, E-mail: Lev.A.Ostrovsky@noaa.gov; Tsyuryupa, Sergey; Sarvazyan, Armen, E-mail: armen@artannlabs.com

In the past decade acoustic radiation force (ARF) became a powerful tool in numerous biomedical applications. ARF from a focused ultrasound beam acts as a virtual “finger” for remote probing of internal anatomical structures and obtaining diagnostic information. This presentation deals with generation of shear waves by nonlinear focused beams. Albeit the ARF has intrinsically nonlinear origin, in most cases the primary ultrasonic wave was considered in the linear approximation. In this presentation, we consider the effects of nonlinearly distorted beams on generation of shear waves by such beams.

Nonlinear aspects of acoustic radiation force in biomedical applications

NASA Astrophysics Data System (ADS)

Ostrovsky, Lev; Tsyuryupa, Sergey; Sarvazyan, Armen

2015-10-01

In the past decade acoustic radiation force (ARF) became a powerful tool in numerous biomedical applications. ARF from a focused ultrasound beam acts as a virtual "finger" for remote probing of internal anatomical structures and obtaining diagnostic information. This presentation deals with generation of shear waves by nonlinear focused beams. Albeit the ARF has intrinsically nonlinear origin, in most cases the primary ultrasonic wave was considered in the linear approximation. In this presentation, we consider the effects of nonlinearly distorted beams on generation of shear waves by such beams.

Harnessing the Power of Light to See and Treat Breast Cancer

DTIC Science & Technology

2011-10-01

generate sarcomas include LSL- KrasG12D/+;Trp53Flox/Flox, BrafCa/+;Trp53 Flox/Flox and BrafCa/Ca;Trp53Flox/Flox.7,8 Soft tissue sarcomas were generated...temporally restricted mouse model of soft tissue sarcoma , Nat Med, 2007. 13(8): p. 992-7. 8. Dankort, D., et al., A new mouse model to explore the...resolution anatomical images of heterogeneous tissue. To do so we are employing the use of two ex vivo test beds: 1) murine sarcoma margins and 2

Generation of induced pluripotent stem cells from a patient with X-linked juvenile retinoschisis.

PubMed

Peng, Chi-Hsien; Huang, Kang-Chieh; Lu, Huai-En; Syu, Shih-Han; Yarmishyn, Aliaksandr A; Lu, Jyh-Feng; Buddhakosai, Waradee; Lin, Tai-Chi; Hsu, Chih-Chien; Hwang, De-Kuang; Shen, Chia-Ning; Chen, Shih-Jen; Chiou, Shih-Hwa

2018-05-01

X-linked juvenile retinoschisis (XLRS) is a hereditary retinal dystrophy manifested as splitting of anatomical layers of retina. In this report, we generated a patient-specific induced pluripotent stem cell (iPSC) line, TVGH-iPSC-013-05, from the peripheral blood mononuclear cells of a male patient with XLRS by using the Sendai-virus delivery system. We believe that XLRS patient-specific iPSCs provide a powerful in vitro model for evaluating the pathological phenotypes of the disease. Copyright © 2018. Published by Elsevier B.V.

Building strategies for tsunami scenarios databases to be used in a tsunami early warning decision support system: an application to western Iberia

NASA Astrophysics Data System (ADS)

Tinti, S.; Armigliato, A.; Pagnoni, G.; Zaniboni, F.

2012-04-01

One of the most challenging goals that the geo-scientific community is facing after the catastrophic tsunami occurred on December 2004 in the Indian Ocean is to develop the so-called "next generation" Tsunami Early Warning Systems (TEWS). Indeed, the meaning of "next generation" does not refer to the aim of a TEWS, which obviously remains to detect whether a tsunami has been generated or not by a given source and, in the first case, to send proper warnings and/or alerts in a suitable time to all the countries and communities that can be affected by the tsunami. Instead, "next generation" identifies with the development of a Decision Support System (DSS) that, in general terms, relies on 1) an integrated set of seismic, geodetic and marine sensors whose objective is to detect and characterise the possible tsunamigenic sources and to monitor instrumentally the time and space evolution of the generated tsunami, 2) databases of pre-computed numerical tsunami scenarios to be suitably combined based on the information coming from the sensor environment and to be used to forecast the degree of exposition of different coastal places both in the near- and in the far-field, 3) a proper overall (software) system architecture. The EU-FP7 TRIDEC Project aims at developing such a DSS and has selected two test areas in the Euro-Mediterranean region, namely the western Iberian margin and the eastern Mediterranean (Turkish coasts). In this study, we discuss the strategies that are being adopted in TRIDEC to build the databases of pre-computed tsunami scenarios and we show some applications to the western Iberian margin. In particular, two different databases are being populated, called "Virtual Scenario Database" (VSDB) and "Matching Scenario Database" (MSDB). The VSDB contains detailed simulations of few selected earthquake-generated tsunamis. The cases provided by the members of the VSDB are computed "real events"; in other words, they represent the unknowns that the TRIDEC platform must be able to recognise and match during the early crisis management phase. The MSDB contains a very large number (order of thousands) of tsunami simulations performed starting from many different simple earthquake sources of different magnitudes and located in the "vicinity" of the virtual scenario earthquake. Examples from both databases will be presented.

The performance of non-invasive tests to rule-in and rule-out significant coronary artery stenosis in patients with stable angina: a meta-analysis focused on post-test disease probability.

PubMed

Knuuti, Juhani; Ballo, Haitham; Juarez-Orozco, Luis Eduardo; Saraste, Antti; Kolh, Philippe; Rutjes, Anne Wilhelmina Saskia; Jüni, Peter; Windecker, Stephan; Bax, Jeroen J; Wijns, William

2018-05-29

To determine the ranges of pre-test probability (PTP) of coronary artery disease (CAD) in which stress electrocardiogram (ECG), stress echocardiography, coronary computed tomography angiography (CCTA), single-photon emission computed tomography (SPECT), positron emission tomography (PET), and cardiac magnetic resonance (CMR) can reclassify patients into a post-test probability that defines (>85%) or excludes (<15%) anatomically (defined by visual evaluation of invasive coronary angiography [ICA]) and functionally (defined by a fractional flow reserve [FFR] ≤0.8) significant CAD. A broad search in electronic databases until August 2017 was performed. Studies on the aforementioned techniques in >100 patients with stable CAD that utilized either ICA or ICA with FFR measurement as reference, were included. Study-level data was pooled using a hierarchical bivariate random-effects model and likelihood ratios were obtained for each technique. The PTP ranges for each technique to rule-in or rule-out significant CAD were defined. A total of 28 664 patients from 132 studies that used ICA as reference and 4131 from 23 studies using FFR, were analysed. Stress ECG can rule-in and rule-out anatomically significant CAD only when PTP is ≥80% (76-83) and ≤19% (15-25), respectively. Coronary computed tomography angiography is able to rule-in anatomic CAD at a PTP ≥58% (45-70) and rule-out at a PTP ≤80% (65-94). The corresponding PTP values for functionally significant CAD were ≥75% (67-83) and ≤57% (40-72) for CCTA, and ≥71% (59-81) and ≤27 (24-31) for ICA, demonstrating poorer performance of anatomic imaging against FFR. In contrast, functional imaging techniques (PET, stress CMR, and SPECT) are able to rule-in functionally significant CAD when PTP is ≥46-59% and rule-out when PTP is ≤34-57%. The various diagnostic modalities have different optimal performance ranges for the detection of anatomically and functionally significant CAD. Stress ECG appears to have very limited diagnostic power. The selection of a diagnostic technique for any given patient to rule-in or rule-out CAD should be based on the optimal PTP range for each test and on the assumed reference standard.

Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures

PubMed Central

2010-01-01

Background Papaver somniferum (opium poppy) is the source for several pharmaceutical benzylisoquinoline alkaloids including morphine, the codeine and sanguinarine. In response to treatment with a fungal elicitor, the biosynthesis and accumulation of sanguinarine is induced along with other plant defense responses in opium poppy cell cultures. The transcriptional induction of alkaloid metabolism in cultured cells provides an opportunity to identify components of this process via the integration of deep transcriptome and proteome databases generated using next-generation technologies. Results A cDNA library was prepared for opium poppy cell cultures treated with a fungal elicitor for 10 h. Using 454 GS-FLX Titanium pyrosequencing, 427,369 expressed sequence tags (ESTs) with an average length of 462 bp were generated. Assembly of these sequences yielded 93,723 unigenes, of which 23,753 were assigned Gene Ontology annotations. Transcripts encoding all known sanguinarine biosynthetic enzymes were identified in the EST database, 5 of which were represented among the 50 most abundant transcripts. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) of total protein extracts from cell cultures treated with a fungal elicitor for 50 h facilitated the identification of 1,004 proteins. Proteins were fractionated by one-dimensional SDS-PAGE and digested with trypsin prior to LC-MS/MS analysis. Query of an opium poppy-specific EST database substantially enhanced peptide identification. Eight out of 10 known sanguinarine biosynthetic enzymes and many relevant primary metabolic enzymes were represented in the peptide database. Conclusions The integration of deep transcriptome and proteome analyses provides an effective platform to catalogue the components of secondary metabolism, and to identify genes encoding uncharacterized enzymes. The establishment of corresponding transcript and protein databases generated by next-generation technologies in a system with a well-defined metabolite profile facilitates an improved linkage between genes, enzymes, and pathway components. The proteome database represents the most relevant alkaloid-producing enzymes, compared with the much deeper and more complete transcriptome library. The transcript database contained full-length mRNAs encoding most alkaloid biosynthetic enzymes, which is a key requirement for the functional characterization of novel gene candidates. PMID:21083930

Omics databases on kidney disease: where they can be found and how to benefit from them.

PubMed

Papadopoulos, Theofilos; Krochmal, Magdalena; Cisek, Katryna; Fernandes, Marco; Husi, Holger; Stevens, Robert; Bascands, Jean-Loup; Schanstra, Joost P; Klein, Julie

2016-06-01

In the recent decades, the evolution of omics technologies has led to advances in all biological fields, creating a demand for effective storage, management and exchange of rapidly generated data and research discoveries. To address this need, the development of databases of experimental outputs has become a common part of scientific practice in order to serve as knowledge sources and data-sharing platforms, providing information about genes, transcripts, proteins or metabolites. In this review, we present omics databases available currently, with a special focus on their application in kidney research and possibly in clinical practice. Databases are divided into two categories: general databases with a broad information scope and kidney-specific databases distinctively concentrated on kidney pathologies. In research, databases can be used as a rich source of information about pathophysiological mechanisms and molecular targets. In the future, databases will support clinicians with their decisions, providing better and faster diagnoses and setting the direction towards more preventive, personalized medicine. We also provide a test case demonstrating the potential of biological databases in comparing multi-omics datasets and generating new hypotheses to answer a critical and common diagnostic problem in nephrology practice. In the future, employment of databases combined with data integration and data mining should provide powerful insights into unlocking the mysteries of kidney disease, leading to a potential impact on pharmacological intervention and therapeutic disease management.

[Surgery of prostate cancer: Technical principles and perioperative complications].

PubMed

Salomon, L; Rozet, F; Soulié, M

2015-11-01

To describe the surgical procedure of localized prostate cancer treated by radical prostatectomy. Bibliography search was performed from the Medline database (National Library of Medicine, PubMed) selected according to the scientific relevance. The research was focused on historic of radical prostatectomy, surgical anatomy, surgical technics of radical prostatectomy and lymph nodes excision, and complications. During the last 30 years, evolution of radical prostatectomy was important, from open to mini-invasive surgery with or without robotic assistance. Anatomical knowledge of the prostate was useful to describe the different anatomical structure as urinary sphincter and fascias, and to develop different procedure of neurovascular bundles preservation to ameliorate functional results. Complications are well-known and their taking-over more precise. Results of radical prostatectomy depend less of the surgical approach but more of the attitude of the surgeon according to the characteristics of the tumor and the functional status of the patient. Radical prostatectomy is an elaborate and challenging procedure when carcinological risk balances with functional results. Nevertheless, complications are quite rare. Improvement of results is due to adequation between surgical procedure and oncological and functional status. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

A unified anatomy ontology of the vertebrate skeletal system.

PubMed

Dahdul, Wasila M; Balhoff, James P; Blackburn, David C; Diehl, Alexander D; Haendel, Melissa A; Hall, Brian K; Lapp, Hilmar; Lundberg, John G; Mungall, Christopher J; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E; Vickaryous, Matthew K; Westerfield, Monte; Mabee, Paula M

2012-01-01

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

A Unified Anatomy Ontology of the Vertebrate Skeletal System

PubMed Central

Dahdul, Wasila M.; Balhoff, James P.; Blackburn, David C.; Diehl, Alexander D.; Haendel, Melissa A.; Hall, Brian K.; Lapp, Hilmar; Lundberg, John G.; Mungall, Christopher J.; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E.; Vickaryous, Matthew K.; Westerfield, Monte; Mabee, Paula M.

2012-01-01

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity. PMID:23251424

Developing a Large Lexical Database for Information Retrieval, Parsing, and Text Generation Systems.

ERIC Educational Resources Information Center

Conlon, Sumali Pin-Ngern; And Others

1993-01-01

Important characteristics of lexical databases and their applications in information retrieval and natural language processing are explained. An ongoing project using various machine-readable sources to build a lexical database is described, and detailed designs of individual entries with examples are included. (Contains 66 references.) (EAM)

Chapter 4 - The LANDFIRE Prototype Project reference database

Treesearch

John F. Caratti

2006-01-01

This chapter describes the data compilation process for the Landscape Fire and Resource Management Planning Tools Prototype Project (LANDFIRE Prototype Project) reference database (LFRDB) and explains the reference data applications for LANDFIRE Prototype maps and models. The reference database formed the foundation for all LANDFIRE tasks. All products generated by the...

Building an integrated neurodegenerative disease database at an academic health center.

PubMed

Xie, Sharon X; Baek, Young; Grossman, Murray; Arnold, Steven E; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M-Y; Trojanowski, John Q

2011-07-01

It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration. These comparative studies rely on powerful database tools to quickly generate data sets that match diverse and complementary criteria set by them. In this article, we present a novel integrated neurodegenerative disease (INDD) database, which was developed at the University of Pennsylvania (Penn) with the help of a consortium of Penn investigators. Because the work of these investigators are based on Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration, it allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used the Microsoft SQL server as a platform, with built-in "backwards" functionality to provide Access as a frontend client to interface with the database. We used PHP Hypertext Preprocessor to create the "frontend" web interface and then used a master lookup table to integrate individual neurodegenerative disease databases. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Using the INDD database, we compared the results of a biomarker study with those using an alternative approach by querying individual databases separately. We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies on several neurodegenerative diseases. Copyright © 2011 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

Toward the automated generation of genome-scale metabolic networks in the SEED.

PubMed

DeJongh, Matthew; Formsma, Kevin; Boillot, Paul; Gould, John; Rycenga, Matthew; Best, Aaron

2007-04-26

Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis). We have implemented our tools and database within the SEED, an open-source software environment for comparative genome annotation and analysis. Our method sets the stage for the automated generation of substantially complete metabolic networks for over 400 complete genome sequences currently in the SEED. With each genome that is processed using our tools, the database of common components grows to cover more of the diversity of metabolic pathways. This increases the likelihood that components of reaction networks for subsequently processed genomes can be retrieved from the database, rather than assembled and verified manually.

Generation of synthetic CT data using patient specific daily MR image data and image registration

NASA Astrophysics Data System (ADS)

Melanie Kraus, Kim; Jäkel, Oliver; Niebuhr, Nina I.; Pfaffenberger, Asja

2017-02-01

To fully exploit the advantages of magnetic resonance imaging (MRI) for radiotherapy (RT) treatment planning, a method is required to overcome the problem of lacking electron density information. We aim to establish and evaluate a new method for computed tomography (CT) data generation based on MRI and image registration. The thereby generated CT data is used for dose accumulation. We developed a process flow based on an initial pair of rigidly co-registered CT and T2-weighted MR image representing the same anatomical situation. Deformable image registration using anatomical landmarks is performed between the initial MRI data and daily MR images. The resulting transformation is applied to the initial CT, thus fractional CT data is generated. Furthermore, the dose for a photon intensity modulated RT (IMRT) or intensity modulated proton therapy (IMPT) plan is calculated on the generated fractional CT and accumulated on the initial CT via inverse transformation. The method is evaluated by the use of phantom CT and MRI data. Quantitative validation is performed by evaluation of the mean absolute error (MAE) between the measured and the generated CT. The effect on dose accumulation is examined by means of dose-volume parameters. One patient case is presented to demonstrate the applicability of the method introduced here. Overall, CT data derivation lead to MAEs with a median of 37.0 HU ranging from 29.9 to 66.6 HU for all investigated tissues. The accuracy of image registration showed to be limited in the case of unexpected air cavities and at tissue boundaries. The comparisons of dose distributions based on measured and generated CT data agree well with the published literature. Differences in dose volume parameters kept within 1.6% and 3.2% for photon and proton RT, respectively. The method presented here is particularly suited for application in adaptive RT in current clinical routine, since only minor additional technical equipment is required.

Interhemispheric Plasticity following Intermittent Theta Burst Stimulation in Chronic Poststroke Aphasia

PubMed Central

Griffis, Joseph C.; Nenert, Rodolphe; Allendorfer, Jane B.; Szaflarski, Jerzy P.

2016-01-01

The effects of noninvasive neurostimulation on brain structure and function in chronic poststroke aphasia are poorly understood. We investigated the effects of intermittent theta burst stimulation (iTBS) applied to residual language-responsive cortex in chronic patients using functional and anatomical MRI data acquired before and after iTBS. Lateralization index (LI) analyses, along with comparisons of inferior frontal gyrus (IFG) activation and connectivity during covert verb generation, were used to assess changes in cortical language function. Voxel-based morphometry (VBM) was used to assess effects on regional grey matter (GM). LI analyses revealed a leftward shift in IFG activity after treatment. While left IFG activation increased, right IFG activation decreased. Changes in right to left IFG connectivity during covert verb generation also decreased after iTBS. Behavioral correlations revealed a negative relationship between changes in right IFG activation and improvements in fluency. While anatomical analyses did not reveal statistically significant changes in grey matter volume, the fMRI results provide evidence for changes in right and left IFG function after iTBS. The negative relationship between post-iTBS changes in right IFG activity during covert verb generation and improvements in fluency suggests that iTBS applied to residual left-hemispheric language areas may reduce contralateral responses related to language production and facilitate recruitment of residual language areas after stroke. PMID:26881111

Interhemispheric Plasticity following Intermittent Theta Burst Stimulation in Chronic Poststroke Aphasia.

PubMed

Griffis, Joseph C; Nenert, Rodolphe; Allendorfer, Jane B; Szaflarski, Jerzy P

2016-01-01

The effects of noninvasive neurostimulation on brain structure and function in chronic poststroke aphasia are poorly understood. We investigated the effects of intermittent theta burst stimulation (iTBS) applied to residual language-responsive cortex in chronic patients using functional and anatomical MRI data acquired before and after iTBS. Lateralization index (LI) analyses, along with comparisons of inferior frontal gyrus (IFG) activation and connectivity during covert verb generation, were used to assess changes in cortical language function. Voxel-based morphometry (VBM) was used to assess effects on regional grey matter (GM). LI analyses revealed a leftward shift in IFG activity after treatment. While left IFG activation increased, right IFG activation decreased. Changes in right to left IFG connectivity during covert verb generation also decreased after iTBS. Behavioral correlations revealed a negative relationship between changes in right IFG activation and improvements in fluency. While anatomical analyses did not reveal statistically significant changes in grey matter volume, the fMRI results provide evidence for changes in right and left IFG function after iTBS. The negative relationship between post-iTBS changes in right IFG activity during covert verb generation and improvements in fluency suggests that iTBS applied to residual left-hemispheric language areas may reduce contralateral responses related to language production and facilitate recruitment of residual language areas after stroke.

Funding anatomic pathology research: a retrospective analysis of an intramural funding mechanism.

PubMed

McDaniel, Andrew; Fullen, Douglas R; Cho, Kathleen R; Lucas, David R; Giordano, Thomas J; Greenson, Joel; Lieberman, Andrew P; Kunju, Lakshmi P; Myers, Jeffrey L; Roh, Michael H

2013-09-01

In 2006, the department of pathology at our institution established an intramural research funding mechanism to support anatomic pathology research projects for faculty and trainee development. A review committee consisting of faculty members with diverse academic interests evaluated applications; proposals were eligible for a maximum award amount of $30 000 per project with a maximum program cost of $150 000 annually. To report our experience based on a retrospective review of the research proposals submitted to the committee since the inception of the Anatomic Pathology Research Fund and evaluate the outcomes of the funded projects. We retrospectively analyzed all project applications that were received by the committee. Outcome data were collected by reviewing progress reports, abstracts for national and international meetings, PubMed search results, and/or direct communication with investigators. To date, a total of 59 individual projects have been awarded funding, for a total amount of $349 792, with an average award amount of $5381 per project. A total of 26 faculty members have secured funding for projects through this mechanism, and 27 resident and fellow trainees have been engaged in the funded projects. Spanning 11 subspecialty disciplines in anatomic pathology, 32 abstracts (54%) have been presented at national meetings and 26 (44%) have been published in the peer-reviewed literature to date. One project generated data used to secure an extramural (R01) grant. Our funding mechanism could serve as a model used by other academic departments to support research activities, thereby fostering faculty development through scholarly activities.

Towards Anatomic Scale Agent-Based Modeling with a Massively Parallel Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT_HPC)

PubMed Central

Cockrell, Robert Chase; Christley, Scott; Chang, Eugene; An, Gary

2015-01-01

Perhaps the greatest challenge currently facing the biomedical research community is the ability to integrate highly detailed cellular and molecular mechanisms to represent clinical disease states as a pathway to engineer effective therapeutics. This is particularly evident in the representation of organ-level pathophysiology in terms of abnormal tissue structure, which, through histology, remains a mainstay in disease diagnosis and staging. As such, being able to generate anatomic scale simulations is a highly desirable goal. While computational limitations have previously constrained the size and scope of multi-scale computational models, advances in the capacity and availability of high-performance computing (HPC) resources have greatly expanded the ability of computational models of biological systems to achieve anatomic, clinically relevant scale. Diseases of the intestinal tract are exemplary examples of pathophysiological processes that manifest at multiple scales of spatial resolution, with structural abnormalities present at the microscopic, macroscopic and organ-levels. In this paper, we describe a novel, massively parallel computational model of the gut, the Spatially Explicitly General-purpose Model of Enteric Tissue_HPC (SEGMEnT_HPC), which extends an existing model of the gut epithelium, SEGMEnT, in order to create cell-for-cell anatomic scale simulations. We present an example implementation of SEGMEnT_HPC that simulates the pathogenesis of ileal pouchitis, and important clinical entity that affects patients following remedial surgery for ulcerative colitis. PMID:25806784

Development and Feasibility Testing of a Critical Care EEG Monitoring Database for Standardized Clinical Reporting and Multicenter Collaborative Research.

PubMed

Lee, Jong Woo; LaRoche, Suzette; Choi, Hyunmi; Rodriguez Ruiz, Andres A; Fertig, Evan; Politsky, Jeffrey M; Herman, Susan T; Loddenkemper, Tobias; Sansevere, Arnold J; Korb, Pearce J; Abend, Nicholas S; Goldstein, Joshua L; Sinha, Saurabh R; Dombrowski, Keith E; Ritzl, Eva K; Westover, Michael B; Gavvala, Jay R; Gerard, Elizabeth E; Schmitt, Sarah E; Szaflarski, Jerzy P; Ding, Kan; Haas, Kevin F; Buchsbaum, Richard; Hirsch, Lawrence J; Wusthoff, Courtney J; Hopp, Jennifer L; Hahn, Cecil D

2016-04-01

The rapid expansion of the use of continuous critical care electroencephalogram (cEEG) monitoring and resulting multicenter research studies through the Critical Care EEG Monitoring Research Consortium has created the need for a collaborative data sharing mechanism and repository. The authors describe the development of a research database incorporating the American Clinical Neurophysiology Society standardized terminology for critical care EEG monitoring. The database includes flexible report generation tools that allow for daily clinical use. Key clinical and research variables were incorporated into a Microsoft Access database. To assess its utility for multicenter research data collection, the authors performed a 21-center feasibility study in which each center entered data from 12 consecutive intensive care unit monitoring patients. To assess its utility as a clinical report generating tool, three large volume centers used it to generate daily clinical critical care EEG reports. A total of 280 subjects were enrolled in the multicenter feasibility study. The duration of recording (median, 25.5 hours) varied significantly between the centers. The incidence of seizure (17.6%), periodic/rhythmic discharges (35.7%), and interictal epileptiform discharges (11.8%) was similar to previous studies. The database was used as a clinical reporting tool by 3 centers that entered a total of 3,144 unique patients covering 6,665 recording days. The Critical Care EEG Monitoring Research Consortium database has been successfully developed and implemented with a dual role as a collaborative research platform and a clinical reporting tool. It is now available for public download to be used as a clinical data repository and report generating tool.

Generation of large scale urban environments to support advanced sensor and seeker simulation

NASA Astrophysics Data System (ADS)

Giuliani, Joseph; Hershey, Daniel; McKeown, David, Jr.; Willis, Carla; Van, Tan

2009-05-01

One of the key aspects for the design of a next generation weapon system is the need to operate in cluttered and complex urban environments. Simulation systems rely on accurate representation of these environments and require automated software tools to construct the underlying 3D geometry and associated spectral and material properties that are then formatted for various objective seeker simulation systems. Under an Air Force Small Business Innovative Research (SBIR) contract, we have developed an automated process to generate 3D urban environments with user defined properties. These environments can be composed from a wide variety of source materials, including vector source data, pre-existing 3D models, and digital elevation models, and rapidly organized into a geo-specific visual simulation database. This intermediate representation can be easily inspected in the visible spectrum for content and organization and interactively queried for accuracy. Once the database contains the required contents, it can then be exported into specific synthetic scene generation runtime formats, preserving the relationship between geometry and material properties. To date an exporter for the Irma simulation system developed and maintained by AFRL/Eglin has been created and a second exporter to Real Time Composite Hardbody and Missile Plume (CHAMP) simulation system for real-time use is currently being developed. This process supports significantly more complex target environments than previous approaches to database generation. In this paper we describe the capabilities for content creation for advanced seeker processing algorithms simulation and sensor stimulation, including the overall database compilation process and sample databases produced and exported for the Irma runtime system. We also discuss the addition of object dynamics and viewer dynamics within the visual simulation into the Irma runtime environment.

SU-F-J-201: Validation Study of Proton Radiography Against CT Data for Quantitative Imaging of Anatomical Changes in Head and Neck Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hammi, A; Weber, D; Lomax, A

2016-06-15

Purpose: In clinical pencil-beam-scanned (PBS) proton therapy, the advantage of the characteristic sharp dose fall-off after the Bragg Peak (BP) becomes a disadvantage if the BP positions of a plan’s constituent pencil beams are shifted, eg.due to anatomical changes. Thus, for fractionated PBS proton therapy, accurate knowledge of the water equivalent path length (WEPL) of the traversed anatomy is critical. In this work we investigate the feasibility of using 2D proton range maps (proton radiography, PR) with the active-scanning gantry at PSI. Methods: We simulated our approach using Monte Carlo methods (MC) to simulate proton beam interactions in patients usingmore » clinical imaging data. We selected six head and neck cases having significant anatomical changes detected in per-treatment CTs.PRs (two at 0°/90°) were generated from MC simulations of low-dose pencil beams at 230MeV. Each beam’s residual depth-dose was propagated through the patient geometry (from CT) and detected on exiting the patient anatomy in an ideal depth-resolved detector (eg. range telescope). Firstly, to validate the technique, proton radiographs were compared to the ground truth, which was the WEPL from ray-tracing in the patient CT at the pencil beam location. Secondly, WEPL difference maps (per-treatment – planning imaging timepoints) were then generated to locate the anatomical changes, both in the CT (ground truth) and in the PRs. Binomial classification was performed to evaluate the efficacy of the technique relative to CT. Results: Over the projections simulated over all six patients, 70%, 79% and 95% of the grid points agreed with the ground truth proton range to within ±0.5%, ±1%, and ±3% respectively. The sensitivity, specificity, precision and accuracy were high (mean±1σ, 83±8%, 87±13%, 95±10%, 83±7% respectively). Conclusion: We show that proton-based radiographic images can accurately monitor patient positioning and in vivo range verification, while providing equivalent WEPL information to a CT scan, with the advantage of a much lower imaging dose.« less

SU-G-IeP2-08: Investigation On Signal Detectability in Volumetric Cone Beam CT Images with Anatomical Background

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, M; Baek, J

2016-06-15

Purpose: To investigate the slice direction dependent detectability in cone beam CT images with anatomical background. Methods: We generated 3D anatomical background images using breast anatomy model. To generate 3D breast anatomy, we filtered 3D Gaussian noise with a square root of 1/f{sup 3}, and then assigned the attenuation coefficient of glandular (0.8cm{sup −1}) and adipose (0.46 cm{sup −1}) tissues based on voxel values. Projections were acquired by forward projection, and quantum noise was added to the projection data. The projection data were reconstructed by FDK algorithm. We compared the detectability of a 3 mm spherical signal in the imagemore » reconstructed from four different backprojection Methods: Hanning weighted ramp filter with linear interpolation (RECON1), Hanning weighted ramp filter with Fourier interpolation (RECON2), ramp filter with linear interpolation (RECON3), and ramp filter with Fourier interpolation (RECON4), respectively. We computed task SNR of the spherical signal in transverse and longitudinal planes using channelized Hotelling observer with Laguerre-Gauss channels. Results: Transverse plane has similar task SNR values for different backprojection methods, while longitudinal plane has a maximum task SNR value in RECON1. For all backprojection methods, longitudinal plane has higher task SNR than transverse plane. Conclusion: In this work, we investigated detectability for different slice direction in cone beam CT images with anatomical background. Longitudinal plane has a higher task SNR than transverse plane, and backprojection with hanning weighted ramp filter with linear interpolation method (i.e., RECON1) produced the highest task SNR among four different backprojection methods. This research was supported by the MSIP (Ministry of Science, ICT and Future Planning), Korea, under the IT Consilience Creative Programs(IITP-2015-R0346-15-1008) supervised by the IITP (Institute for Information & Communications Technology Promotion), Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the MSIP (2015R1C1A1A01052268) and framework of international cooperation program managed by NRF (NRF-2015K2A1A2067635).« less

SU-G-BRA-07: An Innovative Fiducial-Less Tracking Method for Radiation Treatment of Abdominal Tumors by Diaphragm Disparity Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dick, D; Zhao, W; Wu, X

2016-06-15

Purpose: To investigate the feasibility of tracking abdominal tumors without the use of gold fiducial markers Methods: In this simulation study, an abdominal 4DCT dataset, acquired previously and containing 8 phases of the breathing cycle, was used as the testing data. Two sets of DRR images (45 and 135 degrees) were generated for each phase. Three anatomical points along the lung-diaphragm interface on each of the Digital Reconstructed Radiograph(DRR) images were identified by cross-correlation. The gallbladder, which simulates the tumor, was contoured for each phase of the breathing cycle and the corresponding centroid values serve as the measured center ofmore » the tumor. A linear model was created to correlate the diaphragm’s disparity of the three identified anatomical points with the center of the tumor. To verify the established linear model, we sequentially removed one phase of the data (i.e., 3 anatomical points and the corresponding tumor center) and created new linear models with the remaining 7 phases. Then we substituted the eliminated phase data (disparities of the 3 anatomical points) into the corresponding model to compare model-generated tumor center and the measured tumor center. Results: The maximum difference between the modeled and the measured centroid values across the 8 phases were 0.72, 0.29 and 0.30 pixels in the x, y and z directions respectively, which yielded a maximum mean-squared-error value of 0.75 pixels. The outcomes of the verification process, by eliminating each phase, produced mean-squared-errors ranging from 0.41 to 1.28 pixels. Conclusion: Gold fiducial markers, requiring surgical procedures to be implanted, are conventionally used in radiation therapy. The present work shows the feasibility of a fiducial-less tracking method for localizing abdominal tumors. Through developed diaphragm disparity analysis, the established linear model was verified with clinically accepted errors. The tracking method in real time under different radiation therapy platforms will be further investigated.« less

An Extended IEEE 118-Bus Test System With High Renewable Penetration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pena, Ivonne; Martinez-Anido, Carlo Brancucci; Hodge, Bri-Mathias

This article describes a new publicly available version of the IEEE 118-bus test system, named NREL-118. The database is based on the transmission representation (buses and lines) of the IEEE 118-bus test system, with a reconfigured generation representation using three regions of the US Western Interconnection from the latest Western Electricity Coordination Council (WECC) 2024 Common Case [1]. Time-synchronous hourly load, wind, and solar time series are provided for over one year (8784 hours). The public database presented and described in this manuscript will allow researchers to model a test power system using detailed transmission, generation, load, wind, and solarmore » data. This database includes key additional features that add to the current IEEE 118-bus test model, such as: the inclusion of 10 generation technologies with different heat rate functions, minimum stable levels and ramping rates, GHG emissions rates, regulation and contingency reserves, and hourly time series data for one full year for load, wind and solar generation.« less

CT-based manual segmentation and evaluation of paranasal sinuses.

PubMed

Pirner, S; Tingelhoff, K; Wagner, I; Westphal, R; Rilk, M; Wahl, F M; Bootz, F; Eichhorn, Klaus W G

2009-04-01

Manual segmentation of computed tomography (CT) datasets was performed for robot-assisted endoscope movement during functional endoscopic sinus surgery (FESS). Segmented 3D models are needed for the robots' workspace definition. A total of 50 preselected CT datasets were each segmented in 150-200 coronal slices with 24 landmarks being set. Three different colors for segmentation represent diverse risk areas. Extension and volumetric measurements were performed. Three-dimensional reconstruction was generated after segmentation. Manual segmentation took 8-10 h for each CT dataset. The mean volumes were: right maxillary sinus 17.4 cm(3), left side 17.9 cm(3), right frontal sinus 4.2 cm(3), left side 4.0 cm(3), total frontal sinuses 7.9 cm(3), sphenoid sinus right side 5.3 cm(3), left side 5.5 cm(3), total sphenoid sinus volume 11.2 cm(3). Our manually segmented 3D-models present the patient's individual anatomy with a special focus on structures in danger according to the diverse colored risk areas. For safe robot assistance, the high-accuracy models represent an average of the population for anatomical variations, extension and volumetric measurements. They can be used as a database for automatic model-based segmentation. None of the segmentation methods so far described provide risk segmentation. The robot's maximum distance to the segmented border can be adjusted according to the differently colored areas.

Generating patient specific pseudo-CT of the head from MR using atlas-based regression

NASA Astrophysics Data System (ADS)

Sjölund, J.; Forsberg, D.; Andersson, M.; Knutsson, H.

2015-01-01

Radiotherapy planning and attenuation correction of PET images require simulation of radiation transport. The necessary physical properties are typically derived from computed tomography (CT) images, but in some cases, including stereotactic neurosurgery and combined PET/MR imaging, only magnetic resonance (MR) images are available. With these applications in mind, we describe how a realistic, patient-specific, pseudo-CT of the head can be derived from anatomical MR images. We refer to the method as atlas-based regression, because of its similarity to atlas-based segmentation. Given a target MR and an atlas database comprising MR and CT pairs, atlas-based regression works by registering each atlas MR to the target MR, applying the resulting displacement fields to the corresponding atlas CTs and, finally, fusing the deformed atlas CTs into a single pseudo-CT. We use a deformable registration algorithm known as the Morphon and augment it with a certainty mask that allows a tailoring of the influence certain regions are allowed to have on the registration. Moreover, we propose a novel method of fusion, wherein the collection of deformed CTs is iteratively registered to their joint mean and find that the resulting mean CT becomes more similar to the target CT. However, the voxelwise median provided even better results; at least as good as earlier work that required special MR imaging techniques. This makes atlas-based regression a good candidate for clinical use.

Joint Clustering and Component Analysis of Correspondenceless Point Sets: Application to Cardiac Statistical Modeling.

PubMed

Gooya, Ali; Lekadir, Karim; Alba, Xenia; Swift, Andrew J; Wild, Jim M; Frangi, Alejandro F

2015-01-01

Construction of Statistical Shape Models (SSMs) from arbitrary point sets is a challenging problem due to significant shape variation and lack of explicit point correspondence across the training data set. In medical imaging, point sets can generally represent different shape classes that span healthy and pathological exemplars. In such cases, the constructed SSM may not generalize well, largely because the probability density function (pdf) of the point sets deviates from the underlying assumption of Gaussian statistics. To this end, we propose a generative model for unsupervised learning of the pdf of point sets as a mixture of distinctive classes. A Variational Bayesian (VB) method is proposed for making joint inferences on the labels of point sets, and the principal modes of variations in each cluster. The method provides a flexible framework to handle point sets with no explicit point-to-point correspondences. We also show that by maximizing the marginalized likelihood of the model, the optimal number of clusters of point sets can be determined. We illustrate this work in the context of understanding the anatomical phenotype of the left and right ventricles in heart. To this end, we use a database containing hearts of healthy subjects, patients with Pulmonary Hypertension (PH), and patients with Hypertrophic Cardiomyopathy (HCM). We demonstrate that our method can outperform traditional PCA in both generalization and specificity measures.

Spatial and symbolic queries for 3D image data

NASA Astrophysics Data System (ADS)

Benson, Daniel C.; Zick, Gregory L.

1992-04-01

We present a query system for an object-oriented biomedical imaging database containing 3-D anatomical structures and their corresponding 2-D images. The graphical interface facilitates the formation of spatial queries, nonspatial or symbolic queries, and combined spatial/symbolic queries. A query editor is used for the creation and manipulation of 3-D query objects as volumes, surfaces, lines, and points. Symbolic predicates are formulated through a combination of text fields and multiple choice selections. Query results, which may include images, image contents, composite objects, graphics, and alphanumeric data, are displayed in multiple views. Objects returned by the query may be selected directly within the views for further inspection or modification, or for use as query objects in subsequent queries. Our image database query system provides visual feedback and manipulation of spatial query objects, multiple views of volume data, and the ability to combine spatial and symbolic queries. The system allows for incremental enhancement of existing objects and the addition of new objects and spatial relationships. The query system is designed for databases containing symbolic and spatial data. This paper discuses its application to data acquired in biomedical 3- D image reconstruction, but it is applicable to other areas such as CAD/CAM, geographical information systems, and computer vision.

Autophagic compound database: A resource connecting autophagy-modulating compounds, their potential targets and relevant diseases.

PubMed

Deng, Yiqi; Zhu, Lingjuan; Cai, Haoyang; Wang, Guan; Liu, Bo

2018-06-01

Autophagy, a highly conserved lysosomal degradation process in eukaryotic cells, can digest long-lived proteins and damaged organelles through vesicular trafficking pathways. Nowadays, mechanisms of autophagy have been gradually elucidated and thus the discovery of small-molecule drugs targeting autophagy has always been drawing much attention. So far, some autophagy-related web servers have been available online to facilitate scientists to obtain the information relevant to autophagy conveniently, such as HADb, CTLPScanner, iLIR server and ncRDeathDB. However, to the best of our knowledge, there is not any web server available about the autophagy-modulating compounds. According to published articles, all the compounds and their relations with autophagy were anatomized. Subsequently, an online Autophagic Compound Database (ACDB) (http://www.acdbliulab.com/) was constructed, which contained information of 357 compounds with 164 corresponding signalling pathways and potential targets in different diseases. We achieved a great deal of information of autophagy-modulating compounds, including compounds, targets/pathways and diseases. ACDB is a valuable resource for users to access to more than 300 curated small-molecule compounds correlated with autophagy. Autophagic compound database will facilitate to the discovery of more novel therapeutic drugs in the near future. © 2017 John Wiley & Sons Ltd.

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

PubMed Central

Brozovic, Matija; Dantec, Christelle; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maelle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Lowe, Elijah K; Mendez, Mickael; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Kenta; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie; Veeman, Michael; Volff, Jean-Nicolas

2018-01-01

Abstract ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates. PMID:29149270

Data-driven grasp synthesis using shape matching and task-based pruning.

PubMed

Li, Ying; Fu, Jiaxin L; Pollard, Nancy S

2007-01-01

Human grasps, especially whole-hand grasps, are difficult to animate because of the high number of degrees of freedom of the hand and the need for the hand to conform naturally to the object surface. Captured human motion data provides us with a rich source of examples of natural grasps. However, for each new object, we are faced with the problem of selecting the best grasp from the database and adapting it to that object. This paper presents a data-driven approach to grasp synthesis. We begin with a database of captured human grasps. To identify candidate grasps for a new object, we introduce a novel shape matching algorithm that matches hand shape to object shape by identifying collections of features having similar relative placements and surface normals. This step returns many grasp candidates, which are clustered and pruned by choosing the grasp best suited for the intended task. For pruning undesirable grasps, we develop an anatomically-based grasp quality measure specific to the human hand. Examples of grasp synthesis are shown for a variety of objects not present in the original database. This algorithm should be useful both as an animator tool for posing the hand and for automatic grasp synthesis in virtual environments.

Automated CFD Database Generation for a 2nd Generation Glide-Back-Booster

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.; Rogers, Stuart E.; Aftosmis, Michael J.; Pandya, Shishir A.; Ahmad, Jasim U.; Tejmil, Edward

2003-01-01

A new software tool, AeroDB, is used to compute thousands of Euler and Navier-Stokes solutions for a 2nd generation glide-back booster in one week. The solution process exploits a common job-submission grid environment using 13 computers located at 4 different geographical sites. Process automation and web-based access to the database greatly reduces the user workload, removing much of the tedium and tendency for user input errors. The database consists of forces, moments, and solution files obtained by varying the Mach number, angle of attack, and sideslip angle. The forces and moments compare well with experimental data. Stability derivatives are also computed using a monotone cubic spline procedure. Flow visualization and three-dimensional surface plots are used to interpret and characterize the nature of computed flow fields.

Aptamer Database

PubMed Central

Lee, Jennifer F.; Hesselberth, Jay R.; Meyers, Lauren Ancel; Ellington, Andrew D.

2004-01-01

The aptamer database is designed to contain comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods. Such data are not normally collected in ‘natural’ sequence databases, such as GenBank. Besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility, the database serves as a valuable resource for theoretical biologists who describe and explore fitness landscapes. The database is updated monthly and is publicly available at http://aptamer.icmb.utexas.edu/. PMID:14681367

3D printing materials and their use in medical education: a review of current technology and trends for the future

PubMed Central

Garcia, Justine; Yang, ZhiLin; Mongrain, Rosaire; Leask, Richard L; Lachapelle, Kevin

2018-01-01

3D printing is a new technology in constant evolution. It has rapidly expanded and is now being used in health education. Patient-specific models with anatomical fidelity created from imaging dataset have the potential to significantly improve the knowledge and skills of a new generation of surgeons. This review outlines five technical steps required to complete a printed model: They include (1) selecting the anatomical area of interest, (2) the creation of the 3D geometry, (3) the optimisation of the file for the printing and the appropriate selection of (4) the 3D printer and (5) materials. All of these steps require time, expertise and money. A thorough understanding of educational needs is therefore essential in order to optimise educational value. At present, most of the available printing materials are rigid and therefore not optimum for flexibility and elasticity unlike biological tissue. We believe that the manipuation and tuning of material properties through the creation of composites and/or blending materials will eventually allow for the creation of patient-specific models which have both anatomical and tissue fidelity. PMID:29354281

3D printing materials and their use in medical education: a review of current technology and trends for the future.

PubMed

Garcia, Justine; Yang, ZhiLin; Mongrain, Rosaire; Leask, Richard L; Lachapelle, Kevin

2018-01-01

3D printing is a new technology in constant evolution. It has rapidly expanded and is now being used in health education. Patient-specific models with anatomical fidelity created from imaging dataset have the potential to significantly improve the knowledge and skills of a new generation of surgeons. This review outlines five technical steps required to complete a printed model: They include (1) selecting the anatomical area of interest, (2) the creation of the 3D geometry, (3) the optimisation of the file for the printing and the appropriate selection of (4) the 3D printer and (5) materials. All of these steps require time, expertise and money. A thorough understanding of educational needs is therefore essential in order to optimise educational value. At present, most of the available printing materials are rigid and therefore not optimum for flexibility and elasticity unlike biological tissue. We believe that the manipuation and tuning of material properties through the creation of composites and/or blending materials will eventually allow for the creation of patient-specific models which have both anatomical and tissue fidelity.

An anatomically comprehensive atlas of the adult human brain transcriptome

PubMed Central

Guillozet-Bongaarts, Angela L.; Shen, Elaine H.; Ng, Lydia; Miller, Jeremy A.; van de Lagemaat, Louie N.; Smith, Kimberly A.; Ebbert, Amanda; Riley, Zackery L.; Abajian, Chris; Beckmann, Christian F.; Bernard, Amy; Bertagnolli, Darren; Boe, Andrew F.; Cartagena, Preston M.; Chakravarty, M. Mallar; Chapin, Mike; Chong, Jimmy; Dalley, Rachel A.; David Daly, Barry; Dang, Chinh; Datta, Suvro; Dee, Nick; Dolbeare, Tim A.; Faber, Vance; Feng, David; Fowler, David R.; Goldy, Jeff; Gregor, Benjamin W.; Haradon, Zeb; Haynor, David R.; Hohmann, John G.; Horvath, Steve; Howard, Robert E.; Jeromin, Andreas; Jochim, Jayson M.; Kinnunen, Marty; Lau, Christopher; Lazarz, Evan T.; Lee, Changkyu; Lemon, Tracy A.; Li, Ling; Li, Yang; Morris, John A.; Overly, Caroline C.; Parker, Patrick D.; Parry, Sheana E.; Reding, Melissa; Royall, Joshua J.; Schulkin, Jay; Sequeira, Pedro Adolfo; Slaughterbeck, Clifford R.; Smith, Simon C.; Sodt, Andy J.; Sunkin, Susan M.; Swanson, Beryl E.; Vawter, Marquis P.; Williams, Derric; Wohnoutka, Paul; Zielke, H. Ronald; Geschwind, Daniel H.; Hof, Patrick R.; Smith, Stephen M.; Koch, Christof; Grant, Seth G. N.; Jones, Allan R.

2014-01-01

Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray profiling of ~900 neuroanatomically precise subdivisions in two individuals. Transcriptional regulation varies enormously by anatomical location, with different regions and their constituent cell types displaying robust molecular signatures that are highly conserved between individuals. Analysis of differential gene expression and gene co-expression relationships demonstrates that brain-wide variation strongly reflects the distributions of major cell classes such as neurons, oligodendrocytes, astrocytes and microglia. Local neighbourhood relationships between fine anatomical subdivisions are associated with discrete neuronal subtypes and genes involved with synaptic transmission. The neocortex displays a relatively homogeneous transcriptional pattern, but with distinct features associated selectively with primary sensorimotor cortices and with enriched frontal lobe expression. Notably, the spatial topography of the neocortex is strongly reflected in its molecular topography— the closer two cortical regions, the more similar their transcriptomes. This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function. PMID:22996553

Analysis of Mass Averaged Tissue Doses in CAM, CAF, MAX, and FAX

NASA Technical Reports Server (NTRS)

Slaba, Tony C.; Qualls, Garry D.; Clowdsley, Martha S.; Blattnig, Steve R.; Simonsen, Lisa C.; Walker, Steven A.; Singleterry, Robert C.

2009-01-01

To estimate astronaut health risk due to space radiation, one must have the ability to calculate exposure-related quantities averaged over specific organs and tissue types. In this study, we first examine the anatomical properties of the Computerized Anatomical Man (CAM), Computerized Anatomical Female (CAF), Male Adult voXel (MAX), and Female Adult voXel (FAX) models by comparing the masses of various tissues to the reference values specified by the International Commission on Radiological Protection (ICRP). Major discrepancies are found between the CAM and CAF tissue masses and the ICRP reference data for almost all of the tissues. We next examine the distribution of target points used with the deterministic transport code HZETRN to compute mass averaged exposure quantities. A numerical algorithm is used to generate multiple point distributions for many of the effective dose tissues identified in CAM, CAF, MAX, and FAX. It is concluded that the previously published CAM and CAF point distributions were under-sampled and that the set of point distributions presented here should be adequate for future studies involving CAM, CAF, MAX, or FAX. It is concluded that MAX and FAX are more accurate than CAM and CAF for space radiation analyses.

Comparison of mechanical energy profiles of passive and active below-knee prostheses: a case study.

PubMed

Takahashi, Kota Z; Horne, John R; Stanhope, Steven J

2015-04-01

With the recent technological advancements of prosthetic lower limbs, there is currently a great desire to objectively evaluate existing prostheses. Using a novel biomechanical analysis, the purpose of this case study was to compare the mechanical energy profiles of anatomical and two disparate prostheses: a passive prosthesis and an active prosthesis. An individual with a transtibial amputation who customarily wears a passive prosthesis (Elation, Össur) and an active prosthesis (BiOM, iWalk, Inc.) and 11 healthy subjects participated in an instrumented gait analysis. The total mechanical power and work of below-knee structures during stance were quantified using a unified deformable segment power analysis. Active prosthesis generated greater peak power and total positive work than passive prosthesis and healthy anatomical limbs. The case study will enhance future efforts to objectively evaluate prosthetic functions during gait in individuals with transtibial amputations. A prosthetic limb should closely replicate the mechanical energy profiles of anatomical limbs. The unified deformable (UD) analysis may be valuable to facilitate future clinical prescription and guide fine adjustments of prosthetic componentry to optimize gait outcomes. © The International Society for Prosthetics and Orthotics 2014.

An improved distance-to-dose correlation for predicting bladder and rectum dose-volumes in knowledge-based VMAT planning for prostate cancer

NASA Astrophysics Data System (ADS)

Wall, Phillip D. H.; Carver, Robert L.; Fontenot, Jonas D.

2018-01-01

The overlap volume histogram (OVH) is an anatomical metric commonly used to quantify the geometric relationship between an organ at risk (OAR) and target volume when predicting expected dose-volumes in knowledge-based planning (KBP). This work investigated the influence of additional variables contributing to variations in the assumed linear DVH-OVH correlation for the bladder and rectum in VMAT plans of prostate patients, with the goal of increasing prediction accuracy and achievability of knowledge-based planning methods. VMAT plans were retrospectively generated for 124 prostate patients using multi-criteria optimization. DVHs quantified patient dosimetric data while OVHs quantified patient anatomical information. The DVH-OVH correlations were calculated for fractional bladder and rectum volumes of 30, 50, 65, and 80%. Correlations between potential influencing factors and dose were quantified using the Pearson product-moment correlation coefficient (R). Factors analyzed included the derivative of the OVH, prescribed dose, PTV volume, bladder volume, rectum volume, and in-field OAR volume. Out of the selected factors, only the in-field bladder volume (mean R  =  0.86) showed a strong correlation with bladder doses. Similarly, only the in-field rectal volume (mean R  =  0.76) showed a strong correlation with rectal doses. Therefore, an OVH formalism accounting for in-field OAR volumes was developed to determine the extent to which it improved the DVH-OVH correlation. Including the in-field factor improved the DVH-OVH correlation, with the mean R values over the fractional volumes studied improving from  -0.79 to  -0.85 and  -0.82 to  -0.86 for the bladder and rectum, respectively. A re-planning study was performed on 31 randomly selected database patients to verify the increased accuracy of KBP dose predictions by accounting for bladder and rectum volume within treatment fields. The in-field OVH led to significantly more precise and fewer unachievable KBP predictions, especially for lower bladder and rectum dose-volumes.

Anatomical based registration of multi-sector x-ray images for panorama reconstruction

NASA Astrophysics Data System (ADS)

Ben-Zikri, Yehuda Kfir; Mendez, Stacy; Linte, Cristian A.

2017-03-01

Accurate measurement of long limb alignment is an essential stage of the pre-operative planning of realignment surgery. This alignment is quantified according to the hip-knee-ankle (HKA) angle of the mechanical axis of the lower extremity and is measured based on a full-length weight-bearing X-ray or standard computed radiography (CR) image of the patient in standing position. Due to the limited field-of-view of the traditionally employed digital X-ray imaging systems, several sector images are required to capture the posture of a standing individual. These sector images need to then be "stitched" together to reconstruct the standing posture. To eliminate user-induced variability and time constraints associated with the traditional manual "stitching" protocol, we have created an image processing application to automate the stitching process, when there are no reliable external markers available in the images, by only relying on the most reliable anatomical content of the image. The application starts with a rough segmentation of the tibia and the sector images are then registered by evaluating the DICE coefficient between the edges of these corresponding bones along the medial edge. The identified translations are then used to register the original sector images into the standing panorama image. To test the robustness of our method, we randomly selected 40 datasets from a variant database consisting of nearly 100 patient X-ray images acquired for patient screening as part of a multi-site clinical trial. The resulting horizontal and vertical translation values from the automated registration were compared to the homologous translations recorded during the manual panorama generation conducted by a knowledgeable X-ray imaging technician. The mean and standard deviation of the differences for the horizontal translation parameters was -0:27+/-1:14 mm and 0:31+/-1:86 mm for the left and right tibia, respectively. The vertical translation differences for the left and right tibia were 1:05+/-5:24 mm and 1:32+/-4:77 mm, respectively. For these differences, the expert radiologist reported no difference in the hip-knee-ankle angular assessment.

New model for distributed multimedia databases and its application to networking of museums

NASA Astrophysics Data System (ADS)

Kuroda, Kazuhide; Komatsu, Naohisa; Komiya, Kazumi; Ikeda, Hiroaki

1998-02-01

This paper proposes a new distributed multimedia data base system where the databases storing MPEG-2 videos and/or super high definition images are connected together through the B-ISDN's, and also refers to an example of the networking of museums on the basis of the proposed database system. The proposed database system introduces a new concept of the 'retrieval manager' which functions an intelligent controller so that the user can recognize a set of image databases as one logical database. A user terminal issues a request to retrieve contents to the retrieval manager which is located in the nearest place to the user terminal on the network. Then, the retrieved contents are directly sent through the B-ISDN's to the user terminal from the server which stores the designated contents. In this case, the designated logical data base dynamically generates the best combination of such a retrieving parameter as a data transfer path referring to directly or data on the basis of the environment of the system. The generated retrieving parameter is then executed to select the most suitable data transfer path on the network. Therefore, the best combination of these parameters fits to the distributed multimedia database system.

Colloquium paper: bioenergetics, the origins of complexity, and the ascent of man.

PubMed

Wallace, Douglas C

2010-05-11

Complex structures are generated and maintained through energy flux. Structures embody information, and biological information is stored in nucleic acids. The progressive increase in biological complexity over geologic time is thus the consequence of the information-generating power of energy flow plus the information-accumulating capacity of DNA, winnowed by natural selection. Consequently, the most important component of the biological environment is energy flow: the availability of calories and their use for growth, survival, and reproduction. Animals can exploit and adapt to available energy resources at three levels. They can evolve different anatomical forms through nuclear DNA (nDNA) mutations permitting exploitation of alternative energy reservoirs, resulting in new species. They can evolve modified bioenergetic physiologies within a species, primarily through the high mutation rate of mitochondrial DNA (mtDNA)-encoded bioenergetic genes, permitting adjustment to regional energetic environments. They can alter the epigenomic regulation of the thousands of dispersed bioenergetic genes via mitochondrially generated high-energy intermediates permitting individual accommodation to short-term environmental energetic fluctuations. Because medicine pertains to a single species, Homo sapiens, functional human variation often involves sequence changes in bioenergetic genes, most commonly mtDNA mutations, plus changes in the expression of bioenergetic genes mediated by the epigenome. Consequently, common nDNA polymorphisms in anatomical genes may represent only a fraction of the genetic variation associated with the common "complex" diseases, and the ascent of man has been the product of 3.5 billion years of information generation by energy flow, accumulated and preserved in DNA and edited by natural selection.

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas.

PubMed

Ecker, Joseph R; Geschwind, Daniel H; Kriegstein, Arnold R; Ngai, John; Osten, Pavel; Polioudakis, Damon; Regev, Aviv; Sestan, Nenad; Wickersham, Ian R; Zeng, Hongkui

2017-11-01

A comprehensive characterization of neuronal cell types, their distributions, and patterns of connectivity is critical for understanding the properties of neural circuits and how they generate behaviors. Here we review the experiences of the BRAIN Initiative Cell Census Consortium, ten pilot projects funded by the U.S. BRAIN Initiative, in developing, validating, and scaling up emerging genomic and anatomical mapping technologies for creating a complete inventory of neuronal cell types and their connections in multiple species and during development. These projects lay the foundation for a larger and longer-term effort to generate whole-brain cell atlases in species including mice and humans. Copyright © 2017 Elsevier Inc. All rights reserved.

The Clinical Next-Generation Sequencing Database: A Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.

PubMed

Nishio, Shin-Ya; Usami, Shin-Ichi

2017-03-01

Recent advances in next-generation sequencing (NGS) have given rise to new challenges due to the difficulties in variant pathogenicity interpretation and large dataset management, including many kinds of public population databases as well as public or commercial disease-specific databases. Here, we report a new database development tool, named the "Clinical NGS Database," for improving clinical NGS workflow through the unified management of variant information and clinical information. This database software offers a two-feature approach to variant pathogenicity classification. The first of these approaches is a phenotype similarity-based approach. This database allows the easy comparison of the detailed phenotype of each patient with the average phenotype of the same gene mutation at the variant or gene level. It is also possible to browse patients with the same gene mutation quickly. The other approach is a statistical approach to variant pathogenicity classification based on the use of the odds ratio for comparisons between the case and the control for each inheritance mode (families with apparently autosomal dominant inheritance vs. control, and families with apparently autosomal recessive inheritance vs. control). A number of case studies are also presented to illustrate the utility of this database. © 2016 The Authors. **Human Mutation published by Wiley Periodicals, Inc.

Generation of comprehensive thoracic oncology database--tool for translational research.

PubMed

Surati, Mosmi; Robinson, Matthew; Nandi, Suvobroto; Faoro, Leonardo; Demchuk, Carley; Kanteti, Rajani; Ferguson, Benjamin; Gangadhar, Tara; Hensing, Thomas; Hasina, Rifat; Husain, Aliya; Ferguson, Mark; Karrison, Theodore; Salgia, Ravi

2011-01-22

The Thoracic Oncology Program Database Project was created to serve as a comprehensive, verified, and accessible repository for well-annotated cancer specimens and clinical data to be available to researchers within the Thoracic Oncology Research Program. This database also captures a large volume of genomic and proteomic data obtained from various tumor tissue studies. A team of clinical and basic science researchers, a biostatistician, and a bioinformatics expert was convened to design the database. Variables of interest were clearly defined and their descriptions were written within a standard operating manual to ensure consistency of data annotation. Using a protocol for prospective tissue banking and another protocol for retrospective banking, tumor and normal tissue samples from patients consented to these protocols were collected. Clinical information such as demographics, cancer characterization, and treatment plans for these patients were abstracted and entered into an Access database. Proteomic and genomic data have been included in the database and have been linked to clinical information for patients described within the database. The data from each table were linked using the relationships function in Microsoft Access to allow the database manager to connect clinical and laboratory information during a query. The queried data can then be exported for statistical analysis and hypothesis generation.

Global Thermal Power Plants Database: Unit-Based CO2, SO2, NOX and PM2.5 Emissions in 2010

NASA Astrophysics Data System (ADS)

Tong, D.; Qiang, Z.; Davis, S. J.

2016-12-01

There are more than 30,000 thermal power plants now operating worldwide, reflecting a tremendously diverse infrastructure that includes units burning oil, natural gas, coal and biomass and ranging in capacity from <1MW to >1GW. Although the electricity generated by this infrastructure is vital to economic activities across the world, it also produces more CO2 and air pollution emissions than any other industry sector. Here we present a new database of global thermal power-generating units and their emissions as of 2010, GPED (Global Power Emissions Database), including the detailed unit information of installed capacity, operation year, geographic location, fuel type and control measures for more than 70000 units. In this study, we have compiled, combined, and harmonized the available underlying data related to thermal power-generating units (e.g. eGRID of USA, CPED of China and published Indian power plants database), and then analyzed the generating capacity, capacity factor, fuel type, age, location, and installed pollution-control technology in order to determine those units with disproportionately high levels of emissions. In total, this work is of great importance for improving spatial distribution of global thermal power plants emissions and exploring their environmental impacts at global scale.

Facilitating Collaboration, Knowledge Construction and Communication with Web-Enabled Databases.

ERIC Educational Resources Information Center

McNeil, Sara G.; Robin, Bernard R.

This paper presents an overview of World Wide Web-enabled databases that dynamically generate Web materials and focuses on the use of this technology to support collaboration, knowledge construction, and communication. Database applications have been used in classrooms to support learning activities for over a decade, but, although business and…

Comparison Study of Overlap among 21 Scientific Databases in Searching Pesticide Information.

ERIC Educational Resources Information Center

Meyer, Daniel E.; And Others

1983-01-01

Evaluates overlapping coverage of 21 scientific databases used in 10 online pesticide searches in an attempt to identify minimum number of databases needed to generate 90 percent of unique, relevant citations for given search. Comparison of searches combined under given pesticide usage (herbicide, fungicide, insecticide) is discussed. Nine…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langan, Roisin T.; Archibald, Richard K.; Lamberti, Vincent

We have applied a new imputation-based method for analyzing incomplete data, called Monte Carlo Bayesian Database Generation (MCBDG), to the Spent Fuel Isotopic Composition (SFCOMPO) database. About 60% of the entries are absent for SFCOMPO. The method estimates missing values of a property from a probability distribution created from the existing data for the property, and then generates multiple instances of the completed database for training a machine learning algorithm. Uncertainty in the data is represented by an empirical or an assumed error distribution. The method makes few assumptions about the underlying data, and compares favorably against results obtained bymore » replacing missing information with constant values.« less

Predicting Student Performance in Sonographic Scanning Using Spatial Ability as an Ability Determinent of Skill Acquisition

ERIC Educational Resources Information Center

Clem, Douglas Wayne

2012-01-01

Spatial ability refers to an individual's capacity to visualize and mentally manipulate three dimensional objects. Since sonographers manually manipulate 2D and 3D sonographic images to generate multi-viewed, logical, sequential renderings of an anatomical structure, it can be assumed that spatial ability is central to the perception and…

Figuring fact from fiction: unbiased polling of memory T cells.

PubMed

Gerlach, Carmen; Loughhead, Scott M; von Andrian, Ulrich H

2015-05-07

Immunization generates several memory T cell subsets that differ in their migratory properties, anatomic distribution, and, hence, accessibility to investigation. In this issue, Steinert et al. demonstrate that what was believed to be a minor memory cell subset in peripheral tissues has been dramatically underestimated. Thus, current models of protective immunity require revision. Copyright © 2015 Elsevier Inc. All rights reserved.

An experimental investigation of masking in the US FDA adverse event reporting system database.

PubMed

Wang, Hsin-wei; Hochberg, Alan M; Pearson, Ronald K; Hauben, Manfred

2010-12-01

A phenomenon of 'masking' or 'cloaking' in pharmacovigilance data mining has been described, which can potentially cause signals of disproportionate reporting (SDRs) to be missed, particularly in pharmaceutical company databases. Masking has been predicted theoretically, observed anecdotally or studied to a limited extent in both pharmaceutical company and health authority databases, but no previous publication systematically assesses its occurrence in a large health authority database. To explore the nature, extent and possible consequences of masking in the US FDA Adverse Event Reporting System (AERS) database by applying various experimental unmasking protocols to a set of drugs and events representing realistic pharmacovigilance analysis conditions. This study employed AERS data from 2001 through 2005. For a set of 63 Medical Dictionary for Regulatory Activities (MedDRA®) Preferred Terms (PTs), disproportionality analysis was carried out with respect to all drugs included in the AERS database, using a previously described urn-model-based algorithm. We specifically sought masking in which drug removal induced an increase in the statistical representation of a drug-event combination (DEC) that resulted in the emergence of a new SDR. We performed a series of unmasking experiments selecting drugs for removal using rational statistical decision rules based on the requirement of a reporting ratio (RR) >1, top-ranked statistical unexpectedness (SU) and relatedness as reflected in the WHO Anatomical Therapeutic Chemical level 4 (ATC4) grouping. In order to assess the possible extent of residual masking we performed two supplemental purely empirical analyses on a limited subset of data. This entailed testing every drug and drug group to determine which was most influential in uncovering masked SDRs. We assessed the strength of external evidence for a causal association for a small number of masked SDRs involving a subset of 29 drugs for which level of evidence adjudication was available from a previous study. The original disproportionality analysis identified 8719 SDRs for the 63 PTs. The SU-based unmasking protocols generated variable numbers of masked SDRs ranging from 38 to 156, representing a 0.43-1.8% increase over the number of baseline SDRs. A significant number of baseline SDRs were also lost in the course of our experiments. The trend in the number of gained SDRs per report removed was inversely related to the number of lost SDRs per protocol. Both the number and nature of the reports removed influenced the number of gained SDRs observed. The purely empirical protocols unmasked up to ten times as many SDRs. None of the masked SDRs had strong external evidence supporting a causal association. Most involved associations for which there was no external supporting evidence or were in the original product label. For two masked SDRs, there was external evidence of a possible causal association. We documented masking in the FDA AERS database. Attempts at unmasking SDRs using practically implementable protocols produced only small changes in the output of SDRs in our analysis. This is undoubtedly related to the large size and diversity of the database, but the complex interdependencies between drugs and events in authentic spontaneous reporting system (SRS) databases, and the impact of measures of statistical variability that are typically used in real-world disproportionality analysis, may be additional factors that constrain the discovery of masked SDRs and which may also operate in pharmaceutical company databases. Empirical determination of the most influential drugs may uncover significantly more SDRs than protocols based on predetermined statistical selection rules but are impractical except possibly for evaluating specific events. Routine global exercises to elicit masking, especially in large health authority databases are not justified based on results available to date. Exercises to elicit unmasking should be driven by prior knowledge or obvious data imbalances.

Afferent and Efferent Aspects of Mandibular Sensorimotor Control in Adults who Stutter

PubMed Central

Daliri, Ayoub; Prokopenko, Roman A.; Max, Ludo

2013-01-01

Purpose Individuals who stutter show sensorimotor deficiencies in speech and nonspeech movements. For the mandibular system, we dissociated the sense of kinesthesia from the efferent control component to examine whether kinesthetic integrity itself is compromised in stuttering or whether deficiencies occur only when generating motor commands. Method We investigated 11 stuttering and 11 nonstuttering adults’ kinesthetic sensitivity threshold and kinesthetic accuracy for passive jaw movements as well as their minimal displacement threshold and positioning accuracy for active jaw movements. We also investigated the correlation with an anatomical index of jaw size. Results The groups showed no statistically significant differences on sensory measures for passive jaw movements. Although some stuttering individuals performed more poorly than any nonstuttering participants on the active movement tasks, between-group differences for active movements were also not statistically significant. Unlike fluent speakers, however, the stuttering group showed a statistically significant correlation between mandibular size and performance in the active and passive near-threshold tasks. Conclusions Previously reported minimal movement differences were not replicated. Instead, stuttering individuals’ performance varied with anatomical properties. These correlational results are consistent with the hypothesis that stuttering participants generate and perceive movements based on less accurate internal models of the involved neuromechanical systems. PMID:23816664

Medical 3D Printing for the Radiologist

PubMed Central

Mitsouras, Dimitris; Liacouras, Peter; Imanzadeh, Amir; Giannopoulos, Andreas A.; Cai, Tianrun; Kumamaru, Kanako K.; George, Elizabeth; Wake, Nicole; Caterson, Edward J.; Pomahac, Bohdan; Ho, Vincent B.; Grant, Gerald T.

2015-01-01

While use of advanced visualization in radiology is instrumental in diagnosis and communication with referring clinicians, there is an unmet need to render Digital Imaging and Communications in Medicine (DICOM) images as three-dimensional (3D) printed models capable of providing both tactile feedback and tangible depth information about anatomic and pathologic states. Three-dimensional printed models, already entrenched in the nonmedical sciences, are rapidly being embraced in medicine as well as in the lay community. Incorporating 3D printing from images generated and interpreted by radiologists presents particular challenges, including training, materials and equipment, and guidelines. The overall costs of a 3D printing laboratory must be balanced by the clinical benefits. It is expected that the number of 3D-printed models generated from DICOM images for planning interventions and fabricating implants will grow exponentially. Radiologists should at a minimum be familiar with 3D printing as it relates to their field, including types of 3D printing technologies and materials used to create 3D-printed anatomic models, published applications of models to date, and clinical benefits in radiology. Online supplemental material is available for this article. ©RSNA, 2015 PMID:26562233

A spiking neural network model of the midbrain superior colliculus that generates saccadic motor commands.

PubMed

Kasap, Bahadir; van Opstal, A John

2017-08-01

Single-unit recordings suggest that the midbrain superior colliculus (SC) acts as an optimal controller for saccadic gaze shifts. The SC is proposed to be the site within the visuomotor system where the nonlinear spatial-to-temporal transformation is carried out: the population encodes the intended saccade vector by its location in the motor map (spatial), and its trajectory and velocity by the distribution of firing rates (temporal). The neurons' burst profiles vary systematically with their anatomical positions and intended saccade vectors, to account for the nonlinear main-sequence kinematics of saccades. Yet, the underlying collicular mechanisms that could result in these firing patterns are inaccessible to current neurobiological techniques. Here, we propose a simple spiking neural network model that reproduces the spike trains of saccade-related cells in the intermediate and deep SC layers during saccades. The model assumes that SC neurons have distinct biophysical properties for spike generation that depend on their anatomical position in combination with a center-surround lateral connectivity. Both factors are needed to account for the observed firing patterns. Our model offers a basis for neuronal algorithms for spatiotemporal transformations and bio-inspired optimal controllers.

Medical 3D Printing for the Radiologist.

PubMed

Mitsouras, Dimitris; Liacouras, Peter; Imanzadeh, Amir; Giannopoulos, Andreas A; Cai, Tianrun; Kumamaru, Kanako K; George, Elizabeth; Wake, Nicole; Caterson, Edward J; Pomahac, Bohdan; Ho, Vincent B; Grant, Gerald T; Rybicki, Frank J

2015-01-01

While use of advanced visualization in radiology is instrumental in diagnosis and communication with referring clinicians, there is an unmet need to render Digital Imaging and Communications in Medicine (DICOM) images as three-dimensional (3D) printed models capable of providing both tactile feedback and tangible depth information about anatomic and pathologic states. Three-dimensional printed models, already entrenched in the nonmedical sciences, are rapidly being embraced in medicine as well as in the lay community. Incorporating 3D printing from images generated and interpreted by radiologists presents particular challenges, including training, materials and equipment, and guidelines. The overall costs of a 3D printing laboratory must be balanced by the clinical benefits. It is expected that the number of 3D-printed models generated from DICOM images for planning interventions and fabricating implants will grow exponentially. Radiologists should at a minimum be familiar with 3D printing as it relates to their field, including types of 3D printing technologies and materials used to create 3D-printed anatomic models, published applications of models to date, and clinical benefits in radiology. Online supplemental material is available for this article. (©)RSNA, 2015.

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.

PubMed

Chiba, Hirokazu; Uchiyama, Ikuo

2017-02-08

Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL Protocol and RDF Query Language (SPARQL) provides a basis for exploiting RDF databases, writing SPARQL code is burdensome for users including bioinformaticians. Thus, an easy-to-use interface is necessary. We developed SPANG, a SPARQL client that has unique features for querying RDF datasets. SPANG dynamically generates typical SPARQL queries according to specified arguments. It can also call SPARQL template libraries constructed in a local system or published on the Web. Further, it enables combinatorial execution of multiple queries, each with a distinct target database. These features facilitate easy and effective access to RDF datasets and integrative analysis of distributed data. SPANG helps users to exploit RDF datasets by generation and reuse of SPARQL queries through a simple interface. This client will enhance integrative exploitation of biological RDF datasets distributed across the Web. This software package is freely available at http://purl.org/net/spang .

Power Plant Model Validation Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

The PPMV is used to validate generator model using disturbance recordings. The PPMV tool contains a collection of power plant models and model validation studies, as well as disturbance recordings from a number of historic grid events. The user can import data from a new disturbance into the database, which converts PMU and SCADA data into GE PSLF format, and then run the tool to validate (or invalidate) the model for a specific power plant against its actual performance. The PNNL PPMV tool enables the automation of the process of power plant model validation using disturbance recordings. The tool usesmore » PMU and SCADA measurements as input information. The tool automatically adjusts all required EPCL scripts and interacts with GE PSLF in the batch mode. The main tool features includes: The tool interacts with GE PSLF; The tool uses GE PSLF Play-In Function for generator model validation; Database of projects (model validation studies); Database of the historic events; Database of the power plant; The tool has advanced visualization capabilities; and The tool automatically generates reports« less

Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology.

PubMed

Bibault, Jean-Emmanuel; Zapletal, Eric; Rance, Bastien; Giraud, Philippe; Burgun, Anita

2018-01-01

Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. We present the ontology we developed to address this issue. Radiation Oncology anatomical and target volumes were categorized in anatomical and treatment planning classes. International delineation guidelines specific to radiation oncology were used for lymph nodes areas and target volumes. Hierarchical classes were created to generate The Radiation Oncology Structures (ROS) Ontology. The ROS was then applied to the data from our institution. Four hundred and seventeen classes were created with a maximum of 14 children classes (average = 5). The ontology was then converted into a Web Ontology Language (.owl) format and made available online on Bioportal and GitHub under an Apache 2.0 License. We extracted all structures delineated in our department since the opening in 2001. 20,758 structures were exported from our "record-and-verify" system, demonstrating a significant heterogeneity within a single center. All structures were matched to the ROS ontology before integration into our clinical data warehouse (CDW). In this study we describe a new ontology, specific to radiation oncology, that reports all anatomical and treatment planning structures that can be delineated. This ontology will be used to integrate dosimetric data in the Assistance Publique-Hôpitaux de Paris CDW that stores data from 6.5 million patients (as of February 2017).

Morphometric analysis of the relationships between intervertebral disc and vertebral body heights: an anatomical and radiographic study of the human thoracic spine

PubMed Central

Kunkel, Maria E; Herkommer, Andrea; Reinehr, Michael; Böckers, Tobias M; Wilke, Hans-Joachim

2011-01-01

The main aim of this study was to provide anatomical data on the heights of the human intervertebral discs for all levels of the thoracic spine by direct and radiographic measurements. Additionally, the heights of the neighboring vertebral bodies were measured, and the prediction of the disc heights based only on the size of the vertebral bodies was investigated. The anterior (ADH), middle (MDH) and posterior heights (PDH) of the discs were measured directly and on radiographs of 72 spine segments from 30 donors (age 57.43 ± 11.27 years). The radiographic measurement error and the reliability of the measurements were calculated. Linear and non-linear regression analyses were employed for investigation of statistical correlations between the heights of the thoracic disc and vertebrae. Radiographic measurements displayed lower repeatability and were shorter than the anatomical ones (approximately 9% for ADH and 37% for PDH). The thickness of the discs varied from 4.5 to 7.2 mm, with the MDH approximately 22.7% greater. The disc heights showed good correlations with the vertebral body heights (R2, 0.659–0.835, P-values < 0.005; anova), allowing the generation of 10 prediction equations. New data on thoracic disc morphometry were provided in this study. The generated set of regression equations could be used to predict thoracic disc heights from radiographic measurement of the vertebral body height posterior. For the creation of parameterized models of the human thoracic discs, the use of the prediction equations could eliminate the need for direct measurement on intervertebral discs. Moreover, the error produced by radiographic measurements could be reduced at least for the PDH. PMID:21615399

A possible anatomical and biomechanical explanation of the 10% rule used in the clinical assessment of prehensile hand movements and handed dominance.

PubMed

Yielder, P; Gutnik, B; Kobrin, V; Hudson, G

2009-12-01

A current doctrine in the dynamometric approach to determine lateralization of hand function states that in 10% of cases, the non-dominant hand will be stronger than the dominant hand. In this study, a novel MRI based modelling approach was applied to the first dorsal introsseus muscle (FDI), to determine whether the 10% rule may be applied to the FDI and may be partially explained by the arrangement of the anatomical components of the FDI. Initially the force generated by the thumb segment during an isometric pushing task in the horizontal plane was measured from 25 strongly right-handed young males. Nine of these participants then had structural magnetic resonance imaging (sMRI) of the thumb and index osseous compartment. A modelling technique was developed to extract the muscle data and quantify the muscle line of action onto to the first metacarpal bone segment in order to quantify the muscle force at the point of momentary rotation--equilibrium. Eight of 25 subjects exhibited stronger force from the left hand. Six out of nine subjects from the MRI possessed significantly greater angles of attachment of the index osseous compartment on the left (non-dominant) hand. These six subjects also generated greater maximal isometric forces from the FDI of the left side. There was a significantly greater muscle volume for the right FDI muscle as compared to the left as measured from the reconstructed MRI slice data. The calculated force produced by the muscle is related to the angle of attachment of the muscle to bone in the index osseous compartment. The MRI findings indicate that the 10% rule may be anatomically and biomechanically explained.

Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology

PubMed Central

Zapletal, Eric; Rance, Bastien; Giraud, Philippe; Burgun, Anita

2018-01-01

Purpose Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. We present the ontology we developed to address this issue. Methods Radiation Oncology anatomical and target volumes were categorized in anatomical and treatment planning classes. International delineation guidelines specific to radiation oncology were used for lymph nodes areas and target volumes. Hierarchical classes were created to generate The Radiation Oncology Structures (ROS) Ontology. The ROS was then applied to the data from our institution. Results Four hundred and seventeen classes were created with a maximum of 14 children classes (average = 5). The ontology was then converted into a Web Ontology Language (.owl) format and made available online on Bioportal and GitHub under an Apache 2.0 License. We extracted all structures delineated in our department since the opening in 2001. 20,758 structures were exported from our “record-and-verify” system, demonstrating a significant heterogeneity within a single center. All structures were matched to the ROS ontology before integration into our clinical data warehouse (CDW). Conclusion In this study we describe a new ontology, specific to radiation oncology, that reports all anatomical and treatment planning structures that can be delineated. This ontology will be used to integrate dosimetric data in the Assistance Publique—Hôpitaux de Paris CDW that stores data from 6.5 million patients (as of February 2017). PMID:29351341

Standards for Clinical Grade Genomic Databases.

PubMed

Yohe, Sophia L; Carter, Alexis B; Pfeifer, John D; Crawford, James M; Cushman-Vokoun, Allison; Caughron, Samuel; Leonard, Debra G B

2015-11-01

Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation. To define CGGD and the categories of information contained in CGGDs and to frame recommendations for the structure and use of these databases in clinical patient care. Members of the College of American Pathologists Personalized Health Care Committee reviewed the literature and existing state of genomic databases and developed a framework for guiding CGGD development in the future. Clinical-grade genomic databases may provide different types of information. This work group defined 3 layers of information in CGGDs: clinical genomic variant repositories, genomic medical data repositories, and genomic medicine evidence databases. The layers are differentiated by the types of genomic and medical information contained and the utility in assisting with clinical interpretation of genomic variants. Clinical-grade genomic databases must meet specific standards regarding submission, curation, and retrieval of data, as well as the maintenance of privacy and security. These organizing principles for CGGDs should serve as a foundation for future development of specific standards that support the use of such databases for patient care.

Multi-template analysis of human perirhinal cortex in brain MRI: Explicitly accounting for anatomical variability

PubMed Central

Xie, Long; Pluta, John B.; Das, Sandhitsu R.; Wisse, Laura E.M.; Wang, Hongzhi; Mancuso, Lauren; Kliot, Dasha; Avants, Brian B.; Ding, Song-Lin; Manjón, José V.; Wolk, David A.; Yushkevich, Paul A.

2016-01-01

Rational The human perirhinal cortex (PRC) plays critical roles in episodic and semantic memory and visual perception. The PRC consists of Brodmann areas 35 and 36 (BA35, BA36). In Alzheimer's disease (AD), BA35 is the first cortical site affected by neurofibrillary tangle pathology, which is closely linked to neural injury in AD. Large anatomical variability, manifested in the form of different cortical folding and branching patterns, makes it difficult to segment the PRC in MRI scans. Pathology studies have found that in ~97% of specimens, the PRC falls into one of three discrete anatomical variants. However, current methods for PRC segmentation and morphometry in MRI are based on single-template approaches, which may not be able to accurately model these discrete variants Methods A multi-template analysis pipeline that explicitly accounts for anatomical variability is used to automatically label the PRC and measure its thickness in T2-weighted MRI scans. The pipeline uses multi-atlas segmentation to automatically label medial temporal lobe cortices including entorhinal cortex, PRC and the parahippocampal cortex. Pairwise registration between label maps and clustering based on residual dissimilarity after registration are used to construct separate templates for the anatomical variants of the PRC. An optimal path of deformations linking these templates is used to establish correspondences between all the subjects. Experimental evaluation focuses on the ability of single-template and multi-template analyses to detect differences in the thickness of medial temporal lobe cortices between patients with amnestic mild cognitive impairment (aMCI, n=41) and age-matched controls (n=44). Results The proposed technique is able to generate templates that recover the three dominant discrete variants of PRC and establish more meaningful correspondences between subjects than a single-template approach. The largest reduction in thickness associated with aMCI, in absolute terms, was found in left BA35 using both regional and summary thickness measures. Further, statistical maps of regional thickness difference between aMCI and controls revealed different patterns for the three anatomical variants. PMID:27702610

Data, knowledge and method bases in chemical sciences. Part IV. Current status in databases.

PubMed

Braibanti, Antonio; Rao, Rupenaguntla Sambasiva; Rao, Gollapalli Nagesvara; Ramam, Veluri Anantha; Rao, Sattiraju Veera Venkata Satyanarayana

2002-01-01

Computer readable databases have become an integral part of chemical research right from planning data acquisition to interpretation of the information generated. The databases available today are numerical, spectral and bibliographic. Data representation by different schemes--relational, hierarchical and objects--is demonstrated. Quality index (QI) throws light on the quality of data. The objective, prospects and impact of database activity on expert systems are discussed. The number and size of corporate databases available on international networks crossed manageable number leading to databases about their contents. Subsets of corporate or small databases have been developed by groups of chemists. The features and role of knowledge-based or intelligent databases are described.

Customer satisfaction in anatomic pathology. A College of American Pathologists Q-Probes study of 3065 physician surveys from 94 laboratories.

PubMed

Zarbo, Richard J; Nakhleh, Raouf E; Walsh, Molly

2003-01-01

Measurement of physicians' and patients' satisfaction with laboratory services has recently become a requirement of health care accreditation agencies in the United States. To our knowledge, this is the first customer satisfaction survey of anatomic pathology services to provide a standardized tool and benchmarks for subsequent measures of satisfaction. This Q-Probes study assessed physician satisfaction with anatomic pathology laboratory services and sought to determine characteristics that correlate with a high level of physician satisfaction. In January 2001, each laboratory used standardized survey forms to assess physician customer satisfaction with 10 specific elements of service in anatomic pathology and an overall satisfaction rating based on a scale of rankings from a 5 for excellent to a 1 for poor. Data from up to 50 surveys returned per laboratory were compiled and analyzed by the College of American Pathologists. A general questionnaire collected information about types of services offered and each laboratory's quality assurance initiatives to determine characteristics that correlate with a high level of physician satisfaction. Hospital-based laboratories in the United States (95.8%), as well as others from Canada and Australia. Ninety-four voluntary subscriber laboratories in the College of American Pathologists Q-Probes quality improvement program participated in this survey. Roughly 70% of respondents were from hospitals with occupied bedsizes of 300 or less, 65% were private nonprofit institutions, just over half were located in cities, one third were teaching hospitals, and 19% had pathology residency training programs. Overall physician satisfaction with anatomic pathology and 10 selected aspects of the laboratory service (professional interaction, diagnostic accuracy, pathologist responsiveness to problems, pathologist accessibility for frozen section, tumor board presentations, courtesy of secretarial and technical staff, communication of relevant information, teaching conferences and courses, notification of significant abnormal results, and timeliness of reporting). The database of 3065 physician surveys was derived from 94 laboratories. An average of 32.6 surveys (median 30) was returned per institution, with a range of 5 to 50 surveys per institution. The mean response rate was 35.6% (median 32.5%). The median (50th percentile) laboratory had an overall median satisfaction score of 4.4. The lowest satisfaction scores that were obtained all related to poor communication, which included timeliness of reporting, communication of relevant information, and notification of significant abnormal results. Statistically significant associations of customer satisfaction with certain institutional characteristics and laboratory performance improvement activities were identified. The importance of this satisfaction survey lies not in its requirement as an exercise for accrediting agencies but in understanding the needs of the customer (in this case the physician) to direct performance improvement in the delivery of quality anatomic pathology laboratory services.

The Design and Product of National 1:1000000 Cartographic Data of Topographic Map

NASA Astrophysics Data System (ADS)

Wang, Guizhi

2016-06-01

National administration of surveying, mapping and geoinformation started to launch the project of national fundamental geographic information database dynamic update in 2012. Among them, the 1:50000 database was updated once a year, furthermore the 1:250000 database was downsized and linkage-updated on the basis. In 2014, using the latest achievements of 1:250000 database, comprehensively update the 1:1000000 digital line graph database. At the same time, generate cartographic data of topographic map and digital elevation model data. This article mainly introduce national 1:1000000 cartographic data of topographic map, include feature content, database structure, Database-driven Mapping technology, workflow and so on.

Comparative Evaluation of Registration Algorithms in Different Brain Databases With Varying Difficulty: Results and Insights

PubMed Central

Akbari, Hamed; Bilello, Michel; Da, Xiao; Davatzikos, Christos

2015-01-01

Evaluating various algorithms for the inter-subject registration of brain magnetic resonance images (MRI) is a necessary topic receiving growing attention. Existing studies evaluated image registration algorithms in specific tasks or using specific databases (e.g., only for skull-stripped images, only for single-site images, etc.). Consequently, the choice of registration algorithms seems task- and usage/parameter-dependent. Nevertheless, recent large-scale, often multi-institutional imaging-related studies create the need and raise the question whether some registration algorithms can 1) generally apply to various tasks/databases posing various challenges; 2) perform consistently well, and while doing so, 3) require minimal or ideally no parameter tuning. In seeking answers to this question, we evaluated 12 general-purpose registration algorithms, for their generality, accuracy and robustness. We fixed their parameters at values suggested by algorithm developers as reported in the literature. We tested them in 7 databases/tasks, which present one or more of 4 commonly-encountered challenges: 1) inter-subject anatomical variability in skull-stripped images; 2) intensity homogeneity, noise and large structural differences in raw images; 3) imaging protocol and field-of-view (FOV) differences in multi-site data; and 4) missing correspondences in pathology-bearing images. Totally 7,562 registrations were performed. Registration accuracies were measured by (multi-)expert-annotated landmarks or regions of interest (ROIs). To ensure reproducibility, we used public software tools, public databases (whenever possible), and we fully disclose the parameter settings. We show evaluation results, and discuss the performances in light of algorithms’ similarity metrics, transformation models and optimization strategies. We also discuss future directions for the algorithm development and evaluations. PMID:24951685

What approach to brain partial volume correction is best for PET/MRI?

NASA Astrophysics Data System (ADS)

Hutton, B. F.; Thomas, B. A.; Erlandsson, K.; Bousse, A.; Reilhac-Laborde, A.; Kazantsev, D.; Pedemonte, S.; Vunckx, K.; Arridge, S. R.; Ourselin, S.

2013-02-01

Many partial volume correction approaches make use of anatomical information, readily available in PET/MRI systems but it is not clear what approach is best. Seven novel approaches to partial volume correction were evaluated, including several post-reconstruction methods and several reconstruction methods that incorporate anatomical information. These were compared with an MRI-independent approach (reblurred van Cittert ) and uncorrected data. Monte Carlo PET data were generated for activity distributions representing both 18F FDG and amyloid tracer uptake. Post-reconstruction methods provided the best recovery with ideal segmentation but were particularly sensitive to mis-registration. Alternative approaches performed better in maintaining lesion contrast (unseen in MRI) with good noise control. These were also relatively insensitive to mis-registration errors. The choice of method will depend on the specific application and reliability of segmentation and registration algorithms.

Modulation of Respiratory Frequency by Peptidergic Input to Rhythmogenic Neurons in the PreBötzinger Complex

PubMed Central

Gray, Paul A.; Rekling, Jens C.; Bocchiaro, Christopher M.; Feldman, Jack L.

2010-01-01

Neurokinin-1 receptor (NK1R) and μ-opioid receptor (μOR) agonists affected respiratory rhythm when injected directly into the preBötzinger Complex (preBötC), the hypothesized site for respiratory rhythmogenesis in mammals. These effects were mediated by actions on preBötC rhythmogenic neurons. The distribution of NK1R+ neurons anatomically defined the preBötC. Type 1 neurons in the preBötC, which have rhythmogenic properties, expressed both NK1Rs and μORs, whereas type 2 neurons expressed only NK1Rs. These findings suggest that the preBötC is a definable anatomic structure with unique physiological function and that a subpopulation of neurons expressing both NK1Rs and μORs generate respiratory rhythm and modulate respiratory frequency. PMID:10567264

Generation and evaluation of 3D digital casts of maxillary defects based on multisource data registration: A pilot clinical study.

PubMed

Ye, Hongqiang; Ma, Qijun; Hou, Yuezhong; Li, Man; Zhou, Yongsheng

2017-12-01

Digital techniques are not clinically applied for 1-piece maxillary prostheses containing an obturator and removable partial denture retained by the remaining teeth because of the difficulty in obtaining sufficiently accurate 3-dimensional (3D) images. The purpose of this pilot clinical study was to generate 3D digital casts of maxillary defects, including the defective region and the maxillary dentition, based on multisource data registration and to evaluate their effectiveness. Twelve participants with maxillary defects were selected. The maxillofacial region was scanned with spiral computer tomography (CT), and the maxillary arch and palate were scanned using an intraoral optical scanner. The 3D images from the CT and intraoral scanner were registered and merged to form a 3D digital cast of the maxillary defect containing the anatomic structures needed for the maxillary prosthesis. This included the defect cavity, maxillary dentition, and palate. Traditional silicone impressions were also made, and stone casts were poured. The accuracy of the digital cast in comparison with that of the stone cast was evaluated by measuring the distance between 4 anatomic landmarks. Differences and consistencies were assessed using paired Student t tests and the intraclass correlation coefficient (ICC). In 3 participants, physical resin casts were produced by rapid prototyping from digital casts. Based on the resin casts, maxillary prostheses were fabricated by using conventional methods and then evaluated in the participants to assess the clinical applicability of the digital casts. Digital casts of the maxillary defects were generated and contained all the anatomic details needed for the maxillary prosthesis. Comparing the digital and stone casts, a paired Student t test indicated that differences in the linear distances between landmarks were not statistically significant (P>.05). High ICC values (0.977 to 0.998) for the interlandmark distances further indicated the high degree of consistency between the digital and stone casts. The maxillary prostheses showed good clinical effectiveness, indicating that the corresponding digital casts met the requirements for clinical application. Based on multisource data from spiral CT and the intraoral scanner, 3D digital casts of maxillary defects were generated using the registration technique. These casts were consistent with conventional stone casts in terms of accuracy and were suitable for clinical use. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

ADAM-M Data and Information

Atmospheric Science Data Center

2017-05-11

... Information Creating a Unified Airborne Database for Assessment and Validation of Global Models of Atmospheric ...  (3)  To generate a standardized in-situ observational database with best possible matching temporal and spatial scales to model ...

Database on Performance of Neutron Irradiated FeCrAl Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Field, Kevin G.; Briggs, Samuel A.; Littrell, Ken

The present report summarizes and discusses the database on radiation tolerance for Generation I, Generation II, and commercial FeCrAl alloys. This database has been built upon mechanical testing and microstructural characterization on selected alloys irradiated within the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL) up to doses of 13.8 dpa at temperatures ranging from 200°C to 550°C. The structure and performance of these irradiated alloys were characterized using advanced microstructural characterization techniques and mechanical testing. The primary objective of developing this database is to enhance the rapid development of a mechanistic understanding on the radiation tolerancemore » of FeCrAl alloys, thereby enabling informed decisions on the optimization of composition and microstructure of FeCrAl alloys for application as an accident tolerant fuel (ATF) cladding. This report is structured to provide a brief summary of critical results related to the database on radiation tolerance of FeCrAl alloys.« less

Development and expansion of high-quality control region databases to improve forensic mtDNA evidence interpretation.

PubMed

Irwin, Jodi A; Saunier, Jessica L; Strouss, Katharine M; Sturk, Kimberly A; Diegoli, Toni M; Just, Rebecca S; Coble, Michael D; Parson, Walther; Parsons, Thomas J

2007-06-01

In an effort to increase the quantity, breadth and availability of mtDNA databases suitable for forensic comparisons, we have developed a high-throughput process to generate approximately 5000 control region sequences per year from regional US populations, global populations from which the current US population is derived and global populations currently under-represented in available forensic databases. The system utilizes robotic instrumentation for all laboratory steps from pre-extraction through sequence detection, and a rigorous eight-step, multi-laboratory data review process with entirely electronic data transfer. Over the past 3 years, nearly 10,000 control region sequences have been generated using this approach. These data are being made publicly available and should further address the need for consistent, high-quality mtDNA databases for forensic testing.

Development and operation of NEW-KOTIS : In-house technical information database of Nippon Kokan Corp.

NASA Astrophysics Data System (ADS)

Yagi, Yukio; Takahashi, Kaei

The purpose of this report is to describe how the activities for managing technical information has been and is now being conducted by the Engineering department of Nippon Kokan Corp. In addition, as a practical example of database generation promoted by the department, this book gives whole aspects of the NEW-KOTIS (background of its development, history, features, functional details, control and operation method, use in search operations, and so forth). The NEW-KOTIS (3rd-term system) is an "in-house technical information database system," which started its operation on May, 1987. This database system now contains approximately 65,000 information items (research reports, investigation reports, technical reports, etc.) generated within the company, and this information is available to anyone in any department through the network connecting all the company's structures.

Social media based NPL system to find and retrieve ARM data: Concept paper

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devarakonda, Ranjeet; Giansiracusa, Michael T.; Kumar, Jitendra

Information connectivity and retrieval has a role in our daily lives. The most pervasive source of online information is databases. The amount of data is growing at rapid rate and database technology is improving and having a profound effect. Almost all online applications are storing and retrieving information from databases. One challenge in supplying the public with wider access to informational databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it may notmore » be practical to make the public aware of the structure of the database. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide more intuitive method for generating database queries and delivering responses. Social media makes it possible to interact with a wide section of the population. Through this medium, and with the help of Natural Language Processing (NLP) we can make the data of the Atmospheric Radiation Measurement Data Center (ADC) more accessible to the public. We propose an architecture for using Apache Lucene/Solr [1], OpenML [2,3], and Kafka [4] to generate an automated query/response system with inputs from Twitter5, our Cassandra DB, and our log database. Using the Twitter API and NLP we can give the public the ability to ask questions of our database and get automated responses.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Devarakonda, Ranjeet; Giansiracusa, Michael T.; Kumar, Jitendra

Information connectivity and retrieval has a role in our daily lives. The most pervasive source of online information is databases. The amount of data is growing at rapid rate and database technology is improving and having a profound effect. Almost all online applications are storing and retrieving information from databases. One challenge in supplying the public with wider access to informational databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it may notmore » be practical to make the public aware of the structure of the database. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide more intuitive method for generating database queries and delivering responses. Social media makes it possible to interact with a wide section of the population. Through this medium, and with the help of Natural Language Processing (NLP) we can make the data of the Atmospheric Radiation Measurement Data Center (ADC) more accessible to the public. We propose an architecture for using Apache Lucene/Solr [1], OpenML [2,3], and Kafka [4] to generate an automated query/response system with inputs from Twitter5, our Cassandra DB, and our log database. Using the Twitter API and NLP we can give the public the ability to ask questions of our database and get automated responses.« less

Database Access Manager for the Software Engineering Laboratory (DAMSEL) user's guide

NASA Technical Reports Server (NTRS)

1990-01-01

Operating instructions for the Database Access Manager for the Software Engineering Laboratory (DAMSEL) system are presented. Step-by-step instructions for performing various data entry and report generation activities are included. Sample sessions showing the user interface display screens are also included. Instructions for generating reports are accompanied by sample outputs for each of the reports. The document groups the available software functions by the classes of users that may access them.

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Druzinsky, Robert E.; Balhoff, James P.; Crompton, Alfred W.

Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repositorymore » for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). Lastly, we compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.« less

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

DOE PAGES

Druzinsky, Robert E.; Balhoff, James P.; Crompton, Alfred W.; ...

2016-02-12

Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repositorymore » for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). Lastly, we compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.« less

The prevalence and morphology of the corona mortis (Crown of death): A meta-analysis with implications in abdominal wall and pelvic surgery.

PubMed

Sanna, Beatrice; Henry, Brandon Michael; Vikse, Jens; Skinningsrud, Bendik; Pękala, Jakub R; Walocha, Jerzy A; Cirocchi, Roberto; Tomaszewski, Krzysztof A

2018-02-01

Corona mortis is a highly variable vascular connection between the obturator and external iliac or inferior epigastric arteries or veins located behind the superior pubic ramus in the retropubic space (space of Retzius). Due to the significant variation in this collateral circulation, detailed anatomical knowledge of the corona mortis is vital to enhance the prevention of possible iatrogenic errors in hernia repair and other pubic surgical procedures. The aim of our meta-analysis was to provide comprehensive data on the prevalence, anatomical characteristics, and ethnic variations of the corona mortis vessel. An extensive search was conducted through the major electronic databases to identify eligible articles. Data extracted included investigative method, prevalence of the corona mortis vessels among hemi-pelvises (overall, arterial only, venous only, and combined), distance from the corona mortis to pubic symphysis, and assessment of gender, side, laterality, and ethnicity subgroups. A total of 21 studies (n=2184 hemi-pelvises) were included in the meta-analysis. The overall prevalence of the corona mortis in hemi-pelvises is high (49.3%). A venous corona mortis is more prevalent than an arterial corona mortis (41.7% vs. 17.0%). The corona mortis is more common in Asia (59.3%) than in Europe (42.8%) and North America (44.3%). As a corona mortis is present in an about half of all hemi-pelvises, it is important to consider the possibilities of its presence when undertaking surgical procedures and plan accordingly to avoid injuries. All surgeons operating in the retropubic region should have a thorough understanding of the anatomical characteristics and surgical implications of a corona mortis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Automated segmentation of 3D anatomical structures on CT images by using a deep convolutional network based on end-to-end learning approach

NASA Astrophysics Data System (ADS)

Zhou, Xiangrong; Takayama, Ryosuke; Wang, Song; Zhou, Xinxin; Hara, Takeshi; Fujita, Hiroshi

2017-02-01

We have proposed an end-to-end learning approach that trained a deep convolutional neural network (CNN) for automatic CT image segmentation, which accomplished a voxel-wised multiple classification to directly map each voxel on 3D CT images to an anatomical label automatically. The novelties of our proposed method were (1) transforming the anatomical structures segmentation on 3D CT images into a majority voting of the results of 2D semantic image segmentation on a number of 2D-slices from different image orientations, and (2) using "convolution" and "deconvolution" networks to achieve the conventional "coarse recognition" and "fine extraction" functions which were integrated into a compact all-in-one deep CNN for CT image segmentation. The advantage comparing to previous works was its capability to accomplish real-time image segmentations on 2D slices of arbitrary CT-scan-range (e.g. body, chest, abdomen) and produced correspondingly-sized output. In this paper, we propose an improvement of our proposed approach by adding an organ localization module to limit CT image range for training and testing deep CNNs. A database consisting of 240 3D CT scans and a human annotated ground truth was used for training (228 cases) and testing (the remaining 12 cases). We applied the improved method to segment pancreas and left kidney regions, respectively. The preliminary results showed that the accuracies of the segmentation results were improved significantly (pancreas was 34% and kidney was 8% increased in Jaccard index from our previous results). The effectiveness and usefulness of proposed improvement for CT image segmentations were confirmed.

Controversies In The Surgical Management Of Shoulder Instability: Associated Soft Tissue Procedures

PubMed Central

Moros Marco, Santos; Ávila Lafuente, José Luis; Ruiz Ibán, Miguel Angel; Diaz Heredia, Jorge

2017-01-01

Background: The glenohumeral joint is a ball-and-socket joint that is inherently unstable and thus, susceptible to dislocation. The traditional and most common anatomic finding is the Bankart lesion (anterior-inferior capsule labral complex avulsion), but there is a wide variety of anatomic alterations that can cause shoulder instability or may be present as a concomitant injury or in combination, including bone loss (glenoid or humeral head), complex capsule-labral tears, rotator cuff tears, Kim´s lesions (injuries to the posterior-inferior labrum) and rotator interval pathology. Methods: A review of articles related to shoulder anatomy and soft tissue procedures that are performed during shoulder instability arthroscopic management was conducted by querying the Pubmed database and conclusions and controversies regarding this injury were exposed. Results: Due to the complex anatomy of the shoulder and the large range of movement of this joint, a wide variety of anatomic injuries and conditions can lead to shoulder instability, specially present in young population. Recognizing and treating all of them including Bankart repair, capsule-labral plicatures, SLAP repair, circumferential approach to pan-labral lesions, rotator interval closure, rotator cuff injuries and HAGL lesion repair is crucial to achieve the goal of a stable, full range of movement and not painful joint. Conclusion: Physicians must be familiarized with all the lesions involved in shoulder instability, and should be able to recognize and subsequently treat them to achieve the goal of a stable non-painful shoulder. Unrecognized or not treated lesions may result in recurrence of instability episodes and pain while overuse of some of the techniques previously described can lead to stiffness, thus the importance of an accurate diagnosis and treatment when facing a shoulder instability. PMID:28979603

Controversies In The Surgical Management Of Shoulder Instability: Associated Soft Tissue Procedures.

PubMed

Marco, Santos Moros; Lafuente, José Luis Ávila; Ibán, Miguel Angel Ruiz; Heredia, Jorge Diaz

2017-01-01

The glenohumeral joint is a ball-and-socket joint that is inherently unstable and thus, susceptible to dislocation. The traditional and most common anatomic finding is the Bankart lesion (anterior-inferior capsule labral complex avulsion), but there is a wide variety of anatomic alterations that can cause shoulder instability or may be present as a concomitant injury or in combination, including bone loss (glenoid or humeral head), complex capsule-labral tears, rotator cuff tears, Kim´s lesions (injuries to the posterior-inferior labrum) and rotator interval pathology. A review of articles related to shoulder anatomy and soft tissue procedures that are performed during shoulder instability arthroscopic management was conducted by querying the Pubmed database and conclusions and controversies regarding this injury were exposed. Due to the complex anatomy of the shoulder and the large range of movement of this joint, a wide variety of anatomic injuries and conditions can lead to shoulder instability, specially present in young population. Recognizing and treating all of them including Bankart repair, capsule-labral plicatures, SLAP repair, circumferential approach to pan-labral lesions, rotator interval closure, rotator cuff injuries and HAGL lesion repair is crucial to achieve the goal of a stable, full range of movement and not painful joint. Physicians must be familiarized with all the lesions involved in shoulder instability, and should be able to recognize and subsequently treat them to achieve the goal of a stable non-painful shoulder. Unrecognized or not treated lesions may result in recurrence of instability episodes and pain while overuse of some of the techniques previously described can lead to stiffness, thus the importance of an accurate diagnosis and treatment when facing a shoulder instability.

Tobacco use predicts a more difficult episode of care after anatomic total shoulder arthroplasty.

PubMed

Wells, Daniel B; Holt, Andrew M; Smith, Richard A; Brolin, Tyler J; Azar, Frederick M; Throckmorton, Thomas W

2018-01-01

In the current health care environment, it is becoming increasingly important to recognize risks factors that may affect a patient's postoperative outcome. To determine the potential impact of tobacco as a risk factor, we evaluated postoperative pain, narcotic use, length of stay, reoperations, and complications in the global 90-day episode of care for patients undergoing anatomic total shoulder arthroplasty (TSA) who were current tobacco users, former users, or nonusers. Database search identified 163 patients with primary anatomic TSA done for glenohumeral arthritis; these were divided into 3 groups: current tobacco users (28), nonusers (88), and former users (47). All surgeries were done with the same technique and implants. Patients in the current tobacco use group had significantly higher visual analog scale scores preoperatively and at 12 weeks postoperatively than nonusers and former users. Mean improvement in visual analog scale scores was significantly less in current tobacco users. Cumulative oral morphine equivalent use at 12 weeks was significantly higher in current tobacco users than in nonusers and former users. The average oral morphine equivalent per day was also significantly higher in the current tobacco users than in nonusers and former users. There were no significant differences in length of stay or complications. Although length of stay, complication rates, hospital readmissions, and reoperation rates were not significantly different, tobacco users reported increased postoperative pain and narcotic use in the global period after TSA. Former tobacco users were found to have a postoperative course similar to that of nonusers, suggesting that discontinuation of tobacco use can improve a patient's episode of care performance after TSA. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Clinical features and prognosis of eyeball rupture: eye injury vitrectomy study.

PubMed

Feng, Kang; Wang, Chang-guan; Hu, Yun-tao; Yao, Yi; Jiang, Yan-rong; Shen, Li-jun; Pang, Xiu-qin; Nie, Hong-ping; Ma, Zhi-zhong

2015-01-01

The objective of the study was to delineate clinical characteristics, surgical interventions, anatomic and visual outcomes of ruptured eye balls after trauma, and establish the prognostic indicators, which can assist clinicians in making correct surgical decisions during globe exploration for ruptured eyes. The study design used was a multicentre prospective cohort study, including six university-affiliated tertiary hospitals. We selected 242 cases of ruptured globe from the Eye Injury Vitrectomy Study database, until 31 December 2012. All selected cases underwent vitreoretinal surgery, enucleation or evisceration, and were followed up for at least 6 months. Age, visual acuity (VA) after injury, ocular trauma zone, time to surgery, corneal laceration, scleral wound, extrusion of iris or lens, ciliary body damage, intraocular haemorrhage, retinal detachment or defect, proliferative vitreoretinopathy (PVR) and choroidal damage were the predisposing factors evaluated by logistic regression models. We compared the pre-surgical indicators between cases of anatomically restored eyes with VA of 4/200 or better, or eyes with initial no light perception restored light perception or better, and cases of VA worse than 4/200, silicone oil-sustained eyes, phthisis or enucleation. Nearly 40% of cases with ruptured globe were anatomically restored through vitreoretinal surgery. The closed-funnel retinal detachment or extensive retinal loss (odds ratio [OR] = 3.38, P = 0.026), PVR-C (OR = 3.45, P = 0.008), and choroidal damage (OR = 4.20, P = 0.004) were correlated with poor outcomes. The closed-funnel retinal detachment or extensive retinal loss, PVR-C, and choroidal damage are the risk factors for unfavourable outcomes in globe ruptures. © 2015 Royal Australian and New Zealand College of Ophthalmologists.

FDI World Dental Federation - clinical criteria for the evaluation of direct and indirect restorations. Update and clinical examples.

PubMed

Hickel, Reinhard; Peschke, Arnd; Tyas, Martin; Mjör, Ivar; Bayne, Stephen; Peters, Mathilde; Hiller, Karl-Anton; Randall, Ross; Vanherle, Guido; Heintze, Siegward D

2010-08-01

In 2007, new clinical criteria were approved by the FDI World Dental Federation and simultaneously published in three dental journals. The criteria were categorized into three groups: esthetic parameters (four criteria), functional parameters (six criteria), and biological parameters (six criteria). Each criterion can be expressed with five scores, three for acceptable and two for non-acceptable (one for reparable and one for replacement). The criteria have been used in several clinical studies since 2007, and the resulting experience in their application has led to a requirement to modify some of the criteria and scores. The two major alterations involve staining and approximal contacts. As staining of the margins and the surface have different causes, both phenomena do not appear simultaneously. Thus, staining has been differentiated into marginal staining and surface staining. The approximal contact now appears under the name "approximal anatomic form" as the approximal contour is a specific, often non-esthetic issue that cannot be integrated into the criterion "esthetic anatomical form". In 2008, a web-based training and calibration tool called e-calib (www.e-calib.info) was made available. Clinical investigators and other research workers can train and calibrate themselves interactively by assessing clinical cases of posterior restorations, which are presented as high quality pictures. Currently, about 300 clinical cases are included in the database which is regularly updated. Training for 8 of the 16 clinical criteria is available in the program: "Surface luster"; "Staining (surface, margins)"; "Color match and translucency"; "Esthetic anatomical form"; "Fracture of material and retention"; "Marginal adaptation"; "Recurrence of caries, erosion, abfraction"; and "Tooth integrity (enamel cracks, tooth fractures)". Typical clinical cases are presented for each of these eight criteria and their corresponding five scores.

VirtualDose: a software for reporting organ doses from CT for adult and pediatric patients

NASA Astrophysics Data System (ADS)

Ding, Aiping; Gao, Yiming; Liu, Haikuan; Caracappa, Peter F.; Long, Daniel J.; Bolch, Wesley E.; Liu, Bob; Xu, X. George

2015-07-01

This paper describes the development and testing of VirtualDose—a software for reporting organ doses for adult and pediatric patients who undergo x-ray computed tomography (CT) examinations. The software is based on a comprehensive database of organ doses derived from Monte Carlo (MC) simulations involving a library of 25 anatomically realistic phantoms that represent patients of different ages, body sizes, body masses, and pregnant stages. Models of GE Lightspeed Pro 16 and Siemens SOMATOM Sensation 16 scanners were carefully validated for use in MC dose calculations. The software framework is designed with the ‘software as a service (SaaS)’ delivery concept under which multiple clients can access the web-based interface simultaneously from any computer without having to install software locally. The RESTful web service API also allows a third-party picture archiving and communication system software package to seamlessly integrate with VirtualDose’s functions. Software testing showed that VirtualDose was compatible with numerous operating systems including Windows, Linux, Apple OS X, and mobile and portable devices. The organ doses from VirtualDose were compared against those reported by CT-Expo and ImPACT—two dosimetry tools that were based on the stylized pediatric and adult patient models that were known to be anatomically simple. The organ doses reported by VirtualDose differed from those reported by CT-Expo and ImPACT by as much as 300% in some of the patient models. These results confirm the conclusion from past studies that differences in anatomical realism offered by stylized and voxel phantoms have caused significant discrepancies in CT dose estimations.

Left Septal Slow Pathway Ablation for Atrioventricular Nodal Reentrant Tachycardia.

PubMed

Katritsis, Demosthenes G; John, Roy M; Latchamsetty, Rakesh; Muthalaly, Rahul G; Zografos, Theodoros; Katritsis, George D; Stevenson, William G; Efimov, Igor R; Morady, Fred

2018-03-01

Immunohistochemistry studies suggest that the anatomic substrate of the slow pathway in atrioventricular nodal reentrant tachycardia (AVNRT) is the left inferior nodal extension. We hypothesized that slow pathway ablation from the left septum is an effective alternative to right-sided ablation. We analyzed our databases of AVNRT in search of cases that had used slow pathway ablation from the left septum because of failure of right septal ablation, and then prospectively subjected consenting patients to a left septal-only procedure. Of 1342 patients subjected to right septal slow pathway ablation for AVNRT, 15 patients, 11 with typical and 4 with atypical AVNRT, had a left septal approach after unsuccessful right-sided ablation (R+L group). Eleven patients were subjected to a left septal-only approach for slow pathway ablation without a previous right septal attempt (L group). Fluoroscopy times in the R+L and L groups were 30.5 (21.0-44.0) and 20.0 (17.0-25.0) minutes, respectively ( P =0.061), and radiofrequency current delivery times were 11.3 (5.0-19.1) and 10.0 (7.0-12.0) minutes, respectively ( P =0.897). There was no need for additional ablation lesions at other anatomic sites in either group, and no cases of atrioventricular block were encountered. Recurrence rates of the arrhythmia for the R+L and L groups were 6.7% and 0%, respectively, in the 3 months after ablation ( P =1.000). Left septal ablation at the anatomic site of the left inferior nodal extension is an alternative for ablation of both typical and atypical AVNRT when ablation at the right posterior septum is ineffective. © 2018 American Heart Association, Inc.

Neurological outcomes by mode of delivery for fetuses with open neural tube defects: A systematic review and meta-analysis.

PubMed

Tolcher, Mary C; Shazly, Sherif A; Shamshirsaz, Alireza A; Whitehead, William E; Espinoza, Jimmy; Vidaeff, Alex C; Belfort, Michael A; Nassr, Ahmed A

2018-06-20

Controversy exists regarding the optimal mode of delivery for fetuses with open neural tube defects. To compare neurological outcomes among infants with open neural tube defects who underwent vaginal compared to caesarean delivery. Electronic databases MEDLINE, EMBASE, Scopus, and Clinicaltrials. gov were searched from inception to November 2017. Eligible studies included observational or randomised studies comparing vaginal and caesarean delivery in pregnancies with fetal open neural tube defects who did not undergo prenatal repair. Two reviewers independently reviewed abstracts and full text articles. Outcomes were compared between vaginal and caesarean delivery and prelabour caesarean versus labour. The primary outcome was motor-anatomic level difference. Secondary outcomes included shunt requirement, sac disruption, meningitis, and ambulation at 2 years. Meta-analysis was performed and mean difference or odds ratios with 95% confidence interval calculated. Of 201 abstracts identified in the primary search, 9 studies (672 women) met eligibility criteria. Comparing vaginal and caesarean delivery, there was no significant difference in motor-anatomic level difference (mean difference -0.10, 95% CI -0.58-0.38; I 2 =57%). The vaginal delivery group was less likely to require a shunt or have sac disruption (OR 0.37, 95% CI 0.14-0.95 and OR 0.46, 95% CI 0.23-0.90, respectively). Comparisons by prelabour caesarean versus labour showed no significant difference in motor-anatomic level difference (OR 1.29, 95% CI -0.63-3.21) or ambulation at 2 years (OR 2.13, 95% CI 0.35-13.12). Caesarean delivery was not associated with improved neurological outcomes among fetuses with open neural tube defects. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

3D Topography of the Young Adult Anal Sphincter Complex Reconstructed from Undeformed Serial Anatomical Sections

PubMed Central

Wu, Yi; Dabhoiwala, Noshir F.; Hagoort, Jaco; Shan, Jin-Lu; Tan, Li-Wen; Fang, Bin-Ji; Zhang, Shao-Xiang; Lamers, Wouter H.

2015-01-01

Background Pelvic-floor anatomy is usually studied by artifact-prone dissection or imaging, which requires prior anatomical knowledge. We used the serial-section approach to settle contentious issues and an interactive 3D-pdf to make the results widely accessible. Method 3D reconstructions of undeformed thin serial anatomical sections of 4 females and 2 males (21–35y) of the Chinese Visible Human database. Findings Based on tendinous septa and muscle-fiber orientation as segmentation guides, the anal-sphincter complex (ASC) comprised the subcutaneous external anal sphincter (EAS) and the U-shaped puborectal muscle, a part of the levator ani muscle (LAM). The anococcygeal ligament fixed the EAS to the coccygeal bone. The puborectal-muscle loops, which define the levator hiatus, passed around the anorectal junction and inserted anteriorly on the perineal body and pubic bone. The LAM had a common anterior attachment to the pubic bone, but separated posteriorly into puborectal and “pubovisceral” muscles. This pubovisceral muscle was bilayered: its internal layer attached to the conjoint longitudinal muscle of the rectum and the rectococcygeal fascia, while its outer, patchy layer reinforced the inner layer. ASC contraction makes the ano-rectal bend more acute and lifts the pelvic floor. Extensions of the rectal longitudinal smooth muscle to the coccygeal bone (rectococcygeal muscle), perineal body (rectoperineal muscle), and endopelvic fascia (conjoint longitudinal and pubovisceral muscles) formed a “diaphragm” at the inferior boundary of the mesorectum that suspended the anorectal junction. Its contraction should straighten the anorectal bend. Conclusion The serial-section approach settled contentious topographic issues of the pelvic floor. We propose that the ASC is involved in continence and the rectal diaphragm in defecation. PMID:26305117

The 2002 RPA Plot Summary database users manual

Treesearch

Patrick D. Miles; John S. Vissage; W. Brad Smith

2004-01-01

Describes the structure of the RPA 2002 Plot Summary database and provides information on generating estimates of forest statistics from these data. The RPA 2002 Plot Summary database provides a consistent framework for storing forest inventory data across all ownerships across the entire United States. The data represents the best available data as of October 2001....

Computer Cataloging of Electronic Journals in Unstable Aggregator Databases: The Hong Kong Baptist University Library Experience.

ERIC Educational Resources Information Center

Li, Yiu-On; Leung, Shirley W.

2001-01-01

Discussion of aggregator databases focuses on a project at the Hong Kong Baptist University library to integrate full-text electronic journal titles from three unstable aggregator databases into its online public access catalog (OPAC). Explains the development of the electronic journal computer program (EJCOP) to generate MARC records for…

Age-related changes in thoracic skeletal geometry of elderly females.

PubMed

Holcombe, Sven A; Wang, Stewart C; Grotberg, James B

2017-05-29

Both females and the elderly have been identified as vulnerable populations with increased injury and mortality risk in multiple crash scenarios. Particularly in frontal impacts, older females show higher risk to the chest and thorax than their younger or male counterparts. Thoracic geometry plays a role in this increase, and this study aims to quantify key parts of that geometry in a way that can directly inform human body models that incorporate the concept of person age. Computed tomography scans from 2 female subject groups aged 20-35 and 65-99 were selected from the International Center for Automotive Medicine scan database representing young and old female populations. A model of thoracic skeletal anatomy was built for each subject from independent parametric models of the spine, ribs, and sternum, along with further parametric models of those components' spatial relationships. Parameter values between the 2 groups are directly compared, and average parameter values within each group are used to generate statistically average skeletal geometry for young and old females. In addition to the anatomic measures explicitly used in the parameterization scheme, key measures of rib cage depth and spine curvature are taken from both the underlying subject pool and from the resultant representative geometries. Statistically significant differences were seen between the young and old groups' spine and rib anatomic components, with no significant differences in local sternal geometry found. Vertebral segments in older females had higher angles relative to their inferior neighbors, providing a quantification of the kyphotic curvature known to be associated with age. Ribs in older females had greater end-to-end span, greater aspect ratio, and reduced out-of-plane deviation, producing an elongated and overall flatter curvature that leads to distal rib ends extending further anteriorly in older individuals. Combined differences in spine curvature and rib geometry led to an 18-mm difference in anterior placement of the sternum between young and old subjects. This study provides new geometric data regarding the variability in anthropometry of adult females with age and has utility in advancing the veracity of current human body models. A simplified scaffold representation of underlying 3-dimensional bones within the thorax is presented, and the reported young and old female parameter sets can be used to characterize the anatomic differences expected with age and to both validate and drive morphing algorithms for aged human body models. The modular approach taken allows model parameters to hold inherent and intuitive meaning, offering advantages over more generalized methods such as principal component analysis. Geometry can be assessed on a component level or a whole thorax level, and the parametric representation of thorax shape allows direct comparisons between the current study and other individuals or human body models.

A set of 4D pediatric XCAT reference phantoms for multimodality research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norris, Hannah, E-mail: Hannah.norris@duke.edu; Zhang, Yakun; Bond, Jason

Purpose: The authors previously developed an adult population of 4D extended cardiac-torso (XCAT) phantoms for multimodality imaging research. In this work, the authors develop a reference set of 4D pediatric XCAT phantoms consisting of male and female anatomies at ages of newborn, 1, 5, 10, and 15 years. These models will serve as the foundation from which the authors will create a vast population of pediatric phantoms for optimizing pediatric CT imaging protocols. Methods: Each phantom was based on a unique set of CT data from a normal patient obtained from the Duke University database. The datasets were selected tomore » best match the reference values for height and weight for the different ages and genders according to ICRP Publication 89. The major organs and structures were segmented from the CT data and used to create an initial pediatric model defined using nonuniform rational B-spline surfaces. The CT data covered the entire torso and part of the head. To complete the body, the authors manually added on the top of the head and the arms and legs using scaled versions of the XCAT adult models or additional models created from cadaver data. A multichannel large deformation diffeomorphic metric mapping algorithm was then used to calculate the transform from a template XCAT phantom (male or female 50th percentile adult) to the target pediatric model. The transform was applied to the template XCAT to fill in any unsegmented structures within the target phantom and to implement the 4D cardiac and respiratory models in the new anatomy. The masses of the organs in each phantom were matched to the reference values given in ICRP Publication 89. The new reference models were checked for anatomical accuracy via visual inspection. Results: The authors created a set of ten pediatric reference phantoms that have the same level of detail and functionality as the original XCAT phantom adults. Each consists of thousands of anatomical structures and includes parameterized models for the cardiac and respiratory motions. Based on patient data, the phantoms capture the anatomic variations of childhood, such as the development of bone in the skull, pelvis, and long bones, and the growth of the vertebrae and organs. The phantoms can be combined with existing simulation packages to generate realistic pediatric imaging data from different modalities. Conclusions: The development of patient-derived pediatric computational phantoms is useful in providing variable anatomies for simulation. Future work will expand this ten-phantom base to a host of pediatric phantoms representative of the public at large. This can provide a means to evaluate and improve pediatric imaging devices and to optimize CT protocols in terms of image quality and radiation dose.« less

Time-Tag Generation Script

NASA Technical Reports Server (NTRS)

Jackson, Dan E.

2010-01-01

Time-Tag Generation Script (TTaGS) is an application program, written in the AWK scripting language, for generating commands for aiming one Ku-band antenna and two S-band antennas for communicating with spacecraft. TTaGS saves between 2 and 4 person-hours per every 24 hours by automating the repetitious process of building between 150 and 180 antenna-control commands. TTaGS reads a text database of communication satellite schedules and a text database of satellite rise and set times and cross-references items in the two databases. It then compares the scheduled start and stop with the geometric rise and set to compute the times to execute antenna control commands. While so doing, TTaGS determines whether to generate commands for guidance, navigation, and control computers to tell them which satellites to track. To help prevent Ku-band irradiation of the Earth, TTaGS accepts input from the user about horizon tolerance and accordingly restricts activation and effects deactivation of the transmitter. TTaGS can be modified easily to enable tracking of additional satellites and for such other tasks as reading Sun-rise/set tables to generate commands to point the solar photovoltaic arrays of the International Space Station at the Sun.

Endoscopic colloid cyst excision: surgical techniques and nuances.

PubMed

Azab, Waleed Abdelfattah; Najibullah, Mustafa; Yosef, Waleed

2017-06-01

Endoscopic excision of colloid cysts is currently well established as a minimally invasive and highly effective technique that is associated with less morbidity in comparison to microsurgical resection. Operative charts and videos of patients undergoing endoscopic colloid cyst excision were retrieved from the senior author's database of endoscopic procedures and reviewed. This revealed nine trans-foraminal and three trans-septal procedures. Description of the surgical techniques was then formulated. Variation of the technique is based on the specific patho-anatomical features of the colloid cyst being resected. For the trans-foraminal approach, we think that the rotational technique is associated with a more complete removal of the cyst wall and consequently lower recurrence rate.

International LCA

EPA Science Inventory

To provide global guidance on the establishment and maintenance of LCA databases, as the basis for improved dataset exchangeability and interlinkages of databases worldwide. Increase the credibility of existing LCA data, the generation of more data and their overall accessibilit...

Combining evidence from multiple electronic health care databases: performances of one-stage and two-stage meta-analysis in matched case-control studies.

PubMed

La Gamba, Fabiola; Corrao, Giovanni; Romio, Silvana; Sturkenboom, Miriam; Trifirò, Gianluca; Schink, Tania; de Ridder, Maria

2017-10-01

Clustering of patients in databases is usually ignored in one-stage meta-analysis of multi-database studies using matched case-control data. The aim of this study was to compare bias and efficiency of such a one-stage meta-analysis with a two-stage meta-analysis. First, we compared the approaches by generating matched case-control data under 5 simulated scenarios, built by varying: (1) the exposure-outcome association; (2) its variability among databases; (3) the confounding strength of one covariate on this association; (4) its variability; and (5) the (heterogeneous) confounding strength of two covariates. Second, we made the same comparison using empirical data from the ARITMO project, a multiple database study investigating the risk of ventricular arrhythmia following the use of medications with arrhythmogenic potential. In our study, we specifically investigated the effect of current use of promethazine. Bias increased for one-stage meta-analysis with increasing (1) between-database variance of exposure effect and (2) heterogeneous confounding generated by two covariates. The efficiency of one-stage meta-analysis was slightly lower than that of two-stage meta-analysis for the majority of investigated scenarios. Based on ARITMO data, there were no evident differences between one-stage (OR = 1.50, CI = [1.08; 2.08]) and two-stage (OR = 1.55, CI = [1.12; 2.16]) approaches. When the effect of interest is heterogeneous, a one-stage meta-analysis ignoring clustering gives biased estimates. Two-stage meta-analysis generates estimates at least as accurate and precise as one-stage meta-analysis. However, in a study using small databases and rare exposures and/or outcomes, a correct one-stage meta-analysis becomes essential. Copyright © 2017 John Wiley & Sons, Ltd.

Current issues with standards in the measurement and documentation of human skeletal anatomy.

PubMed

Magee, Justin; McClelland, Brian; Winder, John

2012-09-01

Digital modeling of human anatomy has become increasingly important and relies on well-documented quantitative anatomy literature. This type of documentation is common for the spine and pelvis; however, significant issues exist due to the lack of standardization in measurement and technique. Existing literature on quantitative anatomy for the spine and pelvis of white adults (aged 18-65 years, separated into decadal categories) was reviewed from the disciplines of anatomy, manipulative therapy, anthropometrics, occupational ergonomics, biomechanics and forensic science. The data were unified into a single normative model of the sub-axial spine. Two-dimensional orthographic drawings were produced from the 590 individual measurements identified, which informed the development of a 3D digital model. A similar review of full range of motion data was conducted as a meta-analysis and the results were applied to the existing model, providing an inter-connected, articulated digital spine. During these data analysis processes several inconsistencies were observed accompanied by an evidential lack of standardization with measurement and recording of data. These have been categorized as: anatomical terminology; scaling of measurements; measurement methodology, dimension and anatomical reference positions; global coordinate systems. There is inconsistency in anatomical terminology where independent researchers use the same terms to describe different aspects of anatomy or different terms for the same anatomy. Published standards exist for measurement methods of the human body regarding spatial interaction, anthropometric databases, automotive applications, clothing industries and for computer manikins, but none exists for skeletal anatomy. Presentation of measurements often lacks formal structure in clinical publications, seldom providing geometric reference points, therefore making digital reconstruction difficult. Published quantitative data does not follow existing international published standards relating to engineering drawing and visual communication. Large variations are also evident in standards or guidelines used for global coordinate systems across biomechanics, ergonomics, software systems and 3D software applications. This paper identifies where established good practice exists and suggests additional recommendations, informing an improved communication protocol, to assist reconstruction of skeletal anatomy using 3D digital modeling. © 2012 The Authors. Journal of Anatomy © 2012 Anatomical Society.

Nuclear Forensics Analysis with Missing and Uncertain Data

DOE PAGES

Langan, Roisin T.; Archibald, Richard K.; Lamberti, Vincent

2015-10-05

We have applied a new imputation-based method for analyzing incomplete data, called Monte Carlo Bayesian Database Generation (MCBDG), to the Spent Fuel Isotopic Composition (SFCOMPO) database. About 60% of the entries are absent for SFCOMPO. The method estimates missing values of a property from a probability distribution created from the existing data for the property, and then generates multiple instances of the completed database for training a machine learning algorithm. Uncertainty in the data is represented by an empirical or an assumed error distribution. The method makes few assumptions about the underlying data, and compares favorably against results obtained bymore » replacing missing information with constant values.« less

Finer parcellation reveals detailed correlational structure of resting-state fMRI signals.

PubMed

Dornas, João V; Braun, Jochen

2018-01-15

Even in resting state, the human brain generates functional signals (fMRI) with complex correlational structure. To simplify this structure, it is common to parcellate a standard brain into coarse chunks. Finer parcellations are considered less reproducible and informative, due to anatomical and functional variability of individual brains. Grouping signals with similar local correlation profiles, restricted to each anatomical region (Tzourio-Mazoyer et al., 2002), we divide a standard brain into 758 'functional clusters' averaging 1.7cm 3 gray matter volume ('MD758' parcellation). We compare 758 'spatial clusters' of similar size ('S758'). 'Functional clusters' are spatially contiguous and cluster quality (integration and segregation of temporal variance) is far superior to 'spatial clusters', comparable to multi-modal parcellations of half the resolution (Craddock et al., 2012; Glasser et al., 2016). Moreover, 'functional clusters' capture many long-range functional correlations, with O(10 5 ) reproducibly correlated cluster pairs in different anatomical regions. The pattern of functional correlations closely mirrors long-range anatomical connectivity established by fibre tracking. MD758 is comparable to coarser parcellations (Craddock et al., 2012; Glasser et al., 2016) in terms of cluster quality, correlational structure (54% relative mutual entropy vs 60% and 61%), and sparseness (35% significant pairwise correlations vs 36% and 44%). We describe and evaluate a simple path to finer functional parcellations of the human brain. Detailed correlational structure is surprisingly consistent between individuals, opening new possibilities for comparing functional correlations between cognitive conditions, states of health, or pharmacological interventions. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Automatic construction of subject-specific human airway geometry including trifurcations based on a CT-segmented airway skeleton and surface

PubMed Central

Miyawaki, Shinjiro; Tawhai, Merryn H.; Hoffman, Eric A.; Wenzel, Sally E.; Lin, Ching-Long

2016-01-01

We propose a method to construct three-dimensional airway geometric models based on airway skeletons, or centerlines (CLs). Given a CT-segmented airway skeleton and surface, the proposed CL-based method automatically constructs subject-specific models that contain anatomical information regarding branches, include bifurcations and trifurcations, and extend from the trachea to terminal bronchioles. The resulting model can be anatomically realistic with the assistance of an image-based surface; alternatively a model with an idealized skeleton and/or branch diameters is also possible. This method systematically identifies and classifies trifurcations to successfully construct the models, which also provides the number and type of trifurcations for the analysis of the airways from an anatomical point of view. We applied this method to 16 normal and 16 severe asthmatic subjects using their computed tomography images. The average distance between the surface of the model and the image-based surface was 11% of the average voxel size of the image. The four most frequent locations of trifurcations were the left upper division bronchus, left lower lobar bronchus, right upper lobar bronchus, and right intermediate bronchus. The proposed method automatically constructed accurate subject-specific three-dimensional airway geometric models that contain anatomical information regarding branches using airway skeleton, diameters, and image-based surface geometry. The proposed method can construct (i) geometry automatically for population-based studies, (ii) trifurcations to retain the original airway topology, (iii) geometry that can be used for automatic generation of computational fluid dynamics meshes, and (iv) geometry based only on a skeleton and diameters for idealized branches. PMID:27704229

Regenerative Medicine and Restoration of Joint Function

DTIC Science & Technology

2012-10-01

identify the parameters that generate anatomically shaped bone substitutes of optimal composition and structure with an articulating profile. 2) to develop...strengths. An in vivo study in rabbits to evaluate these materials are ongoing. Task 2. Optimization of SFF Rolling Compaction Parameters : The work is...ongoing related to optimizing SFF rolling compaction parameters to control the density of green samples. We have used CPP powders for these studies

Regenerative Medicine and Restoration of Joint Function

DTIC Science & Technology

2014-12-01

to resist fracture and excessive deformation under antici- pated mechanical loading conditions both during the early healing process and for longer...per sample type), the results sug- gest a correlation between percent fractured sinter neck area and mechanical properties with the lowest bending...joint replacement are used to treat a joint with an intra-articular fracture or destroyed by a combat injury. Generation of personalized, anatomically

Principal component analysis-based anatomical motion models for use in adaptive radiation therapy of head and neck cancer patients

NASA Astrophysics Data System (ADS)

Chetvertkov, Mikhail A.

Purpose: To develop standard and regularized principal component analysis (PCA) models of anatomical changes from daily cone beam CTs (CBCTs) of head and neck (H&N) patients, assess their potential use in adaptive radiation therapy (ART), and to extract quantitative information for treatment response assessment. Methods: Planning CT (pCT) images of H&N patients were artificially deformed to create "digital phantom" images, which modeled systematic anatomical changes during Radiation Therapy (RT). Artificial deformations closely mirrored patients' actual deformations, and were interpolated to generate 35 synthetic CBCTs, representing evolving anatomy over 35 fractions. Deformation vector fields (DVFs) were acquired between pCT and synthetic CBCTs (i.e., digital phantoms), and between pCT and clinical CBCTs. Patient-specific standard PCA (SPCA) and regularized PCA (RPCA) models were built from these synthetic and clinical DVF sets. Eigenvectors, or eigenDVFs (EDVFs), having the largest eigenvalues were hypothesized to capture the major anatomical deformations during treatment. Modeled anatomies were used to assess the dose deviations with respect to the planned dose distribution. Results: PCA models achieve variable results, depending on the size and location of anatomical change. Random changes prevent or degrade SPCA's ability to detect underlying systematic change. RPCA is able to detect smaller systematic changes against the background of random fraction-to-fraction changes, and is therefore more successful than SPCA at capturing systematic changes early in treatment. SPCA models were less successful at modeling systematic changes in clinical patient images, which contain a wider range of random motion than synthetic CBCTs, while the regularized approach was able to extract major modes of motion. For dose assessment it has been shown that the modeled dose distribution was different from the planned dose for the parotid glands due to their shrinkage and shift into the higher dose volumes during the radiotherapy course. Modeled DVHs still underestimated the effect of parotid shrinkage due to the large compression factor (CF) used to acquire DVFs. Conclusion: Leading EDVFs from both PCA approaches have the potential to capture systematic anatomical changes during H&N radiotherapy when systematic changes are large enough with respect to random fraction-to-fraction changes. In all cases the RPCA approach appears to be more reliable than SPCA at capturing systematic changes, enabling dosimetric consequences to be projected to the future treatment fractions based on trends established early in a treatment course, or, potentially, based on population models. This work showed that PCA has a potential in identifying the major mode of anatomical changes during the radiotherapy course and subsequent use of this information in future dose predictions is feasible. Use of smaller CF values for DVFs is preferred, otherwise anatomical motion will be underestimated.

Pleasure systems in the brain

PubMed Central

Berridge, Kent C.; Kringelbach, Morten L.

2015-01-01

Pleasure is mediated by well-developed mesocorticolimbic circuitry, and serves adaptive functions. In affective disorders anhedonia (lack of pleasure) or dysphoria (negative affect) can result from breakdowns of that hedonic system. Human neuroimaging studies indicate that surprisingly similar circuitry is activated by quite diverse pleasures, suggesting a common neural currency shared by all. Wanting for rewards is generated by a large and distributed brain system. Liking, or pleasure itself, is generated by a smaller set of hedonic hotspots within limbic circuitry. Those hotspots also can be embedded in broader anatomical patterns of valence organization, such as in a keyboard pattern of nucleus accumbens generators for desire versus dread. In contrast, some of the best known textbook candidates for pleasure generators, including classic pleasure electrodes and the mesolimbic dopamine system, may not generate pleasure after all. These emerging insights into brain pleasure mechanisms may eventually facilitate better treatments for affective disorders. PMID:25950633

Multi-Resolution Playback of Network Trace Files

DTIC Science & Technology

2015-06-01

a com- plete MySQL database, C++ developer tools and the libraries utilized in the development of the system (Boost and Libcrafter), and Wireshark...XE suite has a limit to the allowed size of each database. In order to be scalable, the project had to switch to the MySQL database suite. The...programs that access the database use the MySQL C++ connector, provided by Oracle, and the supplied methods and libraries. 4.4 Flow Generator Chapter 3

Reporting to Improve Reproducibility and Facilitate Validity Assessment for Healthcare Database Studies V1.0.

PubMed

Wang, Shirley V; Schneeweiss, Sebastian; Berger, Marc L; Brown, Jeffrey; de Vries, Frank; Douglas, Ian; Gagne, Joshua J; Gini, Rosa; Klungel, Olaf; Mullins, C Daniel; Nguyen, Michael D; Rassen, Jeremy A; Smeeth, Liam; Sturkenboom, Miriam

2017-09-01

Defining a study population and creating an analytic dataset from longitudinal healthcare databases involves many decisions. Our objective was to catalogue scientific decisions underpinning study execution that should be reported to facilitate replication and enable assessment of validity of studies conducted in large healthcare databases. We reviewed key investigator decisions required to operate a sample of macros and software tools designed to create and analyze analytic cohorts from longitudinal streams of healthcare data. A panel of academic, regulatory, and industry experts in healthcare database analytics discussed and added to this list. Evidence generated from large healthcare encounter and reimbursement databases is increasingly being sought by decision-makers. Varied terminology is used around the world for the same concepts. Agreeing on terminology and which parameters from a large catalogue are the most essential to report for replicable research would improve transparency and facilitate assessment of validity. At a minimum, reporting for a database study should provide clarity regarding operational definitions for key temporal anchors and their relation to each other when creating the analytic dataset, accompanied by an attrition table and a design diagram. A substantial improvement in reproducibility, rigor and confidence in real world evidence generated from healthcare databases could be achieved with greater transparency about operational study parameters used to create analytic datasets from longitudinal healthcare databases. © 2017 The Authors. Pharmacoepidemiology & Drug Safety Published by John Wiley & Sons Ltd.

Challenges of the information age: the impact of false discovery on pathway identification.

PubMed

Rog, Colin J; Chekuri, Srinivasa C; Edgerton, Mary E

2012-11-21

Pathways with members that have known relevance to a disease are used to support hypotheses generated from analyses of gene expression and proteomic studies. Using cancer as an example, the pitfalls of searching pathways databases as support for genes and proteins that could represent false discoveries are explored. The frequency with which networks could be generated from 100 instances each of randomly selected five and ten genes sets as input to MetaCore, a commercial pathways database, was measured. A PubMed search enumerated cancer-related literature published for any gene in the networks. Using three, two, and one maximum intervening step between input genes to populate the network, networks were generated with frequencies of 97%, 77%, and 7% using ten gene sets and 73%, 27%, and 1% using five gene sets. PubMed reported an average of 4225 cancer-related articles per network gene. This can be attributed to the richly populated pathways databases and the interest in the molecular basis of cancer. As information sources become enriched, they are more likely to generate plausible mechanisms for false discoveries.

Generation of dense statistical connectomes from sparse morphological data

PubMed Central

Egger, Robert; Dercksen, Vincent J.; Udvary, Daniel; Hege, Hans-Christian; Oberlaender, Marcel

2014-01-01

Sensory-evoked signal flow, at cellular and network levels, is primarily determined by the synaptic wiring of the underlying neuronal circuitry. Measurements of synaptic innervation, connection probabilities and subcellular organization of synaptic inputs are thus among the most active fields of research in contemporary neuroscience. Methods to measure these quantities range from electrophysiological recordings over reconstructions of dendrite-axon overlap at light-microscopic levels to dense circuit reconstructions of small volumes at electron-microscopic resolution. However, quantitative and complete measurements at subcellular resolution and mesoscopic scales to obtain all local and long-range synaptic in/outputs for any neuron within an entire brain region are beyond present methodological limits. Here, we present a novel concept, implemented within an interactive software environment called NeuroNet, which allows (i) integration of sparsely sampled (sub)cellular morphological data into an accurate anatomical reference frame of the brain region(s) of interest, (ii) up-scaling to generate an average dense model of the neuronal circuitry within the respective brain region(s) and (iii) statistical measurements of synaptic innervation between all neurons within the model. We illustrate our approach by generating a dense average model of the entire rat vibrissal cortex, providing the required anatomical data, and illustrate how to measure synaptic innervation statistically. Comparing our results with data from paired recordings in vitro and in vivo, as well as with reconstructions of synaptic contact sites at light- and electron-microscopic levels, we find that our in silico measurements are in line with previous results. PMID:25426033

Freight Transportation Energy Use : Volume 3. Freight Network and Operations Database.

DOT National Transportation Integrated Search

1979-07-01

The data sources, procedures, and assumptions used to generate the TSC national freight network and operations database are documented. National rail, highway, waterway, and pipeline networks are presented, and estimates of facility capacity, travel ...

Eglin virtual range database for hardware-in-the-loop testing

NASA Astrophysics Data System (ADS)

Talele, Sunjay E.; Pickard, J. W., Jr.; Owens, Monte A.; Foster, Joseph; Watson, John S.; Amick, Mary Amenda; Anthony, Kenneth

1998-07-01

Realistic backgrounds are necessary to support high fidelity hardware-in-the-loop testing. Advanced avionics and weapon system sensors are driving the requirement for higher resolution imagery. The model-test-model philosophy being promoted by the T&E community is resulting in the need for backgrounds that are realistic or virtual representations of actual test areas. Combined, these requirements led to a major upgrade of the terrain database used for hardware-in-the-loop testing at the Guided Weapons Evaluation Facility (GWEF) at Eglin Air Force Base, Florida. This paper will describe the process used to generate the high-resolution (1-foot) database of ten sites totaling over 20 square kilometers of the Eglin range. this process involved generating digital elevation maps from stereo aerial imagery and classifying ground cover material using the spectral content. These databases were then optimized for real-time operation at 90 Hz.

Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification.

PubMed

Schuemie, Martijn J; Mons, Barend; Weeber, Marc; Kors, Jan A

2007-06-01

Gene and protein name identification in text requires a dictionary approach to relate synonyms to the same gene or protein, and to link names to external databases. However, existing dictionaries are incomplete. We investigate two complementary methods for automatic generation of a comprehensive dictionary: combination of information from existing gene and protein databases and rule-based generation of spelling variations. Both methods have been reported in literature before, but have hitherto not been combined and evaluated systematically. We combined gene and protein names from several existing databases of four different organisms. The combined dictionaries showed a substantial increase in recall on three different test sets, as compared to any single database. Application of 23 spelling variation rules to the combined dictionaries further increased recall. However, many rules appeared to have no effect and some appear to have a detrimental effect on precision.

Expert system development for commonality analysis in space programs

NASA Technical Reports Server (NTRS)

Yeager, Dorian P.

1987-01-01

This report is a combination of foundational mathematics and software design. A mathematical model of the Commonality Analysis problem was developed and some important properties discovered. The complexity of the problem is described herein and techniques, both deterministic and heuristic, for reducing that complexity are presented. Weaknesses are pointed out in the existing software (System Commonality Analysis Tool) and several improvements are recommended. It is recommended that: (1) an expert system for guiding the design of new databases be developed; (2) a distributed knowledge base be created and maintained for the purpose of encoding the commonality relationships between design items in commonality databases; (3) a software module be produced which automatically generates commonality alternative sets from commonality databases using the knowledge associated with those databases; and (4) a more complete commonality analysis module be written which is capable of generating any type of feasible solution.

The DrugAge database of aging-related drugs.

PubMed

Barardo, Diogo; Thornton, Daniel; Thoppil, Harikrishnan; Walsh, Michael; Sharifi, Samim; Ferreira, Susana; Anžič, Andreja; Fernandes, Maria; Monteiro, Patrick; Grum, Tjaša; Cordeiro, Rui; De-Souza, Evandro Araújo; Budovsky, Arie; Araujo, Natali; Gruber, Jan; Petrascheck, Michael; Fraifeld, Vadim E; Zhavoronkov, Alexander; Moskalev, Alexey; de Magalhães, João Pedro

2017-06-01

Aging is a major worldwide medical challenge. Not surprisingly, identifying drugs and compounds that extend lifespan in model organisms is a growing research area. Here, we present DrugAge (http://genomics.senescence.info/drugs/), a curated database of lifespan-extending drugs and compounds. At the time of writing, DrugAge contains 1316 entries featuring 418 different compounds from studies across 27 model organisms, including worms, flies, yeast and mice. Data were manually curated from 324 publications. Using drug-gene interaction data, we also performed a functional enrichment analysis of targets of lifespan-extending drugs. Enriched terms include various functional categories related to glutathione and antioxidant activity, ion transport and metabolic processes. In addition, we found a modest but significant overlap between targets of lifespan-extending drugs and known aging-related genes, suggesting that some but not most aging-related pathways have been targeted pharmacologically in longevity studies. DrugAge is freely available online for the scientific community and will be an important resource for biogerontologists. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Hold your horses: A comparison of human laryngomalacia with analogous equine airway pathology.

PubMed

Lawrence, Rachael J; Butterell, Matthew J; Constable, James D; Daniel, Matija

2018-02-01

Laryngomalacia is the most common cause of stridor in infants. Dynamic airway collapse is also a well-recognised entity in horses and an important cause of surgical veterinary intervention. We compare the aetiology, clinical features and management of human laryngomalacia with equine dynamic airway collapse. A structured review of the PubMed, the Ovid Medline and the Cochrane Collaboration databases (Cochrane Central Register of Controlled Trials, Cochrane Database of Systemic Reviews). There are numerous equine conditions that cause dynamic airway collapse defined specifically by the anatomical structures involved. Axial Deviation of the Aryepiglottic Folds (ADAF) is the condition most clinically analogous to laryngomalacia in humans, and is likewise most prevalent in the immature equine airway. Both conditions are managed either conservatively, or if symptoms require it, with surgical intervention. The operative procedures performed for ADAF and laryngomalacia are technically comparable. Dynamic collapse of the equine larynx, especially ADAF, is clinically similar to human laryngomalacia, and both are treated in a similar fashion. Copyright © 2017 Elsevier B.V. All rights reserved.

Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes

PubMed Central

Pantazatos, Spiro P.; Li, Jianrong; Pavlidis, Paul; Lussier, Yves A.

2009-01-01

An approach towards heterogeneous neuroscience dataset integration is proposed that uses Natural Language Processing (NLP) and a knowledge-based phenotype organizer system (PhenOS) to link ontology-anchored terms to underlying data from each database, and then maps these terms based on a computable model of disease (SNOMED CT®). The approach was implemented using sample datasets from fMRIDC, GEO, The Whole Brain Atlas and Neuronames, and allowed for complex queries such as “List all disorders with a finding site of brain region X, and then find the semantically related references in all participating databases based on the ontological model of the disease or its anatomical and morphological attributes”. Precision of the NLP-derived coding of the unstructured phenotypes in each dataset was 88% (n = 50), and precision of the semantic mapping between these terms across datasets was 98% (n = 100). To our knowledge, this is the first example of the use of both semantic decomposition of disease relationships and hierarchical information found in ontologies to integrate heterogeneous phenotypes across clinical and molecular datasets. PMID:20495688

Using Web Database Tools To Facilitate the Construction of Knowledge in Online Courses.

ERIC Educational Resources Information Center

McNeil, Sara G.; Robin, Bernard R.

This paper presents an overview of database tools that dynamically generate World Wide Web materials and focuses on the use of these tools to support research activities, as well as teaching and learning. Database applications have been used in classrooms to support learning activities for over a decade, but, although business and e-commerce have…

Creating and virtually screening databases of fluorescently-labelled compounds for the discovery of target-specific molecular probes

NASA Astrophysics Data System (ADS)

Kamstra, Rhiannon L.; Dadgar, Saedeh; Wigg, John; Chowdhury, Morshed A.; Phenix, Christopher P.; Floriano, Wely B.

2014-11-01

Our group has recently demonstrated that virtual screening is a useful technique for the identification of target-specific molecular probes. In this paper, we discuss some of our proof-of-concept results involving two biologically relevant target proteins, and report the development of a computational script to generate large databases of fluorescence-labelled compounds for computer-assisted molecular design. The virtual screening of a small library of 1,153 fluorescently-labelled compounds against two targets, and the experimental testing of selected hits reveal that this approach is efficient at identifying molecular probes, and that the screening of a labelled library is preferred over the screening of base compounds followed by conjugation of confirmed hits. The automated script for library generation explores the known reactivity of commercially available dyes, such as NHS-esters, to create large virtual databases of fluorescence-tagged small molecules that can be easily synthesized in a laboratory. A database of 14,862 compounds, each tagged with the ATTO680 fluorophore was generated with the automated script reported here. This library is available for downloading and it is suitable for virtual ligand screening aiming at the identification of target-specific fluorescent molecular probes.

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.

PubMed

Hume, Maxwell A; Barrera, Luis A; Gisselbrecht, Stephen S; Bulyk, Martha L

2015-01-01

The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k ('k-mers'). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Prevalence, correlates, and impact of coronary calcification on adverse events following PCI with newer-generation DES: Findings from a large multiethnic registry.

PubMed

Copeland-Halperin, Robert S; Baber, Usman; Aquino, Melissa; Rajamanickam, Anitha; Roy, Swathi; Hasan, Choudhury; Barman, Nitin; Kovacic, Jason C; Moreno, Pedro; Krishnan, Prakash; Sweeny, Joseph M; Mehran, Roxana; Dangas, George; Kini, Annapoorna S; Sharma, Samin K

2018-04-01

We sought to determine the prevalence, predictors, and clinical impact of target lesion calcification in patients undergoing percutaneous coronary intervention (PCI) with newer generation drug-eluting stents (DES) and devices. Coronary calcification is independently associated with adverse outcomes following PCI. While newer DES and contemporary devices are considered safer and more efficacious, their influence on outcomes following PCI of heavily calcified lesions is unknown. We performed a retrospective analysis of a large, multiethnic cohort of patients undergoing PCI with new generation DES at an academic center between 2009 and 2013. Coronary calcification was qualitatively assessed as none/mild, moderate, or severe. Independent demographic, clinical, and anatomic predictors of moderate/severe calcification were identified using logistic regression. Associations between coronary calcification and 1-year MACE (death, myocardial infarction, or target vessel revascularization) were examined using Cox modeling. Compared to patients with none/mild (n = 10,180; 82.0%), those with moderate (n = 1,271; 10.0%) or severe (n = 994; 8.0%) calcification were older, more often Caucasian, had more complex target lesions, and worse renal function. The strongest demographic, clinical, and anatomic correlates of moderate/severe calcification were age, Caucasian race, renal dysfunction, lesion length, and left main location. Unadjusted MACE rates among those with none/mild, moderate, and severe calcification were 8.3, 14.6, and 17.8%, respectively (P < 0.001). After multivariable adjustment, the hazard ratio (95% CI) for MACE associated with moderate or severe coronary calcification was 1.63. Target lesion calcification remains independently associated with adverse outcomes in patients treated with newer generation DES and modern devices. © 2017 Wiley Periodicals, Inc.

The utility of international shoulder joint replacement registries and databases: a comparative analytic review of two hundred and sixty one thousand, four hundred and eighty four cases.

PubMed

Bayona, Carlos Eduardo Afanador; Somerson, Jeremy S; Matsen, Frederick A

2018-02-01

National registries are valuable tools for understanding the results of shoulder arthroplasty across populations. These databases provide an unselected view of shoulder joint replacement within geographical areas that cannot be obtained from case series or prospective studies. They can be particularly helpful in determining which diagnoses, patients, procedures, and prostheses have higher than expected rates of revision. In an attempt to determine the generalizability of registry data, we asked, 'how similar are the patients and procedures among the different national registries?' We analyzed national shoulder arthroplasty registries and databases accessed via Internet portals and through a PubMed literature search. Seven national/regional registries and five publications regarding national shoulder arthroplasty data were identified; these sources contained a combined total of 261,484 shoulder arthroplasty cases. The percentages of hemiarthroplasty, anatomic (aTSA) and reverse total shoulders (rTSA), the diagnoses leading to arthroplasty, the mean patient age, and the distribution of patient gender varied significantly among these different databases. This study indicates that the indications for and application of shoulder arthroplasty have important geographical variations and that these variations must be considered when comparing outcomes of shoulder arthroplasty from different locations. Without controlling for age, gender, diagnosis and procedure type, the results from one national registry may not be applicable to patients from a different location. In that national data provide the opportunity to reduce costs by identifying implants and procedures with higher failure rates, the funding of registries needs to be free of conflicts of interest.

Comparison of anti-diabetic drug prescribing in children and adolescents in seven European countries.

PubMed

Neubert, Antje; Hsia, Yingfen; de Jong-van den Berg, Lolkje T W; Janhsen, Katrin; Glaeske, Gerd; Furu, Kari; Kieler, Helle; Nørgaard, Mette; Clavenna, Antonio; Wong, Ian C K

2011-12-01

The aim of this study was to compare the prevalence of diabetes in children across seven European countries, when using prescribing of anti-diabetics as a proxy for diabetes. A secondary aim was to assess the potential for collaboration between countries using different databases in diabetes research. Data were obtained from population-based clinical databases in seven European countries. The study population comprised children aged 0-18 years. Prescriptions were categorized using the Anatomic Therapeutic Chemical (ATC) classification. The one-year user prevalence in 2008 was calculated for each country and stratified by age and sex. We studied a total of 5.8 million children and adolescents. The prevalence of insulin prescribing varied between 1.1 and 3.5 per 1000 population, being highest in Sweden and lowest in Italy. In all countries, novel insulin analogues were the most commonly used insulins. The prevalence of oral anti-diabetic prescribing ranged from 0.08 per 1000 individuals in Sweden and Germany to 0.21 per 1000 population in the UK. Overall, the absolute number of oral anti-diabetic users was very low. This study shows that there is a varying frequency of type 1 diabetes in children and adolescents across Europe. We also demonstrated that it is possible to obtain similar information from different clinical databases within Europe, which would allow continuous monitoring of type 1 diabetes. Owing to the lack of indications in most of the databases, this approach is less suitable for type 2 diabetes. © 2011 The Authors. British Journal of Clinical Pharmacology © 2011 The British Pharmacological Society.

Deep learning of the sectional appearances of 3D CT images for anatomical structure segmentation based on an FCN voting method.

PubMed

Zhou, Xiangrong; Takayama, Ryosuke; Wang, Song; Hara, Takeshi; Fujita, Hiroshi

2017-10-01

We propose a single network trained by pixel-to-label deep learning to address the general issue of automatic multiple organ segmentation in three-dimensional (3D) computed tomography (CT) images. Our method can be described as a voxel-wise multiple-class classification scheme for automatically assigning labels to each pixel/voxel in a 2D/3D CT image. We simplify the segmentation algorithms of anatomical structures (including multiple organs) in a CT image (generally in 3D) to a majority voting scheme over the semantic segmentation of multiple 2D slices drawn from different viewpoints with redundancy. The proposed method inherits the spirit of fully convolutional networks (FCNs) that consist of "convolution" and "deconvolution" layers for 2D semantic image segmentation, and expands the core structure with 3D-2D-3D transformations to adapt to 3D CT image segmentation. All parameters in the proposed network are trained pixel-to-label from a small number of CT cases with human annotations as the ground truth. The proposed network naturally fulfills the requirements of multiple organ segmentations in CT cases of different sizes that cover arbitrary scan regions without any adjustment. The proposed network was trained and validated using the simultaneous segmentation of 19 anatomical structures in the human torso, including 17 major organs and two special regions (lumen and content inside of stomach). Some of these structures have never been reported in previous research on CT segmentation. A database consisting of 240 (95% for training and 5% for testing) 3D CT scans, together with their manually annotated ground-truth segmentations, was used in our experiments. The results show that the 19 structures of interest were segmented with acceptable accuracy (88.1% and 87.9% voxels in the training and testing datasets, respectively, were labeled correctly) against the ground truth. We propose a single network based on pixel-to-label deep learning to address the challenging issue of anatomical structure segmentation in 3D CT cases. The novelty of this work is the policy of deep learning of the different 2D sectional appearances of 3D anatomical structures for CT cases and the majority voting of the 3D segmentation results from multiple crossed 2D sections to achieve availability and reliability with better efficiency, generality, and flexibility than conventional segmentation methods, which must be guided by human expertise. © 2017 The Authors. Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Composite Bone Models in Orthopaedic Surgery Research and Education

PubMed Central

Elfar, John; Stanbury, Spencer; Menorca, Ron Martin Garcia; Reed, Jeffrey Douglas

2014-01-01

Composite bone models are increasingly used in orthopaedic biomechanics research and surgical education—applications that traditionally relied on cadavers. Cadaver bones are suboptimal for myriad reasons, including issues of cost, availability, preservation, and inconsistency between specimens. Further, cadaver samples disproportionately represent the elderly, whose bone quality may not be representative of the greater orthopaedic population. The current fourth-generation composite bone models provide an accurate reproduction of the biomechanical properties of human bone when placed under bending, axial, and torsional loads. The combination of glass fiber and epoxy resin components into a single phase has enabled manufacturing by injection molding. The high anatomic fidelity of the cadaver-based molds and negligible shrinkage properties of the epoxy resin results in a process that allows for excellent definition of anatomic detail in the cortical wall and optimized consistency of features between models. Recent biomechanical studies of composites have validated their use as a suitable substitute for cadaver specimens. PMID:24486757

Textural analysis of optical coherence tomography skin images: quantitative differentiation between healthy and cancerous tissues

NASA Astrophysics Data System (ADS)

Adabi, Saba; Conforto, Silvia; Hosseinzadeh, Matin; Noe, Shahryar; Daveluy, Steven; Mehregan, Darius; Nasiriavanaki, Mohammadreza

2017-02-01

Optical Coherence Tomography (OCT) offers real-time high-resolution three-dimensional images of tissue microstructures. In this study, we used OCT skin images acquired from ten volunteers, neither of whom had any skin conditions addressing the features of their anatomic location. OCT segmented images are analyzed based on their optical properties (attenuation coefficient) and textural image features e.g., contrast, correlation, homogeneity, energy, entropy, etc. Utilizing the information and referring to their clinical insight, we aim to make a comprehensive computational model for the healthy skin. The derived parameters represent the OCT microstructural morphology and might provide biological information for generating an atlas of normal skin from different anatomic sites of human skin and may allow for identification of cell microstructural changes in cancer patients. We then compared the parameters of healthy samples with those of abnormal skin and classified them using a linear Support Vector Machines (SVM) with 82% accuracy.

Composite bone models in orthopaedic surgery research and education.

PubMed

Elfar, John; Menorca, Ron Martin Garcia; Reed, Jeffrey Douglas; Stanbury, Spencer

2014-02-01

Composite bone models are increasingly used in orthopaedic biomechanics research and surgical education-applications that traditionally relied on cadavers. Cadaver bones are suboptimal for many reasons, including issues of cost, availability, preservation, and inconsistency between specimens. Further, cadaver samples disproportionately represent the elderly, whose bone quality may not be representative of the greater orthopaedic population. The current fourth-generation composite bone models provide an accurate reproduction of the biomechanical properties of human bone when placed under bending, axial, and torsional loads. The combination of glass fiber and epoxy resin components into a single phase has enabled manufacturing by injection molding. The high level of anatomic fidelity of the cadaver-based molds and negligible shrinkage properties of the epoxy resin results in a process that allows for excellent definition of anatomic detail in the cortical wall and optimized consistency of features between models. Recent biomechanical studies of composites have validated their use as a suitable substitute for cadaver specimens.

Innervation of taste buds revealed with Brainbow-labeling in mouse.

PubMed

Zaidi, Faisal N; Cicchini, Vanessa; Kaufman, Daniel; Ko, Elizabeth; Ko, Abraham; Van Tassel, Heather; Whitehead, Mark C

2016-12-01

Nerve fibers that surround and innervate the taste bud were visualized with inherent fluorescence using Brainbow transgenic mice that were generated by mating the founder line L with nestin-cre mice. Multicolor fluorescence revealed perigemmal fibers as branched within the non-taste epithelium and ending in clusters of multiple rounded swellings surrounding the taste pore. Brainbow-labeling also revealed the morphology and branching pattern of single intragemmal fibers. These taste bud fibers frequently innervated both the peripheral bud, where immature gemmal cells are located, and the central bud, where mature, differentiated cells are located. The fibers typically bore preterminal and terminal swellings, growth cones with filopodia, swellings, and rounded retraction bulbs. These results establish an anatomical substrate for taste nerve fibers to contact and remodel among receptor cells at all stages of their differentiation, an interpretation that was supported by staining with GAP-43, a marker for growing fibers and growth cones. © 2016 Anatomical Society.

Linked exploratory visualizations for uncertain MR spectroscopy data

NASA Astrophysics Data System (ADS)

Feng, David; Kwock, Lester; Lee, Yueh; Taylor, Russell M., II

2010-01-01

We present a system for visualizing magnetic resonance spectroscopy (MRS) data sets. Using MRS, radiologists generate multiple 3D scalar fields of metabolite concentrations within the brain and compare them to anatomical magnetic resonance imaging. By understanding the relationship between metabolic makeup and anatomical structure, radiologists hope to better diagnose and treat tumors and lesions. Our system consists of three linked visualizations: a spatial glyph-based technique we call Scaled Data-Driven Spheres, a parallel coordinates visualization augmented to incorporate uncertainty in the data, and a slice plane for accurate data value extraction. The parallel coordinates visualization uses specialized brush interactions designed to help users identify nontrivial linear relationships between scalar fields. We describe two novel contributions to parallel coordinates visualizations: linear function brushing and new axis construction. Users have discovered significant relationships among metabolites and anatomy by linking interactions between the three visualizations.

Linked Exploratory Visualizations for Uncertain MR Spectroscopy Data

PubMed Central

Feng, David; Kwock, Lester; Lee, Yueh; Taylor, Russell M.

2010-01-01

We present a system for visualizing magnetic resonance spectroscopy (MRS) data sets. Using MRS, radiologists generate multiple 3D scalar fields of metabolite concentrations within the brain and compare them to anatomical magnetic resonance imaging. By understanding the relationship between metabolic makeup and anatomical structure, radiologists hope to better diagnose and treat tumors and lesions. Our system consists of three linked visualizations: a spatial glyph-based technique we call Scaled Data-Driven Spheres, a parallel coordinates visualization augmented to incorporate uncertainty in the data, and a slice plane for accurate data value extraction. The parallel coordinates visualization uses specialized brush interactions designed to help users identify nontrivial linear relationships between scalar fields. We describe two novel contributions to parallel coordinates visualizations: linear function brushing and new axis construction. Users have discovered significant relationships among metabolites and anatomy by linking interactions between the three visualizations. PMID:21152337

Whole-brain activity mapping onto a zebrafish brain atlas.

PubMed

Randlett, Owen; Wee, Caroline L; Naumann, Eva A; Nnaemeka, Onyeka; Schoppik, David; Fitzgerald, James E; Portugues, Ruben; Lacoste, Alix M B; Riegler, Clemens; Engert, Florian; Schier, Alexander F

2015-11-01

In order to localize the neural circuits involved in generating behaviors, it is necessary to assign activity onto anatomical maps of the nervous system. Using brain registration across hundreds of larval zebrafish, we have built an expandable open-source atlas containing molecular labels and definitions of anatomical regions, the Z-Brain. Using this platform and immunohistochemical detection of phosphorylated extracellular signal–regulated kinase (ERK) as a readout of neural activity, we have developed a system to create and contextualize whole-brain maps of stimulus- and behavior-dependent neural activity. This mitogen-activated protein kinase (MAP)-mapping assay is technically simple, and data analysis is completely automated. Because MAP-mapping is performed on freely swimming fish, it is applicable to studies of nearly any stimulus or behavior. Here we demonstrate our high-throughput approach using pharmacological, visual and noxious stimuli, as well as hunting and feeding. The resultant maps outline hundreds of areas associated with behaviors.

From anatomical 'competence' to complex capability. The views and experiences of UK tutors on how we should teach anatomy to medical students.

PubMed

Regan de Bere, Sam; Mattick, Karen

2010-10-01

Developments in clinical education have recently challenged the identity of anatomy teaching and learning, leading to high profile debate over the potential implications for the competence levels of new doctors. However, the emphasis remains on methods of teaching, rather than a review of what well-rounded anatomical learning actually entails, and how teaching can address contemporary learning needs. This paper identifies and addresses some of these issues, drawing on expert views captured in qualitative research with anatomy tutors at twenty different medical schools in the UK. Three main themes emerging from our analysis are described: anatomy as a subject matter, the challenges of teaching or learning anatomy, and the use of teaching methods. We also detail how inductive analysis generated new hypotheses worthy of further consideration. These fall into two key categories: (1) improving anatomy curriculum design and (2) advancing anatomy education research.

A modeling framework for deriving the structural and functional architecture of a short-term memory microcircuit.

PubMed

Fisher, Dimitry; Olasagasti, Itsaso; Tank, David W; Aksay, Emre R F; Goldman, Mark S

2013-09-04

Although many studies have identified neural correlates of memory, relatively little is known about the circuit properties connecting single-neuron physiology to behavior. Here we developed a modeling framework to bridge this gap and identify circuit interactions capable of maintaining short-term memory. Unlike typical studies that construct a phenomenological model and test whether it reproduces select aspects of neuronal data, we directly fit the synaptic connectivity of an oculomotor memory circuit to a broad range of anatomical, electrophysiological, and behavioral data. Simultaneous fits to all data, combined with sensitivity analyses, revealed complementary roles of synaptic and neuronal recruitment thresholds in providing the nonlinear interactions required to generate the observed circuit behavior. This work provides a methodology for identifying the cellular and synaptic mechanisms underlying short-term memory and demonstrates how the anatomical structure of a circuit may belie its functional organization. Copyright © 2013 Elsevier Inc. All rights reserved.

Altered cortical anatomical networks in temporal lobe epilepsy

NASA Astrophysics Data System (ADS)

Lv, Bin; He, Huiguang; Lu, Jingjing; Li, Wenjing; Dai, Dai; Li, Meng; Jin, Zhengyu

2011-03-01

Temporal lobe epilepsy (TLE) is one of the most common epilepsy syndromes with focal seizures generated in the left or right temporal lobes. With the magnetic resonance imaging (MRI), many evidences have demonstrated that the abnormalities in hippocampal volume and the distributed atrophies in cortical cortex. However, few studies have investigated if TLE patients have the alternation in the structural networks. In the present study, we used the cortical thickness to establish the morphological connectivity networks, and investigated the network properties using the graph theoretical methods. We found that all the morphological networks exhibited the small-world efficiency in left TLE, right TLE and normal groups. And the betweenness centrality analysis revealed that there were statistical inter-group differences in the right uncus region. Since the right uncus located at the right temporal lobe, these preliminary evidences may suggest that there are topological alternations of the cortical anatomical networks in TLE, especially for the right TLE.

Vincenc Alexandr Bohdálek (1801-1883): Czech anatomist and neuroscientist of the nineteenth century.

PubMed

Chvátal, Alexandr; Kachlík, David

2017-01-01

Vincenc Alexandr Bohdálek (Vincenz Alexander Bochdalek) was a well-known anatomist and pathologist in the nineteenth century. Today, however, his name is all but forgotten. Bohdálek described a number of anatomical structures; some of them became eponyms. Unfortunately, his findings concerning the innervation of the eye, upper jaw, hard palate, auditory system, and meninges are little known today. This current overview is based on available archival sources and provides an insight into his results in the field of nervous system research, which account for almost half his work. Bohdálek can clearly be considered a pioneer in the field we now call functional anatomy, as he tried to find a physiological explanation for the anatomical and pathological findings he observed. The work and results of this truly outstanding neuroscientist of his time are thus again available to current and future generations of neuroscientists and neuroanatomists.

The ADAMS interactive interpreter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rietscha, E.R.

1990-12-17

The ADAMS (Advanced DAta Management System) project is exploring next generation database technology. Database management does not follow the usual programming paradigm. Instead, the database dictionary provides an additional name space environment that should be interactively created and tested before writing application code. This document describes the implementation and operation of the ADAMS Interpreter, an interactive interface to the ADAMS data dictionary and runtime system. The Interpreter executes individual statements of the ADAMS Interface Language, providing a fast, interactive mechanism to define and access persistent databases. 5 refs.

Prevalence and profile of musculoskeletal injuries in ballet dancers: A systematic review and meta-analysis.

PubMed

Smith, Toby O; Davies, Leigh; de Medici, Akbar; Hakim, Allan; Haddad, Fares; Macgregor, Alex

2016-05-01

To determine the prevalence of musculoskeletal disorders and anatomical regions which are most frequently injured in ballet dancers. Published (AMED, CiNAHL, EMBASE, SPORTDiscus, psycINFO, MEDLINE, the Cochrane Library) and grey literature databases (OpenGrey, the WHO International Clinical Trials Registry Platform, Current Controlled Trials and the UK National Research Register Archive) were searched from their inception to 25th May 2015 for papers presenting data on injury prevalence in ballet dancers. Two reviewers independently identified all eligible papers, data extracted and critically appraised studies. Study appraisal was conducted using the CASP appraisal tool. Pooled prevalence data with 95% confidence intervals were estimated to determine period prevalence of musculoskeletal disorders and anatomical regions affected. Nineteen studies were eligible, reporting 7332 injuries in 2617 ballet dancers. The evidence was moderate in quality. Period prevalence of musculoskeletal injury was 280% (95% CI: 217-343%). The most prevalent musculoskeletal disorders included: hamstring strain (51%), ankle tendinopathy (19%) and generalized low back pain (14%). No papers explored musculoskeletal disorders in retired ballet dancers. Whilst we have identified which regions and what musculoskeletal disorders are commonly seen ballet dancers. The long-term injury impact of musculoskeletal disorders in retired ballet dancers remains unknown. Copyright © 2016 Elsevier Ltd. All rights reserved.

Portal vascular anomalies in Down syndrome: spectrum of clinical presentation and management approach.

PubMed

Golewale, Nazar; Paltiel, Harriet J; Fishman, Steven J; Alomari, Ahmad I

2010-08-01

The occurrence of portal vascular anomalies in Down syndrome has been sporadically reported in the literature. These rare disorders have a wide spectrum of anatomical and clinical presentations. The aim of this communication was to describe the clinical course, imaging features, and management approaches in patients with this association. We conducted a comprehensive search of the databases of the Vascular Anomalies Center and the Department of Radiology at Children's Hospital Boston for patients with Down syndrome and portal vascular anomalies. Medical records and imaging studies of varying modalities were reviewed. Three children with Down syndrome and portal anomalies (portosystemic shunt, simple arterioportal shunt, complex arterioportal shunt) were managed at our institution. The portosystemic shunt was clinically insignificant and resolved without any intervention. The simple arterioportal shunt was successfully treated with embolization. The complex arterioportal shunt was associated with major congenital cardiac defects and the child ultimately expired despite a decrease in the arterioportal shunting after embolization. Three is a wide spectrum of clinical and anatomical features of portal vascular shunts in Down syndrome. The management approach should be tailored based on the severity of symptoms. Percutaneous embolization can offer a safe, effective, and minimally invasive alternative to the surgical approach in selective cases. Copyright 2010 Elsevier Inc. All rights reserved.

A novel 3D shape descriptor for automatic retrieval of anatomical structures from medical images

NASA Astrophysics Data System (ADS)

Nunes, Fátima L. S.; Bergamasco, Leila C. C.; Delmondes, Pedro H.; Valverde, Miguel A. G.; Jackowski, Marcel P.

2017-03-01

Content-based image retrieval (CBIR) aims at retrieving from a database objects that are similar to an object provided by a query, by taking into consideration a set of extracted features. While CBIR has been widely applied in the two-dimensional image domain, the retrieval of3D objects from medical image datasets using CBIR remains to be explored. In this context, the development of descriptors that can capture information specific to organs or structures is desirable. In this work, we focus on the retrieval of two anatomical structures commonly imaged by Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) techniques, the left ventricle of the heart and blood vessels. Towards this aim, we developed the Area-Distance Local Descriptor (ADLD), a novel 3D local shape descriptor that employs mesh geometry information, namely facet area and distance from centroid to surface, to identify shape changes. Because ADLD only considers surface meshes extracted from volumetric medical images, it substantially diminishes the amount of data to be analyzed. A 90% precision rate was obtained when retrieving both convex (left ventricle) and non-convex structures (blood vessels), allowing for detection of abnormalities associated with changes in shape. Thus, ADLD has the potential to aid in the diagnosis of a wide range of vascular and cardiac diseases.

PACS-based interface for 3D anatomical structure visualization and surgical planning

NASA Astrophysics Data System (ADS)

Koehl, Christophe; Soler, Luc; Marescaux, Jacques

2002-05-01

The interpretation of radiological image is routine but it remains a rather difficult task for physicians. It requires complex mental processes, that permit translation from 2D slices into 3D localization and volume determination of visible diseases. An easier and more extensive visualization and exploitation of medical images can be reached through the use of computer-based systems that provide real help from patient admission to post-operative followup. In this way, we have developed a 3D visualization interface linked to a PACS database that allows manipulation and interaction on virtual organs delineated from CT-scan or MRI. This software provides the 3D real-time surface rendering of anatomical structures, an accurate evaluation of volumes and distances and the improvement of radiological image analysis and exam annotation through a negatoscope tool. It also provides a tool for surgical planning allowing the positioning of an interactive laparoscopic instrument and the organ resection. The software system could revolutionize the field of computerized imaging technology. Indeed, it provides a handy and portable tool for pre-operative and intra-operative analysis of anatomy and pathology in various medical fields. This constitutes the first step of the future development of augmented reality and surgical simulation systems.

The AJCC 8th Edition Staging System for Soft Tissue Sarcoma of the Extremities or Trunk: A Cohort Study of the SEER Database.

PubMed

Cates, Justin M M

2018-02-01

Background: The AJCC recently published the 8th edition of its cancer staging system. Significant changes were made to the staging algorithm for soft tissue sarcoma (STS) of the extremities or trunk, including the addition of 2 additional T (size) classifications in lieu of tumor depth and grouping lymph node metastasis (LNM) with distant metastasis as stage IV disease. Whether these changes improve staging system performance is questionable. Patients and Methods: This retrospective cohort analysis of 21,396 adult patients with STS of the extremity or trunk in the SEER database compares the AJCC 8th edition staging system with the 7th edition and a newly proposed staging algorithm using a variety of statistical techniques. The effect of tumor size on disease-specific survival was assessed by flexible, nonlinear Cox proportional hazard regression using restricted cubic splines and fractional polynomials. Results: The slope of covariate-adjusted log hazards for sarcoma-specific survival decreases for tumors >8 cm in greatest dimension, limiting prognostic information contributed by the new T4 classification in the AJCC 8th edition. Anatomic depth independently provides significant prognostic information. LNM is not equivalent to distant, non-nodal metastasis. Based on these findings, an alternative staging system is proposed and demonstrated to outperform both AJCC staging schemes. The analyses presented also disclose no evidence of improved clinical performance of the 8th edition compared with the previous edition. Conclusions: The AJCC 8th edition staging system for STS is no better than the previous 7th edition. Instead, a proposed staging system based on histologic grade, tumor size, and anatomic depth shows significantly higher predictive accuracy, with higher model concordance than either AJCC staging system. Changes to existing staging systems should improve the performance of prognostic models. Until such improvements are documented, AJCC committees should refrain from modifying established staging schemes. Copyright © 2018 by the National Comprehensive Cancer Network.

Pharyngeal Residue Severity Rating Scales Based on Fiberoptic Endoscopic Evaluation of Swallowing: A Systematic Review.

PubMed

Neubauer, Paul D; Hersey, Denise P; Leder, Steven B

2016-06-01

Identification of pharyngeal residue severity located in the valleculae and pyriform sinuses has always been a primary goal during fiberoptic endoscopic evaluation of swallowing (FEES). Pharyngeal residue is a clinical sign of potential prandial aspiration making an accurate description of its severity an important but difficult challenge. A reliable, validated, and generalizable pharyngeal residue severity rating scale for FEES would be beneficial. A systematic review of the published English language literature since 1995 was conducted to determine the quality of existing pharyngeal residue severity rating scales based on FEES. Databases were searched using controlled vocabulary words and synonymous free text words for topics of interest (deglutition disorders, pharyngeal residue, endoscopy, videofluoroscopy, fiberoptic technology, aspiration, etc.) and outcomes of interest (scores, scales, grades, tests, FEES, etc.). Search strategies were adjusted for syntax appropriate for each database/platform. Data sources included MEDLINE (OvidSP 1946-April Week 3 2015), Embase (OvidSP 1974-2015 April 20), Scopus (Elsevier), and the unindexed material in PubMed (NLM/NIH) were searched for relevant articles. Supplementary efforts to identify studies included checking reference lists of articles retrieved. Scales were compared using qualitative properties (sample size, severity definitions, number of raters, and raters' experience and training) and psychometric analyses (randomization, intra- and inter-rater reliability, and construct validity). Seven articles describing pharyngeal residue severity rating scales met inclusion criteria. Six of seven scales had insufficient data to support their use as evidenced by methodological weaknesses with both qualitative properties and psychometric analyses. There is a need for qualitative and psychometrically reliable, validated, and generalizable pharyngeal residue severity rating scales that are anatomically specific, image-based, and easily learned by both novice and experienced clinicians. Only the Yale Pharyngeal Residue Severity Rating Scale, an anatomically defined and image-based tool, met all qualitative and psychometric criteria necessary for a valid, reliable, and generalizable vallecula and pyriform sinus severity rating scale based on FEES.

Engineering anatomically shaped vascularized bone grafts with hASCs and 3D-printed PCL scaffolds.

PubMed

Temple, Joshua P; Hutton, Daphne L; Hung, Ben P; Huri, Pinar Yilgor; Cook, Colin A; Kondragunta, Renu; Jia, Xiaofeng; Grayson, Warren L

2014-12-01

The treatment of large craniomaxillofacial bone defects is clinically challenging due to the limited availability of transplantable autologous bone grafts and the complex geometry of the bones. The ability to regenerate new bone tissues that faithfully replicate the anatomy would revolutionize treatment options. Advances in the field of bone tissue engineering over the past few decades offer promising new treatment alternatives using biocompatible scaffold materials and autologous cells. This approach combined with recent advances in three-dimensional (3D) printing technologies may soon allow the generation of large, bioartificial bone grafts with custom, patient-specific architecture. In this study, we use a custom-built 3D printer to develop anatomically shaped polycaprolactone (PCL) scaffolds with varying internal porosities. These scaffolds are assessed for their ability to support induction of human adipose-derived stem cells (hASCs) to form vasculature and bone, two essential components of functional bone tissue. The development of functional tissues is assessed in vitro and in vivo. Finally, we demonstrate the ability to print large mandibular and maxillary bone scaffolds that replicate fine details extracted from patient's computed tomography scans. The findings of this study illustrate the capabilities and potential of 3D printed scaffolds to be used for engineering autologous, anatomically shaped, vascularized bone grafts. © 2014 Wiley Periodicals, Inc.