Development and evaluation of a crowdsourcing methodology for knowledge base construction: identifying relationships between clinical problems and medications

PubMed Central

Wright, Adam; Laxmisan, Archana; Ottosen, Madelene J; McCoy, Jacob A; Butten, David; Sittig, Dean F

2012-01-01

Objective We describe a novel, crowdsourcing method for generating a knowledge base of problem–medication pairs that takes advantage of manually asserted links between medications and problems. Methods Through iterative review, we developed metrics to estimate the appropriateness of manually entered problem–medication links for inclusion in a knowledge base that can be used to infer previously unasserted links between problems and medications. Results Clinicians manually linked 231 223 medications (55.30% of prescribed medications) to problems within the electronic health record, generating 41 203 distinct problem–medication pairs, although not all were accurate. We developed methods to evaluate the accuracy of the pairs, and after limiting the pairs to those meeting an estimated 95% appropriateness threshold, 11 166 pairs remained. The pairs in the knowledge base accounted for 183 127 total links asserted (76.47% of all links). Retrospective application of the knowledge base linked 68 316 medications not previously linked by a clinician to an indicated problem (36.53% of unlinked medications). Expert review of the combined knowledge base, including inferred and manually linked problem–medication pairs, found a sensitivity of 65.8% and a specificity of 97.9%. Conclusion Crowdsourcing is an effective, inexpensive method for generating a knowledge base of problem–medication pairs that is automatically mapped to local terminologies, up-to-date, and reflective of local prescribing practices and trends. PMID:22582202

Effects of gross motor function and manual function levels on performance-based ADL motor skills of children with spastic cerebral palsy.

PubMed

Park, Myoung-Ok

2017-02-01

[Purpose] The purpose of this study was to determine effects of Gross Motor Function Classification System and Manual Ability Classification System levels on performance-based motor skills of children with spastic cerebral palsy. [Subjects and Methods] Twenty-three children with cerebral palsy were included. The Assessment of Motor and Process Skills was used to evaluate performance-based motor skills in daily life. Gross motor function was assessed using Gross Motor Function Classification Systems, and manual function was measured using the Manual Ability Classification System. [Results] Motor skills in daily activities were significantly different on Gross Motor Function Classification System level and Manual Ability Classification System level. According to the results of multiple regression analysis, children categorized as Gross Motor Function Classification System level III scored lower in terms of performance based motor skills than Gross Motor Function Classification System level I children. Also, when analyzed with respect to Manual Ability Classification System level, level II was lower than level I, and level III was lower than level II in terms of performance based motor skills. [Conclusion] The results of this study indicate that performance-based motor skills differ among children categorized based on Gross Motor Function Classification System and Manual Ability Classification System levels of cerebral palsy.

Comparison of liver volumetry on contrast‐enhanced CT images: one semiautomatic and two automatic approaches

PubMed Central

Cai, Wei; He, Baochun; Fang, Chihua

2016-01-01

This study was to evaluate the accuracy, consistency, and efficiency of three liver volumetry methods— one interactive method, an in‐house‐developed 3D medical Image Analysis (3DMIA) system, one automatic active shape model (ASM)‐based segmentation, and one automatic probabilistic atlas (PA)‐guided segmentation method on clinical contrast‐enhanced CT images. Forty‐two datasets, including 27 normal liver and 15 space‐occupying liver lesion patients, were retrospectively included in this study. The three methods — one semiautomatic 3DMIA, one automatic ASM‐based, and one automatic PA‐based liver volumetry — achieved an accuracy with VD (volume difference) of −1.69%,−2.75%, and 3.06% in the normal group, respectively, and with VD of −3.20%,−3.35%, and 4.14% in the space‐occupying lesion group, respectively. However, the three methods achieved an efficiency of 27.63 mins, 1.26 mins, 1.18 mins on average, respectively, compared with the manual volumetry, which took 43.98 mins. The high intraclass correlation coefficient between the three methods and the manual method indicated an excellent agreement on liver volumetry. Significant differences in segmentation time were observed between the three methods (3DMIA, ASM, and PA) and the manual volumetry (p<0.001), as well as between the automatic volumetries (ASM and PA) and the semiautomatic volumetry (3DMIA) (p<0.001). The semiautomatic interactive 3DMIA, automatic ASM‐based, and automatic PA‐based liver volumetry agreed well with manual gold standard in both the normal liver group and the space‐occupying lesion group. The ASM‐ and PA‐based automatic segmentation have better efficiency in clinical use. PACS number(s): 87.55.‐x PMID:27929487

Bone marrow cavity segmentation using graph-cuts with wavelet-based texture feature.

PubMed

Shigeta, Hironori; Mashita, Tomohiro; Kikuta, Junichi; Seno, Shigeto; Takemura, Haruo; Ishii, Masaru; Matsuda, Hideo

2017-10-01

Emerging bioimaging technologies enable us to capture various dynamic cellular activities [Formula: see text]. As large amounts of data are obtained these days and it is becoming unrealistic to manually process massive number of images, automatic analysis methods are required. One of the issues for automatic image segmentation is that image-taking conditions are variable. Thus, commonly, many manual inputs are required according to each image. In this paper, we propose a bone marrow cavity (BMC) segmentation method for bone images as BMC is considered to be related to the mechanism of bone remodeling, osteoporosis, and so on. To reduce manual inputs to segment BMC, we classified the texture pattern using wavelet transformation and support vector machine. We also integrated the result of texture pattern classification into the graph-cuts-based image segmentation method because texture analysis does not consider spatial continuity. Our method is applicable to a particular frame in an image sequence in which the condition of fluorescent material is variable. In the experiment, we evaluated our method with nine types of mother wavelets and several sets of scale parameters. The proposed method with graph-cuts and texture pattern classification performs well without manual inputs by a user.

Battery Calendar Life Estimator Manual Modeling and Simulation

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

Jon P. Christophersen; Ira Bloom; Ed Thomas

2012-10-01

The Battery Life Estimator (BLE) Manual has been prepared to assist developers in their efforts to estimate the calendar life of advanced batteries for automotive applications. Testing requirements and procedures are defined by the various manuals previously published under the United States Advanced Battery Consortium (USABC). The purpose of this manual is to describe and standardize a method for estimating calendar life based on statistical models and degradation data acquired from typical USABC battery testing.

Battery Life Estimator Manual Linear Modeling and Simulation

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

Jon P. Christophersen; Ira Bloom; Ed Thomas

2009-08-01

The Battery Life Estimator (BLE) Manual has been prepared to assist developers in their efforts to estimate the calendar life of advanced batteries for automotive applications. Testing requirements and procedures are defined by the various manuals previously published under the United States Advanced Battery Consortium (USABC). The purpose of this manual is to describe and standardize a method for estimating calendar life based on statistical models and degradation data acquired from typical USABC battery testing.

Development and Evaluation of a Manual for Extended Brief Intervention for Alcohol Misuse for Adults with Mild to Moderate Intellectual Disabilities Living in the Community: The EBI-LD Study Manual

ERIC Educational Resources Information Center

Kouimtsidis, Christos; Scior, Katrina; Baio, Gianluca; Hunter, Rachael; Pezzoni, Vittoria; Hassiotis, Angela

2017-01-01

Background: Extended brief interventions for alcohol misuse are effective in the general population. The process of manualising the first ever such intervention for people with mild to moderate intellectual disabilities in the UK is the focus of this study. Methods: The manual was an adaptation of existing manuals based on Motivational Enhancement…

MEthods of ASsessing blood pressUre: identifying thReshold and target valuEs (MeasureBP): a review & study protocol.

PubMed

Blom, Kimberly C; Farina, Sasha; Gomez, Yessica-Haydee; Campbell, Norm R C; Hemmelgarn, Brenda R; Cloutier, Lyne; McKay, Donald W; Dawes, Martin; Tobe, Sheldon W; Bolli, Peter; Gelfer, Mark; McLean, Donna; Bartlett, Gillian; Joseph, Lawrence; Featherstone, Robin; Schiffrin, Ernesto L; Daskalopoulou, Stella S

2015-04-01

Despite progress in automated blood pressure measurement (BPM) technology, there is limited research linking hard outcomes to automated office BPM (OBPM) treatment targets and thresholds. Equivalences for automated BPM devices have been estimated from approximations of standardized manual measurements of 140/90 mmHg. Until outcome-driven targets and thresholds become available for automated measurement methods, deriving evidence-based equivalences between automated methods and standardized manual OBPM is the next best solution. The MeasureBP study group was initiated by the Canadian Hypertension Education Program to close this critical knowledge gap. MeasureBP aims to define evidence-based equivalent values between standardized manual OBPM and automated BPM methods by synthesizing available evidence using a systematic review and individual subject-level data meta-analyses. This manuscript provides a review of the literature and MeasureBP study protocol. These results will lay the evidenced-based foundation to resolve uncertainties within blood pressure guidelines which, in turn, will improve the management of hypertension.

Applications of "Integrated Data Viewer'' (IDV) in the classroom

NASA Astrophysics Data System (ADS)

Nogueira, R.; Cutrim, E. M.

2006-06-01

Conventionally, weather products utilized in synoptic meteorology reduce phenomena occurring in four dimensions to a 2-dimensional form. This constitutes a road-block for non-atmospheric-science majors who need to take meteorology as a non-mathematical and complementary course to their major programs. This research examines the use of Integrated Data Viewer-IDV as a teaching tool, as it allows a 4-dimensional representation of weather products. IDV was tested in the teaching of synoptic meteorology, weather analysis, and weather map interpretation to non-science students in the laboratory sessions of an introductory meteorology class at Western Michigan University. Comparison of student exam scores according to the laboratory teaching techniques, i.e., traditional lab manual and IDV was performed for short- and long-term learning. Results of the statistical analysis show that the Fall 2004 students in the IDV-based lab session retained learning. However, in the Spring 2005 the exam scores did not reflect retention in learning when compared with IDV-based and MANUAL-based lab scores (short term learning, i.e., exam taken one week after the lab exercise). Testing the long-term learning, seven weeks between the two exams in the Spring 2005, show no statistically significant difference between IDV-based group scores and MANUAL-based group scores. However, the IDV group obtained exam score average slightly higher than the MANUAL group. Statistical testing of the principal hypothesis in this study, leads to the conclusion that the IDV-based method did not prove to be a better teaching tool than the traditional paper-based method. Future studies could potentially find significant differences in the effectiveness of both manual and IDV methods if the conditions had been more controlled. That is, students in the control group should not be exposed to the weather analysis using IDV during lecture.

Reproducible segmentation of white matter hyperintensities using a new statistical definition.

PubMed

Damangir, Soheil; Westman, Eric; Simmons, Andrew; Vrenken, Hugo; Wahlund, Lars-Olof; Spulber, Gabriela

2017-06-01

We present a method based on a proposed statistical definition of white matter hyperintensities (WMH), which can work with any combination of conventional magnetic resonance (MR) sequences without depending on manually delineated samples. T1-weighted, T2-weighted, FLAIR, and PD sequences acquired at 1.5 Tesla from 119 subjects from the Kings Health Partners-Dementia Case Register (healthy controls, mild cognitive impairment, Alzheimer's disease) were used. The segmentation was performed using a proposed definition for WMH based on the one-tailed Kolmogorov-Smirnov test. The presented method was verified, given all possible combinations of input sequences, against manual segmentations and a high similarity (Dice 0.85-0.91) was observed. Comparing segmentations with different input sequences to one another also yielded a high similarity (Dice 0.83-0.94) that exceeded intra-rater similarity (Dice 0.75-0.91). We compared the results with those of other available methods and showed that the segmentation based on the proposed definition has better accuracy and reproducibility in the test dataset used. Overall, the presented definition is shown to produce accurate results with higher reproducibility than manual delineation. This approach can be an alternative to other manual or automatic methods not only because of its accuracy, but also due to its good reproducibility.

Computer aided manual validation of mass spectrometry-based proteomic data.

PubMed

Curran, Timothy G; Bryson, Bryan D; Reigelhaupt, Michael; Johnson, Hannah; White, Forest M

2013-06-15

Advances in mass spectrometry-based proteomic technologies have increased the speed of analysis and the depth provided by a single analysis. Computational tools to evaluate the accuracy of peptide identifications from these high-throughput analyses have not kept pace with technological advances; currently the most common quality evaluation methods are based on statistical analysis of the likelihood of false positive identifications in large-scale data sets. While helpful, these calculations do not consider the accuracy of each identification, thus creating a precarious situation for biologists relying on the data to inform experimental design. Manual validation is the gold standard approach to confirm accuracy of database identifications, but is extremely time-intensive. To palliate the increasing time required to manually validate large proteomic datasets, we provide computer aided manual validation software (CAMV) to expedite the process. Relevant spectra are collected, catalogued, and pre-labeled, allowing users to efficiently judge the quality of each identification and summarize applicable quantitative information. CAMV significantly reduces the burden associated with manual validation and will hopefully encourage broader adoption of manual validation in mass spectrometry-based proteomics. Copyright © 2013 Elsevier Inc. All rights reserved.

Automatic and manual segmentation of healthy retinas using high-definition optical coherence tomography.

PubMed

Golbaz, Isabelle; Ahlers, Christian; Goesseringer, Nina; Stock, Geraldine; Geitzenauer, Wolfgang; Prünte, Christian; Schmidt-Erfurth, Ursula Margarethe

2011-03-01

This study compared automatic- and manual segmentation modalities in the retina of healthy eyes using high-definition optical coherence tomography (HD-OCT). Twenty retinas in 20 healthy individuals were examined using an HD-OCT system (Carl Zeiss Meditec, Inc.). Three-dimensional imaging was performed with an axial resolution of 6 μm at a maximum scanning speed of 25,000 A-scans/second. Volumes of 6 × 6 × 2 mm were scanned. Scans were analysed using a matlab-based algorithm and a manual segmentation software system (3D-Doctor). The volume values calculated by the two methods were compared. Statistical analysis revealed a high correlation between automatic and manual modes of segmentation. The automatic mode of measuring retinal volume and the corresponding three-dimensional images provided similar results to the manual segmentation procedure. Both methods were able to visualize retinal and subretinal features accurately. This study compared two methods of assessing retinal volume using HD-OCT scans in healthy retinas. Both methods were able to provide realistic volumetric data when applied to raster scan sets. Manual segmentation methods represent an adequate tool with which to control automated processes and to identify clinically relevant structures, whereas automatic procedures will be needed to obtain data in larger patient populations. © 2009 The Authors. Journal compilation © 2009 Acta Ophthalmol.

Manualized Family-Based Treatment for Anorexia Nervosa: A Case Series.

ERIC Educational Resources Information Center

Le Grange, Daniel; Binford, Roslyn; Loeb, Katharine L.

2005-01-01

Objective: The purpose of this study was to describe a case series of children and adolescents (mean age = 14.5 years, SD = 2.3; range 9-18) with anorexia nervosa who received manualized family-based treatment for their eating disorder. Method: Forty-five patients with anorexia nervosa were compared pre- and post-treatment on weight and menstrual…

Negation’s Not Solved: Generalizability Versus Optimizability in Clinical Natural Language Processing

PubMed Central

Wu, Stephen; Miller, Timothy; Masanz, James; Coarr, Matt; Halgrim, Scott; Carrell, David; Clark, Cheryl

2014-01-01

A review of published work in clinical natural language processing (NLP) may suggest that the negation detection task has been “solved.” This work proposes that an optimizable solution does not equal a generalizable solution. We introduce a new machine learning-based Polarity Module for detecting negation in clinical text, and extensively compare its performance across domains. Using four manually annotated corpora of clinical text, we show that negation detection performance suffers when there is no in-domain development (for manual methods) or training data (for machine learning-based methods). Various factors (e.g., annotation guidelines, named entity characteristics, the amount of data, and lexical and syntactic context) play a role in making generalizability difficult, but none completely explains the phenomenon. Furthermore, generalizability remains challenging because it is unclear whether to use a single source for accurate data, combine all sources into a single model, or apply domain adaptation methods. The most reliable means to improve negation detection is to manually annotate in-domain training data (or, perhaps, manually modify rules); this is a strategy for optimizing performance, rather than generalizing it. These results suggest a direction for future work in domain-adaptive and task-adaptive methods for clinical NLP. PMID:25393544

Brain tumor segmentation in MR slices using improved GrowCut algorithm

NASA Astrophysics Data System (ADS)

Ji, Chunhong; Yu, Jinhua; Wang, Yuanyuan; Chen, Liang; Shi, Zhifeng; Mao, Ying

2015-12-01

The detection of brain tumor from MR images is very significant for medical diagnosis and treatment. However, the existing methods are mostly based on manual or semiautomatic segmentation which are awkward when dealing with a large amount of MR slices. In this paper, a new fully automatic method for the segmentation of brain tumors in MR slices is presented. Based on the hypothesis of the symmetric brain structure, the method improves the interactive GrowCut algorithm by further using the bounding box algorithm in the pre-processing step. More importantly, local reflectional symmetry is used to make up the deficiency of the bounding box method. After segmentation, 3D tumor image is reconstructed. We evaluate the accuracy of the proposed method on MR slices with synthetic tumors and actual clinical MR images. Result of the proposed method is compared with the actual position of simulated 3D tumor qualitatively and quantitatively. In addition, our automatic method produces equivalent performance as manual segmentation and the interactive GrowCut with manual interference while providing fully automatic segmentation.

Impervious surface mapping with Quickbird imagery

PubMed Central

Lu, Dengsheng; Hetrick, Scott; Moran, Emilio

2010-01-01

This research selects two study areas with different urban developments, sizes, and spatial patterns to explore the suitable methods for mapping impervious surface distribution using Quickbird imagery. The selected methods include per-pixel based supervised classification, segmentation-based classification, and a hybrid method. A comparative analysis of the results indicates that per-pixel based supervised classification produces a large number of “salt-and-pepper” pixels, and segmentation based methods can significantly reduce this problem. However, neither method can effectively solve the spectral confusion of impervious surfaces with water/wetland and bare soils and the impacts of shadows. In order to accurately map impervious surface distribution from Quickbird images, manual editing is necessary and may be the only way to extract impervious surfaces from the confused land covers and the shadow problem. This research indicates that the hybrid method consisting of thresholding techniques, unsupervised classification and limited manual editing provides the best performance. PMID:21643434

Haptic exploratory behavior during object discrimination: a novel automatic annotation method.

PubMed

Jansen, Sander E M; Bergmann Tiest, Wouter M; Kappers, Astrid M L

2015-01-01

In order to acquire information concerning the geometry and material of handheld objects, people tend to execute stereotypical hand movement patterns called haptic Exploratory Procedures (EPs). Manual annotation of haptic exploration trials with these EPs is a laborious task that is affected by subjectivity, attentional lapses, and viewing angle limitations. In this paper we propose an automatic EP annotation method based on position and orientation data from motion tracking sensors placed on both hands and inside a stimulus. A set of kinematic variables is computed from these data and compared to sets of predefined criteria for each of four EPs. Whenever all criteria for a specific EP are met, it is assumed that that particular hand movement pattern was performed. This method is applied to data from an experiment where blindfolded participants haptically discriminated between objects differing in hardness, roughness, volume, and weight. In order to validate the method, its output is compared to manual annotation based on video recordings of the same trials. Although mean pairwise agreement is less between human-automatic pairs than between human-human pairs (55.7% vs 74.5%), the proposed method performs much better than random annotation (2.4%). Furthermore, each EP is linked to a specific object property for which it is optimal (e.g., Lateral Motion for roughness). We found that the percentage of trials where the expected EP was found does not differ between manual and automatic annotation. For now, this method cannot yet completely replace a manual annotation procedure. However, it could be used as a starting point that can be supplemented by manual annotation.

Tree and brush control for county road right-of-way.

DOT National Transportation Integrated Search

2002-10-01

This manual summarizes the roadside tree and brush control methods used by all of Iowa's 99 : counties. It is based on interviews conducted in Spring 2002 with county engineers, roadside : managers and others. The target audience of this manual is th...

Semiautomated Device for Batch Extraction of Metabolites from Tissue Samples

PubMed Central

2012-01-01

Metabolomics has become a mainstream analytical strategy for investigating metabolism. The quality of data derived from these studies is proportional to the consistency of the sample preparation. Although considerable research has been devoted to finding optimal extraction protocols, most of the established methods require extensive sample handling. Manual sample preparation can be highly effective in the hands of skilled technicians, but an automated tool for purifying metabolites from complex biological tissues would be of obvious utility to the field. Here, we introduce the semiautomated metabolite batch extraction device (SAMBED), a new tool designed to simplify metabolomics sample preparation. We discuss SAMBED’s design and show that SAMBED-based extractions are of comparable quality to extracts produced through traditional methods (13% mean coefficient of variation from SAMBED versus 16% from manual extractions). Moreover, we show that aqueous SAMBED-based methods can be completed in less than a quarter of the time required for manual extractions. PMID:22292466

A semiautomatic CT-based ensemble segmentation of lung tumors: comparison with oncologists' delineations and with the surgical specimen.

PubMed

Rios Velazquez, Emmanuel; Aerts, Hugo J W L; Gu, Yuhua; Goldgof, Dmitry B; De Ruysscher, Dirk; Dekker, Andre; Korn, René; Gillies, Robert J; Lambin, Philippe

2012-11-01

To assess the clinical relevance of a semiautomatic CT-based ensemble segmentation method, by comparing it to pathology and to CT/PET manual delineations by five independent radiation oncologists in non-small cell lung cancer (NSCLC). For 20 NSCLC patients (stages Ib-IIIb) the primary tumor was delineated manually on CT/PET scans by five independent radiation oncologists and segmented using a CT based semi-automatic tool. Tumor volume and overlap fractions between manual and semiautomatic-segmented volumes were compared. All measurements were correlated with the maximal diameter on macroscopic examination of the surgical specimen. Imaging data are available on www.cancerdata.org. High overlap fractions were observed between the semi-automatically segmented volumes and the intersection (92.5±9.0, mean±SD) and union (94.2±6.8) of the manual delineations. No statistically significant differences in tumor volume were observed between the semiautomatic segmentation (71.4±83.2 cm(3), mean±SD) and manual delineations (81.9±94.1 cm(3); p=0.57). The maximal tumor diameter of the semiautomatic-segmented tumor correlated strongly with the macroscopic diameter of the primary tumor (r=0.96). Semiautomatic segmentation of the primary tumor on CT demonstrated high agreement with CT/PET manual delineations and strongly correlated with the macroscopic diameter considered as the "gold standard". This method may be used routinely in clinical practice and could be employed as a starting point for treatment planning, target definition in multi-center clinical trials or for high throughput data mining research. This method is particularly suitable for peripherally located tumors. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Comparative study of Sperm Motility Analysis System and conventional microscopic semen analysis

PubMed Central

KOMORI, KAZUHIKO; ISHIJIMA, SUMIO; TANJAPATKUL, PHANU; FUJITA, KAZUTOSHI; MATSUOKA, YASUHIRO; TAKAO, TETSUYA; MIYAGAWA, YASUSHI; TAKADA, SHINGO; OKUYAMA, AKIHIKO

2006-01-01

Background and Aim:  Conventional manual sperm analysis still shows variations in structure, process and outcome although World Health Organization (WHO) guidelines present an appropriate method for sperm analysis. In the present study a new system for sperm analysis, Sperm Motility Analysis System (SMAS), was compared with manual semen analysis based on WHO guidelines. Materials and methods:  Samples from 30 infertility patients and 21 healthy volunteers were subjected to manual microscopic analysis and SMAS analysis, simultaneously. We compared these two methods with respect to sperm concentration and percent motility. Results:  Sperm concentrations obtained by SMAS (Csmas) and manual microscopic analyses on WHO guidelines (Cwho) were strongly correlated (Cwho = 1.325 × Csmas; r = 0.95, P < 0.001). If we excluded subjects with Csmas values >30 × 106 sperm/mL, the results were more similar (Cwho = 1.022 × Csmas; r = 0.81, P < 0.001). Percent motility obtained by SMAS (Msmas) and manual analysis on WHO guidelines (Mwho) were strongly correlated (Mwho = 1.214 × Msmas; r = 0.89, P < 0.001). Conclusions:  The data indicate that the results of SMAS and those of manual microscopic sperm analyses based on WHO guidelines are strongly correlated. SMAS is therefore a promising system for sperm analysis. (Reprod Med Biol 2006; 5: 195–200) PMID:29662398

Battery Test Manual For Plug-In Hybrid Electric Vehicles

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

Jeffrey R. Belt

2010-09-01

This battery test procedure manual was prepared for the United States Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy (EERE), Vehicle Technologies Program. It is based on technical targets established for energy storage development projects aimed at meeting system level DOE goals for Plug-in Hybrid Electric Vehicles (PHEV). The specific procedures defined in this manual support the performance and life characterization of advanced battery devices under development for PHEV’s. However, it does share some methods described in the previously published battery test manual for power-assist hybrid electric vehicles. Due to the complexity of some of the proceduresmore » and supporting analysis, a revision including some modifications and clarifications of these procedures is expected. As in previous battery and capacitor test manuals, this version of the manual defines testing methods for full-size battery systems, along with provisions for scaling these tests for modules, cells or other subscale level devices.« less

Battery Test Manual For Plug-In Hybrid Electric Vehicles

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

Jeffrey R. Belt

2010-12-01

This battery test procedure manual was prepared for the United States Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy (EERE), Vehicle Technologies Program. It is based on technical targets established for energy storage development projects aimed at meeting system level DOE goals for Plug-in Hybrid Electric Vehicles (PHEV). The specific procedures defined in this manual support the performance and life characterization of advanced battery devices under development for PHEV’s. However, it does share some methods described in the previously published battery test manual for power-assist hybrid electric vehicles. Due to the complexity of some of the proceduresmore » and supporting analysis, a revision including some modifications and clarifications of these procedures is expected. As in previous battery and capacitor test manuals, this version of the manual defines testing methods for full-size battery systems, along with provisions for scaling these tests for modules, cells or other subscale level devices.« less

Viscous wing theory development. Volume 2: GRUMWING computer program user's manual

NASA Technical Reports Server (NTRS)

Chow, R. R.; Ogilvie, P. L.

1986-01-01

This report is a user's manual which describes the operation of the computer program, GRUMWING. The program computes the viscous transonic flow over three-dimensional wings using a boundary layer type viscid-inviscid interaction approach. The inviscid solution is obtained by an approximate factorization (AFZ)method for the full potential equation. The boundary layer solution is based on integral entrainment methods.

WE-AB-BRA-05: Fully Automatic Segmentation of Male Pelvic Organs On CT Without Manual Intervention

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

Gao, Y; Lian, J; Chen, R

Purpose: We aim to develop a fully automatic tool for accurate contouring of major male pelvic organs in CT images for radiotherapy without any manual initialization, yet still achieving superior performance than the existing tools. Methods: A learning-based 3D deformable shape model was developed for automatic contouring. Specifically, we utilized a recent machine learning method, random forest, to jointly learn both image regressor and classifier for each organ. In particular, the image regressor is trained to predict the 3D displacement from each vertex of the 3D shape model towards the organ boundary based on the local image appearance around themore » location of this vertex. The predicted 3D displacements are then used to drive the 3D shape model towards the target organ. Once the shape model is deformed close to the target organ, it is further refined by an organ likelihood map estimated by the learned classifier. As the organ likelihood map provides good guideline for the organ boundary, the precise contouring Result could be achieved, by deforming the 3D shape model locally to fit boundaries in the organ likelihood map. Results: We applied our method to 29 previously-treated prostate cancer patients, each with one planning CT scan. Compared with manually delineated pelvic organs, our method obtains overlap ratios of 85.2%±3.74% for the prostate, 94.9%±1.62% for the bladder, and 84.7%±1.97% for the rectum, respectively. Conclusion: This work demonstrated feasibility of a novel machine-learning based approach for accurate and automatic contouring of major male pelvic organs. It shows the potential to replace the time-consuming and inconsistent manual contouring in the clinic. Also, compared with the existing works, our method is more accurate and also efficient since it does not require any manual intervention, such as manual landmark placement. Moreover, our method obtained very similar contouring results as the clinical experts. Project is partially support by a grant from NCI 1R01CA140413.« less

Comparison of manual and automatic techniques for substriatal segmentation in 11C-raclopride high-resolution PET studies.

PubMed

Johansson, Jarkko; Alakurtti, Kati; Joutsa, Juho; Tohka, Jussi; Ruotsalainen, Ulla; Rinne, Juha O

2016-10-01

The striatum is the primary target in regional C-raclopride-PET studies, and despite its small volume, it contains several functional and anatomical subregions. The outcome of the quantitative dopamine receptor study using C-raclopride-PET depends heavily on the quality of the region-of-interest (ROI) definition of these subregions. The aim of this study was to evaluate subregional analysis techniques because new approaches have emerged, but have not yet been compared directly. In this paper, we compared manual ROI delineation with several automatic methods. The automatic methods used either direct clustering of the PET image or individualization of chosen brain atlases on the basis of MRI or PET image normalization. State-of-the-art normalization methods and atlases were applied, including those provided in the FreeSurfer, Statistical Parametric Mapping8, and FSL software packages. Evaluation of the automatic methods was based on voxel-wise congruity with the manual delineations and the test-retest variability and reliability of the outcome measures using data from seven healthy male participants who were scanned twice with C-raclopride-PET on the same day. The results show that both manual and automatic methods can be used to define striatal subregions. Although most of the methods performed well with respect to the test-retest variability and reliability of binding potential, the smallest average test-retest variability and SEM were obtained using a connectivity-based atlas and PET normalization (test-retest variability=4.5%, SEM=0.17). The current state-of-the-art automatic ROI methods can be considered good alternatives for subjective and laborious manual segmentation in C-raclopride-PET studies.

Peak Detection Method Evaluation for Ion Mobility Spectrometry by Using Machine Learning Approaches

PubMed Central

Hauschild, Anne-Christin; Kopczynski, Dominik; D’Addario, Marianna; Baumbach, Jörg Ingo; Rahmann, Sven; Baumbach, Jan

2013-01-01

Ion mobility spectrometry with pre-separation by multi-capillary columns (MCC/IMS) has become an established inexpensive, non-invasive bioanalytics technology for detecting volatile organic compounds (VOCs) with various metabolomics applications in medical research. To pave the way for this technology towards daily usage in medical practice, different steps still have to be taken. With respect to modern biomarker research, one of the most important tasks is the automatic classification of patient-specific data sets into different groups, healthy or not, for instance. Although sophisticated machine learning methods exist, an inevitable preprocessing step is reliable and robust peak detection without manual intervention. In this work we evaluate four state-of-the-art approaches for automated IMS-based peak detection: local maxima search, watershed transformation with IPHEx, region-merging with VisualNow, and peak model estimation (PME). We manually generated a gold standard with the aid of a domain expert (manual) and compare the performance of the four peak calling methods with respect to two distinct criteria. We first utilize established machine learning methods and systematically study their classification performance based on the four peak detectors’ results. Second, we investigate the classification variance and robustness regarding perturbation and overfitting. Our main finding is that the power of the classification accuracy is almost equally good for all methods, the manually created gold standard as well as the four automatic peak finding methods. In addition, we note that all tools, manual and automatic, are similarly robust against perturbations. However, the classification performance is more robust against overfitting when using the PME as peak calling preprocessor. In summary, we conclude that all methods, though small differences exist, are largely reliable and enable a wide spectrum of real-world biomedical applications. PMID:24957992

Peak detection method evaluation for ion mobility spectrometry by using machine learning approaches.

PubMed

Hauschild, Anne-Christin; Kopczynski, Dominik; D'Addario, Marianna; Baumbach, Jörg Ingo; Rahmann, Sven; Baumbach, Jan

2013-04-16

Ion mobility spectrometry with pre-separation by multi-capillary columns (MCC/IMS) has become an established inexpensive, non-invasive bioanalytics technology for detecting volatile organic compounds (VOCs) with various metabolomics applications in medical research. To pave the way for this technology towards daily usage in medical practice, different steps still have to be taken. With respect to modern biomarker research, one of the most important tasks is the automatic classification of patient-specific data sets into different groups, healthy or not, for instance. Although sophisticated machine learning methods exist, an inevitable preprocessing step is reliable and robust peak detection without manual intervention. In this work we evaluate four state-of-the-art approaches for automated IMS-based peak detection: local maxima search, watershed transformation with IPHEx, region-merging with VisualNow, and peak model estimation (PME).We manually generated Metabolites 2013, 3 278 a gold standard with the aid of a domain expert (manual) and compare the performance of the four peak calling methods with respect to two distinct criteria. We first utilize established machine learning methods and systematically study their classification performance based on the four peak detectors' results. Second, we investigate the classification variance and robustness regarding perturbation and overfitting. Our main finding is that the power of the classification accuracy is almost equally good for all methods, the manually created gold standard as well as the four automatic peak finding methods. In addition, we note that all tools, manual and automatic, are similarly robust against perturbations. However, the classification performance is more robust against overfitting when using the PME as peak calling preprocessor. In summary, we conclude that all methods, though small differences exist, are largely reliable and enable a wide spectrum of real-world biomedical applications.

Aircraft noise prediction program user's manual

NASA Technical Reports Server (NTRS)

Gillian, R. E.

1982-01-01

The Aircraft Noise Prediction Program (ANOPP) predicts aircraft noise with the best methods available. This manual is designed to give the user an understanding of the capabilities of ANOPP and to show how to formulate problems and obtain solutions by using these capabilities. Sections within the manual document basic ANOPP concepts, ANOPP usage, ANOPP functional modules, ANOPP control statement procedure library, and ANOPP permanent data base. appendixes to the manual include information on preparing job decks for the operating systems in use, error diagnostics and recovery techniques, and a glossary of ANOPP terms.

Automatic sentence extraction for the detection of scientific paper relations

NASA Astrophysics Data System (ADS)

Sibaroni, Y.; Prasetiyowati, S. S.; Miftachudin, M.

2018-03-01

The relations between scientific papers are very useful for researchers to see the interconnection between scientific papers quickly. By observing the inter-article relationships, researchers can identify, among others, the weaknesses of existing research, performance improvements achieved to date, and tools or data typically used in research in specific fields. So far, methods that have been developed to detect paper relations include machine learning and rule-based methods. However, a problem still arises in the process of sentence extraction from scientific paper documents, which is still done manually. This manual process causes the detection of scientific paper relations longer and inefficient. To overcome this problem, this study performs an automatic sentences extraction while the paper relations are identified based on the citation sentence. The performance of the built system is then compared with that of the manual extraction system. The analysis results suggested that the automatic sentence extraction indicates a very high level of performance in the detection of paper relations, which is close to that of manual sentence extraction.

Bridging the gap between the science and service of HIV prevention: transferring effective research-based HIV prevention interventions to community AIDS service providers.

PubMed Central

Kelly, J A; Somlai, A M; DiFranceisco, W J; Otto-Salaj, L L; McAuliffe, T L; Hackl, K L; Heckman, T G; Holtgrave, D R; Rompa, D

2000-01-01

OBJECTIVES: AIDS service organizations (ASOs) rarely have access to the information needed to implement research-based HIV prevention interventions for their clients. We compared the effectiveness of 3 dissemination strategies for transferring HIV prevention models from the research arena to community providers of HIV prevention services. METHODS: Interviews were conducted with the directors of 74 ASOs to assess current HIV prevention services. ASOs were randomized to programs that provided (1) technical assistance manuals describing how to implement research-based HIV prevention interventions, (2) manuals plus a staff training workshop on how to conduct the implementation, or (3) manuals, the training workshop, and follow-up telephone consultation calls. Follow-up interviews determined whether the intervention model had been adopted. RESULTS: The dissemination package that provided ASOs with implementation manuals, staff training workshops, and follow-up consultation resulted in more frequent adoption and use of the research-based HIV prevention intervention for gay men, women, and other client populations. CONCLUSIONS: Strategies are needed to quickly transfer research-based HIV prevention methods to community providers of HIV prevention services. Active collaboration between researchers and service agencies results in more successful program adoption than distribution of implementation packages alone. PMID:10897186

Computer-aided target tracking in motion analysis studies

NASA Astrophysics Data System (ADS)

Burdick, Dominic C.; Marcuse, M. L.; Mislan, J. D.

1990-08-01

Motion analysis studies require the precise tracking of reference objects in sequential scenes. In a typical situation, events of interest are captured at high frame rates using special cameras, and selected objects or targets are tracked on a frame by frame basis to provide necessary data for motion reconstruction. Tracking is usually done using manual methods which are slow and prone to error. A computer based image analysis system has been developed that performs tracking automatically. The objective of this work was to eliminate the bottleneck due to manual methods in high volume tracking applications such as the analysis of crash test films for the automotive industry. The system has proven to be successful in tracking standard fiducial targets and other objects in crash test scenes. Over 95 percent of target positions which could be located using manual methods can be tracked by the system, with a significant improvement in throughput over manual methods. Future work will focus on the tracking of clusters of targets and on tracking deformable objects such as airbags.

TU-AB-BRA-11: Evaluation of Fully Automatic Volumetric GBM Segmentation in the TCGA-GBM Dataset: Prognosis and Correlation with VASARI Features

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

Rios Velazquez, E; Meier, R; Dunn, W

Purpose: Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. Methods: MRI sets of 67 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA), including necrosis, edema, contrast enhancing and non-enhancing tumor. Spearman’s correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Results: Auto-segmented sub-volumes showedmore » high agreement with manually delineated volumes (range (r): 0.65 – 0.91). Also showed higher correlation with VASARI features (auto r = 0.35, 0.60 and 0.59; manual r = 0.29, 0.50, 0.43, for contrast-enhancing, necrosis and edema, respectively). The contrast-enhancing volume and post-contrast abnormal volume showed the highest C-index (0.73 and 0.72), comparable to manually defined volumes (p = 0.22 and p = 0.07, respectively). The non-enhancing region defined by BraTumIA showed a significantly higher prognostic value (CI = 0.71) than the edema (CI = 0.60), both of which could not be distinguished by manual delineation. Conclusion: BraTumIA tumor sub-compartments showed higher correlation with VASARI data, and equivalent performance in terms of prognosis compared to manual sub-volumes. This method can enable more reproducible definition and quantification of imaging based biomarkers and has a large potential in high-throughput medical imaging research.« less

Reliability of lower limb alignment measures using an established landmark-based method with a customized computer software program

PubMed Central

Sled, Elizabeth A.; Sheehy, Lisa M.; Felson, David T.; Costigan, Patrick A.; Lam, Miu; Cooke, T. Derek V.

2010-01-01

The objective of the study was to evaluate the reliability of frontal plane lower limb alignment measures using a landmark-based method by (1) comparing inter- and intra-reader reliability between measurements of alignment obtained manually with those using a computer program, and (2) determining inter- and intra-reader reliability of computer-assisted alignment measures from full-limb radiographs. An established method for measuring alignment was used, involving selection of 10 femoral and tibial bone landmarks. 1) To compare manual and computer methods, we used digital images and matching paper copies of five alignment patterns simulating healthy and malaligned limbs drawn using AutoCAD. Seven readers were trained in each system. Paper copies were measured manually and repeat measurements were performed daily for 3 days, followed by a similar routine with the digital images using the computer. 2) To examine the reliability of computer-assisted measures from full-limb radiographs, 100 images (200 limbs) were selected as a random sample from 1,500 full-limb digital radiographs which were part of the Multicenter Osteoarthritis (MOST) Study. Three trained readers used the software program to measure alignment twice from the batch of 100 images, with two or more weeks between batch handling. Manual and computer measures of alignment showed excellent agreement (intraclass correlations [ICCs] 0.977 – 0.999 for computer analysis; 0.820 – 0.995 for manual measures). The computer program applied to full-limb radiographs produced alignment measurements with high inter- and intra-reader reliability (ICCs 0.839 – 0.998). In conclusion, alignment measures using a bone landmark-based approach and a computer program were highly reliable between multiple readers. PMID:19882339

A Manual-Based Intervention to Address Clinical Crises and Retain Patients in the Treatment of Adolescents with Depression Study (TADS)

ERIC Educational Resources Information Center

May, Diane E.; Kratochvil, Christopher J.; Puumala, Susan E.; Silva, Susan G.; Rezac, Amy J.; Hallin, Mary J.; Reinecke, Mark A.; Vitiello, Benedetto; Weller, Elizabeth B.; Pathak, Sanjeev; Simons, Anne D.; March, John S.

2007-01-01

Objective: To describe a manual-based intervention to address clinical crises and retain participants in the Treatment for Adolescents with Depression Study (TADS). Method: The use of adjunct services for attrition prevention (ASAP) is described for adolescents (ages 12-17 years) during the 12-week acute treatment in TADS, from 2000 to 2003.…

Systems thinking applied to safety during manual handling tasks in the transport and storage industry.

PubMed

Goode, Natassia; Salmon, Paul M; Lenné, Michael G; Hillard, Peter

2014-07-01

Injuries resulting from manual handling tasks represent an on-going problem for the transport and storage industry. This article describes an application of a systems theory-based approach, Rasmussen's (1997. Safety Science 27, 183), risk management framework, to the analysis of the factors influencing safety during manual handling activities in a freight handling organisation. Observations of manual handling activities, cognitive decision method interviews with workers (n=27) and interviews with managers (n=35) were used to gather information about three manual handling activities. Hierarchical task analysis and thematic analysis were used to identify potential risk factors and performance shaping factors across the levels of Rasmussen's framework. These different data sources were then integrated using Rasmussen's Accimap technique to provide an overall analysis of the factors influencing safety during manual handling activities in this context. The findings demonstrate how a systems theory-based approach can be applied to this domain, and suggest that policy-orientated, rather than worker-orientated, changes are required to prevent future manual handling injuries. Copyright © 2013 Elsevier Ltd. All rights reserved.

Interactive 3D segmentation using connected orthogonal contours.

PubMed

de Bruin, P W; Dercksen, V J; Post, F H; Vossepoel, A M; Streekstra, G J; Vos, F M

2005-05-01

This paper describes a new method for interactive segmentation that is based on cross-sectional design and 3D modelling. The method represents a 3D model by a set of connected contours that are planar and orthogonal. Planar contours overlayed on image data are easily manipulated and linked contours reduce the amount of user interaction.1 This method solves the contour-to-contour correspondence problem and can capture extrema of objects in a more flexible way than manual segmentation of a stack of 2D images. The resulting 3D model is guaranteed to be free of geometric and topological errors. We show that manual segmentation using connected orthogonal contours has great advantages over conventional manual segmentation. Furthermore, the method provides effective feedback and control for creating an initial model for, and control and steering of, (semi-)automatic segmentation methods.

Computer-assisted determination of left ventricular endocardial borders reduces variability in the echocardiographic assessment of ejection fraction

PubMed Central

Maret, Eva; Brudin, Lars; Lindstrom, Lena; Nylander, Eva; Ohlsson, Jan L; Engvall, Jan E

2008-01-01

Background Left ventricular size and function are important prognostic factors in heart disease. Their measurement is the most frequent reason for sending patients to the echo lab. These measurements have important implications for therapy but are sensitive to the skill of the operator. Earlier automated echo-based methods have not become widely used. The aim of our study was to evaluate an automatic echocardiographic method (with manual correction if needed) for determining left ventricular ejection fraction (LVEF) based on an active appearance model of the left ventricle (syngo®AutoEF, Siemens Medical Solutions). Comparisons were made with manual planimetry (manual Simpson), visual assessment and automatically determined LVEF from quantitative myocardial gated single photon emission computed tomography (SPECT). Methods 60 consecutive patients referred for myocardial perfusion imaging (MPI) were included in the study. Two-dimensional echocardiography was performed within one hour of MPI at rest. Image quality did not constitute an exclusion criterion. Analysis was performed by five experienced observers and by two novices. Results LVEF (%), end-diastolic and end-systolic volume/BSA (ml/m2) were for uncorrected AutoEF 54 ± 10, 51 ± 16, 24 ± 13, for corrected AutoEF 53 ± 10, 53 ± 18, 26 ± 14, for manual Simpson 51 ± 11, 56 ± 20, 28 ± 15, and for MPI 52 ± 12, 67 ± 26, 35 ± 23. The required time for analysis was significantly different for all four echocardiographic methods and was for uncorrected AutoEF 79 ± 5 s, for corrected AutoEF 159 ± 46 s, for manual Simpson 177 ± 66 s, and for visual assessment 33 ± 14 s. Compared with the expert manual Simpson, limits of agreement for novice corrected AutoEF was lower than for novice manual Simpson (0.8 ± 10.5 vs. -3.2 ± 11.4 LVEF percentage points). Calculated for experts and with LVEF (%) categorized into < 30, 30–44, 45–54 and ≥ 55, kappa measure of agreement was moderate (0.44–0.53) for all method comparisons (uncorrected AutoEF not evaluated). Conclusion Corrected AutoEF reduces the variation in measurements compared with manual planimetry, without increasing the time required. The method seems especially suited for unexperienced readers. PMID:19014461

Characterization of shallow unconsolidated aquifers in West Africa using different hydrogeological data sources as a contribution to the promotion of manual drilling and low cost techniques for groundwater exploration

NASA Astrophysics Data System (ADS)

Fussi, Fabio; Fumagalli, Letizia; Bonomi, Tullia; Kane, Cheikh H.; Fava, Francesco; Di Mauro, Biagio; Hamidou, Barry; Niang, Magatte; Wade, Souleye; Colombo, Roberto

2016-04-01

Manual drilling refers to several drilling methods that rely on human energy to construct a borehole and complete a water supply (Danert, 2015). It can be an effective strategy to increase access to groundwater in low income countries , but manual drilling can be applied only where shallow geological layers are relatively soft and water table is not too deep. It is important therefore to identify those zones where shallow hydrogeological conditions are suitable, investigating the characteristics of shallow porous aquifers. Existing hydrogeological studies are generally focused in the characterization of deep fractures aquifers, more productive and able to ensure water supply for large settlements. Information concerning shallow porous aquifers are limited. This research has been carried out in two different study areas in West Africa (North-Western Senegal and Eastern Guinea). Aim of the research is the characterization of shallow aquifer using different methods and the identification of hydrogeological condition suitable for manual drilling implementation. Three different methods to estimate geometry and hydraulic properties of shallow unconsolidated aquifers have been used: The first method is based on the analysis of stratigraphic data obtained from borehole logs of the national water point database in both countries. The following steps have been implemented on the original information using the software TANGAFRIC, specifically designed for this study: a) identification of most frequent terms used for hydrogeological description in Senegal and Guinea database; b) definition of standard categories and manual codification of data; c) automatic extraction of average distribution of textural classes at different depth intervals in the unconsolidated aquifer; d) estimation of hydraulic parameters using conversion tables between texture and hydraulic conductivity available in the literature. . The second method is based on the interpretation of pump and recovery test in large diameter wells. K values obtained from these tests provide direct information on hydraulic parameters of shallow porous aquifers (while pump tests data obtained from deep mechanized boreholes, exploiting fractured aquifers, cannot be considered representative for the target shallow aquifer of manual drilling). The third method is based on the interpretation of stratigraphic logs and simplified pump test from manual drilled wells carried out since 2012 in Guinea. In this country a standard and systematic procedure to collect hydrogeological data from these wells (therefore indicating properties of shallow aquifer) has been put in place in 2011; it is considered one of the best example worldwide about technical data collection and systematization from manual drilling activities, but its development has been stopped because of the outbreak of Ebola in this country. The integration of these 3 methods allow to estimate geometry and hydraulic behavior of shallow unconsolidated aquifer, identifying those areas where manual drilling is feasible and estimating potential yield that can be extracted. In the mean time this research provides relevant indications concerning the use of data obtained from low cost open hand dug or manually drilled wells (rarely used in hydrogeological research) for groundwater exploration of shallow aquifers.

Three-dimensional murine airway segmentation in micro-CT images

NASA Astrophysics Data System (ADS)

Shi, Lijun; Thiesse, Jacqueline; McLennan, Geoffrey; Hoffman, Eric A.; Reinhardt, Joseph M.

2007-03-01

Thoracic imaging for small animals has emerged as an important tool for monitoring pulmonary disease progression and therapy response in genetically engineered animals. Micro-CT is becoming the standard thoracic imaging modality in small animal imaging because it can produce high-resolution images of the lung parenchyma, vasculature, and airways. Segmentation, measurement, and visualization of the airway tree is an important step in pulmonary image analysis. However, manual analysis of the airway tree in micro-CT images can be extremely time-consuming since a typical dataset is usually on the order of several gigabytes in size. Automated and semi-automated tools for micro-CT airway analysis are desirable. In this paper, we propose an automatic airway segmentation method for in vivo micro-CT images of the murine lung and validate our method by comparing the automatic results to manual tracing. Our method is based primarily on grayscale morphology. The results show good visual matches between manually segmented and automatically segmented trees. The average true positive volume fraction compared to manual analysis is 91.61%. The overall runtime for the automatic method is on the order of 30 minutes per volume compared to several hours to a few days for manual analysis.

Enabling Requirements-Based Programming for Highly-Dependable Complex Parallel and Distributed Systems

NASA Technical Reports Server (NTRS)

Hinchey, Michael G.; Rash, James L.; Rouff, Christopher A.

2005-01-01

The manual application of formal methods in system specification has produced successes, but in the end, despite any claims and assertions by practitioners, there is no provable relationship between a manually derived system specification or formal model and the customer's original requirements. Complex parallel and distributed system present the worst case implications for today s dearth of viable approaches for achieving system dependability. No avenue other than formal methods constitutes a serious contender for resolving the problem, and so recognition of requirements-based programming has come at a critical juncture. We describe a new, NASA-developed automated requirement-based programming method that can be applied to certain classes of systems, including complex parallel and distributed systems, to achieve a high degree of dependability.

Fully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features.

PubMed

Rios Velazquez, Emmanuel; Meier, Raphael; Dunn, William D; Alexander, Brian; Wiest, Roland; Bauer, Stefan; Gutman, David A; Reyes, Mauricio; Aerts, Hugo J W L

2015-11-18

Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. MRI sets of 109 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA). Spearman's correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Auto-segmented sub-volumes showed moderate to high agreement with manually delineated volumes (range (r): 0.4 - 0.86). Also, the auto and manual volumes showed similar correlation with VASARI features (auto r = 0.35, 0.43 and 0.36; manual r = 0.17, 0.67, 0.41, for contrast-enhancing, necrosis and edema, respectively). The auto-segmented contrast-enhancing volume and post-contrast abnormal volume showed the highest AUC (0.66, CI: 0.55-0.77 and 0.65, CI: 0.54-0.76), comparable to manually defined volumes (0.64, CI: 0.53-0.75 and 0.63, CI: 0.52-0.74, respectively). BraTumIA and manual tumor sub-compartments showed comparable performance in terms of prognosis and correlation with VASARI features. This method can enable more reproducible definition and quantification of imaging based biomarkers and has potential in high-throughput medical imaging research.

Validation of a fibula graft cutting guide for mandibular reconstruction: experiment with rapid prototyping mandible model.

PubMed

Lim, Se-Ho; Kim, Yeon-Ho; Kim, Moon-Key; Nam, Woong; Kang, Sang-Hoon

2016-12-01

We examined whether cutting a fibula graft with a surgical guide template, prepared with computer-aided design/computer-aided manufacturing (CAD/CAM), would improve the precision and accuracy of mandibular reconstruction. Thirty mandibular rapid prototype (RP) models were allocated to experimental (N = 15) and control (N = 15) groups. Thirty identical fibular RP models were assigned randomly, 15 to each group. For reference, we prepared a reconstructed mandibular RP model with a three-dimensional printer, based on surgical simulation. In the experimental group, a stereolithography (STL) surgical guide template, based on simulation, was used for cutting the fibula graft. In the control group, the fibula graft was cut manually, with reference to the reconstructed RP mandible model. The mandibular reconstructions were compared to the surgical simulation, and errors were calculated for both the STL surgical guide and the manual methods. The average differences in three-dimensional, minimum distances between the reconstruction and simulation were 9.87 ± 6.32 mm (mean ± SD) for the STL surgical guide method and 14.76 ± 10.34 mm (mean ± SD) for the manual method. The STL surgical guide method incurred less error than the manual method in mandibular reconstruction. A fibula cutting guide improved the precision of reconstructing the mandible with a fibula graft.

Operating manual-based usability evaluation of medical devices: an effective patient safety screening method.

PubMed

Turley, James P; Johnson, Todd R; Smith, Danielle Paige; Zhang, Jaijie; Brixey, Juliana J

2006-04-01

Use of medical devices often directly contributes to medical errors. Because it is difficult or impossible to change the design of existing devices, the best opportunity for improving medical device safety is during the purchasing process. However, most hospital personnel are not familiar with the usability evaluation methods designed to identify aspects of a user interface that do not support intuitive and safe use. A review of medical device operating manuals is proposed as a more practical method of usability evaluation. Operating manuals for five volumetric infusion pumps from three manufacturers were selected for this study (January-April 2003). Each manual's safety message content was evaluated to determine whether the message indicated a device design characteristic that violated known usability principles (heuristics) or indicated a violation of an affordance of the device. "Minimize memory load," with 65 violations, was the heuristic violated most frequently across pumps. Variations between pumps, including the frequency and severity of violations for each, were noted. Results suggest that manual review can provide a proxy for heuristic evaluation of the actual medical device. This method, intended to be a component of prepurchasing evaluation, can complement more formal usability evaluation methods and be used to select a subset of devices for more extensive and formal testing.

Structure-based manual screening and automatic networking for systematically exploring sansanmycin analogues using high performance liquid chromatography tandem mass spectroscopy.

PubMed

Jiang, Zhi-Bo; Ren, Wei-Cong; Shi, Yuan-Yuan; Li, Xing-Xing; Lei, Xuan; Fan, Jia-Hui; Zhang, Cong; Gu, Ren-Jie; Wang, Li-Fei; Xie, Yun-Ying; Hong, Bin

2018-05-18

Sansanmycins (SS), one of several known uridyl peptide antibiotics (UPAs) possessing a unique chemical scaffold, showed a good inhibitory effect on the highly refractory pathogens Pseudomonas aeruginosa and Mycobacterium tuberculosis, especially on the multi-drug resistant M. tuberculosis. This study employed high performance liquid chromatography-mass spectrometry detector (HPLC-MSD) ion trap and LTQ orbitrap tandem mass spectrometry (MS/MS) to explore sansanmycin analogues manually and automatically by re-analysis of the Streptomyces sp. SS fermentation broth. The structure-based manual screening method, based on analysis of the fragmentation pathway of known UPAs and on comparisons of the MS/MS spectra with that of sansanmycin A (SS-A), resulted in identifying twenty sansanmycin analogues, including twelve new structures (1-12). Furthermore, to deeply explore sansanmycin analogues, we utilized a GNPS based molecular networking workflow to re-analyze the HPLC-MS/MS data automatically. As a result, eight more new sansanmycins (13-20) were discovered. Compound 1 was discovered to lose two amino acids of residue 1 (AA 1 ) and (2S, 3S)-N 3 -methyl-2,3-diamino butyric acid (DABA) from the N-terminus, and compounds 6, 11 and 12 were found to contain a 2',3'-dehydrated 4',5'-enamine-3'-deoxyuridyl moiety, which have not been reported before. Interestingly, three trace components with novel 5,6-dihydro-5'-aminouridyl group (16-18) were detected for the first time in the sansanmycin-producing strain. Their structures were primarily determined by detail analysis of the data from MS/MS. Compounds 8 and 10 were further confirmed by nuclear magnetic resonance (NMR) data, which proved the efficiency and accuracy of the method of HPLC-MS/MS for exploration of novel UPAs. Comparing to manual screening, the networking method can provide systematic visualization results. Manual screening and networking method may complement with each other to facilitate the mining of novel UPAs. Copyright © 2018 Elsevier B.V. All rights reserved.

Phantom Study Investigating the Accuracy of Manual and Automatic Image Fusion with the GE Logiq E9: Implications for use in Percutaneous Liver Interventions.

PubMed

Burgmans, Mark Christiaan; den Harder, J Michiel; Meershoek, Philippa; van den Berg, Nynke S; Chan, Shaun Xavier Ju Min; van Leeuwen, Fijs W B; van Erkel, Arian R

2017-06-01

To determine the accuracy of automatic and manual co-registration methods for image fusion of three-dimensional computed tomography (CT) with real-time ultrasonography (US) for image-guided liver interventions. CT images of a skills phantom with liver lesions were acquired and co-registered to US using GE Logiq E9 navigation software. Manual co-registration was compared to automatic and semiautomatic co-registration using an active tracker. Also, manual point registration was compared to plane registration with and without an additional translation point. Finally, comparison was made between manual and automatic selection of reference points. In each experiment, accuracy of the co-registration method was determined by measurement of the residual displacement in phantom lesions by two independent observers. Mean displacements for a superficial and deep liver lesion were comparable after manual and semiautomatic co-registration: 2.4 and 2.0 mm versus 2.0 and 2.5 mm, respectively. Both methods were significantly better than automatic co-registration: 5.9 and 5.2 mm residual displacement (p < 0.001; p < 0.01). The accuracy of manual point registration was higher than that of plane registration, the latter being heavily dependent on accurate matching of axial CT and US images by the operator. Automatic reference point selection resulted in significantly lower registration accuracy compared to manual point selection despite lower root-mean-square deviation (RMSD) values. The accuracy of manual and semiautomatic co-registration is better than that of automatic co-registration. For manual co-registration using a plane, choosing the correct plane orientation is an essential first step in the registration process. Automatic reference point selection based on RMSD values is error-prone.

A guide to best practices for Gene Ontology (GO) manual annotation

PubMed Central

Balakrishnan, Rama; Harris, Midori A.; Huntley, Rachael; Van Auken, Kimberly; Cherry, J. Michael

2013-01-01

The Gene Ontology Consortium (GOC) is a community-based bioinformatics project that classifies gene product function through the use of structured controlled vocabularies. A fundamental application of the Gene Ontology (GO) is in the creation of gene product annotations, evidence-based associations between GO definitions and experimental or sequence-based analysis. Currently, the GOC disseminates 126 million annotations covering >374 000 species including all the kingdoms of life. This number includes two classes of GO annotations: those created manually by experienced biocurators reviewing the literature or by examination of biological data (1.1 million annotations covering 2226 species) and those generated computationally via automated methods. As manual annotations are often used to propagate functional predictions between related proteins within and between genomes, it is critical to provide accurate consistent manual annotations. Toward this goal, we present here the conventions defined by the GOC for the creation of manual annotation. This guide represents the best practices for manual annotation as established by the GOC project over the past 12 years. We hope this guide will encourage research communities to annotate gene products of their interest to enhance the corpus of GO annotations available to all. Database URL: http://www.geneontology.org PMID:23842463

Phantom Study Investigating the Accuracy of Manual and Automatic Image Fusion with the GE Logiq E9: Implications for use in Percutaneous Liver Interventions

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

Burgmans, Mark Christiaan, E-mail: m.c.burgmans@lumc.nl; Harder, J. Michiel den, E-mail: chiel.den.harder@gmail.com; Meershoek, Philippa, E-mail: P.Meershoek@lumc.nl

PurposeTo determine the accuracy of automatic and manual co-registration methods for image fusion of three-dimensional computed tomography (CT) with real-time ultrasonography (US) for image-guided liver interventions.Materials and MethodsCT images of a skills phantom with liver lesions were acquired and co-registered to US using GE Logiq E9 navigation software. Manual co-registration was compared to automatic and semiautomatic co-registration using an active tracker. Also, manual point registration was compared to plane registration with and without an additional translation point. Finally, comparison was made between manual and automatic selection of reference points. In each experiment, accuracy of the co-registration method was determined bymore » measurement of the residual displacement in phantom lesions by two independent observers.ResultsMean displacements for a superficial and deep liver lesion were comparable after manual and semiautomatic co-registration: 2.4 and 2.0 mm versus 2.0 and 2.5 mm, respectively. Both methods were significantly better than automatic co-registration: 5.9 and 5.2 mm residual displacement (p < 0.001; p < 0.01). The accuracy of manual point registration was higher than that of plane registration, the latter being heavily dependent on accurate matching of axial CT and US images by the operator. Automatic reference point selection resulted in significantly lower registration accuracy compared to manual point selection despite lower root-mean-square deviation (RMSD) values.ConclusionThe accuracy of manual and semiautomatic co-registration is better than that of automatic co-registration. For manual co-registration using a plane, choosing the correct plane orientation is an essential first step in the registration process. Automatic reference point selection based on RMSD values is error-prone.« less

Assessing the economics of processing end-of-life vehicles through manual dismantling.

PubMed

Tian, Jin; Chen, Ming

2016-10-01

Most dismantling enterprises in a number of developing countries, such as China, usually adopt the "manual+mechanical" dismantling approach to process end-of-life vehicles. However, the automobile industry does not have a clear indicator to reasonably and effectively determine the manual dismantling degree for end-of-life vehicles. In this study, five different dismantling scenarios and an economic system for end-of-life vehicles were developed based on the actual situation of end-of-life vehicles. The fuzzy analytic hierarchy process was applied to set the weights of direct costs, indirect costs, and sales and to obtain an optimal manual dismantling scenario. Results showed that although the traditional method of "dismantling to the end" can guarantee the highest recycling rate, this method is not the best among all the scenarios. The profit gained in the optimal scenario is 100.6% higher than that in the traditional scenario. The optimal manual dismantling scenario showed that enterprises are required to select suitable parts to process through manual dismantling. Selecting suitable parts maximizes economic profit and improves dismantling speed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Determination of the human spine curve based on laser triangulation.

PubMed

Poredoš, Primož; Čelan, Dušan; Možina, Janez; Jezeršek, Matija

2015-02-05

The main objective of the present method was to automatically obtain a spatial curve of the thoracic and lumbar spine based on a 3D shape measurement of a human torso with developed scoliosis. Manual determination of the spine curve, which was based on palpation of the thoracic and lumbar spinous processes, was found to be an appropriate way to validate the method. Therefore a new, noninvasive, optical 3D method for human torso evaluation in medical practice is introduced. Twenty-four patients with confirmed clinical diagnosis of scoliosis were scanned using a specially developed 3D laser profilometer. The measuring principle of the system is based on laser triangulation with one-laser-plane illumination. The measurement took approximately 10 seconds at 700 mm of the longitudinal translation along the back. The single point measurement accuracy was 0.1 mm. Computer analysis of the measured surface returned two 3D curves. The first curve was determined by manual marking (manual curve), and the second was determined by detecting surface curvature extremes (automatic curve). The manual and automatic curve comparison was given as the root mean square deviation (RMSD) for each patient. The intra-operator study involved assessing 20 successive measurements of the same person, and the inter-operator study involved assessing measurements from 8 operators. The results obtained for the 24 patients showed that the typical RMSD between the manual and automatic curve was 5.0 mm in the frontal plane and 1.0 mm in the sagittal plane, which is a good result compared with palpatory accuracy (9.8 mm). The intra-operator repeatability of the presented method in the frontal and sagittal planes was 0.45 mm and 0.06 mm, respectively. The inter-operator repeatability assessment shows that that the presented method is invariant to the operator of the computer program with the presented method. The main novelty of the presented paper is the development of a new, non-contact method that provides a quick, precise and non-invasive way to determine the spatial spine curve for patients with developed scoliosis and the validation of the presented method using the palpation of the spinous processes, where no harmful ionizing radiation is present.

The paradox of sham therapy and placebo effect in osteopathy

PubMed Central

Cerritelli, Francesco; Verzella, Marco; Cicchitti, Luca; D’Alessandro, Giandomenico; Vanacore, Nicola

2016-01-01

Abstract Background: Placebo, defined as “false treatment,” is a common gold-standard method to assess the validity of a therapy both in pharmacological trials and manual medicine research where placebo is also referred to as “sham therapy.” In the medical literature, guidelines have been proposed on how to conduct robust placebo-controlled trials, but mainly in a drug-based scenario. In contrast, there are not precise guidelines on how to conduct a placebo-controlled in manual medicine trials (particularly osteopathy). The aim of the present systematic review was to report how and what type of sham methods, dosage, operator characteristics, and patient types were used in osteopathic clinical trials and, eventually, assess sham clinical effectiveness. Methods: A systematic Cochrane-based review was conducted by analyzing the osteopathic trials that used both manual and nonmanual placebo control. Searches were conducted on 8 databases from journal inception to December 2015 using a pragmatic literature search approach. Two independent reviewers conducted the study selection and data extraction for each study. The risk of bias was evaluated according to the Cochrane methods. Results: A total of 64 studies were eligible for analysis collecting a total of 5024 participants. More than half (43 studies) used a manual placebo; 9 studies used a nonmanual placebo; and 12 studies used both manual and nonmanual placebo. Data showed lack of reporting sham therapy information across studies. Risk of bias analysis demonstrated a high risk of bias for allocation, blinding of personnel and participants, selective, and other bias. To explore the clinical effects of sham therapies used, a quantitative analysis was planned. However, due to the high heterogeneity of sham approaches used no further analyses were performed. Conclusion: High heterogeneity regarding placebo used between studies, lack of reporting information on placebo methods and within-study variability between sham and real treatment procedures suggest prudence in reading and interpreting study findings in manual osteopathic randomized controlled trials (RCTs). Efforts must be made to promote guidelines to design the most reliable placebo for manual RCTs as a means of increasing the internal validity and improve external validity of findings. PMID:27583913

Segmentation of Image Ensembles via Latent Atlases

PubMed Central

Van Leemput, Koen; Menze, Bjoern H.; Wells, William M.; Golland, Polina

2010-01-01

Spatial priors, such as probabilistic atlases, play an important role in MRI segmentation. However, the availability of comprehensive, reliable and suitable manual segmentations for atlas construction is limited. We therefore propose a method for joint segmentation of corresponding regions of interest in a collection of aligned images that does not require labeled training data. Instead, a latent atlas, initialized by at most a single manual segmentation, is inferred from the evolving segmentations of the ensemble. The algorithm is based on probabilistic principles but is solved using partial differential equations (PDEs) and energy minimization criteria. We evaluate the method on two datasets, segmenting subcortical and cortical structures in a multi-subject study and extracting brain tumors in a single-subject multi-modal longitudinal experiment. We compare the segmentation results to manual segmentations, when those exist, and to the results of a state-of-the-art atlas-based segmentation method. The quality of the results supports the latent atlas as a promising alternative when existing atlases are not compatible with the images to be segmented. PMID:20580305

Spatially varying accuracy and reproducibility of prostate segmentation in magnetic resonance images using manual and semiautomated methods.

PubMed

Shahedi, Maysam; Cool, Derek W; Romagnoli, Cesare; Bauman, Glenn S; Bastian-Jordan, Matthew; Gibson, Eli; Rodrigues, George; Ahmad, Belal; Lock, Michael; Fenster, Aaron; Ward, Aaron D

2014-11-01

Three-dimensional (3D) prostate image segmentation is useful for cancer diagnosis and therapy guidance, but can be time-consuming to perform manually and involves varying levels of difficulty and interoperator variability within the prostatic base, midgland (MG), and apex. In this study, the authors measured accuracy and interobserver variability in the segmentation of the prostate on T2-weighted endorectal magnetic resonance (MR) imaging within the whole gland (WG), and separately within the apex, midgland, and base regions. The authors collected MR images from 42 prostate cancer patients. Prostate border delineation was performed manually by one observer on all images and by two other observers on a subset of ten images. The authors used complementary boundary-, region-, and volume-based metrics [mean absolute distance (MAD), Dice similarity coefficient (DSC), recall rate, precision rate, and volume difference (ΔV)] to elucidate the different types of segmentation errors that they observed. Evaluation for expert manual and semiautomatic segmentation approaches was carried out. Compared to manual segmentation, the authors' semiautomatic approach reduces the necessary user interaction by only requiring an indication of the anteroposterior orientation of the prostate and the selection of prostate center points on the apex, base, and midgland slices. Based on these inputs, the algorithm identifies candidate prostate boundary points using learned boundary appearance characteristics and performs regularization based on learned prostate shape information. The semiautomated algorithm required an average of 30 s of user interaction time (measured for nine operators) for each 3D prostate segmentation. The authors compared the segmentations from this method to manual segmentations in a single-operator (mean whole gland MAD = 2.0 mm, DSC = 82%, recall = 77%, precision = 88%, and ΔV = - 4.6 cm(3)) and multioperator study (mean whole gland MAD = 2.2 mm, DSC = 77%, recall = 72%, precision = 86%, and ΔV = - 4.0 cm(3)). These results compared favorably with observed differences between manual segmentations and a simultaneous truth and performance level estimation reference for this data set (whole gland differences as high as MAD = 3.1 mm, DSC = 78%, recall = 66%, precision = 77%, and ΔV = 15.5 cm(3)). The authors found that overall, midgland segmentation was more accurate and repeatable than the segmentation of the apex and base, with the base posing the greatest challenge. The main conclusions of this study were that (1) the semiautomated approach reduced interobserver segmentation variability; (2) the segmentation accuracy of the semiautomated approach, as well as the accuracies of recently published methods from other groups, were within the range of observed expert variability in manual prostate segmentation; and (3) further efforts in the development of computer-assisted segmentation would be most productive if focused on improvement of segmentation accuracy and reduction of variability within the prostatic apex and base.

Evaluation of an automatic MR-based gold fiducial marker localisation method for MR-only prostate radiotherapy

NASA Astrophysics Data System (ADS)

Maspero, Matteo; van den Berg, Cornelis A. T.; Zijlstra, Frank; Sikkes, Gonda G.; de Boer, Hans C. J.; Meijer, Gert J.; Kerkmeijer, Linda G. W.; Viergever, Max A.; Lagendijk, Jan J. W.; Seevinck, Peter R.

2017-10-01

An MR-only radiotherapy planning (RTP) workflow would reduce the cost, radiation exposure and uncertainties introduced by CT-MRI registrations. In the case of prostate treatment, one of the remaining challenges currently holding back the implementation of an RTP workflow is the MR-based localisation of intraprostatic gold fiducial markers (FMs), which is crucial for accurate patient positioning. Currently, MR-based FM localisation is clinically performed manually. This is sub-optimal, as manual interaction increases the workload. Attempts to perform automatic FM detection often rely on being able to detect signal voids induced by the FMs in magnitude images. However, signal voids may not always be sufficiently specific, hampering accurate and robust automatic FM localisation. Here, we present an approach that aims at automatic MR-based FM localisation. This method is based on template matching using a library of simulated complex-valued templates, and exploiting the behaviour of the complex MR signal in the vicinity of the FM. Clinical evaluation was performed on seventeen prostate cancer patients undergoing external beam radiotherapy treatment. Automatic MR-based FM localisation was compared to manual MR-based and semi-automatic CT-based localisation (the current gold standard) in terms of detection rate and the spatial accuracy and precision of localisation. The proposed method correctly detected all three FMs in 15/17 patients. The spatial accuracy (mean) and precision (STD) were 0.9 mm and 0.5 mm respectively, which is below the voxel size of 1.1 × 1.1 × 1.2 mm3 and comparable to MR-based manual localisation. FM localisation failed (3/51 FMs) in the presence of bleeding or calcifications in the direct vicinity of the FM. The method was found to be spatially accurate and precise, which is essential for clinical use. To overcome any missed detection, we envision the use of the proposed method along with verification by an observer. This will result in a semi-automatic workflow facilitating the introduction of an MR-only workflow.

Guide for Planning a High School Environmental Action Conference.

ERIC Educational Resources Information Center

Wanless, Angie, Comp.; And Others

The purpose of this manual is to provide guidelines and suggestions for people organizing an environmental action conference for high school students. The format and planning suggestions are based on the methods used for a conference organized by the Wisconsin Center for Environmental Education in 1991. The bulk of the manual provides structure…

Automated cerebral infarct volume measurement in follow-up noncontrast CT scans of patients with acute ischemic stroke.

PubMed

Boers, A M; Marquering, H A; Jochem, J J; Besselink, N J; Berkhemer, O A; van der Lugt, A; Beenen, L F; Majoie, C B

2013-08-01

Cerebral infarct volume as observed in follow-up CT is an important radiologic outcome measure of the effectiveness of treatment of patients with acute ischemic stroke. However, manual measurement of CIV is time-consuming and operator-dependent. The purpose of this study was to develop and evaluate a robust automated measurement of the CIV. The CIV in early follow-up CT images of 34 consecutive patients with acute ischemic stroke was segmented with an automated intensity-based region-growing algorithm, which includes partial volume effect correction near the skull, midline determination, and ventricle and hemorrhage exclusion. Two observers manually delineated the CIV. Interobserver variability of the manual assessments and the accuracy of the automated method were evaluated by using the Pearson correlation, Bland-Altman analysis, and Dice coefficients. The accuracy was defined as the correlation with the manual assessment as a reference standard. The Pearson correlation for the automated method compared with the reference standard was similar to the manual correlation (R = 0.98). The accuracy of the automated method was excellent with a mean difference of 0.5 mL with limits of agreement of -38.0-39.1 mL, which were more consistent than the interobserver variability of the 2 observers (-40.9-44.1 mL). However, the Dice coefficients were higher for the manual delineation. The automated method showed a strong correlation and accuracy with the manual reference measurement. This approach has the potential to become the standard in assessing the infarct volume as a secondary outcome measure for evaluating the effectiveness of treatment.

The clinical applicability of an automated plethysmographic determination of the ankle-brachial index after vascular surgery.

PubMed

van der Slegt, Jasper; Verbogt, Nathalie Pa; Mulder, Paul Gh; Steunenberg, Stijn L; Steunenberg, Bastiaan E; van der Laan, Lijckle

2016-10-01

An automated ankle-brachial index device could lead to potential time savings and more accuracy in ankle-brachial index-determination after vascular surgery. This prospective cross-sectional study compared postprocedural ankle-brachial indices measured by a manual method with ankle-brachial indices of an automated plethysmographic method. Forty-two patients were included. No significant difference in time performing a measurement was observed (1.1 min, 95% CI: -0.2 to +2.4; P = 0.095). Mean ankle-brachial index with the automated method was 0.105 higher (95% CI: 0.017 to 0.193; P = 0.020) than with the manual method, with limits of agreement of -0.376 and +0.587. Total variance amounted to 0.0759 and the correlation between both methods was 0.60. Reliability expressed as maximum absolute difference (95% level) between duplicate ankle-brachial index-measurements under identical conditions was 0.350 (manual) and 0.152 (automated), although not significant (p = 0.053). Finally, the automated method had 34% points higher failure rate than the manual method. In conclusion based on this study, the automated ankle-brachial index-method seems not to be clinically applicable for measuring ankle-brachial index postoperatively in patients with vascular disease. © The Author(s) 2016.

The accuracy of a designed software for automated localization of craniofacial landmarks on CBCT images.

PubMed

Shahidi, Shoaleh; Bahrampour, Ehsan; Soltanimehr, Elham; Zamani, Ali; Oshagh, Morteza; Moattari, Marzieh; Mehdizadeh, Alireza

2014-09-16

Two-dimensional projection radiographs have been traditionally considered the modality of choice for cephalometric analysis. To overcome the shortcomings of two-dimensional images, three-dimensional computed tomography (CT) has been used to evaluate craniofacial structures. However, manual landmark detection depends on medical expertise, and the process is time-consuming. The present study was designed to produce software capable of automated localization of craniofacial landmarks on cone beam (CB) CT images based on image registration and to evaluate its accuracy. The software was designed using MATLAB programming language. The technique was a combination of feature-based (principal axes registration) and voxel similarity-based methods for image registration. A total of 8 CBCT images were selected as our reference images for creating a head atlas. Then, 20 CBCT images were randomly selected as the test images for evaluating the method. Three experts twice located 14 landmarks in all 28 CBCT images during two examinations set 6 weeks apart. The differences in the distances of coordinates of each landmark on each image between manual and automated detection methods were calculated and reported as mean errors. The combined intraclass correlation coefficient for intraobserver reliability was 0.89 and for interobserver reliability 0.87 (95% confidence interval, 0.82 to 0.93). The mean errors of all 14 landmarks were <4 mm. Additionally, 63.57% of landmarks had a mean error of <3 mm compared with manual detection (gold standard method). The accuracy of our approach for automated localization of craniofacial landmarks, which was based on combining feature-based and voxel similarity-based methods for image registration, was acceptable. Nevertheless we recommend repetition of this study using other techniques, such as intensity-based methods.

Assessing the Agreement Between Eo-Based Semi-Automated Landslide Maps with Fuzzy Manual Landslide Delineation

NASA Astrophysics Data System (ADS)

Albrecht, F.; Hölbling, D.; Friedl, B.

2017-09-01

Landslide mapping benefits from the ever increasing availability of Earth Observation (EO) data resulting from programmes like the Copernicus Sentinel missions and improved infrastructure for data access. However, there arises the need for improved automated landslide information extraction processes from EO data while the dominant method is still manual delineation. Object-based image analysis (OBIA) provides the means for the fast and efficient extraction of landslide information. To prove its quality, automated results are often compared to manually delineated landslide maps. Although there is awareness of the uncertainties inherent in manual delineations, there is a lack of understanding how they affect the levels of agreement in a direct comparison of OBIA-derived landslide maps and manually derived landslide maps. In order to provide an improved reference, we present a fuzzy approach for the manual delineation of landslides on optical satellite images, thereby making the inherent uncertainties of the delineation explicit. The fuzzy manual delineation and the OBIA classification are compared by accuracy metrics accepted in the remote sensing community. We have tested this approach for high resolution (HR) satellite images of three large landslides in Austria and Italy. We were able to show that the deviation of the OBIA result from the manual delineation can mainly be attributed to the uncertainty inherent in the manual delineation process, a relevant issue for the design of validation processes for OBIA-derived landslide maps.

WHO Working Group on revision of the Manual of Laboratory Methods for Testing DTP Vaccines-Report of two meetings held on 20-21 July 2006 and 28-30 March 2007, Geneva, Switzerland.

PubMed

Corbel, Michael J; Das, Rose Gaines; Lei, Dianliang; Xing, Dorothy K L; Horiuchi, Yoshinobu; Dobbelaer, Roland

2008-04-07

This report reflects the discussion and conclusions of a WHO group of experts from National Regulatory Authorities (NRAs), National Control Laboratories (NCLs), vaccine industries and other relevant institutions involved in standardization and control of diphtheria, tetanus and pertussis vaccines (DTP), held on 20-21 July 2006 and 28-30 March 2007, in Geneva Switzerland for the revision of WHO Manual for quality control of DTP vaccines. Taking into account recent developments and standardization in quality control methods and the revision of WHO recommendations for D, T, P vaccines, and a need for updating the manual has been recognized. In these two meetings the current situation of quality control methods in terms of potency, safety and identity tests for DTP vaccines and statistical analysis of data were reviewed. Based on the WHO recommendations and recent validation of testing methods, the content of current manual were reviewed and discussed. The group agreed that the principles to be observed in selecting methods included identifying those critical for assuring safety, efficacy and quality and which were consistent with WHO recommendations/requirements. Methods that were well recognized but not yet included in current Recommendations should be taken into account. These would include in vivo and/or in vitro methods for determining potency, safety testing and identity. The statistical analysis of the data should be revised and updated. It was noted that the mouse based assays for toxoid potency were still quite widely used and it was desirable to establish appropriate standards for these to enable the results to be related to the standard guinea pig assays. The working group was met again to review the first drafts and to input further suggestions or amendments to the contributions of the drafting groups. The revised manual was to be finalized and published by WHO.

MR diffusion-weighted imaging-based subcutaneous tumour volumetry in a xenografted nude mouse model using 3D Slicer: an accurate and repeatable method

PubMed Central

Ma, Zelan; Chen, Xin; Huang, Yanqi; He, Lan; Liang, Cuishan; Liang, Changhong; Liu, Zaiyi

2015-01-01

Accurate and repeatable measurement of the gross tumour volume(GTV) of subcutaneous xenografts is crucial in the evaluation of anti-tumour therapy. Formula and image-based manual segmentation methods are commonly used for GTV measurement but are hindered by low accuracy and reproducibility. 3D Slicer is open-source software that provides semiautomatic segmentation for GTV measurements. In our study, subcutaneous GTVs from nude mouse xenografts were measured by semiautomatic segmentation with 3D Slicer based on morphological magnetic resonance imaging(mMRI) or diffusion-weighted imaging(DWI)(b = 0,20,800 s/mm2) . These GTVs were then compared with those obtained via the formula and image-based manual segmentation methods with ITK software using the true tumour volume as the standard reference. The effects of tumour size and shape on GTVs measurements were also investigated. Our results showed that, when compared with the true tumour volume, segmentation for DWI(P = 0.060–0.671) resulted in better accuracy than that mMRI(P < 0.001) and the formula method(P < 0.001). Furthermore, semiautomatic segmentation for DWI(intraclass correlation coefficient, ICC = 0.9999) resulted in higher reliability than manual segmentation(ICC = 0.9996–0.9998). Tumour size and shape had no effects on GTV measurement across all methods. Therefore, DWI-based semiautomatic segmentation, which is accurate and reproducible and also provides biological information, is the optimal GTV measurement method in the assessment of anti-tumour treatments. PMID:26489359

COMPARISON OF MANUAL AND SEMIAUTOMATED FUNDUS AUTOFLUORESCENCE ANALYSIS OF MACULAR ATROPHY IN STARGARDT DISEASE PHENOTYPE.

PubMed

Kuehlewein, Laura; Hariri, Amir H; Ho, Alexander; Dustin, Laurie; Wolfson, Yulia; Strauss, Rupert W; Scholl, Hendrik P N; Sadda, SriniVas R

2016-06-01

To evaluate manual and semiautomated grading techniques for assessing decreased fundus autofluorescence (DAF) in patients with Stargardt disease phenotype. Certified reading center graders performed manual and semiautomated (region finder-based) grading of confocal scanning laser ophthalmoscopy (cSLO) fundus autofluorescence (FAF) images for 41 eyes of 22 patients. Lesion types were defined based on the black level and sharpness of the border: definite decreased autofluorescence (DDAF), well, and poorly demarcated questionably decreased autofluorescence (WDQDAF, PDQDAF). Agreement in grading between the two methods and inter- and intra-grader agreement was assessed by kappa coefficients (κ) and intraclass correlation coefficients (ICC). The mean ± standard deviation (SD) area was 3.07 ± 3.02 mm for DDAF (n = 31), 1.53 ± 1.52 mm for WDQDAF (n = 9), and 6.94 ± 10.06 mm for PDQDAF (n = 17). The mean ± SD absolute difference in area between manual and semiautomated grading was 0.26 ± 0.28 mm for DDAF, 0.20 ± 0.26 mm for WDQDAF, and 4.05 ± 8.32 mm for PDQDAF. The ICC (95% confidence interval) for method comparison was 0.992 (0.984-0.996) for DDAF, 0.976 (0.922-0.993) for WDQDAF, and 0.648 (0.306-0.842) for PDQDAF. Inter- and intra-grader agreement in manual and semiautomated quantitative grading was better for DDAF (0.981-0.996) and WDQDAF (0.995-0.999) than for PDQDAF (0.715-0.993). Manual and semiautomated grading methods showed similar levels of reproducibility for assessing areas of decreased autofluorescence in patients with Stargardt disease phenotype. Excellent agreement and reproducibility were observed for well demarcated lesions.

Is STAPLE algorithm confident to assess segmentation methods in PET imaging?

NASA Astrophysics Data System (ADS)

Dewalle-Vignion, Anne-Sophie; Betrouni, Nacim; Baillet, Clio; Vermandel, Maximilien

2015-12-01

Accurate tumor segmentation in [18F]-fluorodeoxyglucose positron emission tomography is crucial for tumor response assessment and target volume definition in radiation therapy. Evaluation of segmentation methods from clinical data without ground truth is usually based on physicians’ manual delineations. In this context, the simultaneous truth and performance level estimation (STAPLE) algorithm could be useful to manage the multi-observers variability. In this paper, we evaluated how this algorithm could accurately estimate the ground truth in PET imaging. Complete evaluation study using different criteria was performed on simulated data. The STAPLE algorithm was applied to manual and automatic segmentation results. A specific configuration of the implementation provided by the Computational Radiology Laboratory was used. Consensus obtained by the STAPLE algorithm from manual delineations appeared to be more accurate than manual delineations themselves (80% of overlap). An improvement of the accuracy was also observed when applying the STAPLE algorithm to automatic segmentations results. The STAPLE algorithm, with the configuration used in this paper, is more appropriate than manual delineations alone or automatic segmentations results alone to estimate the ground truth in PET imaging. Therefore, it might be preferred to assess the accuracy of tumor segmentation methods in PET imaging.

Is STAPLE algorithm confident to assess segmentation methods in PET imaging?

PubMed

Dewalle-Vignion, Anne-Sophie; Betrouni, Nacim; Baillet, Clio; Vermandel, Maximilien

2015-12-21

Accurate tumor segmentation in [18F]-fluorodeoxyglucose positron emission tomography is crucial for tumor response assessment and target volume definition in radiation therapy. Evaluation of segmentation methods from clinical data without ground truth is usually based on physicians' manual delineations. In this context, the simultaneous truth and performance level estimation (STAPLE) algorithm could be useful to manage the multi-observers variability. In this paper, we evaluated how this algorithm could accurately estimate the ground truth in PET imaging. Complete evaluation study using different criteria was performed on simulated data. The STAPLE algorithm was applied to manual and automatic segmentation results. A specific configuration of the implementation provided by the Computational Radiology Laboratory was used. Consensus obtained by the STAPLE algorithm from manual delineations appeared to be more accurate than manual delineations themselves (80% of overlap). An improvement of the accuracy was also observed when applying the STAPLE algorithm to automatic segmentations results. The STAPLE algorithm, with the configuration used in this paper, is more appropriate than manual delineations alone or automatic segmentations results alone to estimate the ground truth in PET imaging. Therefore, it might be preferred to assess the accuracy of tumor segmentation methods in PET imaging.

Automated breast segmentation in ultrasound computer tomography SAFT images

NASA Astrophysics Data System (ADS)

Hopp, T.; You, W.; Zapf, M.; Tan, W. Y.; Gemmeke, H.; Ruiter, N. V.

2017-03-01

Ultrasound Computer Tomography (USCT) is a promising new imaging system for breast cancer diagnosis. An essential step before further processing is to remove the water background from the reconstructed images. In this paper we present a fully-automated image segmentation method based on three-dimensional active contours. The active contour method is extended by applying gradient vector flow and encoding the USCT aperture characteristics as additional weighting terms. A surface detection algorithm based on a ray model is developed to initialize the active contour, which is iteratively deformed to capture the breast outline in USCT reflection images. The evaluation with synthetic data showed that the method is able to cope with noisy images, and is not influenced by the position of the breast and the presence of scattering objects within the breast. The proposed method was applied to 14 in-vivo images resulting in an average surface deviation from a manual segmentation of 2.7 mm. We conclude that automated segmentation of USCT reflection images is feasible and produces results comparable to a manual segmentation. By applying the proposed method, reproducible segmentation results can be obtained without manual interaction by an expert.

Volumetric analysis of pelvic hematomas after blunt trauma using semi-automated seeded region growing segmentation: a method validation study.

PubMed

Dreizin, David; Bodanapally, Uttam K; Neerchal, Nagaraj; Tirada, Nikki; Patlas, Michael; Herskovits, Edward

2016-11-01

Manually segmented traumatic pelvic hematoma volumes are strongly predictive of active bleeding at conventional angiography, but the method is time intensive, limiting its clinical applicability. We compared volumetric analysis using semi-automated region growing segmentation to manual segmentation and diameter-based size estimates in patients with pelvic hematomas after blunt pelvic trauma. A 14-patient cohort was selected in an anonymous randomized fashion from a dataset of patients with pelvic binders at MDCT, collected retrospectively as part of a HIPAA-compliant IRB-approved study from January 2008 to December 2013. To evaluate intermethod differences, one reader (R1) performed three volume measurements using the manual technique and three volume measurements using the semi-automated technique. To evaluate interobserver differences for semi-automated segmentation, a second reader (R2) performed three semi-automated measurements. One-way analysis of variance was used to compare differences in mean volumes. Time effort was also compared. Correlation between the two methods as well as two shorthand appraisals (greatest diameter, and the ABC/2 method for estimating ellipsoid volumes) was assessed with Spearman's rho (r). Intraobserver variability was lower for semi-automated compared to manual segmentation, with standard deviations ranging between ±5-32 mL and ±17-84 mL, respectively (p = 0.0003). There was no significant difference in mean volumes between the two readers' semi-automated measurements (p = 0.83); however, means were lower for the semi-automated compared with the manual technique (manual: mean and SD 309.6 ± 139 mL; R1 semi-auto: 229.6 ± 88.2 mL, p = 0.004; R2 semi-auto: 243.79 ± 99.7 mL, p = 0.021). Despite differences in means, the correlation between the two methods was very strong and highly significant (r = 0.91, p < 0.001). Correlations with diameter-based methods were only moderate and nonsignificant. Mean semi-automated segmentation time effort was 2 min and 6 s and 2 min and 35 s for R1 and R2, respectively, vs. 22 min and 8 s for manual segmentation. Semi-automated pelvic hematoma volumes correlate strongly with manually segmented volumes. Since semi-automated segmentation can be performed reliably and efficiently, volumetric analysis of traumatic pelvic hematomas is potentially valuable at the point-of-care.

Automated posterior cranial fossa volumetry by MRI: applications to Chiari malformation type I.

PubMed

Bagci, A M; Lee, S H; Nagornaya, N; Green, B A; Alperin, N

2013-09-01

Quantification of PCF volume and the degree of PCF crowdedness were found beneficial for differential diagnosis of tonsillar herniation and prediction of surgical outcome in CMI. However, lack of automated methods limits the clinical use of PCF volumetry. An atlas-based method for automated PCF segmentation tailored for CMI is presented. The method performance is assessed in terms of accuracy and spatial overlap with manual segmentation. The degree of association between PCF volumes and the lengths of previously proposed linear landmarks is reported. T1-weighted volumetric MR imaging data with 1-mm isotropic resolution obtained with the use of a 3T scanner from 14 patients with CMI and 3 healthy subjects were used for the study. Manually delineated PCF from 9 patients was used to establish a CMI-specific reference for an atlas-based automated PCF parcellation approach. Agreement between manual and automated segmentation of 5 different CMI datasets was verified by means of the t test. Measurement reproducibility was established through the use of 2 repeated scans from 3 healthy subjects. Degree of linear association between PCF volume and 6 linear landmarks was determined by means of Pearson correlation. PCF volumes measured by use of the automated method and with manual delineation were similar, 196.2 ± 8.7 mL versus 196.9 ± 11.0 mL, respectively. The mean relative difference of -0.3 ± 1.9% was not statistically significant. Low measurement variability, with a mean absolute percentage value of 0.6 ± 0.2%, was achieved. None of the PCF linear landmarks were significantly associated with PCF volume. PCF and tissue content volumes can be reliably measured in patients with CMI by use of an atlas-based automated segmentation method.

Three-dimensional morphological analysis of intracranial aneurysms: a fully automated method for aneurysm sac isolation and quantification.

PubMed

Larrabide, Ignacio; Cruz Villa-Uriol, Maria; Cárdenes, Rubén; Pozo, Jose Maria; Macho, Juan; San Roman, Luis; Blasco, Jordi; Vivas, Elio; Marzo, Alberto; Hose, D Rod; Frangi, Alejandro F

2011-05-01

Morphological descriptors are practical and essential biomarkers for diagnosis and treatment selection for intracranial aneurysm management according to the current guidelines in use. Nevertheless, relatively little work has been dedicated to improve the three-dimensional quantification of aneurysmal morphology, to automate the analysis, and hence to reduce the inherent intra and interobserver variability of manual analysis. In this paper we propose a methodology for the automated isolation and morphological quantification of saccular intracranial aneurysms based on a 3D representation of the vascular anatomy. This methodology is based on the analysis of the vasculature skeleton's topology and the subsequent application of concepts from deformable cylinders. These are expanded inside the parent vessel to identify different regions and discriminate the aneurysm sac from the parent vessel wall. The method renders as output the surface representation of the isolated aneurysm sac, which can then be quantified automatically. The proposed method provides the means for identifying the aneurysm neck in a deterministic way. The results obtained by the method were assessed in two ways: they were compared to manual measurements obtained by three independent clinicians as normally done during diagnosis and to automated measurements from manually isolated aneurysms by three independent operators, nonclinicians, experts in vascular image analysis. All the measurements were obtained using in-house tools. The results were qualitatively and quantitatively compared for a set of the saccular intracranial aneurysms (n = 26). Measurements performed on a synthetic phantom showed that the automated measurements obtained from manually isolated aneurysms where the most accurate. The differences between the measurements obtained by the clinicians and the manually isolated sacs were statistically significant (neck width: p <0.001, sac height: p = 0.002). When comparing clinicians' measurements to automatically isolated sacs, only the differences for the neck width were significant (neck width: p <0.001, sac height: p = 0.95). However, the correlation and agreement between the measurements obtained from manually and automatically isolated aneurysms for the neck width: p = 0.43 and sac height: p = 0.95 where found. The proposed method allows the automated isolation of intracranial aneurysms, eliminating the interobserver variability. In average, the computational cost of the automated method (2 min 36 s) was similar to the time required by a manual operator (measurement by clinicians: 2 min 51 s, manual isolation: 2 min 21 s) but eliminating human interaction. The automated measurements are irrespective of the viewing angle, eliminating any bias or difference between the observer criteria. Finally, the qualitative assessment of the results showed acceptable agreement between manually and automatically isolated aneurysms.

A Method for Automated Detection of Usability Problems from Client User Interface Events

PubMed Central

Saadawi, Gilan M.; Legowski, Elizabeth; Medvedeva, Olga; Chavan, Girish; Crowley, Rebecca S.

2005-01-01

Think-aloud usability analysis provides extremely useful data but is very time-consuming and expensive to perform because of the extensive manual video analysis that is required. We describe a simple method for automated detection of usability problems from client user interface events for a developing medical intelligent tutoring system. The method incorporates (1) an agent-based method for communication that funnels all interface events and system responses to a centralized database, (2) a simple schema for representing interface events and higher order subgoals, and (3) an algorithm that reproduces the criteria used for manual coding of usability problems. A correction factor was empirically determining to account for the slower task performance of users when thinking aloud. We tested the validity of the method by simultaneously identifying usability problems using TAU and manually computing them from stored interface event data using the proposed algorithm. All usability problems that did not rely on verbal utterances were detectable with the proposed method. PMID:16779121

Sensitivity-based virtual fields for the non-linear virtual fields method

NASA Astrophysics Data System (ADS)

Marek, Aleksander; Davis, Frances M.; Pierron, Fabrice

2017-09-01

The virtual fields method is an approach to inversely identify material parameters using full-field deformation data. In this manuscript, a new set of automatically-defined virtual fields for non-linear constitutive models has been proposed. These new sensitivity-based virtual fields reduce the influence of noise on the parameter identification. The sensitivity-based virtual fields were applied to a numerical example involving small strain plasticity; however, the general formulation derived for these virtual fields is applicable to any non-linear constitutive model. To quantify the improvement offered by these new virtual fields, they were compared with stiffness-based and manually defined virtual fields. The proposed sensitivity-based virtual fields were consistently able to identify plastic model parameters and outperform the stiffness-based and manually defined virtual fields when the data was corrupted by noise.

NASA Safety Manual. Volume 3: System Safety

NASA Technical Reports Server (NTRS)

1970-01-01

This Volume 3 of the NASA Safety Manual sets forth the basic elements and techniques for managing a system safety program and the technical methods recommended for use in developing a risk evaluation program that is oriented to the identification of hazards in aerospace hardware systems and the development of residual risk management information for the program manager that is based on the hazards identified. The methods and techniques described in this volume are in consonance with the requirements set forth in NHB 1700.1 (VI), Chapter 3. This volume and future volumes of the NASA Safety Manual shall not be rewritten, reprinted, or reproduced in any manner. Installation implementing procedures, if necessary, shall be inserted as page supplements in accordance with the provisions of Appendix A. No portion of this volume or future volumes of the NASA Safety Manual shall be invoked in contracts.

A Manual for Assessing Language Growth in Instructional Settings.

ERIC Educational Resources Information Center

Swinton, Spencer S.

This manual is designed to assist administrators of English-as-a-second-language programs in assessing students' language growth. It begins by reviewing some of the concepts and terminology to be used. It then goes on to suggest and illustrate data-recording formats and methods of summarizing raw gains. This is followed by an example based on…

Comparative performance evaluation of automated segmentation methods of hippocampus from magnetic resonance images of temporal lobe epilepsy patients

PubMed Central

Hosseini, Mohammad-Parsa; Nazem-Zadeh, Mohammad-Reza; Pompili, Dario; Jafari-Khouzani, Kourosh; Elisevich, Kost; Soltanian-Zadeh, Hamid

2016-01-01

Purpose: Segmentation of the hippocampus from magnetic resonance (MR) images is a key task in the evaluation of mesial temporal lobe epilepsy (mTLE) patients. Several automated algorithms have been proposed although manual segmentation remains the benchmark. Choosing a reliable algorithm is problematic since structural definition pertaining to multiple edges, missing and fuzzy boundaries, and shape changes varies among mTLE subjects. Lack of statistical references and guidance for quantifying the reliability and reproducibility of automated techniques has further detracted from automated approaches. The purpose of this study was to develop a systematic and statistical approach using a large dataset for the evaluation of automated methods and establish a method that would achieve results better approximating those attained by manual tracing in the epileptogenic hippocampus. Methods: A template database of 195 (81 males, 114 females; age range 32–67 yr, mean 49.16 yr) MR images of mTLE patients was used in this study. Hippocampal segmentation was accomplished manually and by two well-known tools (FreeSurfer and hammer) and two previously published methods developed at their institution [Automatic brain structure segmentation (ABSS) and LocalInfo]. To establish which method was better performing for mTLE cases, several voxel-based, distance-based, and volume-based performance metrics were considered. Statistical validations of the results using automated techniques were compared with the results of benchmark manual segmentation. Extracted metrics were analyzed to find the method that provided a more similar result relative to the benchmark. Results: Among the four automated methods, ABSS generated the most accurate results. For this method, the Dice coefficient was 5.13%, 14.10%, and 16.67% higher, Hausdorff was 22.65%, 86.73%, and 69.58% lower, precision was 4.94%, −4.94%, and 12.35% higher, and the root mean square (RMS) was 19.05%, 61.90%, and 65.08% lower than LocalInfo, FreeSurfer, and hammer, respectively. The Bland–Altman similarity analysis revealed a low bias for the ABSS and LocalInfo techniques compared to the others. Conclusions: The ABSS method for automated hippocampal segmentation outperformed other methods, best approximating what could be achieved by manual tracing. This study also shows that four categories of input data can cause automated segmentation methods to fail. They include incomplete studies, artifact, low signal-to-noise ratio, and inhomogeneity. Different scanner platforms and pulse sequences were considered as means by which to improve reliability of the automated methods. Other modifications were specially devised to enhance a particular method assessed in this study. PMID:26745947

Fully convolutional networks (FCNs)-based segmentation method for colorectal tumors on T2-weighted magnetic resonance images.

PubMed

Jian, Junming; Xiong, Fei; Xia, Wei; Zhang, Rui; Gu, Jinhui; Wu, Xiaodong; Meng, Xiaochun; Gao, Xin

2018-06-01

Segmentation of colorectal tumors is the basis of preoperative prediction, staging, and therapeutic response evaluation. Due to the blurred boundary between lesions and normal colorectal tissue, it is hard to realize accurate segmentation. Routinely manual or semi-manual segmentation methods are extremely tedious, time-consuming, and highly operator-dependent. In the framework of FCNs, a segmentation method for colorectal tumor was presented. Normalization was applied to reduce the differences among images. Borrowing from transfer learning, VGG-16 was employed to extract features from normalized images. We conducted five side-output blocks from the last convolutional layer of each block of VGG-16 along the network, these side-output blocks can deep dive multiscale features, and produced corresponding predictions. Finally, all of the predictions from side-output blocks were fused to determine the final boundaries of the tumors. A quantitative comparison of 2772 colorectal tumor manual segmentation results from T2-weighted magnetic resonance images shows that the average Dice similarity coefficient, positive predictive value, specificity, sensitivity, Hammoude distance, and Hausdorff distance were 83.56, 82.67, 96.75, 87.85%, 0.2694, and 8.20, respectively. The proposed method is superior to U-net in colorectal tumor segmentation (P < 0.05). There is no difference between cross-entropy loss and Dice-based loss in colorectal tumor segmentation (P > 0.05). The results indicate that the introduction of FCNs contributed to accurate segmentation of colorectal tumors. This method has the potential to replace the present time-consuming and nonreproducible manual segmentation method.

A new background distribution-based active contour model for three-dimensional lesion segmentation in breast DCE-MRI

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

Liu, Hui; Liu, Yiping; Qiu, Tianshuang

2014-08-15

Purpose: To develop and evaluate a computerized semiautomatic segmentation method for accurate extraction of three-dimensional lesions from dynamic contrast-enhanced magnetic resonance images (DCE-MRIs) of the breast. Methods: The authors propose a new background distribution-based active contour model using level set (BDACMLS) to segment lesions in breast DCE-MRIs. The method starts with manual selection of a region of interest (ROI) that contains the entire lesion in a single slice where the lesion is enhanced. Then the lesion volume from the volume data of interest, which is captured automatically, is separated. The core idea of BDACMLS is a new signed pressure functionmore » which is based solely on the intensity distribution combined with pathophysiological basis. To compare the algorithm results, two experienced radiologists delineated all lesions jointly to obtain the ground truth. In addition, results generated by other different methods based on level set (LS) are also compared with the authors’ method. Finally, the performance of the proposed method is evaluated by several region-based metrics such as the overlap ratio. Results: Forty-two studies with 46 lesions that contain 29 benign and 17 malignant lesions are evaluated. The dataset includes various typical pathologies of the breast such as invasive ductal carcinoma, ductal carcinomain situ, scar carcinoma, phyllodes tumor, breast cysts, fibroadenoma, etc. The overlap ratio for BDACMLS with respect to manual segmentation is 79.55% ± 12.60% (mean ± s.d.). Conclusions: A new active contour model method has been developed and shown to successfully segment breast DCE-MRI three-dimensional lesions. The results from this model correspond more closely to manual segmentation, solve the weak-edge-passed problem, and improve the robustness in segmenting different lesions.« less

The paradox of sham therapy and placebo effect in osteopathy: A systematic review.

PubMed

Cerritelli, Francesco; Verzella, Marco; Cicchitti, Luca; D'Alessandro, Giandomenico; Vanacore, Nicola

2016-08-01

Placebo, defined as "false treatment," is a common gold-standard method to assess the validity of a therapy both in pharmacological trials and manual medicine research where placebo is also referred to as "sham therapy." In the medical literature, guidelines have been proposed on how to conduct robust placebo-controlled trials, but mainly in a drug-based scenario. In contrast, there are not precise guidelines on how to conduct a placebo-controlled in manual medicine trials (particularly osteopathy). The aim of the present systematic review was to report how and what type of sham methods, dosage, operator characteristics, and patient types were used in osteopathic clinical trials and, eventually, assess sham clinical effectiveness. A systematic Cochrane-based review was conducted by analyzing the osteopathic trials that used both manual and nonmanual placebo control. Searches were conducted on 8 databases from journal inception to December 2015 using a pragmatic literature search approach. Two independent reviewers conducted the study selection and data extraction for each study. The risk of bias was evaluated according to the Cochrane methods. A total of 64 studies were eligible for analysis collecting a total of 5024 participants. More than half (43 studies) used a manual placebo; 9 studies used a nonmanual placebo; and 12 studies used both manual and nonmanual placebo. Data showed lack of reporting sham therapy information across studies. Risk of bias analysis demonstrated a high risk of bias for allocation, blinding of personnel and participants, selective, and other bias. To explore the clinical effects of sham therapies used, a quantitative analysis was planned. However, due to the high heterogeneity of sham approaches used no further analyses were performed. High heterogeneity regarding placebo used between studies, lack of reporting information on placebo methods and within-study variability between sham and real treatment procedures suggest prudence in reading and interpreting study findings in manual osteopathic randomized controlled trials (RCTs). Efforts must be made to promote guidelines to design the most reliable placebo for manual RCTs as a means of increasing the internal validity and improve external validity of findings.

Comparative performance evaluation of automated segmentation methods of hippocampus from magnetic resonance images of temporal lobe epilepsy patients.

PubMed

Hosseini, Mohammad-Parsa; Nazem-Zadeh, Mohammad-Reza; Pompili, Dario; Jafari-Khouzani, Kourosh; Elisevich, Kost; Soltanian-Zadeh, Hamid

2016-01-01

Segmentation of the hippocampus from magnetic resonance (MR) images is a key task in the evaluation of mesial temporal lobe epilepsy (mTLE) patients. Several automated algorithms have been proposed although manual segmentation remains the benchmark. Choosing a reliable algorithm is problematic since structural definition pertaining to multiple edges, missing and fuzzy boundaries, and shape changes varies among mTLE subjects. Lack of statistical references and guidance for quantifying the reliability and reproducibility of automated techniques has further detracted from automated approaches. The purpose of this study was to develop a systematic and statistical approach using a large dataset for the evaluation of automated methods and establish a method that would achieve results better approximating those attained by manual tracing in the epileptogenic hippocampus. A template database of 195 (81 males, 114 females; age range 32-67 yr, mean 49.16 yr) MR images of mTLE patients was used in this study. Hippocampal segmentation was accomplished manually and by two well-known tools (FreeSurfer and hammer) and two previously published methods developed at their institution [Automatic brain structure segmentation (ABSS) and LocalInfo]. To establish which method was better performing for mTLE cases, several voxel-based, distance-based, and volume-based performance metrics were considered. Statistical validations of the results using automated techniques were compared with the results of benchmark manual segmentation. Extracted metrics were analyzed to find the method that provided a more similar result relative to the benchmark. Among the four automated methods, ABSS generated the most accurate results. For this method, the Dice coefficient was 5.13%, 14.10%, and 16.67% higher, Hausdorff was 22.65%, 86.73%, and 69.58% lower, precision was 4.94%, -4.94%, and 12.35% higher, and the root mean square (RMS) was 19.05%, 61.90%, and 65.08% lower than LocalInfo, FreeSurfer, and hammer, respectively. The Bland-Altman similarity analysis revealed a low bias for the ABSS and LocalInfo techniques compared to the others. The ABSS method for automated hippocampal segmentation outperformed other methods, best approximating what could be achieved by manual tracing. This study also shows that four categories of input data can cause automated segmentation methods to fail. They include incomplete studies, artifact, low signal-to-noise ratio, and inhomogeneity. Different scanner platforms and pulse sequences were considered as means by which to improve reliability of the automated methods. Other modifications were specially devised to enhance a particular method assessed in this study.

Dakota, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis version 6.0 theory manual

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

Adams, Brian M.; Ebeida, Mohamed Salah; Eldred, Michael S

The Dakota (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a exible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quanti cation with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components requiredmore » for iterative systems analyses, the Dakota toolkit provides a exible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quanti cation, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.« less

A motor learning approach to training wheelchair propulsion biomechanics for new manual wheelchair users: A pilot study

PubMed Central

Morgan, Kerri A.; Tucker, Susan M.; Klaesner, Joseph W.; Engsberg, Jack R.

2017-01-01

Context/Objective Developing an evidence-based approach to teaching wheelchair skills and proper propulsion for everyday wheelchair users with a spinal cord injury (SCI) is important to their rehabilitation. The purpose of this project was to pilot test manual wheelchair training based on motor learning and repetition-based approaches for new manual wheelchair users with an SCI. Design A repeated measures within-subject design was used with participants acting as their own controls. Methods Six persons with an SCI requiring the use of a manual wheelchair participated in wheelchair training. The training included nine 90-minute sessions. The primary focus was on wheelchair propulsion biomechanics with a secondary focus on wheelchair skills. Outcome Measures During Pretest 1, Pretest 2, and Posttest, wheelchair propulsion biomechanics were measured using the Wheelchair Propulsion Test and a Video Motion Capture system. During Pretest 2 and Posttest, propulsion forces using the WheelMill System and wheelchair skills using the Wheelchair Skills Test were measured. Results Significant changes in area of the push loop, hand-to-axle relationship, and slope of push forces were found. Changes in propulsion patterns were identified post-training. No significant differences were found in peak and average push forces and wheelchair skills pre- and post-training. Conclusions This project identified trends in change related to a repetition-based motor learning approach for propelling a manual wheelchair. The changes found were related to the propulsion patterns used by participants. Despite some challenges associated with implementing interventions for new manual wheelchair users, such as recruitment, the results of this study show that repetition-based training can improve biomechanics and propulsion patterns for new manual wheelchair users. PMID:26674751

Evaluation of Automated and Semi-Automated Scoring of Polysomnographic Recordings from a Clinical Trial Using Zolpidem in the Treatment of Insomnia

PubMed Central

Svetnik, Vladimir; Ma, Junshui; Soper, Keith A.; Doran, Scott; Renger, John J.; Deacon, Steve; Koblan, Ken S.

2007-01-01

Objective: To evaluate the performance of 2 automated systems, Morpheus and Somnolyzer24X7, with various levels of human review/editing, in scoring polysomnographic (PSG) recordings from a clinical trial using zolpidem in a model of transient insomnia. Methods: 164 all-night PSG recordings from 82 subjects collected during 2 nights of sleep, one under placebo and one under zolpidem (10 mg) treatment were used. For each recording, 6 different methods were used to provide sleep stage scores based on Rechtschaffen & Kales criteria: 1) full manual scoring, 2) automated scoring by Morpheus 3) automated scoring by Somnolyzer24X7, 4) automated scoring by Morpheus with full manual review, 5) automated scoring by Morpheus with partial manual review, 6) automated scoring by Somnolyzer24X7 with partial manual review. Ten traditional clinical efficacy measures of sleep initiation, maintenance, and architecture were calculated. Results: Pair-wise epoch-by-epoch agreements between fully automated and manual scores were in the range of intersite manual scoring agreements reported in the literature (70%-72%). Pair-wise epoch-by-epoch agreements between automated scores manually reviewed were higher (73%-76%). The direction and statistical significance of treatment effect sizes using traditional efficacy endpoints were essentially the same whichever method was used. As the degree of manual review increased, the magnitude of the effect size approached those estimated with fully manual scoring. Conclusion: Automated or semi-automated sleep PSG scoring offers valuable alternatives to costly, time consuming, and intrasite and intersite variable manual scoring, especially in large multicenter clinical trials. Reduction in scoring variability may also reduce the sample size of a clinical trial. Citation: Svetnik V; Ma J; Soper KA; Doran S; Renger JJ; Deacon S; Koblan KS. Evaluation of automated and semi-automated scoring of polysomnographic recordings from a clinical trial using zolpidem in the treatment of insomnia. SLEEP 2007;30(11):1562-1574. PMID:18041489

Generic method for automatic bladder segmentation on cone beam CT using a patient-specific bladder shape model

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

Schoot, A. J. A. J. van de, E-mail: a.j.schootvande@amc.uva.nl; Schooneveldt, G.; Wognum, S.

Purpose: The aim of this study is to develop and validate a generic method for automatic bladder segmentation on cone beam computed tomography (CBCT), independent of gender and treatment position (prone or supine), using only pretreatment imaging data. Methods: Data of 20 patients, treated for tumors in the pelvic region with the entire bladder visible on CT and CBCT, were divided into four equally sized groups based on gender and treatment position. The full and empty bladder contour, that can be acquired with pretreatment CT imaging, were used to generate a patient-specific bladder shape model. This model was used tomore » guide the segmentation process on CBCT. To obtain the bladder segmentation, the reference bladder contour was deformed iteratively by maximizing the cross-correlation between directional grey value gradients over the reference and CBCT bladder edge. To overcome incorrect segmentations caused by CBCT image artifacts, automatic adaptations were implemented. Moreover, locally incorrect segmentations could be adapted manually. After each adapted segmentation, the bladder shape model was expanded and new shape patterns were calculated for following segmentations. All available CBCTs were used to validate the segmentation algorithm. The bladder segmentations were validated by comparison with the manual delineations and the segmentation performance was quantified using the Dice similarity coefficient (DSC), surface distance error (SDE) and SD of contour-to-contour distances. Also, bladder volumes obtained by manual delineations and segmentations were compared using a Bland-Altman error analysis. Results: The mean DSC, mean SDE, and mean SD of contour-to-contour distances between segmentations and manual delineations were 0.87, 0.27 cm and 0.22 cm (female, prone), 0.85, 0.28 cm and 0.22 cm (female, supine), 0.89, 0.21 cm and 0.17 cm (male, supine) and 0.88, 0.23 cm and 0.17 cm (male, prone), respectively. Manual local adaptations improved the segmentation results significantly (p < 0.01) based on DSC (6.72%) and SD of contour-to-contour distances (0.08 cm) and decreased the 95% confidence intervals of the bladder volume differences. Moreover, expanding the shape model improved the segmentation results significantly (p < 0.01) based on DSC and SD of contour-to-contour distances. Conclusions: This patient-specific shape model based automatic bladder segmentation method on CBCT is accurate and generic. Our segmentation method only needs two pretreatment imaging data sets as prior knowledge, is independent of patient gender and patient treatment position and has the possibility to manually adapt the segmentation locally.« less

Synthesis/literature review for determining structural layer coefficients (SLC) of bases.

DOT National Transportation Integrated Search

2014-12-01

FDOTs current method of determining a base material structural layer coefficient (SLC) is detailed in the : Materials Manual, Chapter 2.1, Structural Layer Coefficients for Flexible Pavement Base Materials. : Currently, any new base material not a...

Automated classification of mouse pup isolation syllables: from cluster analysis to an Excel-based "mouse pup syllable classification calculator".

PubMed

Grimsley, Jasmine M S; Gadziola, Marie A; Wenstrup, Jeffrey J

2012-01-01

Mouse pups vocalize at high rates when they are cold or isolated from the nest. The proportions of each syllable type produced carry information about disease state and are being used as behavioral markers for the internal state of animals. Manual classifications of these vocalizations identified 10 syllable types based on their spectro-temporal features. However, manual classification of mouse syllables is time consuming and vulnerable to experimenter bias. This study uses an automated cluster analysis to identify acoustically distinct syllable types produced by CBA/CaJ mouse pups, and then compares the results to prior manual classification methods. The cluster analysis identified two syllable types, based on their frequency bands, that have continuous frequency-time structure, and two syllable types featuring abrupt frequency transitions. Although cluster analysis computed fewer syllable types than manual classification, the clusters represented well the probability distributions of the acoustic features within syllables. These probability distributions indicate that some of the manually classified syllable types are not statistically distinct. The characteristics of the four classified clusters were used to generate a Microsoft Excel-based mouse syllable classifier that rapidly categorizes syllables, with over a 90% match, into the syllable types determined by cluster analysis.

Segmentation of stereo terrain images

NASA Astrophysics Data System (ADS)

George, Debra A.; Privitera, Claudio M.; Blackmon, Theodore T.; Zbinden, Eric; Stark, Lawrence W.

2000-06-01

We have studied four approaches to segmentation of images: three automatic ones using image processing algorithms and a fourth approach, human manual segmentation. We were motivated toward helping with an important NASA Mars rover mission task -- replacing laborious manual path planning with automatic navigation of the rover on the Mars terrain. The goal of the automatic segmentations was to identify an obstacle map on the Mars terrain to enable automatic path planning for the rover. The automatic segmentation was first explored with two different segmentation methods: one based on pixel luminance, and the other based on pixel altitude generated through stereo image processing. The third automatic segmentation was achieved by combining these two types of image segmentation. Human manual segmentation of Martian terrain images was used for evaluating the effectiveness of the combined automatic segmentation as well as for determining how different humans segment the same images. Comparisons between two different segmentations, manual or automatic, were measured using a similarity metric, SAB. Based on this metric, the combined automatic segmentation did fairly well in agreeing with the manual segmentation. This was a demonstration of a positive step towards automatically creating the accurate obstacle maps necessary for automatic path planning and rover navigation.

One Small Step for Manuals: Computer-Assisted Training in Twelve-Step Facilitation*

PubMed Central

Sholomskas, Diane E.; Carroll, Kathleen M.

2008-01-01

Objective The burgeoning number of empirically validated therapies has not been met with systematic evaluation of practical, inexpensive means of teaching large numbers of clinicians to use these treatments effectively. An interactive, computer-assisted training program that sought to impart skills associated with the Project MATCH (Matching Alcoholism Treatments to Client Heterogeneity) Twelve-Step Facilitation (TSF) manual was developed to address this need. Method Twenty-five community-based substance use-treatment clinicians were randomized to one of two training conditions: (1) access to the computer-assisted training program plus the TSF manual or (2) access to the manual only. The primary outcome measure was change from pre- to posttraining in the clinicians' ability to demonstrate key TSF skills. Results The data suggested that the clinicians' ability to implement TSF, as assessed by independent ratings of adherence and skill for the key TSF interventions, was significantly higher after training for those who had access to the computerized training condition than those who were assigned to the manual-only condition. Those assigned to the computer-assisted training condition also demonstrated greater gains in a knowledge test assessing familiarity with concepts presented in the TSF manual. Conclusions Computer-based training may be a feasible and effective means of training larger numbers of clinicians in empirically supported, manual-guided therapies. PMID:17061013

Manual versus automated coding of free-text self-reported medication data in the 45 and Up Study: a validation study.

PubMed

Gnjidic, Danijela; Pearson, Sallie-Anne; Hilmer, Sarah N; Basilakis, Jim; Schaffer, Andrea L; Blyth, Fiona M; Banks, Emily

2015-03-30

Increasingly, automated methods are being used to code free-text medication data, but evidence on the validity of these methods is limited. To examine the accuracy of automated coding of previously keyed in free-text medication data compared with manual coding of original handwritten free-text responses (the 'gold standard'). A random sample of 500 participants (475 with and 25 without medication data in the free-text box) enrolled in the 45 and Up Study was selected. Manual coding involved medication experts keying in free-text responses and coding using Anatomical Therapeutic Chemical (ATC) codes (i.e. chemical substance 7-digit level; chemical subgroup 5-digit; pharmacological subgroup 4-digit; therapeutic subgroup 3-digit). Using keyed-in free-text responses entered by non-experts, the automated approach coded entries using the Australian Medicines Terminology database and assigned corresponding ATC codes. Based on manual coding, 1377 free-text entries were recorded and, of these, 1282 medications were coded to ATCs manually. The sensitivity of automated coding compared with manual coding was 79% (n = 1014) for entries coded at the exact ATC level, and 81.6% (n = 1046), 83.0% (n = 1064) and 83.8% (n = 1074) at the 5, 4 and 3-digit ATC levels, respectively. The sensitivity of automated coding for blank responses was 100% compared with manual coding. Sensitivity of automated coding was highest for prescription medications and lowest for vitamins and supplements, compared with the manual approach. Positive predictive values for automated coding were above 95% for 34 of the 38 individual prescription medications examined. Automated coding for free-text prescription medication data shows very high to excellent sensitivity and positive predictive values, indicating that automated methods can potentially be useful for large-scale, medication-related research.

Model-based segmentation in orbital volume measurement with cone beam computed tomography and evaluation against current concepts.

PubMed

Wagner, Maximilian E H; Gellrich, Nils-Claudius; Friese, Karl-Ingo; Becker, Matthias; Wolter, Franz-Erich; Lichtenstein, Juergen T; Stoetzer, Marcus; Rana, Majeed; Essig, Harald

2016-01-01

Objective determination of the orbital volume is important in the diagnostic process and in evaluating the efficacy of medical and/or surgical treatment of orbital diseases. Tools designed to measure orbital volume with computed tomography (CT) often cannot be used with cone beam CT (CBCT) because of inferior tissue representation, although CBCT has the benefit of greater availability and lower patient radiation exposure. Therefore, a model-based segmentation technique is presented as a new method for measuring orbital volume and compared to alternative techniques. Both eyes from thirty subjects with no known orbital pathology who had undergone CBCT as a part of routine care were evaluated (n = 60 eyes). Orbital volume was measured with manual, atlas-based, and model-based segmentation methods. Volume measurements, volume determination time, and usability were compared between the three methods. Differences in means were tested for statistical significance using two-tailed Student's t tests. Neither atlas-based (26.63 ± 3.15 mm(3)) nor model-based (26.87 ± 2.99 mm(3)) measurements were significantly different from manual volume measurements (26.65 ± 4.0 mm(3)). However, the time required to determine orbital volume was significantly longer for manual measurements (10.24 ± 1.21 min) than for atlas-based (6.96 ± 2.62 min, p < 0.001) or model-based (5.73 ± 1.12 min, p < 0.001) measurements. All three orbital volume measurement methods examined can accurately measure orbital volume, although atlas-based and model-based methods seem to be more user-friendly and less time-consuming. The new model-based technique achieves fully automated segmentation results, whereas all atlas-based segmentations at least required manipulations to the anterior closing. Additionally, model-based segmentation can provide reliable orbital volume measurements when CT image quality is poor.

Model-Based Method for Terrain-Following Display Design

DTIC Science & Technology

1989-06-15

data into a more compact set of model parameters. These model parameters provide insights into the interpretation of the experimental results as well...2.8 presents the VSD display, and is taken from figure 1.95 of the B-IB Flight Manual , NA-77-400. There are two primary elements in the VSD: 1) the...baseline VSD based on figures such as these from the B-lB Flight Manual , a video tape of an operating VSD in the engineering - 21 - research simulator, and

Foot Pedals for Spacecraft Manual Control

NASA Technical Reports Server (NTRS)

Love, Stanley G.; Morin, Lee M.; McCabe, Mary

2010-01-01

Fifty years ago, NASA decided that the cockpit controls in spacecraft should be like the ones in airplanes. But controls based on the stick and rudder may not be best way to manually control a vehicle in space. A different method is based on submersible vehicles controlled with foot pedals. A new pilot can learn the sub's control scheme in minutes and drive it hands-free. We are building a pair of foot pedals for spacecraft control, and will test them in a spacecraft flight simulator.

Calculating the Mean Amplitude of Glycemic Excursions from Continuous Glucose Data Using an Open-Code Programmable Algorithm Based on the Integer Nonlinear Method.

PubMed

Yu, Xuefei; Lin, Liangzhuo; Shen, Jie; Chen, Zhi; Jian, Jun; Li, Bin; Xin, Sherman Xuegang

2018-01-01

The mean amplitude of glycemic excursions (MAGE) is an essential index for glycemic variability assessment, which is treated as a key reference for blood glucose controlling at clinic. However, the traditional "ruler and pencil" manual method for the calculation of MAGE is time-consuming and prone to error due to the huge data size, making the development of robust computer-aided program an urgent requirement. Although several software products are available instead of manual calculation, poor agreement among them is reported. Therefore, more studies are required in this field. In this paper, we developed a mathematical algorithm based on integer nonlinear programming. Following the proposed mathematical method, an open-code computer program named MAGECAA v1.0 was developed and validated. The results of the statistical analysis indicated that the developed program was robust compared to the manual method. The agreement among the developed program and currently available popular software is satisfied, indicating that the worry about the disagreement among different software products is not necessary. The open-code programmable algorithm is an extra resource for those peers who are interested in the related study on methodology in the future.

Classifying zones of suitability for manual drilling using textural and hydraulic parameters of shallow aquifers: a case study in northwestern Senegal

NASA Astrophysics Data System (ADS)

Fussi, F. Fabio; Fumagalli, Letizia; Fava, Francesco; Di Mauro, Biagio; Kane, Cheik Hamidou; Niang, Magatte; Wade, Souleye; Hamidou, Barry; Colombo, Roberto; Bonomi, Tullia

2017-12-01

A method is proposed that uses analysis of borehole stratigraphic logs for the characterization of shallow aquifers and for the assessment of areas suitable for manual drilling. The model is based on available borehole-log parameters: depth to hard rock, depth to water, thickness of laterite and hydraulic transmissivity of the shallow aquifer. The model is applied to a study area in northwestern Senegal. A dataset of boreholes logs has been processed using a software package (TANGAFRIC) developed during the research. After a manual procedure to assign a standard category describing the lithological characteristics, the next step is the automated extraction of different textural parameters and the estimation of hydraulic conductivity using reference values available in the literature. The hydraulic conductivity values estimated from stratigraphic data have been partially validated, by comparing them with measured values from a series of pumping tests carried out in large-diameter wells. The results show that this method is able to produce a reliable interpretation of the shallow hydrogeological context using information generally available in the region. The research contributes to improving the identification of areas where conditions are suitable for manual drilling. This is achieved by applying the described method, based on a structured and semi-quantitative approach, to classify the zones of suitability for given manual drilling techniques using data available in most African countries. Ultimately, this work will support proposed international programs aimed at promoting low-cost water supply in Africa and enhancing access to safe drinking water for the population.

Optimal level of continuous positive airway pressure: auto-adjusting titration versus titration with a predictive equation.

PubMed

Choi, Ji Ho; Jun, Young Joon; Oh, Jeong In; Jung, Jong Yoon; Hwang, Gyu Ho; Kwon, Soon Young; Lee, Heung Man; Kim, Tae Hoon; Lee, Sang Hag; Lee, Seung Hoon

2013-05-01

The aims of the present study were twofold. We sought to compare two methods of titrating the level of continuous positive airway pressure (CPAP) - auto-adjusting titration and titration using a predictive equation - with full-night manual titration used as the benchmark. We also investigated the reliability of the two methods in patients with obstructive sleep apnea syndrome (OSAS). Twenty consecutive adult patients with OSAS who had successful, full-night manual and auto-adjusting CPAP titration participated in this study. The titration pressure level was calculated with a previously developed predictive equation based on body mass index and apnea-hypopnea index. The mean titration pressure levels obtained with the manual, auto-adjusting, and predictive equation methods were 9.0 +/- 3.6, 9.4 +/- 3.0, and 8.1 +/- 1.6 cm H2O,respectively. There was a significant difference in the concordance within the range of +/- 2 cm H2O (p = 0.019) between both the auto-adjusting titration and the titration using the predictive equation compared to the full-night manual titration. However, there was no significant difference in the concordance within the range of +/- 1 cm H2O (p > 0.999). When compared to full-night manual titration as the standard method, auto-adjusting titration appears to be more reliable than using a predictive equation for determining the optimal CPAP level in patients with OSAS.

Region-based multi-step optic disk and cup segmentation from color fundus image

NASA Astrophysics Data System (ADS)

Xiao, Di; Lock, Jane; Manresa, Javier Moreno; Vignarajan, Janardhan; Tay-Kearney, Mei-Ling; Kanagasingam, Yogesan

2013-02-01

Retinal optic cup-disk-ratio (CDR) is a one of important indicators of glaucomatous neuropathy. In this paper, we propose a novel multi-step 4-quadrant thresholding method for optic disk segmentation and a multi-step temporal-nasal segmenting method for optic cup segmentation based on blood vessel inpainted HSL lightness images and green images. The performance of the proposed methods was evaluated on a group of color fundus images and compared with the manual outlining results from two experts. Dice scores of detected disk and cup regions between the auto and manual results were computed and compared. Vertical CDRs were also compared among the three results. The preliminary experiment has demonstrated the robustness of the method for automatic optic disk and cup segmentation and its potential value for clinical application.

Comparison of Manual Versus Automated Data Collection Method for an Evidence-Based Nursing Practice Study

PubMed Central

Byrne, M.D.; Jordan, T.R.; Welle, T.

2013-01-01

Objective The objective of this study was to investigate and improve the use of automated data collection procedures for nursing research and quality assurance. Methods A descriptive, correlational study analyzed 44 orthopedic surgical patients who were part of an evidence-based practice (EBP) project examining post-operative oxygen therapy at a Midwestern hospital. The automation work attempted to replicate a manually-collected data set from the EBP project. Results Automation was successful in replicating data collection for study data elements that were available in the clinical data repository. The automation procedures identified 32 “false negative” patients who met the inclusion criteria described in the EBP project but were not selected during the manual data collection. Automating data collection for certain data elements, such as oxygen saturation, proved challenging because of workflow and practice variations and the reliance on disparate sources for data abstraction. Automation also revealed instances of human error including computational and transcription errors as well as incomplete selection of eligible patients. Conclusion Automated data collection for analysis of nursing-specific phenomenon is potentially superior to manual data collection methods. Creation of automated reports and analysis may require initial up-front investment with collaboration between clinicians, researchers and information technology specialists who can manage the ambiguities and challenges of research and quality assurance work in healthcare. PMID:23650488

Automated estimation of choroidal thickness distribution and volume based on OCT images of posterior visual section.

PubMed

Vupparaboina, Kiran Kumar; Nizampatnam, Srinath; Chhablani, Jay; Richhariya, Ashutosh; Jana, Soumya

2015-12-01

A variety of vision ailments are indicated by anomalies in the choroid layer of the posterior visual section. Consequently, choroidal thickness and volume measurements, usually performed by experts based on optical coherence tomography (OCT) images, have assumed diagnostic significance. Now, to save precious expert time, it has become imperative to develop automated methods. To this end, one requires choroid outer boundary (COB) detection as a crucial step, where difficulty arises as the COB divides the choroidal granularity and the scleral uniformity only notionally, without marked brightness variation. In this backdrop, we measure the structural dissimilarity between choroid and sclera by structural similarity (SSIM) index, and hence estimate the COB by thresholding. Subsequently, smooth COB estimates, mimicking manual delineation, are obtained using tensor voting. On five datasets, each consisting of 97 adult OCT B-scans, automated and manual segmentation results agree visually. We also demonstrate close statistical match (greater than 99.6% correlation) between choroidal thickness distributions obtained algorithmically and manually. Further, quantitative superiority of our method is established over existing results by respective factors of 27.67% and 76.04% in two quotient measures defined relative to observer repeatability. Finally, automated choroidal volume estimation, being attempted for the first time, also yields results in close agreement with that of manual methods. Copyright © 2015 Elsevier Ltd. All rights reserved.

Battery Test Manual For Electric Vehicles, Revision 3

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

Christophersen, Jon P.

2015-06-01

This battery test procedure manual was prepared for the United States Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy (EERE), Vehicle Technologies Office. It is based on technical targets for commercial viability established for energy storage development projects aimed at meeting system level DOE goals for Electric Vehicles (EV). The specific procedures defined in this manual support the performance and life characterization of advanced battery devices under development for EVs. However, it does share some methods described in the previously published battery test manual for plug-in hybrid electric vehicles. Due to the complexity of some of themore » procedures and supporting analysis, future revisions including some modifications and clarifications of these procedures are expected. As in previous battery and capacitor test manuals, this version of the manual defines testing methods for full-size battery systems, along with provisions for scaling these tests for modules, cells or other subscale level devices. The DOE-United States Advanced Battery Consortium (USABC), Technical Advisory Committee (TAC) supported the development of the manual. Technical Team points of contact responsible for its development and revision are Chul Bae of Ford Motor Company and Jon P. Christophersen of the Idaho National Laboratory. The development of this manual was funded by the Unites States Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Technical direction from DOE was provided by David Howell, Energy Storage R&D Manager and Hybrid Electric Systems Team Leader. Comments and questions regarding the manual should be directed to Jon P. Christophersen at the Idaho National Laboratory (jon.christophersen@inl.gov).« less

Automated Bone Segmentation and Surface Evaluation of a Small Animal Model of Post-Traumatic Osteoarthritis.

PubMed

Ramme, Austin J; Voss, Kevin; Lesporis, Jurinus; Lendhey, Matin S; Coughlin, Thomas R; Strauss, Eric J; Kennedy, Oran D

2017-05-01

MicroCT imaging allows for noninvasive microstructural evaluation of mineralized bone tissue, and is essential in studies of small animal models of bone and joint diseases. Automatic segmentation and evaluation of articular surfaces is challenging. Here, we present a novel method to create knee joint surface models, for the evaluation of PTOA-related joint changes in the rat using an atlas-based diffeomorphic registration to automatically isolate bone from surrounding tissues. As validation, two independent raters manually segment datasets and the resulting segmentations were compared to our novel automatic segmentation process. Data were evaluated using label map volumes, overlap metrics, Euclidean distance mapping, and a time trial. Intraclass correlation coefficients were calculated to compare methods, and were greater than 0.90. Total overlap, union overlap, and mean overlap were calculated to compare the automatic and manual methods and ranged from 0.85 to 0.99. A Euclidean distance comparison was also performed and showed no measurable difference between manual and automatic segmentations. Furthermore, our new method was 18 times faster than manual segmentation. Overall, this study describes a reliable, accurate, and automatic segmentation method for mineralized knee structures from microCT images, and will allow for efficient assessment of bony changes in small animal models of PTOA.

Automated brain computed tomographic densitometry of early ischemic changes in acute stroke

PubMed Central

Stoel, Berend C.; Marquering, Henk A.; Staring, Marius; Beenen, Ludo F.; Slump, Cornelis H.; Roos, Yvo B.; Majoie, Charles B.

2015-01-01

Abstract. The Alberta Stroke Program Early CT score (ASPECTS) scoring method is frequently used for quantifying early ischemic changes (EICs) in patients with acute ischemic stroke in clinical studies. Varying interobserver agreement has been reported, however, with limited agreement. Therefore, our goal was to develop and evaluate an automated brain densitometric method. It divides CT scans of the brain into ASPECTS regions using atlas-based segmentation. EICs are quantified by comparing the brain density between contralateral sides. This method was optimized and validated using CT data from 10 and 63 patients, respectively. The automated method was validated against manual ASPECTS, stroke severity at baseline and clinical outcome after 7 to 10 days (NIH Stroke Scale, NIHSS) and 3 months (modified Rankin Scale). Manual and automated ASPECTS showed similar and statistically significant correlations with baseline NIHSS (R=−0.399 and −0.277, respectively) and with follow-up mRS (R=−0.256 and −0.272), except for the follow-up NIHSS. Agreement between automated and consensus ASPECTS reading was similar to the interobserver agreement of manual ASPECTS (differences <1 point in 73% of cases). The automated ASPECTS method could, therefore, be used as a supplementary tool to assist manual scoring. PMID:26158082

Comparison of human septal nuclei MRI measurements using automated segmentation and a new manual protocol based on histology

PubMed Central

Butler, Tracy; Zaborszky, Laszlo; Pirraglia, Elizabeth; Li, Jinyu; Wang, Xiuyuan Hugh; Li, Yi; Tsui, Wai; Talos, Delia; Devinsky, Orrin; Kuchna, Izabela; Nowicki, Krzysztof; French, Jacqueline; Kuzniecky, Rubin; Wegiel, Jerzy; Glodzik, Lidia; Rusinek, Henry; DeLeon, Mony J.; Thesen, Thomas

2014-01-01

Septal nuclei, located in basal forebrain, are strongly connected with hippocampi and important in learning and memory, but have received limited research attention in human MRI studies. While probabilistic maps for estimating septal volume on MRI are now available, they have not been independently validated against manual tracing of MRI, typically considered the gold standard for delineating brain structures. We developed a protocol for manual tracing of the human septal region on MRI based on examination of neuroanatomical specimens. We applied this tracing protocol to T1 MRI scans (n=86) from subjects with temporal epilepsy and healthy controls to measure septal volume. To assess the inter-rater reliability of the protocol, a second tracer used the same protocol on 20 scans that were randomly selected from the 72 healthy controls. In addition to measuring septal volume, maximum septal thickness between the ventricles was measured and recorded. The same scans (n=86) were also analysed using septal probabilistic maps and Dartel toolbox in SPM. Results show that our manual tracing algorithm is reliable, and that septal volume measurements obtained via manual and automated methods correlate significantly with each other (p<001). Both manual and automated methods detected significantly enlarged septal nuclei in patients with temporal lobe epilepsy in accord with a proposed compensatory neuroplastic process related to the strong connections between septal nuclei and hippocampi. Septal thickness, which was simple to measure with excellent inter-rater reliability, correlated well with both manual and automated septal volume, suggesting it could serve as an easy-to-measure surrogate for septal volume in future studies. Our results call attention to the important though understudied human septal region, confirm its enlargement in temporal lobe epilepsy, and provide a reliable new manual delineation protocol that will facilitate continued study of this critical region. PMID:24736183

Comparison of human septal nuclei MRI measurements using automated segmentation and a new manual protocol based on histology.

PubMed

Butler, Tracy; Zaborszky, Laszlo; Pirraglia, Elizabeth; Li, Jinyu; Wang, Xiuyuan Hugh; Li, Yi; Tsui, Wai; Talos, Delia; Devinsky, Orrin; Kuchna, Izabela; Nowicki, Krzysztof; French, Jacqueline; Kuzniecky, Rubin; Wegiel, Jerzy; Glodzik, Lidia; Rusinek, Henry; deLeon, Mony J; Thesen, Thomas

2014-08-15

Septal nuclei, located in basal forebrain, are strongly connected with hippocampi and important in learning and memory, but have received limited research attention in human MRI studies. While probabilistic maps for estimating septal volume on MRI are now available, they have not been independently validated against manual tracing of MRI, typically considered the gold standard for delineating brain structures. We developed a protocol for manual tracing of the human septal region on MRI based on examination of neuroanatomical specimens. We applied this tracing protocol to T1 MRI scans (n=86) from subjects with temporal epilepsy and healthy controls to measure septal volume. To assess the inter-rater reliability of the protocol, a second tracer used the same protocol on 20 scans that were randomly selected from the 72 healthy controls. In addition to measuring septal volume, maximum septal thickness between the ventricles was measured and recorded. The same scans (n=86) were also analyzed using septal probabilistic maps and DARTEL toolbox in SPM. Results show that our manual tracing algorithm is reliable, and that septal volume measurements obtained via manual and automated methods correlate significantly with each other (p<.001). Both manual and automated methods detected significantly enlarged septal nuclei in patients with temporal lobe epilepsy in accord with a proposed compensatory neuroplastic process related to the strong connections between septal nuclei and hippocampi. Septal thickness, which was simple to measure with excellent inter-rater reliability, correlated well with both manual and automated septal volume, suggesting it could serve as an easy-to-measure surrogate for septal volume in future studies. Our results call attention to the important though understudied human septal region, confirm its enlargement in temporal lobe epilepsy, and provide a reliable new manual delineation protocol that will facilitate continued study of this critical region. Copyright © 2014 Elsevier Inc. All rights reserved.

Effects of Selected Task Performance Criteria at Initiating Adaptive Task Real locations

NASA Technical Reports Server (NTRS)

Montgomery, Demaris A.

2001-01-01

In the current report various performance assessment methods used to initiate mode transfers between manual control and automation for adaptive task reallocation were tested. Participants monitored two secondary tasks for critical events while actively controlling a process in a fictional system. One of the secondary monitoring tasks could be automated whenever operators' performance was below acceptable levels. Automation of the secondary task and transfer of the secondary task back to manual control were either human- or machine-initiated. Human-initiated transfers were based on the operator's assessment of the current task demands while machine-initiated transfers were based on the operators' performance. Different performance assessment methods were tested in two separate experiments.

Comparison between manual scaling and Autoscala automatic scaling applied to Sodankylä Geophysical Observatory ionograms

NASA Astrophysics Data System (ADS)

Enell, Carl-Fredrik; Kozlovsky, Alexander; Turunen, Tauno; Ulich, Thomas; Välitalo, Sirkku; Scotto, Carlo; Pezzopane, Michael

2016-03-01

This paper presents a comparison between standard ionospheric parameters manually and automatically scaled from ionograms recorded at the high-latitude Sodankylä Geophysical Observatory (SGO, ionosonde SO166, 64.1° geomagnetic latitude), located in the vicinity of the auroral oval. The study is based on 2610 ionograms recorded during the period June-December 2013. The automatic scaling was made by means of the Autoscala software. A few typical examples are shown to outline the method, and statistics are presented regarding the differences between manually and automatically scaled values of F2, F1, E and sporadic E (Es) layer parameters. We draw the conclusions that: 1. The F2 parameters scaled by Autoscala, foF2 and M(3000)F2, are reliable. 2. F1 is identified by Autoscala in significantly fewer cases (about 50 %) than in the manual routine, but if identified the values of foF1 are reliable. 3. Autoscala frequently (30 % of the cases) detects an E layer when the manual scaling process does not. When identified by both methods, the Autoscala E-layer parameters are close to those manually scaled, foE agreeing to within 0.4 MHz. 4. Es and parameters of Es identified by Autoscala are in many cases different from those of the manual scaling. Scaling of Es at auroral latitudes is often a difficult task.

Evaluation of an automated spike-and-wave complex detection algorithm in the EEG from a rat model of absence epilepsy.

PubMed

Bauquier, Sebastien H; Lai, Alan; Jiang, Jonathan L; Sui, Yi; Cook, Mark J

2015-10-01

The aim of this prospective blinded study was to evaluate an automated algorithm for spike-and-wave discharge (SWD) detection applied to EEGs from genetic absence epilepsy rats from Strasbourg (GAERS). Five GAERS underwent four sessions of 20-min EEG recording. Each EEG was manually analyzed for SWDs longer than one second by two investigators and automatically using an algorithm developed in MATLAB®. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated for the manual (reference) versus the automatic (test) methods. The results showed that the algorithm had specificity, sensitivity, PPV and NPV >94%, comparable to published methods that are based on analyzing EEG changes in the frequency domain. This provides a good alternative as a method designed to mimic human manual marking in the time domain.

Day Care for All Children: Integrating Children with Special Needs into Community Child Care Settings. A Resource and Consultation Manual.

ERIC Educational Resources Information Center

Gaumer, Nancy; And Others

This manual provides guidance on using the consultation method to help meet the needs of families of children with disabilities in integrated community-based day care settings. The introductory section provides an overview, a statement of philosophy, the history of the day care consultation program in Illinois, and instructions for using the…

USEPA MANUAL OF METHODS FOR VIROLOGY

EPA Science Inventory

This chapter describes procedures for the detection of coliphases in water matrices. These procedures are based on those presented in the Supplement to the 20th Edition of Standard Methods for the Examination of Water and Eastewater and EPA Methods 1601 and 1602. Two quantitati...

Comparison of 3D laser-based photonic scans and manual anthropometric measurements of body size and shape in a validation study of 123 young Swiss men

PubMed Central

Zwahlen, Marcel; Wells, Jonathan C.; Bender, Nicole; Henneberg, Maciej

2017-01-01

Background Manual anthropometric measurements are time-consuming and challenging to perform within acceptable intra- and inter-individual error margins in large studies. Three-dimensional (3D) laser body scanners provide a fast and precise alternative: within a few seconds the system produces a 3D image of the body topography and calculates some 150 standardised body size measurements. Objective The aim was to enhance the small number of existing validation studies and compare scan and manual techniques based on five selected measurements. We assessed the agreement between two repeated measurements within the two methods, analysed the direct agreement between the two methods, and explored the differences between the techniques when used in regressions assessing the effect of health related determinants on body shape indices. Methods We performed two repeated body scans on 123 volunteering young men using a Vitus Smart XXL body scanner. We manually measured height, waist, hip, buttock, and chest circumferences twice for each participant according to the WHO guidelines. The participants also filled in a basic questionnaire. Results Mean differences between the two scan measurements were smaller than between the two manual measurements, and precision as well as intra-class correlation coefficients were higher. Both techniques were strongly correlated. When comparing means between both techniques we found significant differences: Height was systematically shorter by 2.1 cm, whereas waist, hip and bust circumference measurements were larger in the scans by 1.17–4.37 cm. In consequence, body shape indices also became larger and the prevalence of overweight was greater when calculated from the scans. Between 4.1% and 7.3% of the probands changed risk category from normal to overweight when classified based on the scans. However, when employing regression analyses the two measurement techniques resulted in very similar coefficients, confidence intervals, and p-values. Conclusion For performing a large number of measurements in a large group of probands in a short time, body scans generally showed good feasibility, reliability, and validity in comparison to manual measurements. The systematic differences between the methods may result from their technical nature (contact vs. non-contact). PMID:28289559

NASA Hydrogen Peroxide Propellant Hazards Technical Manual

NASA Technical Reports Server (NTRS)

Baker, David L.; Greene, Ben; Frazier, Wayne

2005-01-01

The Fire, Explosion, Compatibility and Safety Hazards of Hydrogen Peroxide NASA technical manual was developed at the NASA Johnson Space Center White Sands Test Facility. NASA Technical Memorandum TM-2004-213151 covers topics concerning high concentration hydrogen peroxide including fire and explosion hazards, material and fluid reactivity, materials selection information, personnel and environmental hazards, physical and chemical properties, analytical spectroscopy, specifications, analytical methods, and material compatibility data. A summary of hydrogen peroxide-related accidents, incidents, dose calls, mishaps and lessons learned is included. The manual draws from art extensive literature base and includes recent applicable regulatory compliance documentation. The manual may be obtained by United States government agencies from NASA Johnson Space Center and used as a reference source for hazards and safe handling of hydrogen peroxide.

Automated Literature Searches for Longitudinal Tracking of Cancer Research Training Program Graduates.

PubMed

Padilla, Luz A; Desmond, Renee A; Brooks, C Michael; Waterbor, John W

2018-06-01

A key outcome measure of cancer research training programs is the number of cancer-related peer-reviewed publications after training. Because program graduates do not routinely report their publications, staff must periodically conduct electronic literature searches on each graduate. The purpose of this study is to compare findings of an innovative computer-based automated search program versus repeated manual literature searches to identify post-training peer-reviewed publications. In late 2014, manual searches for publications by former R25 students identified 232 cancer-related articles published by 112 of 543 program graduates. In 2016, a research assistant was instructed in performing Scopus literature searches for comparison with individual PubMed searches on our 543 program graduates. Through 2014, Scopus found 304 cancer publications, 220 of that had been retrieved manually plus an additional 84 papers. However, Scopus missed 12 publications found manually. Together, both methods found 316 publications. The automated method found 96.2 % of the 316 publications while individual searches found only 73.4 %. An automated search method such as using the Scopus database is a key tool for conducting comprehensive literature searches, but it must be supplemented with periodic manual searches to find the initial publications of program graduates. A time-saving feature of Scopus is the periodic automatic alerts of new publications. Although a training period is needed and initial costs can be high, an automated search method is worthwhile due to its high sensitivity and efficiency in the long term.

Automatic multi-camera calibration for deployable positioning systems

NASA Astrophysics Data System (ADS)

Axelsson, Maria; Karlsson, Mikael; Rudner, Staffan

2012-06-01

Surveillance with automated positioning and tracking of subjects and vehicles in 3D is desired in many defence and security applications. Camera systems with stereo or multiple cameras are often used for 3D positioning. In such systems, accurate camera calibration is needed to obtain a reliable 3D position estimate. There is also a need for automated camera calibration to facilitate fast deployment of semi-mobile multi-camera 3D positioning systems. In this paper we investigate a method for automatic calibration of the extrinsic camera parameters (relative camera pose and orientation) of a multi-camera positioning system. It is based on estimation of the essential matrix between each camera pair using the 5-point method for intrinsically calibrated cameras. The method is compared to a manual calibration method using real HD video data from a field trial with a multicamera positioning system. The method is also evaluated on simulated data from a stereo camera model. The results show that the reprojection error of the automated camera calibration method is close to or smaller than the error for the manual calibration method and that the automated calibration method can replace the manual calibration.

Validity of a Manual Soft Tissue Profile Prediction Method Following Mandibular Setback Osteotomy

PubMed Central

Kolokitha, Olga-Elpis

2007-01-01

Objectives The aim of this study was to determine the validity of a manual cephalometric method used for predicting the post-operative soft tissue profiles of patients who underwent mandibular setback surgery and compare it to a computerized cephalometric prediction method (Dentofacial Planner). Lateral cephalograms of 18 adults with mandibular prognathism taken at the end of pre-surgical orthodontics and approximately one year after surgery were used. Methods To test the validity of the manual method the prediction tracings were compared to the actual post-operative tracings. The Dentofacial Planner software was used to develop the computerized post-surgical prediction tracings. Both manual and computerized prediction printouts were analyzed by using the cephalometric system PORDIOS. Statistical analysis was performed by means of t-test. Results Comparison between manual prediction tracings and the actual post-operative profile showed that the manual method results in more convex soft tissue profiles; the upper lip was found in a more prominent position, upper lip thickness was increased and, the mandible and lower lip were found in a less posterior position than that of the actual profiles. Comparison between computerized and manual prediction methods showed that in the manual method upper lip thickness was increased, the upper lip was found in a more anterior position and the lower anterior facial height was increased as compared to the computerized prediction method. Conclusions Cephalometric simulation of post-operative soft tissue profile following orthodontic-surgical management of mandibular prognathism imposes certain limitations related to the methods implied. However, both manual and computerized prediction methods remain a useful tool for patient communication. PMID:19212468

A prospective comparison between auto-registration and manual registration of real-time ultrasound with MR images for percutaneous ablation or biopsy of hepatic lesions.

PubMed

Cha, Dong Ik; Lee, Min Woo; Song, Kyoung Doo; Oh, Young-Taek; Jeong, Ja-Yeon; Chang, Jung-Woo; Ryu, Jiwon; Lee, Kyong Joon; Kim, Jaeil; Bang, Won-Chul; Shin, Dong Kuk; Choi, Sung Jin; Koh, Dalkwon; Seo, Bong Koo; Kim, Kyunga

2017-06-01

To compare the accuracy and required time for image fusion of real-time ultrasound (US) with pre-procedural magnetic resonance (MR) images between positioning auto-registration and manual registration for percutaneous radiofrequency ablation or biopsy of hepatic lesions. This prospective study was approved by the institutional review board, and all patients gave written informed consent. Twenty-two patients (male/female, n = 18/n = 4; age, 61.0 ± 7.7 years) who were referred for planning US to assess the feasibility of radiofrequency ablation (n = 21) or biopsy (n = 1) for focal hepatic lesions were included. One experienced radiologist performed the two types of image fusion methods in each patient. The performance of auto-registration and manual registration was evaluated. The accuracy of the two methods, based on measuring registration error, and the time required for image fusion for both methods were recorded using in-house software and respectively compared using the Wilcoxon signed rank test. Image fusion was successful in all patients. The registration error was not significantly different between the two methods (auto-registration: median, 3.75 mm; range, 1.0-15.8 mm vs. manual registration: median, 2.95 mm; range, 1.2-12.5 mm, p = 0.242). The time required for image fusion was significantly shorter with auto-registration than with manual registration (median, 28.5 s; range, 18-47 s, vs. median, 36.5 s; range, 14-105 s, p = 0.026). Positioning auto-registration showed promising results compared with manual registration, with similar accuracy and even shorter registration time.

What is the best way to contour lung tumors on PET scans? Multiobserver validation of a gradient-based method using a NSCLC digital PET phantom.

PubMed

Werner-Wasik, Maria; Nelson, Arden D; Choi, Walter; Arai, Yoshio; Faulhaber, Peter F; Kang, Patrick; Almeida, Fabio D; Xiao, Ying; Ohri, Nitin; Brockway, Kristin D; Piper, Jonathan W; Nelson, Aaron S

2012-03-01

To evaluate the accuracy and consistency of a gradient-based positron emission tomography (PET) segmentation method, GRADIENT, compared with manual (MANUAL) and constant threshold (THRESHOLD) methods. Contouring accuracy was evaluated with sphere phantoms and clinically realistic Monte Carlo PET phantoms of the thorax. The sphere phantoms were 10-37 mm in diameter and were acquired at five institutions emulating clinical conditions. One institution also acquired a sphere phantom with multiple source-to-background ratios of 2:1, 5:1, 10:1, 20:1, and 70:1. One observer segmented (contoured) each sphere with GRADIENT and THRESHOLD from 25% to 50% at 5% increments. Subsequently, seven physicians segmented 31 lesions (7-264 mL) from 25 digital thorax phantoms using GRADIENT, THRESHOLD, and MANUAL. For spheres <20 mm in diameter, GRADIENT was the most accurate with a mean absolute % error in diameter of 8.15% (10.2% SD) compared with 49.2% (51.1% SD) for 45% THRESHOLD (p < 0.005). For larger spheres, the methods were statistically equivalent. For varying source-to-background ratios, GRADIENT was the most accurate for spheres >20 mm (p < 0.065) and <20 mm (p < 0.015). For digital thorax phantoms, GRADIENT was the most accurate (p < 0.01), with a mean absolute % error in volume of 10.99% (11.9% SD), followed by 25% THRESHOLD at 17.5% (29.4% SD), and MANUAL at 19.5% (17.2% SD). GRADIENT had the least systematic bias, with a mean % error in volume of -0.05% (16.2% SD) compared with 25% THRESHOLD at -2.1% (34.2% SD) and MANUAL at -16.3% (20.2% SD; p value <0.01). Interobserver variability was reduced using GRADIENT compared with both 25% THRESHOLD and MANUAL (p value <0.01, Levene's test). GRADIENT was the most accurate and consistent technique for target volume contouring. GRADIENT was also the most robust for varying imaging conditions. GRADIENT has the potential to play an important role for tumor delineation in radiation therapy planning and response assessment. Copyright © 2012. Published by Elsevier Inc.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

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

Morshed, Nader; Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Echols, Nathaniel, E-mail: nechols@lbl.gov

2015-05-01

A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here,more » the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

U.S. Department of Energy Vehicle Technologies Program: Battery Test Manual For Plug-In Hybrid Electric Vehicles

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

Christophersen, Jon P.

2014-09-01

This battery test procedure manual was prepared for the United States Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy (EERE), Vehicle Technologies Office. It is based on technical targets for commercial viability established for energy storage development projects aimed at meeting system level DOE goals for Plug-in Hybrid Electric Vehicles (PHEV). The specific procedures defined in this manual support the performance and life characterization of advanced battery devices under development for PHEV’s. However, it does share some methods described in the previously published battery test manual for power-assist hybrid electric vehicles. Due to the complexity of somemore » of the procedures and supporting analysis, future revisions including some modifications and clarifications of these procedures are expected. As in previous battery and capacitor test manuals, this version of the manual defines testing methods for full-size battery systems, along with provisions for scaling these tests for modules, cells or other subscale level devices. The DOE-United States Advanced Battery Consortium (USABC), Technical Advisory Committee (TAC) supported the development of the manual. Technical Team points of contact responsible for its development and revision are Renata M. Arsenault of Ford Motor Company and Jon P. Christophersen of the Idaho National Laboratory. The development of this manual was funded by the Unites States Department of Energy, Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Office. Technical direction from DOE was provided by David Howell, Energy Storage R&D Manager and Hybrid Electric Systems Team Leader. Comments and questions regarding the manual should be directed to Jon P. Christophersen at the Idaho National Laboratory (jon.christophersen@inl.gov).« less

Interpretation of ANA Indirect Immunofluorescence Test Outside the Darkroom Using NOVA View Compared to Manual Microscopy

PubMed Central

Copple, Susan S.; Jaskowski, Troy D.; Giles, Rashelle; Hill, Harry R.

2014-01-01

Objective. To evaluate NOVA View with focus on reading archived images versus microscope based manual interpretation of ANA HEp-2 slides by an experienced, certified medical technologist. Methods. 369 well defined sera from: 44 rheumatoid arthritis, 50 systemic lupus erythematosus, 35 scleroderma, 19 Sjögren's syndrome, and 10 polymyositis patients as well as 99 healthy controls were examined. In addition, 12 defined sera from the Centers for Disease Control and 100 random patient sera sent to ARUP Laboratories for ANA HEp-2 IIF testing were included. Samples were read using the archived images on NOVA View and compared to results obtained from manual reading. Results. At a 1 : 40/1 : 80 dilution the resulting comparison demonstrated 94.8%/92.9% positive, 97.4%/97.4% negative, and 96.5%/96.2% total agreements between manual IIF and NOVA View archived images. Agreement of identifiable patterns between methods was 97%, with PCNA and mixed patterns undetermined. Conclusion. Excellent agreements were obtained between reading archived images on NOVA View and manually on a fluorescent microscope. In addition, workflow benefits were observed which need to be analyzed in future studies. PMID:24741573

Purification of Training Samples Based on Spectral Feature and Superpixel Segmentation

NASA Astrophysics Data System (ADS)

Guan, X.; Qi, W.; He, J.; Wen, Q.; Chen, T.; Wang, Z.

2018-04-01

Remote sensing image classification is an effective way to extract information from large volumes of high-spatial resolution remote sensing images. Generally, supervised image classification relies on abundant and high-precision training data, which is often manually interpreted by human experts to provide ground truth for training and evaluating the performance of the classifier. Remote sensing enterprises accumulated lots of manually interpreted products from early lower-spatial resolution remote sensing images by executing their routine research and business programs. However, these manually interpreted products may not match the very high resolution (VHR) image properly because of different dates or spatial resolution of both data, thus, hindering suitability of manually interpreted products in training classification models, or small coverage area of these manually interpreted products. We also face similar problems in our laboratory in 21st Century Aerospace Technology Co. Ltd (short for 21AT). In this work, we propose a method to purify the interpreted product to match newly available VHRI data and provide the best training data for supervised image classifiers in VHR image classification. And results indicate that our proposed method can efficiently purify the input data for future machine learning use.

Quantifying the robustness of [18F]FDG-PET/CT radiomic features with respect to tumor delineation in head and neck and pancreatic cancer patients.

PubMed

Belli, Maria Luisa; Mori, Martina; Broggi, Sara; Cattaneo, Giovanni Mauro; Bettinardi, Valentino; Dell'Oca, Italo; Fallanca, Federico; Passoni, Paolo; Vanoli, Emilia Giovanna; Calandrino, Riccardo; Di Muzio, Nadia; Picchio, Maria; Fiorino, Claudio

2018-05-01

To investigate the robustness of PET radiomic features (RF) against tumour delineation uncertainty in two clinically relevant situations. Twenty-five head-and-neck (HN) and 25 pancreatic cancer patients previously treated with 18 F-Fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT)-based planning optimization were considered. Seven FDG-based contours were delineated for tumour (T) and positive lymph nodes (N, for HN patients only) following manual (2 observers), semi-automatic (based on SUV maximum gradient: PET_Edge) and automatic (40%, 50%, 60%, 70% SUV_max thresholds) methods. Seventy-three RF (14 of first order and 59 of higher order) were extracted using the CGITA software (v.1.4). The impact of delineation on volume agreement and RF was assessed by DICE and Intra-class Correlation Coefficients (ICC). A large disagreement between manual and SUV_max method was found for thresholds  ≥50%. Inter-observer variability showed median DICE values between 0.81 (HN-T) and 0.73 (pancreas). Volumes defined by PET_Edge were better consistent with the manual ones compared to SUV40%. Regarding RF, 19%/19%/47% of the features showed ICC < 0.80 between observers for HN-N/HN-T/pancreas, mostly in the Voxel-alignment matrix and in the intensity-size zone matrix families. RFs with ICC < 0.80 against manual delineation (taking the worst value) increased to 44%/36%/61% for PET_Edge and to 69%/53%/75% for SUV40%. About 80%/50% of 72 RF were consistent between observers for HN/pancreas patients. PET_edge was sufficiently robust against manual delineation while SUV40% showed a worse performance. This result suggests the possibility to replace manual with semi-automatic delineation of HN and pancreas tumours in studies including PET radiomic analyses. Copyright © 2018 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Comparison of manual versus automated data collection method for an evidence-based nursing practice study.

PubMed

Byrne, M D; Jordan, T R; Welle, T

2013-01-01

The objective of this study was to investigate and improve the use of automated data collection procedures for nursing research and quality assurance. A descriptive, correlational study analyzed 44 orthopedic surgical patients who were part of an evidence-based practice (EBP) project examining post-operative oxygen therapy at a Midwestern hospital. The automation work attempted to replicate a manually-collected data set from the EBP project. Automation was successful in replicating data collection for study data elements that were available in the clinical data repository. The automation procedures identified 32 "false negative" patients who met the inclusion criteria described in the EBP project but were not selected during the manual data collection. Automating data collection for certain data elements, such as oxygen saturation, proved challenging because of workflow and practice variations and the reliance on disparate sources for data abstraction. Automation also revealed instances of human error including computational and transcription errors as well as incomplete selection of eligible patients. Automated data collection for analysis of nursing-specific phenomenon is potentially superior to manual data collection methods. Creation of automated reports and analysis may require initial up-front investment with collaboration between clinicians, researchers and information technology specialists who can manage the ambiguities and challenges of research and quality assurance work in healthcare.

Response Evaluation of Malignant Liver Lesions After TACE/SIRT: Comparison of Manual and Semi-Automatic Measurement of Different Response Criteria in Multislice CT.

PubMed

Höink, Anna Janina; Schülke, Christoph; Koch, Raphael; Löhnert, Annika; Kammerer, Sara; Fortkamp, Rasmus; Heindel, Walter; Buerke, Boris

2017-11-01

Purpose  To compare measurement precision and interobserver variability in the evaluation of hepatocellular carcinoma (HCC) and liver metastases in MSCT before and after transarterial local ablative therapies. Materials and Methods  Retrospective study of 72 patients with malignant liver lesions (42 metastases; 30 HCCs) before and after therapy (43 SIRT procedures; 29 TACE procedures). Established (LAD; SAD; WHO) and vitality-based parameters (mRECIST; mLAD; mSAD; EASL) were assessed manually and semi-automatically by two readers. The relative interobserver difference (RID) and intraclass correlation coefficient (ICC) were calculated. Results  The median RID for vitality-based parameters was lower from semi-automatic than from manual measurement of mLAD (manual 12.5 %; semi-automatic 3.4 %), mSAD (manual 12.7 %; semi-automatic 5.7 %) and EASL (manual 10.4 %; semi-automatic 1.8 %). The difference in established parameters was not statistically noticeable (p > 0.05). The ICCs of LAD (manual 0.984; semi-automatic 0.982), SAD (manual 0.975; semi-automatic 0.958) and WHO (manual 0.984; semi-automatic 0.978) are high, both in manual and semi-automatic measurements. The ICCs of manual measurements of mLAD (0.897), mSAD (0.844) and EASL (0.875) are lower. This decrease cannot be found in semi-automatic measurements of mLAD (0.997), mSAD (0.992) and EASL (0.998). Conclusion  Vitality-based tumor measurements of HCC and metastases after transarterial local therapies should be performed semi-automatically due to greater measurement precision, thus increasing the reproducibility and in turn the reliability of therapeutic decisions. Key points   · Liver lesion measurements according to EASL and mRECIST are more precise when performed semi-automatically.. · The higher reproducibility may facilitate a more reliable classification of therapy response.. · Measurements according to RECIST and WHO offer equivalent precision semi-automatically and manually.. Citation Format · Höink AJ, Schülke C, Koch R et al. Response Evaluation of Malignant Liver Lesions After TACE/SIRT: Comparison of Manual and Semi-Automatic Measurement of Different Response Criteria in Multislice CT. Fortschr Röntgenstr 2017; 189: 1067 - 1075. © Georg Thieme Verlag KG Stuttgart · New York.

Machine-Learning Algorithms to Code Public Health Spending Accounts

PubMed Central

Leider, Jonathon P.; Resnick, Beth A.; Alfonso, Y. Natalia; Bishai, David

2017-01-01

Objectives: Government public health expenditure data sets require time- and labor-intensive manipulation to summarize results that public health policy makers can use. Our objective was to compare the performances of machine-learning algorithms with manual classification of public health expenditures to determine if machines could provide a faster, cheaper alternative to manual classification. Methods: We used machine-learning algorithms to replicate the process of manually classifying state public health expenditures, using the standardized public health spending categories from the Foundational Public Health Services model and a large data set from the US Census Bureau. We obtained a data set of 1.9 million individual expenditure items from 2000 to 2013. We collapsed these data into 147 280 summary expenditure records, and we followed a standardized method of manually classifying each expenditure record as public health, maybe public health, or not public health. We then trained 9 machine-learning algorithms to replicate the manual process. We calculated recall, precision, and coverage rates to measure the performance of individual and ensembled algorithms. Results: Compared with manual classification, the machine-learning random forests algorithm produced 84% recall and 91% precision. With algorithm ensembling, we achieved our target criterion of 90% recall by using a consensus ensemble of ≥6 algorithms while still retaining 93% coverage, leaving only 7% of the summary expenditure records unclassified. Conclusions: Machine learning can be a time- and cost-saving tool for estimating public health spending in the United States. It can be used with standardized public health spending categories based on the Foundational Public Health Services model to help parse public health expenditure information from other types of health-related spending, provide data that are more comparable across public health organizations, and evaluate the impact of evidence-based public health resource allocation. PMID:28363034

Validity of a manual soft tissue profile prediction method following mandibular setback osteotomy.

PubMed

Kolokitha, Olga-Elpis

2007-10-01

The aim of this study was to determine the validity of a manual cephalometric method used for predicting the post-operative soft tissue profiles of patients who underwent mandibular setback surgery and compare it to a computerized cephalometric prediction method (Dentofacial Planner). Lateral cephalograms of 18 adults with mandibular prognathism taken at the end of pre-surgical orthodontics and approximately one year after surgery were used. To test the validity of the manual method the prediction tracings were compared to the actual post-operative tracings. The Dentofacial Planner software was used to develop the computerized post-surgical prediction tracings. Both manual and computerized prediction printouts were analyzed by using the cephalometric system PORDIOS. Statistical analysis was performed by means of t-test. Comparison between manual prediction tracings and the actual post-operative profile showed that the manual method results in more convex soft tissue profiles; the upper lip was found in a more prominent position, upper lip thickness was increased and, the mandible and lower lip were found in a less posterior position than that of the actual profiles. Comparison between computerized and manual prediction methods showed that in the manual method upper lip thickness was increased, the upper lip was found in a more anterior position and the lower anterior facial height was increased as compared to the computerized prediction method. Cephalometric simulation of post-operative soft tissue profile following orthodontic-surgical management of mandibular prognathism imposes certain limitations related to the methods implied. However, both manual and computerized prediction methods remain a useful tool for patient communication.

Evaluation of bone formation in calcium phosphate scaffolds with μCT-method validation using SEM.

PubMed

Lewin, S; Barba, A; Persson, C; Franch, J; Ginebra, M-P; Öhman-Mägi, C

2017-10-05

There is a plethora of calcium phosphate (CaP) scaffolds used as synthetic substitutes to bone grafts. The scaffold performance is often evaluated from the quantity of bone formed within or in direct contact with the scaffold. Micro-computed tomography (μCT) allows three-dimensional evaluation of bone formation inside scaffolds. However, the almost identical x-ray attenuation of CaP and bone obtrude the separation of these phases in μCT images. Commonly, segmentation of bone in μCT images is based on gray scale intensity, with manually determined global thresholds. However, image analysis methods, and methods for manual thresholding in particular, lack standardization and may consequently suffer from subjectivity. The aim of the present study was to provide a methodological framework for addressing these issues. Bone formation in two types of CaP scaffold architectures (foamed and robocast), obtained from a larger animal study (a 12 week canine animal model) was evaluated by μCT. In addition, cross-sectional scanning electron microscopy (SEM) images were acquired as references to determine thresholds and to validate the result. μCT datasets were registered to the corresponding SEM reference. Global thresholds were then determined by quantitatively correlating the different area fractions in the μCT image, towards the area fractions in the corresponding SEM image. For comparison, area fractions were also quantified using global thresholds determined manually by two different approaches. In the validation the manually determined thresholds resulted in large average errors in area fraction (up to 17%), whereas for the evaluation using SEM references, the errors were estimated to be less than 3%. Furthermore, it was found that basing the thresholds on one single SEM reference gave lower errors than determining them manually. This study provides an objective, robust and less error prone method to determine global thresholds for the evaluation of bone formation in CaP scaffolds.

A work study of the CAD/CAM method and conventional manual method in the fabrication of spinal orthoses for patients with adolescent idiopathic scoliosis.

PubMed

Wong, M S; Cheng, J C Y; Wong, M W; So, S F

2005-04-01

A study was conducted to compare the CAD/CAM method with the conventional manual method in fabrication of spinal orthoses for patients with adolescent idiopathic scoliosis. Ten subjects were recruited for this study. Efficiency analyses of the two methods were performed from cast filling/ digitization process to completion of cast/image rectification. The dimensional changes of the casts/ models rectified by the two cast rectification methods were also investigated. The results demonstrated that the CAD/CAM method was faster than the conventional manual method in the studied processes. The mean rectification time of the CAD/CAM method was shorter than that of the conventional manual method by 108.3 min (63.5%). This indicated that the CAD/CAM method took about 1/3 of the time of the conventional manual to finish cast rectification. In the comparison of cast/image dimensional differences between the conventional manual method and the CAD/CAM method, five major dimensions in each of the five rectified regions namely the axilla, thoracic, lumbar, abdominal and pelvic regions were involved. There were no significant dimensional differences (p < 0.05) in 19 out of the 25 studied dimensions. This study demonstrated that the CAD/CAM system could save the time in the rectification process and offer a relatively high resemblance in cast rectification as compared with the conventional manual method.

Two-wavelength Lidar inversion algorithm for determining planetary boundary layer height

NASA Astrophysics Data System (ADS)

Liu, Boming; Ma, Yingying; Gong, Wei; Jian, Yang; Ming, Zhang

2018-02-01

This study proposes a two-wavelength Lidar inversion algorithm to determine the boundary layer height (BLH) based on the particles clustering. Color ratio and depolarization ratio are used to analyze the particle distribution, based on which the proposed algorithm can overcome the effects of complex aerosol layers to calculate the BLH. The algorithm is used to determine the top of the boundary layer under different mixing state. Experimental results demonstrate that the proposed algorithm can determine the top of the boundary layer even in a complex case. Moreover, it can better deal with the weak convection conditions. Finally, experimental data from June 2015 to December 2015 were used to verify the reliability of the proposed algorithm. The correlation between the results of the proposed algorithm and the manual method is R2 = 0.89 with a RMSE of 131 m and mean bias of 49 m; the correlation between the results of the ideal profile fitting method and the manual method is R2 = 0.64 with a RMSE of 270 m and a mean bias of 165 m; and the correlation between the results of the wavelet covariance transform method and manual method is R2 = 0.76, with a RMSE of 196 m and mean bias of 23 m. These findings indicate that the proposed algorithm has better reliability and stability than traditional algorithms.

Using deep learning to segment breast and fibroglandular tissue in MRI volumes.

PubMed

Dalmış, Mehmet Ufuk; Litjens, Geert; Holland, Katharina; Setio, Arnaud; Mann, Ritse; Karssemeijer, Nico; Gubern-Mérida, Albert

2017-02-01

Automated segmentation of breast and fibroglandular tissue (FGT) is required for various computer-aided applications of breast MRI. Traditional image analysis and computer vision techniques, such atlas, template matching, or, edge and surface detection, have been applied to solve this task. However, applicability of these methods is usually limited by the characteristics of the images used in the study datasets, while breast MRI varies with respect to the different MRI protocols used, in addition to the variability in breast shapes. All this variability, in addition to various MRI artifacts, makes it a challenging task to develop a robust breast and FGT segmentation method using traditional approaches. Therefore, in this study, we investigated the use of a deep-learning approach known as "U-net." We used a dataset of 66 breast MRI's randomly selected from our scientific archive, which includes five different MRI acquisition protocols and breasts from four breast density categories in a balanced distribution. To prepare reference segmentations, we manually segmented breast and FGT for all images using an in-house developed workstation. We experimented with the application of U-net in two different ways for breast and FGT segmentation. In the first method, following the same pipeline used in traditional approaches, we trained two consecutive (2C) U-nets: first for segmenting the breast in the whole MRI volume and the second for segmenting FGT inside the segmented breast. In the second method, we used a single 3-class (3C) U-net, which performs both tasks simultaneously by segmenting the volume into three regions: nonbreast, fat inside the breast, and FGT inside the breast. For comparison, we applied two existing and published methods to our dataset: an atlas-based method and a sheetness-based method. We used Dice Similarity Coefficient (DSC) to measure the performances of the automated methods, with respect to the manual segmentations. Additionally, we computed Pearson's correlation between the breast density values computed based on manual and automated segmentations. The average DSC values for breast segmentation were 0.933, 0.944, 0.863, and 0.848 obtained from 3C U-net, 2C U-nets, atlas-based method, and sheetness-based method, respectively. The average DSC values for FGT segmentation obtained from 3C U-net, 2C U-nets, and atlas-based methods were 0.850, 0.811, and 0.671, respectively. The correlation between breast density values based on 3C U-net and manual segmentations was 0.974. This value was significantly higher than 0.957 as obtained from 2C U-nets (P < 0.0001, Steiger's Z-test with Bonferoni correction) and 0.938 as obtained from atlas-based method (P = 0.0016). In conclusion, we applied a deep-learning method, U-net, for segmenting breast and FGT in MRI in a dataset that includes a variety of MRI protocols and breast densities. Our results showed that U-net-based methods significantly outperformed the existing algorithms and resulted in significantly more accurate breast density computation. © 2016 American Association of Physicists in Medicine.

A combined learning algorithm for prostate segmentation on 3D CT images.

PubMed

Ma, Ling; Guo, Rongrong; Zhang, Guoyi; Schuster, David M; Fei, Baowei

2017-11-01

Segmentation of the prostate on CT images has many applications in the diagnosis and treatment of prostate cancer. Because of the low soft-tissue contrast on CT images, prostate segmentation is a challenging task. A learning-based segmentation method is proposed for the prostate on three-dimensional (3D) CT images. We combine population-based and patient-based learning methods for segmenting the prostate on CT images. Population data can provide useful information to guide the segmentation processing. Because of inter-patient variations, patient-specific information is particularly useful to improve the segmentation accuracy for an individual patient. In this study, we combine a population learning method and a patient-specific learning method to improve the robustness of prostate segmentation on CT images. We train a population model based on the data from a group of prostate patients. We also train a patient-specific model based on the data of the individual patient and incorporate the information as marked by the user interaction into the segmentation processing. We calculate the similarity between the two models to obtain applicable population and patient-specific knowledge to compute the likelihood of a pixel belonging to the prostate tissue. A new adaptive threshold method is developed to convert the likelihood image into a binary image of the prostate, and thus complete the segmentation of the gland on CT images. The proposed learning-based segmentation algorithm was validated using 3D CT volumes of 92 patients. All of the CT image volumes were manually segmented independently three times by two, clinically experienced radiologists and the manual segmentation results served as the gold standard for evaluation. The experimental results show that the segmentation method achieved a Dice similarity coefficient of 87.18 ± 2.99%, compared to the manual segmentation. By combining the population learning and patient-specific learning methods, the proposed method is effective for segmenting the prostate on 3D CT images. The prostate CT segmentation method can be used in various applications including volume measurement and treatment planning of the prostate. © 2017 American Association of Physicists in Medicine.

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi.

PubMed

Feldmesser, Ester; Rosenwasser, Shilo; Vardi, Assaf; Ben-Dor, Shifra

2014-02-22

The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biotechnological significance, and consequently the understanding of their unique metabolic pathways is essential. Several methods that integrate de novo assembly with genome-based assembly have been proposed. Yet, there are many open challenges in defining genes, particularly where genomes are not available or incomplete. Despite the large numbers of transcriptome assemblies that have been performed, quality control of the transcript building process, particularly on the protein level, is rarely performed if ever. To test and improve the quality of the automated transcriptome reconstruction, we used manually defined and curated genes, several of them experimentally validated. Several approaches to transcript construction were utilized, based on the available data: a draft genome, high quality RNAseq reads, and ESTs. In order to maximize the contribution of the various data, we integrated methods including de novo and genome based assembly, as well as EST clustering. After each step a set of manually curated genes was used for quality assessment of the transcripts. The interplay between the automated pipeline and the quality control indicated which additional processes were required to improve the transcriptome reconstruction. We discovered that E. huxleyi has a very high percentage of non-canonical splice junctions, and relatively high rates of intron retention, which caused unique issues with the currently available tools. While individual tools missed genes and artificially joined overlapping transcripts, combining the results of several tools improved the completeness and quality considerably. The final collection, created from the integration of several quality control and improvement rounds, was compared to the manually defined set both on the DNA and protein levels, and resulted in an improvement of 20% versus any of the read-based approaches alone. To the best of our knowledge, this is the first time that an automated transcript definition is subjected to quality control using manually defined and curated genes and thereafter the process is improved. We recommend using a set of manually curated genes to troubleshoot transcriptome reconstruction.

A comparison of treatment effectiveness between the CAD/CAM method and the manual method for managing adolescent idiopathic scoliosis.

PubMed

Wong, M S; Cheng, J C Y; Lo, K H

2005-04-01

The treatment effectiveness of the CAD/CAM method and the manual method in managing adolescent idiopathic scoliosis (AIS) was compared. Forty subjects were recruited with twenty subjects for each method. The clinical parameters namely Cobb's angle and apical vertebral rotation were evaluated at the pre-brace and the immediate in-brace visits. The results demonstrated that orthotic treatments rendered by the CAD/CAM method and the conventional manual method were effective in providing initial control of Cobb's angle. Significant decreases (p < 0.05) were found between the pre-brace and immediate in-brace visits for both methods. The mean reductions of Cobb's angle were 12.8 degrees (41.9%) for the CAD/CAM method and 9.8 degrees (32.1%) for the manual method. An initial control of the apical vertebral rotation was not shown in this study. In the comparison between the CAD/CAM method and the manual method, no significant difference was found in the control of Cobb's angle and apical vertebral rotation. The current study demonstrated that the CAD/CAM method can provide similar result in the initial stage of treatment as compared with the manual method.

A comparison study of size-specific dose estimate calculation methods.

PubMed

Parikh, Roshni A; Wien, Michael A; Novak, Ronald D; Jordan, David W; Klahr, Paul; Soriano, Stephanie; Ciancibello, Leslie; Berlin, Sheila C

2018-01-01

The size-specific dose estimate (SSDE) has emerged as an improved metric for use by medical physicists and radiologists for estimating individual patient dose. Several methods of calculating SSDE have been described, ranging from patient thickness or attenuation-based (automated and manual) measurements to weight-based techniques. To compare the accuracy of thickness vs. weight measurement of body size to allow for the calculation of the size-specific dose estimate (SSDE) in pediatric body CT. We retrospectively identified 109 pediatric body CT examinations for SSDE calculation. We examined two automated methods measuring a series of level-specific diameters of the patient's body: method A used the effective diameter and method B used the water-equivalent diameter. Two manual methods measured patient diameter at two predetermined levels: the superior endplate of L2, where body width is typically most thin, and the superior femoral head or iliac crest (for scans that did not include the pelvis), where body width is typically most thick; method C averaged lateral measurements at these two levels from the CT projection scan, and method D averaged lateral and anteroposterior measurements at the same two levels from the axial CT images. Finally, we used body weight to characterize patient size, method E, and compared this with the various other measurement methods. Methods were compared across the entire population as well as by subgroup based on body width. Concordance correlation (ρ c ) between each of the SSDE calculation methods (methods A-E) was greater than 0.92 across the entire population, although the range was wider when analyzed by subgroup (0.42-0.99). When we compared each SSDE measurement method with CTDI vol, there was poor correlation, ρ c <0.77, with percentage differences between 20.8% and 51.0%. Automated computer algorithms are accurate and efficient in the calculation of SSDE. Manual methods based on patient thickness provide acceptable dose estimates for pediatric patients <30 cm in body width. Body weight provides a quick and practical method to identify conversion factors that can be used to estimate SSDE with reasonable accuracy in pediatric patients with body width ≥20 cm.

Document Form and Character Recognition using SVM

NASA Astrophysics Data System (ADS)

Park, Sang-Sung; Shin, Young-Geun; Jung, Won-Kyo; Ahn, Dong-Kyu; Jang, Dong-Sik

2009-08-01

Because of development of computer and information communication, EDI (Electronic Data Interchange) has been developing. There is OCR (Optical Character Recognition) of Pattern recognition technology for EDI. OCR contributed to changing many manual in the past into automation. But for the more perfect database of document, much manual is needed for excluding unnecessary recognition. To resolve this problem, we propose document form based character recognition method in this study. Proposed method is divided into document form recognition part and character recognition part. Especially, in character recognition, change character into binarization by using SVM algorithm and extract more correct feature value.

DBCG hypo trial validation of radiotherapy parameters from a national data bank versus manual reporting.

PubMed

Brink, Carsten; Lorenzen, Ebbe L; Krogh, Simon Long; Westberg, Jonas; Berg, Martin; Jensen, Ingelise; Thomsen, Mette Skovhus; Yates, Esben Svitzer; Offersen, Birgitte Vrou

2018-01-01

The current study evaluates the data quality achievable using a national data bank for reporting radiotherapy parameters relative to the classical manual reporting method of selected parameters. The data comparison is based on 1522 Danish patients of the DBCG hypo trial with data stored in the Danish national radiotherapy data bank. In line with standard DBCG trial practice selected parameters were also reported manually to the DBCG database. Categorical variables are compared using contingency tables, and comparison of continuous parameters is presented in scatter plots. For categorical variables 25 differences between the data bank and manual values were located. Of these 23 were related to mistakes in the manual reported value whilst the remaining two were a wrong classification in the data bank. The wrong classification in the data bank was related to lack of dose information, since the two patients had been treated with an electron boost based on a manual calculation, thus data was not exported to the data bank, and this was not detected prior to comparison with the manual data. For a few database fields in the manual data an ambiguity of the parameter definition of the specific field is seen in the data. This was not the case for the data bank, which extract all data consistently. In terms of data quality the data bank is superior to manually reported values. However, there is a need to allocate resources for checking the validity of the available data as well as ensuring that all relevant data is present. The data bank contains more detailed information, and thus facilitates research related to the actual dose distribution in the patients.

Validation of a simple, manual urinary iodine method for estimating the prevalence of iodine-deficiency disorders, and interlaboratory comparison with other methods.

PubMed

May, S L; May, W A; Bourdoux, P P; Pino, S; Sullivan, K M; Maberly, G F

1997-05-01

The measurement of urinary iodine in population-based surveys provides a biological indicator of the severity of iodine-deficiency disorders. We describe the steps performed to validate a simple, inexpensive, manual urinary iodine acid digestion method, and compare the results using this method with those of other urinary iodine methods. Initially, basic performance characteristics were evaluated: the average recovery of added iodine was 100.4 +/- 8.7% (mean +/- SD), within-assay precision (CV) over the assay range 0-0.95 mumol/L (0-12 micrograms/dL) was < 6%, between-assay precision over the same range was < 12%, and assay sensitivity was 0.05 mumol/L (0.6 microgram/dL). There were no apparent effects on the method by thiocyanate, a known interfering substance. In a comparison with five other methods performed in four different laboratories, samples were collected to test the method performance over a wide range of urinary iodine values (0.04-3.7 mumol/L, or 0.5-47 micrograms/dL). There was a high correlation between all methods and the interpretation of the results was consistent. We conclude that the simple, manual acid digestion method is suitable for urinary iodine analysis.

Comparison of a brain-based adaptive system and a manual adaptable system for invoking automation.

PubMed

Bailey, Nathan R; Scerbo, Mark W; Freeman, Frederick G; Mikulka, Peter J; Scott, Lorissa A

2006-01-01

Two experiments are presented examining adaptive and adaptable methods for invoking automation. Empirical investigations of adaptive automation have focused on methods used to invoke automation or on automation-related performance implications. However, no research has addressed whether performance benefits associated with brain-based systems exceed those in which users have control over task allocations. Participants performed monitoring and resource management tasks as well as a tracking task that shifted between automatic and manual modes. In the first experiment, participants worked with an adaptive system that used their electroencephalographic signals to switch the tracking task between automatic and manual modes. Participants were also divided between high- and low-reliability conditions for the system-monitoring task as well as high- and low-complacency potential. For the second experiment, participants operated an adaptable system that gave them manual control over task allocations. Results indicated increased situation awareness (SA) of gauge instrument settings for individuals high in complacency potential using the adaptive system. In addition, participants who had control over automation performed more poorly on the resource management task and reported higher levels of workload. A comparison between systems also revealed enhanced SA of gauge instrument settings and decreased workload in the adaptive condition. The present results suggest that brain-based adaptive automation systems may enhance perceptual level SA while reducing mental workload relative to systems requiring user-initiated control. Potential applications include automated systems for which operator monitoring performance and high-workload conditions are of concern.

Bridging the gap in complementary and alternative medicine research: manualization as a means of promoting standardization and flexibility of treatment in clinical trials of acupuncture.

PubMed

Schnyer, Rosa N; Allen, John J B

2002-10-01

An important methodological challenge encountered in acupuncture clinical research involves the design of treatment protocols that help ensure standardization and replicability while allowing for the necessary flexibility to tailor treatments to each individual. Manualization of protocols used in clinical trials of acupuncture and other traditionally-based complementary and alternative medicine (CAM) systems facilitates the systematic delivery of replicable and standardized, yet individually-tailored treatments. To facilitate high-quality CAM acupuncture research by outlining a method for the systematic design and implementation of protocols used in CAM clinical trials based on the concept of treatment manualization. A series of treatment manuals was developed to systematically articulate the Chinese medical theoretical and clinical framework for a given Western-defined illness, to increase the quality and consistency of treatment, and to standardize the technical aspects of the protocol. In all, three manuals were developed for National Institutes of Health (NIH)-funded clinical trials of acupuncture for depression, spasticity in cerebral palsy, and repetitive stress injury. In Part I, the rationale underlying these manuals and the challenges encountered in creating them are discussed, and qualitative assessments of their utility are provided. In Part II, a methodology to develop treatment manuals for use in clinical trials is detailed, and examples are given. A treatment manual provides a precise way to train and supervise practitioners, enable evaluation of conformity and competence, facilitate the training process, and increase the ability to identify the active therapeutic ingredients in clinical trials of acupuncture.

Screening for Human Immunodeficiency Virus, Hepatitis B Virus, Hepatitis C Virus, and Treponema pallidum by Blood Testing Using a Bio-Flash Technology-Based Algorithm before Gastrointestinal Endoscopy

PubMed Central

Zhen, Chen; QuiuLi, Zhang; YuanQi, An; Casado, Verónica Vocero; Fan, Yuan

2016-01-01

Currently, conventional enzyme immunoassays which use manual gold immunoassays and colloidal tests (GICTs) are used as screening tools to detect Treponema pallidum (syphilis), hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus type 1 (HIV-1), and HIV-2 in patients undergoing surgery. The present observational, cross-sectional study compared the sensitivity, specificity, and work flow characteristics of the conventional algorithm with manual GICTs with those of a newly proposed algorithm that uses the automated Bio-Flash technology as a screening tool in patients undergoing gastrointestinal (GI) endoscopy. A total of 956 patients were examined for the presence of serological markers of infection with HIV-1/2, HCV, HBV, and T. pallidum. The proposed algorithm with the Bio-Flash technology was superior for the detection of all markers (100.0% sensitivity and specificity for detection of anti-HIV and anti-HCV antibodies, HBV surface antigen [HBsAg], and T. pallidum) compared with the conventional algorithm based on the manual method (80.0% sensitivity and 98.6% specificity for the detection of anti-HIV, 75.0% sensitivity for the detection of anti-HCV, 94.7% sensitivity for the detection of HBsAg, and 100% specificity for the detection of anti-HCV and HBsAg) in these patients. The automated Bio-Flash technology-based screening algorithm also reduced the operation time by 85.0% (205 min) per day, saving up to 24 h/week. In conclusion, the use of the newly proposed screening algorithm based on the automated Bio-Flash technology can provide an advantage over the use of conventional algorithms based on manual methods for screening for HIV, HBV, HCV, and syphilis before GI endoscopy. PMID:27707942

Screening for Human Immunodeficiency Virus, Hepatitis B Virus, Hepatitis C Virus, and Treponema pallidum by Blood Testing Using a Bio-Flash Technology-Based Algorithm before Gastrointestinal Endoscopy.

PubMed

Jun, Zhou; Zhen, Chen; QuiuLi, Zhang; YuanQi, An; Casado, Verónica Vocero; Fan, Yuan

2016-12-01

Currently, conventional enzyme immunoassays which use manual gold immunoassays and colloidal tests (GICTs) are used as screening tools to detect Treponema pallidum (syphilis), hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus type 1 (HIV-1), and HIV-2 in patients undergoing surgery. The present observational, cross-sectional study compared the sensitivity, specificity, and work flow characteristics of the conventional algorithm with manual GICTs with those of a newly proposed algorithm that uses the automated Bio-Flash technology as a screening tool in patients undergoing gastrointestinal (GI) endoscopy. A total of 956 patients were examined for the presence of serological markers of infection with HIV-1/2, HCV, HBV, and T. pallidum The proposed algorithm with the Bio-Flash technology was superior for the detection of all markers (100.0% sensitivity and specificity for detection of anti-HIV and anti-HCV antibodies, HBV surface antigen [HBsAg], and T. pallidum) compared with the conventional algorithm based on the manual method (80.0% sensitivity and 98.6% specificity for the detection of anti-HIV, 75.0% sensitivity for the detection of anti-HCV, 94.7% sensitivity for the detection of HBsAg, and 100% specificity for the detection of anti-HCV and HBsAg) in these patients. The automated Bio-Flash technology-based screening algorithm also reduced the operation time by 85.0% (205 min) per day, saving up to 24 h/week. In conclusion, the use of the newly proposed screening algorithm based on the automated Bio-Flash technology can provide an advantage over the use of conventional algorithms based on manual methods for screening for HIV, HBV, HCV, and syphilis before GI endoscopy. Copyright © 2016 Jun et al.

Reproducibility of myelin content-based human habenula segmentation at 3 Tesla.

PubMed

Kim, Joo-Won; Naidich, Thomas P; Joseph, Joshmi; Nair, Divya; Glasser, Matthew F; O'halloran, Rafael; Doucet, Gaelle E; Lee, Won Hee; Krinsky, Hannah; Paulino, Alejandro; Glahn, David C; Anticevic, Alan; Frangou, Sophia; Xu, Junqian

2018-03-26

In vivo morphological study of the human habenula, a pair of small epithalamic nuclei adjacent to the dorsomedial thalamus, has recently gained significant interest for its role in reward and aversion processing. However, segmenting the habenula from in vivo magnetic resonance imaging (MRI) is challenging due to the habenula's small size and low anatomical contrast. Although manual and semi-automated habenula segmentation methods have been reported, the test-retest reproducibility of the segmented habenula volume and the consistency of the boundaries of habenula segmentation have not been investigated. In this study, we evaluated the intra- and inter-site reproducibility of in vivo human habenula segmentation from 3T MRI (0.7-0.8 mm isotropic resolution) using our previously proposed semi-automated myelin contrast-based method and its fully-automated version, as well as a previously published manual geometry-based method. The habenula segmentation using our semi-automated method showed consistent boundary definition (high Dice coefficient, low mean distance, and moderate Hausdorff distance) and reproducible volume measurement (low coefficient of variation). Furthermore, the habenula boundary in our semi-automated segmentation from 3T MRI agreed well with that in the manual segmentation from 7T MRI (0.5 mm isotropic resolution) of the same subjects. Overall, our proposed semi-automated habenula segmentation showed reliable and reproducible habenula localization, while its fully-automated version offers an efficient way for large sample analysis. © 2018 Wiley Periodicals, Inc.

CometBoards Users Manual Release 1.0

NASA Technical Reports Server (NTRS)

Guptill, James D.; Coroneos, Rula M.; Patnaik, Surya N.; Hopkins, Dale A.; Berke, Lazlo

1996-01-01

Several nonlinear mathematical programming algorithms for structural design applications are available at present. These include the sequence of unconstrained minimizations technique, the method of feasible directions, and the sequential quadratic programming technique. The optimality criteria technique and the fully utilized design concept are two other structural design methods. A project was undertaken to bring all these design methods under a common computer environment so that a designer can select any one of these tools that may be suitable for his/her application. To facilitate selection of a design algorithm, to validate and check out the computer code, and to ascertain the relative merits of the design tools, modest finite element structural analysis programs based on the concept of stiffness and integrated force methods have been coupled to each design method. The code that contains both these design and analysis tools, by reading input information from analysis and design data files, can cast the design of a structure as a minimum-weight optimization problem. The code can then solve it with a user-specified optimization technique and a user-specified analysis method. This design code is called CometBoards, which is an acronym for Comparative Evaluation Test Bed of Optimization and Analysis Routines for the Design of Structures. This manual describes for the user a step-by-step procedure for setting up the input data files and executing CometBoards to solve a structural design problem. The manual includes the organization of CometBoards; instructions for preparing input data files; the procedure for submitting a problem; illustrative examples; and several demonstration problems. A set of 29 structural design problems have been solved by using all the optimization methods available in CometBoards. A summary of the optimum results obtained for these problems is appended to this users manual. CometBoards, at present, is available for Posix-based Cray and Convex computers, Iris and Sun workstations, and the VM/CMS system.

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

Natural Language Processing As an Alternative to Manual Reporting of Colonoscopy Quality Metrics

PubMed Central

RAJU, GOTTUMUKKALA S.; LUM, PHILLIP J.; SLACK, REBECCA; THIRUMURTHI, SELVI; LYNCH, PATRICK M.; MILLER, ETHAN; WESTON, BRIAN R.; DAVILA, MARTA L.; BHUTANI, MANOOP S.; SHAFI, MEHNAZ A.; BRESALIER, ROBERT S.; DEKOVICH, ALEXANDER A.; LEE, JEFFREY H.; GUHA, SUSHOVAN; PANDE, MALA; BLECHACZ, BORIS; RASHID, ASIF; ROUTBORT, MARK; SHUTTLESWORTH, GLADIS; MISHRA, LOPA; STROEHLEIN, JOHN R.; ROSS, WILLIAM A.

2015-01-01

BACKGROUND & AIMS The adenoma detection rate (ADR) is a quality metric tied to interval colon cancer occurrence. However, manual extraction of data to calculate and track the ADR in clinical practice is labor-intensive. To overcome this difficulty, we developed a natural language processing (NLP) method to identify patients, who underwent their first screening colonoscopy, identify adenomas and sessile serrated adenomas (SSA). We compared the NLP generated results with that of manual data extraction to test the accuracy of NLP, and report on colonoscopy quality metrics using NLP. METHODS Identification of screening colonoscopies using NLP was compared with that using the manual method for 12,748 patients who underwent colonoscopies from July 2010 to February 2013. Also, identification of adenomas and SSAs using NLP was compared with that using the manual method with 2259 matched patient records. Colonoscopy ADRs using these methods were generated for each physician. RESULTS NLP correctly identified 91.3% of the screening examinations, whereas the manual method identified 87.8% of them. Both the manual method and NLP correctly identified examinations of patients with adenomas and SSAs in the matched records almost perfectly. Both NLP and manual method produce comparable values for ADR for each endoscopist as well as the group as a whole. CONCLUSIONS NLP can correctly identify screening colonoscopies, accurately identify adenomas and SSAs in a pathology database, and provide real-time quality metrics for colonoscopy. PMID:25910665

Automated data mining: an innovative and efficient web-based approach to maintaining resident case logs.

PubMed

Bhattacharya, Pratik; Van Stavern, Renee; Madhavan, Ramesh

2010-12-01

Use of resident case logs has been considered by the Residency Review Committee for Neurology of the Accreditation Council for Graduate Medical Education (ACGME). This study explores the effectiveness of a data-mining program for creating resident logs and compares the results to a manual data-entry system. Other potential applications of data mining to enhancing resident education are also explored. Patient notes dictated by residents were extracted from the Hospital Information System and analyzed using an unstructured mining program. History, examination and ICD codes were obtained and compared to the existing manual log. The automated data History, examination, and ICD codes were gathered for a 30-day period and compared to manual case logs. The automated method extracted all resident dictations with the dates of encounter and transcription. The automated data-miner processed information from all 19 residents, while only 4 residents logged manually. The manual method identified only broad categories of diseases; the major categories were stroke or vascular disorder 53 (27.6%), epilepsy 28 (14.7%), and pain syndromes 26 (13.5%). In the automated method, epilepsy 114 (21.1%), cerebral atherosclerosis 114 (21.1%), and headache 105 (19.4%) were the most frequent primary diagnoses, and headache 89 (16.5%), seizures 94 (17.4%), and low back pain 47 (9%) were the most common chief complaints. More detailed patient information such as tobacco use 227 (42%), alcohol use 205 (38%), and drug use 38 (7%) were extracted by the data-mining method. Manual case logs are time-consuming, provide limited information, and may be unpopular with residents. Data mining is a time-effective tool that may aid in the assessment of resident experience or the ACGME core competencies or in resident clinical research. More study of this method in larger numbers of residency programs is needed.

Extracting BI-RADS Features from Portuguese Clinical Texts.

PubMed

Nassif, Houssam; Cunha, Filipe; Moreira, Inês C; Cruz-Correia, Ricardo; Sousa, Eliana; Page, David; Burnside, Elizabeth; Dutra, Inês

2012-01-01

In this work we build the first BI-RADS parser for Portuguese free texts, modeled after existing approaches to extract BI-RADS features from English medical records. Our concept finder uses a semantic grammar based on the BIRADS lexicon and on iterative transferred expert knowledge. We compare the performance of our algorithm to manual annotation by a specialist in mammography. Our results show that our parser's performance is comparable to the manual method.

NMR-based automated protein structure determination.

PubMed

Würz, Julia M; Kazemi, Sina; Schmidt, Elena; Bagaria, Anurag; Güntert, Peter

2017-08-15

NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures. Copyright © 2017 Elsevier Inc. All rights reserved.

Do centrally pre-prepared solutions achieve more reliable drug concentrations than solutions prepared on the ward?

PubMed

Dehmel, Carola; Braune, Stephan A; Kreymann, Georg; Baehr, Michael; Langebrake, Claudia; Hilgarth, Heike; Nierhaus, Axel; Dartsch, Dorothee C; Kluge, Stefan

2011-08-01

To compare the concentration conformity of infusion solutions manually prepared on intensive care units (ICU) with solutions from pharmacy-based, automated production. A prospective observational study conducted in a university hospital in Germany. Drug concentrations of 100 standardised infusion solutions manually prepared in the ICU and 100 matching solutions from automated production containing amiodarone, noradrenaline or hydrocortisone were measured by high-performance liquid chromatography analysis. Deviations from stated concentrations were calculated, and the quality of achieved concentration conformity of the two production methods was compared. Actual concentrations of 53% of the manually prepared and 16% of the machine-made solutions deviated by >5% above or below the stated concentration. A deviation of >10% was measured in 22% of the manually prepared samples and in 5% of samples from automated production. Of the manually prepared solutions, 15% deviated by >15% above or below the intended concentration. The mean concentration of the manually prepared solutions was 97.2% (SD 12.7%, range 45-129%) and of the machine-made solutions was 101.1% (SD 4.3%, range 90-114%) of the target concentration (p < 0.01). In this preliminary study, ward-based, manually prepared infusion solutions showed clinically relevant deviations in concentration conformity significantly more often than pharmacy-prepared, machine-made solutions. Centralised, automated preparation of standardised infusion solutions may be an effective means to reduce this type of medication error. Further confirmatory studies in larger settings and under conditions of routine automated production are required.

Automated measurements for individualized heart rate correction of the QT interval.

PubMed

Mason, Jay W; Moon, Thomas E

2015-04-01

Subject-specific electrocardiographic QT interval correction for heart rate is often used in clinical trials with frequent electrocardiographic recordings. However, in these studies relatively few 10-s, 12-lead electrocardiograms may be available for calculating the individual correction. Highly automated QT and RR measurement tools have made it practical to measure electrocardiographic intervals on large volumes of continuous electrocardiogram data. The purpose of this study was to determine whether an automated method can be used in lieu of a manual method. In 49 subjects who completed all treatments in a four-armed crossover study we compared two methods for derivation of individualized rate-correction coefficients: manual measurement on 10-s electrocardiograms and automated measurement of QT and RR during continuous 24-h electrocardiogram recordings. The four treatments, received by each subject in a latin-square randomization sequence were placebo, moxifloxacin, and two doses of an investigational drug. Analysis of continuous electrocardiogram data yielded a lower standard deviation of QT:RR regression values than the manual method, though the differences were not statistically significant. The within-subject and within-treatment coefficients of variation between the manual and automated methods were not significantly different. Corrected QT values from the two methods had similar rates of true and false positive identification of moxifloxacin's QT prolonging effect. An automated method for individualized rate correction applied to continuous electrocardiogram data could be advantageous in clinical trials, as the automated method is simpler, is based upon a much larger volume of data, yields similar results, and requires no human over-reading of the measurements. © The Author(s) 2015.

Measurement of thermally ablated lesions in sonoelastographic images using level set methods

NASA Astrophysics Data System (ADS)

Castaneda, Benjamin; Tamez-Pena, Jose Gerardo; Zhang, Man; Hoyt, Kenneth; Bylund, Kevin; Christensen, Jared; Saad, Wael; Strang, John; Rubens, Deborah J.; Parker, Kevin J.

2008-03-01

The capability of sonoelastography to detect lesions based on elasticity contrast can be applied to monitor the creation of thermally ablated lesion. Currently, segmentation of lesions depicted in sonoelastographic images is performed manually which can be a time consuming process and prone to significant intra- and inter-observer variability. This work presents a semi-automated segmentation algorithm for sonoelastographic data. The user starts by planting a seed in the perceived center of the lesion. Fast marching methods use this information to create an initial estimate of the lesion. Subsequently, level set methods refine its final shape by attaching the segmented contour to edges in the image while maintaining smoothness. The algorithm is applied to in vivo sonoelastographic images from twenty five thermal ablated lesions created in porcine livers. The estimated area is compared to results from manual segmentation and gross pathology images. Results show that the algorithm outperforms manual segmentation in accuracy, inter- and intra-observer variability. The processing time per image is significantly reduced.

Plexiform neurofibroma tissue classification

NASA Astrophysics Data System (ADS)

Weizman, L.; Hoch, L.; Ben Sira, L.; Joskowicz, L.; Pratt, L.; Constantini, S.; Ben Bashat, D.

2011-03-01

Plexiform Neurofibroma (PN) is a major complication of NeuroFibromatosis-1 (NF1), a common genetic disease that involving the nervous system. PNs are peripheral nerve sheath tumors extending along the length of the nerve in various parts of the body. Treatment decision is based on tumor volume assessment using MRI, which is currently time consuming and error prone, with limited semi-automatic segmentation support. We present in this paper a new method for the segmentation and tumor mass quantification of PN from STIR MRI scans. The method starts with a user-based delineation of the tumor area in a single slice and automatically detects the PN lesions in the entire image based on the tumor connectivity. Experimental results on seven datasets yield a mean volume overlap difference of 25% as compared to manual segmentation by expert radiologist with a mean computation and interaction time of 12 minutes vs. over an hour for manual annotation. Since the user interaction in the segmentation process is minimal, our method has the potential to successfully become part of the clinical workflow.

[The risk of manual handling loads in the hotel sector].

PubMed

Muraca, G; Martino, L Barbaro; Abbate, A; De Pasquale, D; Barbuzza, O; Brecciaroli, R

2007-01-01

The aim of our study is to evaluate the manual handling risk and the incidence of muscle-skeletal pathologies in the hotel compartment. Our study is conducted on 264 workers of the hotel compartment. The sample is divided on the base of the working turn in the following groups: porter (both to the plans and in the kitchen); waiters to the plans; services (gardeners and workers). The duties have been valued according to the method NIOSH. The presence of muscle-skeletal pathologies has been verified on the base to the accused symptomology, and on the presence of clinical objectivity and to the reports of checks. The data has been compared to a control group. The application of the NIOSH method has showed for each working profile an elevated synthetic index, > 3, and for porter the index is 5. The clinical data has shown an elevated incidence of pathologies of the spine, especially lumbar spine, with a high prevalence in the group of male porters. In conclusion we believe that the manual handling represents a particularly remarkable risk for the workers in the hotel compartment.

Automated in-line mixing system for large scale production of chitosan-based polyplexes.

PubMed

Tavakoli Naeini, Ashkan; Soliman, Ousamah Younoss; Alameh, Mohamad Gabriel; Lavertu, Marc; Buschmann, Michael D

2017-08-15

Chitosan (CS)-based polyplexes are efficient non-viral gene delivery systems that are most commonly prepared by manual mixing. However, manual mixing is not only poorly controlled but also restricted to relatively small preparation volumes, limiting clinical applications. In order to overcome these drawbacks and to produce clinical quantities of CS-based polyplexes, a fully automated in-line mixing platform was developed for production of large batches of small-size and homogeneous CS-based polyplexes. Operational conditions to produce small-sized homogeneous polyplexes were identified. Increasing mixing concentrations of CS and nucleic acid was directly associated with an increase in size and polydispersity of both CS/pDNA and CS/siRNA polyplexes. We also found that although the speed of mixing has a negligible impact on the properties of CS/pDNA polyplexes, the size and polydispersity of CS/siRNA polyplexes are strongly influenced by the mixing speed: the higher the speed, the smaller the size and polydispersity. While in-line and manual CS/pDNA polyplexes had similar size and PDI, CS/siRNA polyplexes were smaller and more homogenous when prepared in-line in the non-laminar flow regime compared to manual method. Finally, we found that in-line mixed CS/siRNA polyplexes have equivalent or higher silencing efficiency of ApoB in HepG2 cells, compared to manually prepared polyplexes. Copyright © 2017 Elsevier Inc. All rights reserved.

Semiautomated segmentation of head and neck cancers in 18F-FDG PET scans: A just-enough-interaction approach

PubMed Central

Beichel, Reinhard R.; Van Tol, Markus; Ulrich, Ethan J.; Bauer, Christian; Chang, Tangel; Plichta, Kristin A.; Smith, Brian J.; Sunderland, John J.; Graham, Michael M.; Sonka, Milan; Buatti, John M.

2016-01-01

Purpose: The purpose of this work was to develop, validate, and compare a highly computer-aided method for the segmentation of hot lesions in head and neck 18F-FDG PET scans. Methods: A semiautomated segmentation method was developed, which transforms the segmentation problem into a graph-based optimization problem. For this purpose, a graph structure around a user-provided approximate lesion centerpoint is constructed and a suitable cost function is derived based on local image statistics. To handle frequently occurring situations that are ambiguous (e.g., lesions adjacent to each other versus lesion with inhomogeneous uptake), several segmentation modes are introduced that adapt the behavior of the base algorithm accordingly. In addition, the authors present approaches for the efficient interactive local and global refinement of initial segmentations that are based on the “just-enough-interaction” principle. For method validation, 60 PET/CT scans from 59 different subjects with 230 head and neck lesions were utilized. All patients had squamous cell carcinoma of the head and neck. A detailed comparison with the current clinically relevant standard manual segmentation approach was performed based on 2760 segmentations produced by three experts. Results: Segmentation accuracy measured by the Dice coefficient of the proposed semiautomated and standard manual segmentation approach was 0.766 and 0.764, respectively. This difference was not statistically significant (p = 0.2145). However, the intra- and interoperator standard deviations were significantly lower for the semiautomated method. In addition, the proposed method was found to be significantly faster and resulted in significantly higher intra- and interoperator segmentation agreement when compared to the manual segmentation approach. Conclusions: Lack of consistency in tumor definition is a critical barrier for radiation treatment targeting as well as for response assessment in clinical trials and in clinical oncology decision-making. The properties of the authors approach make it well suited for applications in image-guided radiation oncology, response assessment, or treatment outcome prediction. PMID:27277044

Semiautomated segmentation of head and neck cancers in 18F-FDG PET scans: A just-enough-interaction approach

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

Beichel, Reinhard R., E-mail: reinhard-beichel@uiowa.edu; Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, Iowa 52242; Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242

Purpose: The purpose of this work was to develop, validate, and compare a highly computer-aided method for the segmentation of hot lesions in head and neck 18F-FDG PET scans. Methods: A semiautomated segmentation method was developed, which transforms the segmentation problem into a graph-based optimization problem. For this purpose, a graph structure around a user-provided approximate lesion centerpoint is constructed and a suitable cost function is derived based on local image statistics. To handle frequently occurring situations that are ambiguous (e.g., lesions adjacent to each other versus lesion with inhomogeneous uptake), several segmentation modes are introduced that adapt the behaviormore » of the base algorithm accordingly. In addition, the authors present approaches for the efficient interactive local and global refinement of initial segmentations that are based on the “just-enough-interaction” principle. For method validation, 60 PET/CT scans from 59 different subjects with 230 head and neck lesions were utilized. All patients had squamous cell carcinoma of the head and neck. A detailed comparison with the current clinically relevant standard manual segmentation approach was performed based on 2760 segmentations produced by three experts. Results: Segmentation accuracy measured by the Dice coefficient of the proposed semiautomated and standard manual segmentation approach was 0.766 and 0.764, respectively. This difference was not statistically significant (p = 0.2145). However, the intra- and interoperator standard deviations were significantly lower for the semiautomated method. In addition, the proposed method was found to be significantly faster and resulted in significantly higher intra- and interoperator segmentation agreement when compared to the manual segmentation approach. Conclusions: Lack of consistency in tumor definition is a critical barrier for radiation treatment targeting as well as for response assessment in clinical trials and in clinical oncology decision-making. The properties of the authors approach make it well suited for applications in image-guided radiation oncology, response assessment, or treatment outcome prediction.« less

Antifungal Susceptibility Testing in HIV/AIDS Patients: a Comparison Between Automated Machine and Manual Method.

PubMed

Nelwan, Erni J; Indrasanti, Evi; Sinto, Robert; Nurchaida, Farida; Sosrosumihardjo, Rustadi

2016-01-01

to evaluate the performance of Vitek2 compact machine (Biomerieux Inc. ver 04.02, France) in reference to manual methods for susceptibility test for Candida resistance among HIV/AIDS patients. a comparison study to evaluate Vitek2 compact machine (Biomerieux Inc. ver 04.02, France) in reference to manual methods for susceptibility test for Candida resistance among HIV/AIDS patient was done. Categorical agreement between manual disc diffusion and Vitek2 machine was calculated using predefined criteria. Time to susceptibility result for automated and manual methods were measured. there were 137 Candida isolates comprising eight Candida species with C.albicans and C. glabrata as the first (56.2%) and second (15.3%) most common species, respectively. For fluconazole drug, among the C. albicans, 2.6% was found resistant on manual disc diffusion methods and no resistant was determined by Vitek2 machine; whereas 100% C. krusei was identified as resistant on both methods. Resistant patterns for C. glabrata to fluconazole, voriconazole and amphotericin B were 52.4%, 23.8%, 23.8% vs. 9.5%, 9.5%, 4.8% respectively between manual diffusion disc methods and Vitek2 machine. Time to susceptibility result for automated methods compared to Vitex2 machine was shorter for all Candida species. there is a good categorical agreement between manual disc diffusion and Vitek2 machine, except for C. glabrata for measuring the antifungal resistant. Time to susceptibility result for automated methods is shorter for all Candida species.

HEp-2 cell image classification method based on very deep convolutional networks with small datasets

NASA Astrophysics Data System (ADS)

Lu, Mengchi; Gao, Long; Guo, Xifeng; Liu, Qiang; Yin, Jianping

2017-07-01

Human Epithelial-2 (HEp-2) cell images staining patterns classification have been widely used to identify autoimmune diseases by the anti-Nuclear antibodies (ANA) test in the Indirect Immunofluorescence (IIF) protocol. Because manual test is time consuming, subjective and labor intensive, image-based Computer Aided Diagnosis (CAD) systems for HEp-2 cell classification are developing. However, methods proposed recently are mostly manual features extraction with low accuracy. Besides, the scale of available benchmark datasets is small, which does not exactly suitable for using deep learning methods. This issue will influence the accuracy of cell classification directly even after data augmentation. To address these issues, this paper presents a high accuracy automatic HEp-2 cell classification method with small datasets, by utilizing very deep convolutional networks (VGGNet). Specifically, the proposed method consists of three main phases, namely image preprocessing, feature extraction and classification. Moreover, an improved VGGNet is presented to address the challenges of small-scale datasets. Experimental results over two benchmark datasets demonstrate that the proposed method achieves superior performance in terms of accuracy compared with existing methods.

A detailed comparison of analysis processes for MCC-IMS data in disease classification—Automated methods can replace manual peak annotations

PubMed Central

Horsch, Salome; Kopczynski, Dominik; Kuthe, Elias; Baumbach, Jörg Ingo; Rahmann, Sven

2017-01-01

Motivation Disease classification from molecular measurements typically requires an analysis pipeline from raw noisy measurements to final classification results. Multi capillary column—ion mobility spectrometry (MCC-IMS) is a promising technology for the detection of volatile organic compounds in the air of exhaled breath. From raw measurements, the peak regions representing the compounds have to be identified, quantified, and clustered across different experiments. Currently, several steps of this analysis process require manual intervention of human experts. Our goal is to identify a fully automatic pipeline that yields competitive disease classification results compared to an established but subjective and tedious semi-manual process. Method We combine a large number of modern methods for peak detection, peak clustering, and multivariate classification into analysis pipelines for raw MCC-IMS data. We evaluate all combinations on three different real datasets in an unbiased cross-validation setting. We determine which specific algorithmic combinations lead to high AUC values in disease classifications across the different medical application scenarios. Results The best fully automated analysis process achieves even better classification results than the established manual process. The best algorithms for the three analysis steps are (i) SGLTR (Savitzky-Golay Laplace-operator filter thresholding regions) and LM (Local Maxima) for automated peak identification, (ii) EM clustering (Expectation Maximization) and DBSCAN (Density-Based Spatial Clustering of Applications with Noise) for the clustering step and (iii) RF (Random Forest) for multivariate classification. Thus, automated methods can replace the manual steps in the analysis process to enable an unbiased high throughput use of the technology. PMID:28910313

Reconstruction of three-dimensional grain structure in polycrystalline iron via an interactive segmentation method

NASA Astrophysics Data System (ADS)

Feng, Min-nan; Wang, Yu-cong; Wang, Hao; Liu, Guo-quan; Xue, Wei-hua

2017-03-01

Using a total of 297 segmented sections, we reconstructed the three-dimensional (3D) structure of pure iron and obtained the largest dataset of 16254 3D complete grains reported to date. The mean values of equivalent sphere radius and face number of pure iron were observed to be consistent with those of Monte Carlo simulated grains, phase-field simulated grains, Ti-alloy grains, and Ni-based super alloy grains. In this work, by finding a balance between automatic methods and manual refinement, we developed an interactive segmentation method to segment serial sections accurately in the reconstruction of the 3D microstructure; this approach can save time as well as substantially eliminate errors. The segmentation process comprises four operations: image preprocessing, breakpoint detection based on mathematical morphology analysis, optimized automatic connection of the breakpoints, and manual refinement by artificial evaluation.

Fully automatic multi-atlas segmentation of CTA for partial volume correction in cardiac SPECT/CT

NASA Astrophysics Data System (ADS)

Liu, Qingyi; Mohy-ud-Din, Hassan; Boutagy, Nabil E.; Jiang, Mingyan; Ren, Silin; Stendahl, John C.; Sinusas, Albert J.; Liu, Chi

2017-05-01

Anatomical-based partial volume correction (PVC) has been shown to improve image quality and quantitative accuracy in cardiac SPECT/CT. However, this method requires manual segmentation of various organs from contrast-enhanced computed tomography angiography (CTA) data. In order to achieve fully automatic CTA segmentation for clinical translation, we investigated the most common multi-atlas segmentation methods. We also modified the multi-atlas segmentation method by introducing a novel label fusion algorithm for multiple organ segmentation to eliminate overlap and gap voxels. To evaluate our proposed automatic segmentation, eight canine 99mTc-labeled red blood cell SPECT/CT datasets that incorporated PVC were analyzed, using the leave-one-out approach. The Dice similarity coefficient of each organ was computed. Compared to the conventional label fusion method, our proposed label fusion method effectively eliminated gaps and overlaps and improved the CTA segmentation accuracy. The anatomical-based PVC of cardiac SPECT images with automatic multi-atlas segmentation provided consistent image quality and quantitative estimation of intramyocardial blood volume, as compared to those derived using manual segmentation. In conclusion, our proposed automatic multi-atlas segmentation method of CTAs is feasible, practical, and facilitates anatomical-based PVC of cardiac SPECT/CT images.

User-guided segmentation for volumetric retinal optical coherence tomography images

PubMed Central

Yin, Xin; Chao, Jennifer R.; Wang, Ruikang K.

2014-01-01

Abstract. Despite the existence of automatic segmentation techniques, trained graders still rely on manual segmentation to provide retinal layers and features from clinical optical coherence tomography (OCT) images for accurate measurements. To bridge the gap between this time-consuming need of manual segmentation and currently available automatic segmentation techniques, this paper proposes a user-guided segmentation method to perform the segmentation of retinal layers and features in OCT images. With this method, by interactively navigating three-dimensional (3-D) OCT images, the user first manually defines user-defined (or sketched) lines at regions where the retinal layers appear very irregular for which the automatic segmentation method often fails to provide satisfactory results. The algorithm is then guided by these sketched lines to trace the entire 3-D retinal layer and anatomical features by the use of novel layer and edge detectors that are based on robust likelihood estimation. The layer and edge boundaries are finally obtained to achieve segmentation. Segmentation of retinal layers in mouse and human OCT images demonstrates the reliability and efficiency of the proposed user-guided segmentation method. PMID:25147962

User-guided segmentation for volumetric retinal optical coherence tomography images.

PubMed

Yin, Xin; Chao, Jennifer R; Wang, Ruikang K

2014-08-01

Despite the existence of automatic segmentation techniques, trained graders still rely on manual segmentation to provide retinal layers and features from clinical optical coherence tomography (OCT) images for accurate measurements. To bridge the gap between this time-consuming need of manual segmentation and currently available automatic segmentation techniques, this paper proposes a user-guided segmentation method to perform the segmentation of retinal layers and features in OCT images. With this method, by interactively navigating three-dimensional (3-D) OCT images, the user first manually defines user-defined (or sketched) lines at regions where the retinal layers appear very irregular for which the automatic segmentation method often fails to provide satisfactory results. The algorithm is then guided by these sketched lines to trace the entire 3-D retinal layer and anatomical features by the use of novel layer and edge detectors that are based on robust likelihood estimation. The layer and edge boundaries are finally obtained to achieve segmentation. Segmentation of retinal layers in mouse and human OCT images demonstrates the reliability and efficiency of the proposed user-guided segmentation method.

Automated coronary artery calcification detection on low-dose chest CT images

NASA Astrophysics Data System (ADS)

Xie, Yiting; Cham, Matthew D.; Henschke, Claudia; Yankelevitz, David; Reeves, Anthony P.

2014-03-01

Coronary artery calcification (CAC) measurement from low-dose CT images can be used to assess the risk of coronary artery disease. A fully automatic algorithm to detect and measure CAC from low-dose non-contrast, non-ECG-gated chest CT scans is presented. Based on the automatically detected CAC, the Agatston score (AS), mass score and volume score were computed. These were compared with scores obtained manually from standard-dose ECG-gated scans and low-dose un-gated scans of the same patient. The automatic algorithm segments the heart region based on other pre-segmented organs to provide a coronary region mask. The mitral valve and aortic valve calcification is identified and excluded. All remaining voxels greater than 180HU within the mask region are considered as CAC candidates. The heart segmentation algorithm was evaluated on 400 non-contrast cases with both low-dose and regular dose CT scans. By visual inspection, 371 (92.8%) of the segmentations were acceptable. The automated CAC detection algorithm was evaluated on 41 low-dose non-contrast CT scans. Manual markings were performed on both low-dose and standard-dose scans for these cases. Using linear regression, the correlation of the automatic AS with the standard-dose manual scores was 0.86; with the low-dose manual scores the correlation was 0.91. Standard risk categories were also computed. The automated method risk category agreed with manual markings of gated scans for 24 cases while 15 cases were 1 category off. For low-dose scans, the automatic method agreed with 33 cases while 7 cases were 1 category off.

Fast cine-magnetic resonance imaging point tracking for prostate cancer radiation therapy planning

NASA Astrophysics Data System (ADS)

Dowling, J.; Dang, K.; Fox, Chris D.; Chandra, S.; Gill, Suki; Kron, T.; Pham, D.; Foroudi, F.

2014-03-01

The analysis of intra-fraction organ motion is important for improving the precision of radiation therapy treatment delivery. One method to quantify this motion is for one or more observers to manually identify anatomic points of interest (POIs) on each slice of a cine-MRI sequence. However this is labour intensive and inter- and intra- observer variation can introduce uncertainty. In this paper a fast method for non-rigid registration based point tracking in cine-MRI sagittal and coronal series is described which identifies POIs in 0.98 seconds per sagittal slice and 1.35 seconds per coronal slice. The manual and automatic points were highly correlated (r>0.99, p<0.001) for all organs and the difference generally less than 1mm. For prostate planning peristalsis and rectal gas can result in unpredictable out of plane motion, suggesting the results may require manual verification.

The design and implementation of an automated system for logging clinical experiences using an anesthesia information management system.

PubMed

Simpao, Allan; Heitz, James W; McNulty, Stephen E; Chekemian, Beth; Brenn, B Randall; Epstein, Richard H

2011-02-01

Residents in anesthesia training programs throughout the world are required to document their clinical cases to help ensure that they receive adequate training. Current systems involve self-reporting, are subject to delayed updates and misreported data, and do not provide a practicable method of validation. Anesthesia information management systems (AIMS) are being used increasingly in training programs and are a logical source for verifiable documentation. We hypothesized that case logs generated automatically from an AIMS would be sufficiently accurate to replace the current manual process. We based our analysis on the data reporting requirements of the American College of Graduate Medical Education (ACGME). We conducted a systematic review of ACGME requirements and our AIMS record, and made modifications after identifying data element and attribution issues. We studied 2 methods (parsing of free text procedure descriptions and CPT4 procedure code mapping) to automatically determine ACGME case categories and generated AIMS-based case logs and compared these to assignments made by manual inspection of the anesthesia records. We also assessed under- and overreporting of cases entered manually by our residents into the ACGME website. The parsing and mapping methods assigned cases to a majority of the ACGME categories with accuracies of 95% and 97%, respectively, as compared with determinations made by 2 residents and 1 attending who manually reviewed all procedure descriptions. Comparison of AIMS-based case logs with reports from the ACGME Resident Case Log System website showed that >50% of residents either underreported or overreported their total case counts by at least 5%. The AIMS database is a source of contemporaneous documentation of resident experience that can be queried to generate valid, verifiable case logs. The extent of AIMS adoption by academic anesthesia departments should encourage accreditation organizations to support uploading of AIMS-based case log files to improve accuracy and to decrease the clerical burden on anesthesia residents.

DESIGN MANUAL: PHOSPHORUS REMOVAL

EPA Science Inventory

This manual summarizes process design information for the best developed methods for removing phosphorus from wastewater. his manual discusses several proven phosphorus removal methods, including phosphorus removal obtainable through biological activity as well as chemical precip...

Bronchial closure methods and risks for bronchopleural fistula in pulmonary resections: how a surgeon may choose the optimum method?

PubMed

Uçvet, Ahmet; Gursoy, Soner; Sirzai, Serdar; Erbaycu, Ahmet E; Ozturk, Ali A; Ceylan, Kenan C; Kaya, Seyda O

2011-04-01

There is debate about which bronchial closure technique is the best to prevent bronchopleural fistulas (BPFs). We aim to assess the effect of bronchial closure procedures and patients' characteristics on BPF occurrence in pulmonary resections. Bronchial closures in 625 consecutive patients were assessed. Stumps were closed by manual suturing in 204 and by mechanical stapling in 421 cases. In the mechanical stapling group, stapling supported by manual suture was performed in 170 cases. BPFs occurred in 3.8%. Of these, stapling was used in 5.0%, whereas manual suturing was used in 1.5% (P=0.04). BPFs were more prevalent among patients who had undergone pneumonectomy (P<0.01), right pneumonectomy (P<0.01), stapler closure (P<0.01), patients with co-factors (P<0.01), and patients who had undergone preoperative neo-adjuvant (P=0.01) or postoperative adjuvant therapy (P=0.03). There was no difference in the frequency of BPF between patients with and without adjuvant support in the stapling group. The optimum bronchial closure method has to be chosen by considering the patient and bronchus based characteristics. This has to be assessed carefully, especially in pneumonectomy and co-factors. The manual closure seems to be the more preferable method in risky patients. An additive support suture on the bronchial stump does not decrease the risk of BPF.

Functional segmentation of dynamic PET studies: Open source implementation and validation of a leader-follower-based algorithm.

PubMed

Mateos-Pérez, José María; Soto-Montenegro, María Luisa; Peña-Zalbidea, Santiago; Desco, Manuel; Vaquero, Juan José

2016-02-01

We present a novel segmentation algorithm for dynamic PET studies that groups pixels according to the similarity of their time-activity curves. Sixteen mice bearing a human tumor cell line xenograft (CH-157MN) were imaged with three different (68)Ga-DOTA-peptides (DOTANOC, DOTATATE, DOTATOC) using a small animal PET-CT scanner. Regional activities (input function and tumor) were obtained after manual delineation of regions of interest over the image. The algorithm was implemented under the jClustering framework and used to extract the same regional activities as in the manual approach. The volume of distribution in the tumor was computed using the Logan linear method. A Kruskal-Wallis test was used to investigate significant differences between the manually and automatically obtained volumes of distribution. The algorithm successfully segmented all the studies. No significant differences were found for the same tracer across different segmentation methods. Manual delineation revealed significant differences between DOTANOC and the other two tracers (DOTANOC - DOTATATE, p=0.020; DOTANOC - DOTATOC, p=0.033). Similar differences were found using the leader-follower algorithm. An open implementation of a novel segmentation method for dynamic PET studies is presented and validated in rodent studies. It successfully replicated the manual results obtained in small-animal studies, thus making it a reliable substitute for this task and, potentially, for other dynamic segmentation procedures. Copyright © 2016 Elsevier Ltd. All rights reserved.

Topological leakage detection and freeze-and-grow propagation for improved CT-based airway segmentation

NASA Astrophysics Data System (ADS)

Nadeem, Syed Ahmed; Hoffman, Eric A.; Sieren, Jered P.; Saha, Punam K.

2018-03-01

Numerous large multi-center studies are incorporating the use of computed tomography (CT)-based characterization of the lung parenchyma and bronchial tree to understand chronic obstructive pulmonary disease status and progression. To the best of our knowledge, there are no fully automated airway tree segmentation methods, free of the need for user review. A failure in even a fraction of segmentation results necessitates manual revision of all segmentation masks which is laborious considering the thousands of image data sets evaluated in large studies. In this paper, we present a novel CT-based airway tree segmentation algorithm using topological leakage detection and freeze-and-grow propagation. The method is fully automated requiring no manual inputs or post-segmentation editing. It uses simple intensity-based connectivity and a freeze-and-grow propagation algorithm to iteratively grow the airway tree starting from an initial seed inside the trachea. It begins with a conservative parameter and then, gradually shifts toward more generous parameter values. The method was applied on chest CT scans of fifteen subjects at total lung capacity. Airway segmentation results were qualitatively assessed and performed comparably to established airway segmentation method with no major visual leakages.

A bibliography on formal methods for system specification, design and validation

NASA Technical Reports Server (NTRS)

Meyer, J. F.; Furchtgott, D. G.; Movaghar, A.

1982-01-01

Literature on the specification, design, verification, testing, and evaluation of avionics systems was surveyed, providing 655 citations. Journal papers, conference papers, and technical reports are included. Manual and computer-based methods were employed. Keywords used in the online search are listed.

Automatic lumbar spine measurement in CT images

NASA Astrophysics Data System (ADS)

Mao, Yunxiang; Zheng, Dong; Liao, Shu; Peng, Zhigang; Yan, Ruyi; Liu, Junhua; Dong, Zhongxing; Gong, Liyan; Zhou, Xiang Sean; Zhan, Yiqiang; Fei, Jun

2017-03-01

Accurate lumbar spine measurement in CT images provides an essential way for quantitative spinal diseases analysis such as spondylolisthesis and scoliosis. In today's clinical workflow, the measurements are manually performed by radiologists and surgeons, which is time consuming and irreproducible. Therefore, automatic and accurate lumbar spine measurement algorithm becomes highly desirable. In this study, we propose a method to automatically calculate five different lumbar spine measurements in CT images. There are three main stages of the proposed method: First, a learning based spine labeling method, which integrates both the image appearance and spine geometry information, is used to detect lumbar and sacrum vertebrae in CT images. Then, a multiatlases based image segmentation method is used to segment each lumbar vertebra and the sacrum based on the detection result. Finally, measurements are derived from the segmentation result of each vertebra. Our method has been evaluated on 138 spinal CT scans to automatically calculate five widely used clinical spine measurements. Experimental results show that our method can achieve more than 90% success rates across all the measurements. Our method also significantly improves the measurement efficiency compared to manual measurements. Besides benefiting the routine clinical diagnosis of spinal diseases, our method also enables the large scale data analytics for scientific and clinical researches.

Early Childhood Longitudinal Study, Kindergarten Class of 2010-11 (ECLS-K:2011). User's Manual for the ECLS-K:2011 Kindergarten Data File and Electronic Codebook, Public Version. NCES 2015-074

ERIC Educational Resources Information Center

Tourangeau, Karen; Nord, Christine; Lê, Thanh; Sorongon, Alberto G.; Hagedorn, Mary C.; Daly, Peggy; Najarian, Michelle

2015-01-01

This manual provides guidance and documentation for users of the kindergarten (or base year) data of the Early Childhood Longitudinal Study, Kindergarten Class of 2010-11 (ECLS-K:2011). It begins with an overview of the ECLS-K:2011. Subsequent chapters provide details on the study data collection instruments and methods; the direct and indirect…

An Overview of Potential Methods for Maintaining Training Area Environments in Arid and Semi-Arid Climates

DTIC Science & Technology

1983-04-01

Shrubs , Ground Covers, and Vines , Technical Manual 5-830-4 (June 1976). This manual provides guidelines and prescribes standard techniques to be used...in planting and the initial care required to successfully establish trees, shrubs , ground covers, and vines . Criteria for selecting materials are...their new location. The planting of trees, shrubs , ground covers, and vines should comply with approved landscape planting plans and should be based on

Extracting BI-RADS Features from Portuguese Clinical Texts

PubMed Central

Nassif, Houssam; Cunha, Filipe; Moreira, Inês C.; Cruz-Correia, Ricardo; Sousa, Eliana; Page, David; Burnside, Elizabeth; Dutra, Inês

2013-01-01

In this work we build the first BI-RADS parser for Portuguese free texts, modeled after existing approaches to extract BI-RADS features from English medical records. Our concept finder uses a semantic grammar based on the BIRADS lexicon and on iterative transferred expert knowledge. We compare the performance of our algorithm to manual annotation by a specialist in mammography. Our results show that our parser’s performance is comparable to the manual method. PMID:23797461

Fully automated registration of first-pass myocardial perfusion MRI using independent component analysis.

PubMed

Milles, J; van der Geest, R J; Jerosch-Herold, M; Reiber, J H C; Lelieveldt, B P F

2007-01-01

This paper presents a novel method for registration of cardiac perfusion MRI. The presented method successfully corrects for breathing motion without any manual interaction using Independent Component Analysis to extract physiologically relevant features together with their time-intensity behavior. A time-varying reference image mimicking intensity changes in the data of interest is computed based on the results of ICA, and used to compute the displacement caused by breathing for each frame. Qualitative and quantitative validation of the method is carried out using 46 clinical quality, short-axis, perfusion MR datasets comprising 100 images each. Validation experiments showed a reduction of the average LV motion from 1.26+/-0.87 to 0.64+/-0.46 pixels. Time-intensity curves are also improved after registration with an average error reduced from 2.65+/-7.89% to 0.87+/-3.88% between registered data and manual gold standard. We conclude that this fully automatic ICA-based method shows an excellent accuracy, robustness and computation speed, adequate for use in a clinical environment.

Interactive surface correction for 3D shape based segmentation

NASA Astrophysics Data System (ADS)

Schwarz, Tobias; Heimann, Tobias; Tetzlaff, Ralf; Rau, Anne-Mareike; Wolf, Ivo; Meinzer, Hans-Peter

2008-03-01

Statistical shape models have become a fast and robust method for segmentation of anatomical structures in medical image volumes. In clinical practice, however, pathological cases and image artifacts can lead to local deviations of the detected contour from the true object boundary. These deviations have to be corrected manually. We present an intuitively applicable solution for surface interaction based on Gaussian deformation kernels. The method is evaluated by two radiological experts on segmentations of the liver in contrast-enhanced CT images and of the left heart ventricle (LV) in MRI data. For both applications, five datasets are segmented automatically using deformable shape models, and the resulting surfaces are corrected manually. The interactive correction step improves the average surface distance against ground truth from 2.43mm to 2.17mm for the liver, and from 2.71mm to 1.34mm for the LV. We expect this method to raise the acceptance of automatic segmentation methods in clinical application.

Rapid detection of Salmonella in pet food: design and evaluation of integrated methods based on real-time PCR detection.

PubMed

Balachandran, Priya; Friberg, Maria; Vanlandingham, V; Kozak, K; Manolis, Amanda; Brevnov, Maxim; Crowley, Erin; Bird, Patrick; Goins, David; Furtado, Manohar R; Petrauskene, Olga V; Tebbs, Robert S; Charbonneau, Duane

2012-02-01

Reducing the risk of Salmonella contamination in pet food is critical for both companion animals and humans, and its importance is reflected by the substantial increase in the demand for pathogen testing. Accurate and rapid detection of foodborne pathogens improves food safety, protects the public health, and benefits food producers by assuring product quality while facilitating product release in a timely manner. Traditional culture-based methods for Salmonella screening are laborious and can take 5 to 7 days to obtain definitive results. In this study, we developed two methods for the detection of low levels of Salmonella in pet food using real-time PCR: (i) detection of Salmonella in 25 g of dried pet food in less than 14 h with an automated magnetic bead-based nucleic acid extraction method and (ii) detection of Salmonella in 375 g of composite dry pet food matrix in less than 24 h with a manual centrifugation-based nucleic acid preparation method. Both methods included a preclarification step using a novel protocol that removes food matrix-associated debris and PCR inhibitors and improves the sensitivity of detection. Validation studies revealed no significant differences between the two real-time PCR methods and the standard U.S. Food and Drug Administration Bacteriological Analytical Manual (chapter 5) culture confirmation method.

Two phase sampling for wheat acreage estimation. [large area crop inventory experiment

NASA Technical Reports Server (NTRS)

Thomas, R. W.; Hay, C. M.

1977-01-01

A two phase LANDSAT-based sample allocation and wheat proportion estimation method was developed. This technique employs manual, LANDSAT full frame-based wheat or cultivated land proportion estimates from a large number of segments comprising a first sample phase to optimally allocate a smaller phase two sample of computer or manually processed segments. Application to the Kansas Southwest CRD for 1974 produced a wheat acreage estimate for that CRD within 2.42 percent of the USDA SRS-based estimate using a lower CRD inventory budget than for a simulated reference LACIE system. Factor of 2 or greater cost or precision improvements relative to the reference system were obtained.

FacetModeller: Software for manual creation, manipulation and analysis of 3D surface-based models

NASA Astrophysics Data System (ADS)

Lelièvre, Peter G.; Carter-McAuslan, Angela E.; Dunham, Michael W.; Jones, Drew J.; Nalepa, Mariella; Squires, Chelsea L.; Tycholiz, Cassandra J.; Vallée, Marc A.; Farquharson, Colin G.

2018-01-01

The creation of 3D models is commonplace in many disciplines. Models are often built from a collection of tessellated surfaces. To apply numerical methods to such models it is often necessary to generate a mesh of space-filling elements that conforms to the model surfaces. While there are meshing algorithms that can do so, they place restrictive requirements on the surface-based models that are rarely met by existing 3D model building software. Hence, we have developed a Java application named FacetModeller, designed for efficient manual creation, modification and analysis of 3D surface-based models destined for use in numerical modelling.

Reproducibility measurements of three methods for calculating in vivo MR-based knee kinematics.

PubMed

Lansdown, Drew A; Zaid, Musa; Pedoia, Valentina; Subburaj, Karupppasamy; Souza, Richard; Benjamin, C; Li, Xiaojuan

2015-08-01

To describe three quantification methods for magnetic resonance imaging (MRI)-based knee kinematic evaluation and to report on the reproducibility of these algorithms. T2 -weighted, fast-spin echo images were obtained of the bilateral knees in six healthy volunteers. Scans were repeated for each knee after repositioning to evaluate protocol reproducibility. Semiautomatic segmentation defined regions of interest for the tibia and femur. The posterior femoral condyles and diaphyseal axes were defined using the previously defined tibia and femur. All segmentation was performed twice to evaluate segmentation reliability. Anterior tibial translation (ATT) and internal tibial rotation (ITR) were calculated using three methods: a tibial-based registration system, a combined tibiofemoral-based registration method with all manual segmentation, and a combined tibiofemoral-based registration method with automatic definition of condyles and axes. Intraclass correlation coefficients and standard deviations across multiple measures were determined. Reproducibility of segmentation was excellent (ATT = 0.98; ITR = 0.99) for both combined methods. ATT and ITR measurements were also reproducible across multiple scans in the combined registration measurements with manual (ATT = 0.94; ITR = 0.94) or automatic (ATT = 0.95; ITR = 0.94) condyles and axes. The combined tibiofemoral registration with automatic definition of the posterior femoral condyle and diaphyseal axes allows for improved knee kinematics quantification with excellent in vivo reproducibility. © 2014 Wiley Periodicals, Inc.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

DOE PAGES

Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

2015-04-25

In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore » diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

The influence of direct compression powder blend transfer method from the container to the tablet press on product critical quality attributes: a case study.

PubMed

Teżyk, Michał; Jakubowska, Emilia; Milczewska, Kasylda; Milanowski, Bartłomiej; Voelkel, Adam; Lulek, Janina

2017-06-01

The aim of this article is to compare the gravitational powder blend loading method to the tablet press and manual loading in terms of their influence on tablets' critical quality attributes (CQA). The results of the study can be of practical relevance to the pharmaceutical industry in the area of direct compression of low-dose formulations, which could be prone to content uniformity (CU) issues. In the preliminary study, particle size distribution (PSD) and surface energy of raw materials were determined using laser diffraction method and inverse gas chromatography, respectively. For trials purpose, a formulation containing two pharmaceutical ingredients (APIs) was used. Tablet samples were collected during the compression progress to analyze their CQAs, namely assay and CU. Results obtained during trials indicate that tested direct compression powder blend is sensitive to applied powder handling method. Mild increase in both APIs content was observed during manual scooping. Gravitational approach (based on discharge into the drum) resulted in a decrease in CU, which is connected to a more pronounced assay increase at the end of tableting than in the case of manual loading. The correct design of blend transfer over single unit processes is an important issue and should be investigated during the development phase since it may influence the final product CQAs. The manual scooping method, although simplistic, can be a temporary solution to improve the results of API's content and uniformity when compared to industrial gravitational transfer.

Putaminal volume and diffusion in early familial Creutzfeldt-Jakob disease.

PubMed

Seror, Ilana; Lee, Hedok; Cohen, Oren S; Hoffmann, Chen; Prohovnik, Isak

2010-01-15

The putamen is centrally implicated in the pathophysiology of Creutzfeldt-Jakob Disease (CJD). To our knowledge, its volume has never been measured in this disease. We investigated whether gross putaminal atrophy can be detected by MRI in early stages, when the diffusion is already reduced. Twelve familial CJD patients with the E200K mutation and 22 healthy controls underwent structural and diffusion MRI scans. The putamen was identified in anatomical scans by two methods: manual tracing by a blinded investigator, and automatic parcellation by a computerized segmentation procedure (FSL FIRST). For each method, volume and mean Apparent Diffusion Coefficient (ADC) were calculated. ADC was significantly lower in CJD patients (697+/-64 microm(2)/s vs. 750+/-31 microm(2)/s, p<0.005), as expected, but the volume was not reduced. The computerized FIRST delineation yielded comparable ADC values to the manual method, but computerized volumes were smaller than manual tracing values. We conclude that significant diffusion reduction in the putamen can be detected by delineating the structure manually or with a computerized algorithm. Our findings confirm and extend previous voxel-based and observational studies. Putaminal volume was not reduced in our early-stage patients, thus confirming that diffusion abnormalities precede detectible atrophy in this structure.

Time warp operating system version 2.7 internals manual

NASA Technical Reports Server (NTRS)

1992-01-01

The Time Warp Operating System (TWOS) is an implementation of the Time Warp synchronization method proposed by David Jefferson. In addition, it serves as an actual platform for running discrete event simulations. The code comprising TWOS can be divided into several different sections. TWOS typically relies on an existing operating system to furnish some very basic services. This existing operating system is referred to as the Base OS. The existing operating system varies depending on the hardware TWOS is running on. It is Unix on the Sun workstations, Chrysalis or Mach on the Butterfly, and Mercury on the Mark 3 Hypercube. The base OS could be an entirely new operating system, written to meet the special needs of TWOS, but, to this point, existing systems have been used instead. The base OS's used for TWOS on various platforms are not discussed in detail in this manual, as they are well covered in their own manuals. Appendix G discusses the interface between one such OS, Mach, and TWOS.

An Unsupervised kNN Method to Systematically Detect Changes in Protein Localization in High-Throughput Microscopy Images.

PubMed

Lu, Alex Xijie; Moses, Alan M

2016-01-01

Despite the importance of characterizing genes that exhibit subcellular localization changes between conditions in proteome-wide imaging experiments, many recent studies still rely upon manual evaluation to assess the results of high-throughput imaging experiments. We describe and demonstrate an unsupervised k-nearest neighbours method for the detection of localization changes. Compared to previous classification-based supervised change detection methods, our method is much simpler and faster, and operates directly on the feature space to overcome limitations in needing to manually curate training sets that may not generalize well between screens. In addition, the output of our method is flexible in its utility, generating both a quantitatively ranked list of localization changes that permit user-defined cut-offs, and a vector for each gene describing feature-wise direction and magnitude of localization changes. We demonstrate that our method is effective at the detection of localization changes using the Δrpd3 perturbation in Saccharomyces cerevisiae, where we capture 71.4% of previously known changes within the top 10% of ranked genes, and find at least four new localization changes within the top 1% of ranked genes. The results of our analysis indicate that simple unsupervised methods may be able to identify localization changes in images without laborious manual image labelling steps.

[Medical image elastic registration smoothed by unconstrained optimized thin-plate spline].

PubMed

Zhang, Yu; Li, Shuxiang; Chen, Wufan; Liu, Zhexing

2003-12-01

Elastic registration of medical image is an important subject in medical image processing. Previous work has concentrated on selecting the corresponding landmarks manually and then using thin-plate spline interpolating to gain the elastic transformation. However, the landmarks extraction is always prone to error, which will influence the registration results. Localizing the landmarks manually is also difficult and time-consuming. We the optimization theory to improve the thin-plate spline interpolation, and based on it, used an automatic method to extract the landmarks. Combining these two steps, we have proposed an automatic, exact and robust registration method and have gained satisfactory registration results.

Smart Extraction and Analysis System for Clinical Research.

PubMed

Afzal, Muhammad; Hussain, Maqbool; Khan, Wajahat Ali; Ali, Taqdir; Jamshed, Arif; Lee, Sungyoung

2017-05-01

With the increasing use of electronic health records (EHRs), there is a growing need to expand the utilization of EHR data to support clinical research. The key challenge in achieving this goal is the unavailability of smart systems and methods to overcome the issue of data preparation, structuring, and sharing for smooth clinical research. We developed a robust analysis system called the smart extraction and analysis system (SEAS) that consists of two subsystems: (1) the information extraction system (IES), for extracting information from clinical documents, and (2) the survival analysis system (SAS), for a descriptive and predictive analysis to compile the survival statistics and predict the future chance of survivability. The IES subsystem is based on a novel permutation-based pattern recognition method that extracts information from unstructured clinical documents. Similarly, the SAS subsystem is based on a classification and regression tree (CART)-based prediction model for survival analysis. SEAS is evaluated and validated on a real-world case study of head and neck cancer. The overall information extraction accuracy of the system for semistructured text is recorded at 99%, while that for unstructured text is 97%. Furthermore, the automated, unstructured information extraction has reduced the average time spent on manual data entry by 75%, without compromising the accuracy of the system. Moreover, around 88% of patients are found in a terminal or dead state for the highest clinical stage of disease (level IV). Similarly, there is an ∼36% probability of a patient being alive if at least one of the lifestyle risk factors was positive. We presented our work on the development of SEAS to replace costly and time-consuming manual methods with smart automatic extraction of information and survival prediction methods. SEAS has reduced the time and energy of human resources spent unnecessarily on manual tasks.

Left ventricular endocardial surface detection based on real-time 3D echocardiographic data

NASA Technical Reports Server (NTRS)

Corsi, C.; Borsari, M.; Consegnati, F.; Sarti, A.; Lamberti, C.; Travaglini, A.; Shiota, T.; Thomas, J. D.

2001-01-01

OBJECTIVE: A new computerized semi-automatic method for left ventricular (LV) chamber segmentation is presented. METHODS: The LV is imaged by real-time three-dimensional echocardiography (RT3DE). The surface detection model, based on level set techniques, is applied to RT3DE data for image analysis. The modified level set partial differential equation we use is solved by applying numerical methods for conservation laws. The initial conditions are manually established on some slices of the entire volume. The solution obtained for each slice is a contour line corresponding with the boundary between LV cavity and LV endocardium. RESULTS: The mathematical model has been applied to sequences of frames of human hearts (volume range: 34-109 ml) imaged by 2D and reconstructed off-line and RT3DE data. Volume estimation obtained by this new semi-automatic method shows an excellent correlation with those obtained by manual tracing (r = 0.992). Dynamic change of LV volume during the cardiac cycle is also obtained. CONCLUSION: The volume estimation method is accurate; edge based segmentation, image completion and volume reconstruction can be accomplished. The visualization technique also allows to navigate into the reconstructed volume and to display any section of the volume.

iTemplate: A template-based eye movement data analysis approach.

PubMed

Xiao, Naiqi G; Lee, Kang

2018-02-08

Current eye movement data analysis methods rely on defining areas of interest (AOIs). Due to the fact that AOIs are created and modified manually, variances in their size, shape, and location are unavoidable. These variances affect not only the consistency of the AOI definitions, but also the validity of the eye movement analyses based on the AOIs. To reduce the variances in AOI creation and modification and achieve a procedure to process eye movement data with high precision and efficiency, we propose a template-based eye movement data analysis method. Using a linear transformation algorithm, this method registers the eye movement data from each individual stimulus to a template. Thus, users only need to create one set of AOIs for the template in order to analyze eye movement data, rather than creating a unique set of AOIs for all individual stimuli. This change greatly reduces the error caused by the variance from manually created AOIs and boosts the efficiency of the data analysis. Furthermore, this method can help researchers prepare eye movement data for some advanced analysis approaches, such as iMap. We have developed software (iTemplate) with a graphic user interface to make this analysis method available to researchers.

Semiautomated segmentation of head and neck cancers in 18F-FDG PET scans: A just-enough-interaction approach.

PubMed

Beichel, Reinhard R; Van Tol, Markus; Ulrich, Ethan J; Bauer, Christian; Chang, Tangel; Plichta, Kristin A; Smith, Brian J; Sunderland, John J; Graham, Michael M; Sonka, Milan; Buatti, John M

2016-06-01

The purpose of this work was to develop, validate, and compare a highly computer-aided method for the segmentation of hot lesions in head and neck 18F-FDG PET scans. A semiautomated segmentation method was developed, which transforms the segmentation problem into a graph-based optimization problem. For this purpose, a graph structure around a user-provided approximate lesion centerpoint is constructed and a suitable cost function is derived based on local image statistics. To handle frequently occurring situations that are ambiguous (e.g., lesions adjacent to each other versus lesion with inhomogeneous uptake), several segmentation modes are introduced that adapt the behavior of the base algorithm accordingly. In addition, the authors present approaches for the efficient interactive local and global refinement of initial segmentations that are based on the "just-enough-interaction" principle. For method validation, 60 PET/CT scans from 59 different subjects with 230 head and neck lesions were utilized. All patients had squamous cell carcinoma of the head and neck. A detailed comparison with the current clinically relevant standard manual segmentation approach was performed based on 2760 segmentations produced by three experts. Segmentation accuracy measured by the Dice coefficient of the proposed semiautomated and standard manual segmentation approach was 0.766 and 0.764, respectively. This difference was not statistically significant (p = 0.2145). However, the intra- and interoperator standard deviations were significantly lower for the semiautomated method. In addition, the proposed method was found to be significantly faster and resulted in significantly higher intra- and interoperator segmentation agreement when compared to the manual segmentation approach. Lack of consistency in tumor definition is a critical barrier for radiation treatment targeting as well as for response assessment in clinical trials and in clinical oncology decision-making. The properties of the authors approach make it well suited for applications in image-guided radiation oncology, response assessment, or treatment outcome prediction.

Automatic aneurysm neck detection using surface Voronoi diagrams.

PubMed

Cárdenes, Rubén; Pozo, José María; Bogunovic, Hrvoje; Larrabide, Ignacio; Frangi, Alejandro F

2011-10-01

A new automatic approach for saccular intracranial aneurysm isolation is proposed in this work. Due to the inter- and intra-observer variability in manual delineation of the aneurysm neck, a definition based on a minimum cost path around the aneurysm sac is proposed that copes with this variability and is able to make consistent measurements along different data sets, as well as to automate and speedup the analysis of cerebral aneurysms. The method is based on the computation of a minimal path along a scalar field obtained on the vessel surface, to find the aneurysm neck in a robust and fast manner. The computation of the scalar field on the surface is obtained using a fast marching approach with a speed function based on the exponential of the distance from the centerline bifurcation between the aneurysm dome and the parent vessels. In order to assure a correct topology of the aneurysm sac, the neck computation is constrained to a region defined by a surface Voronoi diagram obtained from the branches of the vessel centerline. We validate this method comparing our results in 26 real cases with manual aneurysm isolation obtained using a cut-plane, and also with results obtained using manual delineations from three different observers by comparing typical morphological measures. © 2011 IEEE

A Method to Calculate and Analyze Residents' Evaluations by Using a Microcomputer Data-Base Management System.

ERIC Educational Resources Information Center

Mills, Myron L.

1988-01-01

A system developed for more efficient evaluation of graduate medical students' progress uses numerical scoring and a microcomputer database management system as an alternative to manual methods to produce accurate, objective, and meaningful summaries of resident evaluations. (Author/MSE)

A marker-based watershed method for X-ray image segmentation.

PubMed

Zhang, Xiaodong; Jia, Fucang; Luo, Suhuai; Liu, Guiying; Hu, Qingmao

2014-03-01

Digital X-ray images are the most frequent modality for both screening and diagnosis in hospitals. To facilitate subsequent analysis such as quantification and computer aided diagnosis (CAD), it is desirable to exclude image background. A marker-based watershed segmentation method was proposed to segment background of X-ray images. The method consisted of six modules: image preprocessing, gradient computation, marker extraction, watershed segmentation from markers, region merging and background extraction. One hundred clinical direct radiograph X-ray images were used to validate the method. Manual thresholding and multiscale gradient based watershed method were implemented for comparison. The proposed method yielded a dice coefficient of 0.964±0.069, which was better than that of the manual thresholding (0.937±0.119) and that of multiscale gradient based watershed method (0.942±0.098). Special means were adopted to decrease the computational cost, including getting rid of few pixels with highest grayscale via percentile, calculation of gradient magnitude through simple operations, decreasing the number of markers by appropriate thresholding, and merging regions based on simple grayscale statistics. As a result, the processing time was at most 6s even for a 3072×3072 image on a Pentium 4 PC with 2.4GHz CPU (4 cores) and 2G RAM, which was more than one time faster than that of the multiscale gradient based watershed method. The proposed method could be a potential tool for diagnosis and quantification of X-ray images. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Comparison of [{sup 11}C]choline Positron Emission Tomography With T2- and Diffusion-Weighted Magnetic Resonance Imaging for Delineating Malignant Intraprostatic Lesions

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

Chang, Joe H.; University of Melbourne, Victoria; Lim Joon, Daryl

2015-06-01

Purpose: The purpose of this study was to compare the accuracy of [{sup 11}C]choline positron emission tomography (CHOL-PET) with that of the combination of T2-weighted and diffusion-weighted (T2W/DW) magnetic resonance imaging (MRI) for delineating malignant intraprostatic lesions (IPLs) for guiding focal therapies and to investigate factors predicting the accuracy of CHOL-PET. Methods and Materials: This study included 21 patients who underwent CHOL-PET and T2W/DW MRI prior to radical prostatectomy. Two observers manually delineated IPL contours for each scan, and automatic IPL contours were generated on CHOL-PET based on varying proportions of the maximum standardized uptake value (SUV). IPLs identified onmore » prostatectomy specimens defined reference standard contours. The imaging-based contours were compared with the reference standard contours using Dice similarity coefficient (DSC), and sensitivity and specificity values. Factors that could potentially predict the DSC of the best contouring method were analyzed using linear models. Results: The best automatic contouring method, 60% of the maximum SUV (SUV{sub 60}) , had similar correlations (DSC: 0.59) with the manual PET contours (DSC: 0.52, P=.127) and significantly better correlations than the manual MRI contours (DSC: 0.37, P<.001). The sensitivity and specificity values were 72% and 71% for SUV{sub 60}; 53% and 86% for PET manual contouring; and 28% and 92% for MRI manual contouring. The tumor volume and transition zone pattern could independently predict the accuracy of CHOL-PET. Conclusions: CHOL-PET is superior to the combination of T2W/DW MRI for delineating IPLs. The accuracy of CHOL-PET is insufficient for gland-sparing focal therapies but may be accurate enough for focal boost therapies. The transition zone pattern is a new classification that may predict how well CHOL-PET delineates IPLs.« less

Automated classification of Acid Rock Drainage potential from Corescan drill core imagery

NASA Astrophysics Data System (ADS)

Cracknell, M. J.; Jackson, L.; Parbhakar-Fox, A.; Savinova, K.

2017-12-01

Classification of the acid forming potential of waste rock is important for managing environmental hazards associated with mining operations. Current methods for the classification of acid rock drainage (ARD) potential usually involve labour intensive and subjective assessment of drill core and/or hand specimens. Manual methods are subject to operator bias, human error and the amount of material that can be assessed within a given time frame is limited. The automated classification of ARD potential documented here is based on the ARD Index developed by Parbhakar-Fox et al. (2011). This ARD Index involves the combination of five indicators: A - sulphide content; B - sulphide alteration; C - sulphide morphology; D - primary neutraliser content; and E - sulphide mineral association. Several components of the ARD Index require accurate identification of sulphide minerals. This is achieved by classifying Corescan Red-Green-Blue true colour images into the presence or absence of sulphide minerals using supervised classification. Subsequently, sulphide classification images are processed and combined with Corescan SWIR-based mineral classifications to obtain information on sulphide content, indices representing sulphide textures (disseminated versus massive and degree of veining), and spatially associated minerals. This information is combined to calculate ARD Index indicator values that feed into the classification of ARD potential. Automated ARD potential classifications of drill core samples associated with a porphyry Cu-Au deposit are compared to manually derived classifications and those obtained by standard static geochemical testing and X-ray diffractometry analyses. Results indicate a high degree of similarity between automated and manual ARD potential classifications. Major differences between approaches are observed in sulphide and neutraliser mineral percentages, likely due to the subjective nature of manual estimates of mineral content. The automated approach presented here for the classification of ARD potential offers rapid, repeatable and accurate outcomes comparable to manually derived classifications. Methods for automated ARD classifications from digital drill core data represent a step-change for geoenvironmental management practices in the mining industry.

Object-oriented feature extraction approach for mapping supraglacial debris in Schirmacher Oasis using very high-resolution satellite data

NASA Astrophysics Data System (ADS)

Jawak, Shridhar D.; Jadhav, Ajay; Luis, Alvarinho J.

2016-05-01

Supraglacial debris was mapped in the Schirmacher Oasis, east Antarctica, by using WorldView-2 (WV-2) high resolution optical remote sensing data consisting of 8-band calibrated Gram Schmidt (GS)-sharpened and atmospherically corrected WV-2 imagery. This study is a preliminary attempt to develop an object-oriented rule set to extract supraglacial debris for Antarctic region using 8-spectral band imagery. Supraglacial debris was manually digitized from the satellite imagery to generate the ground reference data. Several trials were performed using few existing traditional pixel-based classification techniques and color-texture based object-oriented classification methods to extract supraglacial debris over a small domain of the study area. Multi-level segmentation and attributes such as scale, shape, size, compactness along with spectral information from the data were used for developing the rule set. The quantitative analysis of error was carried out against the manually digitized reference data to test the practicability of our approach over the traditional pixel-based methods. Our results indicate that OBIA-based approach (overall accuracy: 93%) for extracting supraglacial debris performed better than all the traditional pixel-based methods (overall accuracy: 80-85%). The present attempt provides a comprehensive improved method for semiautomatic feature extraction in supraglacial environment and a new direction in the cryospheric research.

Benefits of an Android Based Tablet Application in Primary Screening for Eye Diseases in a Rural Population, India.

PubMed

Imtiaz, Sayed Ahmed; Krishnaiah, Sannapaneni; Yadav, Sunil Kumar; Bharath, Balasubramaniam; Ramani, Ramanathan V

2017-04-01

To investigate the effectiveness, efficiency and cost gains in collecting patient eye health information from remote rural villages of India by trained field investigators through an Android Based Tablet Application namely 'Sankara Electronic Remote Vision Information System (SERVIS)". During January and March 2016, a population based cross-sectional study was conducted in three Indian states employing SERVIS and manual method. The SERVIS application has a 48-items survey instrument programed into the application. Data on 281 individuals were collected for each of these methods as part of screening. The demographic details of individuals between both screening methods were comparable (P>0.05). The mean time (in minutes) to screen an individual by SERVIS was significantly less when compared to manual method (6.57±1.46 versus 11.93±1.53) (P<0.0001). The efficiency of SERVIS in screening was significantly evident as 26% (n = 73) of the patients screened have been referred to campsite and 69.8% (n = 51) of those referred were visited the campsite for a detailed eye examination by an ophthalmologist. The cost of screening through SERVIS is significantly less when compared to manual method; INR 7,633 (USD 113.9) Versus INR 24,780 (USD 370). SERVIS is an effective and efficient tool in terms of patients' referral conversion to the camp site leading to timely detection of potential blinding eye conditions and their appropriate treatment. This ensures timely prevention of avoidable blindness and visual impairment. In addition, the storage and access of eye health epidemiological quality data is helpful to plan appropriate blindness prevention initiatives in rural India.

Hand Rim Wheelchair Propulsion Training Using Biomechanical Real-Time Visual Feedback Based on Motor Learning Theory Principles

PubMed Central

Rice, Ian; Gagnon, Dany; Gallagher, Jere; Boninger, Michael

2010-01-01

Background/Objective: As considerable progress has been made in laboratory-based assessment of manual wheelchair propulsion biomechanics, the necessity to translate this knowledge into new clinical tools and treatment programs becomes imperative. The objective of this study was to describe the development of a manual wheelchair propulsion training program aimed to promote the development of an efficient propulsion technique among long-term manual wheelchair users. Methods: Motor learning theory principles were applied to the design of biomechanical feedback-based learning software, which allows for random discontinuous real-time visual presentation of key spatio-temporal and kinetic parameters. This software was used to train a long-term wheelchair user on a dynamometer during 3 low-intensity wheelchair propulsion training sessions over a 3-week period. Biomechanical measures were recorded with a SmartWheel during over ground propulsion on a 50-m level tile surface at baseline and 3 months after baseline. Results: Training software was refined and administered to a participant who was able to improve his propulsion technique by increasing contact angle while simultaneously reducing stroke cadence, mean resultant force, peak and mean moment out of plane, and peak rate of rise of force applied to the pushrim after training. Conclusions: The proposed propulsion training protocol may lead to favorable changes in manual wheelchair propulsion technique. These changes could limit or prevent upper limb injuries among manual wheelchair users. In addition, many of the motor learning theory–based techniques examined in this study could be applied to training individuals in various stages of rehabilitation to optimize propulsion early on. PMID:20397442

18 CFR 3b.204 - Safeguarding information in manual and computer-based record systems.

Code of Federal Regulations, 2014 CFR

2014-04-01

... information in manual and computer-based record systems. 3b.204 Section 3b.204 Conservation of Power and Water... Collection of Records § 3b.204 Safeguarding information in manual and computer-based record systems. (a) The administrative and physical controls to protect the information in the manual and computer-based record systems...

18 CFR 3b.204 - Safeguarding information in manual and computer-based record systems.

Code of Federal Regulations, 2011 CFR

2011-04-01

... information in manual and computer-based record systems. 3b.204 Section 3b.204 Conservation of Power and Water... Collection of Records § 3b.204 Safeguarding information in manual and computer-based record systems. (a) The administrative and physical controls to protect the information in the manual and computer-based record systems...

18 CFR 3b.204 - Safeguarding information in manual and computer-based record systems.

Code of Federal Regulations, 2012 CFR

2012-04-01

... information in manual and computer-based record systems. 3b.204 Section 3b.204 Conservation of Power and Water... Collection of Records § 3b.204 Safeguarding information in manual and computer-based record systems. (a) The administrative and physical controls to protect the information in the manual and computer-based record systems...

18 CFR 3b.204 - Safeguarding information in manual and computer-based record systems.

Code of Federal Regulations, 2013 CFR

2013-04-01

... information in manual and computer-based record systems. 3b.204 Section 3b.204 Conservation of Power and Water... Collection of Records § 3b.204 Safeguarding information in manual and computer-based record systems. (a) The administrative and physical controls to protect the information in the manual and computer-based record systems...

An iterative method for airway segmentation using multiscale leakage detection

NASA Astrophysics Data System (ADS)

Nadeem, Syed Ahmed; Jin, Dakai; Hoffman, Eric A.; Saha, Punam K.

2017-02-01

There are growing applications of quantitative computed tomography for assessment of pulmonary diseases by characterizing lung parenchyma as well as the bronchial tree. Many large multi-center studies incorporating lung imaging as a study component are interested in phenotypes relating airway branching patterns, wall-thickness, and other morphological measures. To our knowledge, there are no fully automated airway tree segmentation methods, free of the need for user review. Even when there are failures in a small fraction of segmentation results, the airway tree masks must be manually reviewed for all results which is laborious considering that several thousands of image data sets are evaluated in large studies. In this paper, we present a CT-based novel airway tree segmentation algorithm using iterative multi-scale leakage detection, freezing, and active seed detection. The method is fully automated requiring no manual inputs or post-segmentation editing. It uses simple intensity based connectivity and a new leakage detection algorithm to iteratively grow an airway tree starting from an initial seed inside the trachea. It begins with a conservative threshold and then, iteratively shifts toward generous values. The method was applied on chest CT scans of ten non-smoking subjects at total lung capacity and ten at functional residual capacity. Airway segmentation results were compared to an expert's manually edited segmentations. Branch level accuracy of the new segmentation method was examined along five standardized segmental airway paths (RB1, RB4, RB10, LB1, LB10) and two generations beyond these branches. The method successfully detected all branches up to two generations beyond these segmental bronchi with no visual leakages.

High precision localization of intracerebral hemorrhage based on 3D MPR on head CT images

NASA Astrophysics Data System (ADS)

Sun, Jianyong; Hou, Xiaoshuai; Sun, Shujie; Zhang, Jianguo

2017-03-01

The key step for minimally invasive intracerebral hemorrhage surgery is precisely positioning the hematoma location in the brain before and during the hematoma surgery, which can significantly improves the success rate of puncture hematoma. We designed a 3D computerized surgical plan (CSP) workstation precisely to locate brain hematoma based on Multi-Planar Reconstruction (MPR) visualization technique. We used ten patients' CT/MR studies to verify our designed CSP intracerebral hemorrhage localization method. With the doctor's assessment and comparing with the results of manual measurements, the output of CSP WS for hematoma surgery is more precise and reliable than manual procedure.

Towards fully automated structure-based function prediction in structural genomics: a case study.

PubMed

Watson, James D; Sanderson, Steve; Ezersky, Alexandra; Savchenko, Alexei; Edwards, Aled; Orengo, Christine; Joachimiak, Andrzej; Laskowski, Roman A; Thornton, Janet M

2007-04-13

As the global Structural Genomics projects have picked up pace, the number of structures annotated in the Protein Data Bank as hypothetical protein or unknown function has grown significantly. A major challenge now involves the development of computational methods to assign functions to these proteins accurately and automatically. As part of the Midwest Center for Structural Genomics (MCSG) we have developed a fully automated functional analysis server, ProFunc, which performs a battery of analyses on a submitted structure. The analyses combine a number of sequence-based and structure-based methods to identify functional clues. After the first stage of the Protein Structure Initiative (PSI), we review the success of the pipeline and the importance of structure-based function prediction. As a dataset, we have chosen all structures solved by the MCSG during the 5 years of the first PSI. Our analysis suggests that two of the structure-based methods are particularly successful and provide examples of local similarity that is difficult to identify using current sequence-based methods. No one method is successful in all cases, so, through the use of a number of complementary sequence and structural approaches, the ProFunc server increases the chances that at least one method will find a significant hit that can help elucidate function. Manual assessment of the results is a time-consuming process and subject to individual interpretation and human error. We present a method based on the Gene Ontology (GO) schema using GO-slims that can allow the automated assessment of hits with a success rate approaching that of expert manual assessment.

A New Method for Automated Identification and Morphometry of Myelinated Fibers Through Light Microscopy Image Analysis.

PubMed

Novas, Romulo Bourget; Fazan, Valeria Paula Sassoli; Felipe, Joaquim Cezar

2016-02-01

Nerve morphometry is known to produce relevant information for the evaluation of several phenomena, such as nerve repair, regeneration, implant, transplant, aging, and different human neuropathies. Manual morphometry is laborious, tedious, time consuming, and subject to many sources of error. Therefore, in this paper, we propose a new method for the automated morphometry of myelinated fibers in cross-section light microscopy images. Images from the recurrent laryngeal nerve of adult rats and the vestibulocochlear nerve of adult guinea pigs were used herein. The proposed pipeline for fiber segmentation is based on the techniques of competitive clustering and concavity analysis. The evaluation of the proposed method for segmentation of images was done by comparing the automatic segmentation with the manual segmentation. To further evaluate the proposed method considering morphometric features extracted from the segmented images, the distributions of these features were tested for statistical significant difference. The method achieved a high overall sensitivity and very low false-positive rates per image. We detect no statistical difference between the distribution of the features extracted from the manual and the pipeline segmentations. The method presented a good overall performance, showing widespread potential in experimental and clinical settings allowing large-scale image analysis and, thus, leading to more reliable results.

An Academic Library's Experience with Fee-Based Services.

ERIC Educational Resources Information Center

Hornbeck, Julia W.

1983-01-01

Profile of fee-based information services offered by the Information Exchange Center of Georgia Institute of Technology notes history and background, document delivery to commercial clients and on-campus faculty, online and manual literature searching, staff, cost analysis, fee schedule, operating methods, client relations, marketing, and current…

An automated approach for annual layer counting in ice cores

NASA Astrophysics Data System (ADS)

Winstrup, M.; Svensson, A.; Rasmussen, S. O.; Winther, O.; Steig, E.; Axelrod, A.

2012-04-01

The temporal resolution of some ice cores is sufficient to preserve seasonal information in the ice core record. In such cases, annual layer counting represents one of the most accurate methods to produce a chronology for the core. Yet, manual layer counting is a tedious and sometimes ambiguous job. As reliable layer recognition becomes more difficult, a manual approach increasingly relies on human interpretation of the available data. Thus, much may be gained by an automated and therefore objective approach for annual layer identification in ice cores. We have developed a novel method for automated annual layer counting in ice cores, which relies on Bayesian statistics. It uses algorithms from the statistical framework of Hidden Markov Models (HMM), originally developed for use in machine speech recognition. The strength of this layer detection algorithm lies in the way it is able to imitate the manual procedures for annual layer counting, while being based on purely objective criteria for annual layer identification. With this methodology, it is possible to determine the most likely position of multiple layer boundaries in an entire section of ice core data at once. It provides a probabilistic uncertainty estimate of the resulting layer count, hence ensuring a proper treatment of ambiguous layer boundaries in the data. Furthermore multiple data series can be incorporated to be used at once, hence allowing for a full multi-parameter annual layer counting method similar to a manual approach. In this study, the automated layer counting algorithm has been applied to data from the NGRIP ice core, Greenland. The NGRIP ice core has very high temporal resolution with depth, and hence the potential to be dated by annual layer counting far back in time. In previous studies [Andersen et al., 2006; Svensson et al., 2008], manual layer counting has been carried out back to 60 kyr BP. A comparison between the counted annual layers based on the two approaches will be presented and their differences discussed. Within the estimated uncertainties, the two methodologies agree. This shows the potential for a fully automated annual layer counting method to be operational for data sections where the annual layering is unknown.

A Manual of Simplified Laboratory Methods for Operators of Wastewater Treatment Facilities.

ERIC Educational Resources Information Center

Westerhold, Arnold F., Ed.; Bennett, Ernest C., Ed.

This manual is designed to provide the small wastewater treatment plant operator, as well as the new or inexperienced operator, with simplified methods for laboratory analysis of water and wastewater. It is emphasized that this manual is not a replacement for standard methods but a guide for plants with insufficient equipment to perform analyses…

Training sample selection based on self-training for liver cirrhosis classification using ultrasound images

NASA Astrophysics Data System (ADS)

Fujita, Yusuke; Mitani, Yoshihiro; Hamamoto, Yoshihiko; Segawa, Makoto; Terai, Shuji; Sakaida, Isao

2017-03-01

Ultrasound imaging is a popular and non-invasive tool used in the diagnoses of liver disease. Cirrhosis is a chronic liver disease and it can advance to liver cancer. Early detection and appropriate treatment are crucial to prevent liver cancer. However, ultrasound image analysis is very challenging, because of the low signal-to-noise ratio of ultrasound images. To achieve the higher classification performance, selection of training regions of interest (ROIs) is very important that effect to classification accuracy. The purpose of our study is cirrhosis detection with high accuracy using liver ultrasound images. In our previous works, training ROI selection by MILBoost and multiple-ROI classification based on the product rule had been proposed, to achieve high classification performance. In this article, we propose self-training method to select training ROIs effectively. Evaluation experiments were performed to evaluate effect of self-training, using manually selected ROIs and also automatically selected ROIs. Experimental results show that self-training for manually selected ROIs achieved higher classification performance than other approaches, including our conventional methods. The manually ROI definition and sample selection are important to improve classification accuracy in cirrhosis detection using ultrasound images.

Objective Assessment of Joint Stiffness: A Clinically Oriented Hardware and Software Device with an Application to the Shoulder Joint.

PubMed

McQuade, Kevin; Price, Robert; Liu, Nelson; Ciol, Marcia A

2012-08-30

Examination of articular joints is largely based on subjective assessment of the "end-feel" of the joint in response to manually applied forces at different joint orientations. This technical report aims to describe the development of an objective method to examine joints in general, with specific application to the shoulder, and suitable for clinical use. We adapted existing hardware and developed laptop-based software to objectively record the force/displacement behavior of the glenohumeral joint during three common manual joint examination tests with the arm in six positions. An electromagnetic tracking system recorded three-dimensional positions of sensors attached to a clinician examiner and a patient. A hand-held force transducer recorded manually applied translational forces. The force and joint displacement were time-synchronized and the joint stiffness was calculated as a quantitative representation of the joint "end-feel." A methodology and specific system checks were developed to enhance clinical testing reproducibility and precision. The device and testing protocol were tested on 31 subjects (15 with healthy shoulders, and 16 with a variety of shoulder impairments). Results describe the stiffness responses, and demonstrate the feasibility of using the device and methods in clinical settings.

FreeSurfer-initiated fully-automated subcortical brain segmentation in MRI using Large Deformation Diffeomorphic Metric Mapping.

PubMed

Khan, Ali R; Wang, Lei; Beg, Mirza Faisal

2008-07-01

Fully-automated brain segmentation methods have not been widely adopted for clinical use because of issues related to reliability, accuracy, and limitations of delineation protocol. By combining the probabilistic-based FreeSurfer (FS) method with the Large Deformation Diffeomorphic Metric Mapping (LDDMM)-based label-propagation method, we are able to increase reliability and accuracy, and allow for flexibility in template choice. Our method uses the automated FreeSurfer subcortical labeling to provide a coarse-to-fine introduction of information in the LDDMM template-based segmentation resulting in a fully-automated subcortical brain segmentation method (FS+LDDMM). One major advantage of the FS+LDDMM-based approach is that the automatically generated segmentations generated are inherently smooth, thus subsequent steps in shape analysis can directly follow without manual post-processing or loss of detail. We have evaluated our new FS+LDDMM method on several databases containing a total of 50 subjects with different pathologies, scan sequences and manual delineation protocols for labeling the basal ganglia, thalamus, and hippocampus. In healthy controls we report Dice overlap measures of 0.81, 0.83, 0.74, 0.86 and 0.75 for the right caudate nucleus, putamen, pallidum, thalamus and hippocampus respectively. We also find statistically significant improvement of accuracy in FS+LDDMM over FreeSurfer for the caudate nucleus and putamen of Huntington's disease and Tourette's syndrome subjects, and the right hippocampus of Schizophrenia subjects.

Monitoring of endoscope reprocessing with an adenosine triphosphate (ATP) bioluminescence method.

PubMed

Parohl, Nina; Stiefenhöfer, Doris; Heiligtag, Sabine; Reuter, Henning; Dopadlik, Dana; Mosel, Frank; Gerken, Guido; Dechêne, Alexander; Heintschel von Heinegg, Evelyn; Jochum, Christoph; Buer, Jan; Popp, Walter

2017-01-01

Background: The arising challenges over endoscope reprocessing quality proposes to look for possibilities to measure and control the process of endoscope reprocessing. Aim: The goal of this study was to evaluate the feasibility of monitoring endoscope reprocessing with an adenosine triphosphate (ATP) based bioluminescence system. Methods: 60 samples of eight gastroscopes have been assessed from routine clinical use in a major university hospital in Germany. Endoscopes have been assessed with an ATP system and microbial cultures at different timepoints during the reprocessing. Findings: After the bedside flush the mean ATP level in relative light units (RLU) was 19,437 RLU, after the manual cleaning 667 RLU and after the automated endoscope reprocessor (AER) 227 RLU. After the manual cleaning the mean total viable count (TVC) per endoscope was 15.3 CFU/10 ml, and after the AER 5.7 CFU/10 ml. Our results show that there are reprocessing cycles which are not able to clean a patient used endoscope. Conclusion: Our data suggest that monitoring of flexible endoscope with ATP can identify a number of different influence factors, like the endoscope condition and the endoscopic procedure, or especially the quality of the bedside flush and manual cleaning before the AER. More process control is one option to identify and improve influence factors to finally increase the overall reprocessing quality, best of all by different methods. ATP measurement seems to be a valid technique that allows an immediate repeat of the manual cleaning if the ATP results after manual cleaning exceed the established cutoff of 200 RLU.

Robust semi-automatic segmentation of pulmonary subsolid nodules in chest computed tomography scans

NASA Astrophysics Data System (ADS)

Lassen, B. C.; Jacobs, C.; Kuhnigk, J.-M.; van Ginneken, B.; van Rikxoort, E. M.

2015-02-01

The malignancy of lung nodules is most often detected by analyzing changes of the nodule diameter in follow-up scans. A recent study showed that comparing the volume or the mass of a nodule over time is much more significant than comparing the diameter. Since the survival rate is higher when the disease is still in an early stage it is important to detect the growth rate as soon as possible. However manual segmentation of a volume is time-consuming. Whereas there are several well evaluated methods for the segmentation of solid nodules, less work is done on subsolid nodules which actually show a higher malignancy rate than solid nodules. In this work we present a fast, semi-automatic method for segmentation of subsolid nodules. As minimal user interaction the method expects a user-drawn stroke on the largest diameter of the nodule. First, a threshold-based region growing is performed based on intensity analysis of the nodule region and surrounding parenchyma. In the next step the chest wall is removed by a combination of a connected component analyses and convex hull calculation. Finally, attached vessels are detached by morphological operations. The method was evaluated on all nodules of the publicly available LIDC/IDRI database that were manually segmented and rated as non-solid or part-solid by four radiologists (Dataset 1) and three radiologists (Dataset 2). For these 59 nodules the Jaccard index for the agreement of the proposed method with the manual reference segmentations was 0.52/0.50 (Dataset 1/Dataset 2) compared to an inter-observer agreement of the manual segmentations of 0.54/0.58 (Dataset 1/Dataset 2). Furthermore, the inter-observer agreement using the proposed method (i.e. different input strokes) was analyzed and gave a Jaccard index of 0.74/0.74 (Dataset 1/Dataset 2). The presented method provides satisfactory segmentation results with minimal observer effort in minimal time and can reduce the inter-observer variability for segmentation of subsolid nodules in clinical routine.

The use of atlas registration and graph cuts for prostate segmentation in magnetic resonance images

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

Korsager, Anne Sofie, E-mail: asko@hst.aau.dk; Østergaard, Lasse Riis; Fortunati, Valerio

2015-04-15

Purpose: An automatic method for 3D prostate segmentation in magnetic resonance (MR) images is presented for planning image-guided radiotherapy treatment of prostate cancer. Methods: A spatial prior based on intersubject atlas registration is combined with organ-specific intensity information in a graph cut segmentation framework. The segmentation is tested on 67 axial T{sub 2}-weighted MR images in a leave-one-out cross validation experiment and compared with both manual reference segmentations and with multiatlas-based segmentations using majority voting atlas fusion. The impact of atlas selection is investigated in both the traditional atlas-based segmentation and the new graph cut method that combines atlas andmore » intensity information in order to improve the segmentation accuracy. Best results were achieved using the method that combines intensity information, shape information, and atlas selection in the graph cut framework. Results: A mean Dice similarity coefficient (DSC) of 0.88 and a mean surface distance (MSD) of 1.45 mm with respect to the manual delineation were achieved. Conclusions: This approaches the interobserver DSC of 0.90 and interobserver MSD 0f 1.15 mm and is comparable to other studies performing prostate segmentation in MR.« less

Monitoring post-fire vegetation rehabilitation projects: A common approach for non-forested ecosystems

USGS Publications Warehouse

Wirth, Troy A.; Pyke, David A.

2007-01-01

Emergency Stabilization and Rehabilitation (ES&R) and Burned Area Emergency Response (BAER) treatments are short-term, high-intensity treatments designed to mitigate the adverse effects of wildfire on public lands. The federal government expends significant resources implementing ES&R and BAER treatments after wildfires; however, recent reviews have found that existing data from monitoring and research are insufficient to evaluate the effects of these activities. The purpose of this report is to: (1) document what monitoring methods are generally used by personnel in the field; (2) describe approaches and methods for post-fire vegetation and soil monitoring documented in agency manuals; (3) determine the common elements of monitoring programs recommended in these manuals; and (4) describe a common monitoring approach to determine the effectiveness of future ES&R and BAER treatments in non-forested regions. Both qualitative and quantitative methods to measure effectiveness of ES&R treatments are used by federal land management agencies. Quantitative methods are used in the field depending on factors such as funding, personnel, and time constraints. There are seven vegetation monitoring manuals produced by the federal government that address monitoring methods for (primarily) vegetation and soil attributes. These methods vary in their objectivity and repeatability. The most repeatable methods are point-intercept, quadrat-based density measurements, gap intercepts, and direct measurement of soil erosion. Additionally, these manuals recommend approaches for designing monitoring programs for the state of ecosystems or the effect of management actions. The elements of a defensible monitoring program applicable to ES&R and BAER projects that most of these manuals have in common are objectives, stratification, control areas, random sampling, data quality, and statistical analysis. The effectiveness of treatments can be determined more accurately if data are gathered using an approach that incorporates these six monitoring program design elements and objectives, as well as repeatable procedures to measure cover, density, gap intercept, and soil erosion within each ecoregion and plant community. Additionally, using a common monitoring program design with comparable methods, consistently documenting results, and creating and maintaining a central database for query and reporting, will ultimately allow a determination of the effectiveness of post-fire rehabilitation activities region-wide.

Consensus statement: patient safety, healthcare-associated infections and hospital environmental surfaces.

PubMed

Roques, Christine; Al Mousa, Haifaa; Duse, Adriano; Gallagher, Rose; Koburger, Torsten; Lingaas, Egil; Petrosillo, Nicola; Škrlin, Jasenka

2015-01-01

Healthcare-associated infections have serious implications for both patients and hospitals. Environmental surface contamination is the key to transmission of nosocomial pathogens. Routine manual cleaning and disinfection eliminates visible soil and reduces environmental bioburden and risk of transmission, but may not address some surface contamination. Automated area decontamination technologies achieve more consistent and pervasive disinfection than manual methods, but it is challenging to demonstrate their efficacy within a randomized trial of the multiple interventions required to reduce healthcare-associated infection rates. Until data from multicenter observational studies are available, automated area decontamination technologies should be an adjunct to manual cleaning and disinfection within a total, multi-layered system and risk-based approach designed to control environmental pathogens and promote patient safety.

Direct volume estimation without segmentation

NASA Astrophysics Data System (ADS)

Zhen, X.; Wang, Z.; Islam, A.; Bhaduri, M.; Chan, I.; Li, S.

2015-03-01

Volume estimation plays an important role in clinical diagnosis. For example, cardiac ventricular volumes including left ventricle (LV) and right ventricle (RV) are important clinical indicators of cardiac functions. Accurate and automatic estimation of the ventricular volumes is essential to the assessment of cardiac functions and diagnosis of heart diseases. Conventional methods are dependent on an intermediate segmentation step which is obtained either manually or automatically. However, manual segmentation is extremely time-consuming, subjective and highly non-reproducible; automatic segmentation is still challenging, computationally expensive, and completely unsolved for the RV. Towards accurate and efficient direct volume estimation, our group has been researching on learning based methods without segmentation by leveraging state-of-the-art machine learning techniques. Our direct estimation methods remove the accessional step of segmentation and can naturally deal with various volume estimation tasks. Moreover, they are extremely flexible to be used for volume estimation of either joint bi-ventricles (LV and RV) or individual LV/RV. We comparatively study the performance of direct methods on cardiac ventricular volume estimation by comparing with segmentation based methods. Experimental results show that direct estimation methods provide more accurate estimation of cardiac ventricular volumes than segmentation based methods. This indicates that direct estimation methods not only provide a convenient and mature clinical tool for cardiac volume estimation but also enables diagnosis of cardiac diseases to be conducted in a more efficient and reliable way.

Combining population and patient-specific characteristics for prostate segmentation on 3D CT images

NASA Astrophysics Data System (ADS)

Ma, Ling; Guo, Rongrong; Tian, Zhiqiang; Venkataraman, Rajesh; Sarkar, Saradwata; Liu, Xiabi; Tade, Funmilayo; Schuster, David M.; Fei, Baowei

2016-03-01

Prostate segmentation on CT images is a challenging task. In this paper, we explore the population and patient-specific characteristics for the segmentation of the prostate on CT images. Because population learning does not consider the inter-patient variations and because patient-specific learning may not perform well for different patients, we are combining the population and patient-specific information to improve segmentation performance. Specifically, we train a population model based on the population data and train a patient-specific model based on the manual segmentation on three slice of the new patient. We compute the similarity between the two models to explore the influence of applicable population knowledge on the specific patient. By combining the patient-specific knowledge with the influence, we can capture the population and patient-specific characteristics to calculate the probability of a pixel belonging to the prostate. Finally, we smooth the prostate surface according to the prostate-density value of the pixels in the distance transform image. We conducted the leave-one-out validation experiments on a set of CT volumes from 15 patients. Manual segmentation results from a radiologist serve as the gold standard for the evaluation. Experimental results show that our method achieved an average DSC of 85.1% as compared to the manual segmentation gold standard. This method outperformed the population learning method and the patient-specific learning approach alone. The CT segmentation method can have various applications in prostate cancer diagnosis and therapy.

Contour detection improved by context-adaptive surround suppression.

PubMed

Sang, Qiang; Cai, Biao; Chen, Hao

2017-01-01

Recently, many image processing applications have taken advantage of a psychophysical and neurophysiological mechanism, called "surround suppression" to extract object contour from a natural scene. However, these traditional methods often adopt a single suppression model and a fixed input parameter called "inhibition level", which needs to be manually specified. To overcome these drawbacks, we propose a novel model, called "context-adaptive surround suppression", which can automatically control the effect of surround suppression according to image local contextual features measured by a surface estimator based on a local linear kernel. Moreover, a dynamic suppression method and its stopping mechanism are introduced to avoid manual intervention. The proposed algorithm is demonstrated and validated by a broad range of experimental results.

Automated and Semiautomated Segmentation of Rectal Tumor Volumes on Diffusion-Weighted MRI: Can It Replace Manual Volumetry?

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

Heeswijk, Miriam M. van; Department of Surgery, Maastricht University Medical Centre, Maastricht; Lambregts, Doenja M.J., E-mail: d.lambregts@nki.nl

Purpose: Diffusion-weighted imaging (DWI) tumor volumetry is promising for rectal cancer response assessment, but an important drawback is that manual per-slice tumor delineation can be highly time consuming. This study investigated whether manual DWI-volumetry can be reproduced using a (semi)automated segmentation approach. Methods and Materials: Seventy-nine patients underwent magnetic resonance imaging (MRI) that included DWI (highest b value [b1000 or b1100]) before and after chemoradiation therapy (CRT). Tumor volumes were assessed on b1000 (or b1100) DWI before and after CRT by means of (1) automated segmentation (by 2 inexperienced readers), (2) semiautomated segmentation (manual adjustment of the volumes obtained bymore » method 1 by 2 radiologists), and (3) manual segmentation (by 2 radiologists); this last assessment served as the reference standard. Intraclass correlation coefficients (ICC) and Dice similarity indices (DSI) were calculated to evaluate agreement between different methods and observers. Measurement times (from a radiologist's perspective) were recorded for each method. Results: Tumor volumes were not significantly different among the 3 methods, either before or after CRT (P=.08 to .92). ICCs compared to manual segmentation were 0.80 to 0.91 and 0.53 to 0.66 before and after CRT, respectively, for the automated segmentation and 0.91 to 0.97 and 0.61 to 0.75, respectively, for the semiautomated method. Interobserver agreement (ICC) pre and post CRT was 0.82 and 0.59 for automated segmentation, 0.91 and 0.73 for semiautomated segmentation, and 0.91 and 0.75 for manual segmentation, respectively. Mean DSI between the automated and semiautomated method were 0.83 and 0.58 pre-CRT and post-CRT, respectively; DSI between the automated and manual segmentation were 0.68 and 0.42 and 0.70 and 0.41 between the semiautomated and manual segmentation, respectively. Median measurement time for the radiologists was 0 seconds (pre- and post-CRT) for the automated method, 41 to 69 seconds (pre-CRT) and 60 to 67 seconds (post-CRT) for the semiautomated method, and 180 to 296 seconds (pre-CRT) and 84 to 91 seconds (post-CRT) for the manual method. Conclusions: DWI volumetry using a semiautomated segmentation approach is promising and a potentially time-saving alternative to manual tumor delineation, particularly for primary tumor volumetry. Once further optimized, it could be a helpful tool for tumor response assessment in rectal cancer.« less

Active learning for ontological event extraction incorporating named entity recognition and unknown word handling.

PubMed

Han, Xu; Kim, Jung-jae; Kwoh, Chee Keong

2016-01-01

Biomedical text mining may target various kinds of valuable information embedded in the literature, but a critical obstacle to the extension of the mining targets is the cost of manual construction of labeled data, which are required for state-of-the-art supervised learning systems. Active learning is to choose the most informative documents for the supervised learning in order to reduce the amount of required manual annotations. Previous works of active learning, however, focused on the tasks of entity recognition and protein-protein interactions, but not on event extraction tasks for multiple event types. They also did not consider the evidence of event participants, which might be a clue for the presence of events in unlabeled documents. Moreover, the confidence scores of events produced by event extraction systems are not reliable for ranking documents in terms of informativity for supervised learning. We here propose a novel committee-based active learning method that supports multi-event extraction tasks and employs a new statistical method for informativity estimation instead of using the confidence scores from event extraction systems. Our method is based on a committee of two systems as follows: We first employ an event extraction system to filter potential false negatives among unlabeled documents, from which the system does not extract any event. We then develop a statistical method to rank the potential false negatives of unlabeled documents 1) by using a language model that measures the probabilities of the expression of multiple events in documents and 2) by using a named entity recognition system that locates the named entities that can be event arguments (e.g. proteins). The proposed method further deals with unknown words in test data by using word similarity measures. We also apply our active learning method for the task of named entity recognition. We evaluate the proposed method against the BioNLP Shared Tasks datasets, and show that our method can achieve better performance than such previous methods as entropy and Gibbs error based methods and a conventional committee-based method. We also show that the incorporation of named entity recognition into the active learning for event extraction and the unknown word handling further improve the active learning method. In addition, the adaptation of the active learning method into named entity recognition tasks also improves the document selection for manual annotation of named entities.

A Randomized Placebo-Controlled Trial of a School-Based Depression Prevention Program.

ERIC Educational Resources Information Center

Merry, Sally; McDowell, Heather; Wild, Chris J.; Bir, Julliet; Cunliffe, Rachel

2004-01-01

Objective: To conduct a placebo-controlled study of the effectiveness of a universal school-based depression prevention program. Method: Three hundred ninety-two students age 13 to 15 from two schools were randomized to intervention (RAP-Kiwi) and placebo programs run by teachers. RAP-Kiwi was an 11-session manual-based program derived from…

Real-time segmentation of burst suppression patterns in critical care EEG monitoring

PubMed Central

Westover, M. Brandon; Shafi, Mouhsin M.; Ching, ShiNung; Chemali, Jessica J.; Purdon, Patrick L.; Cash, Sydney S.; Brown, Emery N.

2014-01-01

Objective Develop a real-time algorithm to automatically discriminate suppressions from non-suppressions (bursts) in electroencephalograms of critically ill adult patients. Methods A real-time method for segmenting adult ICU EEG data into bursts and suppressions is presented based on thresholding local voltage variance. Results are validated against manual segmentations by two experienced human electroencephalographers. We compare inter-rater agreement between manual EEG segmentations by experts with inter-rater agreement between human vs automatic segmentations, and investigate the robustness of segmentation quality to variations in algorithm parameter settings. We further compare the results of using these segmentations as input for calculating the burst suppression probability (BSP), a continuous measure of depth-of-suppression. Results Automated segmentation was comparable to manual segmentation, i.e. algorithm-vs-human agreement was comparable to human-vs-human agreement, as judged by comparing raw EEG segmentations or the derived BSP signals. Results were robust to modest variations in algorithm parameter settings. Conclusions Our automated method satisfactorily segments burst suppression data across a wide range adult ICU EEG patterns. Performance is comparable to or exceeds that of manual segmentation by human electroencephalographers. Significance Automated segmentation of burst suppression EEG patterns is an essential component of quantitative brain activity monitoring in critically ill and anesthetized adults. The segmentations produced by our algorithm provide a basis for accurate tracking of suppression depth. PMID:23891828

MAC/GMC 4.0 User's Manual: Keywords Manual. Volume 2

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2002-01-01

This document is the second volume in the three volume set of User's Manuals for the Micromechanics Analysis Code with Generalized Method of Cells Version 4.0 (MAC/GMC 4.0). Volume 1 is the Theory Manual, this document is the Keywords Manual, and Volume 3 is the Example Problem Manual. MAC/GMC 4.0 is a composite material and laminate analysis software program developed at the NASA Glenn Research Center. It is based on the generalized method of cells (GMC) micromechanics theory, which provides access to the local stress and strain fields in the composite material. This access grants GMC the ability to accommodate arbitrary local models for inelastic material behavior and various types of damage and failure analysis. MAC/GMC 4.0 has been built around GMC to provide the theory with a user-friendly framework, along with a library of local inelastic, damage, and failure models. Further, applications of simulated thermo-mechanical loading, generation of output results, and selection of architectures to represent the composite material have been automated in MAC/GMC 4.0. Finally, classical lamination theory has been implemented within MAC/GMC 4.0 wherein GMC is used to model the composite material response of each ply. Consequently, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. This volume describes the basic information required to use the MAC/GMC 4.0 software, including a 'Getting Started' section, and an in-depth description of each of the 22 keywords used in the input file to control the execution of the code.

Training Psychiatry Residents in Psychotherapy: The Role of Manualized Treatments.

PubMed

Pagano, Joshua; Kyle, Brandon N; Johnson, Toni L; Saeed, Sy Atezaz

2017-06-01

Evidence-based treatment and manualized psychotherapy have a recent but rich history. As interest and research have progressed, defining the role of treatment manuals in resident training and clinical practice has become more important. Although there is not a universal definition of treatment manual, most clinicians and researchers agree that treatment manuals are an essential piece of evidence-based therapy, and that despite several limitations, they offer advantages in training residents in psychotherapy. Requirements for resident training in psychotherapy have changed over the years, and treatment manuals offer a simple and straightforward way to meet training requirements. In a search limited to only depression, two treatment manuals emerged with the support of research regarding both clinical practice and resident training. In looking toward the future, it will be important for clinicians to remain updated on further advances in evidence based manualized treatment as a tool for training residents in psychotherapy, including recent developments in online and smartphone based treatments.

Application of a semi-automatic cartilage segmentation method for biomechanical modeling of the knee joint.

PubMed

Liukkonen, Mimmi K; Mononen, Mika E; Tanska, Petri; Saarakkala, Simo; Nieminen, Miika T; Korhonen, Rami K

2017-10-01

Manual segmentation of articular cartilage from knee joint 3D magnetic resonance images (MRI) is a time consuming and laborious task. Thus, automatic methods are needed for faster and reproducible segmentations. In the present study, we developed a semi-automatic segmentation method based on radial intensity profiles to generate 3D geometries of knee joint cartilage which were then used in computational biomechanical models of the knee joint. Six healthy volunteers were imaged with a 3T MRI device and their knee cartilages were segmented both manually and semi-automatically. The values of cartilage thicknesses and volumes produced by these two methods were compared. Furthermore, the influences of possible geometrical differences on cartilage stresses and strains in the knee were evaluated with finite element modeling. The semi-automatic segmentation and 3D geometry construction of one knee joint (menisci, femoral and tibial cartilages) was approximately two times faster than with manual segmentation. Differences in cartilage thicknesses, volumes, contact pressures, stresses, and strains between segmentation methods in femoral and tibial cartilage were mostly insignificant (p > 0.05) and random, i.e. there were no systematic differences between the methods. In conclusion, the devised semi-automatic segmentation method is a quick and accurate way to determine cartilage geometries; it may become a valuable tool for biomechanical modeling applications with large patient groups.

Automatic cloud coverage assessment of Formosat-2 image

NASA Astrophysics Data System (ADS)

Hsu, Kuo-Hsien

2011-11-01

Formosat-2 satellite equips with the high-spatial-resolution (2m ground sampling distance) remote sensing instrument. It has been being operated on the daily-revisiting mission orbit by National Space organization (NSPO) of Taiwan since May 21 2004. NSPO has also serving as one of the ground receiving stations for daily processing the received Formosat- 2 images. The current cloud coverage assessment of Formosat-2 image for NSPO Image Processing System generally consists of two major steps. Firstly, an un-supervised K-means method is used for automatically estimating the cloud statistic of Formosat-2 image. Secondly, manual estimation of cloud coverage from Formosat-2 image is processed by manual examination. Apparently, a more accurate Automatic Cloud Coverage Assessment (ACCA) method certainly increases the efficiency of processing step 2 with a good prediction of cloud statistic. In this paper, mainly based on the research results from Chang et al, Irish, and Gotoh, we propose a modified Formosat-2 ACCA method which considered pre-processing and post-processing analysis. For pre-processing analysis, cloud statistic is determined by using un-supervised K-means classification, Sobel's method, Otsu's method, non-cloudy pixels reexamination, and cross-band filter method. Box-Counting fractal method is considered as a post-processing tool to double check the results of pre-processing analysis for increasing the efficiency of manual examination.

Validation of a semi-automatic protocol for the assessment of the tear meniscus central area based on open-source software

NASA Astrophysics Data System (ADS)

Pena-Verdeal, Hugo; Garcia-Resua, Carlos; Yebra-Pimentel, Eva; Giraldez, Maria J.

2017-08-01

Purpose: Different lower tear meniscus parameters can be clinical assessed on dry eye diagnosis. The aim of this study was to propose and analyse the variability of a semi-automatic method for measuring lower tear meniscus central area (TMCA) by using open source software. Material and methods: On a group of 105 subjects, one video of the lower tear meniscus after fluorescein instillation was generated by a digital camera attached to a slit-lamp. A short light beam (3x5 mm) with moderate illumination in the central portion of the meniscus (6 o'clock) was used. Images were extracted from each video by a masked observer. By using an open source software based on Java (NIH ImageJ), a further observer measured in a masked and randomized order the TMCA in the short light beam illuminated area by two methods: (1) manual method, where TMCA images was "manually" measured; (2) semi-automatic method, where TMCA images were transformed in an 8-bit-binary image, then holes inside this shape were filled and on the isolated shape, the area size was obtained. Finally, both measurements, manual and semi-automatic, were compared. Results: Paired t-test showed no statistical difference between both techniques results (p = 0.102). Pearson correlation between techniques show a significant positive near to perfect correlation (r = 0.99; p < 0.001). Conclusions: This study showed a useful tool to objectively measure the frontal central area of the meniscus in photography by free open source software.

Asphalt Raking. Instructor Manual. Trainee Manual.

ERIC Educational Resources Information Center

Laborers-AGC Education and Training Fund, Pomfret Center, CT.

This packet consists of the instructor and trainee manuals for an asphalt raking course. The instructor manual contains a course schedule for 4 days of instruction, content outline, and instructor outline. The trainee manual is divided into five sections: safety, asphalt basics, placing methods, repair and patching, and clean-up and maintenance.…

SU-F-T-358: Is Auto-Planning Useful for Volumetric-Modulated Arc Therapy Planning in Rectal Cancer Radiotherapy?

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

Li, K; Chang, X; Wang, J

Purpose: To evaluate whether Auto-Planning based volumetric-modulated radiotherapy (auto-VMAT) can reduce manual interaction time during treatment planning and improve plan quality for rectal cancer radiotherapy. Methods: Ten rectal cancer patients (stage II and III) after radical resection using Dixon surgery were enrolled. All patients were treated with VMAT technique. The manual VMAT plans (man-VMAT) were designed in the Pinnacle treatment planning system (Version 9.10) following the standard treatment planning procedure developed in our department. Clinical plans were manually designed by our experienced dosimetrists. Additionally, an auto-VMAT plan was created for each patient using Auto-Planning module. However, manual interaction was stillmore » applied to meet the clinical requirements. The treatment planning time and plan quality surrogated by the DVH parameters were compared between manual and automated plans. Results: The total planning time and manual interaction time were 50.38 and 4.47 min for the auto-VMAT and 36.81 and 16.94 min for the man-VMAT (t=60.14,−23.86; p=0.000, 0.000). In terms of plan quality, both plans meet the clinical requirements. The PTV homogeneity index (HI) and conformity index (CI) were 0.054 and 0.822 for the auto-VMAT and 0.059 and 0.815 for the man-VMAT (t=−1.72, 0.36;p=0.119,0.730).Compared to the man-VMAT, the auto-VMAT showed reduction of 11.9% and 0.7% in V40 and V50 of the bladder, respectively.The V30 and D mean were reduced by 14.0% and 5.1Gy in the left femur and 12.2% and 3.8Gy in the right femur. Conclusion: The Auto-Planning based VMAT plans not only shows similar or superior plan quality to the manual ones in the rectal cancer radiotherapy, but also improve the planning efficiency significantly. However, manual interactions are still required to achieve a clinically acceptable plan based on our experiences.« less

A Theory-Based Contextual Nutrition Education Manual Enhanced Nutrition Teaching Skill.

PubMed

Kupolati, Mojisola D; MacIntyre, Una E; Gericke, Gerda J

2018-01-01

Background: A theory-based contextual nutrition education manual (NEM) may enhance effective teaching of nutrition in schools. School nutrition education should lead to the realization of such benefits as improved health, scholarly achievement leading to manpower development and consequently the nation's development. The purpose of the study was to develop a contextual NEM for teachers of Grade 5 and 6 learners in the Bronkhorstspruit district, South Africa, and to assess teachers' perception on the use of the manual for teaching nutrition. Methods: This descriptive case study used an interpretivist paradigm. The study involved teachers ( N = 6) who taught nutrition in Life Skills (LS) and Natural Science and Technology (NST) in a randomly selected primary school in the Bronkhorstspruit district. Findings from a nutrition education needs assessment were integrated with the constructs of the Social cognitive theory (SCT) and the Meaningful learning model (MLM) and the existing curriculum of the Department of Basic Education (DoBE) to develop a contextual NEM. The manual was used by the teachers to teach nutrition to Grades 5 and 6 learners during the 2015 academic year as a pilot project. A focus group discussion (FDG) was conducted with teachers to gauge their perceptions of the usefulness of the NEM. Data were analyzed using the thematic approach of the framework method for qualitative research. Results: Teachers described the NEM as rich in information, easy to use and perceived the supporting materials and activities as being effective. The goal setting activities contained in the NEM were deemed to be ineffective. Teachers felt that they did not have enough time to teach all the important things that the learners needed to know. Conclusion: Teachers perceived the NEM as helpful toward improving their nutrition teaching skills.The NEM template may furthermore guide teachers in planning theory-based nutrition lessons.

Automatic measurement of voice onset time using discriminative structured prediction.

PubMed

Sonderegger, Morgan; Keshet, Joseph

2012-12-01

A discriminative large-margin algorithm for automatic measurement of voice onset time (VOT) is described, considered as a case of predicting structured output from speech. Manually labeled data are used to train a function that takes as input a speech segment of an arbitrary length containing a voiceless stop, and outputs its VOT. The function is explicitly trained to minimize the difference between predicted and manually measured VOT; it operates on a set of acoustic feature functions designed based on spectral and temporal cues used by human VOT annotators. The algorithm is applied to initial voiceless stops from four corpora, representing different types of speech. Using several evaluation methods, the algorithm's performance is near human intertranscriber reliability, and compares favorably with previous work. Furthermore, the algorithm's performance is minimally affected by training and testing on different corpora, and remains essentially constant as the amount of training data is reduced to 50-250 manually labeled examples, demonstrating the method's practical applicability to new datasets.

ISE: An Integrated Search Environment. The manual

NASA Technical Reports Server (NTRS)

Chu, Lon-Chan

1992-01-01

Integrated Search Environment (ISE), a software package that implements hierarchical searches with meta-control, is described in this manual. ISE is a collection of problem-independent routines to support solving searches. Mainly, these routines are core routines for solving a search problem and they handle the control of searches and maintain the statistics related to searches. By separating the problem-dependent and problem-independent components in ISE, new search methods based on a combination of existing methods can be developed by coding a single master control program. Further, new applications solved by searches can be developed by coding the problem-dependent parts and reusing the problem-independent parts already developed. Potential users of ISE are designers of new application solvers and new search algorithms, and users of experimental application solvers and search algorithms. The ISE is designed to be user-friendly and information rich. In this manual, the organization of ISE is described and several experiments carried out on ISE are also described.

User's manual for three dimensional FDTD version D code for scattering from frequency-dependent dielectric and magnetic materials

NASA Technical Reports Server (NTRS)

Beggs, John H.; Luebbers, Raymond J.; Kunz, Karl S.

1992-01-01

The Penn State Finite Difference Time Domain Electromagnetic Scattering Code version D is a 3-D numerical electromagnetic scattering code based upon the finite difference time domain technique (FDTD). The manual provides a description of the code and corresponding results for several scattering problems. The manual is organized into 14 sections: introduction; description of the FDTD method; operation; resource requirements; version D code capabilities; a brief description of the default scattering geometry; a brief description of each subroutine; a description of the include file; a section briefly discussing Radar Cross Section computations; a section discussing some scattering results; a sample problem setup section; a new problem checklist; references and figure titles. The FDTD technique models transient electromagnetic scattering and interactions with objects of arbitrary shape and/or material composition. In the FDTD method, Maxwell's curl equations are discretized in time-space and all derivatives (temporal and spatial) are approximated by central differences.

FIELD OPERATIONS AND METHODS FOR MEASURING THE ECOLOGICAL CONDITION OF NON-WADEABLE RIVERS AND STREAMS

EPA Science Inventory

The methods and instructions for field operations presented in this manual for surveys of non-wadeable streams and rivers were developed and tested based on 55 sample sites in the Mid-Atlantic region and 53 sites in an Oregon study during two years of pilot and demonstration proj...

DeepIED: An epileptic discharge detector for EEG-fMRI based on deep learning.

PubMed

Hao, Yongfu; Khoo, Hui Ming; von Ellenrieder, Nicolas; Zazubovits, Natalja; Gotman, Jean

2018-01-01

Presurgical evaluation that can precisely delineate the epileptogenic zone (EZ) is one important step for successful surgical resection treatment of refractory epilepsy patients. The noninvasive EEG-fMRI recording technique combined with general linear model (GLM) analysis is considered an important tool for estimating the EZ. However, the manual marking of interictal epileptic discharges (IEDs) needed in this analysis is challenging and time-consuming because the quality of the EEG recorded inside the scanner is greatly deteriorated compared to the usual EEG obtained outside the scanner. This is one of main impediments to the widespread use of EEG-fMRI in epilepsy. We propose a deep learning based semi-automatic IED detector that can find the candidate IEDs in the EEG recorded inside the scanner which resemble sample IEDs marked in the EEG recorded outside the scanner. The manual marking burden is greatly reduced as the expert need only edit candidate IEDs. The model is trained on data from 30 patients. Validation of IEDs detection accuracy on another 37 consecutive patients shows our method can improve the median sensitivity from 50.0% for the previously proposed template-based method to 84.2%, with false positive rate as 5 events/min. Reproducibility validation on 15 patients is applied to evaluate if our method can produce similar hemodynamic response maps compared with the manual marking ground truth results. We explore the concordance between the maximum hemodynamic response and the intracerebral EEG defined EZ and find that both methods produce similar percentage of concordance (76.9%, 10 out of 13 patients, electrode was absent in the maximum hemodynamic response in two patients). This tool will make EEG-fMRI analysis more practical for clinical usage.

The influence of IQ stratification on WAIS-III/WMS-III FSIQ-general memory index discrepancy base-rates in the standardization sample.

PubMed

Hawkins, K A; Tulsky, D S

2001-11-01

Since memory performance expectations may be IQ-based, unidirectional base rate data for IQ-Memory Score discrepancies are provided in the WAIS-III/WMS-III Technical Manual. The utility of these data partially rests on the assumption that discrepancy base rates do not vary across ability levels. FSIQ stratified base rate data generated from the standardization sample, however, demonstrate substantial variability across the IQ spectrum. A superiority of memory score over FSIQ is typical at lower IQ levels, whereas the converse is true at higher IQ levels. These data indicate that the use of IQ-memory score unstratified "simple difference" tables could lead to erroneous conclusions for clients with low or high IQ. IQ stratified standardization base rate data are provided as a complement to the "predicted difference" method detailed in the Technical Manual.

40 CFR Table A-1 to Subpart A of... - Summary of Applicable Requirements for Reference and Equivalent Methods for Air Monitoring of...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Methods for Air Monitoring of Criteria Pollutants Pollutant Ref. or equivalent Manual or automated Applicable part 50 appendix Applicable subparts of part 53 A B C D E F SO2 Reference Manual A Equivalent Manual ✓ ✓ Automated ✓ ✓ ✓ CO Reference Automated C ✓ ✓ Equivalent Manual ✓ ✓ Automated ✓ ✓ ✓ O3...

Efficient content-based low-altitude images correlated network and strips reconstruction

NASA Astrophysics Data System (ADS)

He, Haiqing; You, Qi; Chen, Xiaoyong

2017-01-01

The manual intervention method is widely used to reconstruct strips for further aerial triangulation in low-altitude photogrammetry. Clearly the method for fully automatic photogrammetric data processing is not an expected way. In this paper, we explore a content-based approach without manual intervention or external information for strips reconstruction. Feature descriptors in the local spatial patterns are extracted by SIFT to construct vocabulary tree, in which these features are encoded in terms of TF-IDF numerical statistical algorithm to generate new representation for each low-altitude image. Then images correlated network is reconstructed by similarity measure, image matching and geometric graph theory. Finally, strips are reconstructed automatically by tracing straight lines and growing adjacent images gradually. Experimental results show that the proposed approach is highly effective in automatically rearranging strips of lowaltitude images and can provide rough relative orientation for further aerial triangulation.

Surface smoothness: cartilage biomarkers for knee OA beyond the radiologist

NASA Astrophysics Data System (ADS)

Tummala, Sudhakar; Dam, Erik B.

2010-03-01

Fully automatic imaging biomarkers may allow quantification of patho-physiological processes that a radiologist would not be able to assess reliably. This can introduce new insight but is problematic to validate due to lack of meaningful ground truth expert measurements. Rather than quantification accuracy, such novel markers must therefore be validated against clinically meaningful end-goals such as the ability to allow correct diagnosis. We present a method for automatic cartilage surface smoothness quantification in the knee joint. The quantification is based on a curvature flow method used on tibial and femoral cartilage compartments resulting from an automatic segmentation scheme. These smoothness estimates are validated for their ability to diagnose osteoarthritis and compared to smoothness estimates based on manual expert segmentations and to conventional cartilage volume quantification. We demonstrate that the fully automatic markers eliminate the time required for radiologist annotations, and in addition provide a diagnostic marker superior to the evaluated semi-manual markers.

Myocardial scar segmentation from magnetic resonance images using convolutional neural network

NASA Astrophysics Data System (ADS)

Zabihollahy, Fatemeh; White, James A.; Ukwatta, Eranga

2018-02-01

Accurate segmentation of the myocardial fibrosis or scar may provide important advancements for the prediction and management of malignant ventricular arrhythmias in patients with cardiovascular disease. In this paper, we propose a semi-automated method for segmentation of myocardial scar from late gadolinium enhancement magnetic resonance image (LGE-MRI) using a convolutional neural network (CNN). In contrast to image intensitybased methods, CNN-based algorithms have the potential to improve the accuracy of scar segmentation through the creation of high-level features from a combination of convolutional, detection and pooling layers. Our developed algorithm was trained using 2,336,703 image patches extracted from 420 slices of five 3D LGE-MR datasets, then validated on 2,204,178 patches from a testing dataset of seven 3D LGE-MR images including 624 slices, all obtained from patients with chronic myocardial infarction. For evaluation of the algorithm, we compared the algorithmgenerated segmentations to manual delineations by experts. Our CNN-based method reported an average Dice similarity coefficient (DSC), precision, and recall of 94.50 +/- 3.62%, 96.08 +/- 3.10%, and 93.96 +/- 3.75% as the accuracy of segmentation, respectively. As compared to several intensity threshold-based methods for scar segmentation, the results of our developed method have a greater agreement with manual expert segmentation.

WE-EF-210-08: BEST IN PHYSICS (IMAGING): 3D Prostate Segmentation in Ultrasound Images Using Patch-Based Anatomical Feature

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

Yang, X; Rossi, P; Jani, A

Purpose: Transrectal ultrasound (TRUS) is the standard imaging modality for the image-guided prostate-cancer interventions (e.g., biopsy and brachytherapy) due to its versatility and real-time capability. Accurate segmentation of the prostate plays a key role in biopsy needle placement, treatment planning, and motion monitoring. As ultrasound images have a relatively low signal-to-noise ratio (SNR), automatic segmentation of the prostate is difficult. However, manual segmentation during biopsy or radiation therapy can be time consuming. We are developing an automated method to address this technical challenge. Methods: The proposed segmentation method consists of two major stages: the training stage and the segmentation stage.more » During the training stage, patch-based anatomical features are extracted from the registered training images with patient-specific information, because these training images have been mapped to the new patient’ images, and the more informative anatomical features are selected to train the kernel support vector machine (KSVM). During the segmentation stage, the selected anatomical features are extracted from newly acquired image as the input of the well-trained KSVM and the output of this trained KSVM is the segmented prostate of this patient. Results: This segmentation technique was validated with a clinical study of 10 patients. The accuracy of our approach was assessed using the manual segmentation. The mean volume Dice Overlap Coefficient was 89.7±2.3%, and the average surface distance was 1.52 ± 0.57 mm between our and manual segmentation, which indicate that the automatic segmentation method works well and could be used for 3D ultrasound-guided prostate intervention. Conclusion: We have developed a new prostate segmentation approach based on the optimal feature learning framework, demonstrated its clinical feasibility, and validated its accuracy with manual segmentation (gold standard). This segmentation technique could be a useful tool for image-guided interventions in prostate-cancer diagnosis and treatment. This research is supported in part by DOD PCRP Award W81XWH-13-1-0269, and National Cancer Institute (NCI) Grant CA114313.« less

A Manual on Nonviolence and Children.

ERIC Educational Resources Information Center

Judson, Stephanie, Comp.

This manual on teaching children non-violent attitudes and the skills for non-violent conflict resolution suggests teaching activities and methods, describes classrooms in which these methods have been employed, and explains the underlying theory of conflict resolution. The first part of the manual, an outgrowth of the Friends' Nonviolence and…

Validation of Greyscale-Based Quantitative Ultrasound in Manual Wheelchair Users

PubMed Central

Collinger, Jennifer L.; Fullerton, Bradley; Impink, Bradley G.; Koontz, Alicia M.; Boninger, Michael L.

2010-01-01

Objective The primary aim of this study is to establish the validity of greyscale-based quantitative ultrasound (QUS) measures of the biceps and supraspinatus tendons. Design Nine QUS measures of the biceps and supraspinatus tendons were computed from ultrasound images collected from sixty-seven manual wheelchair users. Shoulder pathology was measured using questionnaires, physical examination maneuvers, and a clinical ultrasound grading scale. Results Increased age, duration of wheelchair use, and body mass correlated with a darker, more homogenous tendon appearance. Subjects with pain during physical examination tests for biceps tenderness and acromioclavicular joint tenderness exhibited significantly different supraspinatus QUS values. Even when controlling for tendon depth, QUS measures of the biceps tendon differed significantly between subjects with healthy tendons, mild tendinosis, and severe tendinosis. Clinical grading of supraspinatus tendon health was correlated with QUS measures of the supraspinatus tendon. Conclusions Quantitative ultrasound is valid method to quantify tendinopathy and may allow for early detection of tendinosis. Manual wheelchair users are at a high risk for developing shoulder tendon pathology and may benefit from quantitative ultrasound-based research that focuses on identifying interventions designed to reduce this risk. PMID:20407304

Combining registration and active shape models for the automatic segmentation of the lymph node regions in head and neck CT images

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

Chen Antong; Deeley, Matthew A.; Niermann, Kenneth J.

2010-12-15

Purpose: Intensity-modulated radiation therapy (IMRT) is the state of the art technique for head and neck cancer treatment. It requires precise delineation of the target to be treated and structures to be spared, which is currently done manually. The process is a time-consuming task of which the delineation of lymph node regions is often the longest step. Atlas-based delineation has been proposed as an alternative, but, in the authors' experience, this approach is not accurate enough for routine clinical use. Here, the authors improve atlas-based segmentation results obtained for level II-IV lymph node regions using an active shape model (ASM)more » approach. Methods: An average image volume was first created from a set of head and neck patient images with minimally enlarged nodes. The average image volume was then registered using affine, global, and local nonrigid transformations to the other volumes to establish a correspondence between surface points in the atlas and surface points in each of the other volumes. Once the correspondence was established, the ASMs were created for each node level. The models were then used to first constrain the results obtained with an atlas-based approach and then to iteratively refine the solution. Results: The method was evaluated through a leave-one-out experiment. The ASM- and atlas-based segmentations were compared to manual delineations via the Dice similarity coefficient (DSC) for volume overlap and the Euclidean distance between manual and automatic 3D surfaces. The mean DSC value obtained with the ASM-based approach is 10.7% higher than with the atlas-based approach; the mean and median surface errors were decreased by 13.6% and 12.0%, respectively. Conclusions: The ASM approach is effective in reducing segmentation errors in areas of low CT contrast where purely atlas-based methods are challenged. Statistical analysis shows that the improvements brought by this approach are significant.« less

Left ventricle: fully automated segmentation based on spatiotemporal continuity and myocardium information in cine cardiac magnetic resonance imaging (LV-FAST).

PubMed

Wang, Lijia; Pei, Mengchao; Codella, Noel C F; Kochar, Minisha; Weinsaft, Jonathan W; Li, Jianqi; Prince, Martin R; Wang, Yi

2015-01-01

CMR quantification of LV chamber volumes typically and manually defines the basal-most LV, which adds processing time and user-dependence. This study developed an LV segmentation method that is fully automated based on the spatiotemporal continuity of the LV (LV-FAST). An iteratively decreasing threshold region growing approach was used first from the midventricle to the apex, until the LV area and shape discontinued, and then from midventricle to the base, until less than 50% of the myocardium circumference was observable. Region growth was constrained by LV spatiotemporal continuity to improve robustness of apical and basal segmentations. The LV-FAST method was compared with manual tracing on cardiac cine MRI data of 45 consecutive patients. Of the 45 patients, LV-FAST and manual selection identified the same apical slices at both ED and ES and the same basal slices at both ED and ES in 38, 38, 38, and 41 cases, respectively, and their measurements agreed within -1.6 ± 8.7 mL, -1.4 ± 7.8 mL, and 1.0 ± 5.8% for EDV, ESV, and EF, respectively. LV-FAST allowed LV volume-time course quantitatively measured within 3 seconds on a standard desktop computer, which is fast and accurate for processing the cine volumetric cardiac MRI data, and enables LV filling course quantification over the cardiac cycle.

Automated and Semiautomated Segmentation of Rectal Tumor Volumes on Diffusion-Weighted MRI: Can It Replace Manual Volumetry?

PubMed

van Heeswijk, Miriam M; Lambregts, Doenja M J; van Griethuysen, Joost J M; Oei, Stanley; Rao, Sheng-Xiang; de Graaff, Carla A M; Vliegen, Roy F A; Beets, Geerard L; Papanikolaou, Nikos; Beets-Tan, Regina G H

2016-03-15

Diffusion-weighted imaging (DWI) tumor volumetry is promising for rectal cancer response assessment, but an important drawback is that manual per-slice tumor delineation can be highly time consuming. This study investigated whether manual DWI-volumetry can be reproduced using a (semi)automated segmentation approach. Seventy-nine patients underwent magnetic resonance imaging (MRI) that included DWI (highest b value [b1000 or b1100]) before and after chemoradiation therapy (CRT). Tumor volumes were assessed on b1000 (or b1100) DWI before and after CRT by means of (1) automated segmentation (by 2 inexperienced readers), (2) semiautomated segmentation (manual adjustment of the volumes obtained by method 1 by 2 radiologists), and (3) manual segmentation (by 2 radiologists); this last assessment served as the reference standard. Intraclass correlation coefficients (ICC) and Dice similarity indices (DSI) were calculated to evaluate agreement between different methods and observers. Measurement times (from a radiologist's perspective) were recorded for each method. Tumor volumes were not significantly different among the 3 methods, either before or after CRT (P=.08 to .92). ICCs compared to manual segmentation were 0.80 to 0.91 and 0.53 to 0.66 before and after CRT, respectively, for the automated segmentation and 0.91 to 0.97 and 0.61 to 0.75, respectively, for the semiautomated method. Interobserver agreement (ICC) pre and post CRT was 0.82 and 0.59 for automated segmentation, 0.91 and 0.73 for semiautomated segmentation, and 0.91 and 0.75 for manual segmentation, respectively. Mean DSI between the automated and semiautomated method were 0.83 and 0.58 pre-CRT and post-CRT, respectively; DSI between the automated and manual segmentation were 0.68 and 0.42 and 0.70 and 0.41 between the semiautomated and manual segmentation, respectively. Median measurement time for the radiologists was 0 seconds (pre- and post-CRT) for the automated method, 41 to 69 seconds (pre-CRT) and 60 to 67 seconds (post-CRT) for the semiautomated method, and 180 to 296 seconds (pre-CRT) and 84 to 91 seconds (post-CRT) for the manual method. DWI volumetry using a semiautomated segmentation approach is promising and a potentially time-saving alternative to manual tumor delineation, particularly for primary tumor volumetry. Once further optimized, it could be a helpful tool for tumor response assessment in rectal cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

Fast and accurate semi-automated segmentation method of spinal cord MR images at 3T applied to the construction of a cervical spinal cord template.

PubMed

El Mendili, Mohamed-Mounir; Chen, Raphaël; Tiret, Brice; Villard, Noémie; Trunet, Stéphanie; Pélégrini-Issac, Mélanie; Lehéricy, Stéphane; Pradat, Pierre-François; Benali, Habib

2015-01-01

To design a fast and accurate semi-automated segmentation method for spinal cord 3T MR images and to construct a template of the cervical spinal cord. A semi-automated double threshold-based method (DTbM) was proposed enabling both cross-sectional and volumetric measures from 3D T2-weighted turbo spin echo MR scans of the spinal cord at 3T. Eighty-two healthy subjects, 10 patients with amyotrophic lateral sclerosis, 10 with spinal muscular atrophy and 10 with spinal cord injuries were studied. DTbM was compared with active surface method (ASM), threshold-based method (TbM) and manual outlining (ground truth). Accuracy of segmentations was scored visually by a radiologist in cervical and thoracic cord regions. Accuracy was also quantified at the cervical and thoracic levels as well as at C2 vertebral level. To construct a cervical template from healthy subjects' images (n=59), a standardization pipeline was designed leading to well-centered straight spinal cord images and accurate probability tissue map. Visual scoring showed better performance for DTbM than for ASM. Mean Dice similarity coefficient (DSC) was 95.71% for DTbM and 90.78% for ASM at the cervical level and 94.27% for DTbM and 89.93% for ASM at the thoracic level. Finally, at C2 vertebral level, mean DSC was 97.98% for DTbM compared with 98.02% for TbM and 96.76% for ASM. DTbM showed similar accuracy compared with TbM, but with the advantage of limited manual interaction. A semi-automated segmentation method with limited manual intervention was introduced and validated on 3T images, enabling the construction of a cervical spinal cord template.

Image-based reconstruction of three-dimensional myocardial infarct geometry for patient-specific modeling of cardiac electrophysiology

PubMed Central

Ukwatta, Eranga; Arevalo, Hermenegild; Rajchl, Martin; White, James; Pashakhanloo, Farhad; Prakosa, Adityo; Herzka, Daniel A.; McVeigh, Elliot; Lardo, Albert C.; Trayanova, Natalia A.; Vadakkumpadan, Fijoy

2015-01-01

Purpose: Accurate three-dimensional (3D) reconstruction of myocardial infarct geometry is crucial to patient-specific modeling of the heart aimed at providing therapeutic guidance in ischemic cardiomyopathy. However, myocardial infarct imaging is clinically performed using two-dimensional (2D) late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) techniques, and a method to build accurate 3D infarct reconstructions from the 2D LGE-CMR images has been lacking. The purpose of this study was to address this need. Methods: The authors developed a novel methodology to reconstruct 3D infarct geometry from segmented low-resolution (Lo-res) clinical LGE-CMR images. Their methodology employed the so-called logarithm of odds (LogOdds) function to implicitly represent the shape of the infarct in segmented image slices as LogOdds maps. These 2D maps were then interpolated into a 3D image, and the result transformed via the inverse of LogOdds to a binary image representing the 3D infarct geometry. To assess the efficacy of this method, the authors utilized 39 high-resolution (Hi-res) LGE-CMR images, including 36 in vivo acquisitions of human subjects with prior myocardial infarction and 3 ex vivo scans of canine hearts following coronary ligation to induce infarction. The infarct was manually segmented by trained experts in each slice of the Hi-res images, and the segmented data were downsampled to typical clinical resolution. The proposed method was then used to reconstruct 3D infarct geometry from the downsampled images, and the resulting reconstructions were compared with the manually segmented data. The method was extensively evaluated using metrics based on geometry as well as results of electrophysiological simulations of cardiac sinus rhythm and ventricular tachycardia in individual hearts. Several alternative reconstruction techniques were also implemented and compared with the proposed method. Results: The accuracy of the LogOdds method in reconstructing 3D infarct geometry, as measured by the Dice similarity coefficient, was 82.10% ± 6.58%, a significantly higher value than those of the alternative reconstruction methods. Among outcomes of electrophysiological simulations with infarct reconstructions generated by various methods, the simulation results corresponding to the LogOdds method showed the smallest deviation from those corresponding to the manual reconstructions, as measured by metrics based on both activation maps and pseudo-ECGs. Conclusions: The authors have developed a novel method for reconstructing 3D infarct geometry from segmented slices of Lo-res clinical 2D LGE-CMR images. This method outperformed alternative approaches in reproducing expert manual 3D reconstructions and in electrophysiological simulations. PMID:26233186

Image-based reconstruction of three-dimensional myocardial infarct geometry for patient-specific modeling of cardiac electrophysiology

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

Ukwatta, Eranga, E-mail: eukwatt1@jhu.edu; Arevalo, Hermenegild; Pashakhanloo, Farhad

Purpose: Accurate three-dimensional (3D) reconstruction of myocardial infarct geometry is crucial to patient-specific modeling of the heart aimed at providing therapeutic guidance in ischemic cardiomyopathy. However, myocardial infarct imaging is clinically performed using two-dimensional (2D) late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) techniques, and a method to build accurate 3D infarct reconstructions from the 2D LGE-CMR images has been lacking. The purpose of this study was to address this need. Methods: The authors developed a novel methodology to reconstruct 3D infarct geometry from segmented low-resolution (Lo-res) clinical LGE-CMR images. Their methodology employed the so-called logarithm of odds (LogOdds) function to implicitlymore » represent the shape of the infarct in segmented image slices as LogOdds maps. These 2D maps were then interpolated into a 3D image, and the result transformed via the inverse of LogOdds to a binary image representing the 3D infarct geometry. To assess the efficacy of this method, the authors utilized 39 high-resolution (Hi-res) LGE-CMR images, including 36 in vivo acquisitions of human subjects with prior myocardial infarction and 3 ex vivo scans of canine hearts following coronary ligation to induce infarction. The infarct was manually segmented by trained experts in each slice of the Hi-res images, and the segmented data were downsampled to typical clinical resolution. The proposed method was then used to reconstruct 3D infarct geometry from the downsampled images, and the resulting reconstructions were compared with the manually segmented data. The method was extensively evaluated using metrics based on geometry as well as results of electrophysiological simulations of cardiac sinus rhythm and ventricular tachycardia in individual hearts. Several alternative reconstruction techniques were also implemented and compared with the proposed method. Results: The accuracy of the LogOdds method in reconstructing 3D infarct geometry, as measured by the Dice similarity coefficient, was 82.10% ± 6.58%, a significantly higher value than those of the alternative reconstruction methods. Among outcomes of electrophysiological simulations with infarct reconstructions generated by various methods, the simulation results corresponding to the LogOdds method showed the smallest deviation from those corresponding to the manual reconstructions, as measured by metrics based on both activation maps and pseudo-ECGs. Conclusions: The authors have developed a novel method for reconstructing 3D infarct geometry from segmented slices of Lo-res clinical 2D LGE-CMR images. This method outperformed alternative approaches in reproducing expert manual 3D reconstructions and in electrophysiological simulations.« less

Comparison of Manual Refraction Versus Autorefraction in 60 Diabetic Retinopathy Patients

PubMed Central

Shirzadi, Keyvan; Shahraki, Kourosh; Yahaghi, Emad; Makateb, Ali; Khosravifard, Keivan

2016-01-01

Aim: The purpose of the study was to evaluate the comparison of manual refraction versus autorefraction in diabetic retinopathy patients. Material and Methods: The study was conducted at the Be’sat Army Hospital from 2013-2015. In the present study differences between two common refractometry methods (manual refractometry and Auto refractometry) in diagnosis and follow up of retinopathy in patients affected with diabetes is investigated. Results: Our results showed that there is a significant difference in visual acuity score of patients between manual and auto refractometry. Despite this fact, spherical equivalent scores of two methods of refractometry did not show a significant statistical difference in the patients. Conclusion: Although use of manual refraction is comparable with autorefraction in evaluating spherical equivalent scores in diabetic patients affected with retinopathy, but in the case of visual acuity results from these two methods are not comparable. PMID:27703289

Mapping snow depth distribution in forested terrain using unmanned aerial vehicles and structure-from-motion

NASA Astrophysics Data System (ADS)

Webster, C.; Bühler, Y.; Schirmer, M.; Stoffel, A.; Giulia, M.; Jonas, T.

2017-12-01

Snow depth distribution in forests exhibits strong spatial heterogeneity compared to adjacent open sites. Measurement of snow depths in forests is currently limited to a) manual point measurements, which are sparse and time-intensive, b) ground-penetrating radar surveys, which have limited spatial coverage, or c) airborne LiDAR acquisition, which are expensive and may deteriorate in denser forests. We present the application of unmanned aerial vehicles in combination with structure-from-motion (SfM) methods to photogrammetrically map snow depth distribution in forested terrain. Two separate flights were carried out 10 days apart across a heterogeneous forested area of 900 x 500 m. Corresponding snow depth maps were derived using both, LiDAR-based and SfM-based DTM data, obtained during snow-off conditions. Manual measurements collected following each flight were used to validate the snow depth maps. Snow depths were resolved at 5cm resolution and forest snow depth distribution structures such as tree wells and other areas of preferential melt were represented well. Differential snow depth maps showed maximum ablation in the exposed south sides of trees and smaller differences in the centre of gaps and on the north side of trees. This new application of SfM to map snow depth distribution in forests demonstrates a straightforward method for obtaining information that was previously only available through manual spatially limited ground-based measurements. These methods could therefore be extended to more frequent observation of snow depths in forests as well as estimating snow accumulation and depletion rates.

State of laboratory manual instruction in California community college introductory (non-majors) biology laboratory instruction

NASA Astrophysics Data System (ADS)

Priest, Michelle

College students must complete a life science course prior to graduation for a bachelor's degree. Generally, the course has lecture and laboratory components. It is in the laboratory where there are exceptional opportunities for exploration, challenge and application of the material learned. Optimally, this would utilize the best of inquiry based approaches. Most community colleges are using a home-grown or self written laboratory manual for the direction of work in the laboratory period. Little was known about the motivation, development and adaptation of use. It was also not known about the future of the laboratory manuals in light of the recent learning reform in California Community Colleges, Student Learning Outcomes. Extensive interviews were conducted with laboratory manual authors to determine the motivation, process of development, who was involved and learning framework used in the creation of the manuals. It was further asked of manual authors their ideas about the future of the manual, the development of staff and faculty and finally, the role Student Learning Outcomes would play in the manual. Science faculty currently teaching the non-majors biology laboratories for at least two semesters were surveyed on-line about actual practice of the manual, assessment, manual flexibility, faculty training and incorporation of Student Learning Outcomes. Finally, an evaluation of the laboratory manual was done using an established Laboratory Task Analysis Instrument. Laboratory manuals were evaluated on a variety of categories to determine the level of inquiry instruction done by students in the laboratory section. The results were that the development of homegrown laboratory manuals was done by community colleges in the Los Angeles and Orange Counties in an effort to minimize the cost of the manual to the students, to utilize all the exercises in a particular lab and to effectively utilize the materials already owned by the department. Further, schools wanted to utilize the current faculty research expertise and knowledge. Unfortunately, laboratory manual authors had no real learning framework in the development of the manual. Based on the LAI, most manuals focused on the lowest levels of inquiry based instruction. Most manuals focused exercises on cell and molecular topics. The manuals had little student exploration, creation or design in the laboratory exercise and no option for repeating the exercise. There was a clear desire of faculty and authors to improve the laboratory experience and manual. Authors and faculty wished to include more inquiry and utilize the best of Student Learning Outcome (SLO) methodologies. Authors and the laboratory manuals have a major disconnect in that authors have clear desires inquiry based learning for the manual but do not effectively implement the inquiry based learning for various reasons. The manuals themselves, laboratory manuals themselves are not robust inquiry based learning models to maximize student learning. Authors and faculty are disconnected in that authors know what they want their manuals to do...but do not effectively communicate that to faculty. Finally, schools are in a "wait and see" approach as to when to integrate the latest learning theory mandated by the Chancellors Office -- Student Learning Outcomes.

Man vs. Machine: An interactive poll to evaluate hydrological model performance of a manual and an automatic calibration

NASA Astrophysics Data System (ADS)

Wesemann, Johannes; Burgholzer, Reinhard; Herrnegger, Mathew; Schulz, Karsten

2017-04-01

In recent years, a lot of research in hydrological modelling has been invested to improve the automatic calibration of rainfall-runoff models. This includes for example (1) the implementation of new optimisation methods, (2) the incorporation of new and different objective criteria and signatures in the optimisation and (3) the usage of auxiliary data sets apart from runoff. Nevertheless, in many applications manual calibration is still justifiable and frequently applied. The hydrologist performing the manual calibration, with his expert knowledge, is able to judge the hydrographs simultaneously concerning details but also in a holistic view. This integrated eye-ball verification procedure available to man can be difficult to formulate in objective criteria, even when using a multi-criteria approach. Comparing the results of automatic and manual calibration is not straightforward. Automatic calibration often solely involves objective criteria such as Nash-Sutcliffe Efficiency Coefficient or the Kling-Gupta-Efficiency as a benchmark during the calibration. Consequently, a comparison based on such measures is intrinsically biased towards automatic calibration. Additionally, objective criteria do not cover all aspects of a hydrograph leaving questions concerning the quality of a simulation open. This contribution therefore seeks to examine the quality of manually and automatically calibrated hydrographs by interactively involving expert knowledge in the evaluation. Simulations have been performed for the Mur catchment in Austria with the rainfall-runoff model COSERO using two parameter sets evolved from a manual and an automatic calibration. A subset of resulting hydrographs for observation and simulation, representing the typical flow conditions and events, will be evaluated in this study. In an interactive crowdsourcing approach experts attending the session can vote for their preferred simulated hydrograph without having information on the calibration method that produced the respective hydrograph. Therefore, the result of the poll can be seen as an additional quality criterion for the comparison of the two different approaches and help in the evaluation of the automatic calibration method.

Ecological Momentary Assessments and Automated Time Series Analysis to Promote Tailored Health Care: A Proof-of-Principle Study

PubMed Central

Emerencia, Ando C; Bos, Elisabeth H; Rosmalen, Judith GM; Riese, Harriëtte; Aiello, Marco; Sytema, Sjoerd; de Jonge, Peter

2015-01-01

Background Health promotion can be tailored by combining ecological momentary assessments (EMA) with time series analysis. This combined method allows for studying the temporal order of dynamic relationships among variables, which may provide concrete indications for intervention. However, application of this method in health care practice is hampered because analyses are conducted manually and advanced statistical expertise is required. Objective This study aims to show how this limitation can be overcome by introducing automated vector autoregressive modeling (VAR) of EMA data and to evaluate its feasibility through comparisons with results of previously published manual analyses. Methods We developed a Web-based open source application, called AutoVAR, which automates time series analyses of EMA data and provides output that is intended to be interpretable by nonexperts. The statistical technique we used was VAR. AutoVAR tests and evaluates all possible VAR models within a given combinatorial search space and summarizes their results, thereby replacing the researcher’s tasks of conducting the analysis, making an informed selection of models, and choosing the best model. We compared the output of AutoVAR to the output of a previously published manual analysis (n=4). Results An illustrative example consisting of 4 analyses was provided. Compared to the manual output, the AutoVAR output presents similar model characteristics and statistical results in terms of the Akaike information criterion, the Bayesian information criterion, and the test statistic of the Granger causality test. Conclusions Results suggest that automated analysis and interpretation of times series is feasible. Compared to a manual procedure, the automated procedure is more robust and can save days of time. These findings may pave the way for using time series analysis for health promotion on a larger scale. AutoVAR was evaluated using the results of a previously conducted manual analysis. Analysis of additional datasets is needed in order to validate and refine the application for general use. PMID:26254160

3-D rigid body tracking using vision and depth sensors.

PubMed

Gedik, O Serdar; Alatan, A Aydn

2013-10-01

In robotics and augmented reality applications, model-based 3-D tracking of rigid objects is generally required. With the help of accurate pose estimates, it is required to increase reliability and decrease jitter in total. Among many solutions of pose estimation in the literature, pure vision-based 3-D trackers require either manual initializations or offline training stages. On the other hand, trackers relying on pure depth sensors are not suitable for AR applications. An automated 3-D tracking algorithm, which is based on fusion of vision and depth sensors via extended Kalman filter, is proposed in this paper. A novel measurement-tracking scheme, which is based on estimation of optical flow using intensity and shape index map data of 3-D point cloud, increases 2-D, as well as 3-D, tracking performance significantly. The proposed method requires neither manual initialization of pose nor offline training, while enabling highly accurate 3-D tracking. The accuracy of the proposed method is tested against a number of conventional techniques, and a superior performance is clearly observed in terms of both objectively via error metrics and subjectively for the rendered scenes.

Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

PubMed Central

Meng, Shaowu; Brown, Douglas E; Ebbole, Daniel J; Torto-Alalibo, Trudy; Oh, Yeon Yee; Deng, Jixin; Mitchell, Thomas K; Dean, Ralph A

2009-01-01

Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 . However, a comprehensive manual curation remains to be performed. Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational) GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO). In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57%) being annotated with 1,957 distinct and specific GO terms. Unannotated proteins were assigned to the 3 root terms. The Version 5 GO annotation is publically queryable via the GO site . Additionally, the genome of M. oryzae is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website . The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System. Conclusion Our analysis provides comprehensive and robust GO annotations of the M. oryzae genome assemblies that will be solid foundations for further functional interrogation of M. oryzae. PMID:19278556

Computer-Aided Recognition of Facial Attributes for Fetal Alcohol Spectrum Disorders.

PubMed

Valentine, Matthew; Bihm, Dustin C J; Wolf, Lior; Hoyme, H Eugene; May, Philip A; Buckley, David; Kalberg, Wendy; Abdul-Rahman, Omar A

2017-12-01

To compare the detection of facial attributes by computer-based facial recognition software of 2-D images against standard, manual examination in fetal alcohol spectrum disorders (FASD). Participants were gathered from the Fetal Alcohol Syndrome Epidemiology Research database. Standard frontal and oblique photographs of children were obtained during a manual, in-person dysmorphology assessment. Images were submitted for facial analysis conducted by the facial dysmorphology novel analysis technology (an automated system), which assesses ratios of measurements between various facial landmarks to determine the presence of dysmorphic features. Manual blinded dysmorphology assessments were compared with those obtained via the computer-aided system. Areas under the curve values for individual receiver-operating characteristic curves revealed the computer-aided system (0.88 ± 0.02) to be comparable to the manual method (0.86 ± 0.03) in detecting patients with FASD. Interestingly, cases of alcohol-related neurodevelopmental disorder (ARND) were identified more efficiently by the computer-aided system (0.84 ± 0.07) in comparison to the manual method (0.74 ± 0.04). A facial gestalt analysis of patients with ARND also identified more generalized facial findings compared to the cardinal facial features seen in more severe forms of FASD. We found there was an increased diagnostic accuracy for ARND via our computer-aided method. As this category has been historically difficult to diagnose, we believe our experiment demonstrates that facial dysmorphology novel analysis technology can potentially improve ARND diagnosis by introducing a standardized metric for recognizing FASD-associated facial anomalies. Earlier recognition of these patients will lead to earlier intervention with improved patient outcomes. Copyright © 2017 by the American Academy of Pediatrics.

The 'Arm Force Field' method to predict manual arm strength based on only hand location and force direction.

PubMed

La Delfa, Nicholas J; Potvin, Jim R

2017-03-01

This paper describes the development of a novel method (termed the 'Arm Force Field' or 'AFF') to predict manual arm strength (MAS) for a wide range of body orientations, hand locations and any force direction. This method used an artificial neural network (ANN) to predict the effects of hand location and force direction on MAS, and included a method to estimate the contribution of the arm's weight to the predicted strength. The AFF method predicted the MAS values very well (r 2  = 0.97, RMSD = 5.2 N, n = 456) and maintained good generalizability with external test data (r 2  = 0.842, RMSD = 13.1 N, n = 80). The AFF can be readily integrated within any DHM ergonomics software, and appears to be a more robust, reliable and valid method of estimating the strength capabilities of the arm, when compared to current approaches. Copyright © 2016 Elsevier Ltd. All rights reserved.

Clinical evaluation of multi-atlas based segmentation of lymph node regions in head and neck and prostate cancer patients.

PubMed

Sjöberg, Carl; Lundmark, Martin; Granberg, Christoffer; Johansson, Silvia; Ahnesjö, Anders; Montelius, Anders

2013-10-03

Semi-automated segmentation using deformable registration of selected atlas cases consisting of expert segmented patient images has been proposed to facilitate the delineation of lymph node regions for three-dimensional conformal and intensity-modulated radiotherapy planning of head and neck and prostate tumours. Our aim is to investigate if fusion of multiple atlases will lead to clinical workload reductions and more accurate segmentation proposals compared to the use of a single atlas segmentation, due to a more complete representation of the anatomical variations. Atlases for lymph node regions were constructed using 11 head and neck patients and 15 prostate patients based on published recommendations for segmentations. A commercial registration software (Velocity AI) was used to create individual segmentations through deformable registration. Ten head and neck patients, and ten prostate patients, all different from the atlas patients, were randomly chosen for the study from retrospective data. Each patient was first delineated three times, (a) manually by a radiation oncologist, (b) automatically using a single atlas segmentation proposal from a chosen atlas and (c) automatically by fusing the atlas proposals from all cases in the database using the probabilistic weighting fusion algorithm. In a subsequent step a radiation oncologist corrected the segmentation proposals achieved from step (b) and (c) without using the result from method (a) as reference. The time spent for editing the segmentations was recorded separately for each method and for each individual structure. Finally, the Dice Similarity Coefficient and the volume of the structures were used to evaluate the similarity between the structures delineated with the different methods. For the single atlas method, the time reduction compared to manual segmentation was 29% and 23% for head and neck and pelvis lymph nodes, respectively, while editing the fused atlas proposal resulted in time reductions of 49% and 34%. The average volume of the fused atlas proposals was only 74% of the manual segmentation for the head and neck cases and 82% for the prostate cases due to a blurring effect from the fusion process. After editing of the proposals the resulting volume differences were no longer statistically significant, although a slight influence by the proposals could be noticed since the average edited volume was still slightly smaller than the manual segmentation, 9% and 5%, respectively. Segmentation based on fusion of multiple atlases reduces the time needed for delineation of lymph node regions compared to the use of a single atlas segmentation. Even though the time saving is large, the quality of the segmentation is maintained compared to manual segmentation.

User's manual for UCAP: Unified Counter-Rotation Aero-Acoustics Program

NASA Technical Reports Server (NTRS)

Culver, E. M.; Mccolgan, C. J.

1993-01-01

This is the user's manual for the Unified Counter-rotation Aeroacoustics Program (UCAP), the counter-rotation derivative of the UAAP (Unified Aero-Acoustic Program). The purpose of this program is to predict steady and unsteady air loading on the blades and the noise produced by a counter-rotation Prop-Fan. The aerodynamic method is based on linear potential theory with corrections for nonlinearity associated with axial flux induction, vortex lift on the blades, and rotor-to-rotor interference. The theory for acoustics and the theory for individual blade loading and wakes are derived in Unified Aeroacoustics Analysis for High Speed Turboprop Aerodynamics and Noise, Volume 1 (NASA CR-4329). This user's manual also includes a brief explanation of the theory used for the modelling of counter-rotation.

Teaching artificial neural systems to drive: Manual training techniques for autonomous systems

NASA Technical Reports Server (NTRS)

Shepanski, J. F.; Macy, S. A.

1987-01-01

A methodology was developed for manually training autonomous control systems based on artificial neural systems (ANS). In applications where the rule set governing an expert's decisions is difficult to formulate, ANS can be used to extract rules by associating the information an expert receives with the actions taken. Properly constructed networks imitate rules of behavior that permits them to function autonomously when they are trained on the spanning set of possible situations. This training can be provided manually, either under the direct supervision of a system trainer, or indirectly using a background mode where the networks assimilates training data as the expert performs its day-to-day tasks. To demonstrate these methods, an ANS network was trained to drive a vehicle through simulated freeway traffic.

User's manual for UCAP: Unified Counter-Rotation Aero-Acoustics Program

NASA Astrophysics Data System (ADS)

Culver, E. M.; McColgan, C. J.

1993-04-01

This is the user's manual for the Unified Counter-rotation Aeroacoustics Program (UCAP), the counter-rotation derivative of the UAAP (Unified Aero-Acoustic Program). The purpose of this program is to predict steady and unsteady air loading on the blades and the noise produced by a counter-rotation Prop-Fan. The aerodynamic method is based on linear potential theory with corrections for nonlinearity associated with axial flux induction, vortex lift on the blades, and rotor-to-rotor interference. The theory for acoustics and the theory for individual blade loading and wakes are derived in Unified Aeroacoustics Analysis for High Speed Turboprop Aerodynamics and Noise, Volume 1 (NASA CR-4329). This user's manual also includes a brief explanation of the theory used for the modelling of counter-rotation.

User's manual for three dimensional FDTD version B code for scattering from frequency-dependent dielectric materials

NASA Technical Reports Server (NTRS)

Beggs, John H.; Luebbers, Raymond J.; Kunz, Karl S.

1992-01-01

The Penn State Finite Difference Time Domain Electromagnetic Code Version B is a three dimensional numerical electromagnetic scattering code based upon the Finite Difference Time Domain Technique (FDTD). The supplied version of the code is one version of our current three dimensional FDTD code set. This manual provides a description of the code and corresponding results for several scattering problems. The manual is organized into 14 sections: introduction, description of the FDTD method, operation, resource requirements, Version B code capabilities, a brief description of the default scattering geometry, a brief description of each subroutine, a description of the include file, a discussion of radar cross section computations, a discussion of some scattering results, a sample problem setup section, a new problem checklist, references and figure titles.

Automatic latency equalization in VHDL-implemented complex pipelined systems

NASA Astrophysics Data System (ADS)

Zabołotny, Wojciech M.

2016-09-01

In the pipelined data processing systems it is very important to ensure that parallel paths delay data by the same number of clock cycles. If that condition is not met, the processing blocks receive data not properly aligned in time and produce incorrect results. Manual equalization of latencies is a tedious and error-prone work. This paper presents an automatic method of latency equalization in systems described in VHDL. The proposed method uses simulation to measure latencies and verify introduced correction. The solution is portable between different simulation and synthesis tools. The method does not increase the complexity of the synthesized design comparing to the solution based on manual latency adjustment. The example implementation of the proposed methodology together with a simple design demonstrating its use is available as an open source project under BSD license.

7 CFR 91.23 - Analytical methods.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 3 2014-01-01 2014-01-01 false Analytical methods. 91.23 Section 91.23 Agriculture... SERVICES AND GENERAL INFORMATION Method Manuals § 91.23 Analytical methods. Most analyses are performed according to approved procedures described in manuals of standardized methodology. These standard methods...

7 CFR 91.23 - Analytical methods.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 3 2011-01-01 2011-01-01 false Analytical methods. 91.23 Section 91.23 Agriculture... SERVICES AND GENERAL INFORMATION Method Manuals § 91.23 Analytical methods. Most analyses are performed according to approved procedures described in manuals of standardized methodology. These standard methods...

7 CFR 91.23 - Analytical methods.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 3 2013-01-01 2013-01-01 false Analytical methods. 91.23 Section 91.23 Agriculture... SERVICES AND GENERAL INFORMATION Method Manuals § 91.23 Analytical methods. Most analyses are performed according to approved procedures described in manuals of standardized methodology. These standard methods...

Extracting DNA from FFPE Tissue Biospecimens Using User-Friendly Automated Technology: Is There an Impact on Yield or Quality?

PubMed

Mathieson, William; Guljar, Nafia; Sanchez, Ignacio; Sroya, Manveer; Thomas, Gerry A

2018-05-03

DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissue blocks is amenable to analytical techniques, including sequencing. DNA extraction protocols are typically long and complex, often involving an overnight proteinase K digest. Automated platforms that shorten and simplify the process are therefore an attractive proposition for users wanting a faster turn-around or to process large numbers of biospecimens. It is, however, unclear whether automated extraction systems return poorer DNA yields or quality than manual extractions performed by experienced technicians. We extracted DNA from 42 FFPE clinical tissue biospecimens using the QiaCube (Qiagen) and ExScale (ExScale Biospecimen Solutions) automated platforms, comparing DNA yields and integrities with those from manual extractions. The QIAamp DNA FFPE Spin Column Kit was used for manual and QiaCube DNA extractions and the ExScale extractions were performed using two of the manufacturer's magnetic bead kits: one extracting DNA only and the other simultaneously extracting DNA and RNA. In all automated extraction methods, DNA yields and integrities (assayed using DNA Integrity Numbers from a 4200 TapeStation and the qPCR-based Illumina FFPE QC Assay) were poorer than in the manual method, with the QiaCube system performing better than the ExScale system. However, ExScale was fastest, offered the highest reproducibility when extracting DNA only, and required the least intervention or technician experience. Thus, the extraction methods have different strengths and weaknesses, would appeal to different users with different requirements, and therefore, we cannot recommend one method over another.

Correlation and agreement of a digital and conventional method to measure arch parameters.

PubMed

Nawi, Nes; Mohamed, Alizae Marny; Marizan Nor, Murshida; Ashar, Nor Atika

2018-01-01

The aim of the present study was to determine the overall reliability and validity of arch parameters measured digitally compared to conventional measurement. A sample of 111 plaster study models of Down syndrome (DS) patients were digitized using a blue light three-dimensional (3D) scanner. Digital and manual measurements of defined parameters were performed using Geomagic analysis software (Geomagic Studio 2014 software, 3D Systems, Rock Hill, SC, USA) on digital models and with a digital calliper (Tuten, Germany) on plaster study models. Both measurements were repeated twice to validate the intraexaminer reliability based on intraclass correlation coefficients (ICCs) using the independent t test and Pearson's correlation, respectively. The Bland-Altman method of analysis was used to evaluate the agreement of the measurement between the digital and plaster models. No statistically significant differences (p > 0.05) were found between the manual and digital methods when measuring the arch width, arch length, and space analysis. In addition, all parameters showed a significant correlation coefficient (r ≥ 0.972; p < 0.01) between all digital and manual measurements. Furthermore, a positive agreement between digital and manual measurements of the arch width (90-96%), arch length and space analysis (95-99%) were also distinguished using the Bland-Altman method. These results demonstrate that 3D blue light scanning and measurement software are able to precisely produce 3D digital model and measure arch width, arch length, and space analysis. The 3D digital model is valid to be used in various clinical applications.

Iterative-cuts: longitudinal and scale-invariant segmentation via user-defined templates for rectosigmoid colon in gynecological brachytherapy.

PubMed

Lüddemann, Tobias; Egger, Jan

2016-04-01

Among all types of cancer, gynecological malignancies belong to the fourth most frequent type of cancer among women. In addition to chemotherapy and external beam radiation, brachytherapy is the standard procedure for the treatment of these malignancies. In the progress of treatment planning, localization of the tumor as the target volume and adjacent organs of risks by segmentation is crucial to accomplish an optimal radiation distribution to the tumor while simultaneously preserving healthy tissue. Segmentation is performed manually and represents a time-consuming task in clinical daily routine. This study focuses on the segmentation of the rectum/sigmoid colon as an organ-at-risk in gynecological brachytherapy. The proposed segmentation method uses an interactive, graph-based segmentation scheme with a user-defined template. The scheme creates a directed two-dimensional graph, followed by the minimal cost closed set computation on the graph, resulting in an outlining of the rectum. The graph's outline is dynamically adapted to the last calculated cut. Evaluation was performed by comparing manual segmentations of the rectum/sigmoid colon to results achieved with the proposed method. The comparison of the algorithmic to manual result yielded a dice similarity coefficient value of [Formula: see text], in comparison to [Formula: see text] for the comparison of two manual segmentations by the same physician. Utilizing the proposed methodology resulted in a median time of [Formula: see text], compared to 300 s needed for pure manual segmentation.

Interactive and scale invariant segmentation of the rectum/sigmoid via user-defined templates

NASA Astrophysics Data System (ADS)

Lüddemann, Tobias; Egger, Jan

2016-03-01

Among all types of cancer, gynecological malignancies belong to the 4th most frequent type of cancer among women. Besides chemotherapy and external beam radiation, brachytherapy is the standard procedure for the treatment of these malignancies. In the progress of treatment planning, localization of the tumor as the target volume and adjacent organs of risks by segmentation is crucial to accomplish an optimal radiation distribution to the tumor while simultaneously preserving healthy tissue. Segmentation is performed manually and represents a time-consuming task in clinical daily routine. This study focuses on the segmentation of the rectum/sigmoid colon as an Organ-At-Risk in gynecological brachytherapy. The proposed segmentation method uses an interactive, graph-based segmentation scheme with a user-defined template. The scheme creates a directed two dimensional graph, followed by the minimal cost closed set computation on the graph, resulting in an outlining of the rectum. The graphs outline is dynamically adapted to the last calculated cut. Evaluation was performed by comparing manual segmentations of the rectum/sigmoid colon to results achieved with the proposed method. The comparison of the algorithmic to manual results yielded to a Dice Similarity Coefficient value of 83.85+/-4.08%, in comparison to 83.97+/-8.08% for the comparison of two manual segmentations of the same physician. Utilizing the proposed methodology resulted in a median time of 128 seconds per dataset, compared to 300 seconds needed for pure manual segmentation.

SU-E-J-159: Intra-Patient Deformable Image Registration Uncertainties Quantified Using the Distance Discordance Metric

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

Saleh, Z; Thor, M; Apte, A

2014-06-01

Purpose: The quantitative evaluation of deformable image registration (DIR) is currently challenging due to lack of a ground truth. In this study we test a new method proposed for quantifying multiple-image based DIRrelated uncertainties, for DIR of pelvic images. Methods: 19 patients were analyzed, each with 6 CT scans, who previously had radiotherapy for prostate cancer. Manually delineated structures for rectum and bladder, which served as ground truth structures, were delineated on the planning CT and each subsequent scan. For each patient, voxel-by-voxel DIR-related uncertainties were evaluated, following B-spline based DIR, by applying a previously developed metric, the distance discordancemore » metric (DDM; Saleh et al., PMB (2014) 59:733). The DDM map was superimposed on the first acquired CT scan and DDM statistics were assessed, also relative to two metrics estimating the agreement between the propagated and the manually delineated structures. Results: The highest DDM values which correspond to greatest spatial uncertainties were observed near the body surface and in the bowel due to the presence of gas. The mean rectal and bladder DDM values ranged from 1.1–11.1 mm and 1.5–12.7 mm, respectively. There was a strong correlation in the DDMs between the rectum and bladder (Pearson R = 0.68 for the max DDM). For both structures, DDM was correlated with the ratio between the DIR-propagated and manually delineated volumes (R = 0.74 for the max rectal DDM). The maximum rectal DDM was negatively correlated with the Dice Similarity Coefficient between the propagated and the manually delineated volumes (R= −0.52). Conclusion: The multipleimage based DDM map quantified considerable DIR variability across different structures and among patients. Besides using the DDM for quantifying DIR-related uncertainties it could potentially be used to adjust for uncertainties in DIR-based accumulated dose distributions.« less

Evaluation of heterotrophic plate and chromogenic agar colony counting in water quality laboratories.

PubMed

Hallas, Gary; Monis, Paul

2015-01-01

The enumeration of bacteria using plate-based counts is a core technique used by food and water microbiology testing laboratories. However, manual counting of bacterial colonies is both time and labour intensive, can vary between operators and also requires manual entry of results into laboratory information management systems, which can be a source of data entry error. An alternative is to use automated digital colony counters, but there is a lack of peer-reviewed validation data to allow incorporation into standards. We compared the performance of digital counting technology (ProtoCOL3) against manual counting using criteria defined in internationally recognized standard methods. Digital colony counting provided a robust, standardized system suitable for adoption in a commercial testing environment. The digital technology has several advantages:•Improved measurement of uncertainty by using a standard and consistent counting methodology with less operator error.•Efficiency for labour and time (reduced cost).•Elimination of manual entry of data onto LIMS.•Faster result reporting to customers.

Suggestive, Accelerative Learning and Teaching: A Manual of Classroom Procedures Based on the Lozanov Method.

ERIC Educational Resources Information Center

Schuster, Donald H.; And Others

The Suggestive Accelerative Learning and Teaching Method uses aspects of suggestion and unusual styles of presenting material to accelerate classroom learning. The essence of this technique is the use of a combination of physical relaxation exercises, mental concentration and suggestive principles to strengthen a person's ego and expand his memory…

Method to Identify Deep Cases Based on Relationships between Nouns, Verbs, and Particles

ERIC Educational Resources Information Center

Ide, Daisuke; Kimura, Masaomi

2016-01-01

Deep cases representing the significant meaning of nouns in sentences play a crucial role in semantic analysis. However, a case tends to be manually identified because it requires understanding the meaning and relationships of words. To address this problem, we propose a method to predict deep cases by analyzing the relationship between nouns,…

An Evaluation Method of Words Tendency Depending on Time-Series Variation and Its Improvements.

ERIC Educational Resources Information Center

Atlam, El-Sayed; Okada, Makoto; Shishibori, Masami; Aoe, Jun-ichi

2002-01-01

Discussion of word frequency and keywords in text focuses on a method to estimate automatically the stability classes that indicate a word's popularity with time-series variations based on the frequency change in past electronic text data. Compares the evaluation of decision tree stability class results with manual classification results.…

Determining the biomass fraction of mixed waste fuels: A comparison of existing industry and {sup 14}C-based methodologies

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

Muir, G.K.P., E-mail: Graham.Muir@glasgow.ac.uk; Hayward, S.; Tripney, B.G.

2015-01-15

Highlights: • Compares industry standard and {sup 14}C methods for determining bioenergy content of MSW. • Differences quantified through study at an operational energy from waste plant. • Manual sort and selective dissolution are unreliable measures of feedstock bioenergy. • {sup 14}C methods (esp. AMS) improve precision and reliability of bioenergy determination. • Implications for electricity generators and regulators for award of bio-incentives. - Abstract: {sup 14}C analysis of flue gas by accelerator mass spectrometry (AMS) and liquid scintillation counting (LSC) were used to determine the biomass fraction of mixed waste at an operational energy-from-waste (EfW) plant. Results were convertedmore » to bioenergy (% total) using mathematical algorithms and assessed against existing industry methodologies which involve manual sorting and selective dissolution (SD) of feedstock. Simultaneous determinations using flue gas showed excellent agreement: 44.8 ± 2.7% for AMS and 44.6 ± 12.3% for LSC. Comparable bioenergy results were obtained using a feedstock manual sort procedure (41.4%), whilst a procedure based on selective dissolution of representative waste material is reported as 75.5% (no errors quoted). {sup 14}C techniques present significant advantages in data acquisition, precision and reliability for both electricity generator and industry regulator.« less

An Approach to Evaluate Blurriness in Retinal Images with Vitreous Opacity for Cataract Diagnosis

PubMed Central

Xu, Liang

2017-01-01

Cataract is one of the leading causes of blindness in the world's population. A method to evaluate blurriness for cataract diagnosis in retinal images with vitreous opacity is proposed in this paper. Three types of features are extracted, which include pixel number of visible structures, mean contrast between vessels and background, and local standard deviation. To avoid the wrong detection of vitreous opacity as retinal structures, a morphological method is proposed to detect and remove such lesions from retinal visible structure segmentation. Based on the extracted features, a decision tree is trained to classify retinal images into five grades of blurriness. The proposed approach was tested using 1355 clinical retinal images, and the accuracies of two-class classification and five-grade grading compared with that of manual grading are 92.8% and 81.1%, respectively. The kappa value between automatic grading and manual grading is 0.74 in five-grade grading, in which both variance and P value are less than 0.001. Experimental results show that the grading difference between automatic grading and manual grading is all within 1 grade, which is much improvement compared with that of other available methods. The proposed grading method provides a universal measure of cataract severity and can facilitate the decision of cataract surgery. PMID:29065620

The Influence of Speed and Grade on Wheelchair Propulsion Hand Pattern

PubMed Central

Slowik, Jonathan S.; Requejo, Philip S.; Mulroy, Sara J.; Neptune, Richard R.

2015-01-01

Background The hand pattern used during manual wheelchair propulsion (i.e., full-cycle hand path) can provide insight into an individual's propulsion technique. However, previous analyses of hand patterns have been limited by their focus on a single propulsion condition and reliance on subjective qualitative characterization methods. The purpose of this study was to develop a set of objective quantitative parameters to characterize hand patterns and determine the influence of propulsion speed and grade of incline on the patterns preferred by manual wheelchair users. Methods Kinematic and kinetic data were collected from 170 experienced manual wheelchair users on an ergometer during three conditions: level propulsion at their self-selected speed, level propulsion at their fastest comfortable speed, and graded propulsion (8%) at their level self-selected speed. Hand patterns were quantified using a set of objective parameters and differences across conditions were identified. Findings Increased propulsion speed resulted in a shift away from under-rim hand patterns. Increased grade of incline resulted in the hand remaining near the handrim throughout the cycle. Interpretation Manual wheelchair users change their hand pattern based on task-specific constraints and goals. Further work is needed to investigate how differences between hand patterns influence upper extremity demand and potentially lead to the development of overuse injuries and pain. PMID:26228706

Development of a novel constellation based landmark detection algorithm

NASA Astrophysics Data System (ADS)

Ghayoor, Ali; Vaidya, Jatin G.; Johnson, Hans J.

2013-03-01

Anatomical landmarks such as the anterior commissure (AC) and posterior commissure (PC) are commonly used by researchers for co-registration of images. In this paper, we present a novel, automated approach for landmark detection that combines morphometric constraining and statistical shape models to provide accurate estimation of landmark points. This method is made robust to large rotations in initial head orientation by extracting extra information of the eye centers using a radial Hough transform and exploiting the centroid of head mass (CM) using a novel estimation approach. To evaluate the effectiveness of this method, the algorithm is trained on a set of 20 images with manually selected landmarks, and a test dataset is used to compare the automatically detected against the manually detected landmark locations of the AC, PC, midbrain-pons junction (MPJ), and fourth ventricle notch (VN4). The results show that the proposed method is accurate as the average error between the automatically and manually labeled landmark points is less than 1 mm. Also, the algorithm is highly robust as it was successfully run on a large dataset that included different kinds of images with various orientation, spacing, and origin.

An Automated Method for High-Definition Transcranial Direct Current Stimulation Modeling*

PubMed Central

Huang, Yu; Su, Yuzhuo; Rorden, Christopher; Dmochowski, Jacek; Datta, Abhishek; Parra, Lucas C.

2014-01-01

Targeted transcranial stimulation with electric currents requires accurate models of the current flow from scalp electrodes to the human brain. Idiosyncratic anatomy of individual brains and heads leads to significant variability in such current flows across subjects, thus, necessitating accurate individualized head models. Here we report on an automated processing chain that computes current distributions in the head starting from a structural magnetic resonance image (MRI). The main purpose of automating this process is to reduce the substantial effort currently required for manual segmentation, electrode placement, and solving of finite element models. In doing so, several weeks of manual labor were reduced to no more than 4 hours of computation time and minimal user interaction, while current-flow results for the automated method deviated by less than 27.9% from the manual method. Key facilitating factors are the addition of three tissue types (skull, scalp and air) to a state-of-the-art automated segmentation process, morphological processing to correct small but important segmentation errors, and automated placement of small electrodes based on easily reproducible standard electrode configurations. We anticipate that such an automated processing will become an indispensable tool to individualize transcranial direct current stimulation (tDCS) therapy. PMID:23367144

Segmentation of tumor ultrasound image in HIFU therapy based on texture and boundary encoding

NASA Astrophysics Data System (ADS)

Zhang, Dong; Xu, Menglong; Quan, Long; Yang, Yan; Qin, Qianqing; Zhu, Wenbin

2015-02-01

It is crucial in high intensity focused ultrasound (HIFU) therapy to detect the tumor precisely with less manual intervention for enhancing the therapy efficiency. Ultrasound image segmentation becomes a difficult task due to signal attenuation, speckle effect and shadows. This paper presents an unsupervised approach based on texture and boundary encoding customized for ultrasound image segmentation in HIFU therapy. The approach oversegments the ultrasound image into some small regions, which are merged by using the principle of minimum description length (MDL) afterwards. Small regions belonging to the same tumor are clustered as they preserve similar texture features. The mergence is completed by obtaining the shortest coding length from encoding textures and boundaries of these regions in the clustering process. The tumor region is finally selected from merged regions by a proposed algorithm without manual interaction. The performance of the method is tested on 50 uterine fibroid ultrasound images from HIFU guiding transducers. The segmentations are compared with manual delineations to verify its feasibility. The quantitative evaluation with HIFU images shows that the mean true positive of the approach is 93.53%, the mean false positive is 4.06%, the mean similarity is 89.92%, the mean norm Hausdorff distance is 3.62% and the mean norm maximum average distance is 0.57%. The experiments validate that the proposed method can achieve favorable segmentation without manual initialization and effectively handle the poor quality of the ultrasound guidance image in HIFU therapy, which indicates that the approach is applicable in HIFU therapy.

MAC/GMC 4.0 User's Manual: Example Problem Manual. Volume 3

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2002-01-01

This document is the third volume in the three volume set of User's Manuals for the Micromechanics Analysis Code with Generalized Method of Cells Version 4.0 (MAC/GMC 4.0). Volume 1 is the Theory Manual, Volume 2 is the Keywords Manual, and this document is the Example Problems Manual. MAC/GMC 4.0 is a composite material and laminate analysis software program developed at the NASA Glenn Research Center. It is based on the generalized method of cells (GMC) micromechanics theory, which provides access to the local stress and strain fields in the composite material. This access grants GMC the ability to accommodate arbitrary local models for inelastic material behavior and various types of damage and failure analysis. MAC/GMC 4.0 has been built around GMC to provide the theory with a user-friendly framework, along with a library of local inelastic, damage, and failure models. Further, application of simulated thermo-mechanical loading, generation of output results, and selection of architectures to represent the composite material, have been automated in MAC/GMC 4.0. Finally, classical lamination theory has been implemented within MAC/GMC 4.0 wherein GMC is used to model the composite material response of each ply. Consequently, the full range of GMC composite material capabilities is available for analysis of arbitrary laminate configurations as well. This volume provides in-depth descriptions of 43 example problems, which were specially designed to highlight many of the most important capabilities of the code. The actual input files associated with each example problem are distributed with the MAC/GMC 4.0 software; thus providing the user with a convenient starting point for their own specialized problems of interest.

Resource Manual: Handicapped Children Birth to Five. Part 2.

ERIC Educational Resources Information Center

Leslie, Lin; And Others

The resource manual, in two parts, provides a compilation of methods for enhancing the development of handicapped children from birth to 5 years in the areas of motor, communication, cognition, self help, and social skills. The manual is intended to aid in (1) assessing and identifying target behaviors to be achieved, (2) identifying methods for…

Two Automated Techniques for Carotid Lumen Diameter Measurement: Regional versus Boundary Approaches.

PubMed

Araki, Tadashi; Kumar, P Krishna; Suri, Harman S; Ikeda, Nobutaka; Gupta, Ajay; Saba, Luca; Rajan, Jeny; Lavra, Francesco; Sharma, Aditya M; Shafique, Shoaib; Nicolaides, Andrew; Laird, John R; Suri, Jasjit S

2016-07-01

The degree of stenosis in the carotid artery can be predicted using automated carotid lumen diameter (LD) measured from B-mode ultrasound images. Systolic velocity-based methods for measurement of LD are subjective. With the advancement of high resolution imaging, image-based methods have started to emerge. However, they require robust image analysis for accurate LD measurement. This paper presents two different algorithms for automated segmentation of the lumen borders in carotid ultrasound images. Both algorithms are modeled as a two stage process. Stage one consists of a global-based model using scale-space framework for the extraction of the region of interest. This stage is common to both algorithms. Stage two is modeled using a local-based strategy that extracts the lumen interfaces. At this stage, the algorithm-1 is modeled as a region-based strategy using a classification framework, whereas the algorithm-2 is modeled as a boundary-based approach that uses the level set framework. Two sets of databases (DB), Japan DB (JDB) (202 patients, 404 images) and Hong Kong DB (HKDB) (50 patients, 300 images) were used in this study. Two trained neuroradiologists performed manual LD tracings. The mean automated LD measured was 6.35 ± 0.95 mm for JDB and 6.20 ± 1.35 mm for HKDB. The precision-of-merit was: 97.4 % and 98.0 % w.r.t to two manual tracings for JDB and 99.7 % and 97.9 % w.r.t to two manual tracings for HKDB. Statistical tests such as ANOVA, Chi-Squared, T-test, and Mann-Whitney test were conducted to show the stability and reliability of the automated techniques.

CSTEM User Manual

NASA Technical Reports Server (NTRS)

Hartle, M.; McKnight, R. L.

2000-01-01

This manual is a combination of a user manual, theory manual, and programmer manual. The reader is assumed to have some previous exposure to the finite element method. This manual is written with the idea that the CSTEM (Coupled Structural Thermal Electromagnetic-Computer Code) user needs to have a basic understanding of what the code is actually doing in order to properly use the code. For that reason, the underlying theory and methods used in the code are described to a basic level of detail. The manual gives an overview of the CSTEM code: how the code came into existence, a basic description of what the code does, and the order in which it happens (a flowchart). Appendices provide a listing and very brief description of every file used by the CSTEM code, including the type of file it is, what routine regularly accesses the file, and what routine opens the file, as well as special features included in CSTEM.

Convolutional neural network for high-accuracy functional near-infrared spectroscopy in a brain-computer interface: three-class classification of rest, right-, and left-hand motor execution.

PubMed

Trakoolwilaiwan, Thanawin; Behboodi, Bahareh; Lee, Jaeseok; Kim, Kyungsoo; Choi, Ji-Woong

2018-01-01

The aim of this work is to develop an effective brain-computer interface (BCI) method based on functional near-infrared spectroscopy (fNIRS). In order to improve the performance of the BCI system in terms of accuracy, the ability to discriminate features from input signals and proper classification are desired. Previous studies have mainly extracted features from the signal manually, but proper features need to be selected carefully. To avoid performance degradation caused by manual feature selection, we applied convolutional neural networks (CNNs) as the automatic feature extractor and classifier for fNIRS-based BCI. In this study, the hemodynamic responses evoked by performing rest, right-, and left-hand motor execution tasks were measured on eight healthy subjects to compare performances. Our CNN-based method provided improvements in classification accuracy over conventional methods employing the most commonly used features of mean, peak, slope, variance, kurtosis, and skewness, classified by support vector machine (SVM) and artificial neural network (ANN). Specifically, up to 6.49% and 3.33% improvement in classification accuracy was achieved by CNN compared with SVM and ANN, respectively.

Dissemination of an Electronic Manual to Build Capacity for Implementing Farmers' Markets with Community Health Centers.

PubMed

Guest, M Aaron; Freedman, Darcy; Alia, Kassandra A; Brandt, Heather M; Friedman, Daniela B

2015-10-01

Community-university partnerships can lend themselves to the development of tools that encourage and promote future community health development. The electronic manual, "Building Farmacies," describes an approach for developing capacity and sustaining a community health center-based farmers' market that emerged through a community-university partnership. Manual development was guided by the Knowledge to Action Framework and experiences developing a multivendor, produce-only farmers' market at a community health center in rural South Carolina. The manual was created to illustrate an innovative solution for community health development. The manual was disseminated electronically through 25 listservs and interested individuals voluntarily completed a Web-based survey to access the free manual. During the 6-month dissemination period, 271 individuals downloaded the manual. Findings highlighted the value of translating community-based participatory research into user-friendly manuals to guide future intervention development and dissemination approaches, and demonstrate the need to include capacity building opportunities to support translation and adoption of interventions. © 2015 Wiley Periodicals, Inc.

Dissemination of an Electronic Manual to Build Capacity for Implementing Farmers’ Markets with Community Health Centers

PubMed Central

Guest, M. Aaron; Alia, Kassandra A.; Brandt, Heather M.; Friedman, Daniela B.

2015-01-01

Abstract Community–university partnerships can lend themselves to the development of tools that encourage and promote future community health development. The electronic manual, “Building Farmacies,” describes an approach for developing capacity and sustaining a community health center–based farmers’ market that emerged through a community–university partnership. Manual development was guided by the Knowledge to Action Framework and experiences developing a multivendor, produce‐only farmers’ market at a community health center in rural South Carolina. The manual was created to illustrate an innovative solution for community health development. The manual was disseminated electronically through 25 listservs and interested individuals voluntarily completed a Web‐based survey to access the free manual. During the 6‐month dissemination period, 271 individuals downloaded the manual. Findings highlighted the value of translating community‐based participatory research into user‐friendly manuals to guide future intervention development and dissemination approaches, and demonstrate the need to include capacity building opportunities to support translation and adoption of interventions. PMID:26296392

Treatment manuals, training and successful provision of stop smoking behavioural support.

PubMed

Brose, Leonie S; McEwen, Andy; Michie, Susan; West, Robert; Chew, Xie Yin; Lorencatto, Fabiana

2015-08-01

Translating evidence-based behaviour change interventions into practice is aided by use of treatment manuals specifying the recommended content and format of interventions, and evidence-based training. This study examined whether outcomes of stop smoking behavioural support differed with practitioner's use and evaluation of treatment manuals, or practitioner's training. English stop smoking practitioners were invited to complete an online survey including questions on: practitioners' training, availability, use and perceived utility of manuals, and annual biochemically-validated success rates of quit attempts supported (practitioner-reported). Mean success rates were compared between practitioners with/without access to manuals, those using/not using manuals, perceived utility ratings of manuals, and consecutive levels of training completed. Success rates were higher if practitioners had a manual (Mean (SD) = 54.0 (24.0) versus 48.0 (25.3), t(838) = 2.48, p = 0.013; n = 840), used a manual (F(2,8237) = 4.78, p = 0.009, n = 840), perceived manuals as more useful (F(3,834) = 2.90, p = 0.034, n = 840), and had completed training (F(3,709) = 4.81, p = 0.002, n = 713). Differences were diminished when adjusting for professional and demographic characteristics and no longer reached statistical significance using a conventional alpha for perceived utility of manuals and training status (both p = 0.1). Practitioners' performance in supporting smokers to quit varied with availability and use of treatment manuals. Evidence was weaker for perceived utility of manuals and practitioners' evidence-based training. Ensuring practitioners have access to treatment manuals within their service, promoting manual use, and training practitioners to competently apply manuals is likely to contribute to higher success rates in clinical practice. Copyright © 2015 Elsevier Ltd. All rights reserved.

Achieving Accurate Automatic Sleep Staging on Manually Pre-processed EEG Data Through Synchronization Feature Extraction and Graph Metrics.

PubMed

Chriskos, Panteleimon; Frantzidis, Christos A; Gkivogkli, Polyxeni T; Bamidis, Panagiotis D; Kourtidou-Papadeli, Chrysoula

2018-01-01

Sleep staging, the process of assigning labels to epochs of sleep, depending on the stage of sleep they belong, is an arduous, time consuming and error prone process as the initial recordings are quite often polluted by noise from different sources. To properly analyze such data and extract clinical knowledge, noise components must be removed or alleviated. In this paper a pre-processing and subsequent sleep staging pipeline for the sleep analysis of electroencephalographic signals is described. Two novel methods of functional connectivity estimation (Synchronization Likelihood/SL and Relative Wavelet Entropy/RWE) are comparatively investigated for automatic sleep staging through manually pre-processed electroencephalographic recordings. A multi-step process that renders signals suitable for further analysis is initially described. Then, two methods that rely on extracting synchronization features from electroencephalographic recordings to achieve computerized sleep staging are proposed, based on bivariate features which provide a functional overview of the brain network, contrary to most proposed methods that rely on extracting univariate time and frequency features. Annotation of sleep epochs is achieved through the presented feature extraction methods by training classifiers, which are in turn able to accurately classify new epochs. Analysis of data from sleep experiments on a randomized, controlled bed-rest study, which was organized by the European Space Agency and was conducted in the "ENVIHAB" facility of the Institute of Aerospace Medicine at the German Aerospace Center (DLR) in Cologne, Germany attains high accuracy rates, over 90% based on ground truth that resulted from manual sleep staging by two experienced sleep experts. Therefore, it can be concluded that the above feature extraction methods are suitable for semi-automatic sleep staging.

Achieving Accurate Automatic Sleep Staging on Manually Pre-processed EEG Data Through Synchronization Feature Extraction and Graph Metrics

PubMed Central

Chriskos, Panteleimon; Frantzidis, Christos A.; Gkivogkli, Polyxeni T.; Bamidis, Panagiotis D.; Kourtidou-Papadeli, Chrysoula

2018-01-01

Sleep staging, the process of assigning labels to epochs of sleep, depending on the stage of sleep they belong, is an arduous, time consuming and error prone process as the initial recordings are quite often polluted by noise from different sources. To properly analyze such data and extract clinical knowledge, noise components must be removed or alleviated. In this paper a pre-processing and subsequent sleep staging pipeline for the sleep analysis of electroencephalographic signals is described. Two novel methods of functional connectivity estimation (Synchronization Likelihood/SL and Relative Wavelet Entropy/RWE) are comparatively investigated for automatic sleep staging through manually pre-processed electroencephalographic recordings. A multi-step process that renders signals suitable for further analysis is initially described. Then, two methods that rely on extracting synchronization features from electroencephalographic recordings to achieve computerized sleep staging are proposed, based on bivariate features which provide a functional overview of the brain network, contrary to most proposed methods that rely on extracting univariate time and frequency features. Annotation of sleep epochs is achieved through the presented feature extraction methods by training classifiers, which are in turn able to accurately classify new epochs. Analysis of data from sleep experiments on a randomized, controlled bed-rest study, which was organized by the European Space Agency and was conducted in the “ENVIHAB” facility of the Institute of Aerospace Medicine at the German Aerospace Center (DLR) in Cologne, Germany attains high accuracy rates, over 90% based on ground truth that resulted from manual sleep staging by two experienced sleep experts. Therefore, it can be concluded that the above feature extraction methods are suitable for semi-automatic sleep staging. PMID:29628883

Conventional diamond fraise vs manual spot dermabrasion with drywall sanding screen for scars from skin cancer surgery.

PubMed

Gillard, Montgomery; Wang, Timothy S; Boyd, Charles M; Dunn, Rodney L; Fader, Darrell J; Johnson, Timothy M

2002-08-01

To directly compare cosmetic improvement and postoperative sequelae resulting from dermabrasion of surgical scars with conventional motor-powered diamond fraise vs manual dermabrasion with medium-grade drywall sanding screen. Patients were randomly assigned to receive treatment with conventional diamond fraise dermabrasion to one half of the scar and manual dermabrasion with a drywall sanding screen to the other half in a prospective, comparative clinical study. Blinded observers assessed clinical variables during a 6-month follow-up period. University hospital/cancer center-based cutaneous surgery unit. Twenty-one healthy volunteers, Fitzpatrick skin type I to III, with contour irregularities resulting from granulation (7 patients) or reconstruction (14 patients) after skin cancer excision. One half of the patient's scar was treated with motor-powered diamond fraise dermabrasion and the other half was treated with manual dermabrasion with medium-grade drywall sanding screen. Correction of contour, scarline visibility, time to reepithelialization, presence or absence of milia, degree of postoperative erythema, hypertrophic scarring, patients' subjective reports of postoperative pain, and presence of pigmentary changes were observed for both methods. Standardized scoring systems were used to quantify outcome measures. According to the standardized scoring systems, no differences were found between the 2 methods at any point. In addition, no significant differences were found between the methods for any measure at any of the time points. Both dermabrasion techniques are equally effective in improving the cosmetic appearance of surgical scars.

Classifying injury narratives of large administrative databases for surveillance-A practical approach combining machine learning ensembles and human review.

PubMed

Marucci-Wellman, Helen R; Corns, Helen L; Lehto, Mark R

2017-01-01

Injury narratives are now available real time and include useful information for injury surveillance and prevention. However, manual classification of the cause or events leading to injury found in large batches of narratives, such as workers compensation claims databases, can be prohibitive. In this study we compare the utility of four machine learning algorithms (Naïve Bayes, Single word and Bi-gram models, Support Vector Machine and Logistic Regression) for classifying narratives into Bureau of Labor Statistics Occupational Injury and Illness event leading to injury classifications for a large workers compensation database. These algorithms are known to do well classifying narrative text and are fairly easy to implement with off-the-shelf software packages such as Python. We propose human-machine learning ensemble approaches which maximize the power and accuracy of the algorithms for machine-assigned codes and allow for strategic filtering of rare, emerging or ambiguous narratives for manual review. We compare human-machine approaches based on filtering on the prediction strength of the classifier vs. agreement between algorithms. Regularized Logistic Regression (LR) was the best performing algorithm alone. Using this algorithm and filtering out the bottom 30% of predictions for manual review resulted in high accuracy (overall sensitivity/positive predictive value of 0.89) of the final machine-human coded dataset. The best pairings of algorithms included Naïve Bayes with Support Vector Machine whereby the triple ensemble NB SW =NB BI-GRAM =SVM had very high performance (0.93 overall sensitivity/positive predictive value and high accuracy (i.e. high sensitivity and positive predictive values)) across both large and small categories leaving 41% of the narratives for manual review. Integrating LR into this ensemble mix improved performance only slightly. For large administrative datasets we propose incorporation of methods based on human-machine pairings such as we have done here, utilizing readily-available off-the-shelf machine learning techniques and resulting in only a fraction of narratives that require manual review. Human-machine ensemble methods are likely to improve performance over total manual coding. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Comparison of Manual Refraction Versus Autorefraction in 60 Diabetic Retinopathy Patients.

PubMed

Shirzadi, Keyvan; Shahraki, Kourosh; Yahaghi, Emad; Makateb, Ali; Khosravifard, Keivan

2016-07-27

The purpose of the study was to evaluate the comparison of manual refraction versus autorefraction in diabetic retinopathy patients. The study was conducted at the Be'sat Army Hospital from 2013-2015. In the present study differences between two common refractometry methods (manual refractometry and Auto refractometry) in diagnosis and follow up of retinopathy in patients affected with diabetes is investigated. Our results showed that there is a significant difference in visual acuity score of patients between manual and auto refractometry. Despite this fact, spherical equivalent scores of two methods of refractometry did not show a significant statistical difference in the patients. Although use of manual refraction is comparable with autorefraction in evaluating spherical equivalent scores in diabetic patients affected with retinopathy, but in the case of visual acuity results from these two methods are not comparable.

Unsupervised Ensemble Anomaly Detection Using Time-Periodic Packet Sampling

NASA Astrophysics Data System (ADS)

Uchida, Masato; Nawata, Shuichi; Gu, Yu; Tsuru, Masato; Oie, Yuji

We propose an anomaly detection method for finding patterns in network traffic that do not conform to legitimate (i.e., normal) behavior. The proposed method trains a baseline model describing the normal behavior of network traffic without using manually labeled traffic data. The trained baseline model is used as the basis for comparison with the audit network traffic. This anomaly detection works in an unsupervised manner through the use of time-periodic packet sampling, which is used in a manner that differs from its intended purpose — the lossy nature of packet sampling is used to extract normal packets from the unlabeled original traffic data. Evaluation using actual traffic traces showed that the proposed method has false positive and false negative rates in the detection of anomalies regarding TCP SYN packets comparable to those of a conventional method that uses manually labeled traffic data to train the baseline model. Performance variation due to the probabilistic nature of sampled traffic data is mitigated by using ensemble anomaly detection that collectively exploits multiple baseline models in parallel. Alarm sensitivity is adjusted for the intended use by using maximum- and minimum-based anomaly detection that effectively take advantage of the performance variations among the multiple baseline models. Testing using actual traffic traces showed that the proposed anomaly detection method performs as well as one using manually labeled traffic data and better than one using randomly sampled (unlabeled) traffic data.

Topic detection using paragraph vectors to support active learning in systematic reviews.

PubMed

Hashimoto, Kazuma; Kontonatsios, Georgios; Miwa, Makoto; Ananiadou, Sophia

2016-08-01

Systematic reviews require expert reviewers to manually screen thousands of citations in order to identify all relevant articles to the review. Active learning text classification is a supervised machine learning approach that has been shown to significantly reduce the manual annotation workload by semi-automating the citation screening process of systematic reviews. In this paper, we present a new topic detection method that induces an informative representation of studies, to improve the performance of the underlying active learner. Our proposed topic detection method uses a neural network-based vector space model to capture semantic similarities between documents. We firstly represent documents within the vector space, and cluster the documents into a predefined number of clusters. The centroids of the clusters are treated as latent topics. We then represent each document as a mixture of latent topics. For evaluation purposes, we employ the active learning strategy using both our novel topic detection method and a baseline topic model (i.e., Latent Dirichlet Allocation). Results obtained demonstrate that our method is able to achieve a high sensitivity of eligible studies and a significantly reduced manual annotation cost when compared to the baseline method. This observation is consistent across two clinical and three public health reviews. The tool introduced in this work is available from https://nactem.ac.uk/pvtopic/. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov

PubMed Central

Xu, Jun; Lee, Hee-Jin; Zeng, Jia; Wu, Yonghui; Zhang, Yaoyun; Huang, Liang-Chin; Johnson, Amber; Holla, Vijaykumar; Bailey, Ann M; Cohen, Trevor; Meric-Bernstam, Funda; Bernstam, Elmer V

2016-01-01

Objective: Clinical trials investigating drugs that target specific genetic alterations in tumors are important for promoting personalized cancer therapy. The goal of this project is to create a knowledge base of cancer treatment trials with annotations about genetic alterations from ClinicalTrials.gov. Methods: We developed a semi-automatic framework that combines advanced text-processing techniques with manual review to curate genetic alteration information in cancer trials. The framework consists of a document classification system to identify cancer treatment trials from ClinicalTrials.gov and an information extraction system to extract gene and alteration pairs from the Title and Eligibility Criteria sections of clinical trials. By applying the framework to trials at ClinicalTrials.gov, we created a knowledge base of cancer treatment trials with genetic alteration annotations. We then evaluated each component of the framework against manually reviewed sets of clinical trials and generated descriptive statistics of the knowledge base. Results and Discussion: The automated cancer treatment trial identification system achieved a high precision of 0.9944. Together with the manual review process, it identified 20 193 cancer treatment trials from ClinicalTrials.gov. The automated gene-alteration extraction system achieved a precision of 0.8300 and a recall of 0.6803. After validation by manual review, we generated a knowledge base of 2024 cancer trials that are labeled with specific genetic alteration information. Analysis of the knowledge base revealed the trend of increased use of targeted therapy for cancer, as well as top frequent gene-alteration pairs of interest. We expect this knowledge base to be a valuable resource for physicians and patients who are seeking information about personalized cancer therapy. PMID:27013523

Computer-based coding of free-text job descriptions to efficiently identify occupations in epidemiological studies

PubMed Central

Russ, Daniel E.; Ho, Kwan-Yuet; Colt, Joanne S.; Armenti, Karla R.; Baris, Dalsu; Chow, Wong-Ho; Davis, Faith; Johnson, Alison; Purdue, Mark P.; Karagas, Margaret R.; Schwartz, Kendra; Schwenn, Molly; Silverman, Debra T.; Johnson, Calvin A.; Friesen, Melissa C.

2016-01-01

Background Mapping job titles to standardized occupation classification (SOC) codes is an important step in identifying occupational risk factors in epidemiologic studies. Because manual coding is time-consuming and has moderate reliability, we developed an algorithm called SOCcer (Standardized Occupation Coding for Computer-assisted Epidemiologic Research) to assign SOC-2010 codes based on free-text job description components. Methods Job title and task-based classifiers were developed by comparing job descriptions to multiple sources linking job and task descriptions to SOC codes. An industry-based classifier was developed based on the SOC prevalence within an industry. These classifiers were used in a logistic model trained using 14,983 jobs with expert-assigned SOC codes to obtain empirical weights for an algorithm that scored each SOC/job description. We assigned the highest scoring SOC code to each job. SOCcer was validated in two occupational data sources by comparing SOC codes obtained from SOCcer to expert assigned SOC codes and lead exposure estimates obtained by linking SOC codes to a job-exposure matrix. Results For 11,991 case-control study jobs, SOCcer-assigned codes agreed with 44.5% and 76.3% of manually assigned codes at the 6- and 2-digit level, respectively. Agreement increased with the score, providing a mechanism to identify assignments needing review. Good agreement was observed between lead estimates based on SOCcer and manual SOC assignments (kappa: 0.6–0.8). Poorer performance was observed for inspection job descriptions, which included abbreviations and worksite-specific terminology. Conclusions Although some manual coding will remain necessary, using SOCcer may improve the efficiency of incorporating occupation into large-scale epidemiologic studies. PMID:27102331

Using pattern enumeration to accelerate process development and ramp yield

NASA Astrophysics Data System (ADS)

Zhuang, Linda; Pang, Jenny; Xu, Jessy; Tsai, Mengfeng; Wang, Amy; Zhang, Yifan; Sweis, Jason; Lai, Ya-Chieh; Ding, Hua

2016-03-01

During a new technology node process setup phase, foundries do not initially have enough product chip designs to conduct exhaustive process development. Different operational teams use manually designed simple test keys to set up their process flows and recipes. When the very first version of the design rule manual (DRM) is ready, foundries enter the process development phase where new experiment design data is manually created based on these design rules. However, these IP/test keys contain very uniform or simple design structures. This kind of design normally does not contain critical design structures or process unfriendly design patterns that pass design rule checks but are found to be less manufacturable. It is desired to have a method to generate exhaustive test patterns allowed by design rules at development stage to verify the gap of design rule and process. This paper presents a novel method of how to generate test key patterns which contain known problematic patterns as well as any constructs which designers could possibly draw based on current design rules. The enumerated test key patterns will contain the most critical design structures which are allowed by any particular design rule. A layout profiling method is used to do design chip analysis in order to find potential weak points on new incoming products so fab can take preemptive action to avoid yield loss. It can be achieved by comparing different products and leveraging the knowledge learned from previous manufactured chips to find possible yield detractors.

Similarity regularized sparse group lasso for cup to disc ratio computation.

PubMed

Cheng, Jun; Zhang, Zhuo; Tao, Dacheng; Wong, Damon Wing Kee; Liu, Jiang; Baskaran, Mani; Aung, Tin; Wong, Tien Yin

2017-08-01

Automatic cup to disc ratio (CDR) computation from color fundus images has shown to be promising for glaucoma detection. Over the past decade, many algorithms have been proposed. In this paper, we first review the recent work in the area and then present a novel similarity-regularized sparse group lasso method for automated CDR estimation. The proposed method reconstructs the testing disc image based on a set of reference disc images by integrating the similarity between testing and the reference disc images with the sparse group lasso constraints. The reconstruction coefficients are then used to estimate the CDR of the testing image. The proposed method has been validated using 650 images with manually annotated CDRs. Experimental results show an average CDR error of 0.0616 and a correlation coefficient of 0.7, outperforming other methods. The areas under curve in the diagnostic test reach 0.843 and 0.837 when manual and automatically segmented discs are used respectively, better than other methods as well.

FLAPS (Fatigue Life Analysis Programs): Computer Programs to Predict Cyclic Life Using the Total Strain Version of Strainrange Partitioning and Other Life Prediction Methods. Users' Manual and Example Problems, Version 1.0

NASA Technical Reports Server (NTRS)

Arya, Vinod K.; Halford, Gary R. (Technical Monitor)

2003-01-01

This manual presents computer programs FLAPS for characterizing and predicting fatigue and creep-fatigue resistance of metallic materials in the high-temperature, long-life regime for isothermal and nonisothermal fatigue. The programs use the Total Strain version of Strainrange Partitioning (TS-SRP), and several other life prediction methods described in this manual. The user should be thoroughly familiar with the TS-SRP and these life prediction methods before attempting to use any of these programs. Improper understanding can lead to incorrect use of the method and erroneous life predictions. An extensive database has also been developed in a parallel effort. The database is probably the largest source of high-temperature, creep-fatigue test data available in the public domain and can be used with other life-prediction methods as well. This users' manual, software, and database are all in the public domain and can be obtained by contacting the author. The Compact Disk (CD) accompanying this manual contains an executable file for the FLAPS program, two datasets required for the example problems in the manual, and the creep-fatigue data in a format compatible with these programs.

Percentage exposure of root dentin collagen after application of two irrigation protocols with manual or rotary instrumentation and two methacrylate resin-based sealers.

PubMed

González-López, Santiago; Martín-Altuve, Ernesto; Bolaños-Carmona, Victoria; Sánchez-Sánchez, Purificación; Rodríguez-Navarro, Alejandro

2013-10-01

To compare the percentage of collagen exposed in dentin root thirds after two irrigation protocols with manual or rotary instrumentation using two methacrylate resin-based sealers. Forty-eight single-root human teeth were prepared with manual (n = 24) or nickeltitanium ProFile rotary (n = 24) instrumentation, using 5% NaOCl between instruments and 5 ml 17% EDTA as final irrigant or 20% citric acid + 2% chlorhexidine (CHX) between instruments and as the final irrigant. RealSeal or EndoREZ were used as filling materials. One 1-mm slice per third was abraded and stained with Masson's trichrome method. Mean exposed collagen values were obtained in four areas from each section (at 60X magnification) and a complete factorial ANOVA was used to analyze the influence of the study variables. Non-parametric Mann-Whitney's test was used to compare groups. Differences with p < 0.05 were considered significant. A significantly higher percentage of collagen was exposed in all thirds with the use of the 20% citric acid + 2% CHX protocol with rotary vs manual instrumentation, but percent collagen exposed did not differ as a function of the filling material. After the 5% NaOCl + 17% EDTA protocol, the percentage of collagen exposed did not differ between rotary and manual instrumentation but was higher with the use of RealSeal. The highest percentage exposure of collagen was with 20% citric acid + 2% CHX using rotary instrumentation, regardless of the filling material.

Can pulsed xenon ultraviolet light systems disinfect aerobic bacteria in the absence of manual disinfection?

PubMed

Jinadatha, Chetan; Villamaria, Frank C; Ganachari-Mallappa, Nagaraja; Brown, Donna S; Liao, I-Chia; Stock, Eileen M; Copeland, Laurel A; Zeber, John E

2015-04-01

Whereas pulsed xenon-based ultraviolet light no-touch disinfection systems are being increasingly used for room disinfection after patient discharge with manual cleaning, their effectiveness in the absence of manual disinfection has not been previously evaluated. Our study indicates that pulsed xenon-based ultraviolet light systems effectively reduce aerobic bacteria in the absence of manual disinfection. These data are important for hospitals planning to adopt this technology as adjunct to routine manual disinfection. Published by Elsevier Inc.

Validation of an educative manual for patients with head and neck cancer submitted to radiation therapy 1

PubMed Central

da Cruz, Flávia Oliveira de Almeida Marques; Ferreira, Elaine Barros; Vasques, Christiane Inocêncio; da Mata, Luciana Regina Ferreira; dos Reis, Paula Elaine Diniz

2016-01-01

Abstract Objective: develop the content and face validation of an educative manual for patients with head and neck cancer submitted to radiation therapy. Method: descriptive methodological research. The Theory of Psychometrics was used for the validation process, developed by 15 experts in the theme area of the educative manual and by two language and publicity professionals. A minimum agreement level of 80% was considered to guarantee the validity of the material. Results: the items addressed in the assessment tool of the educative manual were divided in three blocks: objectives, structure and format, and relevance. Only one item, related to the sociocultural level of the target public, obtained an agreement rate <80%, and was reformulated based on the participants' suggestions. All other items were considered appropriate and/or complete appropriate in the three blocks proposed: objectives - 92.38%, structure and form - 89.74%, and relevance - 94.44%. Conclusion: the face and content validation of the educative manual proposed were attended to. This can contribute to the understanding of the therapeutic process the head and neck cancer patient is submitted to during the radiation therapy, besides supporting clinical practice through the nursing consultation. PMID:27305178

Manual unloading of the lumbar spine: can it identify immediate responders to mechanical traction in a low back pain population? A study of reliability and criterion referenced predictive validity

PubMed Central

Swanson, Brian T.; Riley, Sean P.; Cote, Mark P.; Leger, Robin R.; Moss, Isaac L.; Carlos,, John

2016-01-01

Background To date, no research has examined the reliability or predictive validity of manual unloading tests of the lumbar spine to identify potential responders to lumbar mechanical traction. Purpose To determine: (1) the intra and inter-rater reliability of a manual unloading test of the lumbar spine and (2) the criterion referenced predictive validity for the manual unloading test. Methods Ten volunteers with low back pain (LBP) underwent a manual unloading test to establish reliability. In a separate procedure, 30 consecutive patients with LBP (age 50·86±11·51) were assessed for pain in their most provocative standing position (visual analog scale (VAS) 49·53±25·52 mm). Patients were assessed with a manual unloading test in their most provocative position followed by a single application of intermittent mechanical traction. Post traction, pain in the provocative position was reassessed and utilized as the outcome criterion. Results The test of unloading demonstrated substantial intra and inter-rater reliability K = 1·00, P = 0·002, K = 0·737, P = 0·001, respectively. There were statistically significant within group differences for pain response following traction for patients with a positive manual unloading test (P<0·001), while patients with a negative manual unloading test did not demonstrate a statistically significant change (P>0·05). There were significant between group differences for proportion of responders to traction based on manual unloading response (P = 0·031), and manual unloading response demonstrated a moderate to strong relationship with traction response Phi = 0·443, P = 0·015. Discussion and conclusion The manual unloading test appears to be a reliable test and has a moderate to strong correlation with pain relief that exceeds minimal clinically important difference (MCID) following traction supporting the validity of this test. PMID:27559274

Fully Automatic Segmentation of Fluorescein Leakage in Subjects With Diabetic Macular Edema

PubMed Central

Rabbani, Hossein; Allingham, Michael J.; Mettu, Priyatham S.; Cousins, Scott W.; Farsiu, Sina

2015-01-01

Purpose. To create and validate software to automatically segment leakage area in real-world clinical fluorescein angiography (FA) images of subjects with diabetic macular edema (DME). Methods. Fluorescein angiography images obtained from 24 eyes of 24 subjects with DME were retrospectively analyzed. Both video and still-frame images were obtained using a Heidelberg Spectralis 6-mode HRA/OCT unit. We aligned early and late FA frames in the video by a two-step nonrigid registration method. To remove background artifacts, we subtracted early and late FA frames. Finally, after postprocessing steps, including detection and inpainting of the vessels, a robust active contour method was utilized to obtain leakage area in a 1500-μm-radius circular region centered at the fovea. Images were captured at different fields of view (FOVs) and were often contaminated with outliers, as is the case in real-world clinical imaging. Our algorithm was applied to these images with no manual input. Separately, all images were manually segmented by two retina specialists. The sensitivity, specificity, and accuracy of manual interobserver, manual intraobserver, and automatic methods were calculated. Results. The mean accuracy was 0.86 ± 0.08 for automatic versus manual, 0.83 ± 0.16 for manual interobserver, and 0.90 ± 0.08 for manual intraobserver segmentation methods. Conclusions. Our fully automated algorithm can reproducibly and accurately quantify the area of leakage of clinical-grade FA video and is congruent with expert manual segmentation. The performance was reliable for different DME subtypes. This approach has the potential to reduce time and labor costs and may yield objective and reproducible quantitative measurements of DME imaging biomarkers. PMID:25634978

Manual versus Automated Carotid Artery Plaque Component Segmentation in High and Lower Quality 3.0 Tesla MRI Scans

PubMed Central

Smits, Loek P.; van Wijk, Diederik F.; Duivenvoorden, Raphael; Xu, Dongxiang; Yuan, Chun; Stroes, Erik S.; Nederveen, Aart J.

2016-01-01

Purpose To study the interscan reproducibility of manual versus automated segmentation of carotid artery plaque components, and the agreement between both methods, in high and lower quality MRI scans. Methods 24 patients with 30–70% carotid artery stenosis were planned for 3T carotid MRI, followed by a rescan within 1 month. A multicontrast protocol (T1w,T2w, PDw and TOF sequences) was used. After co-registration and delineation of the lumen and outer wall, segmentation of plaque components (lipid-rich necrotic cores (LRNC) and calcifications) was performed both manually and automated. Scan quality was assessed using a visual quality scale. Results Agreement for the detection of LRNC (Cohen’s kappa (k) is 0.04) and calcification (k = 0.41) between both manual and automated segmentation methods was poor. In the high-quality scans (visual quality score ≥ 3), the agreement between manual and automated segmentation increased to k = 0.55 and k = 0.58 for, respectively, the detection of LRNC and calcification larger than 1 mm2. Both manual and automated analysis showed good interscan reproducibility for the quantification of LRNC (intraclass correlation coefficient (ICC) of 0.94 and 0.80 respectively) and calcified plaque area (ICC of 0.95 and 0.77, respectively). Conclusion Agreement between manual and automated segmentation of LRNC and calcifications was poor, despite a good interscan reproducibility of both methods. The agreement between both methods increased to moderate in high quality scans. These findings indicate that image quality is a critical determinant of the performance of both manual and automated segmentation of carotid artery plaque components. PMID:27930665

Using Computer-Extracted Data from Electronic Health Records to Measure the Quality of Adolescent Well-Care

PubMed Central

Gardner, William; Morton, Suzanne; Byron, Sepheen C; Tinoco, Aldo; Canan, Benjamin D; Leonhart, Karen; Kong, Vivian; Scholle, Sarah Hudson

2014-01-01

Objective To determine whether quality measures based on computer-extracted EHR data can reproduce findings based on data manually extracted by reviewers. Data Sources We studied 12 measures of care indicated for adolescent well-care visits for 597 patients in three pediatric health systems. Study Design Observational study. Data Collection/Extraction Methods Manual reviewers collected quality data from the EHR. Site personnel programmed their EHR systems to extract the same data from structured fields in the EHR according to national health IT standards. Principal Findings Overall performance measured via computer-extracted data was 21.9 percent, compared with 53.2 percent for manual data. Agreement measures were high for immunizations. Otherwise, agreement between computer extraction and manual review was modest (Kappa = 0.36) because computer-extracted data frequently missed care events (sensitivity = 39.5 percent). Measure validity varied by health care domain and setting. A limitation of our findings is that we studied only three domains and three sites. Conclusions The accuracy of computer-extracted EHR quality reporting depends on the use of structured data fields, with the highest agreement found for measures and in the setting that had the greatest concentration of structured fields. We need to improve documentation of care, data extraction, and adaptation of EHR systems to practice workflow. PMID:24471935

A computationally efficient method for incorporating spike waveform information into decoding algorithms.

PubMed

Ventura, Valérie; Todorova, Sonia

2015-05-01

Spike-based brain-computer interfaces (BCIs) have the potential to restore motor ability to people with paralysis and amputation, and have shown impressive performance in the lab. To transition BCI devices from the lab to the clinic, decoding must proceed automatically and in real time, which prohibits the use of algorithms that are computationally intensive or require manual tweaking. A common choice is to avoid spike sorting and treat the signal on each electrode as if it came from a single neuron, which is fast, easy, and therefore desirable for clinical use. But this approach ignores the kinematic information provided by individual neurons recorded on the same electrode. The contribution of this letter is a linear decoding model that extracts kinematic information from individual neurons without spike-sorting the electrode signals. The method relies on modeling sample averages of waveform features as functions of kinematics, which is automatic and requires minimal data storage and computation. In offline reconstruction of arm trajectories of a nonhuman primate performing reaching tasks, the proposed method performs as well as decoders based on expertly manually and automatically sorted spikes.

A Minimal Path Searching Approach for Active Shape Model (ASM)-based Segmentation of the Lung.

PubMed

Guo, Shengwen; Fei, Baowei

2009-03-27

We are developing a minimal path searching method for active shape model (ASM)-based segmentation for detection of lung boundaries on digital radiographs. With the conventional ASM method, the position and shape parameters of the model points are iteratively refined and the target points are updated by the least Mahalanobis distance criterion. We propose an improved searching strategy that extends the searching points in a fan-shape region instead of along the normal direction. A minimal path (MP) deformable model is applied to drive the searching procedure. A statistical shape prior model is incorporated into the segmentation. In order to keep the smoothness of the shape, a smooth constraint is employed to the deformable model. To quantitatively assess the ASM-MP segmentation, we compare the automatic segmentation with manual segmentation for 72 lung digitized radiographs. The distance error between the ASM-MP and manual segmentation is 1.75 ± 0.33 pixels, while the error is 1.99 ± 0.45 pixels for the ASM. Our results demonstrate that our ASM-MP method can accurately segment the lung on digital radiographs.

A minimal path searching approach for active shape model (ASM)-based segmentation of the lung

NASA Astrophysics Data System (ADS)

Guo, Shengwen; Fei, Baowei

2009-02-01

We are developing a minimal path searching method for active shape model (ASM)-based segmentation for detection of lung boundaries on digital radiographs. With the conventional ASM method, the position and shape parameters of the model points are iteratively refined and the target points are updated by the least Mahalanobis distance criterion. We propose an improved searching strategy that extends the searching points in a fan-shape region instead of along the normal direction. A minimal path (MP) deformable model is applied to drive the searching procedure. A statistical shape prior model is incorporated into the segmentation. In order to keep the smoothness of the shape, a smooth constraint is employed to the deformable model. To quantitatively assess the ASM-MP segmentation, we compare the automatic segmentation with manual segmentation for 72 lung digitized radiographs. The distance error between the ASM-MP and manual segmentation is 1.75 +/- 0.33 pixels, while the error is 1.99 +/- 0.45 pixels for the ASM. Our results demonstrate that our ASM-MP method can accurately segment the lung on digital radiographs.

A Minimal Path Searching Approach for Active Shape Model (ASM)-based Segmentation of the Lung

PubMed Central

Guo, Shengwen; Fei, Baowei

2013-01-01

We are developing a minimal path searching method for active shape model (ASM)-based segmentation for detection of lung boundaries on digital radiographs. With the conventional ASM method, the position and shape parameters of the model points are iteratively refined and the target points are updated by the least Mahalanobis distance criterion. We propose an improved searching strategy that extends the searching points in a fan-shape region instead of along the normal direction. A minimal path (MP) deformable model is applied to drive the searching procedure. A statistical shape prior model is incorporated into the segmentation. In order to keep the smoothness of the shape, a smooth constraint is employed to the deformable model. To quantitatively assess the ASM-MP segmentation, we compare the automatic segmentation with manual segmentation for 72 lung digitized radiographs. The distance error between the ASM-MP and manual segmentation is 1.75 ± 0.33 pixels, while the error is 1.99 ± 0.45 pixels for the ASM. Our results demonstrate that our ASM-MP method can accurately segment the lung on digital radiographs. PMID:24386531

40 CFR 53.2 - General requirements for a reference method determination.

Code of Federal Regulations, 2010 CFR

2010-07-01

...) Manual methods—(1) Sulfur dioxide (SO 2 ) and lead. For measuring SO2 and lead, appendices A and G of part 50 of this chapter specify unique manual FRM for measuring these pollutants. Except as provided in § 53.16, other manual methods for SO2 and lead will not be considered for FRM determinations under this...

SU-C-BRA-05: Delineating High-Dose Clinical Target Volumes for Head and Neck Tumors Using Machine Learning Algorithms

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

Cardenas, C; The University of Texas Graduate School of Biomedical Sciences, Houston, TX; Wong, A

Purpose: To develop and test population-based machine learning algorithms for delineating high-dose clinical target volumes (CTVs) in H&N tumors. Automating and standardizing the contouring of CTVs can reduce both physician contouring time and inter-physician variability, which is one of the largest sources of uncertainty in H&N radiotherapy. Methods: Twenty-five node-negative patients treated with definitive radiotherapy were selected (6 right base of tongue, 11 left and 9 right tonsil). All patients had GTV and CTVs manually contoured by an experienced radiation oncologist prior to treatment. This contouring process, which is driven by anatomical, pathological, and patient specific information, typically results inmore » non-uniform margin expansions about the GTV. Therefore, we tested two methods to delineate high-dose CTV given a manually-contoured GTV: (1) regression-support vector machines(SVM) and (2) classification-SVM. These models were trained and tested on each patient group using leave-one-out cross-validation. The volume difference(VD) and Dice similarity coefficient(DSC) between the manual and auto-contoured CTV were calculated to evaluate the results. Distances from GTV-to-CTV were computed about each patient’s GTV and these distances, in addition to distances from GTV to surrounding anatomy in the expansion direction, were utilized in the regression-SVM method. The classification-SVM method used categorical voxel-information (GTV, selected anatomical structures, else) from a 3×3×3cm3 ROI centered about the voxel to classify voxels as CTV. Results: Volumes for the auto-contoured CTVs ranged from 17.1 to 149.1cc and 17.4 to 151.9cc; the average(range) VD between manual and auto-contoured CTV were 0.93 (0.48–1.59) and 1.16(0.48–1.97); while average(range) DSC values were 0.75(0.59–0.88) and 0.74(0.59–0.81) for the regression-SVM and classification-SVM methods, respectively. Conclusion: We developed two novel machine learning methods to delineate high-dose CTV for H&N patients. Both methods showed promising results that hint to a solution to the standardization of the contouring process of clinical target volumes. Varian Medical Systems grant.« less

Constraint factor graph cut-based active contour method for automated cellular image segmentation in RNAi screening.

PubMed

Chen, C; Li, H; Zhou, X; Wong, S T C

2008-05-01

Image-based, high throughput genome-wide RNA interference (RNAi) experiments are increasingly carried out to facilitate the understanding of gene functions in intricate biological processes. Automated screening of such experiments generates a large number of images with great variations in image quality, which makes manual analysis unreasonably time-consuming. Therefore, effective techniques for automatic image analysis are urgently needed, in which segmentation is one of the most important steps. This paper proposes a fully automatic method for cells segmentation in genome-wide RNAi screening images. The method consists of two steps: nuclei and cytoplasm segmentation. Nuclei are extracted and labelled to initialize cytoplasm segmentation. Since the quality of RNAi image is rather poor, a novel scale-adaptive steerable filter is designed to enhance the image in order to extract long and thin protrusions on the spiky cells. Then, constraint factor GCBAC method and morphological algorithms are combined to be an integrated method to segment tight clustered cells. Compared with the results obtained by using seeded watershed and the ground truth, that is, manual labelling results by experts in RNAi screening data, our method achieves higher accuracy. Compared with active contour methods, our method consumes much less time. The positive results indicate that the proposed method can be applied in automatic image analysis of multi-channel image screening data.

Association between heart rate variability and manual pulse rate.

PubMed

Hart, John

2013-09-01

One model for neurological assessment in chiropractic pertains to autonomic variability, tested commonly with heart rate variability (HRV). Since HRV may not be convenient to use on all patient visits, more user-friendly methods may help fill-in the gaps. Accordingly, this study tests the association between manual pulse rate and heart rate variability. The manual rates were also compared to the heart rate derived from HRV. Forty-eight chiropractic students were examined with heart rate variability (SDNN and mean heart rate) and two manual radial pulse rate measurements. Inclusion criteria consisted of participants being chiropractic students. Exclusion criteria for 46 of the participants consisted of a body mass index being greater than 30, age greater than 35, and history of: a) dizziness upon standing, b) treatment of psychiatric disorders, and c) diabetes. No exclusion criteria were applied to the remaining two participants who were also convenience sample volunteers. Linear associations between the manual pulse rate methods and the two heart rate variability measures (SDNN and mean heart) were tested with Pearson's correlation and simple linear regression. Moderate strength inverse (expected) correlations were observed between both manual pulse rate methods and SDNN (r = -0.640, 95% CI -0.781, -0.435; r = -0.632, 95% CI -0.776, -0.425). Strong direct (expected) relationships were observed between the manual pulse rate methods and heart rate derived from HRV technology (r = 0.934, 95% CI 0.885, 0.962; r = 0.941, 95% CI 0.897, 0.966). Manual pulse rates may be a useful option for assessing autonomic variability. Furthermore, this study showed a strong relationship between manual pulse rates and heart rate derived from HRV technology.

Comparison of automated erythrocytapheresis versus manual exchange transfusion to treat cerebral macrovasculopathy in sickle cell anemia.

PubMed

Koehl, Bérengère; Sommet, Julie; Holvoet, Laurent; Abdoul, Hendy; Boizeau, Priscilla; Ithier, Ghislaine; Missud, Florence; Couque, Nathalie; Verlhac, Suzanne; Voultoury, Pauline; Sellami, Fatiha; Baruchel, André; Benkerrou, Malika

2016-05-01

Chronic exchange transfusion is effective for primary and secondary prevention of stroke in children with sickle cell anemia (SCA). Erythrocytapheresis is recognized to be the most efficient approach; however, it is not widely implemented and is not suitable for all patients. The aim of our study was to compare automated exchange transfusion (AET) with our manual method of exchange transfusion and, in particular, to evaluate the efficacy, safety, and cost of our manual method. Thirty-nine SCA children with stroke and/or abnormal findings on transcranial Doppler were included in the study. We retrospectively analyzed 1353 exchange sessions, including 333 sessions of AET and 1020 sessions of manual exchange transfusion (MET). Both methods were well tolerated. The median decrease in hemoglobin (Hb)S per session was 21.5% with AET and 18.8% with our manual method (p < 0.0001) with no major increase in red blood cell consumption. Iron overload was well controlled, even with the manual method, with a median (interquartile range) ferritin level of 312 (152-994) µg/L after 24 months of transfusions. The main differences in annual cost relate to equipment costs, which were 74 times higher with the automated method. Our study shows that continuous MET has comparable efficacy to the automated method in terms of stroke prevention, decrease in HbS, and iron overload prevention. It is feasible in all hospital settings and is often combined with AET successively over time. © 2016 AABB.

Somatostatin receptor immunohistochemistry in neuroendocrine tumors: comparison between manual and automated evaluation

PubMed Central

Daniel, Kaemmerer; Maria, Athelogou; Amelie, Lupp; Isabell, Lenhardt; Stefan, Schulz; Luisa, Peter; Merten, Hommann; Vikas, Prasad; Gerd, Binnig; Paul, Baum Richard

2014-01-01

Background: Manual evaluation of somatostatin receptor (SSTR) immunohistochemistry (IHC) is a time-consuming and cost-intensive procedure. Aim of the study was to compare manual evaluation of SSTR subtype IHC to an automated software-based analysis, and to in-vivo imaging by SSTR-based PET/CT. Methods: We examined 25 gastroenteropancreatic neuroendocrine tumor (GEP-NET) patients and correlated their in-vivo SSTR-PET/CT data (determined by the standardized uptake values SUVmax,-mean) with the corresponding ex-vivo IHC data of SSTR subtype (1, 2A, 4, 5) expression. Exactly the same lesions were imaged by PET/CT, resected and analyzed by IHC in each patient. After manual evaluation, the IHC slides were digitized and automatically evaluated for SSTR expression by Definiens XD software. A virtual IHC score “BB1” was created for comparing the manual and automated analysis of SSTR expression. Results: BB1 showed a significant correlation with the corresponding conventionally determined Her2/neu score of the SSTR-subtypes 2A (rs: 0.57), 4 (rs: 0.44) and 5 (rs: 0.43). BB1 of SSTR2A also significantly correlated with the SUVmax (rs: 0.41) and the SUVmean (rs: 0.50). Likewise, a significant correlation was seen between the conventionally evaluated SSTR2A status and the SUVmax (rs: 0.42) and SUVmean (rs: 0.62).Conclusion: Our data demonstrate that the evaluation of the SSTR status by automated analysis (BB1 score), using digitized histopathology slides (“virtual microscopy”), corresponds well with the SSTR2A, 4 and 5 expression as determined by conventional manual histopathology. The BB1 score also exhibited a significant association to the SSTR-PET/CT data in accordance with the high affinity profile of the SSTR analogues used for imaging. PMID:25197368

Machine-Learning Algorithms to Code Public Health Spending Accounts.

PubMed

Brady, Eoghan S; Leider, Jonathon P; Resnick, Beth A; Alfonso, Y Natalia; Bishai, David

Government public health expenditure data sets require time- and labor-intensive manipulation to summarize results that public health policy makers can use. Our objective was to compare the performances of machine-learning algorithms with manual classification of public health expenditures to determine if machines could provide a faster, cheaper alternative to manual classification. We used machine-learning algorithms to replicate the process of manually classifying state public health expenditures, using the standardized public health spending categories from the Foundational Public Health Services model and a large data set from the US Census Bureau. We obtained a data set of 1.9 million individual expenditure items from 2000 to 2013. We collapsed these data into 147 280 summary expenditure records, and we followed a standardized method of manually classifying each expenditure record as public health, maybe public health, or not public health. We then trained 9 machine-learning algorithms to replicate the manual process. We calculated recall, precision, and coverage rates to measure the performance of individual and ensembled algorithms. Compared with manual classification, the machine-learning random forests algorithm produced 84% recall and 91% precision. With algorithm ensembling, we achieved our target criterion of 90% recall by using a consensus ensemble of ≥6 algorithms while still retaining 93% coverage, leaving only 7% of the summary expenditure records unclassified. Machine learning can be a time- and cost-saving tool for estimating public health spending in the United States. It can be used with standardized public health spending categories based on the Foundational Public Health Services model to help parse public health expenditure information from other types of health-related spending, provide data that are more comparable across public health organizations, and evaluate the impact of evidence-based public health resource allocation.

An ensemble deep learning based approach for red lesion detection in fundus images.

PubMed

Orlando, José Ignacio; Prokofyeva, Elena; Del Fresno, Mariana; Blaschko, Matthew B

2018-01-01

Diabetic retinopathy (DR) is one of the leading causes of preventable blindness in the world. Its earliest sign are red lesions, a general term that groups both microaneurysms (MAs) and hemorrhages (HEs). In daily clinical practice, these lesions are manually detected by physicians using fundus photographs. However, this task is tedious and time consuming, and requires an intensive effort due to the small size of the lesions and their lack of contrast. Computer-assisted diagnosis of DR based on red lesion detection is being actively explored due to its improvement effects both in clinicians consistency and accuracy. Moreover, it provides comprehensive feedback that is easy to assess by the physicians. Several methods for detecting red lesions have been proposed in the literature, most of them based on characterizing lesion candidates using hand crafted features, and classifying them into true or false positive detections. Deep learning based approaches, by contrast, are scarce in this domain due to the high expense of annotating the lesions manually. In this paper we propose a novel method for red lesion detection based on combining both deep learned and domain knowledge. Features learned by a convolutional neural network (CNN) are augmented by incorporating hand crafted features. Such ensemble vector of descriptors is used afterwards to identify true lesion candidates using a Random Forest classifier. We empirically observed that combining both sources of information significantly improve results with respect to using each approach separately. Furthermore, our method reported the highest performance on a per-lesion basis on DIARETDB1 and e-ophtha, and for screening and need for referral on MESSIDOR compared to a second human expert. Results highlight the fact that integrating manually engineered approaches with deep learned features is relevant to improve results when the networks are trained from lesion-level annotated data. An open source implementation of our system is publicly available at https://github.com/ignaciorlando/red-lesion-detection. Copyright © 2017 Elsevier B.V. All rights reserved.

TH-CD-206-02: BEST IN PHYSICS (IMAGING): 3D Prostate Segmentation in MR Images Using Patch-Based Anatomical Signature

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

Yang, X; Jani, A; Rossi, P

Purpose: MRI has shown promise in identifying prostate tumors with high sensitivity and specificity for the detection of prostate cancer. Accurate segmentation of the prostate plays a key role various tasks: to accurately localize prostate boundaries for biopsy needle placement and radiotherapy, to initialize multi-modal registration algorithms or to obtain the region of interest for computer-aided detection of prostate cancer. However, manual segmentation during biopsy or radiation therapy can be time consuming and subject to inter- and intra-observer variation. This study’s purpose it to develop an automated method to address this technical challenge. Methods: We present an automated multi-atlas segmentationmore » for MR prostate segmentation using patch-based label fusion. After an initial preprocessing for all images, all the atlases are non-rigidly registered to a target image. And then, the resulting transformation is used to propagate the anatomical structure labels of the atlas into the space of the target image. The top L similar atlases are further chosen by measuring intensity and structure difference in the region of interest around prostate. Finally, using voxel weighting based on patch-based anatomical signature, the label that the majority of all warped labels predict for each voxel is used for the final segmentation of the target image. Results: This segmentation technique was validated with a clinical study of 13 patients. The accuracy of our approach was assessed using the manual segmentation (gold standard). The mean volume Dice Overlap Coefficient was 89.5±2.9% between our and manual segmentation, which indicate that the automatic segmentation method works well and could be used for 3D MRI-guided prostate intervention. Conclusion: We have developed a new prostate segmentation approach based on the optimal feature learning label fusion framework, demonstrated its clinical feasibility, and validated its accuracy. This segmentation technique could be a useful tool in image-guided interventions for prostate-cancer diagnosis and treatment.« less

Computational Methods for Analyzing Health News Coverage

ERIC Educational Resources Information Center

McFarlane, Delano J.

2011-01-01

Researchers that investigate the media's coverage of health have historically relied on keyword searches to retrieve relevant health news coverage, and manual content analysis methods to categorize and score health news text. These methods are problematic. Manual content analysis methods are labor intensive, time consuming, and inherently…

Manuals Used in the National Aquatic Resource Surveys

EPA Pesticide Factsheets

Various manuals are used to communicate the methods and guidelines for the National Aquatic Resource Surveys. The Field Operations Manual: outlines the field protocols that crews will utilize to sample sites.

An automated method for accurate vessel segmentation.

PubMed

Yang, Xin; Liu, Chaoyue; Le Minh, Hung; Wang, Zhiwei; Chien, Aichi; Cheng, Kwang-Ting Tim

2017-05-07

Vessel segmentation is a critical task for various medical applications, such as diagnosis assistance of diabetic retinopathy, quantification of cerebral aneurysm's growth, and guiding surgery in neurosurgical procedures. Despite technology advances in image segmentation, existing methods still suffer from low accuracy for vessel segmentation in the two challenging while common scenarios in clinical usage: (1) regions with a low signal-to-noise-ratio (SNR), and (2) at vessel boundaries disturbed by adjacent non-vessel pixels. In this paper, we present an automated system which can achieve highly accurate vessel segmentation for both 2D and 3D images even under these challenging scenarios. Three key contributions achieved by our system are: (1) a progressive contrast enhancement method to adaptively enhance contrast of challenging pixels that were otherwise indistinguishable, (2) a boundary refinement method to effectively improve segmentation accuracy at vessel borders based on Canny edge detection, and (3) a content-aware region-of-interests (ROI) adjustment method to automatically determine the locations and sizes of ROIs which contain ambiguous pixels and demand further verification. Extensive evaluation of our method is conducted on both 2D and 3D datasets. On a public 2D retinal dataset (named DRIVE (Staal 2004 IEEE Trans. Med. Imaging 23 501-9)) and our 2D clinical cerebral dataset, our approach achieves superior performance to the state-of-the-art methods including a vesselness based method (Frangi 1998 Int. Conf. on Medical Image Computing and Computer-Assisted Intervention) and an optimally oriented flux (OOF) based method (Law and Chung 2008 European Conf. on Computer Vision). An evaluation on 11 clinical 3D CTA cerebral datasets shows that our method can achieve 94% average accuracy with respect to the manual segmentation reference, which is 23% to 33% better than the five baseline methods (Yushkevich 2006 Neuroimage 31 1116-28; Law and Chung 2008 European Conf. on Computer Vision; Law and Chung 2009 IEEE Trans. Image Process. 18 596-612; Wang 2015 J. Neurosci. Methods 241 30-6) with manually optimized parameters. Our system has also been applied clinically for cerebral aneurysm development analysis. Experimental results on 10 patients' data, with two 3D CT scans per patient, show that our system's automatic diagnosis outcomes are consistent with clinicians' manual measurements.

An automated method for accurate vessel segmentation

NASA Astrophysics Data System (ADS)

Yang, Xin; Liu, Chaoyue; Le Minh, Hung; Wang, Zhiwei; Chien, Aichi; (Tim Cheng, Kwang-Ting

2017-05-01

Vessel segmentation is a critical task for various medical applications, such as diagnosis assistance of diabetic retinopathy, quantification of cerebral aneurysm’s growth, and guiding surgery in neurosurgical procedures. Despite technology advances in image segmentation, existing methods still suffer from low accuracy for vessel segmentation in the two challenging while common scenarios in clinical usage: (1) regions with a low signal-to-noise-ratio (SNR), and (2) at vessel boundaries disturbed by adjacent non-vessel pixels. In this paper, we present an automated system which can achieve highly accurate vessel segmentation for both 2D and 3D images even under these challenging scenarios. Three key contributions achieved by our system are: (1) a progressive contrast enhancement method to adaptively enhance contrast of challenging pixels that were otherwise indistinguishable, (2) a boundary refinement method to effectively improve segmentation accuracy at vessel borders based on Canny edge detection, and (3) a content-aware region-of-interests (ROI) adjustment method to automatically determine the locations and sizes of ROIs which contain ambiguous pixels and demand further verification. Extensive evaluation of our method is conducted on both 2D and 3D datasets. On a public 2D retinal dataset (named DRIVE (Staal 2004 IEEE Trans. Med. Imaging 23 501-9)) and our 2D clinical cerebral dataset, our approach achieves superior performance to the state-of-the-art methods including a vesselness based method (Frangi 1998 Int. Conf. on Medical Image Computing and Computer-Assisted Intervention) and an optimally oriented flux (OOF) based method (Law and Chung 2008 European Conf. on Computer Vision). An evaluation on 11 clinical 3D CTA cerebral datasets shows that our method can achieve 94% average accuracy with respect to the manual segmentation reference, which is 23% to 33% better than the five baseline methods (Yushkevich 2006 Neuroimage 31 1116-28; Law and Chung 2008 European Conf. on Computer Vision; Law and Chung 2009 IEEE Trans. Image Process. 18 596-612; Wang 2015 J. Neurosci. Methods 241 30-6) with manually optimized parameters. Our system has also been applied clinically for cerebral aneurysm development analysis. Experimental results on 10 patients’ data, with two 3D CT scans per patient, show that our system’s automatic diagnosis outcomes are consistent with clinicians’ manual measurements.

Carpal tunnel syndrome: Investigating the sensitivity of initial-diagnosis with electro-diagnostic tests in 600 cases and associated risk factors especially manual milking.

PubMed

Tunç, Abdulkadir; Güngen, Belma Doğan

2017-01-01

Electro-diagnostic studies are the most reliable methods in diagnosis of carpal tunnel syndrome (CTS). Although there are many risk factors associated with CTS, there are a limited number of studies in the literature indicating that manual milking, which is frequently seen in Turkey, is a risk factor for CTS. The purpose of this study was to evaluate demographic findings of cases referred due to initial diagnosis of CTS as well as aetiological data especially manual milking and to investigate the sensitivity of initial diagnosis of CTS. Six hundred patients, who were referred to our electromyography laboratory due to initial diagnosis of CTS, were included. Demographic findings, duration of complaints, existence of diabetes mellitus, and manual milking histories of all patients were recorded. Sensitivity of initial diagnosis was investigated based on electro-diagnostic test results. According to electro-diagnostic test results, 289 of the patients were diagnosed with CTS (48.17%). 110 (18.3%) of 600 patients had a history of manual milking. In 94 of this group (85.4%), CTS was detected. Statistically significant correlation was found between CTS and age, female gender, duration of complaints, obesity and manual milking. This study confirms that manual milking is an important risk factor for CTS in addition to female gender, age, symptom duration and obesity. The fact that sensitivity of initial diagnosis of CTS was found to be low according to electro-diagnostic test results indicates importance of detailed clinical evaluation.

User manual for Blossom statistical package for R

USGS Publications Warehouse

Talbert, Marian; Cade, Brian S.

2005-01-01

Blossom is an R package with functions for making statistical comparisons with distance-function based permutation tests developed by P.W. Mielke, Jr. and colleagues at Colorado State University (Mielke and Berry, 2001) and for testing parameters estimated in linear models with permutation procedures developed by B. S. Cade and colleagues at the Fort Collins Science Center, U.S. Geological Survey. This manual is intended to provide identical documentation of the statistical methods and interpretations as the manual by Cade and Richards (2005) does for the original Fortran program, but with changes made with respect to command inputs and outputs to reflect the new implementation as a package for R (R Development Core Team, 2012). This implementation in R has allowed for numerous improvements not supported by the Cade and Richards (2005) Fortran implementation, including use of categorical predictor variables in most routines.

User's manual for three dimensional FDTD version C code for scattering from frequency-independent dielectric and magnetic materials

NASA Technical Reports Server (NTRS)

Beggs, John H.; Luebbers, Raymond J.; Kunz, Karl S.

1991-01-01

The Penn State Finite Difference Time Domain Electromagnetic Scattering Code Version C is a three dimensional numerical electromagnetic scattering code based upon the Finite Difference Time Domain Technique (FDTD). The supplied version of the code is one version of our current three dimensional FDTD code set. This manual provides a description of the code and corresponding results for several scattering problems. The manual is organized into fourteen sections: introduction, description of the FDTD method, operation, resource requirements, Version C code capabilities, a brief description of the default scattering geometry, a brief description of each subroutine, a description of the include file (COMMONC.FOR), a section briefly discussing Radar Cross Section (RCS) computations, a section discussing some scattering results, a sample problem setup section, a new problem checklist, references and figure titles.

User's manual for three dimensional FDTD version D code for scattering from frequency-dependent dielectric and magnetic materials

NASA Technical Reports Server (NTRS)

Beggs, John H.; Luebbers, Raymond J.; Kunz, Karl S.

1991-01-01

The Penn State Finite Difference Time Domain Electromagnetic Scattering Code Version D is a three dimensional numerical electromagnetic scattering code based upon the Finite Difference Time Domain Technique (FDTD). The supplied version of the code is one version of our current three dimensional FDTD code set. This manual provides a description of the code and corresponding results for several scattering problems. The manual is organized into fourteen sections: introduction, description of the FDTD method, operation, resource requirements, Version D code capabilities, a brief description of the default scattering geometry, a brief description of each subroutine, a description of the include file (COMMOND.FOR), a section briefly discussing Radar Cross Section (RCS) computations, a section discussing some scattering results, a sample problem setup section, a new problem checklist, references and figure titles.

User's manual for three dimensional FDTD version A code for scattering from frequency-independent dielectric materials

NASA Technical Reports Server (NTRS)

Beggs, John H.; Luebbers, Raymond J.; Kunz, Karl S.

1992-01-01

The Penn State Finite Difference Time Domain (FDTD) Electromagnetic Scattering Code Version A is a three dimensional numerical electromagnetic scattering code based on the Finite Difference Time Domain technique. The supplied version of the code is one version of our current three dimensional FDTD code set. The manual provides a description of the code and the corresponding results for the default scattering problem. The manual is organized into 14 sections: introduction, description of the FDTD method, operation, resource requirements, Version A code capabilities, a brief description of the default scattering geometry, a brief description of each subroutine, a description of the include file (COMMONA.FOR), a section briefly discussing radar cross section (RCS) computations, a section discussing the scattering results, a sample problem setup section, a new problem checklist, references, and figure titles.

User's manual for three dimensional FDTD version C code for scattering from frequency-independent dielectric and magnetic materials

NASA Technical Reports Server (NTRS)

Beggs, John H.; Luebbers, Raymond J.; Kunz, Karl S.

1992-01-01

The Penn State Finite Difference Time Domain Electromagnetic Scattering Code Version C is a three-dimensional numerical electromagnetic scattering code based on the Finite Difference Time Domain (FDTD) technique. The supplied version of the code is one version of our current three-dimensional FDTD code set. The manual given here provides a description of the code and corresponding results for several scattering problems. The manual is organized into 14 sections: introduction, description of the FDTD method, operation, resource requirements, Version C code capabilities, a brief description of the default scattering geometry, a brief description of each subroutine, a description of the include file (COMMONC.FOR), a section briefly discussing radar cross section computations, a section discussing some scattering results, a new problem checklist, references, and figure titles.

User's manual for three dimensional FDTD version B code for scattering from frequency-dependent dielectric materials

NASA Technical Reports Server (NTRS)

Beggs, John H.; Luebbers, Raymond J.; Kunz, Karl S.

1991-01-01

The Penn State Finite Difference Time Domain Electromagnetic Scattering Code Version B is a three dimensional numerical electromagnetic scattering code based upon the Finite Difference Time Domain Technique (FDTD). The supplied version of the code is one version of our current three dimensional FDTD code set. This manual provides a description of the code and corresponding results for several scattering problems. The manual is organized into fourteen sections: introduction, description of the FDTD method, operation, resource requirements, Version B code capabilities, a brief description of the default scattering geometry, a brief description of each subroutine, a description of the include file (COMMONB.FOR), a section briefly discussing Radar Cross Section (RCS) computations, a section discussing some scattering results, a sample problem setup section, a new problem checklist, references and figure titles.

GRUMFOIL: A computer code for the viscous transonic flow over airfoils

NASA Technical Reports Server (NTRS)

Mead, H. R.; Melnik, R. E.

1985-01-01

A user's manual which describes the operation of the computer program, GRUMFOIL is presented. The program computes the viscous transonic flow over two dimensional airfoils using a boundary layer type viscid-inviscid interaction approach. The inviscid solution is obtained by a multigrid method for the full potential equation. The boundary layer solution is based on integral entrainment methods.

Colorimetric-Solid Phase Extraction Technology for Water Quality Monitoring: Evaluation of C-SPE and Debubbling Methods in Microgravity

NASA Technical Reports Server (NTRS)

Hazen-Bosveld, April; Lipert, Robert J.; Nordling, John; Shih, Chien-Ju; Siperko, Lorraine; Porter, Marc D.; Gazda, Daniel B.; Rutz, Jeff A.; Straub, John E.; Schultz, John R.;

The identification of knowledge content and function in manual labour.

PubMed

Shalin, Valerie; Verdile, Charles

2003-06-10

Calls for an alternative conceptualization of cognition for applied concerns retain the core commitment of the basic research community to abstract cognition detached from a physical environment. The present paper attempts to break out of the dominant, narrow view of cognition and cognitive domains, with a cognitive analysis of digging ditches for the utility industry. To illustrate knowledge-based cognition in manual labour excerpts are presented from the journal entries of a moderately experienced student working a summer job, organized with a representation that distinguishes between the goals and methods of work. The journal entries illustrate the functions of knowledge for interacting with a physical environment; knowledge enables the selection, execution and monitoring of work methods, the interpretation of perceptual information, the application of task completion criteria and the ability for explanation and generalization. To emphasize the generality of the functions of cognition in ditch digging, comparable functions are indicated in a domain rarely regarded as a form of manual labour: the practice of internal medicine. Discussion of the results includes the implications for cognitive theory as well as practical implications for productivity, training and task analysis.

Ergonomic assessment methodologies in manual handling of loads--opportunities in organizations.

PubMed

Pires, Claudia

2012-01-01

The present study was developed based on the analysis of workplaces in the engineering industry, particularly in automotive companies. The main objectives of the study were to evaluate the activities present in the workplace concerning manual handling, using assessment methodologies NIOSH Ergonomic Equation [1] and Manual Material Handling [2], present in ISO 11228 [3-4], and to consider the possibility of developing musculoskeletal injuries associated with these activities, an issue of great concern in all industrial sectors. Similarly, it was also shown the suitability of each method to the task concerned. The study was conducted in three steps. The first step was to collect images and information about the target tasks. As a second step proceeded to the analysis, determining the method to use and to evaluate activities. Finally, we found the results obtained and acted on accordingly. With the study observed situations considered urgent action, according to the methodologies used, and proceeded to develop solutions in order to solve the problems identified, eliminating and / or minimizing embarrassing situations and harmful to employees.

Retinal vessel segmentation using the 2-D Gabor wavelet and supervised classification.

PubMed

Soares, João V B; Leandro, Jorge J G; Cesar Júnior, Roberto M; Jelinek, Herbert F; Cree, Michael J

2006-09-01

We present a method for automated segmentation of the vasculature in retinal images. The method produces segmentations by classifying each image pixel as vessel or nonvessel, based on the pixel's feature vector. Feature vectors are composed of the pixel's intensity and two-dimensional Gabor wavelet transform responses taken at multiple scales. The Gabor wavelet is capable of tuning to specific frequencies, thus allowing noise filtering and vessel enhancement in a single step. We use a Bayesian classifier with class-conditional probability density functions (likelihoods) described as Gaussian mixtures, yielding a fast classification, while being able to model complex decision surfaces. The probability distributions are estimated based on a training set of labeled pixels obtained from manual segmentations. The method's performance is evaluated on publicly available DRIVE (Staal et al., 2004) and STARE (Hoover et al., 2000) databases of manually labeled images. On the DRIVE database, it achieves an area under the receiver operating characteristic curve of 0.9614, being slightly superior than that presented by state-of-the-art approaches. We are making our implementation available as open source MATLAB scripts for researchers interested in implementation details, evaluation, or development of methods.

[Comparison of manual and automated (MagNA Pure) nucleic acid isolation methods in molecular diagnosis of HIV infections].

PubMed

Alp, Alpaslan; Us, Dürdal; Hasçelik, Gülşen

2004-01-01

Rapid quantitative molecular methods are very important for the diagnosis of human immunodeficiency virus (HIV) infections, assessment of prognosis and follow up. The purpose of this study was to compare and evaluate the performances of conventional manual extraction method and automated MagNA Pure system, for the nucleic acid isolation step which is the first and most important step in molecular diagnosis of HIV infections. Plasma samples of 35 patients in which anti-HIV antibodies were found as positive by microparticule enzyme immunoassay and confirmed by immunoblotting method, were included in the study. The nucleic acids obtained simultaneously by manual isolation kit (Cobas Amplicor, HIV-1 Monitor Test, version 1.5, Roche Diagnostics) and automated system (MagNA Pure LC Total Nucleic Acid Isolation Kit, Roche Diagnostics), were amplified and detected in Cobas Amplicor (Roche Diagnostics) instrument. Twenty three of 35 samples (65.7%) were found to be positive, and 9 (25.7%) were negative by both of the methods. The agreement between the methods were detected as 91.4%, for qualitative results. Viral RNA copies detected by manual and MagNA Pure isolation methods were found between 76.0-7.590.000 (mean: 487.143) and 113.0-20.300.0000 (mean: 2.174.097) copies/ml, respectively. When both of the overall and individual results were evaluated, the number of RNA copies obtained with automatized system, were found higher than the manual method (p<0.05). Three samples which had low numbers of nucleic acids (113, 773, 857, respectively) with MagNA Pure, yielded negative results with manual method. In conclusion, the automatized MagNA Pure system was found to be a reliable, rapid and practical method for the isolation of HIV-RNA.

ASPECTS: an automation-assisted SPE method development system.

PubMed

Li, Ming; Chou, Judy; King, Kristopher W; Yang, Liyu

2013-07-01

A typical conventional SPE method development (MD) process usually involves deciding the chemistry of the sorbent and eluent based on information about the analyte; experimentally preparing and trying out various combinations of adsorption chemistry and elution conditions; quantitatively evaluating the various conditions; and comparing quantitative results from all combination of conditions to select the best condition for method qualification. The second and fourth steps have mostly been performed manually until now. We developed an automation-assisted system that expedites the conventional SPE MD process by automating 99% of the second step, and expedites the fourth step by automatically processing the results data and presenting it to the analyst in a user-friendly format. The automation-assisted SPE MD system greatly saves the manual labor in SPE MD work, prevents analyst errors from causing misinterpretation of quantitative results, and shortens data analysis and interpretation time.

An evaluation of coding methodologies for potential use in the Alabama Resource Information System (ARIS)-transportation study for the state of Alabama

NASA Technical Reports Server (NTRS)

Montgomery, O. L.

1977-01-01

Procedures developed for digitizing the transportation arteries, airports, and dock facilities of Alabama and placing them in a computerized format compatible with the Alabama Resource Information System are described. The time required to digitize by the following methods: (a) manual, (b) Telereadex 29 with film reading and digitizing system, and (c) digitizing tablets was evaluated. A method for digitizing and storing information from the U. T. M. grid cell base which was compatible with the system was developed and tested. The highways, navigable waterways, railroads, airports, and docks in the study area were digitized and the data stored. The manual method of digitizing was shown to be best for small amounts of data, while the graphic input from the digitizing tablets would be the best approach for entering the large amounts of data required for an entire state.

Solar and Energy Conserving Food Technologies: A Training Manual. Training for Development. Peace Corps Information Collection & Exchange Training Manual No. T-17.

ERIC Educational Resources Information Center

Farallones Inst., Occidental, CA.

Based on experience in the field, this training manual was developed to help Peace Corps trainers plan and implement inservice training programs in solar and other energy conserving food technologies for Peace Corps volunteers and community workers. Using a competency-based format, the manual contains 20 sessions (learning modules) that focus on…

Multi-atlas propagation based left atrium segmentation coupled with super-voxel based pulmonary veins delineation in late gadolinium-enhanced cardiac MRI

NASA Astrophysics Data System (ADS)

Yang, Guang; Zhuang, Xiahai; Khan, Habib; Haldar, Shouvik; Nyktari, Eva; Li, Lei; Ye, Xujiong; Slabaugh, Greg; Wong, Tom; Mohiaddin, Raad; Keegan, Jennifer; Firmin, David

2017-02-01

Late Gadolinium-Enhanced Cardiac MRI (LGE CMRI) is a non-invasive technique, which has shown promise in detecting native and post-ablation atrial scarring. To visualize the scarring, a precise segmentation of the left atrium (LA) and pulmonary veins (PVs) anatomy is performed as a first step—usually from an ECG gated CMRI roadmap acquisition—and the enhanced scar regions from the LGE CMRI images are superimposed. The anatomy of the LA and PVs in particular is highly variable and manual segmentation is labor intensive and highly subjective. In this paper, we developed a multi-atlas propagation based whole heart segmentation (WHS) to delineate the LA and PVs from ECG gated CMRI roadmap scans. While this captures the anatomy of the atrium well, the PVs anatomy is less easily visualized. The process is therefore augmented by semi-automated manual strokes for PVs identification in the registered LGE CMRI data. This allows us to extract more accurate anatomy than the fully automated WHS. Both qualitative visualization and quantitative assessment with respect to manual segmented ground truth showed that our method is efficient and effective with an overall mean Dice score of 0.91.

Comparison of cell counting methods in rodent pulmonary toxicity studies: automated and manual protocols and considerations for experimental design

PubMed Central

Zeidler-Erdely, Patti C.; Antonini, James M.; Meighan, Terence G.; Young, Shih-Houng; Eye, Tracy J.; Hammer, Mary Ann; Erdely, Aaron

2016-01-01

Pulmonary toxicity studies often use bronchoalveolar lavage (BAL) to investigate potential adverse lung responses to a particulate exposure. The BAL cellular fraction is counted, using automated (i.e. Coulter Counter®), flow cytometry or manual (i.e. hemocytometer) methods, to determine inflammatory cell influx. The goal of the study was to compare the different counting methods to determine which is optimal for examining BAL cell influx after exposure by inhalation or intratracheal instillation (ITI) to different particles with varying inherent pulmonary toxicities in both rat and mouse models. General findings indicate that total BAL cell counts using the automated and manual methods tended to agree after inhalation or ITI exposure to particle samples that are relatively nontoxic or at later time points after exposure to a pneumotoxic particle when the response resolves. However, when the initial lung inflammation and cytotoxicity was high after exposure to a pneumotoxic particle, significant differences were observed when comparing cell counts from the automated, flow cytometry and manual methods. When using total BAL cell count for differential calculations from the automated method, depending on the cell diameter size range cutoff, the data suggest that the number of lung polymorphonuclear leukocytes (PMN) varies. Importantly, the automated counts, regardless of the size cutoff, still indicated a greater number of total lung PMN when compared with the manual method, which agreed more closely with flow cytometry. The results suggest that either the manual method or flow cytometry would be better suited for BAL studies where cytotoxicity is an unknown variable. PMID:27251196

Comparison of cell counting methods in rodent pulmonary toxicity studies: automated and manual protocols and considerations for experimental design.

PubMed

Zeidler-Erdely, Patti C; Antonini, James M; Meighan, Terence G; Young, Shih-Houng; Eye, Tracy J; Hammer, Mary Ann; Erdely, Aaron

2016-08-01

Pulmonary toxicity studies often use bronchoalveolar lavage (BAL) to investigate potential adverse lung responses to a particulate exposure. The BAL cellular fraction is counted, using automated (i.e. Coulter Counter®), flow cytometry or manual (i.e. hemocytometer) methods, to determine inflammatory cell influx. The goal of the study was to compare the different counting methods to determine which is optimal for examining BAL cell influx after exposure by inhalation or intratracheal instillation (ITI) to different particles with varying inherent pulmonary toxicities in both rat and mouse models. General findings indicate that total BAL cell counts using the automated and manual methods tended to agree after inhalation or ITI exposure to particle samples that are relatively nontoxic or at later time points after exposure to a pneumotoxic particle when the response resolves. However, when the initial lung inflammation and cytotoxicity was high after exposure to a pneumotoxic particle, significant differences were observed when comparing cell counts from the automated, flow cytometry and manual methods. When using total BAL cell count for differential calculations from the automated method, depending on the cell diameter size range cutoff, the data suggest that the number of lung polymorphonuclear leukocytes (PMN) varies. Importantly, the automated counts, regardless of the size cutoff, still indicated a greater number of total lung PMN when compared with the manual method, which agreed more closely with flow cytometry. The results suggest that either the manual method or flow cytometry would be better suited for BAL studies where cytotoxicity is an unknown variable.

Determination of albumin in bronchoalveolar lavage fluid by flow-injection fluorometry using chromazurol S.

PubMed

Sato, Takaji; Saito, Yoshihiro; Chikuma, Masahiko; Saito, Yutaka; Nagai, Sonoko

2008-03-01

A highly sensitive flow injection fluorometry for the determination of albumin was developed and applied to the determination of albumin in human bronchoalveolar lavage fluids (BALF). This method is based on binding of chromazurol S (CAS) to albumin. The calibration curve was linear in the range of 5-200 microg/ml of albumin. A highly linear correlation (r=0.986) was observed between the albumin level in BALF samples (n=25) determined by the proposed method and by a conventional fluorometric method using CAS (CAS manual method). The IgG interference was lower in the CAS flow injection method than in the CAS manual method. The albumin level in BALF collected from healthy volunteers (n=10) was 58.5+/-13.1 microg/ml. The albumin levels in BALF samples obtained from patients with sarcoidosis and idiopathic pulmonary fibrosis were increased. This finding shows that the determination of albumin levels in BALF samples is useful for investigating lung diseases and that CAS flow injection method is promising in the determination of trace albumin in BALF samples, because it is sensitive and precise.

Myocardial infarct sizing by late gadolinium-enhanced MRI: Comparison of manual, full-width at half-maximum, and n-standard deviation methods.

PubMed

Zhang, Lin; Huttin, Olivier; Marie, Pierre-Yves; Felblinger, Jacques; Beaumont, Marine; Chillou, Christian DE; Girerd, Nicolas; Mandry, Damien

2016-11-01

To compare three widely used methods for myocardial infarct (MI) sizing on late gadolinium-enhanced (LGE) magnetic resonance (MR) images: manual delineation and two semiautomated techniques (full-width at half-maximum [FWHM] and n-standard deviation [SD]). 3T phase-sensitive inversion-recovery (PSIR) LGE images of 114 patients after an acute MI (2-4 days and 6 months) were analyzed by two independent observers to determine both total and core infarct sizes (TIS/CIS). Manual delineation served as the reference for determination of optimal thresholds for semiautomated methods after thresholding at multiple values. Reproducibility and accuracy were expressed as overall bias ± 95% limits of agreement. Mean infarct sizes by manual methods were 39.0%/24.4% for the acute MI group (TIS/CIS) and 29.7%/17.3% for the chronic MI group. The optimal thresholds (ie, providing the closest mean value to the manual method) were FWHM30% and 3SD for the TIS measurement and FWHM45% and 6SD for the CIS measurement (paired t-test; all P > 0.05). The best reproducibility was obtained using FWHM. For TIS measurement in the acute MI group, intra-/interobserver agreements, from Bland-Altman analysis, with FWHM30%, 3SD, and manual were -0.02 ± 7.74%/-0.74 ± 5.52%, 0.31 ± 9.78%/2.96 ± 16.62% and -2.12 ± 8.86%/0.18 ± 16.12, respectively; in the chronic MI group, the corresponding values were 0.23 ± 3.5%/-2.28 ± 15.06, -0.29 ± 10.46%/3.12 ± 13.06% and 1.68 ± 6.52%/-2.88 ± 9.62%, respectively. A similar trend for reproducibility was obtained for CIS measurement. However, semiautomated methods produced inconsistent results (variabilities of 24-46%) compared to manual delineation. The FWHM technique was the most reproducible method for infarct sizing both in acute and chronic MI. However, both FWHM and n-SD methods showed limited accuracy compared to manual delineation. J. Magn. Reson. Imaging 2016;44:1206-1217. © 2016 International Society for Magnetic Resonance in Medicine.

Chemically assisted somatic cell nuclear transfer without micromanipulator in the goat: effects of demecolcine, cytochalasin-B, and MG-132 on the efficiency of a manual method of oocyte enucleation using a pulled Pasteur pipette.

PubMed

Hosseini, S M; Hajian, M; Forouzanfar, M; Ostadhosseini, S; Moulavi, F; Ghanaei, H R; Gourbai, H; Shahverdi, A H; Vosough, A D; Nasr-Esfahani, M H

2015-07-01

The present study aimed to facilitate widespread application of a previously described manual method of somatic cell nuclear transfer (SCNT) by investigating the effects of demecolcine (a microtubule-depolymerizing chemical), cytochalasin-B (a microfilament-depolymerizing chemical: 2.5μg/ml for 15min) and MG-132 (a proteasome inhibitor chemical) on the (i) incidence of cytoplasmic protrusion of MII chromosomes, (ii) improvement of manual oocyte enucleation, and (iii) in vitro and in vivo developmental competence of SCNT embryos in the goat. Following in vitro maturation, around 65% of goat oocytes contained a characteristic cytoplasmic protrusion of MII-chromosomes. Treatment with demecolcine (0.4μg/ml for 30min) significantly increased this rate to 92.2±4.5%. Treatment with MG-132 (2μM for 30min) could not improve this rate when used alone (61.4±11.5%), but when combined with demecolcine (86.4±8.1%). Treatment with cytochalasin-B completely suppressed this rate whenever used, either alone (7.7±5.1%) or in combination with demecolcine (3.9±1.3%). In a direct comparison, there was no significant difference in quantity and quality of embryos propagated by the manual vs. micromanipulation-based methods of SCNT (cleavage: 85.3±4.5 vs. 89.5±8.9%, blastocyst: 19.5±4.3 vs. 24.3±4.4%, grade 1 and 2 blastocyst: 33.8±7.1 vs. 29.5±6.3%, total cell count: 125±11.1 vs. 122±10.5, respectively). Furthermore, development to live kids at term was not significant between the two SCNT methods. From both technical and economical points of view, the overall in vitro and in vivo efficiency of this manual method of SCNT proved it a simple, fast and efficient alternative for large scale production of cloned goats. Copyright © 2015 Elsevier B.V. All rights reserved.

Robust estimation of carotid artery wall motion using the elasticity-based state-space approach.

PubMed

Gao, Zhifan; Xiong, Huahua; Liu, Xin; Zhang, Heye; Ghista, Dhanjoo; Wu, Wanqing; Li, Shuo

2017-04-01

The dynamics of the carotid artery wall has been recognized as a valuable indicator to evaluate the status of atherosclerotic disease in the preclinical stage. However, it is still a challenge to accurately measure this dynamics from ultrasound images. This paper aims at developing an elasticity-based state-space approach for accurately measuring the two-dimensional motion of the carotid artery wall from the ultrasound imaging sequences. In our approach, we have employed a linear elasticity model of the carotid artery wall, and converted it into the state space equation. Then, the two-dimensional motion of carotid artery wall is computed by solving this state-space approach using the H ∞ filter and the block matching method. In addition, a parameter training strategy is proposed in this study for dealing with the parameter initialization problem. In our experiment, we have also developed an evaluation function to measure the tracking accuracy of the motion of the carotid artery wall by considering the influence of the sizes of the two blocks (acquired by our approach and the manual tracing) containing the same carotid wall tissue and their overlapping degree. Then, we have compared the performance of our approach with the manual traced results drawn by three medical physicians on 37 healthy subjects and 103 unhealthy subjects. The results have showed that our approach was highly correlated (Pearson's correlation coefficient equals 0.9897 for the radial motion and 0.9536 for the longitudinal motion), and agreed well (width the 95% confidence interval is 89.62 µm for the radial motion and 387.26 µm for the longitudinal motion) with the manual tracing method. We also compared our approach to the three kinds of previous methods, including conventional block matching methods, Kalman-based block matching methods and the optical flow. Altogether, we have been able to successfully demonstrate the efficacy of our elasticity-model based state-space approach (EBS) for more accurate tracking of the 2-dimensional motion of the carotid artery wall, towards more effective assessment of the status of atherosclerotic disease in the preclinical stage. Copyright © 2017 Elsevier B.V. All rights reserved.

An advanced method for classifying atmospheric circulation types based on prototypes connectivity graph

NASA Astrophysics Data System (ADS)

Zagouras, Athanassios; Argiriou, Athanassios A.; Flocas, Helena A.; Economou, George; Fotopoulos, Spiros

2012-11-01

Classification of weather maps at various isobaric levels as a methodological tool is used in several problems related to meteorology, climatology, atmospheric pollution and to other fields for many years. Initially the classification was performed manually. The criteria used by the person performing the classification are features of isobars or isopleths of geopotential height, depending on the type of maps to be classified. Although manual classifications integrate the perceptual experience and other unquantifiable qualities of the meteorology specialists involved, these are typically subjective and time consuming. Furthermore, during the last years different approaches of automated methods for atmospheric circulation classification have been proposed, which present automated and so-called objective classifications. In this paper a new method of atmospheric circulation classification of isobaric maps is presented. The method is based on graph theory. It starts with an intelligent prototype selection using an over-partitioning mode of fuzzy c-means (FCM) algorithm, proceeds to a graph formulation for the entire dataset and produces the clusters based on the contemporary dominant sets clustering method. Graph theory is a novel mathematical approach, allowing a more efficient representation of spatially correlated data, compared to the classical Euclidian space representation approaches, used in conventional classification methods. The method has been applied to the classification of 850 hPa atmospheric circulation over the Eastern Mediterranean. The evaluation of the automated methods is performed by statistical indexes; results indicate that the classification is adequately comparable with other state-of-the-art automated map classification methods, for a variable number of clusters.

SRM Manual, Selected Resource Materials: Description and Evaluation.

ERIC Educational Resources Information Center

Alberta Dept. of Education, Edmonton. Special Educational Services Branch.

Provided in the manual is descriptive and evaluative information on 67 instructional materials or programs frequently used with exceptional children in Alberta schools. A flow chart describes the three methods of using the manual: l) to obtain descriptive and evaluative information of an instruction program in the manual 2) to classify and record…

Validation of newly developed and redesigned key indicator methods for assessment of different working conditions with physical workloads based on mixed-methods design: a study protocol

PubMed Central

Liebers, Falk; Brandstädt, Felix; Schust, Marianne; Serafin, Patrick; Schäfer, Andreas; Gebhardt, Hansjürgen; Hartmann, Bernd; Steinberg, Ulf

2017-01-01

Introduction The impact of work-related musculoskeletal disorders is considerable. The assessment of work tasks with physical workloads is crucial to estimate the work-related health risks of exposed employees. Three key indicator methods are available for risk assessment regarding manual lifting, holding and carrying of loads; manual pulling and pushing of loads; and manual handling operations. Three further KIMs for risk assessment regarding whole-body forces, awkward body postures and body movement have been developed de novo. In addition, the development of a newly drafted combined method for mixed exposures is planned. All methods will be validated regarding face validity, reliability, convergent validity, criterion validity and further aspects of utility under practical conditions. Methods and analysis As part of the joint project MEGAPHYS (multilevel risk assessment of physical workloads), a mixed-methods study is being designed for the validation of KIMs and conducted in companies of different sizes and branches in Germany. Workplaces are documented and analysed by observations, applying KIMs, interviews and assessment of environmental conditions. Furthermore, a survey among the employees at the respective workplaces takes place with standardised questionnaires, interviews and physical examinations. It is intended to include 1200 employees at 120 different workplaces. For analysis of the quality criteria, recommendations of the COSMIN checklist (COnsensus-based Standards for the selection of health Measurement INstruments) will be taken into account. Ethics and dissemination The study was planned and conducted in accordance with the German Medical Professional Code and the Declaration of Helsinki as well as the German Federal Data Protection Act. The design of the study was approved by ethics committees. We intend to publish the validated KIMs in 2018. Results will be published in peer-reviewed journals, presented at international meetings and disseminated to actual users for practical application. PMID:28827239

SU-E-J-168: Automated Pancreas Segmentation Based On Dynamic MRI

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

Gou, S; Rapacchi, S; Hu, P

2014-06-01

Purpose: MRI guided radiotherapy is particularly attractive for abdominal targets with low CT contrast. To fully utilize this modality for pancreas tracking, automated segmentation tools are needed. A hybrid gradient, region growth and shape constraint (hGReS) method to segment 2D upper abdominal dynamic MRI is developed for this purpose. Methods: 2D coronal dynamic MR images of 2 healthy volunteers were acquired with a frame rate of 5 f/second. The regions of interest (ROIs) included the liver, pancreas and stomach. The first frame was used as the source where the centers of the ROIs were annotated. These center locations were propagatedmore » to the next dynamic MRI frame. 4-neighborhood region transfer growth was performed from these initial seeds for rough segmentation. To improve the results, gradient, edge and shape constraints were applied to the ROIs before final refinement using morphological operations. Results from hGReS and 3 other automated segmentation methods using edge detection, region growth and level set were compared to manual contouring. Results: For the first patient, hGReS resulted in the organ segmentation accuracy as measure by the Dices index (0.77) for the pancreas. The accuracy was slightly superior to the level set method (0.72), and both are significantly more accurate than the edge detection (0.53) and region growth methods (0.42). For the second healthy volunteer, hGReS reliably segmented the pancreatic region, achieving a Dices index of 0.82, 0.92 and 0.93 for the pancreas, stomach and liver, respectively, comparing to manual segmentation. Motion trajectories derived from the hGReS, level set and manual segmentation methods showed high correlation to respiratory motion calculated using a lung blood vessel as the reference while the other two methods showed substantial motion tracking errors. hGReS was 10 times faster than level set. Conclusion: We have shown the feasibility of automated segmentation of the pancreas anatomy based on dynamic MRI.« less

Fast and Accurate Semi-Automated Segmentation Method of Spinal Cord MR Images at 3T Applied to the Construction of a Cervical Spinal Cord Template

PubMed Central

El Mendili, Mohamed-Mounir; Trunet, Stéphanie; Pélégrini-Issac, Mélanie; Lehéricy, Stéphane; Pradat, Pierre-François; Benali, Habib

2015-01-01

Objective To design a fast and accurate semi-automated segmentation method for spinal cord 3T MR images and to construct a template of the cervical spinal cord. Materials and Methods A semi-automated double threshold-based method (DTbM) was proposed enabling both cross-sectional and volumetric measures from 3D T2-weighted turbo spin echo MR scans of the spinal cord at 3T. Eighty-two healthy subjects, 10 patients with amyotrophic lateral sclerosis, 10 with spinal muscular atrophy and 10 with spinal cord injuries were studied. DTbM was compared with active surface method (ASM), threshold-based method (TbM) and manual outlining (ground truth). Accuracy of segmentations was scored visually by a radiologist in cervical and thoracic cord regions. Accuracy was also quantified at the cervical and thoracic levels as well as at C2 vertebral level. To construct a cervical template from healthy subjects’ images (n=59), a standardization pipeline was designed leading to well-centered straight spinal cord images and accurate probability tissue map. Results Visual scoring showed better performance for DTbM than for ASM. Mean Dice similarity coefficient (DSC) was 95.71% for DTbM and 90.78% for ASM at the cervical level and 94.27% for DTbM and 89.93% for ASM at the thoracic level. Finally, at C2 vertebral level, mean DSC was 97.98% for DTbM compared with 98.02% for TbM and 96.76% for ASM. DTbM showed similar accuracy compared with TbM, but with the advantage of limited manual interaction. Conclusion A semi-automated segmentation method with limited manual intervention was introduced and validated on 3T images, enabling the construction of a cervical spinal cord template. PMID:25816143

Merged GIS, GPS data assist siting for gulf gas line

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

Scott, D.R.; Schmidt, J.A.

1998-06-29

A GIS-based decision-support system was developed for a US Gulf of Mexico onshore and offshore pipeline that has assisted in locating a cost-effective pipeline route based on landcover type, wetland distribution, and proximity to other environmentally sensitive resources. Described here are the methods used to integrate various sources of available GIS data with satellite imagery and surveyed information. Costs of collecting and processing these data are compared with benefits of the system over use of manual methods.

Semen analysis with regard to sperm number, sperm morphology and functional aspects

PubMed Central

Eliasson, Rune

2010-01-01

The new World Health Organization (WHO) Manual for Semen Analysis contains several improvements. One is that the 20 million spermatozoa per mL paradigm has been ousted in favour of proper calculations of lower reference limits for semen from men, whose partners had a time-to-pregnancy of 12 months or less. The recommendation to grade the progressive motility as described in the third and fourth editions of the WHO manual was not evidence-based, and WHO was therefore motivated to abandon it. However, the new recommendation is not evidence-based either, and it is difficult to understand the rational for the new assessment. It may have been a compromise to avoid returning to the rather robust system recommended in the first edition (1980). The unconditional recommendation of the 'Tygerberg strict criteria' is not evidence-based, and seems to be the result of an unfortunate bias in the composition of the Committee in favour of individuals known to support the 'strict criteria' method. This recommendation will have negative effects on the development of andrology as a scientific field. Given the importance of the WHO manual, it is unfortunate that the recommendations for such important variables, as motility and morphology, lack evidence-based support. PMID:20111078

Fully automatic registration and segmentation of first-pass myocardial perfusion MR image sequences.

PubMed

Gupta, Vikas; Hendriks, Emile A; Milles, Julien; van der Geest, Rob J; Jerosch-Herold, Michael; Reiber, Johan H C; Lelieveldt, Boudewijn P F

2010-11-01

Derivation of diagnostically relevant parameters from first-pass myocardial perfusion magnetic resonance images involves the tedious and time-consuming manual segmentation of the myocardium in a large number of images. To reduce the manual interaction and expedite the perfusion analysis, we propose an automatic registration and segmentation method for the derivation of perfusion linked parameters. A complete automation was accomplished by first registering misaligned images using a method based on independent component analysis, and then using the registered data to automatically segment the myocardium with active appearance models. We used 18 perfusion studies (100 images per study) for validation in which the automatically obtained (AO) contours were compared with expert drawn contours on the basis of point-to-curve error, Dice index, and relative perfusion upslope in the myocardium. Visual inspection revealed successful segmentation in 15 out of 18 studies. Comparison of the AO contours with expert drawn contours yielded 2.23 ± 0.53 mm and 0.91 ± 0.02 as point-to-curve error and Dice index, respectively. The average difference between manually and automatically obtained relative upslope parameters was found to be statistically insignificant (P = .37). Moreover, the analysis time per slice was reduced from 20 minutes (manual) to 1.5 minutes (automatic). We proposed an automatic method that significantly reduced the time required for analysis of first-pass cardiac magnetic resonance perfusion images. The robustness and accuracy of the proposed method were demonstrated by the high spatial correspondence and statistically insignificant difference in perfusion parameters, when AO contours were compared with expert drawn contours. Copyright © 2010 AUR. Published by Elsevier Inc. All rights reserved.

Evaluation of a Region-of-Interest Approach for Detecting Progressive Glaucomatous Macular Damage on Optical Coherence Tomography

PubMed Central

Weng, Denis S. D.; Thenappan, Abinaya; Ritch, Robert; Hood, Donald C.

2018-01-01

Purpose To evaluate a manual region-of-interest (ROI) approach for detecting progressive macular ganglion cell complex (GCC) changes on optical coherence tomography (OCT) imaging. Methods One hundred forty-six eyes with a clinical diagnosis of glaucoma or suspected glaucoma with macular OCT scans obtained at least 1 year apart were evaluated. Changes in the GCC thickness were identified using a manual ROI approach (ROIM), whereby region(s) of observed or suspected glaucomatous damage were manually identified when using key features from the macular OCT scan on the second visit. Progression was also evaluated using the global GCC thickness and an automatic ROI approach (ROIA), where contiguous region(s) that fell below the 1% lower normative limit and exceeded 288 μm2 in size were evaluated. Longitudinal signal-to-noise ratios (SNRs) were calculated for progressive changes detected by each of these methods using individualized estimates of test–retest variability and age-related changes, obtained from 303 glaucoma and 394 healthy eyes, respectively. Results On average, the longitudinal SNR for the global thickness, ROIA and ROIM methods were −0.90 y−1, −0.91 y−1, and −1.03 y−1, respectively, and was significantly more negative for the ROIM compared with the global thickness (P = 0.003) and ROIA methods (P = 0.021). Conclusions Progressive glaucomatous macular GCC changes were optimally detected with a manual ROI approach. Translational Relevance These findings suggests that an approach based on a qualitative evaluation of OCT imaging information and consideration of known patterns of damage can improve the detection of progressive glaucomatous macular damage. PMID:29616153

Relating the 2010 signalized intersection methodology to alternate approaches in the context of NYC conditions.

DOT National Transportation Integrated Search

2013-11-01

The Highway Capacity Manual (HCM) has had a delay-based level of service methodology for signalized intersections since 1985. : The 2010 HCM has revised the method for calculating delay. This happened concurrent with such jurisdictions as NYC reviewi...

Preparation of ⁶⁸Ga-labelled DOTA-peptides using a manual labelling approach for small-animal PET imaging.

PubMed

Romero, Eduardo; Martínez, Alfonso; Oteo, Marta; García, Angel; Morcillo, Miguel Angel

2016-01-01

(68)Ga-DOTA-peptides are a promising PET radiotracers used in the detection of different tumours types due to their ability for binding specifically receptors overexpressed in these. Furthermore, (68)Ga can be produced by a (68)Ge/(68)Ga generator on site which is a very good alternative to cyclotron-based PET isotopes. Here, we describe a manual labelling approach for the synthesis of (68)Ga-labelled DOTA-peptides based on concentration and purification of the commercial (68)Ga/(68)Ga generator eluate using an anion exchange-cartridge. (68)Ga-DOTA-TATE was used to image a pheochromocytoma xenograft mouse model by a microPET/CT scanner. The method described provides satisfactory results, allowing the subsequent (68)Ga use to label DOTA-peptides. The simplicity of the method along with its implementation reduced cost, makes it useful in preclinical PET studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Epidermal segmentation in high-definition optical coherence tomography.

PubMed

Li, Annan; Cheng, Jun; Yow, Ai Ping; Wall, Carolin; Wong, Damon Wing Kee; Tey, Hong Liang; Liu, Jiang

2015-01-01

Epidermis segmentation is a crucial step in many dermatological applications. Recently, high-definition optical coherence tomography (HD-OCT) has been developed and applied to imaging subsurface skin tissues. In this paper, a novel epidermis segmentation method using HD-OCT is proposed in which the epidermis is segmented by 3 steps: the weighted least square-based pre-processing, the graph-based skin surface detection and the local integral projection-based dermal-epidermal junction detection respectively. Using a dataset of five 3D volumes, we found that this method correlates well with the conventional method of manually marking out the epidermis. This method can therefore serve to effectively and rapidly delineate the epidermis for study and clinical management of skin diseases.

Correction for FDG PET dose extravasations: Monte Carlo validation and quantitative evaluation of patient studies.

PubMed

Silva-Rodríguez, Jesús; Aguiar, Pablo; Sánchez, Manuel; Mosquera, Javier; Luna-Vega, Víctor; Cortés, Julia; Garrido, Miguel; Pombar, Miguel; Ruibal, Alvaro

2014-05-01

Current procedure guidelines for whole body [18F]fluoro-2-deoxy-D-glucose (FDG)-positron emission tomography (PET) state that studies with visible dose extravasations should be rejected for quantification protocols. Our work is focused on the development and validation of methods for estimating extravasated doses in order to correct standard uptake value (SUV) values for this effect in clinical routine. One thousand three hundred sixty-seven consecutive whole body FDG-PET studies were visually inspected looking for extravasation cases. Two methods for estimating the extravasated dose were proposed and validated in different scenarios using Monte Carlo simulations. All visible extravasations were retrospectively evaluated using a manual ROI based method. In addition, the 50 patients with higher extravasated doses were also evaluated using a threshold-based method. Simulation studies showed that the proposed methods for estimating extravasated doses allow us to compensate the impact of extravasations on SUV values with an error below 5%. The quantitative evaluation of patient studies revealed that paravenous injection is a relatively frequent effect (18%) with a small fraction of patients presenting considerable extravasations ranging from 1% to a maximum of 22% of the injected dose. A criterion based on the extravasated volume and maximum concentration was established in order to identify this fraction of patients that might be corrected for paravenous injection effect. The authors propose the use of a manual ROI based method for estimating the effectively administered FDG dose and then correct SUV quantification in those patients fulfilling the proposed criterion.

Manual hyperinflation in airway clearance in pediatric patients: a systematic review

PubMed Central

de Godoy, Vanessa Cristina Waetge Pires; Zanetti, Nathalia Mendonça; Johnston, Cíntia

2013-01-01

Objective To perform an assessment of the available literature on manual hyperinflation as a respiratory physical therapy technique used in pediatric patients, with the main outcome of achieving airway clearance. Methods We reviewed articles included in the Lilacs (Latin American and Caribbean Literature on Health Sciences/Literatura Latino Americana e do Caribe em Ciências da Saúde), Cochrane Library, Medline (via Virtual Health Library and PubMed), SciELO (Scientific Electronic Library), and PEDro (Physiotherapy Evidence Database) databases from 2002 to 2013 using the following search terms: "physiotherapy (techniques)", "respiratory therapy", "intensive care", and "airway clearance". The selected studies were classified according to the level of evidence and grades of recommendation (method of the Oxford Centre for Evidence-Based Medicine) by two examiners, while a third examiner repeated the search and analysis and checked the classification of the articles. Results Three articles were included for analysis, comprising 250 children (aged 0 to 16 years). The main diagnoses were acute respiratory failure, recovery following heart congenital disease and upper abdominal surgery, bone marrow transplantation, asthma, tracheal reconstruction, brain injury, airway injury, and heterogeneous lung diseases. The studies were classified as having a level of evidence 2C and grade of recommendation C. Conclusions Manual hyperinflation appeared useful for airway clearance in the investigated population, although the evidence available in the literature remains insufficient. Therefore, controlled randomized studies are needed to establish the safety and efficacy of manual hyperinflation in pediatric patients. However, manual hyperinflation must be performed by trained physical therapists only. PMID:24213091

Iterative-cuts: longitudinal and scale-invariant segmentation via user-defined templates for rectosigmoid colon in gynecological brachytherapy

PubMed Central

Lüddemann, Tobias; Egger, Jan

2016-01-01

Abstract. Among all types of cancer, gynecological malignancies belong to the fourth most frequent type of cancer among women. In addition to chemotherapy and external beam radiation, brachytherapy is the standard procedure for the treatment of these malignancies. In the progress of treatment planning, localization of the tumor as the target volume and adjacent organs of risks by segmentation is crucial to accomplish an optimal radiation distribution to the tumor while simultaneously preserving healthy tissue. Segmentation is performed manually and represents a time-consuming task in clinical daily routine. This study focuses on the segmentation of the rectum/sigmoid colon as an organ-at-risk in gynecological brachytherapy. The proposed segmentation method uses an interactive, graph-based segmentation scheme with a user-defined template. The scheme creates a directed two-dimensional graph, followed by the minimal cost closed set computation on the graph, resulting in an outlining of the rectum. The graph’s outline is dynamically adapted to the last calculated cut. Evaluation was performed by comparing manual segmentations of the rectum/sigmoid colon to results achieved with the proposed method. The comparison of the algorithmic to manual result yielded a dice similarity coefficient value of 83.85±4.08, in comparison to 83.97±8.08% for the comparison of two manual segmentations by the same physician. Utilizing the proposed methodology resulted in a median time of 128  s/dataset, compared to 300 s needed for pure manual segmentation. PMID:27403448

Ground Snow Measurements: Comparisons of the Hotplate, Weighing and Manual Methods

NASA Astrophysics Data System (ADS)

Wettlaufer, A.; Snider, J.; Campbell, L. S.; Steenburgh, W. J.; Burkhart, M.

2015-12-01

The Yankee Environmental Systems (YES) Hotplate was developed to avoid some of the problems associated with weighing snowfall sensors. This work compares Hotplate, weighing sensor (ETI NOAH-II) and manual measurements of liquid-equivalent depth. The main field site was at low altitude in western New York; Hotplate and ETI comparisons were also made at two forested subalpine sites in southeastern Wyoming. The manual measurement (only conducted at the New York site) was derived by weighing snow cores sampled from a snow board. The two recording gauges (Hotplate and ETI) were located within 5 m of the snow board. Hotplate-derived accumulations were corrected using a wind-speed dependent catch efficiency and the ETI orifice was heated and alter shielded. Three important findings are evident from the comparisons: 1) The Yes-derived accumulations, recorded in a user-accessible file, were compared to accumulations derived using an in-house calibration and fundamental measurements (plate power, long and shortwave radiances, wind speed, and temperature). These accumulations are highly correlated (N=24; r2=0.99), but the YES-derived values are larger by 20%. 2) The in-house Hotplate accumulations are in good agreement with ETI-based accumulations but with larger variability (N=24; r2=0.88). 3) The comparison of in-house Hotplate accumulation versus manual accumulation, expressed as mm of liquid, exhibits a fitted linear relationship Y (in-house) versus X (manual) given by Y = -0.2 (±1.4) + 0.9 (±0.1) · X (N= 20; r2=0.89). Thus, these two methods agree within statistical uncertainty.

Measurement of edge residual stresses in glass by the phase-shifting method

NASA Astrophysics Data System (ADS)

Ajovalasit, A.; Petrucci, G.; Scafidi, M.

2011-05-01

Control and measurement of residual stress in glass is of great importance in the industrial field. Since glass is a birefringent material, the residual stress analysis is based mainly on the photoelastic method. This paper considers two methods of automated analysis of membrane residual stress in glass sheets, based on the phase-shifting concept in monochromatic light. In particular these methods are the automated versions of goniometric compensation methods of Tardy and Sénarmont. The proposed methods can effectively replace manual methods of compensation (goniometric compensation of Tardy and Sénarmont, Babinet and Babinet-Soleil compensators) provided by current standards on the analysis of residual stresses in glasses.

[Manual therapy in general practice].

PubMed

Березуцкий, Владимир И

2016-01-01

The article is devoted to manual therapy practice for diagnostics and treatment of vertebrogenic pain syndrome in general practice. Analytical roundup of sources proves medical advantage of implementation of manual therapy basic methods by general practice specialists.

Application of the 3D slicer chest imaging platform segmentation algorithm for large lung nodule delineation

PubMed Central

Parmar, Chintan; Blezek, Daniel; Estepar, Raul San Jose; Pieper, Steve; Kim, John; Aerts, Hugo J. W. L.

2017-01-01

Purpose Accurate segmentation of lung nodules is crucial in the development of imaging biomarkers for predicting malignancy of the nodules. Manual segmentation is time consuming and affected by inter-observer variability. We evaluated the robustness and accuracy of a publically available semiautomatic segmentation algorithm that is implemented in the 3D Slicer Chest Imaging Platform (CIP) and compared it with the performance of manual segmentation. Methods CT images of 354 manually segmented nodules were downloaded from the LIDC database. Four radiologists performed the manual segmentation and assessed various nodule characteristics. The semiautomatic CIP segmentation was initialized using the centroid of the manual segmentations, thereby generating four contours for each nodule. The robustness of both segmentation methods was assessed using the region of uncertainty (δ) and Dice similarity index (DSI). The robustness of the segmentation methods was compared using the Wilcoxon-signed rank test (pWilcoxon<0.05). The Dice similarity index (DSIAgree) between the manual and CIP segmentations was computed to estimate the accuracy of the semiautomatic contours. Results The median computational time of the CIP segmentation was 10 s. The median CIP and manually segmented volumes were 477 ml and 309 ml, respectively. CIP segmentations were significantly more robust than manual segmentations (median δCIP = 14ml, median dsiCIP = 99% vs. median δmanual = 222ml, median dsimanual = 82%) with pWilcoxon~10−16. The agreement between CIP and manual segmentations had a median DSIAgree of 60%. While 13% (47/354) of the nodules did not require any manual adjustment, minor to substantial manual adjustments were needed for 87% (305/354) of the nodules. CIP segmentations were observed to perform poorly (median DSIAgree≈50%) for non-/sub-solid nodules with subtle appearances and poorly defined boundaries. Conclusion Semi-automatic CIP segmentation can potentially reduce the physician workload for 13% of nodules owing to its computational efficiency and superior stability compared to manual segmentation. Although manual adjustment is needed for many cases, CIP segmentation provides a preliminary contour for physicians as a starting point. PMID:28594880

Camellia v1.0 Manual: Part I

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

Roberts, Nathan V.

2016-09-28

Camellia began as an effort to simplify implementation of efficient solvers for the discontinuous Petrov-Galerkin (DPG) finite element methodology of Demkowicz and Gopalakrishnan. Since then, the feature set has expanded, to allow implementation of traditional continuous Galerkin methods, as well as discontinuous Galerkin (DG) methods, hybridizable DG (HDG) methods, first-order-system least squares (FOSLS), and the primal DPG method. This manual serves as an introduction to using Camellia. We begin, in Section 1.1, by describing some of the core features of Camellia. In Section 1.2 we provide an outline of the manual as a whole.

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

Bogunovic, Hrvoje; Pozo, Jose Maria; Villa-Uriol, Maria Cruz

Purpose: To evaluate the suitability of an improved version of an automatic segmentation method based on geodesic active regions (GAR) for segmenting cerebral vasculature with aneurysms from 3D x-ray reconstruction angiography (3DRA) and time of flight magnetic resonance angiography (TOF-MRA) images available in the clinical routine. Methods: Three aspects of the GAR method have been improved: execution time, robustness to variability in imaging protocols, and robustness to variability in image spatial resolutions. The improved GAR was retrospectively evaluated on images from patients containing intracranial aneurysms in the area of the Circle of Willis and imaged with two modalities: 3DRA andmore » TOF-MRA. Images were obtained from two clinical centers, each using different imaging equipment. Evaluation included qualitative and quantitative analyses of the segmentation results on 20 images from 10 patients. The gold standard was built from 660 cross-sections (33 per image) of vessels and aneurysms, manually measured by interventional neuroradiologists. GAR has also been compared to an interactive segmentation method: isointensity surface extraction (ISE). In addition, since patients had been imaged with the two modalities, we performed an intermodality agreement analysis with respect to both the manual measurements and each of the two segmentation methods. Results: Both GAR and ISE differed from the gold standard within acceptable limits compared to the imaging resolution. GAR (ISE) had an average accuracy of 0.20 (0.24) mm for 3DRA and 0.27 (0.30) mm for TOF-MRA, and had a repeatability of 0.05 (0.20) mm. Compared to ISE, GAR had a lower qualitative error in the vessel region and a lower quantitative error in the aneurysm region. The repeatability of GAR was superior to manual measurements and ISE. The intermodality agreement was similar between GAR and the manual measurements. Conclusions: The improved GAR method outperformed ISE qualitatively as well as quantitatively and is suitable for segmenting 3DRA and TOF-MRA images from clinical routine.« less

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

Pasquier, David; Lacornerie, Thomas; Vermandel, Maximilien

Purpose: Target-volume and organ-at-risk delineation is a time-consuming task in radiotherapy planning. The development of automated segmentation tools remains problematic, because of pelvic organ shape variability. We evaluate a three-dimensional (3D), deformable-model approach and a seeded region-growing algorithm for automatic delineation of the prostate and organs-at-risk on magnetic resonance images. Methods and Materials: Manual and automatic delineation were compared in 24 patients using a sagittal T2-weighted (T2-w) turbo spin echo (TSE) sequence and an axial T1-weighted (T1-w) 3D fast-field echo (FFE) or TSE sequence. For automatic prostate delineation, an organ model-based method was used. Prostates without seminal vesicles were delineatedmore » as the clinical target volume (CTV). For automatic bladder and rectum delineation, a seeded region-growing method was used. Manual contouring was considered the reference method. The following parameters were measured: volume ratio (Vr) (automatic/manual), volume overlap (Vo) (ratio of the volume of intersection to the volume of union; optimal value = 1), and correctly delineated volume (Vc) (percent ratio of the volume of intersection to the manually defined volume; optimal value 100). Results: For the CTV, the Vr, Vo, and Vc were 1.13 ({+-}0.1 SD), 0.78 ({+-}0.05 SD), and 94.75 ({+-}3.3 SD), respectively. For the rectum, the Vr, Vo, and Vc were 0.97 ({+-}0.1 SD), 0.78 ({+-}0.06 SD), and 86.52 ({+-}5 SD), respectively. For the bladder, the Vr, Vo, and Vc were 0.95 ({+-}0.03 SD), 0.88 ({+-}0.03 SD), and 91.29 ({+-}3.1 SD), respectively. Conclusions: Our results show that the organ-model method is robust, and results in reproducible prostate segmentation with minor interactive corrections. For automatic bladder and rectum delineation, magnetic resonance imaging soft-tissue contrast enables the use of region-growing methods.« less

An efficient approach for surveillance of childhood diabetes by type derived from electronic health record data: the SEARCH for Diabetes in Youth Study

PubMed Central

Zhong, Victor W; Obeid, Jihad S; Craig, Jean B; Pfaff, Emily R; Thomas, Joan; Jaacks, Lindsay M; Beavers, Daniel P; Carey, Timothy S; Lawrence, Jean M; Dabelea, Dana; Hamman, Richard F; Bowlby, Deborah A; Pihoker, Catherine; Saydah, Sharon H

2016-01-01

Objective To develop an efficient surveillance approach for childhood diabetes by type across 2 large US health care systems, using phenotyping algorithms derived from electronic health record (EHR) data. Materials and Methods Presumptive diabetes cases <20 years of age from 2 large independent health care systems were identified as those having ≥1 of the 5 indicators in the past 3.5 years, including elevated HbA1c, elevated blood glucose, diabetes-related billing codes, patient problem list, and outpatient anti-diabetic medications. EHRs of all the presumptive cases were manually reviewed, and true diabetes status and diabetes type were determined. Algorithms for identifying diabetes cases overall and classifying diabetes type were either prespecified or derived from classification and regression tree analysis. Surveillance approach was developed based on the best algorithms identified. Results We developed a stepwise surveillance approach using billing code–based prespecified algorithms and targeted manual EHR review, which efficiently and accurately ascertained and classified diabetes cases by type, in both health care systems. The sensitivity and positive predictive values in both systems were approximately ≥90% for ascertaining diabetes cases overall and classifying cases with type 1 or type 2 diabetes. About 80% of the cases with “other” type were also correctly classified. This stepwise surveillance approach resulted in a >70% reduction in the number of cases requiring manual validation compared to traditional surveillance methods. Conclusion EHR data may be used to establish an efficient approach for large-scale surveillance for childhood diabetes by type, although some manual effort is still needed. PMID:27107449

Automatic Measurement of Fetal Brain Development from Magnetic Resonance Imaging: New Reference Data.

PubMed

Link, Daphna; Braginsky, Michael B; Joskowicz, Leo; Ben Sira, Liat; Harel, Shaul; Many, Ariel; Tarrasch, Ricardo; Malinger, Gustavo; Artzi, Moran; Kapoor, Cassandra; Miller, Elka; Ben Bashat, Dafna

2018-01-01

Accurate fetal brain volume estimation is of paramount importance in evaluating fetal development. The aim of this study was to develop an automatic method for fetal brain segmentation from magnetic resonance imaging (MRI) data, and to create for the first time a normal volumetric growth chart based on a large cohort. A semi-automatic segmentation method based on Seeded Region Growing algorithm was developed and applied to MRI data of 199 typically developed fetuses between 18 and 37 weeks' gestation. The accuracy of the algorithm was tested against a sub-cohort of ground truth manual segmentations. A quadratic regression analysis was used to create normal growth charts. The sensitivity of the method to identify developmental disorders was demonstrated on 9 fetuses with intrauterine growth restriction (IUGR). The developed method showed high correlation with manual segmentation (r2 = 0.9183, p < 0.001) as well as mean volume and volume overlap differences of 4.77 and 18.13%, respectively. New reference data on 199 normal fetuses were created, and all 9 IUGR fetuses were at or below the third percentile of the normal growth chart. The proposed method is fast, accurate, reproducible, user independent, applicable with retrospective data, and is suggested for use in routine clinical practice. © 2017 S. Karger AG, Basel.

[Tuitional-based promotion of social competencies and prevention of bullying in adolescence--the fairplayer.manual: results of a pilot evaluation study].

PubMed

Scheithauer, Herbert; Bull, Heike Dele

2010-01-01

The fairplayer.manual (Scheithauer u. Bull, 2008), a manualized, tuitional-based preventive intervention programme to facilitate social competence and prevent school bullying consists of at least 15 to 17 consecutive, ninety-minute-lessons using cognitive-behavioural methods (e. g. role plays, model-learning, social reinforcement, behaviour-feedback) and moral dilemma discussions amongst others. We present results from a pilot evaluation study with 138 students (between 13 and 21 years of age, from comprehensive and vocational school) and their teachers. Students and teachers were administered structured questionnaires considering e. g. the occurrence of bullying, prosocial behavior and student's empathy as well as legitimation of violence. For 113 students we obtained data for the two measurement points (pre-post). Due to a high attrition rate information of an initially recruited control group could not be considered. Results indicated partially impressive positive changes concerning the total number of bullies and victims as well as prosocial behavior. Results concerning legitimation of violence and empathy differed for classes according to treatment integrity.

Analytical methods manual for the Mineral Resource Surveys Program, U.S. Geological Survey

USGS Publications Warehouse

Arbogast, Belinda F.

1996-01-01

The analytical methods validated by the Mineral Resource Surveys Program, Geologic Division, is the subject of this manual. This edition replaces the methods portion of Open-File Report 90-668 published in 1990. Newer methods may be used which have been approved by the quality assurance (QA) project and are on file with the QA coordinator.This manual is intended primarily for use by laboratory scientists; this manual can also assist laboratory users to evaluate the data they receive. The analytical methods are written in a step by step approach so that they may be used as a training tool and provide detailed documentation of the procedures for quality assurance. A "Catalog of Services" is available for customer (submitter) use with brief listings of:the element(s)/species determined,method of determination,reference to cite,contact person,summary of the technique,and analyte concentration range.For a copy please contact the Branch office at (303) 236-1800 or fax (303) 236-3200.

Mixed methods research - the best of both worlds?

PubMed

van Griensven, Hubert; Moore, Ann P; Hall, Valerie

2014-10-01

There has been a bias towards quantitative research approaches within manual therapy, which may have resulted in a narrow understanding of manual therapy practice. The aim of this Masterclass is to make a contribution to the expansion of methodologies used in manual therapy enquiry by discussing mixed methods research (MMR), a methodology which utilises both qualitative and quantitative methods within a single study in order to provide more comprehensive insights. To review rationales for MMR, as well as some of the common design options and potential difficulties. The paper also discusses theoretical frameworks that have been used to underpin qualitative and quantitative research, and ongoing debates about the possibility of combining them. Complexities associated with health and manual therapy cannot always be investigated satisfactorily by using a single research method. Some issues require a more comprehensive understanding, which may be provided by combining the strengths of quantitative and qualitative methods in a mixed methods study. Copyright © 2014 Elsevier Ltd. All rights reserved.

High-Throughput Method for Automated Colony and Cell Counting by Digital Image Analysis Based on Edge Detection

PubMed Central

Choudhry, Priya

2016-01-01

Counting cells and colonies is an integral part of high-throughput screens and quantitative cellular assays. Due to its subjective and time-intensive nature, manual counting has hindered the adoption of cellular assays such as tumor spheroid formation in high-throughput screens. The objective of this study was to develop an automated method for quick and reliable counting of cells and colonies from digital images. For this purpose, I developed an ImageJ macro Cell Colony Edge and a CellProfiler Pipeline Cell Colony Counting, and compared them to other open-source digital methods and manual counts. The ImageJ macro Cell Colony Edge is valuable in counting cells and colonies, and measuring their area, volume, morphology, and intensity. In this study, I demonstrate that Cell Colony Edge is superior to other open-source methods, in speed, accuracy and applicability to diverse cellular assays. It can fulfill the need to automate colony/cell counting in high-throughput screens, colony forming assays, and cellular assays. PMID:26848849

Computed tomography-based volumetric tool for standardized measurement of the maxillary sinus

PubMed Central

Giacomini, Guilherme; Pavan, Ana Luiza Menegatti; Altemani, João Mauricio Carrasco; Duarte, Sergio Barbosa; Fortaleza, Carlos Magno Castelo Branco; Miranda, José Ricardo de Arruda

2018-01-01

Volume measurements of maxillary sinus may be useful to identify diseases affecting paranasal sinuses. However, literature shows a lack of consensus in studies measuring the volume. This may be attributable to different computed tomography data acquisition techniques, segmentation methods, focuses of investigation, among other reasons. Furthermore, methods for volumetrically quantifying the maxillary sinus are commonly manual or semiautomated, which require substantial user expertise and are time-consuming. The purpose of the present study was to develop an automated tool for quantifying the total and air-free volume of the maxillary sinus based on computed tomography images. The quantification tool seeks to standardize maxillary sinus volume measurements, thus allowing better comparisons and determinations of factors that influence maxillary sinus size. The automated tool utilized image processing techniques (watershed, threshold, and morphological operators). The maxillary sinus volume was quantified in 30 patients. To evaluate the accuracy of the automated tool, the results were compared with manual segmentation that was performed by an experienced radiologist using a standard procedure. The mean percent differences between the automated and manual methods were 7.19% ± 5.83% and 6.93% ± 4.29% for total and air-free maxillary sinus volume, respectively. Linear regression and Bland-Altman statistics showed good agreement and low dispersion between both methods. The present automated tool for maxillary sinus volume assessment was rapid, reliable, robust, accurate, and reproducible and may be applied in clinical practice. The tool may be used to standardize measurements of maxillary volume. Such standardization is extremely important for allowing comparisons between studies, providing a better understanding of the role of the maxillary sinus, and determining the factors that influence maxillary sinus size under normal and pathological conditions. PMID:29304130

BIANCA (Brain Intensity AbNormality Classification Algorithm): A new tool for automated segmentation of white matter hyperintensities.

PubMed

Griffanti, Ludovica; Zamboni, Giovanna; Khan, Aamira; Li, Linxin; Bonifacio, Guendalina; Sundaresan, Vaanathi; Schulz, Ursula G; Kuker, Wilhelm; Battaglini, Marco; Rothwell, Peter M; Jenkinson, Mark

2016-11-01

Reliable quantification of white matter hyperintensities of presumed vascular origin (WMHs) is increasingly needed, given the presence of these MRI findings in patients with several neurological and vascular disorders, as well as in elderly healthy subjects. We present BIANCA (Brain Intensity AbNormality Classification Algorithm), a fully automated, supervised method for WMH detection, based on the k-nearest neighbour (k-NN) algorithm. Relative to previous k-NN based segmentation methods, BIANCA offers different options for weighting the spatial information, local spatial intensity averaging, and different options for the choice of the number and location of the training points. BIANCA is multimodal and highly flexible so that the user can adapt the tool to their protocol and specific needs. We optimised and validated BIANCA on two datasets with different MRI protocols and patient populations (a "predominantly neurodegenerative" and a "predominantly vascular" cohort). BIANCA was first optimised on a subset of images for each dataset in terms of overlap and volumetric agreement with a manually segmented WMH mask. The correlation between the volumes extracted with BIANCA (using the optimised set of options), the volumes extracted from the manual masks and visual ratings showed that BIANCA is a valid alternative to manual segmentation. The optimised set of options was then applied to the whole cohorts and the resulting WMH volume estimates showed good correlations with visual ratings and with age. Finally, we performed a reproducibility test, to evaluate the robustness of BIANCA, and compared BIANCA performance against existing methods. Our findings suggest that BIANCA, which will be freely available as part of the FSL package, is a reliable method for automated WMH segmentation in large cross-sectional cohort studies. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Treatment manuals: use in the treatment of bulimia nervosa.

PubMed

Wallace, Laurel M; von Ranson, Kristin M

2011-11-01

As psychology has moved toward emphasizing evidence-based practice, use of treatment manuals has extended from research trials into clinical practice. Minimal research has directly evaluated use of manuals in clinical practice. This survey of international eating disorder professionals examined use of manuals with 259 clinicians' most recent client with bulimia nervosa. Although evidence-based manuals for bulimia nervosa exist, only 35.9% of clinicians reported using a manual. Clinicians were more likely to use a manual if they were younger; were treating an adult client; were clinical psychologists; were involved in research related to eating disorders; and endorsed a cognitive-behavioral orientation. Clinicians were less likely to use a manual if they provided eclectic psychotherapy that incorporated multiple psychotherapeutic approaches. We conclude that psychotherapy provided in clinical practice often does not align with the specific form validated in research trials, and "eclecticism" is at odds with efforts to disseminate manuals into clinical practice. Copyright © 2011 Elsevier Ltd. All rights reserved.

Automated segmentation of blood-flow regions in large thoracic arteries using 3D-cine PC-MRI measurements.

PubMed

van Pelt, Roy; Nguyen, Huy; ter Haar Romeny, Bart; Vilanova, Anna

2012-03-01

Quantitative analysis of vascular blood flow, acquired by phase-contrast MRI, requires accurate segmentation of the vessel lumen. In clinical practice, 2D-cine velocity-encoded slices are inspected, and the lumen is segmented manually. However, segmentation of time-resolved volumetric blood-flow measurements is a tedious and time-consuming task requiring automation. Automated segmentation of large thoracic arteries, based solely on the 3D-cine phase-contrast MRI (PC-MRI) blood-flow data, was done. An active surface model, which is fast and topologically stable, was used. The active surface model requires an initial surface, approximating the desired segmentation. A method to generate this surface was developed based on a voxel-wise temporal maximum of blood-flow velocities. The active surface model balances forces, based on the surface structure and image features derived from the blood-flow data. The segmentation results were validated using volunteer studies, including time-resolved 3D and 2D blood-flow data. The segmented surface was intersected with a velocity-encoded PC-MRI slice, resulting in a cross-sectional contour of the lumen. These cross-sections were compared to reference contours that were manually delineated on high-resolution 2D-cine slices. The automated approach closely approximates the manual blood-flow segmentations, with error distances on the order of the voxel size. The initial surface provides a close approximation of the desired luminal geometry. This improves the convergence time of the active surface and facilitates parametrization. An active surface approach for vessel lumen segmentation was developed, suitable for quantitative analysis of 3D-cine PC-MRI blood-flow data. As opposed to prior thresholding and level-set approaches, the active surface model is topologically stable. A method to generate an initial approximate surface was developed, and various features that influence the segmentation model were evaluated. The active surface segmentation results were shown to closely approximate manual segmentations.

Occupational self-coding and automatic recording (OSCAR): a novel web-based tool to collect and code lifetime job histories in large population-based studies.

PubMed

De Matteis, Sara; Jarvis, Deborah; Young, Heather; Young, Alan; Allen, Naomi; Potts, James; Darnton, Andrew; Rushton, Lesley; Cullinan, Paul

2017-03-01

Objectives The standard approach to the assessment of occupational exposures is through the manual collection and coding of job histories. This method is time-consuming and costly and makes it potentially unfeasible to perform high quality analyses on occupational exposures in large population-based studies. Our aim was to develop a novel, efficient web-based tool to collect and code lifetime job histories in the UK Biobank, a population-based cohort of over 500 000 participants. Methods We developed OSCAR (occupations self-coding automatic recording) based on the hierarchical structure of the UK Standard Occupational Classification (SOC) 2000, which allows individuals to collect and automatically code their lifetime job histories via a simple decision-tree model. Participants were asked to find each of their jobs by selecting appropriate job categories until they identified their job title, which was linked to a hidden 4-digit SOC code. For each occupation a job title in free text was also collected to estimate Cohen's kappa (κ) inter-rater agreement between SOC codes assigned by OSCAR and an expert manual coder. Results OSCAR was administered to 324 653 UK Biobank participants with an existing email address between June and September 2015. Complete 4-digit SOC-coded lifetime job histories were collected for 108 784 participants (response rate: 34%). Agreement between the 4-digit SOC codes assigned by OSCAR and the manual coder for a random sample of 400 job titles was moderately good [κ=0.45, 95% confidence interval (95% CI) 0.42-0.49], and improved when broader job categories were considered (κ=0.64, 95% CI 0.61-0.69 at a 1-digit SOC-code level). Conclusions OSCAR is a novel, efficient, and reasonably reliable web-based tool for collecting and automatically coding lifetime job histories in large population-based studies. Further application in other research projects for external validation purposes is warranted.

An Improved Manual Method for NOx Emission Measurement.

ERIC Educational Resources Information Center

Dee, L. A.; And Others

The current manual NO (x) sampling and analysis method was evaluated. Improved time-integrated sampling and rapid analysis methods were developed. In the new method, the sample gas is drawn through a heated bed of uniquely active, crystalline, Pb02 where NO (x) is quantitatively absorbed. Nitrate ion is later extracted with water and the…

Assessment of ICount software, a precise and fast egg counting tool for the mosquito vector Aedes aegypti.

PubMed

Gaburro, Julie; Duchemin, Jean-Bernard; Paradkar, Prasad N; Nahavandi, Saeid; Bhatti, Asim

2016-11-18

Widespread in the tropics, the mosquito Aedes aegypti is an important vector of many viruses, posing a significant threat to human health. Vector monitoring often requires fecundity estimation by counting eggs laid by female mosquitoes. Traditionally, manual data analyses have been used but this requires a lot of effort and is the methods are prone to errors. An easy tool to assess the number of eggs laid would facilitate experimentation and vector control operations. This study introduces a built-in software called ICount allowing automatic egg counting of the mosquito vector, Aedes aegypti. ICount egg estimation compared to manual counting is statistically equivalent, making the software effective for automatic and semi-automatic data analysis. This technique also allows rapid analysis compared to manual methods. Finally, the software has been used to assess p-cresol oviposition choices under laboratory conditions in order to test the system with different egg densities. ICount is a powerful tool for fast and precise egg count analysis, freeing experimenters from manual data processing. Software access is free and its user-friendly interface allows easy use by non-experts. Its efficiency has been tested in our laboratory with oviposition dual choices of Aedes aegypti females. The next step will be the development of a mobile application, based on the ICount platform, for vector monitoring surveys in the field.

Automatic Evaluation of Collagen Fiber Directions from Polarized Light Microscopy Images.

PubMed

Novak, Kamil; Polzer, Stanislav; Tichy, Michal; Bursa, Jiri

2015-08-01

Mechanical properties of the arterial wall depend largely on orientation and density of collagen fiber bundles. Several methods have been developed for observation of collagen orientation and density; the most frequently applied collagen-specific manual approach is based on polarized light (PL). However, it is very time consuming and the results are operator dependent. We have proposed a new automated method for evaluation of collagen fiber direction from two-dimensional polarized light microscopy images (2D PLM). The algorithm has been verified against artificial images and validated against manual measurements. Finally the collagen content has been estimated. The proposed algorithm was capable of estimating orientation of some 35 k points in 15 min when applied to aortic tissue and over 500 k points in 35 min for Achilles tendon. The average angular disagreement between each operator and the algorithm was -9.3±8.6° and -3.8±8.6° in the case of aortic tissue and -1.6±6.4° and 2.6±7.8° for Achilles tendon. Estimated mean collagen content was 30.3±5.8% and 94.3±2.7% for aortic media and Achilles tendon, respectively. The proposed automated approach is operator independent and several orders faster than manual measurements and therefore has the potential to replace manual measurements of collagen orientation via PLM.

Comparison of the Automated cobas u 701 Urine Microscopy and UF-1000i Flow Cytometry Systems and Manual Microscopy in the Examination of Urine Sediments.

PubMed

Lee, Wonmok; Ha, Jung-Sook; Ryoo, Nam-Hee

2016-09-01

The cobas u 701, a new automated image-based urine sediment analyzer, was introduced recently. In this study, we compared its performance with that of UF-1000i flow cytometry and manual microscopy in the examination of urine sediments. Precision, linearity, and carry-over were determined for the two urine sediment analyzers. For a comparison of the method, 300 urine samples were examined by the automated analyzers and by manual microscopy using a KOVA chamber. Within-run coefficients of variation (CVs) for the control materials were 7.0-8.8% and 1.7-5.7% for the cobas u 701 and UF-1000i systems, respectively. Between-run CVs were 8.5-9.8% and 2.7-5.4%, respectively. Both instruments showed good linearity and negligible carry-over. For red blood cells (RBC), white blood cells (WBC), and epithelial cells (EPI), the overall concordance rates within one grade of difference among the three methods were good (78.6-86.0%, 88.7-93.8%, and 81.3-90.7%, respectively). The concordance rate for casts was poor (66.5-68.9%). Compared with manual microscopy, the two automated sediment analyzers tested in this study showed satisfactory analytical performances for RBC, WBC, and EPI. However, for other urine sediment particles confirmation by visual microscopy is still required. © 2016 Wiley Periodicals, Inc.

Real-time segmentation of burst suppression patterns in critical care EEG monitoring.

PubMed

Brandon Westover, M; Shafi, Mouhsin M; Ching, Shinung; Chemali, Jessica J; Purdon, Patrick L; Cash, Sydney S; Brown, Emery N

2013-09-30

Develop a real-time algorithm to automatically discriminate suppressions from non-suppressions (bursts) in electroencephalograms of critically ill adult patients. A real-time method for segmenting adult ICU EEG data into bursts and suppressions is presented based on thresholding local voltage variance. Results are validated against manual segmentations by two experienced human electroencephalographers. We compare inter-rater agreement between manual EEG segmentations by experts with inter-rater agreement between human vs automatic segmentations, and investigate the robustness of segmentation quality to variations in algorithm parameter settings. We further compare the results of using these segmentations as input for calculating the burst suppression probability (BSP), a continuous measure of depth-of-suppression. Automated segmentation was comparable to manual segmentation, i.e. algorithm-vs-human agreement was comparable to human-vs-human agreement, as judged by comparing raw EEG segmentations or the derived BSP signals. Results were robust to modest variations in algorithm parameter settings. Our automated method satisfactorily segments burst suppression data across a wide range adult ICU EEG patterns. Performance is comparable to or exceeds that of manual segmentation by human electroencephalographers. Automated segmentation of burst suppression EEG patterns is an essential component of quantitative brain activity monitoring in critically ill and anesthetized adults. The segmentations produced by our algorithm provide a basis for accurate tracking of suppression depth. Copyright © 2013 Elsevier B.V. All rights reserved.

Cryo-balloon catheter localization in fluoroscopic images

NASA Astrophysics Data System (ADS)

Kurzendorfer, Tanja; Brost, Alexander; Jakob, Carolin; Mewes, Philip W.; Bourier, Felix; Koch, Martin; Kurzidim, Klaus; Hornegger, Joachim; Strobel, Norbert

2013-03-01

Minimally invasive catheter ablation has become the preferred treatment option for atrial fibrillation. Although the standard ablation procedure involves ablation points set by radio-frequency catheters, cryo-balloon catheters have even been reported to be more advantageous in certain cases. As electro-anatomical mapping systems do not support cryo-balloon ablation procedures, X-ray guidance is needed. However, current methods to provide support for cryo-balloon catheters in fluoroscopically guided ablation procedures rely heavily on manual user interaction. To improve this, we propose a first method for automatic cryo-balloon catheter localization in fluoroscopic images based on a blob detection algorithm. Our method is evaluated on 24 clinical images from 17 patients. The method successfully detected the cryoballoon in 22 out of 24 images, yielding a success rate of 91.6 %. The successful localization achieved an accuracy of 1.00 mm +/- 0.44 mm. Even though our methods currently fails in 8.4 % of the images available, it still offers a significant improvement over manual methods. Furthermore, detecting a landmark point along the cryo-balloon catheter can be a very important step for additional post-processing operations.

Comparison of the manual, semiautomatic, and automatic selection and leveling of hot spots in whole slide images for Ki-67 quantification in meningiomas.

PubMed

Swiderska, Zaneta; Korzynska, Anna; Markiewicz, Tomasz; Lorent, Malgorzata; Zak, Jakub; Wesolowska, Anna; Roszkowiak, Lukasz; Slodkowska, Janina; Grala, Bartlomiej

2015-01-01

Background. This paper presents the study concerning hot-spot selection in the assessment of whole slide images of tissue sections collected from meningioma patients. The samples were immunohistochemically stained to determine the Ki-67/MIB-1 proliferation index used for prognosis and treatment planning. Objective. The observer performance was examined by comparing results of the proposed method of automatic hot-spot selection in whole slide images, results of traditional scoring under a microscope, and results of a pathologist's manual hot-spot selection. Methods. The results of scoring the Ki-67 index using optical scoring under a microscope, software for Ki-67 index quantification based on hot spots selected by two pathologists (resp., once and three times), and the same software but on hot spots selected by proposed automatic methods were compared using Kendall's tau-b statistics. Results. Results show intra- and interobserver agreement. The agreement between Ki-67 scoring with manual and automatic hot-spot selection is high, while agreement between Ki-67 index scoring results in whole slide images and traditional microscopic examination is lower. Conclusions. The agreement observed for the three scoring methods shows that automation of area selection is an effective tool in supporting physicians and in increasing the reliability of Ki-67 scoring in meningioma.

Terminologies for text-mining; an experiment in the lipoprotein metabolism domain

PubMed Central

Alexopoulou, Dimitra; Wächter, Thomas; Pickersgill, Laura; Eyre, Cecilia; Schroeder, Michael

2008-01-01

Background The engineering of ontologies, especially with a view to a text-mining use, is still a new research field. There does not yet exist a well-defined theory and technology for ontology construction. Many of the ontology design steps remain manual and are based on personal experience and intuition. However, there exist a few efforts on automatic construction of ontologies in the form of extracted lists of terms and relations between them. Results We share experience acquired during the manual development of a lipoprotein metabolism ontology (LMO) to be used for text-mining. We compare the manually created ontology terms with the automatically derived terminology from four different automatic term recognition (ATR) methods. The top 50 predicted terms contain up to 89% relevant terms. For the top 1000 terms the best method still generates 51% relevant terms. In a corpus of 3066 documents 53% of LMO terms are contained and 38% can be generated with one of the methods. Conclusions Given high precision, automatic methods can help decrease development time and provide significant support for the identification of domain-specific vocabulary. The coverage of the domain vocabulary depends strongly on the underlying documents. Ontology development for text mining should be performed in a semi-automatic way; taking ATR results as input and following the guidelines we described. Availability The TFIDF term recognition is available as Web Service, described at PMID:18460175

Comparison of the Manual, Semiautomatic, and Automatic Selection and Leveling of Hot Spots in Whole Slide Images for Ki-67 Quantification in Meningiomas

PubMed Central

Swiderska, Zaneta; Korzynska, Anna; Markiewicz, Tomasz; Lorent, Malgorzata; Zak, Jakub; Wesolowska, Anna; Roszkowiak, Lukasz; Slodkowska, Janina; Grala, Bartlomiej

2015-01-01

Background. This paper presents the study concerning hot-spot selection in the assessment of whole slide images of tissue sections collected from meningioma patients. The samples were immunohistochemically stained to determine the Ki-67/MIB-1 proliferation index used for prognosis and treatment planning. Objective. The observer performance was examined by comparing results of the proposed method of automatic hot-spot selection in whole slide images, results of traditional scoring under a microscope, and results of a pathologist's manual hot-spot selection. Methods. The results of scoring the Ki-67 index using optical scoring under a microscope, software for Ki-67 index quantification based on hot spots selected by two pathologists (resp., once and three times), and the same software but on hot spots selected by proposed automatic methods were compared using Kendall's tau-b statistics. Results. Results show intra- and interobserver agreement. The agreement between Ki-67 scoring with manual and automatic hot-spot selection is high, while agreement between Ki-67 index scoring results in whole slide images and traditional microscopic examination is lower. Conclusions. The agreement observed for the three scoring methods shows that automation of area selection is an effective tool in supporting physicians and in increasing the reliability of Ki-67 scoring in meningioma. PMID:26240787

Autoinjectors Preferred for Intramuscular Epinephrine in Anaphylaxis and Allergic Reactions

PubMed Central

Campbell, Ronna L.; Bellolio, M. Fernanda; Motosue, Megan S.; Sunga, Kharmene L.; Lohse, Christine M.; Rudis, Maria I.

2016-01-01

Introduction Epinephrine is the treatment of choice for anaphylaxis. We surveyed emergency department (ED) healthcare providers regarding two methods of intramuscular (IM) epinephrine administration (autoinjector and manual injection) for the management of anaphylaxis and allergic reactions and identified provider perceptions and preferred method of medication delivery. Methods This observational study adhered to survey reporting guidelines. It was performed through a Web-based survey completed by healthcare providers at an academic ED. The primary outcomes were assessment of provider perceptions and identification of the preferred IM epinephrine administration method by ED healthcare providers. Results Of 217 ED healthcare providers invited to participate, 172 (79%) completed the survey. Overall, 82% of respondents preferred the autoinjector method of epinephrine administration. Providers rated the autoinjector method more favorably for time required for training, ease of use, convenience, satisfaction with weight-based dosing, risk of dosing errors, and speed of administration (p<0.001 for all comparisons). However, manual injection use was rated more favorably for risk of provider self-injury and patient cost (p<0.001 for both comparisons). Three participants (2%) reported a finger stick injury from an epinephrine autoinjector. Conclusion ED healthcare providers preferred the autoinjector method of IM epinephrine administration for the management of anaphylaxis or allergic reactions. Epinephrine autoinjector use may reduce barriers to epinephrine administration for the management of anaphylaxis in the ED. PMID:27833688

Research- and community-based clinicians' attitudes on treatment manuals.

PubMed

Barry, Declan T; Fulgieri, Melissa D; Lavery, Meaghan E; Chawarski, Marek C; Najavits, Lisa M; Schottenfeld, Richard S; Pantalon, Michael V

2008-01-01

We assessed the attitudes of 18 research- and 22 community-based substance abuse clinicians on treatment manuals. Research and community clinicians exhibited favorable attitudes toward manuals, and the majority (72% and 77%, respectively) reported an interest in learning more about substance use disorder (SUD) treatment manuals. Among community clinicians, greater years of experience was significantly associated with less favorable attitudes toward treatment manuals. Research clinicians endorsed significantly higher ratings for the importance attached to "theoretical rationale/overview" and "main session points to address" than community clinicians. Findings suggest that community SUD clinicians are already familiar with and have positive attitudes toward manuals, but specific subgroups have concerns that should be addressed.

Parenting Manuals on Underage Drinking: Differences between Alcohol Industry and Non-Industry Publications

ERIC Educational Resources Information Center

Lindsay, Gordon B.; Merrill, Ray M.; Owens, Adam; Barleen, Nathan A.

2008-01-01

Background: There is some debate over the efficacy of alcohol industry parenting manuals. Purpose: This study compares the content and focus of alcohol industry and non-industry "talk to your child about drinking" parenting manuals. Methods: Parenting manuals from Anheuser-Busch and Miller Brewing Company were compared to federal government and…

Cerebella segmentation on MR images of pediatric patients with medulloblastoma

NASA Astrophysics Data System (ADS)

Shan, Zu Y.; Ji, Qing; Glass, John; Gajjar, Amar; Reddick, Wilburn E.

2005-04-01

In this study, an automated method has been developed to identify the cerebellum from T1-weighted MR brain images of patients with medulloblastoma. A new objective function that is similar to Gibbs free energy in classic physics was defined; and the brain structure delineation was viewed as a process of minimizing Gibbs free energy. We used a rigid-body registration and an active contour (snake) method to minimize the Gibbs free energy in this study. The method was applied to 20 patient data sets to generate cerebellum images and volumetric results. The generated cerebellum images were compared with two manually drawn results. Strong correlations were found between the automatically and manually generated volumetric results, the correlation coefficients with each of manual results were 0.971 and 0.974, respectively. The average Jaccard similarities with each of two manual results were 0.89 and 0.88, respectively. The average Kappa indexes with each of two manual results were 0.94 and 0.93, respectively. These results showed this method was both robust and accurate for cerebellum segmentation. The method may be applied to various research and clinical investigation in which cerebellum segmentation and quantitative MR measurement of cerebellum are needed.

The impact of injector-based contrast agent administration in time-resolved MRA.

PubMed

Budjan, Johannes; Attenberger, Ulrike I; Schoenberg, Stefan O; Pietsch, Hubertus; Jost, Gregor

2018-05-01

Time-resolved contrast-enhanced MR angiography (4D-MRA), which allows the simultaneous visualization of the vasculature and blood-flow dynamics, is widely used in clinical routine. In this study, the impact of two different contrast agent injection methods on 4D-MRA was examined in a controlled, standardized setting in an animal model. Six anesthetized Goettingen minipigs underwent two identical 4D-MRA examinations at 1.5 T in a single session. The contrast agent (0.1 mmol/kg body weight gadobutrol, followed by 20 ml saline) was injected using either manual injection or an automated injection system. A quantitative comparison of vascular signal enhancement and quantitative renal perfusion analyses were performed. Analysis of signal enhancement revealed higher peak enhancements and shorter time to peak intervals for the automated injection. Significantly different bolus shapes were found: automated injection resulted in a compact first-pass bolus shape clearly separated from the recirculation while manual injection resulted in a disrupted first-pass bolus with two peaks. In the quantitative perfusion analyses, statistically significant differences in plasma flow values were found between the injection methods. The results of both qualitative and quantitative 4D-MRA depend on the contrast agent injection method, with automated injection providing more defined bolus shapes and more standardized examination protocols. • Automated and manual contrast agent injection result in different bolus shapes in 4D-MRA. • Manual injection results in an undefined and interrupted bolus with two peaks. • Automated injection provides more defined bolus shapes. • Automated injection can lead to more standardized examination protocols.

Evaluation of a Region-of-Interest Approach for Detecting Progressive Glaucomatous Macular Damage on Optical Coherence Tomography.

PubMed

Wu, Zhichao; Weng, Denis S D; Thenappan, Abinaya; Ritch, Robert; Hood, Donald C

2018-04-01

To evaluate a manual region-of-interest (ROI) approach for detecting progressive macular ganglion cell complex (GCC) changes on optical coherence tomography (OCT) imaging. One hundred forty-six eyes with a clinical diagnosis of glaucoma or suspected glaucoma with macular OCT scans obtained at least 1 year apart were evaluated. Changes in the GCC thickness were identified using a manual ROI approach (ROI M ), whereby region(s) of observed or suspected glaucomatous damage were manually identified when using key features from the macular OCT scan on the second visit. Progression was also evaluated using the global GCC thickness and an automatic ROI approach (ROI A ), where contiguous region(s) that fell below the 1% lower normative limit and exceeded 288 μm 2 in size were evaluated. Longitudinal signal-to-noise ratios (SNRs) were calculated for progressive changes detected by each of these methods using individualized estimates of test-retest variability and age-related changes, obtained from 303 glaucoma and 394 healthy eyes, respectively. On average, the longitudinal SNR for the global thickness, ROI A and ROI M methods were -0.90 y -1 , -0.91 y -1 , and -1.03 y -1 , respectively, and was significantly more negative for the ROI M compared with the global thickness ( P = 0.003) and ROI A methods ( P = 0.021). Progressive glaucomatous macular GCC changes were optimally detected with a manual ROI approach. These findings suggests that an approach based on a qualitative evaluation of OCT imaging information and consideration of known patterns of damage can improve the detection of progressive glaucomatous macular damage.

Methods for semi-automated indexing for high precision information retrieval.

PubMed

Berrios, Daniel C; Cucina, Russell J; Fagan, Lawrence M

2002-01-01

To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISAID were faster (average TPM: 5.6) and had higher rates of concordant index generation. There were substantial learning effects, despite our use of a training/run-in phase. Subjects using the full version of ISAID were much faster by the third indexing session (average TPM: 9.1). There was a statistically significant increase in three-subject concordant indexing rate using the full version of ISAID during the second indexing session (p < 0.05). Users of the ISAID indexing system create complex, precise, and accurate indexing for full-text documents much faster than users of manual methods. Furthermore, the natural language processing methods that ISAID uses to suggest indexes contributes substantially to increased indexing speed and accuracy.

Comparing temporal order judgments and choice reaction time tasks as indices of exogenous spatial cuing.

PubMed

Eskes, Gail A; Klein, Raymond M; Dove, Mary Beth; Coolican, Jamesie; Shore, David I

2007-11-30

Attentional disorders are common in individuals with neurological or psychiatric conditions and impact on recovery and outcome. Thus, it is critical to develop theory-based measures of attentional function to understand potential mechanisms underlying the disorder and to evaluate the effect of intervention. The present study compared two alternative methods to measure the effects of attentional cuing that could be used in populations of individuals who may not be able to make manual responses normally or may show overall slowing in responses. Spatial attention was measured with speeded and unspeeded methods using either manual or voice responses in two standard attention paradigms: the cued target discrimination reaction time (RT) paradigm and the unspeeded temporal order judgment (TOJ) task. The comparison of speeded and unspeeded tasks specifically addresses the concern about interpreting RT differences between cued and uncued trials (taken as a proxy for attention) in the context of drastically different baseline RTs. We found significant cuing effects for both tasks (speeded RT and untimed TOJ) and both response types (vocal and manual) giving clinicians and researchers alternative methods with which to measure the effects of attention in different populations who may not be able to perform the standard speeded RT task.

Manual Physical Therapists' Use of Biopsychosocial History Taking in the Management of Patients with Back or Neck Pain in Clinical Practice

PubMed Central

Oostendorp, Rob A. B.; Elvers, Hans; Mikołajewska, Emilia; Laekeman, Marjan; van Trijffel, Emiel; Samwel, Han; Duquet, William

2015-01-01

Objective. To develop and evaluate process indicators relevant to biopsychosocial history taking in patients with chronic back and neck pain. Methods. The SCEBS method, covering the Somatic, Psychological (Cognition, Emotion, and Behavior), and Social dimensions of chronic pain, was used to evaluate biopsychosocial history taking by manual physical therapists (MPTs). In Phase I, process indicators were developed while in Phase II indicators were tested in practice. Results. Literature-based recommendations were transformed into 51 process indicators. Twenty MTPs contributed 108 patient audio recordings. History taking was excellent (98.3%) for the Somatic dimension, very inadequate for Cognition (43.1%) and Behavior (38.3%), weak (27.8%) for Emotion, and low (18.2%) for the Social dimension. MTPs estimated their coverage of the Somatic dimension as excellent (100%), as adequate for Cognition, Emotion, and Behavior (60.1%), and as very inadequate for the Social dimension (39.8%). Conclusion. MTPs perform screening for musculoskeletal pain mainly through the use of somatic dimension of (chronic) pain. Psychological and social dimensions of chronic pain were inadequately covered by MPTs. Furthermore, a substantial discrepancy between actual and self-estimated use of biopsychosocial history taking was noted. We strongly recommend full implementation of the SCEBS method in educational programs in manual physical therapy. PMID:25945358

Accuracy and reliability of coronal and sagittal spinal curvature data based on patient-specific three-dimensional models created by the EOS 2D/3D imaging system.

PubMed

Somoskeöy, Szabolcs; Tunyogi-Csapó, Miklós; Bogyó, Csaba; Illés, Tamás

2012-11-01

Three-dimensional (3D) deformations of the spine are predominantly characterized by two-dimensional (2D) angulation measurements in coronal and sagittal planes, using anteroposterior and lateral X-ray images. For coronal curves, a method originally described by Cobb and for sagittal curves a modified Cobb method are most widely used in practice, and these methods have been shown to exhibit good-to-excellent reliability and reproducibility, carried out either manually or by computer-based tools. Recently, an ultralow radiation dose-integrated radioimaging solution was introduced with special software for realistic 3D visualization and parametric characterization of the spinal column. Comparison of accuracy, correlation of measurement values, intraobserver and interrater reliability of methods by conventional manual 2D and sterEOS 3D measurements in a routine clinical setting. Retrospective nonrandomized study of diagnostic X-ray images created as part of a routine clinical protocol of eligible patients examined at our clinic during a 30-month period between July 2007 and December 2009. In total, 201 individuals (170 females, 31 males; mean age, 19.88 years) including 10 healthy athletes with normal spine and patients with adolescent idiopathic scoliosis (175 cases), adult degenerative scoliosis (11 cases), and Scheuermann hyperkyphosis (5 cases). Overall range of coronal curves was between 2.4° and 117.5°. Analysis of accuracy and reliability of measurements were carried out on a group of all patients and in subgroups based on coronal plane deviation: 0° to 10° (Group 1, n=36), 10° to 25° (Group 2, n=25), 25° to 50° (Group 3, n=69), 50° to 75° (Group 4, n=49), and more than 75° (Group 5, n=22). Coronal and sagittal curvature measurements were determined by three experienced examiners, using either traditional 2D methods or automatic measurements based on sterEOS 3D reconstructions. Manual measurements were performed three times, and sterEOS 3D reconstructions and automatic measurements were performed two times by each examiner. Means comparison t test, Pearson bivariate correlation analysis, reliability analysis by intraclass correlation coefficients for intraobserver reproducibility and interrater reliability were performed using SPSS v16.0 software (IBM Corp., Armonk, NY, USA). No funds were received in support of this work. No benefits in any form have been or will be received from a commercial party related directly or indirectly to the subject of this article. In comparison with manual 2D methods, only small and nonsignificant differences were detectable in sterEOS 3D-based curvature data. Intraobserver reliability was excellent for both methods, and interrater reproducibility was consistently higher for sterEOS 3D methods that was found to be unaffected by the magnitude of coronal curves or sagittal plane deviations. This is the first clinical report on EOS 2D/3D system (EOS Imaging, Paris, France) and its sterEOS 3D software, documenting an excellent capability for accurate, reliable, and reproducible spinal curvature measurements. Copyright © 2012 Elsevier Inc. All rights reserved.

Fourier Spectroscopy: A Simple Analysis Technique

ERIC Educational Resources Information Center

Oelfke, William C.

1975-01-01

Presents a simple method of analysis in which the student can integrate, point by point, any interferogram to obtain its Fourier transform. The manual technique requires no special equipment and is based on relationships that most undergraduate physics students can derive from the Fourier integral equations. (Author/MLH)

Near infrared spectrometers determine stage maturity in channel catfish

USDA-ARS?s Scientific Manuscript database

Maturation is not synchronized in channel catfish and hence, individual fish are frequently handled and manually stage for maturation based on a selective subjective method. Fully matured fish are more responsive to hormone-induced spawning, and often result in better egg quality, higher relative f...

Comparison of manual & automated analysis methods for corneal endothelial cell density measurements by specular microscopy.

PubMed

Huang, Jianyan; Maram, Jyotsna; Tepelus, Tudor C; Modak, Cristina; Marion, Ken; Sadda, SriniVas R; Chopra, Vikas; Lee, Olivia L

2017-08-07

To determine the reliability of corneal endothelial cell density (ECD) obtained by automated specular microscopy versus that of validated manual methods and factors that predict such reliability. Sharp central images from 94 control and 106 glaucomatous eyes were captured with Konan specular microscope NSP-9900. All images were analyzed by trained graders using Konan CellChek Software, employing the fully- and semi-automated methods as well as Center Method. Images with low cell count (input cells number <100) and/or guttata were compared with the Center and Flex-Center Methods. ECDs were compared and absolute error was used to assess variation. The effect on ECD of age, cell count, cell size, and cell size variation was evaluated. No significant difference was observed between the Center and Flex-Center Methods in corneas with guttata (p=0.48) or low ECD (p=0.11). No difference (p=0.32) was observed in ECD of normal controls <40 yrs old between the fully-automated method and manual Center Method. However, in older controls and glaucomatous eyes, ECD was overestimated by the fully-automated method (p=0.034) and semi-automated method (p=0.025) as compared to manual method. Our findings show that automated analysis significantly overestimates ECD in the eyes with high polymegathism and/or large cell size, compared to the manual method. Therefore, we discourage reliance upon the fully-automated method alone to perform specular microscopy analysis, particularly if an accurate ECD value is imperative. Copyright © 2017. Published by Elsevier España, S.L.U.

Sample registration software for process automation in the Neutron Activation Analysis (NAA) Facility in Malaysia nuclear agency

NASA Astrophysics Data System (ADS)

Rahman, Nur Aira Abd; Yussup, Nolida; Salim, Nazaratul Ashifa Bt. Abdullah; Ibrahim, Maslina Bt. Mohd; Mokhtar, Mukhlis B.; Soh@Shaari, Syirrazie Bin Che; Azman, Azraf B.; Ismail, Nadiah Binti

2015-04-01

Neutron Activation Analysis (NAA) had been established in Nuclear Malaysia since 1980s. Most of the procedures established were done manually including sample registration. The samples were recorded manually in a logbook and given ID number. Then all samples, standards, SRM and blank were recorded on the irradiation vial and several forms prior to irradiation. These manual procedures carried out by the NAA laboratory personnel were time consuming and not efficient. Sample registration software is developed as part of IAEA/CRP project on `Development of Process Automation in the Neutron Activation Analysis (NAA) Facility in Malaysia Nuclear Agency (RC17399)'. The objective of the project is to create a pc-based data entry software during sample preparation stage. This is an effective method to replace redundant manual data entries that needs to be completed by laboratory personnel. The software developed will automatically generate sample code for each sample in one batch, create printable registration forms for administration purpose, and store selected parameters that will be passed to sample analysis program. The software is developed by using National Instruments Labview 8.6.

A simplified form of cardiotocography for antenatal fetal assessment.

PubMed

Mahomed, K; Gupta, B K; Matikiti, L; Murape, T S

1992-12-01

Antenatal cardiotocography has become the primary method of evaluation of fetal wellbeing, and the relationship between the presence of fetal heart rate accelerations in response to fetal movement and subsequent good fetal outcome has been demonstrated. However, in areas where electronic monitors are few or not available it would be useful if such accelerations could be demonstrated using the Pinard stethoscope. A prospective study involving 200 women with a singleton pregnancy of more than 34 weeks gestation was performed at Harare Maternity Hospital, Harare, Zimbabwe, when a 6 min electronic trace using an external transducer was compared with simultaneously performed 6 min manual record using the Pinard stethoscope. The findings showed that the manual record has a sensitivity of 75% and although traces with excessive base line variability would show an acceleration on the manual record, in no case with a flat trace was an acceleration noted on the manual record. This acceptable degree of sensitivity would allow for a significant decrease in the number of women being referred for electronic tracing and would be a more appropriate use of limited resources in terms of manpower and equipment.

The effectiveness of manual therapy in treating cervicogenic dizziness: a systematic review.

PubMed

Yaseen, Khalid; Hendrick, Paul; Ismail, Ayah; Felemban, Mohannad; Alshehri, Mansour Abdullah

2018-01-01

[Purpose] This review provides an evaluation of the evidence for the effectiveness of using manual therapy to treat cervicogenic dizziness. [Subjects and Methods] The literature was systematically searched on the May 2, 2016 using the following online databases: Medline, EMBASE, CINAHL and PEDro. This review included randomised controlled trials and compared the efficacy of manual therapy for the treatment of cervicogenic dizziness, compared to other types of intervention. This study measured changes based on dizziness intensity and frequency. [Results] The primary search found 30 articles, but only four articles met the inclusion criteria. Assessment of methodological quality was performed by two researchers using the PEDro scale. The level of evidence was determined using a recognised grading scale. Three out of the four articles were deemed to have high methodological quality, while the fourth was rated as moderate quality. The attributed level of evidence was moderate (level 2). [Conclusion] Manual therapy is potentially effective for managing cervicogenic dizziness. However, due to the heterogeneity of the results and techniques and the low number of studies, further research is recommended to provide conclusive evidence.

Mapping land cover through time with the Rapid Land Cover Mapper—Documentation and user manual

USGS Publications Warehouse

Cotillon, Suzanne E.; Mathis, Melissa L.

2017-02-15

The Rapid Land Cover Mapper is an Esri ArcGIS® Desktop add-in, which was created as an alternative to automated or semiautomated mapping methods. Based on a manual photo interpretation technique, the tool facilitates mapping over large areas and through time, and produces time-series raster maps and associated statistics that characterize the changing landscapes. The Rapid Land Cover Mapper add-in can be used with any imagery source to map various themes (for instance, land cover, soils, or forest) at any chosen mapping resolution. The user manual contains all essential information for the user to make full use of the Rapid Land Cover Mapper add-in. This manual includes a description of the add-in functions and capabilities, and step-by-step procedures for using the add-in. The Rapid Land Cover Mapper add-in was successfully used by the U.S. Geological Survey West Africa Land Use Dynamics team to accurately map land use and land cover in 17 West African countries through time (1975, 2000, and 2013).

2D and 3D Method of Characteristic Tools for Complex Nozzle Development

NASA Technical Reports Server (NTRS)

Rice, Tharen

2003-01-01

This report details the development of a 2D and 3D Method of Characteristic (MOC) tool for the design of complex nozzle geometries. These tools are GUI driven and can be run on most Windows-based platforms. The report provides a user's manual for these tools as well as explains the mathematical algorithms used in the MOC solutions.

Exponential error reduction in pretransfusion testing with automation.

PubMed

South, Susan F; Casina, Tony S; Li, Lily

2012-08-01

Protecting the safety of blood transfusion is the top priority of transfusion service laboratories. Pretransfusion testing is a critical element of the entire transfusion process to enhance vein-to-vein safety. Human error associated with manual pretransfusion testing is a cause of transfusion-related mortality and morbidity and most human errors can be eliminated by automated systems. However, the uptake of automation in transfusion services has been slow and many transfusion service laboratories around the world still use manual blood group and antibody screen (G&S) methods. The goal of this study was to compare error potentials of commonly used manual (e.g., tiles and tubes) versus automated (e.g., ID-GelStation and AutoVue Innova) G&S methods. Routine G&S processes in seven transfusion service laboratories (four with manual and three with automated G&S methods) were analyzed using failure modes and effects analysis to evaluate the corresponding error potentials of each method. Manual methods contained a higher number of process steps ranging from 22 to 39, while automated G&S methods only contained six to eight steps. Corresponding to the number of the process steps that required human interactions, the risk priority number (RPN) of the manual methods ranged from 5304 to 10,976. In contrast, the RPN of the automated methods was between 129 and 436 and also demonstrated a 90% to 98% reduction of the defect opportunities in routine G&S testing. This study provided quantitative evidence on how automation could transform pretransfusion testing processes by dramatically reducing error potentials and thus would improve the safety of blood transfusion. © 2012 American Association of Blood Banks.

TECHNICAL MANUAL: A SURVEY OF EQUIPMENT AND METHODS FOR PARTICULATE SAMPLING IN INDUSTRIAL PROCESS STREAMS

EPA Science Inventory

The manual lists and describes the instruments and techniques that are available for measuring the concentration or size distribution of particles suspended in process streams. The standard, official, well established methods are described as well as some experimental methods and...

California Publicly-Owned Utilities (POUs) – LBNL ‘Beyond Widgets’ Project. Task: ambient lighting and occupancy-based plug load control. System Program Manual

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

Robinson, Alastair; Mathew, Paul A.; Regnier, Cynthia

This program manual contains detailed technical information for implementing an incentive program for task-ambient lighting and occupancy-based plug load control. This manual was developed by Lawrence Berkeley National Laboratory, in collaboration with the California Publicly-Owned Utilities (CA POUs) as a partner in the ‘Beyond Widgets’ program funded by the U.S. Department of Energy Building Technologies Office. The primary audience for this manual is the program staff of the various CA POUs. It may also be used by other utility incentive programs to help develop similar programs. It is anticipated that the content of this manual be utilized by the CAmore » POU staff for developing related documents such as the Technical Resource Manual and other filings pertaining to the rollout of an energy systems-based rebate incentive program.« less

Automated Dissolution for Enteric-Coated Aspirin Tablets: A Case Study for Method Transfer to a RoboDis II.

PubMed

Ibrahim, Sarah A; Martini, Luigi

2014-08-01

Dissolution method transfer is a complicated yet common process in the pharmaceutical industry. With increased pharmaceutical product manufacturing and dissolution acceptance requirements, dissolution testing has become one of the most labor-intensive quality control testing methods. There is an increased trend for automation in dissolution testing, particularly for large pharmaceutical companies to reduce variability and increase personnel efficiency. There is no official guideline for dissolution testing method transfer from a manual, semi-automated, to automated dissolution tester. In this study, a manual multipoint dissolution testing procedure for an enteric-coated aspirin tablet was transferred effectively and reproducibly to a fully automated dissolution testing device, RoboDis II. Enteric-coated aspirin samples were used as a model formulation to assess the feasibility and accuracy of media pH change during continuous automated dissolution testing. Several RoboDis II parameters were evaluated to ensure the integrity and equivalency of dissolution method transfer from a manual dissolution tester. This current study provides a systematic outline for the transfer of the manual dissolution testing protocol to an automated dissolution tester. This study further supports that automated dissolution testers compliant with regulatory requirements and similar to manual dissolution testers facilitate method transfer. © 2014 Society for Laboratory Automation and Screening.

A neurite quality index and machine vision software for improved quantification of neurodegeneration.

PubMed

Romero, Peggy; Miller, Ted; Garakani, Arman

2009-12-01

Current methods to assess neurodegradation in dorsal root ganglion cultures as a model for neurodegenerative diseases are imprecise and time-consuming. Here we describe two new methods to quantify neuroprotection in these cultures. The neurite quality index (NQI) builds upon earlier manual methods, incorporating additional morphological events to increase detection sensitivity for the detection of early degeneration events. Neurosight is a machine vision-based method that recapitulates many of the strengths of NQI while enabling high-throughput screening applications with decreased costs.

Petrographic methods of examining hardened concrete : a petrographic manual.

DOT National Transportation Integrated Search

1997-11-01

This manual was undertaken to record for all persons wishing to do concrete : petrography the petrographic procedures that have been found useful at the : Virginia Transportation Research Council. The manual is made up of an : introduction and chapte...

Calibration of highway safety manual work zone crash modification factors.

DOT National Transportation Integrated Search

2014-06-01

The Highway Safety Manual is the national safety manual that provides quantitative methods for analyzing highway safety. The : HSM presents crash modification factors related to work zone characteristics such as work zone duration and length. These c...

A Customized Attention-Based Long Short-Term Memory Network for Distant Supervised Relation Extraction.

PubMed

He, Dengchao; Zhang, Hongjun; Hao, Wenning; Zhang, Rui; Cheng, Kai

2017-07-01

Distant supervision, a widely applied approach in the field of relation extraction can automatically generate large amounts of labeled training corpus with minimal manual effort. However, the labeled training corpus may have many false-positive data, which would hurt the performance of relation extraction. Moreover, in traditional feature-based distant supervised approaches, extraction models adopt human design features with natural language processing. It may also cause poor performance. To address these two shortcomings, we propose a customized attention-based long short-term memory network. Our approach adopts word-level attention to achieve better data representation for relation extraction without manually designed features to perform distant supervision instead of fully supervised relation extraction, and it utilizes instance-level attention to tackle the problem of false-positive data. Experimental results demonstrate that our proposed approach is effective and achieves better performance than traditional methods.

Validation of newly developed and redesigned key indicator methods for assessment of different working conditions with physical workloads based on mixed-methods design: a study protocol.

PubMed

Klussmann, Andre; Liebers, Falk; Brandstädt, Felix; Schust, Marianne; Serafin, Patrick; Schäfer, Andreas; Gebhardt, Hansjürgen; Hartmann, Bernd; Steinberg, Ulf

2017-08-21

The impact of work-related musculoskeletal disorders is considerable. The assessment of work tasks with physical workloads is crucial to estimate the work-related health risks of exposed employees. Three key indicator methods are available for risk assessment regarding manual lifting, holding and carrying of loads; manual pulling and pushing of loads; and manual handling operations. Three further KIMs for risk assessment regarding whole-body forces, awkward body postures and body movement have been developed de novo. In addition, the development of a newly drafted combined method for mixed exposures is planned. All methods will be validated regarding face validity, reliability, convergent validity, criterion validity and further aspects of utility under practical conditions. As part of the joint project MEGAPHYS (multilevel risk assessment of physical workloads), a mixed-methods study is being designed for the validation of KIMs and conducted in companies of different sizes and branches in Germany. Workplaces are documented and analysed by observations, applying KIMs, interviews and assessment of environmental conditions. Furthermore, a survey among the employees at the respective workplaces takes place with standardised questionnaires, interviews and physical examinations. It is intended to include 1200 employees at 120 different workplaces. For analysis of the quality criteria, recommendations of the COSMIN checklist (COnsensus-based Standards for the selection of health Measurement INstruments) will be taken into account. The study was planned and conducted in accordance with the German Medical Professional Code and the Declaration of Helsinki as well as the German Federal Data Protection Act. The design of the study was approved by ethics committees. We intend to publish the validated KIMs in 2018. Results will be published in peer-reviewed journals, presented at international meetings and disseminated to actual users for practical application. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Fully automatic segmentation of fluorescein leakage in subjects with diabetic macular edema.

PubMed

Rabbani, Hossein; Allingham, Michael J; Mettu, Priyatham S; Cousins, Scott W; Farsiu, Sina

2015-01-29

To create and validate software to automatically segment leakage area in real-world clinical fluorescein angiography (FA) images of subjects with diabetic macular edema (DME). Fluorescein angiography images obtained from 24 eyes of 24 subjects with DME were retrospectively analyzed. Both video and still-frame images were obtained using a Heidelberg Spectralis 6-mode HRA/OCT unit. We aligned early and late FA frames in the video by a two-step nonrigid registration method. To remove background artifacts, we subtracted early and late FA frames. Finally, after postprocessing steps, including detection and inpainting of the vessels, a robust active contour method was utilized to obtain leakage area in a 1500-μm-radius circular region centered at the fovea. Images were captured at different fields of view (FOVs) and were often contaminated with outliers, as is the case in real-world clinical imaging. Our algorithm was applied to these images with no manual input. Separately, all images were manually segmented by two retina specialists. The sensitivity, specificity, and accuracy of manual interobserver, manual intraobserver, and automatic methods were calculated. The mean accuracy was 0.86 ± 0.08 for automatic versus manual, 0.83 ± 0.16 for manual interobserver, and 0.90 ± 0.08 for manual intraobserver segmentation methods. Our fully automated algorithm can reproducibly and accurately quantify the area of leakage of clinical-grade FA video and is congruent with expert manual segmentation. The performance was reliable for different DME subtypes. This approach has the potential to reduce time and labor costs and may yield objective and reproducible quantitative measurements of DME imaging biomarkers. Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc.

Advantages of combined touch screen technology and text hyperlink for the pathology grossing manual: a simple approach to access instructive information in biohazardous environments.

PubMed

Qu, Zhenhong; Ghorbani, Rhonda P; Li, Hongyan; Hunter, Robert L; Hannah, Christina D

2007-03-01

Gross examination, encompassing description, dissection, and sampling, is a complex task and an essential component of surgical pathology. Because of the complexity of the task, standardized protocols to guide the gross examination often become a bulky manual that is difficult to use. This problem is further compounded by the high specimen volume and biohazardous nature of the task. As a result, such a manual is often underused, leading to errors that are potentially harmful and time consuming to correct-a common chronic problem affecting many pathology laboratories. To combat this problem, we have developed a simple method that incorporates complex text and graphic information of a typical procedure manual and yet allows easy access to any intended instructive information in the manual. The method uses the Object-Linking-and-Embedding function of Microsoft Word (Microsoft, Redmond, WA) to establish hyperlinks among different contents, and then it uses the touch screen technology to facilitate navigation through the manual on a computer screen installed at the cutting bench with no need for a physical keyboard or a mouse. It takes less than 4 seconds to reach any intended information in the manual by 3 to 4 touches on the screen. A 3-year follow-up study shows that this method has increased use of the manual and has improved the quality of gross examination. The method is simple and can be easily tailored to different formats of instructive information, allowing flexible organization, easy access, and quick navigation. Increased compliance to instructive information reduces errors at the grossing bench and improves work efficiency.

Rapid Contour-based Segmentation for 18F-FDG PET Imaging of Lung Tumors by Using ITK-SNAP: Comparison to Expert-based Segmentation.

PubMed

Besson, Florent L; Henry, Théophraste; Meyer, Céline; Chevance, Virgile; Roblot, Victoire; Blanchet, Elise; Arnould, Victor; Grimon, Gilles; Chekroun, Malika; Mabille, Laurence; Parent, Florence; Seferian, Andrei; Bulifon, Sophie; Montani, David; Humbert, Marc; Chaumet-Riffaud, Philippe; Lebon, Vincent; Durand, Emmanuel

2018-04-03

Purpose To assess the performance of the ITK-SNAP software for fluorodeoxyglucose (FDG) positron emission tomography (PET) segmentation of complex-shaped lung tumors compared with an optimized, expert-based manual reference standard. Materials and Methods Seventy-six FDG PET images of thoracic lesions were retrospectively segmented by using ITK-SNAP software. Each tumor was manually segmented by six raters to generate an optimized reference standard by using the simultaneous truth and performance level estimate algorithm. Four raters segmented 76 FDG PET images of lung tumors twice by using ITK-SNAP active contour algorithm. Accuracy of ITK-SNAP procedure was assessed by using Dice coefficient and Hausdorff metric. Interrater and intrarater reliability were estimated by using intraclass correlation coefficients of output volumes. Finally, the ITK-SNAP procedure was compared with currently recommended PET tumor delineation methods on the basis of thresholding at 41% volume of interest (VOI; VOI 41 ) and 50% VOI (VOI 50 ) of the tumor's maximal metabolism intensity. Results Accuracy estimates for the ITK-SNAP procedure indicated a Dice coefficient of 0.83 (95% confidence interval: 0.77, 0.89) and a Hausdorff distance of 12.6 mm (95% confidence interval: 9.82, 15.32). Interrater reliability was an intraclass correlation coefficient of 0.94 (95% confidence interval: 0.91, 0.96). The intrarater reliabilities were intraclass correlation coefficients above 0.97. Finally, VOI 41 and VOI 50 accuracy metrics were as follows: Dice coefficient, 0.48 (95% confidence interval: 0.44, 0.51) and 0.34 (95% confidence interval: 0.30, 0.38), respectively, and Hausdorff distance, 25.6 mm (95% confidence interval: 21.7, 31.4) and 31.3 mm (95% confidence interval: 26.8, 38.4), respectively. Conclusion ITK-SNAP is accurate and reliable for active-contour-based segmentation of heterogeneous thoracic PET tumors. ITK-SNAP surpassed the recommended PET methods compared with ground truth manual segmentation. © RSNA, 2018.

Application of surface geophysics to ground-water investigations

USGS Publications Warehouse

Zohdy, Adel A.R.; Eaton, Gordon P.; Mabey, Don R.

1974-01-01

This manual reviews the standard methods of surface geophysics applicable to ground-water investigations. It covers electrical methods, seismic and gravity methods, and magnetic methods. The general physical principles underlying each method and its capabilities and limitations are described. Possibilities for non-uniqueness of interpretation of geophysical results are noted. Examples of actual use of the methods are given to illustrate applications and interpretation in selected geohydrologic environments. The objective of the manual is to provide the hydrogeologist with a sufficient understanding of the capabilities, imitations, and relative cost of geophysical methods to make sound decisions as to when to use of these methods is desirable. The manual also provides enough information for the hydrogeologist to work with a geophysicist in designing geophysical surveys that differentiate significant hydrogeologic changes.

Supervised segmentation of microelectrode recording artifacts using power spectral density.

PubMed

Bakstein, Eduard; Schneider, Jakub; Sieger, Tomas; Novak, Daniel; Wild, Jiri; Jech, Robert

2015-08-01

Appropriate detection of clean signal segments in extracellular microelectrode recordings (MER) is vital for maintaining high signal-to-noise ratio in MER studies. Existing alternatives to manual signal inspection are based on unsupervised change-point detection. We present a method of supervised MER artifact classification, based on power spectral density (PSD) and evaluate its performance on a database of 95 labelled MER signals. The proposed method yielded test-set accuracy of 90%, which was close to the accuracy of annotation (94%). The unsupervised methods achieved accuracy of about 77% on both training and testing data.

Validation of a low cost computer-based method for quantification of immunohistochemistry-stained sections.

PubMed

Montgomery, Jill D; Hensler, Heather R; Jacobson, Lisa P; Jenkins, Frank J

2008-07-01

The aim of the present study was to determine if the Alpha DigiDoc RT system would be an effective method of quantifying immunohistochemical staining as compared with a manual counting method, which is considered the gold standard. Two readers were used to count 31 samples by both methods. The results obtained using the Bland-Altman for concordance deemed no statistical difference between the 2 methods. Thus, the Alpha DigiDoc RT system is an effective, low cost method to quantify immunohistochemical data.

Development of a computer-aided design software for dental splint in orthognathic surgery

NASA Astrophysics Data System (ADS)

Chen, Xiaojun; Li, Xing; Xu, Lu; Sun, Yi; Politis, Constantinus; Egger, Jan

2016-12-01

In the orthognathic surgery, dental splints are important and necessary to help the surgeon reposition the maxilla or mandible. However, the traditional methods of manual design of dental splints are difficult and time-consuming. The research on computer-aided design software for dental splints is rarely reported. Our purpose is to develop a novel special software named EasySplint to design the dental splints conveniently and efficiently. The design can be divided into two steps, which are the generation of initial splint base and the Boolean operation between it and the maxilla-mandibular model. The initial splint base is formed by ruled surfaces reconstructed using the manually picked points. Then, a method to accomplish Boolean operation based on the distance filed of two meshes is proposed. The interference elimination can be conducted on the basis of marching cubes algorithm and Boolean operation. The accuracy of the dental splint can be guaranteed since the original mesh is utilized to form the result surface. Using EasySplint, the dental splints can be designed in about 10 minutes and saved as a stereo lithography (STL) file for 3D printing in clinical applications. Three phantom experiments were conducted and the efficiency of our method was demonstrated.

Task-based evaluation of segmentation algorithms for diffusion-weighted MRI without using a gold standard

PubMed Central

Jha, Abhinav K.; Kupinski, Matthew A.; Rodríguez, Jeffrey J.; Stephen, Renu M.; Stopeck, Alison T.

2012-01-01

In many studies, the estimation of the apparent diffusion coefficient (ADC) of lesions in visceral organs in diffusion-weighted (DW) magnetic resonance images requires an accurate lesion-segmentation algorithm. To evaluate these lesion-segmentation algorithms, region-overlap measures are used currently. However, the end task from the DW images is accurate ADC estimation, and the region-overlap measures do not evaluate the segmentation algorithms on this task. Moreover, these measures rely on the existence of gold-standard segmentation of the lesion, which is typically unavailable. In this paper, we study the problem of task-based evaluation of segmentation algorithms in DW imaging in the absence of a gold standard. We first show that using manual segmentations instead of gold-standard segmentations for this task-based evaluation is unreliable. We then propose a method to compare the segmentation algorithms that does not require gold-standard or manual segmentation results. The no-gold-standard method estimates the bias and the variance of the error between the true ADC values and the ADC values estimated using the automated segmentation algorithm. The method can be used to rank the segmentation algorithms on the basis of both accuracy and precision. We also propose consistency checks for this evaluation technique. PMID:22713231

Self-Supervised Chinese Ontology Learning from Online Encyclopedias

PubMed Central

Shao, Zhiqing; Ruan, Tong

2014-01-01

Constructing ontology manually is a time-consuming, error-prone, and tedious task. We present SSCO, a self-supervised learning based chinese ontology, which contains about 255 thousand concepts, 5 million entities, and 40 million facts. We explore the three largest online Chinese encyclopedias for ontology learning and describe how to transfer the structured knowledge in encyclopedias, including article titles, category labels, redirection pages, taxonomy systems, and InfoBox modules, into ontological form. In order to avoid the errors in encyclopedias and enrich the learnt ontology, we also apply some machine learning based methods. First, we proof that the self-supervised machine learning method is practicable in Chinese relation extraction (at least for synonymy and hyponymy) statistically and experimentally and train some self-supervised models (SVMs and CRFs) for synonymy extraction, concept-subconcept relation extraction, and concept-instance relation extraction; the advantages of our methods are that all training examples are automatically generated from the structural information of encyclopedias and a few general heuristic rules. Finally, we evaluate SSCO in two aspects, scale and precision; manual evaluation results show that the ontology has excellent precision, and high coverage is concluded by comparing SSCO with other famous ontologies and knowledge bases; the experiment results also indicate that the self-supervised models obviously enrich SSCO. PMID:24715819

Development of a computer-aided design software for dental splint in orthognathic surgery

PubMed Central

Chen, Xiaojun; Li, Xing; Xu, Lu; Sun, Yi; Politis, Constantinus; Egger, Jan

2016-01-01

In the orthognathic surgery, dental splints are important and necessary to help the surgeon reposition the maxilla or mandible. However, the traditional methods of manual design of dental splints are difficult and time-consuming. The research on computer-aided design software for dental splints is rarely reported. Our purpose is to develop a novel special software named EasySplint to design the dental splints conveniently and efficiently. The design can be divided into two steps, which are the generation of initial splint base and the Boolean operation between it and the maxilla-mandibular model. The initial splint base is formed by ruled surfaces reconstructed using the manually picked points. Then, a method to accomplish Boolean operation based on the distance filed of two meshes is proposed. The interference elimination can be conducted on the basis of marching cubes algorithm and Boolean operation. The accuracy of the dental splint can be guaranteed since the original mesh is utilized to form the result surface. Using EasySplint, the dental splints can be designed in about 10 minutes and saved as a stereo lithography (STL) file for 3D printing in clinical applications. Three phantom experiments were conducted and the efficiency of our method was demonstrated. PMID:27966601

Development of a computer-aided design software for dental splint in orthognathic surgery.

PubMed

Chen, Xiaojun; Li, Xing; Xu, Lu; Sun, Yi; Politis, Constantinus; Egger, Jan

2016-12-14

In the orthognathic surgery, dental splints are important and necessary to help the surgeon reposition the maxilla or mandible. However, the traditional methods of manual design of dental splints are difficult and time-consuming. The research on computer-aided design software for dental splints is rarely reported. Our purpose is to develop a novel special software named EasySplint to design the dental splints conveniently and efficiently. The design can be divided into two steps, which are the generation of initial splint base and the Boolean operation between it and the maxilla-mandibular model. The initial splint base is formed by ruled surfaces reconstructed using the manually picked points. Then, a method to accomplish Boolean operation based on the distance filed of two meshes is proposed. The interference elimination can be conducted on the basis of marching cubes algorithm and Boolean operation. The accuracy of the dental splint can be guaranteed since the original mesh is utilized to form the result surface. Using EasySplint, the dental splints can be designed in about 10 minutes and saved as a stereo lithography (STL) file for 3D printing in clinical applications. Three phantom experiments were conducted and the efficiency of our method was demonstrated.

Self-supervised Chinese ontology learning from online encyclopedias.

PubMed

Hu, Fanghuai; Shao, Zhiqing; Ruan, Tong

2014-01-01

Constructing ontology manually is a time-consuming, error-prone, and tedious task. We present SSCO, a self-supervised learning based chinese ontology, which contains about 255 thousand concepts, 5 million entities, and 40 million facts. We explore the three largest online Chinese encyclopedias for ontology learning and describe how to transfer the structured knowledge in encyclopedias, including article titles, category labels, redirection pages, taxonomy systems, and InfoBox modules, into ontological form. In order to avoid the errors in encyclopedias and enrich the learnt ontology, we also apply some machine learning based methods. First, we proof that the self-supervised machine learning method is practicable in Chinese relation extraction (at least for synonymy and hyponymy) statistically and experimentally and train some self-supervised models (SVMs and CRFs) for synonymy extraction, concept-subconcept relation extraction, and concept-instance relation extraction; the advantages of our methods are that all training examples are automatically generated from the structural information of encyclopedias and a few general heuristic rules. Finally, we evaluate SSCO in two aspects, scale and precision; manual evaluation results show that the ontology has excellent precision, and high coverage is concluded by comparing SSCO with other famous ontologies and knowledge bases; the experiment results also indicate that the self-supervised models obviously enrich SSCO.

Hippocampal volume change measurement: quantitative assessment of the reproducibility of expert manual outlining and the automated methods FreeSurfer and FIRST.

PubMed

Mulder, Emma R; de Jong, Remko A; Knol, Dirk L; van Schijndel, Ronald A; Cover, Keith S; Visser, Pieter J; Barkhof, Frederik; Vrenken, Hugo

2014-05-15

To measure hippocampal volume change in Alzheimer's disease (AD) or mild cognitive impairment (MCI), expert manual delineation is often used because of its supposed accuracy. It has been suggested that expert outlining yields poorer reproducibility as compared to automated methods, but this has not been investigated. To determine the reproducibilities of expert manual outlining and two common automated methods for measuring hippocampal atrophy rates in healthy aging, MCI and AD. From the Alzheimer's Disease Neuroimaging Initiative (ADNI), 80 subjects were selected: 20 patients with AD, 40 patients with mild cognitive impairment (MCI) and 20 healthy controls (HCs). Left and right hippocampal volume change between baseline and month-12 visit was assessed by using expert manual delineation, and by the automated software packages FreeSurfer (longitudinal processing stream) and FIRST. To assess reproducibility of the measured hippocampal volume change, both back-to-back (BTB) MPRAGE scans available for each visit were analyzed. Hippocampal volume change was expressed in μL, and as a percentage of baseline volume. Reproducibility of the 1-year hippocampal volume change was estimated from the BTB measurements by using linear mixed model to calculate the limits of agreement (LoA) of each method, reflecting its measurement uncertainty. Using the delta method, approximate p-values were calculated for the pairwise comparisons between methods. Statistical analyses were performed both with inclusion and exclusion of visibly incorrect segmentations. Visibly incorrect automated segmentation in either one or both scans of a longitudinal scan pair occurred in 7.5% of the hippocampi for FreeSurfer and in 6.9% of the hippocampi for FIRST. After excluding these failed cases, reproducibility analysis for 1-year percentage volume change yielded LoA of ±7.2% for FreeSurfer, ±9.7% for expert manual delineation, and ±10.0% for FIRST. Methods ranked the same for reproducibility of 1-year μL volume change, with LoA of ±218 μL for FreeSurfer, ±319 μL for expert manual delineation, and ±333 μL for FIRST. Approximate p-values indicated that reproducibility was better for FreeSurfer than for manual or FIRST, and that manual and FIRST did not differ. Inclusion of failed automated segmentations led to worsening of reproducibility of both automated methods for 1-year raw and percentage volume change. Quantitative reproducibility values of 1-year microliter and percentage hippocampal volume change were roughly similar between expert manual outlining, FIRST and FreeSurfer, but FreeSurfer reproducibility was statistically significantly superior to both manual outlining and FIRST after exclusion of failed segmentations. Copyright © 2014 Elsevier Inc. All rights reserved.

Dynamic delivery of the National Transit Database Sampling Manual.

DOT National Transportation Integrated Search

2013-02-01

This project improves the National Transit Database (NTD) Sampling Manual and develops an Internet-based, WordPress-powered interactive Web tool to deliver the new NTD Sampling Manual dynamically. The new manual adds guidance and a tool for transit a...

Dynamic delivery of the National Transit Database sampling manual.

DOT National Transportation Integrated Search

2013-02-01

This project improves the National Transit Database (NTD) Sampling Manual and develops an Internet-based, WordPress-powered interactive Web tool to deliver the new NTD Sampling Manual dynamically. The new manual adds guidance and a tool for transit a...

Diet manuals to practice manuals: the evolution of nutrition care.

PubMed

Chima, Cinda S

2007-02-01

Although the role of nutrition as a therapy for the sick has been recognized for centuries, the science of nutrition is a relatively young discipline. The first modern attempt to document and standardize appropriate nutrition care was the diet manual. The evolution from "diet manual" to "practice manual" is less a change in purpose than an expansion of scope. This paper reviews the history of diet manuals in the United States, focusing on the evolution of nutrition therapy and the transformation of diet manuals into practice manuals for nutrition care providers. Included is a practice-oriented summary of 7 diet manuals published by Cleveland Metropolitan General Hospital in Cleveland from 1939 to 1984, when the hospital began using nationally distributed practice manuals. These manuals exemplify changes in the practice of medicine and in the role of nutrition providers on the healthcare team. A review of the evolution of clinical decision-making as documented in diet and practice manuals reflects increasing rigor in referencing scientific evidence. Nutrition therapies that seem quaint to us now reflect the traditional origins of many medical practices that persist today. Knowledge of this history should motivate us to critically evaluate the research base that supports all aspects of nutrition therapy, develop protocols to assess practices that remain unexamined, and embrace the discipline of evidence-based practice.

Applicator Training Manual for: Public Health Pest Control.

ERIC Educational Resources Information Center

Moore, E. E.

This manual gives the life cycle and habitats, public health importance, methods of non-chemical control, and pesticides and methods of application for mosquitoes, flies, bedbugs, fleas, lice, cockroaches, venomous anthropods, ticks and chiggers, and rodents. (BB)

Applying the highway safety manual to Georgia.

DOT National Transportation Integrated Search

2015-08-01

This report examines the Highway Safety Manual (HSM) from the perspective of applying its : methods and approaches within the state of Georgia. The work presented here focuses : specifically on data requirements and methods that may be of particular ...

The Influence of Endmember Selection Method in Extracting Impervious Surface from Airborne Hyperspectral Imagery

NASA Astrophysics Data System (ADS)

Wang, J.; Feng, B.

2016-12-01

Impervious surface area (ISA) has long been studied as an important input into moisture flux models. In general, ISA impedes groundwater recharge, increases stormflow/flood frequency, and alters in-stream and riparian habitats. Urban area is recognized as one of the richest ISA environment. Urban ISA mapping assists flood prevention and urban planning. Hyperspectral imagery (HI), for its ability to detect subtle spectral signature, becomes an ideal candidate in urban ISA mapping. To map ISA from HI involves endmember (EM) selection. The high degree of spatial and spectral heterogeneity of urban environment puts great difficulty in this task: a compromise point is needed between the automatic degree and the good representativeness of the method. The study tested one manual and two semi-automatic EM selection strategies. The manual and the first semi-automatic methods have been widely used in EM selection. The second semi-automatic EM selection method is rather new and has been only proposed for moderate spatial resolution satellite. The manual method visually selected the EM candidates from eight landcover types in the original image. The first semi-automatic method chose the EM candidates using a threshold over the pixel purity index (PPI) map. The second semi-automatic method used the triangle shape of the HI scatter plot in the n-Dimension visualizer to identify the V-I-S (vegetation-impervious surface-soil) EM candidates: the pixels locate at the triangle points. The initial EM candidates from the three methods were further refined by three indexes (EM average RMSE, minimum average spectral angle, and count based EM selection) and generated three spectral libraries, which were used to classify the test image. Spectral angle mapper was applied. The accuracy reports for the classification results were generated. The overall accuracy are 85% for the manual method, 81% for the PPI method, and 87% for the V-I-S method. The V-I-S EM selection method performs best in this study. This fact proves the value of V-I-S EM selection method in not only moderate spatial resolution satellite image but also the more and more accessible high spatial resolution airborne image. This semi-automatic EM selection method can be adopted into a wide range of remote sensing images and provide ISA map for hydrology analysis.

Computer-Aided Diagnosis of Acute Lymphoblastic Leukaemia

PubMed Central

2018-01-01

Leukaemia is a form of blood cancer which affects the white blood cells and damages the bone marrow. Usually complete blood count (CBC) and bone marrow aspiration are used to diagnose the acute lymphoblastic leukaemia. It can be a fatal disease if not diagnosed at the earlier stage. In practice, manual microscopic evaluation of stained sample slide is used for diagnosis of leukaemia. But manual diagnostic methods are time-consuming, less accurate, and prone to errors due to various human factors like stress, fatigue, and so forth. Therefore, different automated systems have been proposed to wrestle the glitches in the manual diagnostic methods. In recent past, some computer-aided leukaemia diagnosis methods are presented. These automated systems are fast, reliable, and accurate as compared to manual diagnosis methods. This paper presents review of computer-aided diagnosis systems regarding their methodologies that include enhancement, segmentation, feature extraction, classification, and accuracy. PMID:29681996

Comparison of Manual and Automated Measurements of Tracheobronchial Airway Geometry in Three Balb/c Mice.

PubMed

Islam, Asef; Oldham, Michael J; Wexler, Anthony S

2017-11-01

Mammalian lungs are comprised of large numbers of tracheobronchial airways that transition from the trachea to alveoli. Studies as wide ranging as pollutant deposition and lung development rely on accurate characterization of these airways. Advancements in CT imaging and the value of computational approaches in eliminating the burden of manual measurement are providing increased efficiency in obtaining this geometric data. In this study, we compare an automated method to a manual one for the first six generations of three Balb/c mouse lungs. We find good agreement between manual and automated methods and that much of the disagreement can be attributed to method precision. Using the automated method, we then provide anatomical data for the entire tracheobronchial airway tree from three Balb/C mice. Anat Rec, 2017. © 2017 Wiley Periodicals, Inc. Anat Rec, 300:2046-2057, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Methods for the Determination of Chemical Contaminants in Drinking Water. Training Manual.

ERIC Educational Resources Information Center

Office of Water Program Operations (EPA), Cincinnati, OH. National Training and Operational Technology Center.

This training manual, intended for chemists and technicians with little or no experience in chemical procedures required to monitor drinking water, covers analytical methods for inorganic and organic chemical contaminants listed in the interim primary drinking water regulations. Topics include methods for heavy metals, nitrate, and organic…

Illustrated surface mining methods

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

Not Available

1979-01-01

This manual provides a visual synopsis of surface coal mining methods in the United States. The manual presents various surface mining methods and techniques through artist renderings and appropriate descriptions. The productive coal fields of the United States were divided into four regions according to geology and physiography. A glossay of terminology is included. (DP)

Analytical Methods for Trace Metals. Training Manual.

ERIC Educational Resources Information Center

Office of Water Program Operations (EPA), Cincinnati, OH. National Training and Operational Technology Center.

This training manual presents material on the theoretical concepts involved in the methods listed in the Federal Register as approved for determination of trace metals. Emphasis is on laboratory operations. This course is intended for chemists and technicians with little or no experience in analytical methods for trace metals. Students should have…

Stereophotogrammetry in studies of riparian vegetation dynamics

NASA Astrophysics Data System (ADS)

Hortobagyi, Borbala; Vautier, Franck; Corenblit, Dov; Steiger, Johannes

2014-05-01

Riparian vegetation responds to hydrogeomorphic disturbances and also controls sediment deposition and erosion. Spatio-temporal riparian vegetation dynamics within fluvial corridors have been quantified in many studies using aerial photographs and GIS. However, this approach does not allow the consideration of woody vegetation growth rates (i.e. vertical dimension) which are fundamental when studying feedbacks between the processes of fluvial landform construction and vegetation establishment and succession. We built 3D photogrammetric models of vegetation height based on aerial argentic and digital photographs from sites of the Allier and Garonne Rivers (France). The models were realized at two different spatial scales and with two different methods. The "large" scale corresponds to the reach of the river corridor on the Allier river (photograph taken in 2009) and the "small" scale to river bars of the Allier (photographs taken in 2002, 2009) and Garonne Rivers (photographs taken in 2000, 2002, 2006 and 2010). At the corridor scale, we generated vegetation height models using an automatic procedure. This method is fast but can only be used with digital photographs. At the bar scale, we constructed the models manually using a 3D visualization on the screen. This technique showed good results for digital and also argentic photographs but is very time-consuming. A diachronic study was performed in order to investigate vegetation succession by distinguishing three different classes according to the vegetation height: herbs (<1 m), shrubs (1-4 m) or trees (>4 m). Both methods, i.e. automatic and manual, were employed to study the evolution of the three vegetation classes and the recruitment of new vegetation patches. A comparison was conducted between the vegetation height given by models (automatic and manual) and the vegetation height measured in the field. The manually produced models (small scale) were of a precision of 0.5-1 m, allowing the quantification of woody vegetation growth rates. Thus, our results show that the manual method we developed is accurate to quantify vegetation growth rates at small scales, whereas the less accurate automatic method is appropriate to study vegetation succession at the corridor scale. Both methods are complementary and will contribute to a further exploration of the mutual relationships between hydrogeomorphic processes, topography and vegetation dynamics within alluvial systems, adding the quantification of the vertical dimension of riparian vegetation to their spatio-temporal characteristics.

An automated microplate-based method for monitoring DNA strand breaks in plasmids and bacterial artificial chromosomes

PubMed Central

Rock, Cassandra; Shamlou, Parviz Ayazi; Levy, M. Susana

2003-01-01

A method is described for high-throughput monitoring of DNA backbone integrity in plasmids and artificial chromosomes in solution. The method is based on the denaturation properties of double-stranded DNA in alkaline conditions and uses PicoGreen fluorochrome to monitor denaturation. In the present method, fluorescence enhancement of PicoGreen at pH 12.4 is normalised by its value at pH 8 to give a ratio that is proportional to the average backbone integrity of the DNA molecules in the sample. A good regression fit (r2 > 0.98) was obtained when results derived from the present method and those derived from agarose gel electrophoresis were compared. Spiking experiments indicated that the method is sensitive enough to detect a proportion of 6% (v/v) molecules with an average of less than two breaks per molecule. Under manual operation, validation parameters such as inter-assay and intra-assay variation gave values of <5% coefficient of variation. Automation of the method showed equivalence to the manual procedure with high reproducibility and low variability within wells. The method described requires as little as 0.5 ng of DNA per well and a 96-well microplate can be analysed in 12 min providing an attractive option for analysis of high molecular weight vectors. A preparation of a 116 kb bacterial artificial chromosome was subjected to chemical and shear degradation and DNA integrity was tested using the method. Good correlation was obtained between time of chemical degradation and shear rate with fluorescence response. Results obtained from pulsed- field electrophoresis of sheared samples were in agreement with those obtained using the microplate-based method. PMID:12771229

Dialects for the Stage: A Manual and Two Casette Tapes.

ERIC Educational Resources Information Center

Machlin, Evangeline

This document contains a manual and two cassette tapes designed to help actors and actresses learn to speak various dialects. The tapes and the manual are arranged for the play-it-and-say-it method of dialect acquisition. The first three parts discuss the tapes and the manual in general, the dialect texts and dialect data, and the steps involved…

Coupled rotor/airframe vibration analysis program manual manual. Volume 1: User's and programmer's instructions

NASA Technical Reports Server (NTRS)

Cassarino, S.; Sopher, R.

1982-01-01

user instruction and software descriptions for the base program of the coupled rotor/airframe vibration analysis are provided. The functional capabilities and procedures for running the program are provided. Interfaces with external programs are discussed. The procedure of synthesizing a dynamic system and the various solution methods are described. Input data and output results are presented. Detailed information is provided on the program structure. Sample test case results for five representative dynamic configurations are provided and discussed. System response are plotted to demonstrate the plots capabilities available. Instructions to install and execute SIMVIB on the CDC computer system are provided.

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.

Distribution Characteristics of Air-Bone Gaps – Evidence of Bias in Manual Audiometry

PubMed Central

Margolis, Robert H.; Wilson, Richard H.; Popelka, Gerald R.; Eikelboom, Robert H.; Swanepoel, De Wet; Saly, George L.

2015-01-01

Objective Five databases were mined to examine distributions of air-bone gaps obtained by automated and manual audiometry. Differences in distribution characteristics were examined for evidence of influences unrelated to the audibility of test signals. Design The databases provided air- and bone-conduction thresholds that permitted examination of air-bone gap distributions that were free of ceiling and floor effects. Cases with conductive hearing loss were eliminated based on air-bone gaps, tympanometry, and otoscopy, when available. The analysis is based on 2,378,921 threshold determinations from 721,831 subjects from five databases. Results Automated audiometry produced air-bone gaps that were normally distributed suggesting that air- and bone-conduction thresholds are normally distributed. Manual audiometry produced air-bone gaps that were not normally distributed and show evidence of biasing effects of assumptions of expected results. In one database, the form of the distributions showed evidence of inclusion of conductive hearing losses. Conclusions Thresholds obtained by manual audiometry show tester bias effects from assumptions of the patient’s hearing loss characteristics. Tester bias artificially reduces the variance of bone-conduction thresholds and the resulting air-bone gaps. Because the automated method is free of bias from assumptions of expected results, these distributions are hypothesized to reflect the true variability of air- and bone-conduction thresholds and the resulting air-bone gaps. PMID:26627469

Unsupervised Ontology Generation from Unstructured Text. CRESST Report 827

ERIC Educational Resources Information Center

Mousavi, Hamid; Kerr, Deirdre; Iseli, Markus R.

2013-01-01

Ontologies are a vital component of most knowledge acquisition systems, and recently there has been a huge demand for generating ontologies automatically since manual or supervised techniques are not scalable. In this paper, we introduce "OntoMiner", a rule-based, iterative method to extract and populate ontologies from unstructured or…

Saliency-aware food image segmentation for personal dietary assessment using a wearable computer

USDA-ARS?s Scientific Manuscript database

Image-based dietary assessment has recently received much attention in the community of obesity research. In this assessment, foods in digital pictures are specified, and their portion sizes (volumes) are estimated. Although manual processing is currently the most utilized method, image processing h...

A COMPARISON OF MAPPED ESTIMATES OF LONG-TERM RUNOFF IN THE NORTHEAST UNITED STATES

EPA Science Inventory

We evaluated the relative accuracy of four methods of producing maps of long-term runoff for part of the northeast United States: MAN, a manual procedure that incorporates expert opinion in contour placement; RPRIS, an automated procedure based on water balance considerations, Pn...

Terminologie de Base de la Documentation. (Basic Terminology of Documentation).

ERIC Educational Resources Information Center

Commission des Communautes Europeennes (Luxembourg). Bureau de Terminologie.

This glossary is designed to aid non-specialists whose activities require that they have some familiarity with the terminology of the modern methods of documentation. Definitions have been assembled from various dictionaries, manuals, etc., with particular attention being given to the publications of UNESCO and the International Standards…

Case Study: Longitudinal Treatment of Adolescents with Depression and Inflammatory Bowel Disease

ERIC Educational Resources Information Center

Szigethy, Eva; Carpenter, Johanna; Baum, Emily; Kenney, Elyse; Baptista-Neto, Lourival; Beardslee, William R.; DeMaso, David Ray

2006-01-01

Objective: To assess longitudinal maintenance of improvements in depression, anxiety, global functioning, and physical health perception in 11 adolescents at 6 and 12 months following completion of manual-based cognitive-behavioral therapy. Method: Standardized instruments assessed follow-up changes in depression, anxiety, physical health, and…

Corpus-Based Optimization of Language Models Derived from Unification Grammars

NASA Technical Reports Server (NTRS)

Rayner, Manny; Hockey, Beth Ann; James, Frankie; Bratt, Harry; Bratt, Elizabeth O.; Gawron, Mark; Goldwater, Sharon; Dowding, John; Bhagat, Amrita

2000-01-01

We describe a technique which makes it feasible to improve the performance of a language model derived from a manually constructed unification grammar, using low-quality untranscribed speech data and a minimum of human annotation. The method is on a medium-vocabulary spoken language command and control task.

Experimental Evaluation of the Training Structure of the Picture Exchange Communication System (PECS)

ERIC Educational Resources Information Center

Cummings, Anne R.; Carr, James E.; LeBlanc, Linda A.

2012-01-01

The Picture Exchange Communication System (PECS) is a picture-based alternative communication method that is widely accepted and utilized with individuals with disabilities. Although prior studies have examined the clinical efficacy of PECS, none have experimentally evaluated its manualized training structure. We experimentally evaluated the…

Carotid stenosis assessment with multi-detector CT angiography: comparison between manual and automatic segmentation methods.

PubMed

Zhu, Chengcheng; Patterson, Andrew J; Thomas, Owen M; Sadat, Umar; Graves, Martin J; Gillard, Jonathan H

2013-04-01

Luminal stenosis is used for selecting the optimal management strategy for patients with carotid artery disease. The aim of this study is to evaluate the reproducibility of carotid stenosis quantification using manual and automated segmentation methods using submillimeter through-plane resolution Multi-Detector CT angiography (MDCTA). 35 patients having carotid artery disease with >30 % luminal stenosis as identified by carotid duplex imaging underwent contrast enhanced MDCTA. Two experienced CT readers quantified carotid stenosis from axial source images, reconstructed maximum intensity projection (MIP) and 3D-carotid geometry which was automatically segmented by an open-source toolkit (Vascular Modelling Toolkit, VMTK) using NASCET criteria. Good agreement among the measurement using axial images, MIP and automatic segmentation was observed. Automatic segmentation methods show better inter-observer agreement between the readers (intra-class correlation coefficient (ICC): 0.99 for diameter stenosis measurement) than manual measurement of axial (ICC = 0.82) and MIP (ICC = 0.86) images. Carotid stenosis quantification using an automatic segmentation method has higher reproducibility compared with manual methods.

Methods for automatic detection of artifacts in microelectrode recordings.

PubMed

Bakštein, Eduard; Sieger, Tomáš; Wild, Jiří; Novák, Daniel; Schneider, Jakub; Vostatek, Pavel; Urgošík, Dušan; Jech, Robert

2017-10-01

Extracellular microelectrode recording (MER) is a prominent technique for studies of extracellular single-unit neuronal activity. In order to achieve robust results in more complex analysis pipelines, it is necessary to have high quality input data with a low amount of artifacts. We show that noise (mainly electromagnetic interference and motion artifacts) may affect more than 25% of the recording length in a clinical MER database. We present several methods for automatic detection of noise in MER signals, based on (i) unsupervised detection of stationary segments, (ii) large peaks in the power spectral density, and (iii) a classifier based on multiple time- and frequency-domain features. We evaluate the proposed methods on a manually annotated database of 5735 ten-second MER signals from 58 Parkinson's disease patients. The existing methods for artifact detection in single-channel MER that have been rigorously tested, are based on unsupervised change-point detection. We show on an extensive real MER database that the presented techniques are better suited for the task of artifact identification and achieve much better results. The best-performing classifiers (bagging and decision tree) achieved artifact classification accuracy of up to 89% on an unseen test set and outperformed the unsupervised techniques by 5-10%. This was close to the level of agreement among raters using manual annotation (93.5%). We conclude that the proposed methods are suitable for automatic MER denoising and may help in the efficient elimination of undesirable signal artifacts. Copyright © 2017 Elsevier B.V. All rights reserved.

Automated and Adaptable Quantification of Cellular Alignment from Microscopic Images for Tissue Engineering Applications

PubMed Central

Xu, Feng; Beyazoglu, Turker; Hefner, Evan; Gurkan, Umut Atakan

2011-01-01

Cellular alignment plays a critical role in functional, physical, and biological characteristics of many tissue types, such as muscle, tendon, nerve, and cornea. Current efforts toward regeneration of these tissues include replicating the cellular microenvironment by developing biomaterials that facilitate cellular alignment. To assess the functional effectiveness of the engineered microenvironments, one essential criterion is quantification of cellular alignment. Therefore, there is a need for rapid, accurate, and adaptable methodologies to quantify cellular alignment for tissue engineering applications. To address this need, we developed an automated method, binarization-based extraction of alignment score (BEAS), to determine cell orientation distribution in a wide variety of microscopic images. This method combines a sequenced application of median and band-pass filters, locally adaptive thresholding approaches and image processing techniques. Cellular alignment score is obtained by applying a robust scoring algorithm to the orientation distribution. We validated the BEAS method by comparing the results with the existing approaches reported in literature (i.e., manual, radial fast Fourier transform-radial sum, and gradient based approaches). Validation results indicated that the BEAS method resulted in statistically comparable alignment scores with the manual method (coefficient of determination R2=0.92). Therefore, the BEAS method introduced in this study could enable accurate, convenient, and adaptable evaluation of engineered tissue constructs and biomaterials in terms of cellular alignment and organization. PMID:21370940

Wind Tunnel Force Balance Calibration Study - Interim Results

NASA Technical Reports Server (NTRS)

Rhew, Ray D.

2012-01-01

Wind tunnel force balance calibration is preformed utilizing a variety of different methods and does not have a direct traceable standard such as standards used for most calibration practices (weights, and voltmeters). These different calibration methods and practices include, but are not limited to, the loading schedule, the load application hardware, manual and automatic systems, re-leveling and non-re-leveling. A study of the balance calibration techniques used by NASA was undertaken to develop metrics for reviewing and comparing results using sample calibrations. The study also includes balances of different designs, single and multi-piece. The calibration systems include, the manual, and the automatic that are provided by NASA and its vendors. The results to date will be presented along with the techniques for comparing the results. In addition, future planned calibrations and investigations based on the results will be provided.

PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics1[OPEN

PubMed Central

Poeschl, Yvonne; Plötner, Romina

2017-01-01

Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw-puzzle-shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited, because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based, and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell junctions and three-cell junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient, and reproducible quantitative analysis of PC shape characteristics that can easily be applied to study PC development in large data sets. PMID:28931626

Evaluation and costs of different haemoglobin methods for use in district hospitals in Malawi

PubMed Central

Medina Lara, A; Mundy, C; Kandulu, J; Chisuwo, L; Bates, I

2005-01-01

Aims: To evaluate the characteristics of manual haemoglobin methods in use in Malawi and provide evidence for the Ministry of Health in Malawi to enable them to choose a suitable method for district hospitals. Methods: Criteria on accuracy, clinical usefulness, user friendliness, speed, training time, and economic costs were determined by local health professionals and used to compare six different manual haemoglobin methods. These were introduced sequentially into use in a district hospital in Malawi alongside the reference method. Results: HemoCue was the optimal method based on most of the outcome measures but was also the most expensive (US$0.75/test). DHT meter and Jenway colorimeter were the second choice because they were cheaper (US$0.20–0.35/test), but they were not as accurate or user friendly as HemoCue. Conclusions: The process for choosing appropriate laboratory methods is complex and very little guidance is available for health managers in poorer countries. This paper describes the development and testing of a practical model for gathering evidence about test efficiency that could be adapted for use in other resource poor settings. PMID:15623483

Family-Based Treatment of a 17-Year-Old Twin Presenting with Emerging Anorexia Nervosa: A Case Study Using the "Maudsley Method"

ERIC Educational Resources Information Center

Loeb, Katharine L.; Hirsch, Alicia M.; Greif, Rebecca; Hildebrandt, Thomas B.

2009-01-01

This article describes the successful application of family-based treatment (FBT) for a 17-year-old identical twin presenting with a 4-month history of clinically significant symptoms of anorexia nervosa (AN). FBT is a manualized treatment that has been studied in randomized controlled trials for adolescents with AN. This case study illustrates…

ANSI/ASHRAE/IES Standard 90.1-2010 Performance Rating Method Reference Manual

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

Goel, Supriya; Rosenberg, Michael I.

This document is intended to be a reference manual for the Appendix G Performance Rating Method (PRM) of ANSI/ASHRAE/IES Standard 90.1- 2010 (Standard 90.1-2010).The PRM is used for rating the energy efficiency of commercial and high-rise residential buildings with designs that exceed the requirements of Standard 90.1. The procedures and processes described in this manual are designed to provide consistency and accuracy by filling in gaps and providing additional details needed by users of the PRM. It should be noted that this document is created independently from ASHRAE and SSPC 90.1 and is not sanctioned nor approved by either ofmore » those entities . Potential users of this manual include energy modelers, software developers and implementers of “beyond code” energy programs. Energy modelers using ASHRAE Standard 90.1-2010 for beyond code programs can use this document as a reference manual for interpreting requirements of the Performance Rating method. Software developers, developing tools for automated creation of the baseline model can use this reference manual as a guideline for developing the rules for the baseline model.« less

LOCALIZING THE RANGELAND HEALTH METHOD FOR SOUTHEASTERN ARIZONA

EPA Science Inventory

The interagency manual Interpreting Indicators of Rangeland Health, Version 4 (Technical Reference 1734-6) provides a method for making rangeland health assessments. The manual recommends that the rangeland health assessment approach be adapted to local conditions. This technica...

Validity and reliability of computerized measurement of lumbar intervertebral disc height and volume from magnetic resonance images.

PubMed

Neubert, Ales; Fripp, Jurgen; Engstrom, Craig; Gal, Yaniv; Crozier, Stuart; Kingsley, Michael I C

2014-11-01

Magnetic resonance (MR) examinations of morphologic characteristics of intervertebral discs (IVDs) have been used extensively for biomechanical studies and clinical investigations of the lumbar spine. Traditionally, the morphologic measurements have been performed using time- and expertise-intensive manual segmentation techniques not well suited for analyses of large-scale studies.. The purpose of this study is to introduce and validate a semiautomated method for measuring IVD height and mean sagittal area (and volume) from MR images to determine if it can replace the manual assessment and enable analyses of large MR cohorts. This study compares semiautomated and manual measurements and assesses their reliability and agreement using data from repeated MR examinations. Seven healthy asymptomatic males underwent 1.5-T MR examinations of the lumbar spine involving sagittal T2-weighted fast spin-echo images obtained at baseline, pre-exercise, and postexercise conditions. Measures of the mean height and the mean sagittal area of lumbar IVDs (L1-L2 to L4-L5) were compared for two segmentation approaches: a conventional manual method (10-15 minutes to process one IVD) and a specifically developed semiautomated method (requiring only a few mouse clicks to process each subject). Both methods showed strong test-retest reproducibility evaluated on baseline and pre-exercise examinations with strong intraclass correlations for the semiautomated and manual methods for mean IVD height (intraclass correlation coefficient [ICC]=0.99, 0.98) and mean IVD area (ICC=0.98, 0.99), respectively. A bias (average deviation) of 0.38 mm (4.1%, 95% confidence interval 0.18-0.59 mm) was observed between the manual and semiautomated methods for the IVD height, whereas there was no statistically significant difference for the mean IVD area (0.1%±3.5%). The semiautomated and manual methods both detected significant exercise-induced changes in IVD height (0.20 and 0.28 mm) and mean IVD area (5.7 and 8.3 mm(2)), respectively. The presented semiautomated method provides an alternative to time- and expertise-intensive manual procedures for analysis of larger, cross-sectional, interventional, and longitudinal MR studies for morphometric analyses of lumbar IVDs. Copyright © 2014 Elsevier Inc. All rights reserved.

Automated image analysis for quantification of reactive oxygen species in plant leaves.

PubMed

Sekulska-Nalewajko, Joanna; Gocławski, Jarosław; Chojak-Koźniewska, Joanna; Kuźniak, Elżbieta

2016-10-15

The paper presents an image processing method for the quantitative assessment of ROS accumulation areas in leaves stained with DAB or NBT for H 2 O 2 and O 2 - detection, respectively. Three types of images determined by the combination of staining method and background color are considered. The method is based on the principle of supervised machine learning with manually labeled image patterns used for training. The method's algorithm is developed as a JavaScript macro in the public domain Fiji (ImageJ) environment. It allows to select the stained regions of ROS-mediated histochemical reactions, subsequently fractionated according to the weak, medium and intense staining intensity and thus ROS accumulation. It also evaluates total leaf blade area. The precision of ROS accumulation area detection is validated by the Dice Similarity Coefficient in the case of manual patterns. The proposed framework reduces the computation complexity, once prepared, requires less image processing expertise than the competitive methods and represents a routine quantitative imaging assay for a general histochemical image classification. Copyright © 2016 Elsevier Inc. All rights reserved.

Dynamic CT myocardial perfusion imaging: performance of 3D semi-automated evaluation software.

PubMed

Ebersberger, Ullrich; Marcus, Roy P; Schoepf, U Joseph; Lo, Gladys G; Wang, Yining; Blanke, Philipp; Geyer, Lucas L; Gray, J Cranston; McQuiston, Andrew D; Cho, Young Jun; Scheuering, Michael; Canstein, Christian; Nikolaou, Konstantin; Hoffmann, Ellen; Bamberg, Fabian

2014-01-01

To evaluate the performance of three-dimensional semi-automated evaluation software for the assessment of myocardial blood flow (MBF) and blood volume (MBV) at dynamic myocardial perfusion computed tomography (CT). Volume-based software relying on marginal space learning and probabilistic boosting tree-based contour fitting was applied to CT myocardial perfusion imaging data of 37 subjects. In addition, all image data were analysed manually and both approaches were compared with SPECT findings. Study endpoints included time of analysis and conventional measures of diagnostic accuracy. Of 592 analysable segments, 42 showed perfusion defects on SPECT. Average analysis times for the manual and software-based approaches were 49.1 ± 11.2 and 16.5 ± 3.7 min respectively (P < 0.01). There was strong agreement between the two measures of interest (MBF, ICC = 0.91, and MBV, ICC = 0.88, both P < 0.01) and no significant difference in MBF/MBV with respect to diagnostic accuracy between the two approaches for both MBF and MBV for manual versus software-based approach; respectively; all comparisons P > 0.05. Three-dimensional semi-automated evaluation of dynamic myocardial perfusion CT data provides similar measures and diagnostic accuracy to manual evaluation, albeit with substantially reduced analysis times. This capability may aid the integration of this test into clinical workflows. • Myocardial perfusion CT is attractive for comprehensive coronary heart disease assessment. • Traditional image analysis methods are cumbersome and time-consuming. • Automated 3D perfusion software shortens analysis times. • Automated 3D perfusion software increases standardisation of myocardial perfusion CT. • Automated, standardised analysis fosters myocardial perfusion CT integration into clinical practice.

Research on key technology of the verification system of steel rule based on vision measurement

NASA Astrophysics Data System (ADS)

Jia, Siyuan; Wang, Zhong; Liu, Changjie; Fu, Luhua; Li, Yiming; Lu, Ruijun

2018-01-01

The steel rule plays an important role in quantity transmission. However, the traditional verification method of steel rule based on manual operation and reading brings about low precision and low efficiency. A machine vison based verification system of steel rule is designed referring to JJG1-1999-Verificaiton Regulation of Steel Rule [1]. What differentiates this system is that it uses a new calibration method of pixel equivalent and decontaminates the surface of steel rule. Experiments show that these two methods fully meet the requirements of the verification system. Measuring results strongly prove that these methods not only meet the precision of verification regulation, but also improve the reliability and efficiency of the verification system.

A computer program to obtain time-correlated gust loads for nonlinear aircraft using the matched-filter-based method

NASA Technical Reports Server (NTRS)

Scott, Robert C.; Pototzky, Anthony S.; Perry, Boyd, III

1994-01-01

NASA Langley Research Center has, for several years, conducted research in the area of time-correlated gust loads for linear and nonlinear aircraft. The results of this work led NASA to recommend that the Matched-Filter-Based One-Dimensional Search Method be used for gust load analyses of nonlinear aircraft. This manual describes this method, describes a FORTRAN code which performs this method, and presents example calculations for a sample nonlinear aircraft model. The name of the code is MFD1DS (Matched-Filter-Based One-Dimensional Search). The program source code, the example aircraft equations of motion, a sample input file, and a sample program output are all listed in the appendices.

A new computer-based Farnsworth Munsell 100-hue test for evaluation of color vision.

PubMed

Ghose, Supriyo; Parmar, Twinkle; Dada, Tanuj; Vanathi, Murugesan; Sharma, Sourabh

2014-08-01

To evaluate a computer-based Farnsworth-Munsell (FM) 100-hue test and compare it with a manual FM 100-hue test in normal and congenital color-deficient individuals. Fifty color defective subjects and 200 normal subjects with a best-corrected visual acuity ≥ 6/12 were compared using a standard manual FM 100-hue test and a computer-based FM 100-hue test under standard operating conditions as recommended by the manufacturer after initial trial testing. Parameters evaluated were total error scores (TES), type of defect and testing time. Pearson's correlation coefficient was used to determine the relationship between the test scores. Cohen's kappa was used to assess agreement of color defect classification between the two tests. A receiver operating characteristic curve was used to determine the optimal cut-off score for the computer-based FM 100-hue test. The mean time was 16 ± 1.5 (range 6-20) min for the manual FM 100-hue test and 7.4 ± 1.4 (range 5-13) min for the computer-based FM 100-hue test, thus reducing testing time to <50 % (p < 0.05). For grading color discrimination, Pearson's correlation coefficient for TES between the two tests was 0.91 (p < 0.001). For color defect classification, Cohen's agreement coefficient was 0.98 (p < 0.01). The computer-based FM 100-hue is an effective and rapid method for detecting, classifying and grading color vision anomalies.

Maximum speed limits. Volume 3, A programmed implementation manual for setting a speed limit based on the 85th percentile

DOT National Transportation Integrated Search

1970-10-01

This report contains the implementation manual developed as a part of the project "Maximum Speed Limits." The manual consists of a programed educational unit and a field workguide concerning the setting of speed limits based on the 85th percentile sp...

Students' Reactions to Manual-Based Treatments for Substance Abuse: An Exploratory Study

ERIC Educational Resources Information Center

Simons, Lori; Jacobucci, Raymond; Houston, Hank

2006-01-01

A quasi-experimental research design with quantitative and qualitative methodologies was conducted to explore reactions of 21 students to treatment manuals for substance abuse. Students were randomized to experimental (n = 11) and attention-control (n = 10) groups involving exposure to one of two manual-based therapy interventions. Quantitative…

Occupational and Physical Therapy Services, School Based Programs: An Organizational Manual, 1982-83.

ERIC Educational Resources Information Center

McKee, Marlene, Comp.; And Others

A 1982-83 manual on school-based occupational therapy and physical therapy (OT/PT) services in Texas is presented. Contents include: guidelines, evaluation forms, student and therapists' documentation forms, and policy/procedures manuals for a suburban independent school district and a rural independent school district. Part I provides the…

Surface-Based fMRI-Driven Diffusion Tractography in the Presence of Significant Brain Pathology: A Study Linking Structure and Function in Cerebral Palsy

PubMed Central

Cunnington, Ross; Boyd, Roslyn N.; Rose, Stephen E.

2016-01-01

Diffusion MRI (dMRI) tractography analyses are difficult to perform in the presence of brain pathology. Automated methods that rely on cortical parcellation for structural connectivity studies often fail, while manually defining regions is extremely time consuming and can introduce human error. Both methods also make assumptions about structure-function relationships that may not hold after cortical reorganisation. Seeding tractography with functional-MRI (fMRI) activation is an emerging method that reduces these confounds, but inherent smoothing of fMRI signal may result in the inclusion of irrelevant pathways. This paper describes a novel fMRI-seeded dMRI-analysis pipeline based on surface-meshes that reduces these issues and utilises machine-learning to generate task specific white matter pathways, minimising the requirement for manually-drawn ROIs. We directly compared this new strategy to a standard voxelwise fMRI-dMRI approach, by investigating correlations between clinical scores and dMRI metrics of thalamocortical and corticomotor tracts in 31 children with unilateral cerebral palsy. The surface-based approach successfully processed more participants (87%) than the voxel-based approach (65%), and provided significantly more-coherent tractography. Significant correlations between dMRI metrics and five clinical scores of function were found for the more superior regions of these tracts. These significant correlations were stronger and more frequently found with the surface-based method (15/20 investigated were significant; R2 = 0.43–0.73) than the voxelwise analysis (2 sig. correlations; 0.38 & 0.49). More restricted fMRI signal, better-constrained tractography, and the novel track-classification method all appeared to contribute toward these differences. PMID:27487011

Ecological Momentary Assessments and Automated Time Series Analysis to Promote Tailored Health Care: A Proof-of-Principle Study.

PubMed

van der Krieke, Lian; Emerencia, Ando C; Bos, Elisabeth H; Rosmalen, Judith Gm; Riese, Harriëtte; Aiello, Marco; Sytema, Sjoerd; de Jonge, Peter

2015-08-07

Health promotion can be tailored by combining ecological momentary assessments (EMA) with time series analysis. This combined method allows for studying the temporal order of dynamic relationships among variables, which may provide concrete indications for intervention. However, application of this method in health care practice is hampered because analyses are conducted manually and advanced statistical expertise is required. This study aims to show how this limitation can be overcome by introducing automated vector autoregressive modeling (VAR) of EMA data and to evaluate its feasibility through comparisons with results of previously published manual analyses. We developed a Web-based open source application, called AutoVAR, which automates time series analyses of EMA data and provides output that is intended to be interpretable by nonexperts. The statistical technique we used was VAR. AutoVAR tests and evaluates all possible VAR models within a given combinatorial search space and summarizes their results, thereby replacing the researcher's tasks of conducting the analysis, making an informed selection of models, and choosing the best model. We compared the output of AutoVAR to the output of a previously published manual analysis (n=4). An illustrative example consisting of 4 analyses was provided. Compared to the manual output, the AutoVAR output presents similar model characteristics and statistical results in terms of the Akaike information criterion, the Bayesian information criterion, and the test statistic of the Granger causality test. Results suggest that automated analysis and interpretation of times series is feasible. Compared to a manual procedure, the automated procedure is more robust and can save days of time. These findings may pave the way for using time series analysis for health promotion on a larger scale. AutoVAR was evaluated using the results of a previously conducted manual analysis. Analysis of additional datasets is needed in order to validate and refine the application for general use.

Use of the smartphone for end vertebra selection in scoliosis.

PubMed

Pepe, Murad; Kocadal, Onur; Iyigun, Abdullah; Gunes, Zafer; Aksahin, Ertugrul; Aktekin, Cem Nuri

2017-03-01

The aim of our study was to develop a smartphone-aided end vertebra selection method and to investigate its effectiveness in Cobb angle measurement. Twenty-nine adolescent idiopathic scoliosis patients' pre-operative posteroanterior scoliosis radiographs were used for end vertebra selection and Cobb angle measurement by standard method and smartphone-aided method. Measurements were performed by 7 examiners. The intraclass correlation coefficient was used to analyze selection and measurement reliability. Summary statistics of variance calculations were used to provide 95% prediction limits for the error in Cobb angle measurements. A paired 2-tailed t test was used to analyze end vertebra selection differences. Mean absolute Cobb angle difference was 3.6° for the manual method and 1.9° for the smartphone-aided method. Both intraobserver and interobserver reliability were found excellent in manual and smartphone set for Cobb angle measurement. Both intraobserver and interobserver reliability were found excellent in manual and smartphone set for end vertebra selection. But reliability values of manual set were lower than smartphone. Two observers selected significantly different end vertebra in their repeated selections for manual method. Smartphone-aided method for end vertebra selection and Cobb angle measurement showed excellent reliability. We can expect a reduction in measurement error rates with the widespread use of this method in clinical practice. Level III, Diagnostic study. Copyright © 2016 Turkish Association of Orthopaedics and Traumatology. Production and hosting by Elsevier B.V. All rights reserved.

Linking GPS and travel diary data using sequence alignment in a study of children's independent mobility

PubMed Central

2011-01-01

Background Global positioning systems (GPS) are increasingly being used in health research to determine the location of study participants. Combining GPS data with data collected via travel/activity diaries allows researchers to assess where people travel in conjunction with data about trip purpose and accompaniment. However, linking GPS and diary data is problematic and to date the only method has been to match the two datasets manually, which is time consuming and unlikely to be practical for larger data sets. This paper assesses the feasibility of a new sequence alignment method of linking GPS and travel diary data in comparison with the manual matching method. Methods GPS and travel diary data obtained from a study of children's independent mobility were linked using sequence alignment algorithms to test the proof of concept. Travel diaries were assessed for quality by counting the number of errors and inconsistencies in each participant's set of diaries. The success of the sequence alignment method was compared for higher versus lower quality travel diaries, and for accompanied versus unaccompanied trips. Time taken and percentage of trips matched were compared for the sequence alignment method and the manual method. Results The sequence alignment method matched 61.9% of all trips. Higher quality travel diaries were associated with higher match rates in both the sequence alignment and manual matching methods. The sequence alignment method performed almost as well as the manual method and was an order of magnitude faster. However, the sequence alignment method was less successful at fully matching trips and at matching unaccompanied trips. Conclusions Sequence alignment is a promising method of linking GPS and travel diary data in large population datasets, especially if limitations in the trip detection algorithm are addressed. PMID:22142322

The diagnostic performance of leak-plugging automated segmentation versus manual tracing of breast lesions on ultrasound images.

PubMed

Xiong, Hui; Sultan, Laith R; Cary, Theodore W; Schultz, Susan M; Bouzghar, Ghizlane; Sehgal, Chandra M

2017-05-01

To assess the diagnostic performance of a leak-plugging segmentation method that we have developed for delineating breast masses on ultrasound images. Fifty-two biopsy-proven breast lesion images were analyzed by three observers using the leak-plugging and manual segmentation methods. From each segmentation method, grayscale and morphological features were extracted and classified as malignant or benign by logistic regression analysis. The performance of leak-plugging and manual segmentations was compared by: size of the lesion, overlap area ( O a ) between the margins, and area under the ROC curves ( A z ). The lesion size from leak-plugging segmentation correlated closely with that from manual tracing ( R 2 of 0.91). O a was higher for leak plugging, 0.92 ± 0.01 and 0.86 ± 0.06 for benign and malignant masses, respectively, compared to 0.80 ± 0.04 and 0.73 ± 0.02 for manual tracings. Overall O a between leak-plugging and manual segmentations was 0.79 ± 0.14 for benign and 0.73 ± 0.14 for malignant lesions. A z for leak plugging was consistently higher (0.910 ± 0.003) compared to 0.888 ± 0.012 for manual tracings. The coefficient of variation of A z between three observers was 0.29% for leak plugging compared to 1.3% for manual tracings. The diagnostic performance, size measurements, and observer variability for automated leak-plugging segmentations were either comparable to or better than those of manual tracings.

Quantification of organ motion based on an adaptive image-based scale invariant feature method

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

Paganelli, Chiara; Peroni, Marta; Baroni, Guido

2013-11-15

Purpose: The availability of corresponding landmarks in IGRT image series allows quantifying the inter and intrafractional motion of internal organs. In this study, an approach for the automatic localization of anatomical landmarks is presented, with the aim of describing the nonrigid motion of anatomo-pathological structures in radiotherapy treatments according to local image contrast.Methods: An adaptive scale invariant feature transform (SIFT) was developed from the integration of a standard 3D SIFT approach with a local image-based contrast definition. The robustness and invariance of the proposed method to shape-preserving and deformable transforms were analyzed in a CT phantom study. The application ofmore » contrast transforms to the phantom images was also tested, in order to verify the variation of the local adaptive measure in relation to the modification of image contrast. The method was also applied to a lung 4D CT dataset, relying on manual feature identification by an expert user as ground truth. The 3D residual distance between matches obtained in adaptive-SIFT was then computed to verify the internal motion quantification with respect to the expert user. Extracted corresponding features in the lungs were used as regularization landmarks in a multistage deformable image registration (DIR) mapping the inhale vs exhale phase. The residual distances between the warped manual landmarks and their reference position in the inhale phase were evaluated, in order to provide a quantitative indication of the registration performed with the three different point sets.Results: The phantom study confirmed the method invariance and robustness properties to shape-preserving and deformable transforms, showing residual matching errors below the voxel dimension. The adapted SIFT algorithm on the 4D CT dataset provided automated and accurate motion detection of peak to peak breathing motion. The proposed method resulted in reduced residual errors with respect to standard SIFT, providing a motion description comparable to expert manual identification, as confirmed by DIR.Conclusions: The application of the method to a 4D lung CT patient dataset demonstrated adaptive-SIFT potential as an automatic tool to detect landmarks for DIR regularization and internal motion quantification. Future works should include the optimization of the computational cost and the application of the method to other anatomical sites and image modalities.« less

System Hazard Analysis of TACOM’s Crew Station/Turret Motion Base Simulator

DTIC Science & Technology

1992-01-01

Safety devices have been located on the equipment where necessary and are described in the Contraves USA Manual No. IM-27751, "INSTRUCTION MANUAL FOR...OF TACOM’s CREW STATION/TURRET MOTION BASE SIMULATOR" and Contraves USA Manual No. IM-27751, "INSTRUCTION MANUAL FOR TACOM" in an attempt to satisfy... Contraves USA and assembled jointly by Contraves USA and TACOM. All control compensation was performed by TACOM. The CS/TMBS is expected to open doors

Misclassification of OSA Severity With Automated Scoring of Home Sleep Recordings

PubMed Central

Aurora, R. Nisha; Swartz, Rachel

2015-01-01

BACKGROUND: The advent of home sleep testing has allowed for the development of an ambulatory care model for OSA that most health-care providers can easily deploy. Although automated algorithms that accompany home sleep monitors can identify and classify disordered breathing events, it is unclear whether manual scoring followed by expert review of home sleep recordings is of any value. Thus, this study examined the agreement between automated and manual scoring of home sleep recordings. METHODS: Two type 3 monitors (ApneaLink Plus [ResMed] and Embletta [Embla Systems]) were examined in distinct study samples. Data from manual and automated scoring were available for 200 subjects. Two thresholds for oxygen desaturation (≥ 3% and ≥ 4%) were used to define disordered breathing events. Agreement between manual and automated scoring was examined using Pearson correlation coefficients and Bland-Altman analyses. RESULTS: Automated scoring consistently underscored disordered breathing events compared with manual scoring for both sleep monitors irrespective of whether a ≥ 3% or ≥ 4% oxygen desaturation threshold was used to define the apnea-hypopnea index (AHI). For the ApneaLink Plus monitor, Bland-Altman analyses revealed an average AHI difference between manual and automated scoring of 6.1 (95% CI, 4.9-7.3) and 4.6 (95% CI, 3.5-5.6) events/h for the ≥ 3% and ≥ 4% oxygen desaturation thresholds, respectively. Similarly for the Embletta monitor, the average difference between manual and automated scoring was 5.3 (95% CI, 3.2-7.3) and 8.4 (95% CI, 7.2-9.6) events/h, respectively. CONCLUSIONS: Although agreement between automated and manual scoring of home sleep recordings varies based on the device used, modest agreement was observed between the two approaches. However, manual review of home sleep test recordings can decrease the misclassification of OSA severity, particularly for those with mild disease. TRIAL REGISTRY: ClinicalTrials.gov; No.: NCT01503164; www.clinicaltrials.gov PMID:25411804

Can Family-Based Treatment of Anorexia Nervosa Be Manualized?

PubMed Central

Lock, James; Le Grange, Daniel

2001-01-01

The authors report on the development of a manual for treating adolescents with anorexia nervosa modeled on a family-based intervention originating at the Maudsley Hospital in London. The manual provides the first detailed account of a clinical approach shown to be consistently efficacious in randomized clinical trials for this disorder. Manualized family therapy appears to be acceptable to therapists, patients, and families. Preliminary outcomes are comparable to what would be expected in clinically supervised sessions. These results suggest that through the use of this manual a valuable treatment approach can now be tested more broadly in controlled and uncontrolled settings. PMID:11696652