Comparison of mathematic models for assessment of glomerular filtration rate with electron-beam CT in pigs.

PubMed

Daghini, Elena; Juillard, Laurent; Haas, John A; Krier, James D; Romero, Juan C; Lerman, Lilach O

2007-02-01

To prospectively compare in pigs three mathematic models for assessment of glomerular filtration rate (GFR) on electron-beam (EB) computed tomographic (CT) images, with concurrent inulin clearance serving as the reference standard. This study was approved by the institutional animal care and use committee. Inulin clearance was measured in nine pigs (18 kidneys) and compared with single-kidney GFR assessed from renal time-attenuation curves (TACs) obtained with EB CT before and after infusion of the vasodilator acetylcholine. CT-derived GFR was calculated with the original and modified Patlak methods and with previously validated extended gamma variate modeling of first-pass cortical TACs. Statistical analysis was performed to assess correlation between CT methods and inulin clearance for estimation of GFR with least-squares regression analysis and Bland-Altman graphical representation. Comparisons within groups were performed with a paired t test. GFR assessed with the original Patlak method indicated poor correlation with inulin clearance, whereas GFR assessed with the modified Patlak method (P < .001, r = 0.75) and with gamma variate modeling (P < .001, r = 0.79) correlated significantly with inulin clearance and indicated an increase in response to acetylcholine. CT-derived estimates of GFR can be significantly improved by modifications in image analysis methods (eg, use of a cortical region of interest). (c) RSNA, 2007.

Quantification of 18F-Fluoride Kinetics: Evaluation of Simplified Methods.

PubMed

Raijmakers, Pieter; Temmerman, Olivier P P; Saridin, Carrol P; Heyligers, Ide C; Becking, Alfred G; van Lingen, Arthur; Lammertsma, Adriaan A

2014-07-01

(18)F-fluoride PET is a promising noninvasive method for measuring bone metabolism and bone blood flow. The purpose of this study was to assess the performance of various clinically useful simplified methods by comparing them with full kinetic analysis. In addition, the validity of deriving bone blood flow from K1 of (18)F-fluoride was investigated using (15)O-H2O as a reference. Twenty-two adults (mean age ± SD, 44.8 ± 25.2 y), including 16 patients scheduled for bone surgery and 6 healthy volunteers, were studied. All patients underwent dynamic (15)O-H2O and (18)F-fluoride scans before surgery. Ten of these patients had serial PET measurements before and at 2 time points after local bone surgery. During all PET scans, arterial blood was monitored continuously. (18)F-fluoride data were analyzed using nonlinear regression (NLR) and several simplified methods (Patlak and standardized uptake value [SUV]). SUV was evaluated for different time intervals after injection and after normalizing to body weight, lean body mass, and body surface area, and simplified measurements were compared with NLR results. In addition, changes in SUV and Patlak-derived fluoride influx rate (Ki) after surgery were compared with corresponding changes in NLR-derived Ki. Finally, (18)F-fluoride K1 was compared with bone blood flow derived from (15)O-H2O data, using the standard single-tissue-compartment model. K1 of (18)F-fluoride correlated with measured blood flow, but the correlation coefficient was relatively low (r = 0.35, P < 0.001). NLR resulted in a mean Ki of 0.0160 ± 0.0122, whereas Patlak analysis, for the interval 10-60 min after injection, resulted in an almost-identical mean Ki of 0.0161 ± 0.0117. The Patlak-derived Ki, for 10-60 min after injection, showed a high correlation with the NLR-derived Ki (r = 0.976). The highest correlation between Ki and lean body mass-normalized SUV was found for the interval 50-60 min (r = 0.958). Finally, changes in SUV correlated significantly with those in Ki (r = 0.97). The present data support the use of both Patlak and SUV for assessing fluoride kinetics in humans. However, (18)F-fluoride PET has only limited accuracy in monitoring bone blood flow. © 2014 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Convergence optimization of parametric MLEM reconstruction for estimation of Patlak plot parameters.

PubMed

Angelis, Georgios I; Thielemans, Kris; Tziortzi, Andri C; Turkheimer, Federico E; Tsoumpas, Charalampos

2011-07-01

In dynamic positron emission tomography data many researchers have attempted to exploit kinetic models within reconstruction such that parametric images are estimated directly from measurements. This work studies a direct parametric maximum likelihood expectation maximization algorithm applied to [(18)F]DOPA data using reference-tissue input function. We use a modified version for direct reconstruction with a gradually descending scheme of subsets (i.e. 18-6-1) initialized with the FBP parametric image for faster convergence and higher accuracy. The results compared with analytic reconstructions show quantitative robustness (i.e. minimal bias) and clinical reproducibility within six human acquisitions in the region of clinical interest. Bland-Altman plots for all the studies showed sufficient quantitative agreement between the direct reconstructed parametric maps and the indirect FBP (--0.035x+0.48E--5). Copyright © 2011 Elsevier Ltd. All rights reserved.

Whole-body PET parametric imaging employing direct 4D nested reconstruction and a generalized non-linear Patlak model

NASA Astrophysics Data System (ADS)

Karakatsanis, Nicolas A.; Rahmim, Arman

2014-03-01

Graphical analysis is employed in the research setting to provide quantitative estimation of PET tracer kinetics from dynamic images at a single bed. Recently, we proposed a multi-bed dynamic acquisition framework enabling clinically feasible whole-body parametric PET imaging by employing post-reconstruction parameter estimation. In addition, by incorporating linear Patlak modeling within the system matrix, we enabled direct 4D reconstruction in order to effectively circumvent noise amplification in dynamic whole-body imaging. However, direct 4D Patlak reconstruction exhibits a relatively slow convergence due to the presence of non-sparse spatial correlations in temporal kinetic analysis. In addition, the standard Patlak model does not account for reversible uptake, thus underestimating the influx rate Ki. We have developed a novel whole-body PET parametric reconstruction framework in the STIR platform, a widely employed open-source reconstruction toolkit, a) enabling accelerated convergence of direct 4D multi-bed reconstruction, by employing a nested algorithm to decouple the temporal parameter estimation from the spatial image update process, and b) enhancing the quantitative performance particularly in regions with reversible uptake, by pursuing a non-linear generalized Patlak 4D nested reconstruction algorithm. A set of published kinetic parameters and the XCAT phantom were employed for the simulation of dynamic multi-bed acquisitions. Quantitative analysis on the Ki images demonstrated considerable acceleration in the convergence of the nested 4D whole-body Patlak algorithm. In addition, our simulated and patient whole-body data in the postreconstruction domain indicated the quantitative benefits of our extended generalized Patlak 4D nested reconstruction for tumor diagnosis and treatment response monitoring.

Transport parameter estimation from lymph measurements and the Patlak equation.

PubMed

Watson, P D; Wolf, M B

1992-01-01

Two methods of estimating protein transport parameters for plasma-to-lymph transport data are presented. Both use IBM-compatible computers to obtain least-squares parameters for the solvent drag reflection coefficient and the permeability-surface area product using the Patlak equation. A matrix search approach is described, and the speed and convenience of this are compared with a commercially available gradient method. The results from both of these methods were different from those of a method reported by Reed, Townsley, and Taylor [Am. J. Physiol. 257 (Heart Circ. Physiol. 26): H1037-H1041, 1989]. It is shown that the Reed et al. method contains a systematic error. It is also shown that diffusion always plays an important role for transmembrane transport at the exit end of a membrane channel under all conditions of lymph flow rate and that the statement that diffusion becomes zero at high lymph flow rate depends on a mathematical definition of diffusion.

First demonstration of in vivo mapping for regional brain monoacylglycerol lipase using PET with [11C]SAR127303.

PubMed

Yamasaki, Tomoteru; Mori, Wakana; Zhang, Yiding; Hatori, Akiko; Fujinaga, Masayuki; Wakizaka, Hidekatsu; Kurihara, Yusuke; Wang, Lu; Nengaki, Nobuki; Ohya, Tomoyuki; Liang, Steven H; Zhang, Ming-Rong

2018-08-01

Monoacylglycerol lipase (MAGL) is a main regulator of the endocannabinoid system within the central nervous system (CNS). Recently, [ 11 C]SAR127303 was developed as a promising radioligand for MAGL imaging. In this study, we aimed to quantify regional MAGL concentrations in the rat brain using positron emission tomography (PET) with [ 11 C]SAR127303. An irreversible two-tissue compartment model (2-TCMi, k 4  = 0) analysis was conducted to estimate quantitative parameters (k 3 , K i 2-TCMi , and λk 3 ). These parameters were successfully obtained with high identifiability (<10 %COV) for the following regions ranked in order from highest to lowest: cingulate cortex > striatum > hippocampus > thalamus > cerebellum > hypothalamus ≈ pons. In vitro autoradiographs using [ 11 C]SAR127303 showed a heterogeneous distribution of radioactivity, as seen in the PET images. The K i 2-TCMi and λk 3 values correlated relatively highly with in vitro binding (r > 0.4, P < 0.005). The K i 2-TCMi values showed high correlation and low underestimation (<10%) compared with the slope of a Patlak plot analysis with linear regression (K i Patlak ). In conclusion, we successfully estimated regional net uptake value of [ 11 C]SAR127303 reflecting MAGL concentrations in rat brain regions for the first time. Copyright © 2018 Elsevier Inc. All rights reserved.

Correcting (18)F-fluoride PET static scan measurements of skeletal plasma clearance for tracer efflux from bone.

PubMed

Siddique, Musib; Frost, Michelle L; Moore, Amelia E B; Fogelman, Ignac; Blake, Glen M

2014-03-01

The aim of the study was to examine whether (18)F-fluoride PET ((18)F-PET) static scan measurements of bone plasma clearance (Ki) can be corrected for tracer efflux from bone from the time of injection. The efflux of tracer from bone mineral to plasma was described by a first-order rate constant kloss. A modified Patlak analysis was applied to 60-min dynamic (18)F-PET scans of the spine and hip acquired during trials on the bone anabolic agent teriparatide to find the best-fit values of kloss at the lumbar spine, total hip and femoral shaft. The resulting values of kloss were used to extrapolate the modified Patlak plots to 120 min after injection and derive a sequence of static scan estimates of Ki at 4-min intervals that were compared with the Patlak Ki values from the 60-min dynamic scans. A comparison was made with the results of the standard static scan analysis, which assumes kloss=0. The best-fit values of kloss for the spine and hip regions of interest averaged 0.006/min and did not change when patients were treated with teriparatide. Static scan values of Ki calculated using the modified analysis with kloss=0.006/min were independent of time between 10 and 120 min after injection and were in close agreement with findings from the dynamic scans. In contrast, by 2 h after injection the static scan Ki values calculated using the standard analysis underestimated the dynamic scan results by 20%. Using a modified analysis that corrects for F efflux from bone, estimates of Ki from static PET scans can be corrected for time up to 2 h after injection. This simplified approach may obviate the need to perform dynamic scans and hence shorten the scanning procedure for the patient and reduce the cost of studies. It also enables reliable estimates of Ki to be obtained from multiple skeletal sites with a single injection of tracer.

Repeatable noninvasive measurement of mouse myocardial glucose uptake with 18F-FDG: evaluation of tracer kinetics in a type 1 diabetes model.

PubMed

Thorn, Stephanie L; deKemp, Robert A; Dumouchel, Tyler; Klein, Ran; Renaud, Jennifer M; Wells, R Glenn; Gollob, Michael H; Beanlands, Rob S; DaSilva, Jean N

2013-09-01

A noninvasive and repeatable method for assessing mouse myocardial glucose uptake with (18)F-FDG PET and Patlak kinetic analysis was systematically assessed using the vena cava image-derived blood input function (IDIF). Contrast CT and computer modeling was used to determine the vena cava recovery coefficient. Vena cava IDIF (n = 7) was compared with the left ventricular cavity IDIF, with blood and liver activity measured ex vivo at 60 min. The test-retest repeatability (n = 9) of Patlak influx constant K(i) at 10-40 min was assessed quantitatively using Bland-Altman analysis. Myocardial glucose uptake rates (rMGU) using the vena cava IDIF were calculated at baseline (n = 8), after induction of type 1 diabetes (streptozotocin [50 mg/kg] intraperitoneally, 5 d), and after acute insulin stimulation (0.08 mU/kg of body weight intraperitoneally). These changes were analyzed with a standardized uptake value calculation at 20 and 40 min after injection to correlate to the Patlak time interval. The proximal mouse vena cava diameter was 2.54 ± 0.30 mm. The estimated recovery coefficient, calculated using nonlinear image reconstruction, decreased from 0.76 initially (time 0 to peak activity) to 0.61 for the duration of the scan. There was a 17% difference in the image-derived vena cava blood activity at 60 min, compared with the ex vivo blood activity measured in the γ-counter. The coefficient of variability for Patlak K(i) values between mice was found to be 23% with the proposed method, compared with 51% when using the left ventricular cavity IDIF (P < 0.05). No significant bias in K(i) was found between repeated scans with a coefficient of repeatability of 0.16 mL/min/g. Calculated rMGU values were reduced by 60% in type 1 diabetic mice from baseline scans (P < 0.03, ANOVA), with a subsequent increase of 40% to a level not significantly different from baseline after acute insulin treatment. These results were confirmed with a standardized uptake value measured at 20 and 40 min. The mouse vena cava IDIF provides repeatable assessment of the blood time-activity curve for Patlak kinetic modeling of rMGU. An expected significant reduction in myocardial glucose uptake was demonstrated in a type 1 diabetic mouse model, with significant recovery after acute insulin treatment, using a mouse vena cava IDIF approach.

Simulation-based validation and arrival-time correction for Patlak analyses of Perfusion-CT scans

NASA Astrophysics Data System (ADS)

Bredno, Jörg; Hom, Jason; Schneider, Thomas; Wintermark, Max

2009-02-01

Blood-brain-barrier (BBB) breakdown is a hypothesized mechanism for hemorrhagic transformation in acute stroke. The Patlak analysis of a Perfusion Computed Tomography (PCT) scan measures the BBB permeability, but the method yields higher estimates when applied to the first pass of the contrast bolus compared to a delayed phase. We present a numerical phantom that simulates vascular and parenchymal time-attenuation curves to determine the validity of permeability measurements obtained with different acquisition protocols. A network of tubes represents the major cerebral arteries ipsi- and contralateral to an ischemic event. These tubes branch off into smaller segments that represent capillary beds. Blood flow in the phantom is freely defined and simulated as non-Newtonian tubular flow. Diffusion of contrast in the vessels and permeation through vessel walls is part of the simulation. The phantom allows us to compare the results of a permeability measurement to the simulated vessel wall status. A Patlak analysis reliably detects areas with BBB breakdown for acquisitions of 240s duration, whereas results obtained from the first pass are biased in areas of reduced blood flow. Compensating for differences in contrast arrival times reduces this bias and gives good estimates of BBB permeability for PCT acquisitions of 90-150s duration.

Direct Patlak Reconstruction From Dynamic PET Data Using the Kernel Method With MRI Information Based on Structural Similarity.

PubMed

Gong, Kuang; Cheng-Liao, Jinxiu; Wang, Guobao; Chen, Kevin T; Catana, Ciprian; Qi, Jinyi

2018-04-01

Positron emission tomography (PET) is a functional imaging modality widely used in oncology, cardiology, and neuroscience. It is highly sensitive, but suffers from relatively poor spatial resolution, as compared with anatomical imaging modalities, such as magnetic resonance imaging (MRI). With the recent development of combined PET/MR systems, we can improve the PET image quality by incorporating MR information into image reconstruction. Previously, kernel learning has been successfully embedded into static and dynamic PET image reconstruction using either PET temporal or MRI information. Here, we combine both PET temporal and MRI information adaptively to improve the quality of direct Patlak reconstruction. We examined different approaches to combine the PET and MRI information in kernel learning to address the issue of potential mismatches between MRI and PET signals. Computer simulations and hybrid real-patient data acquired on a simultaneous PET/MR scanner were used to evaluate the proposed methods. Results show that the method that combines PET temporal information and MRI spatial information adaptively based on the structure similarity index has the best performance in terms of noise reduction and resolution improvement.

MRI and quantitative autoradiographic studies following bolus injections of unlabeled and 14C-labeled gadolinium-diethylenetriamine-pentaacetic acid in a rat model of stroke yield similar distribution volumes and blood-to-brain influx rate constants

PubMed Central

Nagaraja, Tavarekere N.; Ewing, James R.; Karki, Kishor; Jacobs, Paul E.; Divine, George W.; Fenstermacher, Joseph D.; Patlak, Clifford S.; Knight, Robert A.

2012-01-01

In previous studies on a rat model of transient cerebral ischemia, the blood and brain concentrations of gadolinium-diethylenetriaminepentaacetic acid (Gd-DTPA) following intravenous bolus injection were repeatedly assessed by dynamic contrast-enhanced (DCE)-MRI, and blood-to-brain influx rate constants (Ki) were calculated from Patlak plots of the data in areas with blood–brain barrier (BBB) opening. For concurrent validation of these findings, after completing the DCE-MRI study, radiolabeled sucrose or α-aminoisobutyric acid was injected intravenously, and the brain disposition and Ki values were calculated by quantitative autoradiography (QAR) assay employing the single-time equation. To overcome two of the shortcomings of this comparison, the present experiments were carried out with a radiotracer virtually identical to Gd-DTPA, Gd-[14C]DTPA, and Ki was calculated from both sets of data by the single-time equation. The protocol included 3 h of middle cerebral artery occlusion and 2.5 h of reperfusion in male Wistar rats (n = 15) preceding the DCE-MRI Gd-DTPA and QAR Gd-[14C]DTPA measurements. In addition to Ki, the tissue-to-blood concentration ratios, or volumes of distribution (VR), were calculated. The regions of BBB opening were similar on the MRI maps and autoradiograms. Within them, VR was nearly identical for Gd-DTPA and Gd-[14C]DTPA, and Ki was slightly, but not significantly, higher for Gd-DTPA than for Gd-[14C]DTPA. The Ki values were well correlated (r = 0.67; p = 0.001). When the arterial concentration–time curve of Gd-DTPA was adjusted to match that of Gd-[14C]DTPA, the two sets of Ki values were equal and statistically comparable with those obtained previously by Patlak plots (the preferred, less model-dependent, approach) of the same data (p = 0.2–0.5). These findings demonstrate that this DCE-MRI technique accurately measures the Gd-DTPA concentration in blood and brain, and that Ki estimates based on such data are good quantitative indicators of BBB injury. PMID:21674656

[Methodological aspects related to the determination of the relative renal function using 99mTC MAG3].

PubMed

Ladrón De Guevara Hernández, D; Ham, H; Franken, P; Piepsz, A; Lobo Sotomayor, G

2002-01-01

The aim of the study was to evaluate three different methods for calculating the split renal function in patients with only one functioning kidney, keeping in mind that the split function should be zero on the side of the non-functioning kidney. We retrospectively selected 28 99mTc MAG3 renograms performed in children, 12 with unilateral nephrectomy, 4 with unilateral agenesis and 12 with a non-functioning kidney. A renal and perirenal region of interest (ROI) were delineated around the functioning kidney. The ROIs around the empty kidney were drawn symmetrically to the contralateral side. The split renal function was calculated using three different methods, the integral method, the slope method and the Patlak-Rutland algorithm. For the whole group of 28 kidneys as well as for the three categories of patients, the three methods provided a split function on the side of the non-functioning kidney close to the zero value, regardless of whether the empty kidney was the left or the right one. We recommend the use of the integral method for the whole range of split renal function with 99mTc MAG3. No significant improvement was obtained by means of the more sophisticated Patlak-Rutland method.

Parametric Net Influx Rate Images of 68Ga-DOTATOC and 68Ga-DOTATATE: Quantitative Accuracy and Improved Image Contrast.

PubMed

Ilan, Ezgi; Sandström, Mattias; Velikyan, Irina; Sundin, Anders; Eriksson, Barbro; Lubberink, Mark

2017-05-01

68 Ga-DOTATOC and 68 Ga-DOTATATE are radiolabeled somatostatin analogs used for the diagnosis of somatostatin receptor-expressing neuroendocrine tumors (NETs), and SUV measurements are suggested for treatment monitoring. However, changes in net influx rate ( K i ) may better reflect treatment effects than those of the SUV, and accordingly there is a need to compute parametric images showing K i at the voxel level. The aim of this study was to evaluate parametric methods for computation of parametric K i images by comparison to volume of interest (VOI)-based methods and to assess image contrast in terms of tumor-to-liver ratio. Methods: Ten patients with metastatic NETs underwent a 45-min dynamic PET examination followed by whole-body PET/CT at 1 h after injection of 68 Ga-DOTATOC and 68 Ga-DOTATATE on consecutive days. Parametric K i images were computed using a basis function method (BFM) implementation of the 2-tissue-irreversible-compartment model and the Patlak method using a descending aorta image-derived input function, and mean tumor K i values were determined for 50% isocontour VOIs and compared with K i values based on nonlinear regression (NLR) of the whole-VOI time-activity curve. A subsample of healthy liver was delineated in the whole-body and K i images, and tumor-to-liver ratios were calculated to evaluate image contrast. Correlation ( R 2 ) and agreement between VOI-based and parametric K i values were assessed using regression and Bland-Altman analysis. Results: The R 2 between NLR-based and parametric image-based (BFM) tumor K i values was 0.98 (slope, 0.81) and 0.97 (slope, 0.88) for 68 Ga-DOTATOC and 68 Ga-DOTATATE, respectively. For Patlak analysis, the R 2 between NLR-based and parametric-based (Patlak) tumor K i was 0.95 (slope, 0.71) and 0.92 (slope, 0.74) for 68 Ga-DOTATOC and 68 Ga-DOTATATE, respectively. There was no bias between NLR and parametric-based K i values. Tumor-to-liver contrast was 1.6 and 2.0 times higher in the parametric BFM K i images and 2.3 and 3.0 times in the Patlak images than in the whole-body images for 68 Ga-DOTATOC and 68 Ga-DOTATATE, respectively. Conclusion: A high R 2 and agreement between NLR- and parametric-based K i values was found, showing that K i images are quantitatively accurate. In addition, tumor-to-liver contrast was superior in the parametric K i images compared with whole-body images for both 68 Ga-DOTATOC and 68 Ga DOTATATE. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Dynamic whole body PET parametric imaging: II. Task-oriented statistical estimation

PubMed Central

Karakatsanis, Nicolas A.; Lodge, Martin A.; Zhou, Y.; Wahl, Richard L.; Rahmim, Arman

2013-01-01

In the context of oncology, dynamic PET imaging coupled with standard graphical linear analysis has been previously employed to enable quantitative estimation of tracer kinetic parameters of physiological interest at the voxel level, thus, enabling quantitative PET parametric imaging. However, dynamic PET acquisition protocols have been confined to the limited axial field-of-view (~15–20cm) of a single bed position and have not been translated to the whole-body clinical imaging domain. On the contrary, standardized uptake value (SUV) PET imaging, considered as the routine approach in clinical oncology, commonly involves multi-bed acquisitions, but is performed statically, thus not allowing for dynamic tracking of the tracer distribution. Here, we pursue a transition to dynamic whole body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. In a companion study, we presented a novel clinically feasible dynamic (4D) multi-bed PET acquisition protocol as well as the concept of whole body PET parametric imaging employing Patlak ordinary least squares (OLS) regression to estimate the quantitative parameters of tracer uptake rate Ki and total blood distribution volume V. In the present study, we propose an advanced hybrid linear regression framework, driven by Patlak kinetic voxel correlations, to achieve superior trade-off between contrast-to-noise ratio (CNR) and mean squared error (MSE) than provided by OLS for the final Ki parametric images, enabling task-based performance optimization. Overall, whether the observer's task is to detect a tumor or quantitatively assess treatment response, the proposed statistical estimation framework can be adapted to satisfy the specific task performance criteria, by adjusting the Patlak correlation-coefficient (WR) reference value. The multi-bed dynamic acquisition protocol, as optimized in the preceding companion study, was employed along with extensive Monte Carlo simulations and an initial clinical FDG patient dataset to validate and demonstrate the potential of the proposed statistical estimation methods. Both simulated and clinical results suggest that hybrid regression in the context of whole-body Patlak Ki imaging considerably reduces MSE without compromising high CNR. Alternatively, for a given CNR, hybrid regression enables larger reductions than OLS in the number of dynamic frames per bed, allowing for even shorter acquisitions of ~30min, thus further contributing to the clinical adoption of the proposed framework. Compared to the SUV approach, whole body parametric imaging can provide better tumor quantification, and can act as a complement to SUV, for the task of tumor detection. PMID:24080994

Dynamic whole-body PET parametric imaging: II. Task-oriented statistical estimation.

PubMed

Karakatsanis, Nicolas A; Lodge, Martin A; Zhou, Y; Wahl, Richard L; Rahmim, Arman

2013-10-21

In the context of oncology, dynamic PET imaging coupled with standard graphical linear analysis has been previously employed to enable quantitative estimation of tracer kinetic parameters of physiological interest at the voxel level, thus, enabling quantitative PET parametric imaging. However, dynamic PET acquisition protocols have been confined to the limited axial field-of-view (~15-20 cm) of a single-bed position and have not been translated to the whole-body clinical imaging domain. On the contrary, standardized uptake value (SUV) PET imaging, considered as the routine approach in clinical oncology, commonly involves multi-bed acquisitions, but is performed statically, thus not allowing for dynamic tracking of the tracer distribution. Here, we pursue a transition to dynamic whole-body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. In a companion study, we presented a novel clinically feasible dynamic (4D) multi-bed PET acquisition protocol as well as the concept of whole-body PET parametric imaging employing Patlak ordinary least squares (OLS) regression to estimate the quantitative parameters of tracer uptake rate Ki and total blood distribution volume V. In the present study, we propose an advanced hybrid linear regression framework, driven by Patlak kinetic voxel correlations, to achieve superior trade-off between contrast-to-noise ratio (CNR) and mean squared error (MSE) than provided by OLS for the final Ki parametric images, enabling task-based performance optimization. Overall, whether the observer's task is to detect a tumor or quantitatively assess treatment response, the proposed statistical estimation framework can be adapted to satisfy the specific task performance criteria, by adjusting the Patlak correlation-coefficient (WR) reference value. The multi-bed dynamic acquisition protocol, as optimized in the preceding companion study, was employed along with extensive Monte Carlo simulations and an initial clinical (18)F-deoxyglucose patient dataset to validate and demonstrate the potential of the proposed statistical estimation methods. Both simulated and clinical results suggest that hybrid regression in the context of whole-body Patlak Ki imaging considerably reduces MSE without compromising high CNR. Alternatively, for a given CNR, hybrid regression enables larger reductions than OLS in the number of dynamic frames per bed, allowing for even shorter acquisitions of ~30 min, thus further contributing to the clinical adoption of the proposed framework. Compared to the SUV approach, whole-body parametric imaging can provide better tumor quantification, and can act as a complement to SUV, for the task of tumor detection.

Dynamic PET image reconstruction integrating temporal regularization associated with respiratory motion correction for applications in oncology

NASA Astrophysics Data System (ADS)

Merlin, Thibaut; Visvikis, Dimitris; Fernandez, Philippe; Lamare, Frédéric

2018-02-01

Respiratory motion reduces both the qualitative and quantitative accuracy of PET images in oncology. This impact is more significant for quantitative applications based on kinetic modeling, where dynamic acquisitions are associated with limited statistics due to the necessity of enhanced temporal resolution. The aim of this study is to address these drawbacks, by combining a respiratory motion correction approach with temporal regularization in a unique reconstruction algorithm for dynamic PET imaging. Elastic transformation parameters for the motion correction are estimated from the non-attenuation-corrected PET images. The derived displacement matrices are subsequently used in a list-mode based OSEM reconstruction algorithm integrating a temporal regularization between the 3D dynamic PET frames, based on temporal basis functions. These functions are simultaneously estimated at each iteration, along with their relative coefficients for each image voxel. Quantitative evaluation has been performed using dynamic FDG PET/CT acquisitions of lung cancer patients acquired on a GE DRX system. The performance of the proposed method is compared with that of a standard multi-frame OSEM reconstruction algorithm. The proposed method achieved substantial improvements in terms of noise reduction while accounting for loss of contrast due to respiratory motion. Results on simulated data showed that the proposed 4D algorithms led to bias reduction values up to 40% in both tumor and blood regions for similar standard deviation levels, in comparison with a standard 3D reconstruction. Patlak parameter estimations on reconstructed images with the proposed reconstruction methods resulted in 30% and 40% bias reduction in the tumor and lung region respectively for the Patlak slope, and a 30% bias reduction for the intercept in the tumor region (a similar Patlak intercept was achieved in the lung area). Incorporation of the respiratory motion correction using an elastic model along with a temporal regularization in the reconstruction process of the PET dynamic series led to substantial quantitative improvements and motion artifact reduction. Future work will include the integration of a linear FDG kinetic model, in order to directly reconstruct parametric images.

Dynamic PET image reconstruction integrating temporal regularization associated with respiratory motion correction for applications in oncology.

PubMed

Merlin, Thibaut; Visvikis, Dimitris; Fernandez, Philippe; Lamare, Frédéric

2018-02-13

Respiratory motion reduces both the qualitative and quantitative accuracy of PET images in oncology. This impact is more significant for quantitative applications based on kinetic modeling, where dynamic acquisitions are associated with limited statistics due to the necessity of enhanced temporal resolution. The aim of this study is to address these drawbacks, by combining a respiratory motion correction approach with temporal regularization in a unique reconstruction algorithm for dynamic PET imaging. Elastic transformation parameters for the motion correction are estimated from the non-attenuation-corrected PET images. The derived displacement matrices are subsequently used in a list-mode based OSEM reconstruction algorithm integrating a temporal regularization between the 3D dynamic PET frames, based on temporal basis functions. These functions are simultaneously estimated at each iteration, along with their relative coefficients for each image voxel. Quantitative evaluation has been performed using dynamic FDG PET/CT acquisitions of lung cancer patients acquired on a GE DRX system. The performance of the proposed method is compared with that of a standard multi-frame OSEM reconstruction algorithm. The proposed method achieved substantial improvements in terms of noise reduction while accounting for loss of contrast due to respiratory motion. Results on simulated data showed that the proposed 4D algorithms led to bias reduction values up to 40% in both tumor and blood regions for similar standard deviation levels, in comparison with a standard 3D reconstruction. Patlak parameter estimations on reconstructed images with the proposed reconstruction methods resulted in 30% and 40% bias reduction in the tumor and lung region respectively for the Patlak slope, and a 30% bias reduction for the intercept in the tumor region (a similar Patlak intercept was achieved in the lung area). Incorporation of the respiratory motion correction using an elastic model along with a temporal regularization in the reconstruction process of the PET dynamic series led to substantial quantitative improvements and motion artifact reduction. Future work will include the integration of a linear FDG kinetic model, in order to directly reconstruct parametric images.

Quantification of Dynamic [18F]FDG Pet Studies in Acute Lung Injury.

PubMed

Grecchi, Elisabetta; Veronese, Mattia; Moresco, Rosa Maria; Bellani, Giacomo; Pesenti, Antonio; Messa, Cristina; Bertoldo, Alessandra

2016-02-01

This work aims to investigate lung glucose metabolism using 2-deoxy-2-[(18)F]fluoro-D-glucose ([(18)F]FDG) positron emission tomography (PET) imaging in acute lung injury (ALI) patients. Eleven ALI patients and five healthy controls underwent a dynamic [(18)F]FDG PET/X-ray computed tomography (CT) scan. The standardized uptake values (SUV) and three different methods for the quantification of glucose metabolism (i.e., ratio, Patlak, and spectral analysis iterative filter, SAIF) were applied both at the region and the voxel levels. SUV reported a lower correlation than the ratio with the net tracer uptake. Patlak and SAIF analyses did not show any significant spatial or quantitative (R(2) > 0.80) difference. The additional information provided by SAIF showed that in lung inflammation, elevated tracer uptake is coupled with abnormal tracer exchanges within and between lung tissue compartments. Full kinetic modeling provides a multi-parametric description of glucose metabolism in the lungs. This allows characterizing the spatial distribution of lung inflammation as well as returning the functional state of the tissues.

Preclinical evaluation of parametric image reconstruction of [18F]FMISO PET: correlation with ex vivo immunohistochemistry

NASA Astrophysics Data System (ADS)

Cheng, Xiaoyin; Bayer, Christine; Maftei, Constantin-Alin; Astner, Sabrina T.; Vaupel, Peter; Ziegler, Sibylle I.; Shi, Kuangyu

2014-01-01

Compared to indirect methods, direct parametric image reconstruction (PIR) has the advantage of high quality and low statistical errors. However, it is not yet clear if this improvement in quality is beneficial for physiological quantification. This study aimed to evaluate direct PIR for the quantification of tumor hypoxia using the hypoxic fraction (HF) assessed from immunohistological data as a physiological reference. Sixteen mice with xenografted human squamous cell carcinomas were scanned with dynamic [18F]FMISO PET. Afterward, tumors were sliced and stained with H&E and the hypoxia marker pimonidazole. The hypoxic signal was segmented using k-means clustering and HF was specified as the ratio of the hypoxic area over the viable tumor area. The parametric Patlak slope images were obtained by indirect voxel-wise modeling on reconstructed images using filtered back projection and ordered-subset expectation maximization (OSEM) and by direct PIR (e.g., parametric-OSEM, POSEM). The mean and maximum Patlak slopes of the tumor area were investigated and compared with HF. POSEM resulted in generally higher correlations between slope and HF among the investigated methods. A strategy for the delineation of the hypoxic tumor volume based on thresholding parametric images at half maximum of the slope is recommended based on the results of this study.

Dynamic-contrast-enhanced-MRI with extravasating contrast reagent: Rat cerebral glioma blood volume determination

NASA Astrophysics Data System (ADS)

Li, Xin; Rooney, William D.; Várallyay, Csanád G.; Gahramanov, Seymur; Muldoon, Leslie L.; Goodman, James A.; Tagge, Ian J.; Selzer, Audrey H.; Pike, Martin M.; Neuwelt, Edward A.; Springer, Charles S.

2010-10-01

The accurate mapping of the tumor blood volume (TBV) fraction ( vb) is a highly desired imaging biometric goal. It is commonly thought that achieving this is difficult, if not impossible, when small molecule contrast reagents (CRs) are used for the T1-weighted (Dynamic-Contrast-Enhanced) DCE-MRI technique. This is because angiogenic malignant tumor vessels allow facile CR extravasation. Here, a three-site equilibrium water exchange model is applied to DCE-MRI data from the cerebrally-implanted rat brain U87 glioma, a tumor exhibiting rapid CR extravasation. Analyses of segments of the (and the entire) DCE data time-course with this "shutter-speed" pharmacokinetic model, which admits finite water exchange kinetics, allow TBV estimation from the first-pass segment. Pairwise parameter determinances were tested with grid searches of 2D parametric error surfaces. Tumor blood volume ( vb), as well as ve (the extracellular, extravascular space volume fraction), and Ktrans (a CR extravasation rate measure) parametric maps are presented. The role of the Patlak Plot in DCE-MRI is also considered.

Optimal acquisition and modeling parameters for accurate assessment of low Ktrans blood-brain barrier permeability using dynamic contrast-enhanced MRI.

PubMed

Barnes, Samuel R; Ng, Thomas S C; Montagne, Axel; Law, Meng; Zlokovic, Berislav V; Jacobs, Russell E

2016-05-01

To determine optimal parameters for acquisition and processing of dynamic contrast-enhanced MRI (DCE-MRI) to detect small changes in near normal low blood-brain barrier (BBB) permeability. Using a contrast-to-noise ratio metric (K-CNR) for Ktrans precision and accuracy, the effects of kinetic model selection, scan duration, temporal resolution, signal drift, and length of baseline on the estimation of low permeability values was evaluated with simulations. The Patlak model was shown to give the highest K-CNR at low Ktrans . The Ktrans transition point, above which other models yielded superior results, was highly dependent on scan duration and tissue extravascular extracellular volume fraction (ve ). The highest K-CNR for low Ktrans was obtained when Patlak model analysis was combined with long scan times (10-30 min), modest temporal resolution (<60 s/image), and long baseline scans (1-4 min). Signal drift as low as 3% was shown to affect the accuracy of Ktrans estimation with Patlak analysis. DCE acquisition and modeling parameters are interdependent and should be optimized together for the tissue being imaged. Appropriately optimized protocols can detect even the subtlest changes in BBB integrity and may be used to probe the earliest changes in neurodegenerative diseases such as Alzheimer's disease and multiple sclerosis. © 2015 Wiley Periodicals, Inc.

Nonlinear PET parametric image reconstruction with MRI information using kernel method

NASA Astrophysics Data System (ADS)

Gong, Kuang; Wang, Guobao; Chen, Kevin T.; Catana, Ciprian; Qi, Jinyi

2017-03-01

Positron Emission Tomography (PET) is a functional imaging modality widely used in oncology, cardiology, and neurology. It is highly sensitive, but suffers from relatively poor spatial resolution, as compared with anatomical imaging modalities, such as magnetic resonance imaging (MRI). With the recent development of combined PET/MR systems, we can improve the PET image quality by incorporating MR information. Previously we have used kernel learning to embed MR information in static PET reconstruction and direct Patlak reconstruction. Here we extend this method to direct reconstruction of nonlinear parameters in a compartment model by using the alternating direction of multiplier method (ADMM) algorithm. Simulation studies show that the proposed method can produce superior parametric images compared with existing methods.

Tracer kinetic modelling for DCE-MRI quantification of subtle blood-brain barrier permeability.

PubMed

Heye, Anna K; Thrippleton, Michael J; Armitage, Paul A; Valdés Hernández, Maria Del C; Makin, Stephen D; Glatz, Andreas; Sakka, Eleni; Wardlaw, Joanna M

2016-01-15

There is evidence that subtle breakdown of the blood-brain barrier (BBB) is a pathophysiological component of several diseases, including cerebral small vessel disease and some dementias. Dynamic contrast-enhanced MRI (DCE-MRI) combined with tracer kinetic modelling is widely used for assessing permeability and perfusion in brain tumours and body tissues where contrast agents readily accumulate in the extracellular space. However, in diseases where leakage is subtle, the optimal approach for measuring BBB integrity is likely to differ since the magnitude and rate of enhancement caused by leakage are extremely low; several methods have been reported in the literature, yielding a wide range of parameters even in healthy subjects. We hypothesised that the Patlak model is a suitable approach for measuring low-level BBB permeability with low temporal resolution and high spatial resolution and brain coverage, and that normal levels of scanner instability would influence permeability measurements. DCE-MRI was performed in a cohort of mild stroke patients (n=201) with a range of cerebral small vessel disease severity. We fitted these data to a set of nested tracer kinetic models, ranking their performance according to the Akaike information criterion. To assess the influence of scanner drift, we scanned 15 healthy volunteers that underwent a "sham" DCE-MRI procedure without administration of contrast agent. Numerical simulations were performed to investigate model validity and the effect of scanner drift. The Patlak model was found to be most appropriate for fitting low-permeability data, and the simulations showed vp and K(Trans) estimates to be reasonably robust to the model assumptions. However, signal drift (measured at approximately 0.1% per minute and comparable to literature reports in other settings) led to systematic errors in calculated tracer kinetic parameters, particularly at low permeabilities. Our findings justify the growing use of the Patlak model in low-permeability states, which has the potential to provide valuable information regarding BBB integrity in a range of diseases. However, absolute values of the resulting tracer kinetic parameters should be interpreted with extreme caution, and the size and influence of signal drift should be measured where possible. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Tracer kinetic modelling for DCE-MRI quantification of subtle blood–brain barrier permeability

PubMed Central

Heye, Anna K.; Thrippleton, Michael J.; Armitage, Paul A.; Valdés Hernández, Maria del C.; Makin, Stephen D.; Glatz, Andreas; Sakka, Eleni; Wardlaw, Joanna M.

2016-01-01

There is evidence that subtle breakdown of the blood–brain barrier (BBB) is a pathophysiological component of several diseases, including cerebral small vessel disease and some dementias. Dynamic contrast-enhanced MRI (DCE-MRI) combined with tracer kinetic modelling is widely used for assessing permeability and perfusion in brain tumours and body tissues where contrast agents readily accumulate in the extracellular space. However, in diseases where leakage is subtle, the optimal approach for measuring BBB integrity is likely to differ since the magnitude and rate of enhancement caused by leakage are extremely low; several methods have been reported in the literature, yielding a wide range of parameters even in healthy subjects. We hypothesised that the Patlak model is a suitable approach for measuring low-level BBB permeability with low temporal resolution and high spatial resolution and brain coverage, and that normal levels of scanner instability would influence permeability measurements. DCE-MRI was performed in a cohort of mild stroke patients (n = 201) with a range of cerebral small vessel disease severity. We fitted these data to a set of nested tracer kinetic models, ranking their performance according to the Akaike information criterion. To assess the influence of scanner drift, we scanned 15 healthy volunteers that underwent a “sham” DCE-MRI procedure without administration of contrast agent. Numerical simulations were performed to investigate model validity and the effect of scanner drift. The Patlak model was found to be most appropriate for fitting low-permeability data, and the simulations showed vp and KTrans estimates to be reasonably robust to the model assumptions. However, signal drift (measured at approximately 0.1% per minute and comparable to literature reports in other settings) led to systematic errors in calculated tracer kinetic parameters, particularly at low permeabilities. Our findings justify the growing use of the Patlak model in low-permeability states, which has the potential to provide valuable information regarding BBB integrity in a range of diseases. However, absolute values of the resulting tracer kinetic parameters should be interpreted with extreme caution, and the size and influence of signal drift should be measured where possible. PMID:26477653

PET Pharmacokinetic Modelling

NASA Astrophysics Data System (ADS)

Müller-Schauenburg, Wolfgang; Reimold, Matthias

Positron Emission Tomography is a well-established technique that allows imaging and quantification of tissue properties in-vivo. The goal of pharmacokinetic modelling is to estimate physiological parameters, e.g. perfusion or receptor density from the measured time course of a radiotracer. After a brief overview of clinical application of PET, we summarize the fundamentals of modelling: distribution volume, Fick's principle of local balancing, extraction and perfusion, and how to calculate equilibrium data from measurements after bolus injection. Three fundamental models are considered: (i) the 1-tissue compartment model, e.g. for regional cerebral blood flow (rCBF) with the short-lived tracer [15O]water, (ii) the 2-tissue compartment model accounting for trapping (one exponential + constant), e.g. for glucose metabolism with [18F]FDG, (iii) the reversible 2-tissue compartment model (two exponentials), e.g. for receptor binding. Arterial blood sampling is required for classical PET modelling, but can often be avoided by comparing regions with specific binding with so called reference regions with negligible specific uptake, e.g. in receptor imaging. To estimate the model parameters, non-linear least square fits are the standard. Various linearizations have been proposed for rapid parameter estimation, e.g. on a pixel-by-pixel basis, for the prize of a bias. Such linear approaches exist for all three models; e.g. the PATLAK-plot for trapping substances like FDG, and the LOGAN-plot to obtain distribution volumes for reversibly binding tracers. The description of receptor modelling is dedicated to the approaches of the subsequent lecture (chapter) of Millet, who works in the tradition of Delforge with multiple-injection investigations.

In-vivo imaging of blood-brain barrier permeability using positron emission tomography with 2-amino-[3-11C]isobutyric acid.

PubMed

Okada, Maki; Kikuchi, Tatsuya; Okamura, Toshimitsu; Ikoma, Yoko; Tsuji, Atsushi B; Wakizaka, Hidekatsu; Kamakura, Tomoo; Aoki, Ichio; Zhang, Ming-Rong; Kato, Koichi

2015-12-01

The blood-brain barrier (BBB) limits the entry of some therapeutics into the brain, resulting in reduced efficacy. BBB-opening techniques have been developed to enhance the entry into the brain. However, a noninvasive, highly sensitive and quantitative method for evaluating the changes in BBB permeability induced by such techniques is needed to optimize treatment protocols. We evaluated 2-amino-[3-C]isobutyric acid ([3-C]AIB) as a PET probe to quantify BBB permeability in model rats. BBB opening was induced by a lipopolysaccharide injection or focused ultrasound (FUS) sonication. [3-C]AIB distribution in the brain was evaluated by autoradiography and PET and compared with that of Evans blue, a traditional BBB permeability marker. Kinetics of [3-C]AIB was compared with that of gadolinium-diethylenetriamine pentaacetic acid (Gd-DTPA)-enhanced MRI. The unidirectional blood-brain transfer constant (Ki) of [3-C]AIB was estimated using the Patlak plot. [3-C]AIB uptake in the lesion area was significantly higher than that in the control area and radioactivity colocalized with Evans blue in both models. [3-C]AIB uptake in the FUS-sonicated region decreased over time after sonication. The ratio of [3-C]AIB accumulation in the FUS-treated to the contralateral side increased during the experimental period, whereas that of the Gd-DTPA intensity reached a maximum at 10 min after injection and decreased thereafter. The [3-C]AIB Ki values were significantly higher in the lesion area than the control area. [3-C]AIB PET is a promising, highly sensitive and quantitative imaging method for assessment of BBB permeability.

Dynamic contrast-enhanced perfusion area-detector CT assessed with various mathematical models: Its capability for therapeutic outcome prediction for non-small cell lung cancer patients with chemoradiotherapy as compared with that of FDG-PET/CT.

PubMed

Ohno, Yoshiharu; Fujisawa, Yasuko; Koyama, Hisanobu; Kishida, Yuji; Seki, Shinichiro; Sugihara, Naoki; Yoshikawa, Takeshi

2017-01-01

To directly compare the capability of dynamic first-pass contrast-enhanced (CE-) perfusion area-detector CT (ADCT) and PET/CT for early prediction of treatment response, disease progression and overall survival of non-small cell carcinoma (NSCLC) patients treated with chemoradiotherapy. Fifty-three consecutive Stage IIIB NSCLC patients who had undergone PET/CT, dynamic first-pass CE-perfusion ADCT, chemoradiotherapy, and follow-up examination were enrolled in this study. They were divided into two groups: 1) complete or partial response (CR+PR) and 2) stable or progressive disease (SD+PD). Pulmonary arterial and systemic arterial perfusions and total perfusion were assessed at targeted lesions with the dual-input maximum slope method, permeability surface and distribution volume with the Patlak plot method, tumor perfusion with the single-input maximum slope method, and SUV max , and results were averaged to determine final values for each patient. Next, step-wise regression analysis was used to determine which indices were the most useful for predicting therapeutic effect. Finally, overall survival of responders and non-responders assessed by using the indices that had a significant effect on prediction of therapeutic outcome was statistically compared. The step-wise regression test showed that therapeutic effect (r 2 =0.63, p=0.01) was significantly affected by the following three factors in order of magnitude of impact: systemic arterial perfusion, total perfusion, and SUV max . Mean overall survival showed a significant difference for total perfusion (p=0.003) and systemic arterial perfusion (p=0.04). Dynamic first-pass CE-perfusion ADCT as well as PET/CT are useful for treatment response prediction in NSCLC patients treated with chemoradiotherapy. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Measurement of regional cerebral blood flow with copper-62-PTSM and a three-compartment model.

PubMed

Okazawa, H; Yonekura, Y; Fujibayashi, Y; Mukai, T; Nishizawa, S; Magata, Y; Ishizu, K; Tamaki, N; Konishi, J

1996-07-01

We evaluated quantitatively 62Cu-labeled pyruvaldehyde bis(N4-methylthiosemicarbazone) copper II (62Cu-PTSM) as a brain perfusion tracer for positron emission tomography (PET). For quantitative measurement, the octanol extraction method is needed to correct for arterial radioactivity in estimating the lipophilic input function, but the procedure is not practical for clinical studies. To measure regional cerebral blood flow (rCBF) by 62Cu-PTSM with simple arterial blood sampling, a standard curve of the octanol extraction ratio and a three-compartment model were applied. We performed both 15O-labeled water PET and 62 Cu-PTSM PET with dynamic data acquisition and arterial sampling in six subjects. Data obtained in 10 subjects studied previously were used for the standard octanol extraction curve. Arterial activity was measured and corrected to obtain the true input function using the standard curve. Graphical analysis (Gjedde-Patlak plot) with the data for each subject fitted by a straight regression line suggested that 62Cu-PTSM can be analyzed by the three-compartment model with negligible K4. Using this model, K1-K3 were estimated from curve fitting of the cerebral time-activity curve and the corrected input function. The fractional uptake of 62Cu-PTSM was corrected to rCBF with the individual extraction at steady state calculated from K1-K3. The influx rates (Ki) obtained from three-compartment model and graphical analyses were compared for the validation of the model. A comparison of rCBF values obtained from 62Cu-PTSM and 150-water studies demonstrated excellent correlation. The results suggest the potential feasibility of quantitation of cerebral perfusion with 62Cu-PTSM accompanied by dynamic PET and simple arterial sampling.

Pseudo-extravasation rate constant of dynamic susceptibility contrast-MRI determined from pharmacokinetic first principles.

PubMed

Li, Xin; Varallyay, Csanad G; Gahramanov, Seymur; Fu, Rongwei; Rooney, William D; Neuwelt, Edward A

2017-11-01

Dynamic susceptibility contrast-magnetic resonance imaging (DSC-MRI) is widely used to obtain informative perfusion imaging biomarkers, such as the relative cerebral blood volume (rCBV). The related post-processing software packages for DSC-MRI are available from major MRI instrument manufacturers and third-party vendors. One unique aspect of DSC-MRI with low-molecular-weight gadolinium (Gd)-based contrast reagent (CR) is that CR molecules leak into the interstitium space and therefore confound the DSC signal detected. Several approaches to correct this leakage effect have been proposed throughout the years. Amongst the most popular is the Boxerman-Schmainda-Weisskoff (BSW) K 2 leakage correction approach, in which the K 2 pseudo-first-order rate constant quantifies the leakage. In this work, we propose a new method for the BSW leakage correction approach. Based on the pharmacokinetic interpretation of the data, the commonly adopted R 2 * expression accounting for contributions from both intravascular and extravasating CR components is transformed using a method mathematically similar to Gjedde-Patlak linearization. Then, the leakage rate constant (K L ) can be determined as the slope of the linear portion of a plot of the transformed data. Using the DSC data of high-molecular-weight (~750 kDa), iron-based, intravascular Ferumoxytol (FeO), the pharmacokinetic interpretation of the new paradigm is empirically validated. The primary objective of this work is to empirically demonstrate that a linear portion often exists in the graph of the transformed data. This linear portion provides a clear definition of the Gd CR pseudo-leakage rate constant, which equals the slope derived from the linear segment. A secondary objective is to demonstrate that transformed points from the initial transient period during the CR wash-in often deviate from the linear trend of the linearized graph. The inclusion of these points will have a negative impact on the accuracy of the leakage rate constant, and even make it time dependent. Copyright © 2017 John Wiley & Sons, Ltd.

Quantitative graphical analysis of simultaneous dynamic PET/MRI for assessment of prostate cancer.

PubMed

Rosenkrantz, Andrew B; Koesters, Thomas; Vahle, Anne-Kristin; Friedman, Kent; Bartlett, Rachel M; Taneja, Samir S; Ding, Yu-Shin; Logan, Jean

2015-04-01

Dynamic FDG imaging for prostate cancer characterization is limited by generally small size and low uptake in prostate tumors. Our aim in this pilot study was to explore feasibility of simultaneous PET/MRI to guide localization of prostate lesions for dynamic FDG analysis using a graphical approach. Three patients with biopsy-proven prostate cancer underwent simultaneous FDG PET/MRI, incorporating dynamic prostate imaging. Histology and multiparametric MRI findings were used to localize tumors, which in turn guided identification of tumors on FDG images. Regions of interest were manually placed on tumor and benign prostate tissue. Blood activity was extracted from a region of interest placed on the femoral artery on PET images. FDG data were analyzed by graphical analysis using the influx constant Ki (Patlak analysis) when FDG binding seemed irreversible and distribution volume VT (reversible graphical analysis) when FDG binding seemed reversible given the presence of washout. Given inherent coregistration, simultaneous acquisition facilitated use of MRI data to localize small lesions on PET and subsequent graphical analysis in all cases. In 2 cases with irreversible binding, tumor had higher Ki than benign using Patlak analysis (0.023 vs 0.006 and 0.019 vs 0.008 mL/cm3 per minute). In 1 case appearing reversible, tumor had higher VT than benign using reversible graphical analysis (0.68 vs 0.52 mL/cm3). Simultaneous PET/MRI allows localization of small prostate tumors for dynamic PET analysis. By taking advantage of inclusion of the femoral arteries in the FOV, we applied advanced PET data analysis methods beyond conventional static measures and without blood sampling.

Textural features of dynamic contrast-enhanced MRI derived model-free and model-based parameter maps in glioma grading.

PubMed

Xie, Tian; Chen, Xiao; Fang, Jingqin; Kang, Houyi; Xue, Wei; Tong, Haipeng; Cao, Peng; Wang, Sumei; Yang, Yizeng; Zhang, Weiguo

2018-04-01

Presurgical glioma grading by dynamic contrast-enhanced MRI (DCE-MRI) has unresolved issues. The aim of this study was to investigate the ability of textural features derived from pharmacokinetic model-based or model-free parameter maps of DCE-MRI in discriminating between different grades of gliomas, and their correlation with pathological index. Retrospective. Forty-two adults with brain gliomas. 3.0T, including conventional anatomic sequences and DCE-MRI sequences (variable flip angle T1-weighted imaging and three-dimensional gradient echo volumetric imaging). Regions of interest on the cross-sectional images with maximal tumor lesion. Five commonly used textural features, including Energy, Entropy, Inertia, Correlation, and Inverse Difference Moment (IDM), were generated. All textural features of model-free parameters (initial area under curve [IAUC], maximal signal intensity [Max SI], maximal up-slope [Max Slope]) could effectively differentiate between grade II (n = 15), grade III (n = 13), and grade IV (n = 14) gliomas (P < 0.05). Two textural features, Entropy and IDM, of four DCE-MRI parameters, including Max SI, Max Slope (model-free parameters), vp (Extended Tofts), and vp (Patlak) could differentiate grade III and IV gliomas (P < 0.01) in four measurements. Both Entropy and IDM of Patlak-based K trans and vp could differentiate grade II (n = 15) from III (n = 13) gliomas (P < 0.01) in four measurements. No textural features of any DCE-MRI parameter maps could discriminate between subtypes of grade II and III gliomas (P < 0.05). Both Entropy and IDM of Extended Tofts- and Patlak-based vp showed highest area under curve in discriminating between grade III and IV gliomas. However, intraclass correlation coefficient (ICC) of these features revealed relatively lower inter-observer agreement. No significant correlation was found between microvascular density and textural features, compared with a moderate correlation found between cellular proliferation index and those features. Textural features of DCE-MRI parameter maps displayed a good ability in glioma grading. 3 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018;47:1099-1111. © 2017 International Society for Magnetic Resonance in Medicine.

Tunnel formation by Reticulitermes flavipes and Coptotermes formosanus (Isoptera: Rhinotermitidae) in response to wood in sand.

PubMed

Puche, H; Su, N Y

2001-12-01

The tunneling responses of two subterranean termite species, Coptotermes formosanus Shiraki and Reticulitermes flavipes (Kollar), to the presence of sound wood in laboratory arenas were studied. Branching pattern and the speed of tunnel construction between R. flavipes and C. formosanus also were compared. Patlak's residence index (rho) was generated using the length, width, speed of construction, and area of the primary tunnels built by termites. In the same allotted time, C. formosanus built wider and shorter primary tunnels, whereas R. flavipes built thinner and longer primary tunnels. The presence of wood did not affect termite tunnel formation. This lack of variation in tunnel formation parameters was evidenced by the inability of the termites to locate wood sources over distance, even as short as 2.5 mm, and by the similar tunneling behaviors in areas of the arena with or without wood. Patlak's model predicted the densities of tunnels with an error between 9 and 28%. in experiments with R. flavipes exposed to a range of 0-8,000 g of wood, and between 61 and 87% in experiments with C. formosanus. These results indicated that the residence index can provide a qualitative measure of the effect of habitat heterogeneity on the individual termite tunnels. The tunneling constructions strategy of these subterranean termites is discussed.

Quantitative assessment of cerebral blood flow in genetically confirmed spinocerebellar ataxia type 6.

PubMed

Honjo, Kie; Ohshita, Tomohiko; Kawakami, Hideshi; Naka, Hiromitsu; Imon, Yukari; Maruyama, Hirofumi; Mimori, Yasuyo; Matsumoto, Masayasu

2004-06-01

Spinocerebellar ataxia type 6 (SCA6) is an autosomal dominant cerebellar ataxia caused by CAG trinucleotide expansion. The characteristics of regional cerebral blood flow (rCBF) in SCA6 patients have not been established, whereas it has been reported that decreased rCBF in the cerebrum seems to be a remote effect of cerebellar impairment in other cerebellar disorders. To clarify the characteristics of rCBF, including cerebro-cerebellar relationship, and its correlation with clinical manifestations in patients with genetically confirmed SCA6 using quantitative assessment of rCBF by brain single-photon emission computed tomography (SPECT). Technetium Tc 99m ethyl cysteinate dimer SPECT study using a Patlak plot. Patients Hiroshima University Hospital, Hiroshima, Japan. Ten patients with SCA6 and 9 healthy controls. Main Outcome Measure The rCBF of the cerebellar vermis, cerebellar hemisphere, and frontal lobes. In SCA6 patients, rCBF was decreased only in the cerebellar vermis and hemisphere compared with healthy controls, and this was inversely correlated with duration of illness. The rCBF in the frontal lobes was slightly correlated with duration of illness without statistical significance. The rCBF in the vermis was inversely correlated with severity of dysarthria, but there was no significant correlation with CAG repeated expansions. Decrease in rCBF was found only in the cerebellum and was associated with duration of illness, dysarthria and ataxia, and cerebellar atrophy. No remote effect of cerebellar hypoperfusion was found in the SCA6 patients.

Dynamic Contrast-Enhanced Perfusion Area-Detector CT: Preliminary Comparison of Diagnostic Performance for N Stage Assessment With FDG PET/CT in Non-Small Cell Lung Cancer.

PubMed

Ohno, Yoshiharu; Fujisawa, Yasuko; Sugihara, Naoki; Kishida, Yuji; Seki, Shinichiro; Koyama, Hisanobu; Yoshikawa, Takeshi

2017-11-01

The objective of our study was to directly compare the capability of dynamic first-pass contrast-enhanced (CE) perfusion area-detector CT (ADCT) and FDG PET/CT for differentiation of metastatic from nonmetastatic lymph nodes and assessment of N stage in patients with non-small cell lung carcinoma (NSCLC). Seventy-seven consecutive patients, 45 men (mean age ± SD, 70.4 ± 5.9 years) and 32 women (71.2 ± 7.7 years), underwent dynamic first-pass CE-perfusion ADCT at two or three different positions for covering the entire thorax, FDG PET/CT, surgical treatment, and pathologic examination. From all ADCT data for each of the subjects, a whole-chest perfusion map was computationally generated using the dual- and single-input maximum slope and Patlak plot methods. For quantitative N stage assessment, perfusion parameters and the maximum standardized uptake value (SUV max ) for each lymph node were determined by measuring the relevant ROI. ROC curve analyses were performed for comparing the diagnostic capability of each of the methods on a per-node basis. N stages evaluated by each of the indexes were then statistically compared with the final pathologic diagnosis by means of chi-square and kappa statistics. The area under the ROC curve (A z ) values of systemic arterial perfusion (A z = 0.89), permeability surface (A z = 0.78), and SUV max (A z = 0.85) were significantly larger than the A z values of total perfusion (A z = 0.70, p < 0.05) and distribution volume (A z = 0.55, p < 0.05). For each of the threshold values, agreement for systemic arterial perfusion calculated using the dual-input maximum slope model was substantial (κ = 0.70, p < 0.0001), and agreement for SUV max was moderate (κ = 0.60, p < 0.0001). Dynamic first-pass CE-perfusion ADCT is as useful as FDG PET/CT for the differentiation of metastatic from nonmetastatic lymph nodes and assessment of N stage in patients with NSCLC.

[Heart rate variability study based on a novel RdR RR Intervals Scatter Plot].

PubMed

Lu, Hongwei; Lu, Xiuyun; Wang, Chunfang; Hua, Youyuan; Tian, Jiajia; Liu, Shihai

2014-08-01

On the basis of Poincare scatter plot and first order difference scatter plot, a novel heart rate variability (HRV) analysis method based on scatter plots of RR intervals and first order difference of RR intervals (namely, RdR) was proposed. The abscissa of the RdR scatter plot, the x-axis, is RR intervals and the ordinate, y-axis, is the difference between successive RR intervals. The RdR scatter plot includes the information of RR intervals and the difference between successive RR intervals, which captures more HRV information. By RdR scatter plot analysis of some records of MIT-BIH arrhythmias database, we found that the scatter plot of uncoupled premature ventricular contraction (PVC), coupled ventricular bigeminy and ventricular trigeminy PVC had specific graphic characteristics. The RdR scatter plot method has higher detecting performance than the Poincare scatter plot method, and simpler and more intuitive than the first order difference method.

Optimal design of a plot cluster for monitoring

Treesearch

Charles T. Scott

1993-01-01

Traveling costs incurred during extensive forest surveys make cluster sampling cost-effective. Clusters are specified by the type of plots, plot size, number of plots, and the distance between plots within the cluster. A method to determine the optimal cluster design when different plot types are used for different forest resource attributes is described. The method...

Is There a Direct Correlation Between Microvascular Wall Structure and k-Trans Values Obtained From Perfusion CT Measurements in Lymphomas?

PubMed

Horger, Marius; Fallier-Becker, Petra; Thaiss, Wolfgang M; Sauter, Alexander; Bösmüller, Hans; Martella, Manuela; Preibsch, Heike; Fritz, Jan; Nikolaou, Konstantin; Kloth, Christopher

2018-05-03

This study aimed to test the hypothesis that ultrastructural wall abnormalities of lymphoma vessels correlate with perfusion computed tomography (PCT) kinetics. Our local institutional review board approved this prospective study. Between February 2013 and June 2016, we included 23 consecutive subjects with newly diagnosed lymphoma, who were referred for computed tomography-guided biopsy (6 women, 17 men; mean age, 60.61 ± 12.43 years; range, 28-74 years) and additionally agreed to undergo PCT of the target lymphoma tissues. PCT was obtained for 40 seconds using 80 kV, 120 mAs, 64 × 0.6-mm collimation, 6.9-cm z-axis coverage, and 26 volume measurements. Mean and maximum k-trans (mL/100 mL/min), blood flow (BF; mL/100 mL/min) and blood volume (BV) were quantified using the deconvolution and the maximum slope + Patlak calculation models. Immunohistochemical staining was performed for microvessel density quantification (vessels/m 2 ), and electron microscopy was used to determine the presence or absence of tight junctions, endothelial fenestration, basement membrane, and pericytes, and to measure extracellular matrix thickness. Extracellular matrix thickness as well as the presence or absence of tight junctions, basal lamina, and pericytes did not correlate with computed tomography perfusion parameters. Endothelial fenestrations correlated significantly with mean BF deconvolution (P = .047, r = 0.418) and additionally was significantly associated with higher mean BV deconvolution (P < .005). Mean k-trans Patlak correlated strongly with mean k-trans deconvolution (r = 0.939, P = .001), and both correlated with mean BF deconvolution (P = .001, r = 0.748), max BF deconvolution (P = .028, r = 0.564), mean BV deconvolution (P = .001, r = 0.752), and max BV deconvolution (P = .001, r = 0.771). Microvessel density correlated with max k-trans deconvolution (r = 0.564, P = .023). Vascular endothelial growth factor receptor-3 expression (receptor specific for lymphatics) correlated significantly with max k-trans Patlak (P = .041, r = 0.686) and mean BF deconvolution (P = .038, r = 0.695). k-Trans values of PCT do not correlate with ultrastructural microvessel features, whereas endothelial fenestrations correlate with increased intra-tumoral BVs. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Theoretical considerations in measurement of time discrepancies between input and myocardial time-signal intensity curves in estimates of regional myocardial perfusion with first-pass contrast-enhanced MRI.

PubMed

Natsume, Takahiro; Ishida, Masaki; Kitagawa, Kakuya; Nagata, Motonori; Sakuma, Hajime; Ichihara, Takashi

2015-11-01

The purpose of this study was to develop a method to determine time discrepancies between input and myocardial time-signal intensity (TSI) curves for accurate estimation of myocardial perfusion with first-pass contrast-enhanced MRI. Estimation of myocardial perfusion with contrast-enhanced MRI using kinetic models requires faithful recording of contrast content in the blood and myocardium. Typically, the arterial input function (AIF) is obtained by setting a region of interest in the left ventricular cavity. However, there is a small delay between the AIF and the myocardial curves, and such time discrepancies can lead to errors in flow estimation using Patlak plot analysis. In this study, the time discrepancies between the arterial TSI curve and the myocardial tissue TSI curve were estimated based on the compartment model. In the early phase after the arrival of the contrast agent in the myocardium, the relationship between rate constant K1 and the concentrations of Gd-DTPA contrast agent in the myocardium and arterial blood (LV blood) can be described by the equation K1={dCmyo(tpeak)/dt}/Ca(tpeak), where Cmyo(t) and Ca(t) are the relative concentrations of Gd-DTPA contrast agent in the myocardium and in the LV blood, respectively, and tpeak is the time corresponding to the peak of Ca(t). In the ideal case, the time corresponding to the maximum upslope of Cmyo(t), tmax, is equal to tpeak. In practice, however, there is a small difference in the arrival times of the contrast agent into the LV and into the myocardium. This difference was estimated to correspond to the difference between tpeak and tmax. The magnitudes of such time discrepancies and the effectiveness of the correction for these time discrepancies were measured in 18 subjects who underwent myocardial perfusion MRI under rest and stress conditions. The effects of the time discrepancies could be corrected effectively in the myocardial perfusion estimates. Copyright © 2015 Elsevier Inc. All rights reserved.

Dynamic 68Ga-DOTATOC PET/CT and static image in NET patients. Correlation of parameters during PRRT.

PubMed

Van Binnebeek, Sofie; Koole, Michel; Terwinghe, Christelle; Baete, Kristof; Vanbilloen, Bert; Haustermans, Karine; Clement, Paul M; Bogaerts, Kris; Verbruggen, Alfons; Nackaerts, Kris; Van Cutsem, Eric; Verslype, Chris; Mottaghy, Felix M; Deroose, Christophe M

2016-06-28

To investigate the relationship between the dynamic parameters (Ki) and static image-derived parameters of 68Ga-DOTATOC-PET, to determine which static parameter best reflects underlying somatostatin-receptor-expression (SSR) levels on neuroendocrine tumours (NETs). 20 patients with metastasized NETs underwent a dynamic and static 68Ga-DOTATOC-PET before PRRT and at 7 and 40 weeks after the first administration of 90Y-DOTATOC (in total 4 cycles were planned); 175 lesions were defined and analyzed on the dynamic as well as static scans. Quantitative analysis was performed using the software PMOD. One to five target lesions per patient were chosen and delineated manually on the baseline dynamic scan and further, on the corresponding static 68Ga-DOTATOC-PET and the dynamic and static 68Ga-DOTATOC-PET at the other time-points; SUVmax and SUVmean of the lesions was assessed on the other six scans. The input function was retrieved from the abdominal aorta on the images. Further on, Ki was calculated using the Patlak-Plot. At last, 5 reference regions for normalization of SUVtumour were delineated on the static scans resulting in 5 ratios (SUVratio). SUVmax and SUVmean of the tumoural lesions on the dynamic 68Ga-DOTATOC-PET had a very strong correlation with the corresponding parameters in the static scan (R²: 0.94 and 0.95 respectively). SUVmax, SUVmean and Ki of the lesions showed a good linear correlation; the SUVratios correlated poorly with Ki. A significantly better correlation was noticed between Ki and SUVtumour(max and mean) (p < 0.0001). As the dynamic parameter Ki correlates best with the absolute SUVtumour, SUVtumour best reflects underlying SSR-levels in NETs.

CT perfusion imaging of the liver and the spleen in patients with cirrhosis: Is there a correlation between perfusion and portal venous hypertension?

PubMed

Talakić, Emina; Schaffellner, Silvia; Kniepeiss, Daniela; Mueller, Helmut; Stauber, Rudolf; Quehenberger, Franz; Schoellnast, Helmut

2017-10-01

To correlate hepatic and splenic CT perfusion parameters with hepatic venous pressure gradient (HVPG) measurements in patients with cirrhosis. Twenty-one patients with cirrhosis (males, 17; females, 4; mean ± SD age, 57 ± 7 years) underwent hepatic and splenic perfusion CT on a 320-detector row volume scanner as well as invasive measurement of HVPG. Different CT perfusion algorithms (maximum slope analysis and Patlak plot) were used to measure hepatic arterial flow (HAF), portal venous flow (PVF), hepatic perfusion index (HPI), splenic arterial flow (SAF), splenic blood volume (SBV) and splenic clearance (SCL). Hepatic and splenic perfusion parameters were correlated with HVPG, and sensitivity and specificity for detection of severe portal hypertension (≥12 mmHg) were calculated. The Spearman correlation coefficient was -0.53 (p < 0.05) between SAF and HVPG, and -0.68 (p < 0.01) between HVPG and SCL. Using a cut-off value of 125 ml/min/100 ml for SCL, sensitivity for detection of a HVPG of ≥12 mmHg was 94%, and specificity 100%. There was no significant correlation between hepatic perfusion parameters and HVPG. CT perfusion in patients with cirrhosis showed a strong correlation between SCL and HVPG and may be used for detection of severe portal hypertension. • SAF and SCL are statistically significantly correlated with HVPG • SCL showed stronger correlation with HVPG than SAF • 125 ml/min/100 ml SCL-cut-off yielded 94 % sensitivity, 100 % specificity for severe PH • HAF, PVF and HPI showed no statistically significant correlation with HVPG.

Influence of O-methylated metabolite penetrating the blood-brain barrier to estimation of dopamine synthesis capacity in human L-[β-(11)C]DOPA PET.

PubMed

Matsubara, Keisuke; Ikoma, Yoko; Okada, Maki; Ibaraki, Masanobu; Suhara, Tetsuya; Kinoshita, Toshibumi; Ito, Hiroshi

2014-02-01

O-methyl metabolite (L-[β-(11)C]OMD) of (11)C-labeled L-3,4-dihydroxyphenylalanine (L-[β-(11)C]DOPA) can penetrate into brain tissue through the blood-brain barrier, and can complicate the estimation of dopamine synthesis capacity by positron emission tomography (PET) study with L-[β-(11)C]DOPA. We evaluated the impact of L-[β-(11)C]OMD on the estimation of the dopamine synthesis capacity in a human L-[β-(11)C]DOPA PET study. The metabolite correction with mathematical modeling of L-[β-(11)C]OMD kinetics in a reference region without decarboxylation and further metabolism, proposed by a previous [(18)F]FDOPA PET study, were implemented to estimate radioactivity of tissue L-[β-(11)C]OMD in 10 normal volunteers. The component of L-[β-(11)C]OMD in tissue time-activity curves (TACs) in 10 regions were subtracted by the estimated radioactivity of L-[β-(11)C]OMD. To evaluate the influence of omitting blood sampling and metabolite correction, relative dopamine synthesis rate (kref) was estimated by Gjedde-Patlak analysis with reference tissue input function, as well as the net dopamine synthesis rate (Ki) by Gjedde-Patlak analysis with the arterial input function and TAC without and with metabolite correction. Overestimation of Ki was observed without metabolite correction. However, the kref and Ki with metabolite correction were significantly correlated. These data suggest that the influence of L-[β-(11)C]OMD is minimal for the estimation of kref as dopamine synthesis capacity.

Partial differential equation techniques for analysing animal movement: A comparison of different methods.

PubMed

Wang, Yi-Shan; Potts, Jonathan R

2017-03-07

Recent advances in animal tracking have allowed us to uncover the drivers of movement in unprecedented detail. This has enabled modellers to construct ever more realistic models of animal movement, which aid in uncovering detailed patterns of space use in animal populations. Partial differential equations (PDEs) provide a popular tool for mathematically analysing such models. However, their construction often relies on simplifying assumptions which may greatly affect the model outcomes. Here, we analyse the effect of various PDE approximations on the analysis of some simple movement models, including a biased random walk, central-place foraging processes and movement in heterogeneous landscapes. Perhaps the most commonly-used PDE method dates back to a seminal paper of Patlak from 1953. However, our results show that this can be a very poor approximation in even quite simple models. On the other hand, more recent methods, based on transport equation formalisms, can provide more accurate results, as long as the kernel describing the animal's movement is sufficiently smooth. When the movement kernel is not smooth, we show that both the older and newer methods can lead to quantitatively misleading results. Our detailed analysis will aid future researchers in the appropriate choice of PDE approximation for analysing models of animal movement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Visualizing the deep end of sound: plotting multi-parameter results from infrasound data analysis

NASA Astrophysics Data System (ADS)

Perttu, A. B.; Taisne, B.

2016-12-01

Infrasound is sound below the threshold of human hearing: approximately 20 Hz. The field of infrasound research, like other waveform based fields relies on several standard processing methods and data visualizations, including waveform plots and spectrograms. The installation of the International Monitoring System (IMS) global network of infrasound arrays, contributed to the resurgence of infrasound research. Array processing is an important method used in infrasound research, however, this method produces data sets with a large number of parameters, and requires innovative plotting techniques. The goal in designing new figures is to be able to present easily comprehendible, and information-rich plots by careful selection of data density and plotting methods.

A fast hidden line algorithm for plotting finite element models

NASA Technical Reports Server (NTRS)

Jones, G. K.

1982-01-01

Effective plotting of finite element models requires the use of fast hidden line plot techniques that provide interactive response. A high speed hidden line technique was developed to facilitate the plotting of NASTRAN finite element models. Based on testing using 14 different models, the new hidden line algorithm (JONES-D) appears to be very fast: its speed equals that for normal (all lines visible) plotting and when compared to other existing methods it appears to be substantially faster. It also appears to be very reliable: no plot errors were observed using the new method to plot NASTRAN models. The new algorithm was made part of the NPLOT NASTRAN plot package and was used by structural analysts for normal production tasks.

Maintaining a permanent plot data base for growth and yield research: Solutions to some recurring problems

Treesearch

John C. Byrne

1993-01-01

Methods for solving some recurring problems of maintaining a permanent plot data base for growth and yield reseuch are described. These methods include documenting data from diverse sampling designs, changing sampling designs, changing field procedures, and coordinating activities in the plots with the land management agency. Managing a permanent plot data base (...

Possibility of using NURBS for surface plotting by survey data

NASA Astrophysics Data System (ADS)

Pravdina, E. A.; Lepikhina, O. J.

2018-05-01

Different methods of surface plotting were discussed in this article. Constructing the surface with the help of the Delaunay triangulation algorithm is described. The TIN-surfaces (triangles irregular net) method is used in the entire CAD software. This type of surfaces is plotting by results of laser scanning and stadia surveying. Possibility of using spline surfaces (NURBS) for surface plotting is studied. For a defined number of points by Mathcad software, the curvilinear function that described two-dimensional spline surfaces was calculated and plotted.

Graphical Data Analysis on the Circle: Wrap-Around Time Series Plots for (Interrupted) Time Series Designs.

PubMed

Rodgers, Joseph Lee; Beasley, William Howard; Schuelke, Matthew

2014-01-01

Many data structures, particularly time series data, are naturally seasonal, cyclical, or otherwise circular. Past graphical methods for time series have focused on linear plots. In this article, we move graphical analysis onto the circle. We focus on 2 particular methods, one old and one new. Rose diagrams are circular histograms and can be produced in several different forms using the RRose software system. In addition, we propose, develop, illustrate, and provide software support for a new circular graphical method, called Wrap-Around Time Series Plots (WATS Plots), which is a graphical method useful to support time series analyses in general but in particular in relation to interrupted time series designs. We illustrate the use of WATS Plots with an interrupted time series design evaluating the effect of the Oklahoma City bombing on birthrates in Oklahoma County during the 10 years surrounding the bombing of the Murrah Building in Oklahoma City. We compare WATS Plots with linear time series representations and overlay them with smoothing and error bands. Each method is shown to have advantages in relation to the other; in our example, the WATS Plots more clearly show the existence and effect size of the fertility differential.

Interactive computer methods for generating mineral-resource maps

USGS Publications Warehouse

Calkins, James Alfred; Crosby, A.S.; Huffman, T.E.; Clark, A.L.; Mason, G.T.; Bascle, R.J.

1980-01-01

Inasmuch as maps are a basic tool of geologists, the U.S. Geological Survey's CRIB (Computerized Resources Information Bank) was constructed so that the data it contains can be used to generate mineral-resource maps. However, by the standard methods used-batch processing and off-line plotting-the production of a finished map commonly takes 2-3 weeks. To produce computer-generated maps more rapidly, cheaply, and easily, and also to provide an effective demonstration tool, we have devised two related methods for plotting maps as alternatives to conventional batch methods. These methods are: 1. Quick-Plot, an interactive program whose output appears on a CRT (cathode-ray-tube) device, and 2. The Interactive CAM (Cartographic Automatic Mapping system), which combines batch and interactive runs. The output of the Interactive CAM system is final compilation (not camera-ready) paper copy. Both methods are designed to use data from the CRIB file in conjunction with a map-plotting program. Quick-Plot retrieves a user-selected subset of data from the CRIB file, immediately produces an image of the desired area on a CRT device, and plots data points according to a limited set of user-selected symbols. This method is useful for immediate evaluation of the map and for demonstrating how trial maps can be made quickly. The Interactive CAM system links the output of an interactive CRIB retrieval to a modified version of the CAM program, which runs in the batch mode and stores plotting instructions on a disk, rather than on a tape. The disk can be accessed by a CRT, and, thus, the user can view and evaluate the map output on a CRT immediately after a batch run, without waiting 1-3 days for an off-line plot. The user can, therefore, do most of the layout and design work in a relatively short time by use of the CRT, before generating a plot tape and having the map plotted on an off-line plotter.

Tracking Changes in Cardiac Output: Statistical Considerations on the 4-Quadrant Plot and the Polar Plot Methodology.

PubMed

Saugel, Bernd; Grothe, Oliver; Wagner, Julia Y

2015-08-01

When comparing 2 technologies for measuring hemodynamic parameters with regard to their ability to track changes, 2 graphical tools are omnipresent in the literature: the 4-quadrant plot and the polar plot recently proposed by Critchley et al. The polar plot is thought to be the more advanced statistical tool, but care should be taken when it comes to its interpretation. The polar plot excludes possibly important measurements from the data. The polar plot transforms the data nonlinearily, which may prevent it from being seen clearly. In this article, we compare the 4-quadrant and the polar plot in detail and thoroughly describe advantages and limitations of each. We also discuss pitfalls concerning the methods to prepare the researcher for the sound use of both methods. Finally, we briefly revisit the Bland-Altman plot for the use in this context.

Identifying hidden common causes from bivariate time series: a method using recurrence plots.

PubMed

Hirata, Yoshito; Aihara, Kazuyuki

2010-01-01

We propose a method for inferring the existence of hidden common causes from observations of bivariate time series. We detect related time series by excessive simultaneous recurrences in the corresponding recurrence plots. We also use a noncoverage property of a recurrence plot by the other to deny the existence of a directional coupling. We apply the proposed method to real wind data.

Double sampling to estimate density and population trends in birds

USGS Publications Warehouse

Bart, Jonathan; Earnst, Susan L.

2002-01-01

We present a method for estimating density of nesting birds based on double sampling. The approach involves surveying a large sample of plots using a rapid method such as uncorrected point counts, variable circular plot counts, or the recently suggested double-observer method. A subsample of those plots is also surveyed using intensive methods to determine actual density. The ratio of the mean count on those plots (using the rapid method) to the mean actual density (as determined by the intensive searches) is used to adjust results from the rapid method. The approach works well when results from the rapid method are highly correlated with actual density. We illustrate the method with three years of shorebird surveys from the tundra in northern Alaska. In the rapid method, surveyors covered ~10 ha h-1 and surveyed each plot a single time. The intensive surveys involved three thorough searches, required ~3 h ha-1, and took 20% of the study effort. Surveyors using the rapid method detected an average of 79% of birds present. That detection ratio was used to convert the index obtained in the rapid method into an essentially unbiased estimate of density. Trends estimated from several years of data would also be essentially unbiased. Other advantages of double sampling are that (1) the rapid method can be changed as new methods become available, (2) domains can be compared even if detection rates differ, (3) total population size can be estimated, and (4) valuable ancillary information (e.g. nest success) can be obtained on intensive plots with little additional effort. We suggest that double sampling be used to test the assumption that rapid methods, such as variable circular plot and double-observer methods, yield density estimates that are essentially unbiased. The feasibility of implementing double sampling in a range of habitats needs to be evaluated.

Microarray-based Resequencing of Multiple Bacillus anthracis Isolates

DTIC Science & Technology

2004-12-17

generated an Unweighted Pair Group Method Arithmetic Mean ( UPGMA ) tree (see methods [56]; Figure 3). The strains group together in a manner broadly similar...was created using DNADIST, plotted as a UPGMA tree using NEIGHBOR and the tree plotted using DRAWGRAM [56]. The B1 strain A0465 was used as an...distance matrix was created using DNADIST, plotted as a UPGMA tree using NEIGHBOR and the tree plotted using DRAWGRAM [57]. Additional data files The

Exploring and accounting for publication bias in mental health: a brief overview of methods.

PubMed

Mavridis, Dimitris; Salanti, Georgia

2014-02-01

OBJECTIVE Publication bias undermines the integrity of published research. The aim of this paper is to present a synopsis of methods for exploring and accounting for publication bias. METHODS We discussed the main features of the following methods to assess publication bias: funnel plot analysis; trim-and-fill methods; regression techniques and selection models. We applied these methods to a well-known example of antidepressants trials that compared trials submitted to the Food and Drug Administration (FDA) for regulatory approval. RESULTS The funnel plot-related methods (visual inspection, trim-and-fill, regression models) revealed an association between effect size and SE. Contours of statistical significance showed that asymmetry in the funnel plot is probably due to publication bias. Selection model found a significant correlation between effect size and propensity for publication. CONCLUSIONS Researchers should always consider the possible impact of publication bias. Funnel plot-related methods should be seen as a means of examining for small-study effects and not be directly equated with publication bias. Possible causes for funnel plot asymmetry should be explored. Contours of statistical significance may help disentangle whether asymmetry in a funnel plot is caused by publication bias or not. Selection models, although underused, could be useful resource when publication bias and heterogeneity are suspected because they address directly the problem of publication bias and not that of small-study effects.

Using T-Z plots as a graphical method to infer lithological variations from growth strata

NASA Astrophysics Data System (ADS)

Castelltort, Sébastien; Pochat, Stéphane; Van Den Driessche, Jean

2004-08-01

The 'T-Z plot' method consists of plotting the throw of sedimentary horizons across a growth fault versus their depth in the hanging wall. This method has been initially developed for the analysis of growth fault kinematics from seismic data. A brief analytical examination of such plots shows that they can also provide valuable information about the evolution of fault topography. When growth is a continuous process, stages of topography creation (fault scarp) and filling (of the space available in the hanging-wall) are related to non-dynamic (draping, mud-prone pelagic settling) and dynamic (sand-prone, dynamically deposited) sedimentation, respectively. In this case, the T-Z plot analysis becomes a powerful tool to predict major lithological variations on seismic profiles in faulted settings.

Coarse-graining time series data: Recurrence plot of recurrence plots and its application for music

NASA Astrophysics Data System (ADS)

Fukino, Miwa; Hirata, Yoshito; Aihara, Kazuyuki

2016-02-01

We propose a nonlinear time series method for characterizing two layers of regularity simultaneously. The key of the method is using the recurrence plots hierarchically, which allows us to preserve the underlying regularities behind the original time series. We demonstrate the proposed method with musical data. The proposed method enables us to visualize both the local and the global musical regularities or two different features at the same time. Furthermore, the determinism scores imply that the proposed method may be useful for analyzing emotional response to the music.

Coarse-graining time series data: Recurrence plot of recurrence plots and its application for music.

PubMed

Fukino, Miwa; Hirata, Yoshito; Aihara, Kazuyuki

2016-02-01

We propose a nonlinear time series method for characterizing two layers of regularity simultaneously. The key of the method is using the recurrence plots hierarchically, which allows us to preserve the underlying regularities behind the original time series. We demonstrate the proposed method with musical data. The proposed method enables us to visualize both the local and the global musical regularities or two different features at the same time. Furthermore, the determinism scores imply that the proposed method may be useful for analyzing emotional response to the music.

Validity of the t-plot method to assess microporosity in hierarchical micro/mesoporous materials.

PubMed

Galarneau, Anne; Villemot, François; Rodriguez, Jeremy; Fajula, François; Coasne, Benoit

2014-11-11

The t-plot method is a well-known technique which allows determining the micro- and/or mesoporous volumes and the specific surface area of a sample by comparison with a reference adsorption isotherm of a nonporous material having the same surface chemistry. In this paper, the validity of the t-plot method is discussed in the case of hierarchical porous materials exhibiting both micro- and mesoporosities. Different hierarchical zeolites with MCM-41 type ordered mesoporosity are prepared using pseudomorphic transformation. For comparison, we also consider simple mechanical mixtures of microporous and mesoporous materials. We first show an intrinsic failure of the t-plot method; this method does not describe the fact that, for a given surface chemistry and pressure, the thickness of the film adsorbed in micropores or small mesopores (< 10σ, σ being the diameter of the adsorbate) increases with decreasing the pore size (curvature effect). We further show that such an effect, which arises from the fact that the surface area and, hence, the free energy of the curved gas/liquid interface decreases with increasing the film thickness, is captured using the simple thermodynamical model by Derjaguin. The effect of such a drawback on the ability of the t-plot method to estimate the micro- and mesoporous volumes of hierarchical samples is then discussed, and an abacus is given to correct the underestimated microporous volume by the t-plot method.

Establishment of monitoring plots and evaluation of trees injured by ozone

Treesearch

Daniel Duriscoe; Kenneth Stolte; John Pronos

1996-01-01

By establishing long–term monitoring plots, it is possible to record environmental and biological conditions of the plot and individual trees, evaluate the condition of crowns of trees in the plot, and determine the extent of ozone injury to western conifers. This chapter recommends various methods for recording data and selecting plots, and provides information for...

Boundary pint corrections for variable radius plots - simulation results

Treesearch

Margaret Penner; Sam Otukol

2000-01-01

The boundary plot problem is encountered when a forest inventory plot includes two or more forest conditions. Depending on the correction method used, the resulting estimates can be biased. The various correction alternatives are reviewed. No correction, area correction, half sweep, and toss-back methods are evaluated using simulation on an actual data set. Based on...

Despite irreversible binding, PET tracer [11C]-SA5845 is suitable for imaging of drug competition at sigma receptors-the cases of ketamine and haloperidol.

PubMed

Kortekaas, Rudie; Maguire, R Paul; van Waarde, Aren; Leenders, Klaus L; Elsinga, Philip H

2008-07-01

Many psychotropic compounds bind to sigma receptors and several new sigma ligands are in development for psychiatric indications such as anxiety, attention deficit hyperactivity disorder, depression and psychosis. Of special interest for drug development are tomographic methods that can quantify the binding of promising sigma ligands in a regional manner. Here we present the development of such a method and the first evaluation of sigma ligand [11C]-SA5845 in a primate. Extensive pharmacokinetic modeling was done on tissue curves and a heart lumen curve. The effects of pretreatment and challenge with haloperidol were studied as well as those of pretreatment with +/- -ketamine. The tracer had a plasma half-life of 77+/-1.7min and was rapidly taken up by all brain areas. The binding pattern was consistent with binding to sigma receptors and compartment modeling showed there was considerable specific binding that was irreversible. We therefore calculated the net influx rate, Ki, with the Gjedde-Patlak linearization, as a measure of free receptors. As expected, Ki was very sensitive to the presence of competing ligands - -ketamine and/or haloperidol. Summarizing, the tracer is well suited for visualizing sigma receptors in the brain and moreover, the presented method is able to quantify, on a regional basis, specific binding of unlabeled ligands to sigma receptors.

Dynamic whole-body PET parametric imaging: I. Concept, acquisition protocol optimization and clinical application.

PubMed

Karakatsanis, Nicolas A; Lodge, Martin A; Tahari, Abdel K; Zhou, Y; Wahl, Richard L; Rahmim, Arman

2013-10-21

Static whole-body PET/CT, employing the standardized uptake value (SUV), is considered the standard clinical approach to diagnosis and treatment response monitoring for a wide range of oncologic malignancies. Alternative PET protocols involving dynamic acquisition of temporal images have been implemented in the research setting, allowing quantification of tracer dynamics, an important capability for tumor characterization and treatment response monitoring. Nonetheless, dynamic protocols have been confined to single-bed-coverage limiting the axial field-of-view to ~15-20 cm, and have not been translated to the routine clinical context of whole-body PET imaging for the inspection of disseminated disease. Here, we pursue a transition to dynamic whole-body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. We investigate solutions to address the challenges of: (i) long acquisitions, (ii) small number of dynamic frames per bed, and (iii) non-invasive quantification of kinetics in the plasma. In the present study, a novel dynamic (4D) whole-body PET acquisition protocol of ~45 min total length is presented, composed of (i) an initial 6 min dynamic PET scan (24 frames) over the heart, followed by (ii) a sequence of multi-pass multi-bed PET scans (six passes × seven bed positions, each scanned for 45 s). Standard Patlak linear graphical analysis modeling was employed, coupled with image-derived plasma input function measurements. Ordinary least squares Patlak estimation was used as the baseline regression method to quantify the physiological parameters of tracer uptake rate Ki and total blood distribution volume V on an individual voxel basis. Extensive Monte Carlo simulation studies, using a wide set of published kinetic FDG parameters and GATE and XCAT platforms, were conducted to optimize the acquisition protocol from a range of ten different clinically acceptable sampling schedules examined. The framework was also applied to six FDG PET patient studies, demonstrating clinical feasibility. Both simulated and clinical results indicated enhanced contrast-to-noise ratios (CNRs) for Ki images in tumor regions with notable background FDG concentration, such as the liver, where SUV performed relatively poorly. Overall, the proposed framework enables enhanced quantification of physiological parameters across the whole body. In addition, the total acquisition length can be reduced from 45 to ~35 min and still achieve improved or equivalent CNR compared to SUV, provided the true Ki contrast is sufficiently high. In the follow-up companion paper, a set of advanced linear regression schemes is presented to particularly address the presence of noise, and attempt to achieve a better trade-off between the mean-squared error and the CNR metrics, resulting in enhanced task-based imaging.

Dynamic whole body PET parametric imaging: I. Concept, acquisition protocol optimization and clinical application

PubMed Central

Karakatsanis, Nicolas A.; Lodge, Martin A.; Tahari, Abdel K.; Zhou, Y.; Wahl, Richard L.; Rahmim, Arman

2013-01-01

Static whole body PET/CT, employing the standardized uptake value (SUV), is considered the standard clinical approach to diagnosis and treatment response monitoring for a wide range of oncologic malignancies. Alternative PET protocols involving dynamic acquisition of temporal images have been implemented in the research setting, allowing quantification of tracer dynamics, an important capability for tumor characterization and treatment response monitoring. Nonetheless, dynamic protocols have been confined to single bed-coverage limiting the axial field-of-view to ~15–20 cm, and have not been translated to the routine clinical context of whole-body PET imaging for the inspection of disseminated disease. Here, we pursue a transition to dynamic whole body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. We investigate solutions to address the challenges of: (i) long acquisitions, (ii) small number of dynamic frames per bed, and (iii) non-invasive quantification of kinetics in the plasma. In the present study, a novel dynamic (4D) whole body PET acquisition protocol of ~45min total length is presented, composed of (i) an initial 6-min dynamic PET scan (24 frames) over the heart, followed by (ii) a sequence of multi-pass multi-bed PET scans (6 passes x 7 bed positions, each scanned for 45sec). Standard Patlak linear graphical analysis modeling was employed, coupled with image-derived plasma input function measurements. Ordinary least squares (OLS) Patlak estimation was used as the baseline regression method to quantify the physiological parameters of tracer uptake rate Ki and total blood distribution volume V on an individual voxel basis. Extensive Monte Carlo simulation studies, using a wide set of published kinetic FDG parameters and GATE and XCAT platforms, were conducted to optimize the acquisition protocol from a range of 10 different clinically acceptable sampling schedules examined. The framework was also applied to six FDG PET patient studies, demonstrating clinical feasibility. Both simulated and clinical results indicated enhanced contrast-to-noise ratios (CNRs) for Ki images in tumor regions with notable background FDG concentration, such as the liver, where SUV performed relatively poorly. Overall, the proposed framework enables enhanced quantification of physiological parameters across the whole-body. In addition, the total acquisition length can be reduced from 45min to ~35min and still achieve improved or equivalent CNR compared to SUV, provided the true Ki contrast is sufficiently high. In the follow-up companion paper, a set of advanced linear regression schemes is presented to particularly address the presence of noise, and attempt to achieve a better trade-off between the mean-squared error (MSE) and the CNR metrics, resulting in enhanced task-based imaging. PMID:24080962

Dynamic whole-body PET parametric imaging: I. Concept, acquisition protocol optimization and clinical application

NASA Astrophysics Data System (ADS)

Karakatsanis, Nicolas A.; Lodge, Martin A.; Tahari, Abdel K.; Zhou, Y.; Wahl, Richard L.; Rahmim, Arman

2013-10-01

Static whole-body PET/CT, employing the standardized uptake value (SUV), is considered the standard clinical approach to diagnosis and treatment response monitoring for a wide range of oncologic malignancies. Alternative PET protocols involving dynamic acquisition of temporal images have been implemented in the research setting, allowing quantification of tracer dynamics, an important capability for tumor characterization and treatment response monitoring. Nonetheless, dynamic protocols have been confined to single-bed-coverage limiting the axial field-of-view to ˜15-20 cm, and have not been translated to the routine clinical context of whole-body PET imaging for the inspection of disseminated disease. Here, we pursue a transition to dynamic whole-body PET parametric imaging, by presenting, within a unified framework, clinically feasible multi-bed dynamic PET acquisition protocols and parametric imaging methods. We investigate solutions to address the challenges of: (i) long acquisitions, (ii) small number of dynamic frames per bed, and (iii) non-invasive quantification of kinetics in the plasma. In the present study, a novel dynamic (4D) whole-body PET acquisition protocol of ˜45 min total length is presented, composed of (i) an initial 6 min dynamic PET scan (24 frames) over the heart, followed by (ii) a sequence of multi-pass multi-bed PET scans (six passes × seven bed positions, each scanned for 45 s). Standard Patlak linear graphical analysis modeling was employed, coupled with image-derived plasma input function measurements. Ordinary least squares Patlak estimation was used as the baseline regression method to quantify the physiological parameters of tracer uptake rate Ki and total blood distribution volume V on an individual voxel basis. Extensive Monte Carlo simulation studies, using a wide set of published kinetic FDG parameters and GATE and XCAT platforms, were conducted to optimize the acquisition protocol from a range of ten different clinically acceptable sampling schedules examined. The framework was also applied to six FDG PET patient studies, demonstrating clinical feasibility. Both simulated and clinical results indicated enhanced contrast-to-noise ratios (CNRs) for Ki images in tumor regions with notable background FDG concentration, such as the liver, where SUV performed relatively poorly. Overall, the proposed framework enables enhanced quantification of physiological parameters across the whole body. In addition, the total acquisition length can be reduced from 45 to ˜35 min and still achieve improved or equivalent CNR compared to SUV, provided the true Ki contrast is sufficiently high. In the follow-up companion paper, a set of advanced linear regression schemes is presented to particularly address the presence of noise, and attempt to achieve a better trade-off between the mean-squared error and the CNR metrics, resulting in enhanced task-based imaging.

Assessing the kidney function parameters glomerular filtration rate and effective renal plasma flow with dynamic FDG-PET/MRI in healthy subjects.

PubMed

Geist, Barbara K; Baltzer, Pascal; Fueger, Barbara; Hamboeck, Martina; Nakuz, Thomas; Papp, Laszlo; Rasul, Sazan; Sundar, Lalith Kumar Shiyam; Hacker, Marcus; Staudenherz, Anton

2018-05-09

A method was developed to assess the kidney parameters glomerular filtration rate (GFR) and effective renal plasma flow (ERPF) from 2-deoxy-2-[ 18 F]fluoro-D-glucose (FDG) concentration behavior in kidneys, measured with positron emission tomography (PET) scans. Twenty-four healthy adult subjects prospectively underwent dynamic simultaneous PET/magnetic resonance imaging (MRI) examination. Time activity curves (TACs) were obtained from the dynamic PET series, with the guidance of MR information. Patlak analysis was performed to determine the GFR, and based on integrals, ERPF was calculated. Results were compared to intra-individually obtained reference values determined from venous blood samples. Total kidney GFR and ERPF as estimated by dynamic PET/MRI were highly correlated to their reference values (r = 0.88/p < 0.0001 and r = 0.82/p < 0.0001, respectively) with no significant difference between their means. The study is a proof of concept that GFR and ERPF can be assessed with dynamic FDG PET/MRI scans in healthy kidneys. This has advantages for patients getting a routine scan, where additional examinations for kidney function estimation could be avoided. Further studies are required for transferring this PET/MRI method to PET/CT applications.

[Contribution of X-ray computed tomography in the evaluation of kidney performance].

PubMed

Lemoine, Sandrine; Rognant, Nicolas; Collet-Benzaquen, Diane; Juillard, Laurent

2012-07-01

X-ray computer assisted tomography scanner is an imaging method based on the use of X-ray attenuation in tissue. This attenuation is proportional to the density of the tissue (without or after contrast media injection) in each pixel image of the image. Spiral scanner, the electron beam computed tomography (EBCT) scanner and multidetector computed tomography scanner allow renal anatomical measurements, such as cortical and medullary volume, but also the measurement of renal functional parameters, such as regional renal perfusion, renal blood flow and glomerular filtration rate. These functional parameters are extracted from the modeling of the kinetics of the contrast media concentration in the vascular space and the renal tissue, using two main mathematical models (the gamma variate model and the Patlak model). Renal functional imaging allows measuring quantitative parameters on each kidney separately, in a non-invasive manner, providing significant opportunities in nephrology, both for experimental and clinical studies. However, this method uses contrast media that may alter renal function, thus limiting its use in patients with chronic renal failure. Moreover, the increase irradiation delivered to the patient with multi detector computed tomography (MDCT) should be considered. Copyright © 2011 Association Société de néphrologie. Published by Elsevier SAS. All rights reserved.

Spatially Locating FIA Plots from Pixel Values

Treesearch

Greg C. Liknes; Geoffrey R. Holden; Mark D. Nelson; Ronald E. McRoberts

2005-01-01

The USDA Forest Service Forest Inventory and Analysis (FIA) program is required to ensure the confidentiality of the geographic locations of plots. To accommodate user requests for data without releasing actual plot coordinates, FIA creates overlays of plot locations on various geospatial data, including satellite imagery. Methods for reporting pixel values associated...

Presenting simulation results in a nested loop plot.

PubMed

Rücker, Gerta; Schwarzer, Guido

2014-12-12

Statisticians investigate new methods in simulations to evaluate their properties for future real data applications. Results are often presented in a number of figures, e.g., Trellis plots. We had conducted a simulation study on six statistical methods for estimating the treatment effect in binary outcome meta-analyses, where selection bias (e.g., publication bias) was suspected because of apparent funnel plot asymmetry. We varied five simulation parameters: true treatment effect, extent of selection, event proportion in control group, heterogeneity parameter, and number of studies in meta-analysis. In combination, this yielded a total number of 768 scenarios. To present all results using Trellis plots, 12 figures were needed. Choosing bias as criterion of interest, we present a 'nested loop plot', a diagram type that aims to have all simulation results in one plot. The idea was to bring all scenarios into a lexicographical order and arrange them consecutively on the horizontal axis of a plot, whereas the treatment effect estimate is presented on the vertical axis. The plot illustrates how parameters simultaneously influenced the estimate. It can be combined with a Trellis plot in a so-called hybrid plot. Nested loop plots may also be applied to other criteria such as the variance of estimation. The nested loop plot, similar to a time series graph, summarizes all information about the results of a simulation study with respect to a chosen criterion in one picture and provides a suitable alternative or an addition to Trellis plots.

Evaluation of limited blood sampling population input approaches for kinetic quantification of [18F]fluorothymidine PET data.

PubMed

Contractor, Kaiyumars B; Kenny, Laura M; Coombes, Charles R; Turkheimer, Federico E; Aboagye, Eric O; Rosso, Lula

2012-03-24

Quantification of kinetic parameters of positron emission tomography (PET) imaging agents normally requires collecting arterial blood samples which is inconvenient for patients and difficult to implement in routine clinical practice. The aim of this study was to investigate whether a population-based input function (POP-IF) reliant on only a few individual discrete samples allows accurate estimates of tumour proliferation using [18F]fluorothymidine (FLT). Thirty-six historical FLT-PET data with concurrent arterial sampling were available for this study. A population average of baseline scans blood data was constructed using leave-one-out cross-validation for each scan and used in conjunction with individual blood samples. Three limited sampling protocols were investigated including, respectively, only seven (POP-IF7), five (POP-IF5) and three (POP-IF3) discrete samples of the historical dataset. Additionally, using the three-point protocol, we derived a POP-IF3M, the only input function which was not corrected for the fraction of radiolabelled metabolites present in blood. The kinetic parameter for net FLT retention at steady state, Ki, was derived using the modified Patlak plot and compared with the original full arterial set for validation. Small percentage differences in the area under the curve between all the POP-IFs and full arterial sampling IF was found over 60 min (4.2%-5.7%), while there were, as expected, larger differences in the peak position and peak height.A high correlation between Ki values calculated using the original arterial input function and all the population-derived IFs was observed (R2 = 0.85-0.98). The population-based input showed good intra-subject reproducibility of Ki values (R2 = 0.81-0.94) and good correlation (R2 = 0.60-0.85) with Ki-67. Input functions generated using these simplified protocols over scan duration of 60 min estimate net PET-FLT retention with reasonable accuracy.

Field methods and data processing techniques associated with mapped inventory plots

Treesearch

William A. Bechtold; Stanley J. Zarnoch

1999-01-01

The U.S. Forest Inventory and Analysis (FIA) and Forest Health Monitoring (FHM) programs utilize a fixed-area mapped-plot design as the national standard for extensive forest inventories. The mapped-plot design is explained, as well as the rationale for its selection as the national standard. Ratio-of-means estimators am presented as a method to process data from...

A statistically valid method for using FIA plots to guide spectral class rejection in producing stratification maps

Treesearch

Michael L. Hoppus; Andrew J. Lister

2002-01-01

A Landsat TM classification method (iterative guided spectral class rejection) produced a forest cover map of southern West Virginia that provided the stratification layer for producing estimates of timberland area from Forest Service FIA ground plots using a stratified sampling technique. These same high quality and expensive FIA ground plots provided ground reference...

Dispersed and piled woody residues volumes in coastal Douglas-fir cutblocks determined using high-resolution imagery from a UAV and from ground-based surveys.

NASA Astrophysics Data System (ADS)

Trofymow, J. A.; Gougeon, F.

2015-12-01

After forest harvest significant amounts of woody residues are left dispersed on site and some subsequently piled and burned. Quantification of residues is required for estimating C budgets, billable waste, harvest efficiency, bioenergy potential and smoke emissions. Trofymow (et al 2014 CJFR) compared remote sensing methods to ground-based waste and residue survey (WRS) methods for residue piles in 4 cutblocks in the Oyster River (OR) area in coastal BC. Compared to geospatial methods using 15cm orthophotos and LiDAR acquired in 2011 by helicopter, the WRS method underestimated pile wood by 30% to 50% while a USFS volume method overestimated pile wood by 50% if site specific packing ratios were not used. A geospatial method was developed in PCI Geomatica to analyze 2-bit images of logs >15cm diameters to determine dispersed wood residues in OR and compare to WRS methods. Across blocks, geospatial and WRS method wood volumes were correlated (R2=0.69), however volumes were 2.5 times larger for the geospatial vs WRS method. Methods for dispersed residues could not be properly compared as individual WRS plots were not georeferenced, only 12 plots were sampled in total, and low-resolution images poorly resolved logs. Thus, a new study in 2 cutblocks in the Northwest Bay (NWB) area acquired 2cm resolution RGB air-photography in 2014-15 using an Aeryon Sky Ranger UAV prior to and after burn pile construction. A total of 57 dispersed WRS plots and 24 WRS pile or accumulation plots were georeferenced and measured. Stero-pairs were used to generate point-clouds for pile bulk volumes. Images processed to 8-bit grey scale are being analyzed with a revised PCI method that better accounts for log overlaps. WRS methods depend on a good sample of plots and accurate determination of stratum (dispersed, roadside, piles, accumulations) areas. Analysis of NWB blocks shows WRS field methods for stratum area differ by 5-20% from that determined using orthophotos. Plot-level wood volumes in each plot and stratum determined by geospatial and WRS methods will be compared. While geospatial methods for residue determination is a 100% sample, compared to sample-based WRS method, difficulties in resolving logs in the images may mean the best method for determining residues requires a combination of geospatial and ground plot measurements. .

Relative equilibrium plot improves graphical analysis and allows bias correction of SUVR in quantitative [11C]PiB PET studies

PubMed Central

Zhou, Yun; Sojkova, Jitka; Resnick, Susan M.; Wong, Dean F.

2012-01-01

Both the standardized uptake value ratio (SUVR) and the Logan plot result in biased distribution volume ratios (DVR) in ligand-receptor dynamic PET studies. The objective of this study is to use a recently developed relative equilibrium-based graphical plot (RE plot) method to improve and simplify the two commonly used methods for quantification of [11C]PiB PET. Methods The overestimation of DVR in SUVR was analyzed theoretically using the Logan and the RE plots. A bias-corrected SUVR (bcSUVR) was derived from the RE plot. Seventy-eight [11C]PiB dynamic PET scans (66 from controls and 12 from mildly cognitively impaired participants (MCI) from the Baltimore Longitudinal Study of Aging (BLSA)) were acquired over 90 minutes. Regions of interest (ROIs) were defined on coregistered MRIs. Both the ROI and pixelwise time activity curves (TACs) were used to evaluate the estimates of DVR. DVRs obtained using the Logan plot applied to ROI TACs were used as a reference for comparison of DVR estimates. Results Results from the theoretical analysis were confirmed by human studies. ROI estimates from the RE plot and the bcSUVR were nearly identical to those from the Logan plot with ROI TACs. In contrast, ROI estimates from DVR images in frontal, temporal, parietal, cingulate regions, and the striatum were underestimated by the Logan plot (controls 4 – 12%; MCI 9 – 16%) and overestimated by the SUVR (controls 8 – 16%; MCI 16 – 24%). This bias was higher in the MCI group than in controls (p < 0.01) but was not present when data were analyzed using either the RE plot or the bcSUVR. Conclusion The RE plot improves pixel-wise quantification of [11C]PiB dynamic PET compared to the conventional Logan plot. The bcSUVR results in lower bias and higher consistency of DVR estimates compared to SUVR. The RE plot and the bcSUVR are practical quantitative approaches that improve the analysis of [11C]PiB studies. PMID:22414634

Redrawing the baseline: a method for adjusting biased historical forest estimates using a spatial and temporally representative plot network

Treesearch

Sara A. Goeking; Paul L. Patterson

2015-01-01

Users of Forest Inventory and Analysis (FIA) data sometimes compare historic and current forest inventory estimates, despite warnings that such comparisons may be tenuous. The purpose of this study was to demonstrate a method for obtaining a more accurate and representative reference dataset using data collected at co-located plots (i.e., plots that were measured...

[Application of Stata software to test heterogeneity in meta-analysis method].

PubMed

Wang, Dan; Mou, Zhen-yun; Zhai, Jun-xia; Zong, Hong-xia; Zhao, Xiao-dong

2008-07-01

To introduce the application of Stata software to heterogeneity test in meta-analysis. A data set was set up according to the example in the study, and the corresponding commands of the methods in Stata 9 software were applied to test the example. The methods used were Q-test and I2 statistic attached to the fixed effect model forest plot, H statistic and Galbraith plot. The existence of the heterogeneity among studies could be detected by Q-test and H statistic and the degree of the heterogeneity could be detected by I2 statistic. The outliers which were the sources of the heterogeneity could be spotted from the Galbraith plot. Heterogeneity test in meta-analysis can be completed by the four methods in Stata software simply and quickly. H and I2 statistics are more robust, and the outliers of the heterogeneity can be clearly seen in the Galbraith plot among the four methods.

Integrating P3 Data Into P2 Analyses: What is the Added Value

Treesearch

James R. Steinman

2001-01-01

The Forest Inventory and Analysis and Forest Health Monitoring Programs of the USDA Forest Service are integrating field procedures for measuring their networks of plots throughout the United States. These plots are now referred to as Phase 2 (P2) and Phase 3 (P3) plots, respectively, and 1 out of every 16 P2 plots will also be a P3 plot. Mensurational methods will be...

Computer systems and methods for visualizing data

DOEpatents

Stolte, Chris; Hanrahan, Patrick

2010-07-13

A method for forming a visual plot using a hierarchical structure of a dataset. The dataset comprises a measure and a dimension. The dimension consists of a plurality of levels. The plurality of levels form a dimension hierarchy. The visual plot is constructed based on a specification. A first level from the plurality of levels is represented by a first component of the visual plot. A second level from the plurality of levels is represented by a second component of the visual plot. The dataset is queried to retrieve data in accordance with the specification. The data includes all or a portion of the dimension and all or a portion of the measure. The visual plot is populated with the retrieved data in accordance with the specification.

Computer systems and methods for visualizing data

DOEpatents

Stolte, Chris; Hanrahan, Patrick

2013-01-29

A method for forming a visual plot using a hierarchical structure of a dataset. The dataset comprises a measure and a dimension. The dimension consists of a plurality of levels. The plurality of levels form a dimension hierarchy. The visual plot is constructed based on a specification. A first level from the plurality of levels is represented by a first component of the visual plot. A second level from the plurality of levels is represented by a second component of the visual plot. The dataset is queried to retrieve data in accordance with the specification. The data includes all or a portion of the dimension and all or a portion of the measure. The visual plot is populated with the retrieved data in accordance with the specification.

Evaluating Plot Designs for the Tropics

Treesearch

Paul C. van Deusen; Bruce Bayle

1991-01-01

Theory and procedures are reviewed for determining the best type of plot for a given forest inventory. A general methodology is given that clarifies the relationship between different plot designs and the associated methods to produce the inventory estimates.

Analysis of variance calculations for irregular experiments

Treesearch

Jonathan W. Wright

1977-01-01

Irregular experiments may be more useful than much smaller regular experiments and can be analyzed statistically without undue expenditure of time. For a few missing plots, standard methods of calculating missing-plot values can be used. For more missing plots (up to 10 percent), seedlot means or randomly chosen plot means of the same seedlot can be substituted for...

Measurements of smoke from chipped and unchipped plots

Treesearch

Gary L. Achtemeier; Jeff Glitzenstein; Luke P. Naeher

2006-01-01

Smoke data were collected from two instrumented plots located on the Francis Marion National Forest in South Carolina during prescribed burns on Feb. 12, 2003. One of the plots had been subjected to mechanical chipping. Particulate matter (PM2.5) data analyzed by gravimetric methods were collected at nine locations on the downwind sides of each plot. In addition,...

Field Testing New Plot Designs and Methods for Determining Hydrophytic Vegetation during Wetland Delineations in the United States

DTIC Science & Technology

2014-03-01

Trees and woody vines are sampled in large plots with 9 m (30 ft) radii. Saplings, shrubs , and herbs are sampled in nested smaller plots with 2 m (5 ft... woody vines in 9 m (30 ft) radius plots and saplings, shrubs , and herbaceous species in 2 m (5 ft) radius plots. In herbaceous meadows, only the 2 m (5...suggests stratifying vegetation by growth forms of trees, shrubs , herbs, and vines and sampling plant communities by using nested circular plots

[Study on extraction method of Panax notoginseng plots in Wenshan of Yunnan province based on decision tree model].

PubMed

Shi, Ting-Ting; Zhang, Xiao-Bo; Guo, Lan-Ping; Huang, Lu-Qi

2017-11-01

The herbs used as the material for traditional Chinese medicine are always planted in the mountainous area where the natural environment is suitable. As the mountain terrain is complex and the distribution of planting plots is scattered, the traditional survey method is difficult to obtain accurate planting area. It is of great significance to provide decision support for the conservation and utilization of traditional Chinese medicine resources by studying the method of extraction of Chinese herbal medicine planting area based on remote sensing and realizing the dynamic monitoring and reserve estimation of Chinese herbal medicines. In this paper, taking the Panax notoginseng plots in Wenshan prefecture of Yunnan province as an example, the China-made GF-1multispectral remote sensing images with a 16 m×16 m resolution were obtained. Then, the time series that can reflect the difference of spectrum of P. notoginseng shed and the background objects were selected to the maximum extent, and the decision tree model of extraction the of P. notoginseng plots was constructed according to the spectral characteristics of the surface features. The results showed that the remote sensing classification method based on the decision tree model could extract P. notoginseng plots in the study area effectively. The method can provide technical support for extraction of P. notoginseng plots at county level. Copyright© by the Chinese Pharmaceutical Association.

In-situ polymerization PLOT columns I: divinylbenzene

NASA Technical Reports Server (NTRS)

Shen, T. C.

1992-01-01

A novel method for preparation of porous-layer open-tubular (PLOT) columns is described. The method involves a simple and reproducible, straight-forward in-situ polymerization of monomer directly on the metal tube.

Investigation of ODE integrators using interactive graphics. [Ordinary Differential Equations

NASA Technical Reports Server (NTRS)

Brown, R. L.

1978-01-01

Two FORTRAN programs using an interactive graphic terminal to generate accuracy and stability plots for given multistep ordinary differential equation (ODE) integrators are described. The first treats the fixed stepsize linear case with complex variable solutions, and generates plots to show accuracy and error response to step driving function of a numerical solution, as well as the linear stability region. The second generates an analog to the stability region for classes of non-linear ODE's as well as accuracy plots. Both systems can compute method coefficients from a simple specification of the method. Example plots are given.

Evaluation of a new inference method for estimating ammonia volatilisation from multiple agronomic plots

NASA Astrophysics Data System (ADS)

Loubet, Benjamin; Carozzi, Marco; Voylokov, Polina; Cohan, Jean-Pierre; Trochard, Robert; Génermont, Sophie

2018-06-01

Tropospheric ammonia (NH3) is a threat to the environment and human health and is mainly emitted by agriculture. Ammonia volatilisation following application of nitrogen in the field accounts for more than 40 % of the total NH3 emissions in France. This represents a major loss of nitrogen use efficiency which needs to be reduced by appropriate agricultural practices. In this study we evaluate a novel method to infer NH3 volatilisation from small agronomic plots consisting of multiple treatments with repetition. The method is based on the combination of a set of NH3 diffusion sensors exposed for durations of 3 h to 1 week and a short-range atmospheric dispersion model, used to retrieve the emissions from each plot. The method is evaluated by mimicking NH3 emissions from an ensemble of nine plots with a resistance analogue-compensation point-surface exchange scheme over a yearly meteorological database separated into 28-day periods. A multifactorial simulation scheme is used to test the effects of sensor numbers and heights, plot dimensions, source strengths, and background concentrations on the quality of the inference method. We further demonstrate by theoretical considerations in the case of an isolated plot that inferring emissions with diffusion sensors integrating over daily periods will always lead to underestimations due to correlations between emissions and atmospheric transfer. We evaluated these underestimations as -8 % ± 6 % of the emissions for a typical western European climate. For multiple plots, we find that this method would lead to median underestimations of -16 % with an interquartile [-8-22 %] for two treatments differing by a factor of up to 20 and a control treatment with no emissions. We further evaluate the methodology for varying background concentrations and NH3 emissions patterns and demonstrate the low sensitivity of the method to these factors. The method was also tested in a real case and proved to provide sound evaluations of NH3 losses from surface applied and incorporated slurry. We hence showed that this novel method should be robust and suitable for estimating NH3 emissions from agronomic plots. We believe that the method could be further improved by using Bayesian inference and inferring surface concentrations rather than surface fluxes. Validating against controlled source is also a remaining challenge.

Analysis of arson fire debris by low temperature dynamic headspace adsorption porous layer open tubular columns.

PubMed

Nichols, Jessica E; Harries, Megan E; Lovestead, Tara M; Bruno, Thomas J

2014-03-21

In this paper we present results of the application of PLOT-cryoadsorption (PLOT-cryo) to the analysis of ignitable liquids in fire debris. We tested ignitable liquids, broadly divided into fuels and solvents (although the majority of the results presented here were obtained with gasoline and diesel fuel) on three substrates: Douglas fir, oak plywood and Nylon carpet. We determined that PLOT-cryo allows the analyst to distinguish all of the ignitable liquids tested by use of a very rapid sampling protocol, and performs better (more recovered components, higher efficiency, lower elution solvent volumes) than a conventional purge and trap method. We also tested the effect of latency (the time period between applying the ignitable liquid and ignition), and we tested a variety of sampling times and a variety of PLOT capillary lengths. Reliable results can be obtained with sampling time periods as short as 3min, and on PLOT capillaries as short as 20cm. The variability of separate samples was also assessed, a study made possible by the high throughput nature of the PLOT-cryo method. We also determined that the method performs better than the conventional carbon strip method that is commonly used in fire debris analysis. Published by Elsevier B.V.

A curve-fitting approach to estimate the arterial plasma input function for the assessment of glucose metabolic rate and response to treatment.

PubMed

Vriens, Dennis; de Geus-Oei, Lioe-Fee; Oyen, Wim J G; Visser, Eric P

2009-12-01

For the quantification of dynamic (18)F-FDG PET studies, the arterial plasma time-activity concentration curve (APTAC) needs to be available. This can be obtained using serial sampling of arterial blood or an image-derived input function (IDIF). Arterial sampling is invasive and often not feasible in practice; IDIFs are biased because of partial-volume effects and cannot be used when no large arterial blood pool is in the field of view. We propose a mathematic function, consisting of an initial linear rising activity concentration followed by a triexponential decay, to describe the APTAC. This function was fitted to 80 oncologic patients and verified for 40 different oncologic patients by area-under-the-curve (AUC) comparison, Patlak glucose metabolic rate (MR(glc)) estimation, and therapy response monitoring (Delta MR(glc)). The proposed function was compared with the gold standard (serial arterial sampling) and the IDIF. To determine the free parameters of the function, plasma time-activity curves based on arterial samples in 80 patients were fitted after normalization for administered activity (AA) and initial distribution volume (iDV) of (18)F-FDG. The medians of these free parameters were used for the model. In 40 other patients (20 baseline and 20 follow-up dynamic (18)F-FDG PET scans), this model was validated. The population-based curve, individually calibrated by AA and iDV (APTAC(AA/iDV)), by 1 late arterial sample (APTAC(1 sample)), and by the individual IDIF (APTAC(IDIF)), was compared with the gold standard of serial arterial sampling (APTAC(sampled)) using the AUC. Additionally, these 3 methods of APTAC determination were evaluated with Patlak MR(glc) estimation and with Delta MR(glc) for therapy effects using serial sampling as the gold standard. Excellent individual fits to the function were derived with significantly different decay constants (P < 0.001). Correlations between AUC from APTAC(AA/iDV), APTAC(1 sample), and APTAC(IDIF) with the gold standard (APTAC(sampled)) were 0.880, 0.994, and 0.856, respectively. For MR(glc), these correlations were 0.963, 0.994, and 0.966, respectively. In response monitoring, these correlations were 0.947, 0.982, and 0.949, respectively. Additional scaling by 1 late arterial sample showed a significant improvement (P < 0.001). The fitted input function calibrated for AA and iDV performed similarly to IDIF. Performance improved significantly using 1 late arterial sample. The proposed model can be used when an IDIF is not available or when serial arterial sampling is not feasible.

[Recurrence plot analysis of HRV for brain ischemia and asphyxia].

PubMed

Chen, Xiaoming; Qiu, Yihong; Zhu, Yisheng

2008-02-01

Heart rate variability (HRV) is the tiny variability existing in the cycles of the heart beats, which reflects the corresponding balance between sympathetic and vagus nerves. Since the nonlinear characteristic of HRV is confirmed, the Recurrence Plot method, a nonlinear dynamic analysis method based on the complexity, could be used to analyze HRV. The results showed the recurrence plot structures and some quantitative indices (L-Mean, L-Entr) during asphyxia insult vary significantly as compared to those in normal conditions, which offer a new method to monitor brain asphyxia injury.

A new method for the preparation of polymeric porous layer open tubular columns for GC application

NASA Technical Reports Server (NTRS)

Shen, T. C.; Wang, M. L.

1995-01-01

A new method to prepare polymeric PLOT columns by using in situ polymerization technology is described. The method involves a straightforward in situ polymerization of the monomer. The polymer produced is directly coated on the metal tubing. This eliminates many of the steps needed in conventional polymeric PLOT column preparation. Our method is easy to operate and produces very reproducible columns, as shown previously (T. C. Shen. J. Chromatogr. Sci. 30, 239, 1992). The effects of solvents, tubing pretreatments, initiators and reaction temperatures in the preparation of PLOT columns are studied. Several columns have been developed to separate (1) highly polar compounds, such as water and ammonia or water and HCN, and (2) hydrocarbons and inert gases. A recent improvement has allowed us to produce bonded polymeric PLOT columns. These were studied, and the results are included also.

New methods, algorithms, and software for rapid mapping of tree positions in coordinate forest plots

Treesearch

A. Dan Wilson

2000-01-01

The theories and methodologies for two new tree mapping methods, the Sequential-target method and the Plot-origin radial method, are described. The methods accommodate the use of any conventional distance measuring device and compass to collect horizontal distance and azimuth data between source or reference positions (origins) and target trees. Conversion equations...

Measuring larval nematode contamination on cattle pastures: Comparing two herbage sampling methods.

PubMed

Verschave, S H; Levecke, B; Duchateau, L; Vercruysse, J; Charlier, J

2015-06-15

Assessing levels of pasture larval contamination is frequently used to study the population dynamics of the free-living stages of parasitic nematodes of livestock. Direct quantification of infective larvae (L3) on herbage is the most applied method to measure pasture larval contamination. However, herbage collection remains labour intensive and there is a lack of studies addressing the variation induced by the sampling method and the required sample size. The aim of this study was (1) to compare two different sampling methods in terms of pasture larval count results and time required to sample, (2) to assess the amount of variation in larval counts at the level of sample plot, pasture and season, respectively and (3) to calculate the required sample size to assess pasture larval contamination with a predefined precision using random plots across pasture. Eight young stock pastures of different commercial dairy herds were sampled in three consecutive seasons during the grazing season (spring, summer and autumn). On each pasture, herbage samples were collected through both a double-crossed W-transect with samples taken every 10 steps (method 1) and four random located plots of 0.16 m(2) with collection of all herbage within the plot (method 2). The average (± standard deviation (SD)) pasture larval contamination using sampling methods 1 and 2 was 325 (± 479) and 305 (± 444)L3/kg dry herbage (DH), respectively. Large discrepancies in pasture larval counts of the same pasture and season were often seen between methods, but no significant difference (P = 0.38) in larval counts between methods was found. Less time was required to collect samples with method 2. This difference in collection time between methods was most pronounced for pastures with a surface area larger than 1 ha. The variation in pasture larval counts from samples generated by random plot sampling was mainly due to the repeated measurements on the same pasture in the same season (residual variance component = 6.2), rather than due to pasture (variance component = 0.55) or season (variance component = 0.15). Using the observed distribution of L3, the required sample size (i.e. number of plots per pasture) for sampling a pasture through random plots with a particular precision was simulated. A higher relative precision was acquired when estimating PLC on pastures with a high larval contamination and a low level of aggregation compared to pastures with a low larval contamination when the same sample size was applied. In the future, herbage sampling through random plots across pasture (method 2) seems a promising method to develop further as no significant difference in counts between the methods was found and this method was less time consuming. Copyright © 2015 Elsevier B.V. All rights reserved.

Detection and monitoring of invasive exotic plants: a comparison of four sampling methods

Treesearch

Cynthia D. Huebner

2007-01-01

The ability to detect and monitor exotic invasive plants is likely to vary depending on the sampling method employed. Methods with strong qualitative thoroughness for species detection often lack the intensity necessary to monitor vegetation change. Four sampling methods (systematic plot, stratified-random plot, modified Whittaker, and timed meander) in hemlock and red...

On fixed-area plot sampling for downed coarse woody debris

Treesearch

Jeffrey H. Gove; Paul C. Van Deusen

2011-01-01

The use of fixed-area plots for sampling down coarse woody debris is reviewed. A set of clearly defined protocols for two previously described methods is established and a new method, which we call the 'sausage' method, is developed. All methods (protocols) are shown to be unbiased for volume estimation, but not necessarily for estimation of population...

Partitioning soil respiration: examining the artifacts of the trenching method.

NASA Astrophysics Data System (ADS)

Savage, K. E.; Davidson, E. A.; Finzi, A.; Giasson, M. A.; Wehr, R. A.

2014-12-01

Soil respiration (Rs) is a combination of autotrophic (Ra) and heterotrophic respiration (Rh). Several methods have been developed to tease out the components of Rs, such as isotopic analyses, and removing Ra input through tree girdling and root exclusion experiments. Trenching involves severing the rooting system surrounding a plot to remove the Ra component within the plot. This method has some potential limitations. Reduced water uptake in trenched plots could change soil water content, which is one of the environmental controllers of Rs in many ecosystems. Eliminating root inputs could reduce heterotrophic decomposition of SOM via lack of priming. On the other hand, the severed dead roots may temporarily increase available carbon substrate for Rh. At the Harvard Forest, MA, we used the trenching method to partition Rs into its components Ra and Rh. Pre-trenched Rs was measured from spring to fall of 2012. In late fall of 2012, a trench was excavated to 1m depth around a 5x5m area, severing all roots. Plastic tarp was placed along the trench walls and then backfilled. Four automated Rs chambers were placed in the trenched plot and four in an un-trenched plot. Respiration was measured hourly for each chamber along with soil temperature and moisture from spring through fall of 2013 and 2014. Eighty root decomposition bags were placed in the organic soil horizon of the trenched (40) and un-trenched (40) plots at the time of trenching in 2012 and measured in 2013 and 2014. These data are being used to estimate the size and duration of any artifact due to root death. As expected, Rs was lower in the trenched plot (Rh only) than in the un-trenched plot (Rh + Ra) in 2013, but the reverse was unexpectedly observed during a period of low precipitation in 2014. High rates of ET combined with below-average precipitation dried the un-trenched plot to a point where Rh was inhibited, whereas less ET allowed the un-trenched plots to remain measurably wetter.

Imaging of Subacute Blood–Brain Barrier Disruption After Methadone Overdose

PubMed Central

Huisa, Branko N.; Gasparovic, Charles; Taheri, Saeid; Prestopnik, Jillian L.; Rosenberg, Gary A.

2014-01-01

BACKGROUND Methadone intoxication can cause respiratory depression, leading to hypoxia with subsequent coma and death. Delayed postanoxic leukoencephalopathy (DAL) has been reported with intoxication by carbon monoxide, narcotics, and other toxins. OBJECTIVE To investigate the metabolic derangement of the white matter (WM) and blood–brain barrier (BBB) after DAL caused by methadone overdose. DESIGN, SETTING, AND PATIENTS Case report of 2 patients with DAL after a single dose of “diverted” methadone used for pain control. RESULTS In both cases brain magnetic resonance imaging (MRI) revealed initial extensive bilateral restricted diffusion lesions within the WM. Follow-up MRI using proton magnetic resonance spectroscopic imaging (1H-MRSI) showed markedly lower N-acetylaspartate and higher choline within the WM. BBB permeability, calculated by Patlak graphical analysis of MRI T1 data obtained after contrast agent injection, showed disruption of the BBB within the WM lesions, which persisted longer than a year in 1 patient. Neuropsychological evaluation showed executive dysfunction in both patients. After 1 year, one patient recovered whereas the second remained impaired. CONCLUSIONS Methadone overdose can cause DAL with profound disturbances of neural metabolism and the BBB. The time course of these disturbances can be monitored with MR methods. PMID:22211853

Imaging of subacute blood-brain barrier disruption after methadone overdose.

PubMed

Huisa, Branko N; Gasparovic, Charles; Taheri, Saeid; Prestopnik, Jillian L; Rosenberg, Gary A

2013-07-01

Methadone intoxication can cause respiratory depression, leading to hypoxia with subsequent coma and death. Delayed postanoxic leukoencephalopathy (DAL) has been reported with intoxication by carbon monoxide, narcotics, and other toxins. To investigate the metabolic derangement of the white matter (WM) and blood-brain barrier (BBB) after DAL caused by methadone overdose. Case report of 2 patients with DAL after a single dose of "diverted" methadone used for pain control. In both cases brain magnetic resonance imaging (MRI) revealed initial extensive bilateral restricted diffusion lesions within the WM. Follow-up MRI using proton magnetic resonance spectroscopic imaging ((1) H-MRSI) showed markedly lower N-acetylaspartate and higher choline within the WM. BBB permeability, calculated by Patlak graphical analysis of MRI T1 data obtained after contrast agent injection, showed disruption of the BBB within the WM lesions, which persisted longer than a year in 1 patient. Neuropsychological evaluation showed executive dysfunction in both patients. After 1 year, one patient recovered whereas the second remained impaired. Methadone overdose can cause DAL with profound disturbances of neural metabolism and the BBB. The time course of these disturbances can be monitored with MR methods. Copyright © 2011 by the American Society of Neuroimaging.

Experimental strategies in carrying out VCU for tobacco crop I: plot design and size.

PubMed

Toledo, F H R B; Ramalho, M A P; Pulcinelli, C E; Bruzi, A T

2013-09-19

We aimed to establish standards for tobacco Valor de Cultivo e Uso (VCU) in Brazil. We obtained information regarding the size and design of plots of two varietal groups of tobacco (Virginia and Burley). Ten inbred lines of each varietal group were evaluated in a randomized complete block design with four replications. The plot contained 42 plants with six rows of seven columns each. For each experiment plant, considering the position of the respective plant in the plot (row and column) as a reference, cured leaf weight (g/plant), total sugar content (%), and total alkaloid content (%) were determined. The maximum curvature of the variations in coefficients was estimated. Trials with the number of plants per plot ranging from 2 to 41 were simulated. The use of a border was not justified because the interactions between inbred lines x position in the plots were never significant, showing that the behavior of the inbred lines coincided with the different positions. The plant performance varied according to the column position in the plot. To lessen the effect of this factor, the use of plots with more than one row is recommended. Experimental precision, evaluated by the CV%, increased with an increase in plot size; nevertheless, the maximum curvature of the variation coefficient method showed no expressive increase in precision if the number of plants was greater than seven. The result in identification of the best inbred line, in terms of the size of each plot, coincided with the maximum curvature method.

Visual analytics of large multidimensional data using variable binned scatter plots

NASA Astrophysics Data System (ADS)

Hao, Ming C.; Dayal, Umeshwar; Sharma, Ratnesh K.; Keim, Daniel A.; Janetzko, Halldór

2010-01-01

The scatter plot is a well-known method of visualizing pairs of two-dimensional continuous variables. Multidimensional data can be depicted in a scatter plot matrix. They are intuitive and easy-to-use, but often have a high degree of overlap which may occlude a significant portion of data. In this paper, we propose variable binned scatter plots to allow the visualization of large amounts of data without overlapping. The basic idea is to use a non-uniform (variable) binning of the x and y dimensions and plots all the data points that fall within each bin into corresponding squares. Further, we map a third attribute to color for visualizing clusters. Analysts are able to interact with individual data points for record level information. We have applied these techniques to solve real-world problems on credit card fraud and data center energy consumption to visualize their data distribution and cause-effect among multiple attributes. A comparison of our methods with two recent well-known variants of scatter plots is included.

Registration of parametric dynamic F-18-FDG PET/CT breast images with parametric dynamic Gd-DTPA breast images

NASA Astrophysics Data System (ADS)

Magri, Alphonso; Krol, Andrzej; Lipson, Edward; Mandel, James; McGraw, Wendy; Lee, Wei; Tillapaugh-Fay, Gwen; Feiglin, David

2009-02-01

This study was undertaken to register 3D parametric breast images derived from Gd-DTPA MR and F-18-FDG PET/CT dynamic image series. Nonlinear curve fitting (Levenburg-Marquardt algorithm) based on realistic two-compartment models was performed voxel-by-voxel separately for MR (Brix) and PET (Patlak). PET dynamic series consists of 50 frames of 1-minute duration. Each consecutive PET image was nonrigidly registered to the first frame using a finite element method and fiducial skin markers. The 12 post-contrast MR images were nonrigidly registered to the precontrast frame using a free-form deformation (FFD) method. Parametric MR images were registered to parametric PET images via CT using FFD because the first PET time frame was acquired immediately after the CT image on a PET/CT scanner and is considered registered to the CT image. We conclude that nonrigid registration of PET and MR parametric images using CT data acquired during PET/CT scan and the FFD method resulted in their improved spatial coregistration. The success of this procedure was limited due to relatively large target registration error, TRE = 15.1+/-7.7 mm, as compared to spatial resolution of PET (6-7 mm), and swirling image artifacts created in MR parametric images by the FFD. Further refinement of nonrigid registration of PET and MR parametric images is necessary to enhance visualization and integration of complex diagnostic information provided by both modalities that will lead to improved diagnostic performance.

Development of Soil Characteristics and Plant Communities On Reclaimed and Unreclaimed Spoil Heaps After Coal Mining

NASA Astrophysics Data System (ADS)

Cudlín, Ondřej; Řehák, Zdeněk; Cudlín, Pavel

2016-10-01

The aim of this study was to compare soil characteristics, plant communities and the rate of selected ecosystem function performance on reclaimed and unreclaimed plots (left for spontaneous succession) of different age on spoil heaps. Twelve spoil heaps (three circle plots of radius 12.5 m) near the town Kladno in north-west direction from Prague, created after deep coal mining, were compared. Five mixed soil samples from organo-mineral horizons in each plot were analysed for total content of carbon, nitrogen and phosphorus. In addition, active soil pH (pHH2O) was determined. Plant diversity was determined by vegetation releves. The biodiversity value of the habitat according to the Habitat Valuation Method was assessed and the rate of evapotranspiration function by the Method of Valuation Functions and Services of Ecosystems in the Czech Republic were determined. The higher organo-mineral layers and higher amount of total nitrogen content were found on the older reclaimed and unreclaimed plots than in younger plots. The number of plant species and the total contents of carbon and nitrogen were significantly higher at the unreclaimed plots compared to reclaimed plots. The biodiversity values and evapotranspiration function rate were also higher on unreclaimed plots. From this perspective, it is possible to recommend using of spontaneous succession, together with routine reclamation methods to restore habitats after coal mining. Despite the relatively high age of vegetation in some of selected plots (90 years), both the reclaimed and unreclaimed plots have not reached the stage of potential vegetation near to natural climax. Slow development of vegetation was probably due to unsuitable substrate of spoil heaps and a lack of plant and tree species of natural forest habitats in this area. However, it is probable that vegetation communities on observed spoil heaps in both type of management (reclaimed and unreclaimed) will achieve the stage of natural climax and they will provide ecosystem functions more effectively in the future.

Fuzzy recurrence plots

NASA Astrophysics Data System (ADS)

Pham, T. D.

2016-12-01

Recurrence plots display binary texture of time series from dynamical systems with single dots and line structures. Using fuzzy recurrence plots, recurrences of the phase-space states can be visualized as grayscale texture, which is more informative for pattern analysis. The proposed method replaces the crucial similarity threshold required by symmetrical recurrence plots with the number of cluster centers, where the estimate of the latter parameter is less critical than the estimate of the former.

Parametric mapping of [18F]fluoromisonidazole positron emission tomography using basis functions.

PubMed

Hong, Young T; Beech, John S; Smith, Rob; Baron, Jean-Claude; Fryer, Tim D

2011-02-01

In this study, we show a basis function method (BAFPIC) for voxelwise calculation of kinetic parameters (K(1), k(2), k(3), K(i)) and blood volume using an irreversible two-tissue compartment model. BAFPIC was applied to rat ischaemic stroke micro-positron emission tomography data acquired with the hypoxia tracer [(18)F]fluoromisonidazole because irreversible two-tissue compartmental modelling provided good fits to data from both hypoxic and normoxic tissues. Simulated data show that BAFPIC produces kinetic parameters with significantly lower variability and bias than nonlinear least squares (NLLS) modelling in hypoxic tissue. The advantage of BAFPIC over NLLS is less pronounced in normoxic tissue. K(i) determined from BAFPIC has lower variability than that from the Patlak-Gjedde graphical analysis (PGA) by up to 40% and lower bias, except for normoxic tissue at mid-high noise levels. Consistent with the simulation results, BAFPIC parametric maps of real data suffer less noise-induced variability than do NLLS and PGA. Delineation of hypoxia on BAFPIC k(3) maps is aided by low variability in normoxic tissue, which matches that in K(i) maps. BAFPIC produces K(i) values that correlate well with those from PGA (r(2)=0.93 to 0.97; slope 0.99 to 1.05, absolute intercept <0.00002 mL/g per min). BAFPIC is a computationally efficient method of determining parametric maps with low bias and variance.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots.

PubMed

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-11

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots

NASA Astrophysics Data System (ADS)

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-01

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Use of recurrence plots in the analysis of pupil diameter dynamics in narcoleptics

NASA Astrophysics Data System (ADS)

Keegan, Andrew P.; Zbilut, J. P.; Merritt, S. L.; Mercer, P. J.

1993-11-01

Recurrence plots were used to evaluate pupil dynamics of subjects with narcolepsy. Preliminary data indicate that this nonlinear method of analyses may be more useful in revealing underlying deterministic differences than traditional methods like FFT and counting statistics.

Multi-Reader ROC studies with Split-Plot Designs: A Comparison of Statistical Methods

PubMed Central

Obuchowski, Nancy A.; Gallas, Brandon D.; Hillis, Stephen L.

2012-01-01

Rationale and Objectives Multi-reader imaging trials often use a factorial design, where study patients undergo testing with all imaging modalities and readers interpret the results of all tests for all patients. A drawback of the design is the large number of interpretations required of each reader. Split-plot designs have been proposed as an alternative, in which one or a subset of readers interprets all images of a sample of patients, while other readers interpret the images of other samples of patients. In this paper we compare three methods of analysis for the split-plot design. Materials and Methods Three statistical methods are presented: Obuchowski-Rockette method modified for the split-plot design, a newly proposed marginal-mean ANOVA approach, and an extension of the three-sample U-statistic method. A simulation study using the Roe-Metz model was performed to compare the type I error rate, power and confidence interval coverage of the three test statistics. Results The type I error rates for all three methods are close to the nominal level but tend to be slightly conservative. The statistical power is nearly identical for the three methods. The coverage of 95% CIs fall close to the nominal coverage for small and large sample sizes. Conclusions The split-plot MRMC study design can be statistically efficient compared with the factorial design, reducing the number of interpretations required per reader. Three methods of analysis, shown to have nominal type I error rate, similar power, and nominal CI coverage, are available for this study design. PMID:23122570

Confidence limits for contribution plots in multivariate statistical process control using bootstrap estimates.

PubMed

Babamoradi, Hamid; van den Berg, Frans; Rinnan, Åsmund

2016-02-18

In Multivariate Statistical Process Control, when a fault is expected or detected in the process, contribution plots are essential for operators and optimization engineers in identifying those process variables that were affected by or might be the cause of the fault. The traditional way of interpreting a contribution plot is to examine the largest contributing process variables as the most probable faulty ones. This might result in false readings purely due to the differences in natural variation, measurement uncertainties, etc. It is more reasonable to compare variable contributions for new process runs with historical results achieved under Normal Operating Conditions, where confidence limits for contribution plots estimated from training data are used to judge new production runs. Asymptotic methods cannot provide confidence limits for contribution plots, leaving re-sampling methods as the only option. We suggest bootstrap re-sampling to build confidence limits for all contribution plots in online PCA-based MSPC. The new strategy to estimate CLs is compared to the previously reported CLs for contribution plots. An industrial batch process dataset was used to illustrate the concepts. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of a reproductive index to estimate grasshopper sparrow and eastern meadowlark reproductive success

USGS Publications Warehouse

Althoff, Donald P.; Gipson, P.S.; Pontius, J.S.; Japuntich, R.D.

2009-01-01

We compared an index of reproductive success based on breeding behavior to actual nest fates of grasshopper sparrows (Ammodramus savannarum) and eastern meadowlarks (Sturnella magna) on 12 plots (4-ha). Concordance of results between the two methods was 58% for grasshopper sparrows and 42% for eastern meadowlarks on a plot-by-plot basis. The indirect method yielded higher estimates of reproductive activity than nest monitoring for the balance of the plots,. There was little evidence that brown-headed cowbird (Molothrus ater) parasitism influenced the estimates of reproductive success using the indirect method. We concluded that nests and about-to-fledge nestlings were missed during searches on some plots. It may be appropriate to use an indirect method to more efficiently survey territories and/or plots for species with hard-to-find nests or when monitoring large areas. Use of a reproductive index may be appropriate and more time-efficient than nest searching and monitoring for comparing management effects such as burning, grazing, haying, military training, and other localized disturbances that are likely to affect reproductive success of grasshopper sparrows and eastern meadowlarks. However, nest monitoring may be necessary for more precise estimates of productivity necessary for long-term monitoring. Nest monitoring results are also likely to allow for direct comparisons to results from other studies because the index method requires intimate knowledge of the species being evaluated - a factor that could lead to reduced precision because the experience level of technicians relying only on behavioral cues from study-to-study is likely to vary considerably.

Funnel plot control limits to identify poorly performing healthcare providers when there is uncertainty in the value of the benchmark.

PubMed

Manktelow, Bradley N; Seaton, Sarah E; Evans, T Alun

2016-12-01

There is an increasing use of statistical methods, such as funnel plots, to identify poorly performing healthcare providers. Funnel plots comprise the construction of control limits around a benchmark and providers with outcomes falling outside the limits are investigated as potential outliers. The benchmark is usually estimated from observed data but uncertainty in this estimate is usually ignored when constructing control limits. In this paper, the use of funnel plots in the presence of uncertainty in the value of the benchmark is reviewed for outcomes from a Binomial distribution. Two methods to derive the control limits are shown: (i) prediction intervals; (ii) tolerance intervals Tolerance intervals formally include the uncertainty in the value of the benchmark while prediction intervals do not. The probability properties of 95% control limits derived using each method were investigated through hypothesised scenarios. Neither prediction intervals nor tolerance intervals produce funnel plot control limits that satisfy the nominal probability characteristics when there is uncertainty in the value of the benchmark. This is not necessarily to say that funnel plots have no role to play in healthcare, but that without the development of intervals satisfying the nominal probability characteristics they must be interpreted with care. © The Author(s) 2014.

MID Plot: a new lithology technique. [Matrix identification plot

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

Clavier, C.; Rust, D.H.

1976-01-01

Lithology interpretation by the Litho-Porosity (M-N) method has been used for years, but is evidently too cumbersome and ambiguous for widespread acceptance as a field technique. To set aside these objections, another method has been devised. Instead of the log-derived parameters M and N, the MID Plot uses quasi-physical quantities, (rho/sub ma/)/sub a/ and (..delta..t/sub ma/)/sub a/, as its porosity-independent variables. These parameters, taken from suitably scaled Neutron-Density and Sonic-Neutron crossplots, define a unique matrix mineral or mixture for each point on the logs. The matrix points on the MID Plot thus remain constant in spite of changes in mudmore » filtrate, porosity, or neutron tool types (all of which significantly affect the M-N Plot). This new development is expected to bring welcome relief in areas where lithology identification is a routine part of log analysis.« less

SnagPRO: snag and tree sampling and analysis methods for wildlife

Treesearch

Lisa J. Bate; Michael J. Wisdom; Edward O. Garton; Shawn C. Clabough

2008-01-01

We describe sampling methods and provide software to accurately and efficiently estimate snag and tree densities at desired scales to meet a variety of research and management objectives. The methods optimize sampling effort by choosing a plot size appropriate for the specified forest conditions and sampling goals. Plot selection and data analyses are supported by...

Weighted analysis methods for mapped plot forest inventory data: Tables, regressions, maps and graphs

Treesearch

Paul C. Van Deusen; Linda S. Heath

2010-01-01

Weighted estimation methods for analysis of mapped plot forest inventory data are discussed. The appropriate weighting scheme can vary depending on the type of analysis and graphical display. Both statistical issues and user expectations need to be considered in these methods. A weighting scheme is proposed that balances statistical considerations and the logical...

Modeling the uncertainty of estimating forest carbon stocks in China

NASA Astrophysics Data System (ADS)

Yue, T. X.; Wang, Y. F.; Du, Z. P.; Zhao, M. W.; Zhang, L. L.; Zhao, N.; Lu, M.; Larocque, G. R.; Wilson, J. P.

2015-12-01

Earth surface systems are controlled by a combination of global and local factors, which cannot be understood without accounting for both the local and global components. The system dynamics cannot be recovered from the global or local controls alone. Ground forest inventory is able to accurately estimate forest carbon stocks at sample plots, but these sample plots are too sparse to support the spatial simulation of carbon stocks with required accuracy. Satellite observation is an important source of global information for the simulation of carbon stocks. Satellite remote-sensing can supply spatially continuous information about the surface of forest carbon stocks, which is impossible from ground-based investigations, but their description has considerable uncertainty. In this paper, we validated the Lund-Potsdam-Jena dynamic global vegetation model (LPJ), the Kriging method for spatial interpolation of ground sample plots and a satellite-observation-based approach as well as an approach for fusing the ground sample plots with satellite observations and an assimilation method for incorporating the ground sample plots into LPJ. The validation results indicated that both the data fusion and data assimilation approaches reduced the uncertainty of estimating carbon stocks. The data fusion had the lowest uncertainty by using an existing method for high accuracy surface modeling to fuse the ground sample plots with the satellite observations (HASM-SOA). The estimates produced with HASM-SOA were 26.1 and 28.4 % more accurate than the satellite-based approach and spatial interpolation of the sample plots, respectively. Forest carbon stocks of 7.08 Pg were estimated for China during the period from 2004 to 2008, an increase of 2.24 Pg from 1984 to 2008, using the preferred HASM-SOA method.

Problems with sampling desert tortoises: A simulation analysis based on field data

USGS Publications Warehouse

Freilich, J.E.; Camp, R.J.; Duda, J.J.; Karl, A.E.

2005-01-01

The desert tortoise (Gopherus agassizii) was listed as a U.S. threatened species in 1990 based largely on population declines inferred from mark-recapture surveys of 2.59-km2 (1-mi2) plots. Since then, several census methods have been proposed and tested, but all methods still pose logistical or statistical difficulties. We conducted computer simulations using actual tortoise location data from 2 1-mi2 plot surveys in southern California, USA, to identify strengths and weaknesses of current sampling strategies. We considered tortoise population estimates based on these plots as "truth" and then tested various sampling methods based on sampling smaller plots or transect lines passing through the mile squares. Data were analyzed using Schnabel's mark-recapture estimate and program CAPTURE. Experimental subsampling with replacement of the 1-mi2 data using 1-km2 and 0.25-km2 plot boundaries produced data sets of smaller plot sizes, which we compared to estimates from the 1-mi 2 plots. We also tested distance sampling by saturating a 1-mi 2 site with computer simulated transect lines, once again evaluating bias in density estimates. Subsampling estimates from 1-km2 plots did not differ significantly from the estimates derived at 1-mi2. The 0.25-km2 subsamples significantly overestimated population sizes, chiefly because too few recaptures were made. Distance sampling simulations were biased 80% of the time and had high coefficient of variation to density ratios. Furthermore, a prospective power analysis suggested limited ability to detect population declines as high as 50%. We concluded that poor performance and bias of both sampling procedures was driven by insufficient sample size, suggesting that all efforts must be directed to increasing numbers found in order to produce reliable results. Our results suggest that present methods may not be capable of accurately estimating desert tortoise populations.

Graphic report of the results from propensity score method analyses.

PubMed

Shrier, Ian; Pang, Menglan; Platt, Robert W

2017-08-01

To increase transparency in studies reporting propensity scores by using graphical methods that clearly illustrate (1) the number of participant exclusions that occur as a consequence of the analytic strategy and (2) whether treatment effects are constant or heterogeneous across propensity scores. We applied graphical methods to a real-world pharmacoepidemiologic study that evaluated the effect of initiating statin medication on the 1-year all-cause mortality post-myocardial infarction. We propose graphical methods to show the consequences of trimming and matching on the exclusion of participants from the analysis. We also propose the use of meta-analytical forest plots to show the magnitude of effect heterogeneity. A density plot with vertical lines demonstrated the proportion of subjects excluded because of trimming. A frequency plot with horizontal lines demonstrated the proportion of subjects excluded because of matching. An augmented forest plot illustrates the amount of effect heterogeneity present in the data. Our proposed techniques present additional and useful information that helps readers understand the sample that is analyzed with propensity score methods and whether effect heterogeneity is present. Copyright © 2017 Elsevier Inc. All rights reserved.

Multi-reader ROC studies with split-plot designs: a comparison of statistical methods.

PubMed

Obuchowski, Nancy A; Gallas, Brandon D; Hillis, Stephen L

2012-12-01

Multireader imaging trials often use a factorial design, in which study patients undergo testing with all imaging modalities and readers interpret the results of all tests for all patients. A drawback of this design is the large number of interpretations required of each reader. Split-plot designs have been proposed as an alternative, in which one or a subset of readers interprets all images of a sample of patients, while other readers interpret the images of other samples of patients. In this paper, the authors compare three methods of analysis for the split-plot design. Three statistical methods are presented: the Obuchowski-Rockette method modified for the split-plot design, a newly proposed marginal-mean analysis-of-variance approach, and an extension of the three-sample U-statistic method. A simulation study using the Roe-Metz model was performed to compare the type I error rate, power, and confidence interval coverage of the three test statistics. The type I error rates for all three methods are close to the nominal level but tend to be slightly conservative. The statistical power is nearly identical for the three methods. The coverage of 95% confidence intervals falls close to the nominal coverage for small and large sample sizes. The split-plot multireader, multicase study design can be statistically efficient compared to the factorial design, reducing the number of interpretations required per reader. Three methods of analysis, shown to have nominal type I error rates, similar power, and nominal confidence interval coverage, are available for this study design. Copyright © 2012 AUR. All rights reserved.

Using recurrence plot analysis for software execution interpretation and fault detection

NASA Astrophysics Data System (ADS)

Mosdorf, M.

2015-09-01

This paper shows a method targeted at software execution interpretation and fault detection using recurrence plot analysis. In in the proposed approach recurrence plot analysis is applied to software execution trace that contains executed assembly instructions. Results of this analysis are subject to further processing with PCA (Principal Component Analysis) method that simplifies number coefficients used for software execution classification. This method was used for the analysis of five algorithms: Bubble Sort, Quick Sort, Median Filter, FIR, SHA-1. Results show that some of the collected traces could be easily assigned to particular algorithms (logs from Bubble Sort and FIR algorithms) while others are more difficult to distinguish.

Metadata (MD)

Treesearch

Robert E. Keane

2006-01-01

The Metadata (MD) table in the FIREMON database is used to record any information about the sampling strategy or data collected using the FIREMON sampling procedures. The MD method records metadata pertaining to a group of FIREMON plots, such as all plots in a specific FIREMON project. FIREMON plots are linked to metadata using a unique metadata identifier that is...

A method for subsurface-banding poultry litter in plots not accessible with conventional field equipment

USDA-ARS?s Scientific Manuscript database

Subsurface band application of poultry litter has been shown to be effective in reducing nutrients in runoff and leachate, relative to surface broadcast application of litter. Some field plot arrangements, such as plots having adjacent pits in the soil, prevent the use of conventional field equipme...

Smoothed Residual Plots for Generalized Linear Models. Technical Report #450.

ERIC Educational Resources Information Center

Brant, Rollin

Methods for examining the viability of assumptions underlying generalized linear models are considered. By appealing to the likelihood, a natural generalization of the raw residual plot for normal theory models is derived and is applied to investigating potential misspecification of the linear predictor. A smooth version of the plot is also…

Refining FIA plot locations using LiDAR point clouds

Treesearch

Charlie Schrader-Patton; Greg C. Liknes; Demetrios Gatziolis; Brian M. Wing; Mark D. Nelson; Patrick D. Miles; Josh Bixby; Daniel G. Wendt; Dennis Kepler; Abbey Schaaf

2015-01-01

Forest Inventory and Analysis (FIA) plot location coordinate precision is often insufficient for use with high resolution remotely sensed data, thereby limiting the use of these plots for geospatial applications and reducing the validity of models that assume the locations are precise. A practical and efficient method is needed to improve coordinate precision. To...

National FIA plot intensification procedure report

Treesearch

Jock A. Blackard; Paul L. Patterson

2014-01-01

The Forest Inventory and Analysis (FIA) program of the U.S. Forest Service (USFS) measures a spatially distributed base grid of forest inventory plots across the United States. The sampling intensity of plots may be increased in some regions when warranted by specific inventory objectives. Several intensification methods have been developed within FIA and USFS National...

Mapped Plot Patch Size Estimates

Treesearch

Paul C. Van Deusen

2005-01-01

This paper demonstrates that the mapped plot design is relatively easy to analyze and describes existing formulas for mean and variance estimators. New methods are developed for using mapped plots to estimate average patch size of condition classes. The patch size estimators require assumptions about the shape of the condition class, limiting their utility. They may...

Research on tactical information display technology for interactive virtual cockpit

NASA Astrophysics Data System (ADS)

Sun, Zhongyun; Tian, Tao; Su, Feng

2018-04-01

Based on a fact that traditional tactical information display technology suffers from disadvantages of a large number of data to be transferred and low plotting efficiency in an interactive virtual cockpit, a GID protocol-based simulation has been designed. This method dissolves complex tactical information screens into basic plotting units. The indication of plotting units is controlled via the plotting commands, which solves the incompatibility between the tactical information display in traditional simulation and the desktop-based virtual simulation training system. Having been used in desktop systems for helicopters, fighters, and transporters, this method proves to be scientific and reasonable in design and simple and efficient in usage, which exerts a significant value in establishing aviation equipment technology support training products.

Performance of quantitative vegetation sampling methods across gradients of cover in Great Basin plant communities

USGS Publications Warehouse

Pilliod, David S.; Arkle, Robert S.

2013-01-01

Resource managers and scientists need efficient, reliable methods for quantifying vegetation to conduct basic research, evaluate land management actions, and monitor trends in habitat conditions. We examined three methods for quantifying vegetation in 1-ha plots among different plant communities in the northern Great Basin: photography-based grid-point intercept (GPI), line-point intercept (LPI), and point-quarter (PQ). We also evaluated each method for within-plot subsampling adequacy and effort requirements relative to information gain. We found that, for most functional groups, percent cover measurements collected with the use of LPI, GPI, and PQ methods were strongly correlated. These correlations were even stronger when we used data from the upper canopy only (i.e., top “hit” of pin flags) in LPI to estimate cover. PQ was best at quantifying cover of sparse plants such as shrubs in early successional habitats. As cover of a given functional group decreased within plots, the variance of the cover estimate increased substantially, which required more subsamples per plot (i.e., transect lines, quadrats) to achieve reliable precision. For GPI, we found that that six–nine quadrats per hectare were sufficient to characterize the vegetation in most of the plant communities sampled. All three methods reasonably characterized the vegetation in our plots, and each has advantages depending on characteristics of the vegetation, such as cover or heterogeneity, study goals, precision of measurements required, and efficiency needed.

The Application of TD/GC/NICI-MS with an Al2O3-PLOT-S Column for the Determination of Perfluoroalkylcycloalkanes in the Atmosphere.

PubMed

Ren, Yu; Schlager, Hans; Martin, Damien

2014-01-01

A modified method for the quantitative determination of atmospheric perfluoroalkylcycloalkanes (PFCs) using thermal desorption coupled with gas chromatography and detection by negative ion chemical ionization-mass spectrometry was developed. Using an optimized analytical system, a commercially available Al 2 O 3 porous layer open tubular (PLOT) capillary column (30 m × 0.25 mm) deactivated with Na 2 SO 4 was used for separation of PFCs. Improvements in the separation of PFCs, the corresponding identification and the limit of detection of PFCs using this method and column are presented. The method was successfully applied to determine the atmospheric background concentrations of a range of PFCs from a number of samples collected at a rural site in Germany. The results of this study suggest that the method outlined using the Al 2 O 3 -PLOT-S capillary column has good sensitivity and selectivity, and that it can be deployed in a routine laboratory process for the analysis of PFCs in the future research work. In addition, the ability of this column to separate the isomers of one of the lower boiling PFCs (perfluorodimethylcyclobutane) and its ability to resolve perfluoroethylcyclohexane offer the opportunity for single-column analysis for multiple PFCs.

Direct estimation of tracer-kinetic parameter maps from highly undersampled brain dynamic contrast enhanced MRI.

PubMed

Guo, Yi; Lingala, Sajan Goud; Zhu, Yinghua; Lebel, R Marc; Nayak, Krishna S

2017-10-01

The purpose of this work was to develop and evaluate a T 1 -weighted dynamic contrast enhanced (DCE) MRI methodology where tracer-kinetic (TK) parameter maps are directly estimated from undersampled (k,t)-space data. The proposed reconstruction involves solving a nonlinear least squares optimization problem that includes explicit use of a full forward model to convert parameter maps to (k,t)-space, utilizing the Patlak TK model. The proposed scheme is compared against an indirect method that creates intermediate images by parallel imaging and compressed sensing before to TK modeling. Thirteen fully sampled brain tumor DCE-MRI scans with 5-second temporal resolution are retrospectively undersampled at rates R = 20, 40, 60, 80, and 100 for each dynamic frame. TK maps are quantitatively compared based on root mean-squared-error (rMSE) and Bland-Altman analysis. The approach is also applied to four prospectively R = 30 undersampled whole-brain DCE-MRI data sets. In the retrospective study, the proposed method performed statistically better than indirect method at R ≥ 80 for all 13 cases. This approach provided restoration of TK parameter values with less errors in tumor regions of interest, an improvement compared to a state-of-the-art indirect method. Applied prospectively, the proposed method provided whole-brain, high-resolution TK maps with good image quality. Model-based direct estimation of TK maps from k,t-space DCE-MRI data is feasible and is compatible up to 100-fold undersampling. Magn Reson Med 78:1566-1578, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Harvesting tree biomass at the stand level to assess the accuracy of field and airborne biomass estimation in savannas.

PubMed

Colgan, Matthew S; Asner, Gregory P; Swemmer, Tony

2013-07-01

Tree biomass is an integrated measure of net growth and is critical for understanding, monitoring, and modeling ecosystem functions. Despite the importance of accurately measuring tree biomass, several fundamental barriers preclude direct measurement at large spatial scales, including the facts that trees must be felled to be weighed and that even modestly sized trees are challenging to maneuver once felled. Allometric methods allow for estimation of tree mass using structural characteristics, such as trunk diameter. Savanna trees present additional challenges, including limited available allometry and a prevalence of multiple stems per individual. Here we collected airborne lidar data over a semiarid savanna adjacent to the Kruger National Park, South Africa, and then harvested and weighed woody plant biomass at the plot scale to provide a standard against which field and airborne estimation methods could be compared. For an existing airborne lidar method, we found that half of the total error was due to averaging canopy height at the plot scale. This error was eliminated by instead measuring maximum height and crown area of individual trees from lidar data using an object-based method to identify individual tree crowns and estimate their biomass. The best object-based model approached the accuracy of field allometry at both the tree and plot levels, and it more than doubled the accuracy compared to existing airborne methods (17% vs. 44% deviation from harvested biomass). Allometric error accounted for less than one-third of the total residual error in airborne biomass estimates at the plot scale when using allometry with low bias. Airborne methods also gave more accurate predictions at the plot level than did field methods based on diameter-only allometry. These results provide a novel comparison of field and airborne biomass estimates using harvested plots and advance the role of lidar remote sensing in savanna ecosystems.

A method for analyzing temporal patterns of variability of a time series from Poincare plots.

PubMed

Fishman, Mikkel; Jacono, Frank J; Park, Soojin; Jamasebi, Reza; Thungtong, Anurak; Loparo, Kenneth A; Dick, Thomas E

2012-07-01

The Poincaré plot is a popular two-dimensional, time series analysis tool because of its intuitive display of dynamic system behavior. Poincaré plots have been used to visualize heart rate and respiratory pattern variabilities. However, conventional quantitative analysis relies primarily on statistical measurements of the cumulative distribution of points, making it difficult to interpret irregular or complex plots. Moreover, the plots are constructed to reflect highly correlated regions of the time series, reducing the amount of nonlinear information that is presented and thereby hiding potentially relevant features. We propose temporal Poincaré variability (TPV), a novel analysis methodology that uses standard techniques to quantify the temporal distribution of points and to detect nonlinear sources responsible for physiological variability. In addition, the analysis is applied across multiple time delays, yielding a richer insight into system dynamics than the traditional circle return plot. The method is applied to data sets of R-R intervals and to synthetic point process data extracted from the Lorenz time series. The results demonstrate that TPV complements the traditional analysis and can be applied more generally, including Poincaré plots with multiple clusters, and more consistently than the conventional measures and can address questions regarding potential structure underlying the variability of a data set.

The Zombie Plot: A Simple Graphic Method for Visualizing the Efficacy of a Diagnostic Test.

PubMed

Richardson, Michael L

2016-08-09

One of the most important jobs of a radiologist is to pick the most appropriate imaging test for a particular clinical situation. Making a proper selection sometimes requires statistical analysis. The objective of this article is to introduce a simple graphic technique, an ROC plot that has been divided into zones of mostly bad imaging efficacy (ZOMBIE, hereafter referred to as the "zombie plot"), that transforms information about imaging efficacy from the numeric domain into the visual domain. The numeric rationale for the use of zombie plots is given, as are several examples of the clinical use of these plots. Two online calculators are described that simplify the process of producing a zombie plot.

Isotopic Characterisation of Methane Emissions: use of Keeling-plot Methods to Identify Source Signatures in Boreal Wetlands and Other Settings

NASA Astrophysics Data System (ADS)

Fisher, R. E.; Lowry, D.; France, J.; Lanoiselle, M.; Zazzeri, G.; Nisbet, E. G.

2012-12-01

Different methane sources have different δ13CCH4 and δDCH4 signatures, which potentially provides a powerful constraint on models of methane emission budgets. However source signatures remain poorly known and need to be studied in more detail if isotopic measurements of ambient air are to be used to constrain regional and global emissions. The Keeling plot method (plotting δ13CCH4 or δDCH4 against 1/CH4 concentration in samples of ambient air in the close vicinity of known sources) directly assesses the source signature of the methane that is actually emitted to the air. This contrasts with chamber studies, measuring air within a chamber, where local micro-meteorological and microbiological processes are occurring. Keeling plot methods have been applied to a wide variety of settings in this study. The selection of appropriate background measurements for Keeling plot analysis is also considered. The method has been used on a local scale to identify the source signature of summer emissions from subarctic wetlands in Fennoscandia. Samples are collected from low height (0.3-3m) over the wetlands during 24-hour periods, to collect daily emissions maxima (warm late afternoons), inversion maxima (at the coldest time of the 24hr daylight: usually earliest morning), and ambient minima when mixing occurs (often mid afternoon). Some results are comparable to parallel chamber studies, but in other cases there are small but significant shifts between CH4 in chamber air and CH4 that is dispersing in the above-ground air. On a regional to continental scale the isotopic signature of bulk sources of emissions can be identified using Keeling plots. The methodology is very applicable for use in urban and urban-rural settings. For example, the winter SE monsoon sweeps from inland central Asia over China to Hong Kong. Application of back trajectory analysis and Keeling plot methods implied coal emissions may be a significant Chinese source of methane in January, although in other months biological sources dominate. Similarly, in London the method has been used to test the London methane emission inventory.

Plotting Rates of Photosynthesis as a Function of Light Quantity.

ERIC Educational Resources Information Center

Dean, Rob L.

1996-01-01

Discusses methods for plotting rates of photosynthesis as a function of light quantity. Presents evidence that suggests that empirically derived conversion factors, which are used to convert foot candles to photon fluence rates, should be used with extreme caution. Suggests how rate data are best plotted when any kind of light meter is not…

Estimating mapped-plot forest attributes with ratios of means

Treesearch

S.J. Zarnoch; W.A. Bechtold

2000-01-01

The mapped-plot design utilized by the U.S. Department of Agriculture (USDA) Forest Inventory and Analysis and the National Forest Health Monitoring Programs is described. Data from 2458 forested mapped plots systematically spread across 25 States reveal that 35 percent straddle multiple conditions. The ratio-of-means estimator is developed as a method to obtain...

The Gran Plot Analysis of an Acid Mixture. An Undergraduate Experiment to Highlight this Alternate Method.

ERIC Educational Resources Information Center

Boiani, James A.

1986-01-01

Describes an experiment which uses the Gran plot for analyzing free ions as well as those involved in an equilibrium. Discusses the benefits of using Gran plots in the study of acids, as well as other analytes in solutions. Presents background theory along with a description of the experimental procedures. (TW)

Digital data collection in forest dynamics plots

Treesearch

Faith Inman-Narahari; Christian Giardina; Rebecca Ostertag; Susan Cordell; Lawren Sack

2010-01-01

Summary 1. Computers are widely used in all aspects of research but their application to in-field data collection for forest plots has rarely been evaluated. 2. We developed digital data collection methods using ESRI mapping software and ruggedized field computers to map and measure ~30 000 trees in two 4-ha forest dynamics plots in wet and dry...

Biomass Development in SRI Field Under Unmaintained Alternate Wetting-Drying Irrigation

NASA Astrophysics Data System (ADS)

Ardiansyah; Chusnul, A.; Krissandi, W.; Asna, M.

2018-05-01

The aim of this research is to observe biomass development of SRI on farmers practice in three plots with different level. This research observes the farmer practice of SRI and Non-SRI during the uncertainty of irrigation water supply and its effects on paddy biomass development during growth stages and final stage of crop. A farmer group that already understand the principle of SRI, applied this method into several plots of their rented paddy field. Researcher interventions were eliminated from their action, so it is purely on farmers decision on managing their SRI plots. Three plots from both SRI and Non-SRI were chosen based on the position of the plot related their access to water. First plots had direct access to water from tertiary irrigation channel (on farm). Second plots were received water from previous upper plots and drainage water into other plots. Third plots were in the bottom position, where they received water from upper plot, and drainage water into farm drainage channel. Result shows there are similar patterns of root, straw, and leaves of biomass during crop growth. On the other hand, during generative phase, grain development shows different pattern and resulting different biomass in harvest time. Second plot, (of SRI) that has water from first plot has the average of biomass grain per plant of 54.4, higher than first plot and third plot, which are 33.8 g and 38.4. Average biomass in second plot is 74.6 g, higher than first and third plot, which are 49.9 g and 52.3 g.

Experimental conformational energy maps of proteins and peptides.

PubMed

Balaji, Govardhan A; Nagendra, H G; Balaji, Vitukudi N; Rao, Shashidhar N

2017-06-01

We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F. M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ, ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions. Further, we have identified low energy pathways for transitions between various minima in the (ϕ,ψ) plots. We have compared and presented the experimental plots with published theoretical plots obtained from both molecular mechanics and quantum mechanical approaches. In addition, we have developed and employed a root mean square deviation (RMSD) metric for isoenergy contours in various ranges, as a measure (in kcal.mol -1 ) to compare any two plots and determine the extent of correlation and similarity between their isoenergy contours. In general, we observe a greater degree of compatibility with experimental plots for energy maps obtained from molecular mechanics methods compared to most quantum mechanical methods. The experimental energy plots we have investigated could be helpful in refining protein structures obtained from X-ray, NMR, and electron microscopy and in refining force field parameters to enable simulations of peptide and protein structures that have higher degree of consistency with experiments. Proteins 2017; 85:979-1001. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

An Excel macro for generating trilinear plots.

PubMed

Shikaze, Steven G; Crowe, Allan S

2007-01-01

This computer note describes a method for creating trilinear plots in Microsoft Excel. Macros have been created in MS Excel's internal language: Visual Basic for Applications (VBA). A simple form has been set up to allow the user to input data from an Excel worksheet. The VBA macro is used to convert the triangular data (which consist of three columns of percentage data) into X-Y data. The macro then generates the axes, labels, and grid for the trilinear plot. The X-Y data are plotted as scatter data in Excel. By providing this macro in Excel, users can create trilinear plots in a quick, inexpensive manner.

Relative equilibrium plot improves graphical analysis and allows bias correction of standardized uptake value ratio in quantitative 11C-PiB PET studies.

PubMed

Zhou, Yun; Sojkova, Jitka; Resnick, Susan M; Wong, Dean F

2012-04-01

Both the standardized uptake value ratio (SUVR) and the Logan plot result in biased distribution volume ratios (DVRs) in ligand-receptor dynamic PET studies. The objective of this study was to use a recently developed relative equilibrium-based graphical (RE) plot method to improve and simplify the 2 commonly used methods for quantification of (11)C-Pittsburgh compound B ((11)C-PiB) PET. The overestimation of DVR in SUVR was analyzed theoretically using the Logan and the RE plots. A bias-corrected SUVR (bcSUVR) was derived from the RE plot. Seventy-eight (11)C-PiB dynamic PET scans (66 from controls and 12 from participants with mild cognitive impaired [MCI] from the Baltimore Longitudinal Study of Aging) were acquired over 90 min. Regions of interest (ROIs) were defined on coregistered MR images. Both the ROI and the pixelwise time-activity curves were used to evaluate the estimates of DVR. DVRs obtained using the Logan plot applied to ROI time-activity curves were used as a reference for comparison of DVR estimates. Results from the theoretic analysis were confirmed by human studies. ROI estimates from the RE plot and the bcSUVR were nearly identical to those from the Logan plot with ROI time-activity curves. In contrast, ROI estimates from DVR images in frontal, temporal, parietal, and cingulate regions and the striatum were underestimated by the Logan plot (controls, 4%-12%; MCI, 9%-16%) and overestimated by the SUVR (controls, 8%-16%; MCI, 16%-24%). This bias was higher in the MCI group than in controls (P < 0.01) but was not present when data were analyzed using either the RE plot or the bcSUVR. The RE plot improves pixelwise quantification of (11)C-PiB dynamic PET, compared with the conventional Logan plot. The bcSUVR results in lower bias and higher consistency of DVR estimates than of SUVR. The RE plot and the bcSUVR are practical quantitative approaches that improve the analysis of (11)C-PiB studies.

Nebraska's forests, 2005: statistics, methods, and quality assurance

Treesearch

Patrick D. Miles; Dacia M. Meneguzzo; Charles J. Barnett

2011-01-01

The first full annual inventory of Nebraska's forests was completed in 2005 after 8,335 plots were selected and 274 forested plots were visited and measured. This report includes detailed information on forest inventory methods, and data quality estimates. Tables of various important resource statistics are presented. Detailed analysis of the inventory data are...

Kansas's forests, 2005: statistics, methods, and quality assurance

Treesearch

Patrick D. Miles; W. Keith Moser; Charles J. Barnett

2011-01-01

The first full annual inventory of Kansas's forests was completed in 2005 after 8,868 plots were selected and 468 forested plots were visited and measured. This report includes detailed information on forest inventory methods and data quality estimates. Important resource statistics are included in the tables. A detailed analysis of Kansas inventory is presented...

The diagnostic plot analysis of artesian aquifers with case studies in Table Mountain Group of South Africa

NASA Astrophysics Data System (ADS)

Sun, Xiaobin; Xu, Yongxin; Lin, Lixiang

2015-05-01

Parameter estimates of artesian aquifers where piezometric head is above ground level are largely made through free-flowing and recovery tests. The straight-line method proposed by Jacob-Lohman is often used for interpretation of flow rate measured at flowing artesian boreholes. However, the approach fails to interpret the free-flowing test data from two artesian boreholes in the fractured-rock aquifer in Table Mountain Group (TMG) of South Africa. The diagnostic plot method using the reciprocal rate derivative is adapted to evaluate the artesian aquifer properties. The variation of the derivative helps not only identify flow regimes and discern the boundary conditions, but also facilitates conceptualization of the aquifer system and selection of an appropriate model for data interpretation later on. Test data from two free-flowing tests conducted in different sites in TMG are analysed using the diagnostic plot method. Based on the results, conceptual models and appropriate approaches are developed to evaluate the aquifer properties. The advantages and limitations of using the diagnostic plot method on free-flowing test data are discussed.

Seedbed treatment increases dominance of natural loblolly pine reproduction

Treesearch

S. Little; J. J. Mohr

1957-01-01

In 1951 a 30-acre mature stand of loblolly pine on Maryland's Eastern Shore was cut, leaving 10 pine seed trees per acre; and three different methods of seedbed preparation were tried on experimental plots within the stand. Besides a control plot, which was only logged, the plot treatments included: (a) pulling a stump with a small bulldozer before cutting,...

Multiscale Poincaré plots for visualizing the structure of heartbeat time series.

PubMed

Henriques, Teresa S; Mariani, Sara; Burykin, Anton; Rodrigues, Filipa; Silva, Tiago F; Goldberger, Ary L

2016-02-09

Poincaré delay maps are widely used in the analysis of cardiac interbeat interval (RR) dynamics. To facilitate visualization of the structure of these time series, we introduce multiscale Poincaré (MSP) plots. Starting with the original RR time series, the method employs a coarse-graining procedure to create a family of time series, each of which represents the system's dynamics in a different time scale. Next, the Poincaré plots are constructed for the original and the coarse-grained time series. Finally, as an optional adjunct, color can be added to each point to represent its normalized frequency. We illustrate the MSP method on simulated Gaussian white and 1/f noise time series. The MSP plots of 1/f noise time series reveal relative conservation of the phase space area over multiple time scales, while those of white noise show a marked reduction in area. We also show how MSP plots can be used to illustrate the loss of complexity when heartbeat time series from healthy subjects are compared with those from patients with chronic (congestive) heart failure syndrome or with atrial fibrillation. This generalized multiscale approach to Poincaré plots may be useful in visualizing other types of time series.

Nonlinear Dot Plots.

PubMed

Rodrigues, Nils; Weiskopf, Daniel

2018-01-01

Conventional dot plots use a constant dot size and are typically applied to show the frequency distribution of small data sets. Unfortunately, they are not designed for a high dynamic range of frequencies. We address this problem by introducing nonlinear dot plots. Adopting the idea of nonlinear scaling from logarithmic bar charts, our plots allow for dots of varying size so that columns with a large number of samples are reduced in height. For the construction of these diagrams, we introduce an efficient two-way sweep algorithm that leads to a dense and symmetrical layout. We compensate aliasing artifacts at high dot densities by a specifically designed low-pass filtering method. Examples of nonlinear dot plots are compared to conventional dot plots as well as linear and logarithmic histograms. Finally, we include feedback from an expert review.

Vegetation resurvey is robust to plot location uncertainty

PubMed Central

Kopecký, Martin; Macek, Martin

2017-01-01

Aim Resurveys of historical vegetation plots are increasingly used for the assessment of decadal changes in plant species diversity and composition. However, historical plots are usually relocated only approximately. This potentially inflates temporal changes and undermines results. Location Temperate deciduous forests in Central Europe. Methods To explore if robust conclusions can be drawn from resurvey studies despite location uncertainty, we compared temporal changes in species richness, frequency, composition and compositional heterogeneity between exactly and approximately relocated plots. We hypothesized that compositional changes should be lower and changes in species richness should be less variable on exactly relocated plots, because pseudo-turnover inflates temporal changes on approximately relocated plots. Results Temporal changes in species richness were not more variable and temporal changes in species composition and compositional heterogeneity were not higher on approximately relocated plots. Moreover, the frequency of individual species changed similarly on both plot types. Main conclusions The resurvey of historical vegetation plots is robust to uncertainty in original plot location and, when done properly, provides reliable evidence of decadal changes in plant communities. This provides important background for other resurvey studies and opens up the possibility for large-scale assessments of plant community change. PMID:28503083

A new improved graphical and quantitative method for detecting bias in meta-analysis.

PubMed

Furuya-Kanamori, Luis; Barendregt, Jan J; Doi, Suhail A R

2018-04-04

Detection of publication and related biases remains suboptimal and threatens the validity and interpretation of meta-analytical findings. When bias is present, it usually differentially affects small and large studies manifesting as an association between precision and effect size and therefore visual asymmetry of conventional funnel plots. This asymmetry can be quantified and Egger's regression is, by far, the most widely used statistical measure for quantifying funnel plot asymmetry. However, concerns have been raised about both the visual appearance of funnel plots and the sensitivity of Egger's regression to detect such asymmetry, particularly when the number of studies is small. In this article, we propose a new graphical method, the Doi plot, to visualize asymmetry and also a new measure, the LFK index, to detect and quantify asymmetry of study effects in Doi plots. We demonstrate that the visual representation of asymmetry was better for the Doi plot when compared with the funnel plot. We also show that the diagnostic accuracy of the LFK index in discriminating between asymmetry due to simulated publication bias versus chance or no asymmetry was also better with the LFK index which had areas under the receiver operating characteristic curve of 0.74-0.88 with simulations of meta-analyses with five, 10, 15, and 20 studies. The Egger's regression result had lower areas under the receiver operating characteristic curve values of 0.58-0.75 across the same simulations. The LFK index also had a higher sensitivity (71.3-72.1%) than the Egger's regression result (18.5-43.0%). We conclude that the methods proposed in this article can markedly improve the ability of researchers to detect bias in meta-analysis.

Interpreting Medical Information Using Machine Learning and Individual Conditional Expectation.

PubMed

Nohara, Yasunobu; Wakata, Yoshifumi; Nakashima, Naoki

2015-01-01

Recently, machine-learning techniques have spread many fields. However, machine-learning is still not popular in medical research field due to difficulty of interpreting. In this paper, we introduce a method of interpreting medical information using machine learning technique. The method gave new explanation of partial dependence plot and individual conditional expectation plot from medical research field.

Fire Behavior (FB)

Treesearch

Robert E. Keane

2006-01-01

The Fire Behavior (FB) method is used to describe the behavior of the fire and the ambient weather and fuel conditions that influence the fire behavior. Fire behavior methods are not plot based and are collected by fire event and time-date. In general, the fire behavior data are used to interpret the fire effects documented in the plot-level sampling. Unlike the other...

North Dakota's forests, 2005: statistics, methods, and quality assurance

Treesearch

Patrick D. Miles; David E. Haugen; Charles J. Barnett

2011-01-01

The first full annual inventory of North Dakota's forests was completed in 2005 after 7,622 plots were selected and 164 forested plots were visited and measured. This report includes detailed information on forest inventory methods and data quality estimates. Important resource statistics are included in the tables. A detailed analysis of the North Dakota...

South Dakota's forests, 2005: statistics, methods, and quality assurance

Treesearch

Patrick D. Miles; Ronald J. Piva; Charles J. Barnett

2011-01-01

The first full annual inventory of South Dakota's forests was completed in 2005 after 8,302 plots were selected and 325 forested plots were visited and measured. This report includes detailed information on forest inventory methods and data quality estimates. Important resource statistics are included in the tables. A detailed analysis of the South Dakota...

Path Analysis and Residual Plotting as Methods of Environmental Scanning in Higher Education: An Illustration with Applications and Enrollments.

ERIC Educational Resources Information Center

Morcol, Goktug; McLaughlin, Gerald W.

1990-01-01

The study proposes using path analysis and residual plotting as methods supporting environmental scanning in strategic planning for higher education institutions. Path models of three levels of independent variables are developed. Dependent variables measuring applications and enrollments at Virginia Polytechnic Institute and State University are…

A Simple Method for Reproducing Orbital Plots for Illustration Using Microsoft Paint and Microsoft Excel

NASA Astrophysics Data System (ADS)

Niebuhr, Cole

2018-04-01

Papers published in the astronomical community, particularly in the field of double star research, often contain plots that display the positions of the component stars relative to each other on a Cartesian coordinate plane. Due to the complexities of plotting a three-dimensional orbit into a two-dimensional image, it is often difficult to include an accurate reproduction of the orbit for comparison purposes. Methods to circumvent this obstacle do exist; however, many of these protocols result in low-quality blurred images or require specific and often expensive software. Here, a method is reported using Microsoft Paint and Microsoft Excel to produce high-quality images with an accurate reproduction of a partial orbit.

Recurrence Density Enhanced Complex Networks for Nonlinear Time Series Analysis

NASA Astrophysics Data System (ADS)

Costa, Diego G. De B.; Reis, Barbara M. Da F.; Zou, Yong; Quiles, Marcos G.; Macau, Elbert E. N.

We introduce a new method, which is entitled Recurrence Density Enhanced Complex Network (RDE-CN), to properly analyze nonlinear time series. Our method first transforms a recurrence plot into a figure of a reduced number of points yet preserving the main and fundamental recurrence properties of the original plot. This resulting figure is then reinterpreted as a complex network, which is further characterized by network statistical measures. We illustrate the computational power of RDE-CN approach by time series by both the logistic map and experimental fluid flows, which show that our method distinguishes different dynamics sufficiently well as the traditional recurrence analysis. Therefore, the proposed methodology characterizes the recurrence matrix adequately, while using a reduced set of points from the original recurrence plots.

The quartile benefit plot: a middle ear surgery benefit assessment scheme.

PubMed

Schmerber, Sébastien; Karkas, Alexandre; Righini, Christian A; Chahine, Karim A

2008-05-01

The purpose of this study is to present a new method for the assessment of hearing improvement following stapes surgery, taking into account additional, previously omitted evaluation criteria. Retrospective. A quartile plot, based on the currently used Glasgow benefit plot, is structured to include two additional criteria of hearing assessment, namely the absence of postoperative sensorineural hearing loss and the closure of the air-bone gap to <10 dB. Pre- and postoperative hearing results of 132 patients diagnosed with bilateral otosclerosis and treated with bilateral stapes surgery were plotted on both the classical Glasgow benefit plot and the new quartile benefit plot. The difference in success assessment due to stricter assessment criteria is demonstrated. Functional success rate following bilateral stapes surgery as plotted on the traditional Glasgow benefit plot was 51.5%. Success rate for bilateral stapes surgery assessed on the new quartile plot with the addition of the two new criteria was 38.64%. The difference in success rates was found to be statistically significant. The basis of benefit assessment in stapes surgery solely on the mean deficit in air conduction results in overestimation of success rate. This study demonstrates that results that appear satisfactory when judged by the Glasgow benefit plot are of modest success when assessed by the new quartile plot. The quartile benefit plot presented in this paper provides a strict measure of presentation and evaluation of stapes surgery results.

Automated matching of multiple terrestrial laser scans for stem mapping without the use of artificial references

NASA Astrophysics Data System (ADS)

Liu, Jingbin; Liang, Xinlian; Hyyppä, Juha; Yu, Xiaowei; Lehtomäki, Matti; Pyörälä, Jiri; Zhu, Lingli; Wang, Yunsheng; Chen, Ruizhi

2017-04-01

Terrestrial laser scanning has been widely used to analyze the 3D structure of a forest in detail and to generate data at the level of a reference plot for forest inventories without destructive measurements. Multi-scan terrestrial laser scanning is more commonly applied to collect plot-level data so that all of the stems can be detected and analyzed. However, it is necessary to match the point clouds of multiple scans to yield a point cloud with automated processing. Mismatches between datasets will lead to errors during the processing of multi-scan data. Classic registration methods based on flat surfaces cannot be directly applied in forest environments; therefore, artificial reference objects have conventionally been used to assist with scan matching. The use of artificial references requires additional labor and expertise, as well as greatly increasing the cost. In this study, we present an automated processing method for plot-level stem mapping that matches multiple scans without artificial references. In contrast to previous studies, the registration method developed in this study exploits the natural geometric characteristics among a set of tree stems in a plot and combines the point clouds of multiple scans into a unified coordinate system. Integrating multiple scans improves the overall performance of stem mapping in terms of the correctness of tree detection, as well as the bias and the root-mean-square errors of forest attributes such as diameter at breast height and tree height. In addition, the automated processing method makes stem mapping more reliable and consistent among plots, reduces the costs associated with plot-based stem mapping, and enhances the efficiency.

Texture Analysis of Recurrence Plots Based on Wavelets and PSO for Laryngeal Pathologies Detection.

PubMed

Souza, Taciana A; Vieira, Vinícius J D; Correia, Suzete E N; Costa, Silvana L N C; de A Costa, Washington C; Souza, Micael A

2015-01-01

This paper deals with the discrimination between healthy and pathological speech signals using recurrence plots and wavelet transform with texture features. Approximation and detail coefficients are obtained from the recurrence plots using Haar wavelet transform, considering one decomposition level. The considered laryngeal pathologies are: paralysis, Reinke's edema and nodules. Accuracy rates above 86% were obtained by means of the employed method.

Effects of hardwood retention, season of year, and landform on the perceived scenic beauty of forest plots in the Ouachita Mountains

Treesearch

James H. Gramann; Victor A. Rudis

1994-01-01

Results from a study of the within-stand visual effects of alternative reproduction cutting methods on 20 experimental plots in the Ouachita National Forest are presented. Treatments varied in their level of hardwood retention from complete suppression of hardwoods to retention of 30 ft2/acre of basal area. Using color transparency film, plots...

Dalitz Plot Analyses of B- to D+ Pi- Pi-, B+ to Pi+ Pi- Pi+ and D(S)+ to Pi+ Pi- Pi+ at BaBar

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

Dong, Liaoyuan; /Iowa State U.

We report on the Dalitz plot analyses of B{sup -} {yields} D{sup +}{pi}{sup -}{pi}{sup -}, B{sup +} {yields} {pi}{sup +}{pi}{sup -}{pi}{sup +} and D{sub s}{sup +} {yields} {pi}{sup +}{pi}{sup -}{sup +}. The Dalitz plot method and the most recent BABAR results are discussed.

Unbalanced and Minimal Point Equivalent Estimation Second-Order Split-Plot Designs

NASA Technical Reports Server (NTRS)

Parker, Peter A.; Kowalski, Scott M.; Vining, G. Geoffrey

2007-01-01

Restricting the randomization of hard-to-change factors in industrial experiments is often performed by employing a split-plot design structure. From an economic perspective, these designs minimize the experimental cost by reducing the number of resets of the hard-to- change factors. In this paper, unbalanced designs are considered for cases where the subplots are relatively expensive and the experimental apparatus accommodates an unequal number of runs per whole-plot. We provide construction methods for unbalanced second-order split- plot designs that possess the equivalence estimation optimality property, providing best linear unbiased estimates of the parameters; independent of the variance components. Unbalanced versions of the central composite and Box-Behnken designs are developed. For cases where the subplot cost approaches the whole-plot cost, minimal point designs are proposed and illustrated with a split-plot Notz design.

How to regress and predict in a Bland-Altman plot? Review and contribution based on tolerance intervals and correlated-errors-in-variables models.

PubMed

Francq, Bernard G; Govaerts, Bernadette

2016-06-30

Two main methodologies for assessing equivalence in method-comparison studies are presented separately in the literature. The first one is the well-known and widely applied Bland-Altman approach with its agreement intervals, where two methods are considered interchangeable if their differences are not clinically significant. The second approach is based on errors-in-variables regression in a classical (X,Y) plot and focuses on confidence intervals, whereby two methods are considered equivalent when providing similar measures notwithstanding the random measurement errors. This paper reconciles these two methodologies and shows their similarities and differences using both real data and simulations. A new consistent correlated-errors-in-variables regression is introduced as the errors are shown to be correlated in the Bland-Altman plot. Indeed, the coverage probabilities collapse and the biases soar when this correlation is ignored. Novel tolerance intervals are compared with agreement intervals with or without replicated data, and novel predictive intervals are introduced to predict a single measure in an (X,Y) plot or in a Bland-Atman plot with excellent coverage probabilities. We conclude that the (correlated)-errors-in-variables regressions should not be avoided in method comparison studies, although the Bland-Altman approach is usually applied to avert their complexity. We argue that tolerance or predictive intervals are better alternatives than agreement intervals, and we provide guidelines for practitioners regarding method comparison studies. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Refutational Text and Multiple External Representations as a Method to Remediate the Misinterpretation of Box Plots

ERIC Educational Resources Information Center

Lem, Stephanie; Baert, Kathy; Ceulemans, Eva; Onghena, Patrick; Verschaffel, Lieven; Van Dooren, Wim

2017-01-01

The ability to interpret graphs is highly important in modern society, but has proven to be a challenge for many people. In this paper, two teaching methods were used to remediate one specific misinterpretation: the area misinterpretation of box plots. First, we used refutational text to explicitly state and invalidate the area misinterpretation…

Measuring water and sediment discharge from a road plot with a settling basin and tipping bucket

Treesearch

Thomas A. Black; Charles H. Luce

2013-01-01

A simple empirical method quantifies water and sediment production from a forest road surface, and is well suited for calibration and validation of road sediment models. To apply this quantitative method, the hydrologic technician installs bordered plots on existing typical road segments and measures coarse sediment production in a settling tank. When a tipping bucket...

Measuring temperature-dependent activation energy in thermally activated processes: a 2D Arrhenius plot method.

PubMed

Li, Jian V; Johnston, Steven W; Yan, Yanfa; Levi, Dean H

2010-03-01

Thermally activated processes are characterized by two key quantities, activation energy (E(a)) and pre-exponential factor (nu(0)), which may be temperature dependent. The accurate measurement of E(a), nu(0), and their temperature dependence is critical for understanding the thermal activation mechanisms of non-Arrhenius processes. However, the classic 1D Arrhenius plot-based methods cannot unambiguously measure E(a), nu(0), and their temperature dependence due to the mathematical impossibility of resolving two unknown 1D arrays from one 1D experimental data array. Here, we propose a 2D Arrhenius plot method to solve this fundamental problem. Our approach measures E(a) at any temperature from matching the first and second moments of the data calculated with respect to temperature and rate in the 2D temperature-rate plane, and therefore is able to unambiguously solve E(a), nu(0), and their temperature dependence. The case study of deep level emission in a Cu(In,Ga)Se(2) solar cell using the 2D Arrhenius plot method reveals clear temperature dependent behavior of E(a) and nu(0), which has not been observable by its 1D predecessors.

Non-parametric and least squares Langley plot methods

NASA Astrophysics Data System (ADS)

Kiedron, P. W.; Michalsky, J. J.

2016-01-01

Langley plots are used to calibrate sun radiometers primarily for the measurement of the aerosol component of the atmosphere that attenuates (scatters and absorbs) incoming direct solar radiation. In principle, the calibration of a sun radiometer is a straightforward application of the Bouguer-Lambert-Beer law V = V0e-τ ṡ m, where a plot of ln(V) voltage vs. m air mass yields a straight line with intercept ln(V0). This ln(V0) subsequently can be used to solve for τ for any measurement of V and calculation of m. This calibration works well on some high mountain sites, but the application of the Langley plot calibration technique is more complicated at other, more interesting, locales. This paper is concerned with ferreting out calibrations at difficult sites and examining and comparing a number of conventional and non-conventional methods for obtaining successful Langley plots. The 11 techniques discussed indicate that both least squares and various non-parametric techniques produce satisfactory calibrations with no significant differences among them when the time series of ln(V0)'s are smoothed and interpolated with median and mean moving window filters.

The albatross plot: A novel graphical tool for presenting results of diversely reported studies in a systematic review.

PubMed

Harrison, Sean; Jones, Hayley E; Martin, Richard M; Lewis, Sarah J; Higgins, Julian P T

2017-09-01

Meta-analyses combine the results of multiple studies of a common question. Approaches based on effect size estimates from each study are generally regarded as the most informative. However, these methods can only be used if comparable effect sizes can be computed from each study, and this may not be the case due to variation in how the studies were done or limitations in how their results were reported. Other methods, such as vote counting, are then used to summarize the results of these studies, but most of these methods are limited in that they do not provide any indication of the magnitude of effect. We propose a novel plot, the albatross plot, which requires only a 1-sided P value and a total sample size from each study (or equivalently a 2-sided P value, direction of effect and total sample size). The plot allows an approximate examination of underlying effect sizes and the potential to identify sources of heterogeneity across studies. This is achieved by drawing contours showing the range of effect sizes that might lead to each P value for given sample sizes, under simple study designs. We provide examples of albatross plots using data from previous meta-analyses, allowing for comparison of results, and an example from when a meta-analysis was not possible. Copyright © 2017 The Authors. Research Synthesis Methods Published by John Wiley & Sons Ltd.

Volcano plots in analyzing differential expressions with mRNA microarrays.

PubMed

Li, Wentian

2012-12-01

A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray.

Method of Continuous Variations: Applications of Job Plots to the Study of Molecular Associations in Organometallic Chemistry[**

PubMed Central

Renny, Joseph S.; Tomasevich, Laura L.; Tallmadge, Evan H.; Collum, David B.

2014-01-01

Applications of the method of continuous variations—MCV or the Method of Job—to problems of interest to organometallic chemists are described. MCV provides qualitative and quantitative insights into the stoichiometries underlying association of m molecules of A and n molecules of B to form AmBn. Applications to complex ensembles probe associations that form metal clusters and aggregates. Job plots in which reaction rates are monitored provide relative stoichiometries in rate-limiting transition structures. In a specialized variant, ligand- or solvent-dependent reaction rates are dissected into contributions in both the ground states and transition states, which affords insights into the full reaction coordinate from a single Job plot. Gaps in the literature are identified and critiqued. PMID:24166797

A new graphic plot analysis for determination of neuroreceptor binding in positron emission tomography studies.

PubMed

Ito, Hiroshi; Yokoi, Takashi; Ikoma, Yoko; Shidahara, Miho; Seki, Chie; Naganawa, Mika; Takahashi, Hidehiko; Takano, Harumasa; Kimura, Yuichi; Ichise, Masanori; Suhara, Tetsuya

2010-01-01

In positron emission tomography (PET) studies with radioligands for neuroreceptors, tracer kinetics have been described by the standard two-tissue compartment model that includes the compartments of nondisplaceable binding and specific binding to receptors. In the present study, we have developed a new graphic plot analysis to determine the total distribution volume (V(T)) and nondisplaceable distribution volume (V(ND)) independently, and therefore the binding potential (BP(ND)). In this plot, Y(t) is the ratio of brain tissue activity to time-integrated arterial input function, and X(t) is the ratio of time-integrated brain tissue activity to time-integrated arterial input function. The x-intercept of linear regression of the plots for early phase represents V(ND), and the x-intercept of linear regression of the plots for delayed phase after the equilibrium time represents V(T). BP(ND) can be calculated by BP(ND)=V(T)/V(ND)-1. Dynamic PET scanning with measurement of arterial input function was performed on six healthy men after intravenous rapid bolus injection of [(11)C]FLB457. The plot yielded a curve in regions with specific binding while it yielded a straight line through all plot data in regions with no specific binding. V(ND), V(T), and BP(ND) values calculated by the present method were in good agreement with those by conventional non-linear least-squares fitting procedure. This method can be used to distinguish graphically whether the radioligand binding includes specific binding or not.

[Effect of comprehensive control and prevention for chronic disease in demonstration plot of Chongqing].

PubMed

Qi, Li; Ding, Xian-bin; Mao, De-qiang; Feng, Lian-gui; Wang, Yu-lin; Jiao, Yan; Zhang, Chun-hua; Lü, Xiao-yan; Li, Hong; Xia, Yi-yin

2013-03-01

To evaluate the effect of comprehensive control and prevention for chronic diseases in demonstration plot of Chongqing. Residents were enrolled through multi-stage stratified random sampling method from 17 districts or counties which had successfully established demonstration plots and 21 districts or counties which had not established demonstration plots (non-demonstration plot for short) yet on May, 2012. Questionnaire was designed to survey awareness of health knowledge, health behaviors and utilization of health supportive tools. The results were analyzed by SPSS 15.0 software. We investigated 15 108 residents, 6156 of which were in demonstration plot and others (8951) were not. The findings revealed the percentage of the people who were aware the national action of health lifestyle in demonstration plot and in non-demonstration plot were 44.4% (2734/6157) and 40.2% (3598/8951), respectively, and the awareness of the hypertension risk of too much sodium were 72.4% (4458/6156) and 67.5% (6042/8951), respectively, and the awareness of the cardinal vascular disease (CVD) risk of obesity and overweight were 77.2% (4753/6157) and 69.6% (6230/8951), respectively. About the residents' health behaviors in demonstration plot and in non-demonstration plot, the utilization rates of salt restriction scoop or pot were 23.5% (1447/6157) and 17.9% (1602/8951), and the utilization rates of oil restriction pot were 16.7% (1028/6157) and 11.8% (1064/8951), respectively. Totally, 33 of the 37 indexes were shown higher in demonstration plot than that in non-demonstration plot (P < 0.05). The chronic diseases comprehensive control and prevention in demonstration plot was more effective, and the remarkable improvement of health knowledge and behaviors level had been achieved in demonstration plot.

Dynamical density delay maps: simple, new method for visualising the behaviour of complex systems

PubMed Central

2014-01-01

Background Physiologic signals, such as cardiac interbeat intervals, exhibit complex fluctuations. However, capturing important dynamical properties, including nonstationarities may not be feasible from conventional time series graphical representations. Methods We introduce a simple-to-implement visualisation method, termed dynamical density delay mapping (“D3-Map” technique) that provides an animated representation of a system’s dynamics. The method is based on a generalization of conventional two-dimensional (2D) Poincaré plots, which are scatter plots where each data point, x(n), in a time series is plotted against the adjacent one, x(n + 1). First, we divide the original time series, x(n) (n = 1,…, N), into a sequence of segments (windows). Next, for each segment, a three-dimensional (3D) Poincaré surface plot of x(n), x(n + 1), h[x(n),x(n + 1)] is generated, in which the third dimension, h, represents the relative frequency of occurrence of each (x(n),x(n + 1)) point. This 3D Poincaré surface is then chromatised by mapping the relative frequency h values onto a colour scheme. We also generate a colourised 2D contour plot from each time series segment using the same colourmap scheme as for the 3D Poincaré surface. Finally, the original time series graph, the colourised 3D Poincaré surface plot, and its projection as a colourised 2D contour map for each segment, are animated to create the full “D3-Map.” Results We first exemplify the D3-Map method using the cardiac interbeat interval time series from a healthy subject during sleeping hours. The animations uncover complex dynamical changes, such as transitions between states, and the relative amount of time the system spends in each state. We also illustrate the utility of the method in detecting hidden temporal patterns in the heart rate dynamics of a patient with atrial fibrillation. The videos, as well as the source code, are made publicly available. Conclusions Animations based on density delay maps provide a new way of visualising dynamical properties of complex systems not apparent in time series graphs or standard Poincaré plot representations. Trainees in a variety of fields may find the animations useful as illustrations of fundamental but challenging concepts, such as nonstationarity and multistability. For investigators, the method may facilitate data exploration. PMID:24438439

Application of the new Cross Recurrence Plots to multivariate data

NASA Astrophysics Data System (ADS)

Thiel, M.; Romano, C.; Kurths, J.

2003-04-01

We extend and then apply the method of the new Cross Recurrence Plots (XRPs) to multivariate data. After introducing the new method we carry out an analysis of spatiotemporal ecological data. We compute not only the Rényi entropies and cross entropies by XRP, that allow to draw conclusions about the coupling of the systems, but also find a prediction horizon for intermediate time scales.

Impacts of sampling design and estimation methods on nutrient leaching of intensively monitored forest plots in the Netherlands.

PubMed

de Vries, W; Wieggers, H J J; Brus, D J

2010-08-05

Element fluxes through forest ecosystems are generally based on measurements of concentrations in soil solution at regular time intervals at plot locations sampled in a regular grid. Here we present spatially averaged annual element leaching fluxes in three Dutch forest monitoring plots using a new sampling strategy in which both sampling locations and sampling times are selected by probability sampling. Locations were selected by stratified random sampling with compact geographical blocks of equal surface area as strata. In each sampling round, six composite soil solution samples were collected, consisting of five aliquots, one per stratum. The plot-mean concentration was estimated by linear regression, so that the bias due to one or more strata being not represented in the composite samples is eliminated. The sampling times were selected in such a way that the cumulative precipitation surplus of the time interval between two consecutive sampling times was constant, using an estimated precipitation surplus averaged over the past 30 years. The spatially averaged annual leaching flux was estimated by using the modeled daily water flux as an ancillary variable. An important advantage of the new method is that the uncertainty in the estimated annual leaching fluxes due to spatial and temporal variation and resulting sampling errors can be quantified. Results of this new method were compared with the reference approach in which daily leaching fluxes were calculated by multiplying daily interpolated element concentrations with daily water fluxes and then aggregated to a year. Results show that the annual fluxes calculated with the reference method for the period 2003-2005, including all plots, elements and depths, lies only in 53% of the cases within the range of the average +/-2 times the standard error of the new method. Despite the differences in results, both methods indicate comparable N retention and strong Al mobilization in all plots, with Al leaching being nearly equal to the leaching of SO(4) and NO(3) with fluxes expressed in mol(c) ha(-1) yr(-1). This illustrates that Al release, which is the clearest signal of soil acidification, is mainly due to the external input of SO(4) and NO(3).

Estrogen Transport in Surface Runoff from Agricultural Fields Treated with Two Application Methods of Dairy Manure.

PubMed

Mina, Odette; Gall, Heather E; Saporito, Louis S; Kleinman, Peter J A

2016-11-01

This study compares two methods of dairy manure application-surface broadcast and shallow disk injection-on the fate and transport of natural estrogens in surface runoff from 12 field plots in central Pennsylvania. Ten natural surface runoff events were sampled over a 9-mo period after fall manure application. Results show that the range of estrogen concentrations observed in surface runoff from the broadcast plots was several orders of magnitude higher (>5000 ng L) than the concentrations in runoff from the shallow disk injection plots (<10 ng L). Additionally, the transport dynamics differed, with the majority of the estrogen loads from the surface broadcast plots occurring during the first rainfall event after application, whereas the majority of the loads from the shallow disk injection plots occurred more than 6 mo later during a hail storm event. Total estrogen loads were, on average, two orders of magnitude lower for shallow disk injection compared with surface broadcast. Independent of the method of manure application, 17α-estradiol and estrone were preserved in the field for as long as 9 mo after application. Overall, injection of manure shows promise in reducing the potential for off-site losses of hormones from manure-amended soils. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

The albatross plot: A novel graphical tool for presenting results of diversely reported studies in a systematic review

PubMed Central

Jones, Hayley E.; Martin, Richard M.; Lewis, Sarah J.; Higgins, Julian P.T.

2017-01-01

Abstract Meta‐analyses combine the results of multiple studies of a common question. Approaches based on effect size estimates from each study are generally regarded as the most informative. However, these methods can only be used if comparable effect sizes can be computed from each study, and this may not be the case due to variation in how the studies were done or limitations in how their results were reported. Other methods, such as vote counting, are then used to summarize the results of these studies, but most of these methods are limited in that they do not provide any indication of the magnitude of effect. We propose a novel plot, the albatross plot, which requires only a 1‐sided P value and a total sample size from each study (or equivalently a 2‐sided P value, direction of effect and total sample size). The plot allows an approximate examination of underlying effect sizes and the potential to identify sources of heterogeneity across studies. This is achieved by drawing contours showing the range of effect sizes that might lead to each P value for given sample sizes, under simple study designs. We provide examples of albatross plots using data from previous meta‐analyses, allowing for comparison of results, and an example from when a meta‐analysis was not possible. PMID:28453179

Nonideal isentropic gas flow through converging-diverging nozzles

NASA Technical Reports Server (NTRS)

Bober, W.; Chow, W. L.

1990-01-01

A method for treating nonideal gas flows through converging-diverging nozzles is described. The method incorporates the Redlich-Kwong equation of state. The Runge-Kutta method is used to obtain a solution. Numerical results were obtained for methane gas. Typical plots of pressure, temperature, and area ratios as functions of Mach number are given. From the plots, it can be seen that there exists a range of reservoir conditions that require the gas to be treated as nonideal if an accurate solution is to be obtained.

Implementation and Testing of Turbulence Models for the F18-HARV Simulation

NASA Technical Reports Server (NTRS)

Yeager, Jessie C.

1998-01-01

This report presents three methods of implementing the Dryden power spectral density model for atmospheric turbulence. Included are the equations which define the three methods and computer source code written in Advanced Continuous Simulation Language to implement the equations. Time-history plots and sample statistics of simulated turbulence results from executing the code in a test program are also presented. Power spectral densities were computed for sample sequences of turbulence and are plotted for comparison with the Dryden spectra. The three model implementations were installed in a nonlinear six-degree-of-freedom simulation of the High Alpha Research Vehicle airplane. Aircraft simulation responses to turbulence generated with the three implementations are presented as plots.

Automatic Extraction of Small Spatial Plots from Geo-Registered UAS Imagery

NASA Astrophysics Data System (ADS)

Cherkauer, Keith; Hearst, Anthony

2015-04-01

Accurate extraction of spatial plots from high-resolution imagery acquired by Unmanned Aircraft Systems (UAS), is a prerequisite for accurate assessment of experimental plots in many geoscience fields. If the imagery is correctly geo-registered, then it may be possible to accurately extract plots from the imagery based on their map coordinates. To test this approach, a UAS was used to acquire visual imagery of 5 ha of soybean fields containing 6.0 m2 plots in a complex planting scheme. Sixteen artificial targets were setup in the fields before flights and different spatial configurations of 0 to 6 targets were used as Ground Control Points (GCPs) for geo-registration, resulting in a total of 175 geo-registered image mosaics with a broad range of geo-registration accuracies. Geo-registration accuracy was quantified based on the horizontal Root Mean Squared Error (RMSE) of targets used as checkpoints. Twenty test plots were extracted from the geo-registered imagery. Plot extraction accuracy was quantified based on the percentage of the desired plot area that was extracted. It was found that using 4 GCPs along the perimeter of the field minimized the horizontal RMSE and enabled a plot extraction accuracy of at least 70%, with a mean plot extraction accuracy of 92%. The methods developed are suitable for work in many fields where replicates across time and space are necessary to quantify variability.

Determination of variability in leaf biomass densities of conifers and mixed conifers under different environmental conditions in the San Joaquin Valley air basin. Final report

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

Temple, P.J.; Mutters, R.J.; Adams, C.

1995-06-01

Biomass sampling plots were established at 29 locations within the dominant vegetation zones of the study area. Estimates of foliar biomass were made for each plot by three independent methods: regression analysis on the basis of tree diameter, calculation of the amount of light intercepted by the leaf canopy, and extrapolation from branch leaf area. Multivariate regression analysis was used to relate these foliar biomass estimates for oak plots and conifer plots to several independent predictor variables, including elevation, slope, aspect, temperature, precipitation, and soil chemical characteristics.

Electrical Arc Ignition Testing of Spacesuit Materials

NASA Technical Reports Server (NTRS)

Smith, Sarah; Gallus, Tim; Tapia, Susana; Ball, Elizabeth; Beeson, Harold

2006-01-01

A viewgraph presentation on electrical arc ignition testing of spacesuit materials is shown. The topics include: 1) Background; 2) Test Objectives; 3) Test Sample Materials; 4) Test Methods; 5) Scratch Test Objectives; 6) Cotton Scratch Test Video; 7) Scratch Test Results; 8) Entire Date Plot; 9) Closeup Data Plot; 10) Scratch Test Problems; 11) Poke Test Objectives; 12) Poke Test Results; 13) Poke Test Problems; 14) Wire-break Test Objectives; 15) Cotton Wire-Break Test Video; 16) High Speed Cotton Wire-break Test Video; 17) Typical Data Plot; 18) Closeup Data Plot; 19) Wire-break Test Results; 20) Wire-break Tests vs. Scratch Tests; 21) Urethane-coated Nylon; and 22) Moleskin.

CPdock: the complementarity plot for docking of proteins: implementing multi-dielectric continuum electrostatics.

PubMed

Basu, Sankar

2017-12-07

The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (S m , E m ) for amino acid side-chains buried within the protein interior or interface and plots them in a two-dimensional plot having knowledge-based probabilistic quality estimates for the residues as well as for the whole structure. The current report essentially presents an upgraded version of the plot with the implementation of the advanced multi-dielectric functionality (as in Delphi version 6.2 or higher) in the computation of electrostatic complementarity to make the validation tool physico-chemically more realistic. The two methods (single- and multi-dielectric) agree decently in their resultant E m values, and hence, provisions for both methods have been kept in the software suite. So to speak, the global electrostatic balance within a well-folded protein and/or a well-packed interface seems only marginally perturbed by the choice of different internal dielectric values. However, both from theoretical as well as practical grounds, the more advanced multi-dielectric version of the plot is certainly recommended for potentially producing more reliable results. The report also presents a new methodology and a variant plot, namely CP dock , based on the same principles of complementarity specifically designed to be used in the docking of proteins. The efficacy of the method to discriminate between good and bad docked protein complexes has been tested on a recent state-of-the-art docking benchmark. The results unambiguously indicate that CP dock can indeed be effective in the initial screening phase of a docking scoring pipeline before going into more sophisticated and computationally expensive scoring functions. CP dock has been made available at https://github.com/nemo8130/CPdock . Graphical Abstract An example showing the efficacy of CP dock to be used in the initial screening phase of a protein-protein docking scoring pipeline.

Evaluation of the Soil Conservation Service curve number methodology using data from agricultural plots

NASA Astrophysics Data System (ADS)

Lal, Mohan; Mishra, S. K.; Pandey, Ashish; Pandey, R. P.; Meena, P. K.; Chaudhary, Anubhav; Jha, Ranjit Kumar; Shreevastava, Ajit Kumar; Kumar, Yogendra

2017-01-01

The Soil Conservation Service curve number (SCS-CN) method, also known as the Natural Resources Conservation Service curve number (NRCS-CN) method, is popular for computing the volume of direct surface runoff for a given rainfall event. The performance of the SCS-CN method, based on large rainfall (P) and runoff (Q) datasets of United States watersheds, is evaluated using a large dataset of natural storm events from 27 agricultural plots in India. On the whole, the CN estimates from the National Engineering Handbook (chapter 4) tables do not match those derived from the observed P and Q datasets. As a result, the runoff prediction using former CNs was poor for the data of 22 (out of 24) plots. However, the match was little better for higher CN values, consistent with the general notion that the existing SCS-CN method performs better for high rainfall-runoff (high CN) events. Infiltration capacity (fc) was the main explanatory variable for runoff (or CN) production in study plots as it exhibited the expected inverse relationship between CN and fc. The plot-data optimization yielded initial abstraction coefficient (λ) values from 0 to 0.659 for the ordered dataset and 0 to 0.208 for the natural dataset (with 0 as the most frequent value). Mean and median λ values were, respectively, 0.030 and 0 for the natural rainfall-runoff dataset and 0.108 and 0 for the ordered rainfall-runoff dataset. Runoff estimation was very sensitive to λ and it improved consistently as λ changed from 0.2 to 0.03.

An alternative representation of the receptance: The 'elliptical plane' and its modal properties

NASA Astrophysics Data System (ADS)

Montalvão, Diogo; Amafabia, Daerefa-a. Mitsheal

2018-03-01

Modal Identification from Frequency Response Functions (FRFs) has been extensively investigated up to the point its research reached a stagnation state. Yet, a new approach to determine the modal damping factors from FRFs was recently proposed, showing that there still is scope for new findings in the field. Contrary to other modal identification methods which are based on the dynamic motion governing equations, the method used the dissipated energy per cycle of vibration as a starting point. For lightly damped systems with conveniently spaced modes, it produced quite accurate results, especially when compared to the well-known method of the inverse. The method used a plot of the sine of the phase of the receptance against its amplitude, whereby damping was determined from the slope of a linear fit to the resulting plot. In this paper, it is shown that this plot has other (perhaps more important) special properties that were not explored before. Near resonant frequencies, its shape is elliptical, whereby the real and imaginary parts of the modal constants can be determined from numerical curve-fitting. This finding allowed developing a new method which formulation is presented in this paper. The method is discussed through numerical and experimental examples. Although the intention is not to present a new modal identification method that is superior to other existing ones (like the method of the inverse or those based on the Nyquist plot), the authors believe that this new representation of the receptance and its properties may bring valuable insights for other researchers in the field.

Investigation into the Use of Normal and Half-Normal Plots for Interpreting Results from Screening Experiments.

DTIC Science & Technology

1987-03-25

by Lloyd (1952) using generalized least squares instead of ordinary least squares, and by Wilk, % 20 Gnanadesikan , and Freeny (1963) using a maximum...plot. The half-normal distribution is a special case of the gamma distribution proposed by Wilk, Gnanadesikan , and Huyett (1962). VARIATIONS ON THE... Gnanadesikan , R. Probability plotting methods for the analysis of data. Biometrika, 1968, 55, 1-17. This paper describes and discusses graphical techniques

Simpson's paradox visualized: The example of the Rosiglitazone meta-analysis

PubMed Central

Rücker, Gerta; Schumacher, Martin

2008-01-01

Background Simpson's paradox is sometimes referred to in the areas of epidemiology and clinical research. It can also be found in meta-analysis of randomized clinical trials. However, though readers are able to recalculate examples from hypothetical as well as real data, they may have problems to easily figure where it emerges from. Method First, two kinds of plots are proposed to illustrate the phenomenon graphically, a scatter plot and a line graph. Subsequently, these can be overlaid, resulting in a overlay plot. The plots are applied to the recent large meta-analysis of adverse effects of rosiglitazone on myocardial infarction and to an example from the literature. A large set of meta-analyses is screened for further examples. Results As noted earlier by others, occurrence of Simpson's paradox in the meta-analytic setting, if present, is associated with imbalance of treatment arm size. This is well illustrated by the proposed plots. The rosiglitazone meta-analysis shows an effect reversion if all trials are pooled. In a sample of 157 meta-analyses, nine showed an effect reversion after pooling, though non-significant in all cases. Conclusion The plots give insight on how the imbalance of trial arm size works as a confounder, thus producing Simpson's paradox. Readers can see why meta-analytic methods must be used and what is wrong with simple pooling. PMID:18513392

An evaluation of rapid methods for monitoring vegetation characteristics of wetland bird habitat

USGS Publications Warehouse

Tavernia, Brian G.; Lyons, James E.; Loges, Brian W.; Wilson, Andrew; Collazo, Jaime A.; Runge, Michael C.

2016-01-01

Wetland managers benefit from monitoring data of sufficient precision and accuracy to assess wildlife habitat conditions and to evaluate and learn from past management decisions. For large-scale monitoring programs focused on waterbirds (waterfowl, wading birds, secretive marsh birds, and shorebirds), precision and accuracy of habitat measurements must be balanced with fiscal and logistic constraints. We evaluated a set of protocols for rapid, visual estimates of key waterbird habitat characteristics made from the wetland perimeter against estimates from (1) plots sampled within wetlands, and (2) cover maps made from aerial photographs. Estimated percent cover of annuals and perennials using a perimeter-based protocol fell within 10 percent of plot-based estimates, and percent cover estimates for seven vegetation height classes were within 20 % of plot-based estimates. Perimeter-based estimates of total emergent vegetation cover did not differ significantly from cover map estimates. Post-hoc analyses revealed evidence for observer effects in estimates of annual and perennial covers and vegetation height. Median time required to complete perimeter-based methods was less than 7 percent of the time needed for intensive plot-based methods. Our results show that rapid, perimeter-based assessments, which increase sample size and efficiency, provide vegetation estimates comparable to more intensive methods.

DON'T BE TRICKED BY YOUR INTEGRATED RATE PLOT!

EPA Science Inventory

Reaction order can be determined from kinetic data in a variety of ways. Two methods commonly employed are comparison of initial rates (while varying reactant concentration) and plotting integrated rate expressions. Both of these are introduced in general and physical chemistry t...

Quantification of the vertical translocation rate of soil solid-phase material by the magnetic tracer method

NASA Astrophysics Data System (ADS)

Zhidkin, A. P.; Gennadiev, A. N.

2016-07-01

Approaches to the quantification of the vertical translocation rate of soil solid-phase material by the magnetic tracer method have been developed; the tracer penetration depth and rate have been determined, as well as the radial distribution of the tracer in chernozems (Chernozems) and dark gray forest soils (Luvisols) of Belgorod oblast under natural steppe and forest vegetation and in arable lands under agricultural use of different durations. It has been found that the penetration depth of spherical magnetic particles (SMPs) during their 150-year-occurrence in soils of a forest plot is 68 cm under forest, 58 cm on a 100-year old plowland, and only 49 cm on a 150-year-old plowland. In the chernozems of the steppe plot, the penetration depth of SMPs exceeds the studied depth of 70 cm both under natural vegetation and on the plowlands. The penetration rates of SMPs deep into the soil vary significantly among the key plots: 0.92-1.32 mm/year on the forest plot and 1.47-1.63 mm/year on the steppe plot, probably because of the more active recent turbation activity of soil animals.

A new method for estimating the demographic history from DNA sequences: an importance sampling approach

PubMed Central

Ait Kaci Azzou, Sadoune; Larribe, Fabrice; Froda, Sorana

2015-01-01

The effective population size over time (demographic history) can be retraced from a sample of contemporary DNA sequences. In this paper, we propose a novel methodology based on importance sampling (IS) for exploring such demographic histories. Our starting point is the generalized skyline plot with the main difference being that our procedure, skywis plot, uses a large number of genealogies. The information provided by these genealogies is combined according to the IS weights. Thus, we compute a weighted average of the effective population sizes on specific time intervals (epochs), where the genealogies that agree more with the data are given more weight. We illustrate by a simulation study that the skywis plot correctly reconstructs the recent demographic history under the scenarios most commonly considered in the literature. In particular, our method can capture a change point in the effective population size, and its overall performance is comparable with the one of the bayesian skyline plot. We also introduce the case of serially sampled sequences and illustrate that it is possible to improve the performance of the skywis plot in the case of an exponential expansion of the effective population size. PMID:26300910

The isometric log-ratio (ilr)-ion plot: A proposed alternative to the Piper diagram

USGS Publications Warehouse

Shelton, Jenna L.; Engle, Mark A.; Buccianti, Antonella; Blondes, Madalyn S.

2018-01-01

The Piper diagram has been a staple for the analysis of water chemistry data since its introduction in 1944. It was conceived to be a method for water classification, determination of potential water mixing between end-members, and to aid in the identification of chemical reactions controlling a sample set. This study uses the information gleaned over the years since the release of the Piper diagram and proposes an alternative to it, capturing the strengths of the original diagram while adding new ideas to increase its robustness. The new method uses compositional data analysis to create 4 isometric log-ratio coordinates for the 6 major chemical species analyzed in the Piper diagram and transforms the data to a 4-field bi-plot, the ilr-ion plot. This ilr-ion plot conveys all of the information in the Piper diagram (water mixing, water types, and chemical reactions) while also visualizing additional data, the ability to examine Ca2+/Mg2+ versus Cl-/SO42−. The Piper and the ilr-ion plot were also compared using multiple synthetic and real datasets in order to illustrate the caveats and the advantages of using either diagram to analyze water chemistry data. Although there are challenges with using the ilr-ion plot (e.g., missing or zero values zeros in the dataset must be imputed by positive real numbers), it appears that the use of compositional data analysis coupled with the ilr-ion plot provides a more in-depth and complete analysis of water quality data compared to the original Piper diagram.

Using volcano plots and regularized-chi statistics in genetic association studies.

PubMed

Li, Wentian; Freudenberg, Jan; Suh, Young Ju; Yang, Yaning

2014-02-01

Labor intensive experiments are typically required to identify the causal disease variants from a list of disease associated variants in the genome. For designing such experiments, candidate variants are ranked by their strength of genetic association with the disease. However, the two commonly used measures of genetic association, the odds-ratio (OR) and p-value may rank variants in different order. To integrate these two measures into a single analysis, here we transfer the volcano plot methodology from gene expression analysis to genetic association studies. In its original setting, volcano plots are scatter plots of fold-change and t-test statistic (or -log of the p-value), with the latter being more sensitive to sample size. In genetic association studies, the OR and Pearson's chi-square statistic (or equivalently its square root, chi; or the standardized log(OR)) can be analogously used in a volcano plot, allowing for their visual inspection. Moreover, the geometric interpretation of these plots leads to an intuitive method for filtering results by a combination of both OR and chi-square statistic, which we term "regularized-chi". This method selects associated markers by a smooth curve in the volcano plot instead of the right-angled lines which corresponds to independent cutoffs for OR and chi-square statistic. The regularized-chi incorporates relatively more signals from variants with lower minor-allele-frequencies than chi-square test statistic. As rare variants tend to have stronger functional effects, regularized-chi is better suited to the task of prioritization of candidate genes. Copyright © 2013 Elsevier Ltd. All rights reserved.

NASCAP user's manual

NASA Technical Reports Server (NTRS)

Mandell, M. J.; Harvey, J. M.; Katz, I.

1977-01-01

The NASCAP (NASA Charging Analyzer Program) code simulates the charging process for a complex object in either tenuous plasma or ground test environment. Detailed specifications needed to run the code are presented. The object definition section, OBJDEF, allows the test object to be easily defined in the cubic mesh. The test object is composed of conducting sections which may be wholly or partially covered with thin dielectric coatings. The potential section, POTENT, obtains the electrostatic potential in the space surrounding the object. It uses the conjugate gradient method to solve the finite element formulation of Poisson's equation. The CHARGE section of NASCAP treats charge redistribution among the surface cells of the object as well as charging through radiation bombardment. NASCAP has facilities for extensive graphical output, including several types of object display plots, potential contour plots, space charge density contour plots, current density plots, and particle trajectory plots.

How Should Blood Glucose Meter System Analytical Performance Be Assessed?

PubMed

Simmons, David A

2015-08-31

Blood glucose meter system analytical performance is assessed by comparing pairs of meter system and reference instrument blood glucose measurements measured over time and across a broad array of glucose values. Consequently, no single, complete, and ideal parameter can fully describe the difference between meter system and reference results. Instead, a number of assessment tools, both graphical (eg, regression plots, modified Bland-Altman plots, and error grid analysis) and tabular (eg, International Organization for Standardization guidelines, mean absolute difference, and mean absolute relative difference) have been developed to evaluate meter system performance. The strengths and weaknesses of these methods of presenting meter system performance data, including a new method known as Radar Plots, are described here. © 2015 Diabetes Technology Society.

Method and apparatus for determining minority carrier diffusion length in semiconductors

DOEpatents

Goldstein, Bernard; Dresner, Joseph; Szostak, Daniel J.

1983-07-12

Method and apparatus are provided for determining the diffusion length of minority carriers in semiconductor material, particularly amorphous silicon which has a significantly small minority carrier diffusion length using the constant-magnitude surface-photovoltage (SPV) method. An unmodulated illumination provides the light excitation on the surface of the material to generate the SPV. A manually controlled or automatic servo system maintains a constant predetermined value of the SPV. A vibrating Kelvin method-type probe electrode couples the SPV to a measurement system. The operating optical wavelength of an adjustable monochromator to compensate for the wavelength dependent sensitivity of a photodetector is selected to measure the illumination intensity (photon flux) on the silicon. Measurements of the relative photon flux for a plurality of wavelengths are plotted against the reciprocal of the optical absorption coefficient of the material. A linear plot of the data points is extrapolated to zero intensity. The negative intercept value on the reciprocal optical coefficient axis of the extrapolated linear plot is the diffusion length of the minority carriers.

Extended quantification of the generalized recurrence plot

NASA Astrophysics Data System (ADS)

Riedl, Maik; Marwan, Norbert; Kurths, Jürgen

2016-04-01

The generalized recurrence plot is a modern tool for quantification of complex spatial patterns. Its application spans the analysis of trabecular bone structures, Turing structures, turbulent spatial plankton patterns, and fractals. But, it is also successfully applied to the description of spatio-temporal dynamics and the detection of regime shifts, such as in the complex Ginzburg-Landau- equation. The recurrence plot based determinism is a central measure in this framework quantifying the level of regularities in temporal and spatial structures. We extend this measure for the generalized recurrence plot considering additional operations of symmetry than the simple translation. It is tested not only on two-dimensional regular patterns and noise but also on complex spatial patterns reconstructing the parameter space of the complex Ginzburg-Landau-equation. The extended version of the determinism resulted in values which are consistent to the original recurrence plot approach. Furthermore, the proposed method allows a split of the determinism into parts which based on laminar and non-laminar regions of the two-dimensional pattern of the complex Ginzburg-Landau-equation. A comparison of these parts with a standard method of image classification, the co-occurrence matrix approach, shows differences especially in the description of patterns associated with turbulence. In that case, it seems that the extended version of the determinism allows a distinction of phase turbulence and defect turbulence by means of their spatial patterns. This ability of the proposed method promise new insights in other systems with turbulent dynamics coming from climatology, biology, ecology, and social sciences, for example.

Metaplot: A Novel Stata Graph for Assessing Heterogeneity at a Glance

PubMed Central

Poorolajal, J; Mahmoodi, M; Majdzadeh, R; Fotouhi, A

2010-01-01

Background: Heterogeneity is usually a major concern in meta-analysis. Although there are some statistical approaches for assessing variability across studies, here we present a new approach to heterogeneity using “MetaPlot” that investigate the influence of a single study on the overall heterogeneity. Methods: MetaPlot is a two-way (x, y) graph, which can be considered as a complementary graphical approach for testing heterogeneity. This method shows graphically as well as numerically the results of an influence analysis, in which Higgins’ I2 statistic with 95% (Confidence interval) CI are computed omitting one study in each turn and then are plotted against reciprocal of standard error (1/SE) or “precision”. In this graph, “1/SE” lies on x axis and “I2 results” lies on y axe. Results: Having a first glance at MetaPlot, one can predict to what extent omission of a single study may influence the overall heterogeneity. The precision on x-axis enables us to distinguish the size of each trial. The graph describes I2 statistic with 95% CI graphically as well as numerically in one view for prompt comparison. It is possible to implement MetaPlot for meta-analysis of different types of outcome data and summary measures. Conclusion: This method presents a simple graphical approach to identify an outlier and its effect on overall heterogeneity at a glance. We wish to suggest MetaPlot to Stata experts to prepare its module for the software. PMID:23113013

Zipper plot: visualizing transcriptional activity of genomic regions.

PubMed

Avila Cobos, Francisco; Anckaert, Jasper; Volders, Pieter-Jan; Everaert, Celine; Rombaut, Dries; Vandesompele, Jo; De Preter, Katleen; Mestdagh, Pieter

2017-05-02

Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA (lncRNA) annotation are mainly based on evolutionary constraints, which may result in false negatives due to the overall limited conservation of lncRNAs. To tackle this problem we have developed the Zipper plot, a novel visualization and analysis method that enables users to simultaneously interrogate thousands of human putative transcription start sites (TSSs) in relation to various features that are indicative for transcriptional activity. These include publicly available CAGE-sequencing, ChIP-sequencing and DNase-sequencing datasets. Our method only requires three tab-separated fields (chromosome, genomic coordinate of the TSS and strand) as input and generates a report that includes a detailed summary table, a Zipper plot and several statistics derived from this plot. Using the Zipper plot, we found evidence of transcription for a set of well-characterized lncRNAs and observed that fewer mono-exonic lncRNAs have CAGE peaks overlapping with their TSSs compared to multi-exonic lncRNAs. Using publicly available RNA-seq data, we found more than one hundred cases where junction reads connected protein-coding gene exons with a downstream mono-exonic lncRNA, revealing the need for a careful evaluation of lncRNA 5'-boundaries. Our method is implemented using the statistical programming language R and is freely available as a webtool.

Comparison of visual-based helicopter and fixed-wing forward-looking infrared surveys for counting white-tailed deer Odocoileus virginianus

USGS Publications Warehouse

Storm, Daniel J.; Samuel, Michael D.; Van Deelen, Timothy R.; Malcolm, Karl D.; Rolley, Robert E.; Frost, Nancy A.; Bates, Donald P.; Richards, Bryan J.

2011-01-01

Aerial surveys using direct counts of animals are commonly used to estimate deer abundance. Forward-looking infrared (FLIR) technology is increasingly replacing traditional methods such as visual observation from helicopters. Our goals were to compare fixed-wing FLIR and visual, helicopter-based counts in terms of relative bias, influence of snow cover and cost. We surveyed five plots: four 41.4 km2 plots with free-ranging white-tailed deer Odocoileus virginianus populations in Wisconsin and a 5.3 km2 plot with a white-tailed deer population contained by a high fence in Michigan. We surveyed plots using both fixed-wing FLIR and helicopters, both with snow cover and without snow. None of the methods counted more deer than the other when snow was present. Helicopter counts were lower in the absence of snow, but lack of snow cover did not apparently affect FLIR. Group sizes of observed deer were similar regardless of survey method or season. We found that FLIR counts were generally precise (CV = 0.089) when two or three replicate surveys were conducted within a few hours. However, at the plot level, FLIR counts differed greatly between seasons, suggesting that detection rates vary over larger time scales. Fixed-wing FLIR was more costly than visual observers in helicopters and was more restrictive in terms of acceptable survey conditions. Further research is needed to understand what factors influence the detection of deer during FLIR surveys.

Analytical Determination of Fluoride Ion Using Gran's Semi-Antilog Plot.

ERIC Educational Resources Information Center

Barnhard, Ralph J.

1983-01-01

A quantitative determination for fluoride ion using a commercially available fluoride electrode is described. The procedure referred to as known-addition is employed with the data processed on Gran's Plot Paper. Background information, experimental procedures, and advantages/disadvantages of the method are discussed. (JN)

Newer developments on self-modeling curve resolution implementing equality and unimodality constraints.

PubMed

Beyramysoltan, Samira; Abdollahi, Hamid; Rajkó, Róbert

2014-05-27

Analytical self-modeling curve resolution (SMCR) methods resolve data sets to a range of feasible solutions using only non-negative constraints. The Lawton-Sylvestre method was the first direct method to analyze a two-component system. It was generalized as a Borgen plot for determining the feasible regions in three-component systems. It seems that a geometrical view is required for considering curve resolution methods, because the complicated (only algebraic) conceptions caused a stop in the general study of Borgen's work for 20 years. Rajkó and István revised and elucidated the principles of existing theory in SMCR methods and subsequently introduced computational geometry tools for developing an algorithm to draw Borgen plots in three-component systems. These developments are theoretical inventions and the formulations are not always able to be given in close form or regularized formalism, especially for geometric descriptions, that is why several algorithms should have been developed and provided for even the theoretical deductions and determinations. In this study, analytical SMCR methods are revised and described using simple concepts. The details of a drawing algorithm for a developmental type of Borgen plot are given. Additionally, for the first time in the literature, equality and unimodality constraints are successfully implemented in the Lawton-Sylvestre method. To this end, a new state-of-the-art procedure is proposed to impose equality constraint in Borgen plots. Two- and three-component HPLC-DAD data set were simulated and analyzed by the new analytical curve resolution methods with and without additional constraints. Detailed descriptions and explanations are given based on the obtained abstract spaces. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparison of Rain-Fast Bait Stations Versus Foliar Bait Sprays for Control of Oriental Fruit Fly, Bactrocera dorsalis, in Papaya Orchards in Hawaii

PubMed Central

Piñero, Jaime C.; Mau, Ronald F. L.; Vargas, Roger I.

2010-01-01

Bait stations represent an environmentally friendly attract-and-kill approach to fruit fly population suppression. Recently a novel, visually attractive, rain-fast bait station was developed in Hawaii for potential use against multiple species of pestiferous fruit flies. Here, we compared the efficacy of GF-120 NF Naturalyte Fruit Fly Bait applied either as foliar sprays or onto bait stations in reducing female oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), population density and level of fruit infestation in commercial papaya orchards in Hawaii. Trapping and infestation data were used as indicators of the effectiveness of the two bait application methods. For the first 10 weeks of the study, captures of female B. dorsalis in monitoring traps were significantly greater in control plots than in plots treated with foliar sprays or bait stations. Six weeks after the first bait spray, incidence of infestation (i.e. number of fruit with one or more B. dorsalis larvae) of quarter to half-ripe papaya fruit was reduced by 71.4% and 63.1% for plots with bait stations and foliar sprays, respectively, as compared to control plots. Twelve weeks after first spray, incidence of infestation was reduced by only 54.5% and 45.4% for plots with bait stations and foliar sprays, respectively, as compared to control plots. About 42% less GF-120 was used in orchard plots with bait stations compared to those subject to foliar sprays. The impact of field sanitation on the outcome is also discussed. The results indicate that bait stations can provide a simple, efficient, and economical method of applying insecticidal baits to control fruit flies and a safer alternative to foliar sprays. PMID:21067423

Metaplot: a novel stata graph for assessing heterogeneity at a glance.

PubMed

Poorolajal, J; Mahmoodi, M; Majdzadeh, R; Fotouhi, A

2010-01-01

Heterogeneity is usually a major concern in meta-analysis. Although there are some statistical approaches for assessing variability across studies, here we present a new approach to heterogeneity using "MetaPlot" that investigate the influence of a single study on the overall heterogeneity. MetaPlot is a two-way (x, y) graph, which can be considered as a complementary graphical approach for testing heterogeneity. This method shows graphically as well as numerically the results of an influence analysis, in which Higgins' I(2) statistic with 95% (Confidence interval) CI are computed omitting one study in each turn and then are plotted against reciprocal of standard error (1/SE) or "precision". In this graph, "1/SE" lies on x axis and "I(2) results" lies on y axe. Having a first glance at MetaPlot, one can predict to what extent omission of a single study may influence the overall heterogeneity. The precision on x-axis enables us to distinguish the size of each trial. The graph describes I(2) statistic with 95% CI graphically as well as numerically in one view for prompt comparison. It is possible to implement MetaPlot for meta-analysis of different types of outcome data and summary measures. This method presents a simple graphical approach to identify an outlier and its effect on overall heterogeneity at a glance. We wish to suggest MetaPlot to Stata experts to prepare its module for the software.

QUESPOWR MRI: QUantification of Exchange as a function of Saturation Power On the Water Resonance

PubMed Central

Randtke, Edward A.; Pagel, Mark D.; Cárdenas-Rodríguez, Julio

2018-01-01

QUantification of Exchange as a function of Saturation Power On the Water Resonance (QUESPOWR) MRI is a new method that can estimate chemical exchange rates. This method acquires a series of OPARACHEE MRI acquisitions with a range of RF powers for the WALTZ16* pulse train, which are applied on the water resonance. A QUESPOWR plot can be generated from the power dependence of the % water signal, which is similar to a QUESP plot that is generated from CEST MRI acquisition methods with RF saturation applied off-resonance from water. A QUESPOWR plot can be quantitatively analyzed using linear fitting methods to provide estimates of average chemical exchange rates. Analyses of the shapes of QUESPOWR plots can also be used to estimate relative differences in average chemical exchange rates and concentrations of biomolecules. The performance of QUESPOWR MRI was assessed via simulations, an in vitro study with iopamidol, and an in vivo study with a mouse model of mammary carcinoma. The results showed that QUESPOWR MRI is especially sensitive to chemical exchange between water and biomolecules that have intermediate to fast chemical exchange rates and chemical shifts that are close to water, which are notoriously difficult to assess with other CEST MRI methods. In addition, in vivo QUESPOWR MRI detected acidic tumor tissues relative to normal tissues that are pH-neutral, and therefore may be a new paradigm for tumor detection with MRI. PMID:27404128

Application of GPS and Near-Surface Geophysical Methods to Evaluate Agricultural Test Plot Differences

USDA-ARS?s Scientific Manuscript database

A field research facility with two pairs of replicated agricultural test plots (four total) was established at a location in northwest Ohio during 2005 for the purpose of studying water table management strategies. Initial efforts at this field research facility were devoted to evaluating difference...

Michigan's forests, 2004: statistics and quality assurance

Treesearch

Scott A. Pugh; Mark H. Hansen; Gary Brand; Ronald E. McRoberts

2010-01-01

The first annual inventory of Michigan's forests was completed in 2004 after 18,916 plots were selected and 10,355 forested plots were visited. This report includes detailed information on forest inventory methods, quality of estimates, and additional tables. An earlier publication presented analyses of the inventoried data (Pugh et al. 2009).

A note on the generation of phase plane plots on a digital computer. [for solution of nonlinear differential equations

NASA Technical Reports Server (NTRS)

Simon, M. K.

1980-01-01

A technique is presented for generating phase plane plots on a digital computer which circumvents the difficulties associated with more traditional methods of numerical solving nonlinear differential equations. In particular, the nonlinear differential equation of operation is formulated.

Methods of cutting ponderosa pine in the Southwest - Establishment report: Even-aged yield study, Plot 11

Treesearch

Gilbert H. Schubert

1963-01-01

The objectie of the study is to obtain information on the growth and yield of even-aged stands of different stocking levels. The plot will also serve as the start of a detailed growing stock study for the ponderosa pine region.

Plotting landscape perspectives of clearcut units.

Treesearch

Roger H. Twito

1978-01-01

The aesthetics of clearcut units potentially visible from a distance can be improved by judicious design. Screening clearcuts from view or shaping them to characterize natural openings are current methods used for this purpose. Perspective plots illustrating how proposed clearcut units will look from specific off-site viewing points provide an...

Plot Description (PD)

Treesearch

Robert E. Keane

2006-01-01

The Plot Description (PD) form is used to describe general characteristics of the FIREMON macroplot to provide ecological context for data analyses. The PD data characterize the topographical setting, geographic reference point, general plant composition and cover, ground cover, fuels, and soils information. This method provides the general ecological data that can be...

Plotit-method of interactively plotting input data for the vorlax computer program. [computerized aircraft configuration design

NASA Technical Reports Server (NTRS)

Denn, F. M.

1978-01-01

Geometric input plotting to the VORLAX computer program by means of an interactive remote terminal is reported. The software consists of a procedure file and two programs. The programs and procedure file are described and a sample execution is presented.

Normal probability plots with confidence.

PubMed

Chantarangsi, Wanpen; Liu, Wei; Bretz, Frank; Kiatsupaibul, Seksan; Hayter, Anthony J; Wan, Fang

2015-01-01

Normal probability plots are widely used as a statistical tool for assessing whether an observed simple random sample is drawn from a normally distributed population. The users, however, have to judge subjectively, if no objective rule is provided, whether the plotted points fall close to a straight line. In this paper, we focus on how a normal probability plot can be augmented by intervals for all the points so that, if the population distribution is normal, then all the points should fall into the corresponding intervals simultaneously with probability 1-α. These simultaneous 1-α probability intervals provide therefore an objective mean to judge whether the plotted points fall close to the straight line: the plotted points fall close to the straight line if and only if all the points fall into the corresponding intervals. The powers of several normal probability plot based (graphical) tests and the most popular nongraphical Anderson-Darling and Shapiro-Wilk tests are compared by simulation. Based on this comparison, recommendations are given in Section 3 on which graphical tests should be used in what circumstances. An example is provided to illustrate the methods. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Change of physical and chemical composition of soil washing out during vegetation season from differently used fields

NASA Astrophysics Data System (ADS)

Baryła, A.; Pierzgalski, E.; Karczmarczyk, A.

2009-04-01

oil losses due to water erosion not only decrease of soil fertility but also influence on pollution of water bodies. One of the method for limitation of water erosion process is protected soil management and choose suitable plants which requires knowledge about effect and mechanism of erosion under different environmental conditions. The results of measurements of quantity and quality of soil losses from three experimental plots are given in the article. Plots were located in Experimental Agricultural Station Puczniew in central part of Poland. Surface soil layer on the plots had mechanical composition of medium loam soil. On two plots grass and barley were planted. Third plot was used as fallow and tilled land. Measurements were carried out four times in the period May-October 2007. Physical and chemical composition of washed soil material was analyzed.

Gene features selection for three-class disease classification via multiple orthogonal partial least square discriminant analysis and S-plot using microarray data.

PubMed

Yang, Mingxing; Li, Xiumin; Li, Zhibin; Ou, Zhimin; Liu, Ming; Liu, Suhuan; Li, Xuejun; Yang, Shuyu

2013-01-01

DNA microarray analysis is characterized by obtaining a large number of gene variables from a small number of observations. Cluster analysis is widely used to analyze DNA microarray data to make classification and diagnosis of disease. Because there are so many irrelevant and insignificant genes in a dataset, a feature selection approach must be employed in data analysis. The performance of cluster analysis of this high-throughput data depends on whether the feature selection approach chooses the most relevant genes associated with disease classes. Here we proposed a new method using multiple Orthogonal Partial Least Squares-Discriminant Analysis (mOPLS-DA) models and S-plots to select the most relevant genes to conduct three-class disease classification and prediction. We tested our method using Golub's leukemia microarray data. For three classes with subtypes, we proposed hierarchical orthogonal partial least squares-discriminant analysis (OPLS-DA) models and S-plots to select features for two main classes and their subtypes. For three classes in parallel, we employed three OPLS-DA models and S-plots to choose marker genes for each class. The power of feature selection to classify and predict three-class disease was evaluated using cluster analysis. Further, the general performance of our method was tested using four public datasets and compared with those of four other feature selection methods. The results revealed that our method effectively selected the most relevant features for disease classification and prediction, and its performance was better than that of the other methods.

The effect of poultry manure application rate and AlCl(3) treatment on bacterial fecal indicators in runoff.

PubMed

Brooks, J P; Adeli, A; McLaughlin, M R; Miles, D M

2012-12-01

Increasing costs associated with inorganic fertilizer have led to widespread use of broiler litter. Proper land application, typically limiting nutrient loss, is essential to protect surface water. This study was designed to evaluate litter-borne microbial runoff (heterotrophic plate count bacteria, staphylococci, Escherichia coli, enterococci, and Clostridium perfringens) while applying typical nutrient-control methods. Field studies were conducted in which plots with high and low litter rates, inorganic fertilizer, AlCl(3)-treated litter, and controls were rained on five times using a rain generator. Overall, microbial runoff from poultry litter applied plots was consistently greater (2-5 log(10) plot(-1)) than controls. No appreciable effect on microbial runoff was noted from variable litter application rate or AlCl(3) treatments, though rain event, not time, significantly affected runoff load. C. perfringens and staphylococci runoff were consistently associated with poultry litter application, during early rain events, while other indicators were unreliable. Large microbial runoff pulses were observed, ranging from 10(2) to 10(10) CFU plot(-1); however, only a small fraction of litter-borne microbes were recoverable in runoff. This study indicated that microbial runoff from litter-applied plots can be substantial, and that methods intended to reduce nutrient losses do not necessarily reduce microbial runoff.

Strategies for minimizing sample size for use in airborne LiDAR-based forest inventory

USGS Publications Warehouse

Junttila, Virpi; Finley, Andrew O.; Bradford, John B.; Kauranne, Tuomo

2013-01-01

Recently airborne Light Detection And Ranging (LiDAR) has emerged as a highly accurate remote sensing modality to be used in operational scale forest inventories. Inventories conducted with the help of LiDAR are most often model-based, i.e. they use variables derived from LiDAR point clouds as the predictive variables that are to be calibrated using field plots. The measurement of the necessary field plots is a time-consuming and statistically sensitive process. Because of this, current practice often presumes hundreds of plots to be collected. But since these plots are only used to calibrate regression models, it should be possible to minimize the number of plots needed by carefully selecting the plots to be measured. In the current study, we compare several systematic and random methods for calibration plot selection, with the specific aim that they be used in LiDAR based regression models for forest parameters, especially above-ground biomass. The primary criteria compared are based on both spatial representativity as well as on their coverage of the variability of the forest features measured. In the former case, it is important also to take into account spatial auto-correlation between the plots. The results indicate that choosing the plots in a way that ensures ample coverage of both spatial and feature space variability improves the performance of the corresponding models, and that adequate coverage of the variability in the feature space is the most important condition that should be met by the set of plots collected.

Mayday - integrative analytics for expression data

PubMed Central

2010-01-01

Background DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. Results We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved. Conclusions We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension possibilities using compiled plugins and ad-hoc scripting allow for the rapid adaption of Mayday also to very specialized data exploration. Mayday is available at http://microarray-analysis.org. PMID:20214778

Inferring the demographic history from DNA sequences: An importance sampling approach based on non-homogeneous processes.

PubMed

Ait Kaci Azzou, S; Larribe, F; Froda, S

2016-10-01

In Ait Kaci Azzou et al. (2015) we introduced an Importance Sampling (IS) approach for estimating the demographic history of a sample of DNA sequences, the skywis plot. More precisely, we proposed a new nonparametric estimate of a population size that changes over time. We showed on simulated data that the skywis plot can work well in typical situations where the effective population size does not undergo very steep changes. In this paper, we introduce an iterative procedure which extends the previous method and gives good estimates under such rapid variations. In the iterative calibrated skywis plot we approximate the effective population size by a piecewise constant function, whose values are re-estimated at each step. These piecewise constant functions are used to generate the waiting times of non homogeneous Poisson processes related to a coalescent process with mutation under a variable population size model. Moreover, the present IS procedure is based on a modified version of the Stephens and Donnelly (2000) proposal distribution. Finally, we apply the iterative calibrated skywis plot method to a simulated data set from a rapidly expanding exponential model, and we show that the method based on this new IS strategy correctly reconstructs the demographic history. Copyright © 2016. Published by Elsevier Inc.

A Program for Calculating and Plotting Synthetic Common-Source Seismic-Reflection Traces for Multilayered Earth Models.

ERIC Educational Resources Information Center

Ramananantoandro, Ramanantsoa

1988-01-01

Presented is a description of a BASIC program to be used on an IBM microcomputer for calculating and plotting synthetic seismic-reflection traces for multilayered earth models. Discusses finding raypaths for given source-receiver offsets using the "shooting method" and calculating the corresponding travel times. (Author/CW)

A regression-adjusted approach can estimate competing biomass

Treesearch

James H. Miller

1983-01-01

A method is presented for estimating above-ground herbaceous and woody biomass on competition research plots. On a set of destructively-sampled plots, an ocular estimate of biomass by vegetative component is first made, after which vegetation is clipped, dried, and weighed. Linear regressions are then calculated for each component between estimated and actual weights...

Application of GPS and Near-Surface Geophysical Methods to Evaluate Differences Between Agricultural Test Plots

USDA-ARS?s Scientific Manuscript database

A field research facility with two pairs of replicated agricultural test plots (four total) was established at a location in northwest Ohio during 2005 for the purpose of studying water table management strategies. Initial efforts at this field research facility were devoted to evaluating difference...

Prefield methods: streamlining forest or nonforest determinations to increase inventory efficiency

Treesearch

Sara Goeking; Gretchen Moisen; Kevin Megown; Jason Toombs

2009-01-01

Interior West Forest Inventory and Analysis has developed prefield protocols to distinguish forested plots that require field visits from nonforested plots that do not require field visits. Recent innovations have increased the efficiency of the prefield process. First, the incorporation of periodic inventory data into a prefield database increased the amount of...

Continuum of risk analysis methods to assess tillage system sustainability at the experimental plot level

USDA-ARS?s Scientific Manuscript database

The primary goal of this study was to evaluate the efficacy of stochastic dominance and stochastic efficiency with respect to a function (SERF) methodology for ranking conventional and conservation tillage systems using 14 years (1990-2003) of economic budget data collected from 36 plots at the Iowa...

The Wally plot approach to assess the calibration of clinical prediction models.

PubMed

Blanche, Paul; Gerds, Thomas A; Ekstrøm, Claus T

2017-12-06

A prediction model is calibrated if, roughly, for any percentage x we can expect that x subjects out of 100 experience the event among all subjects that have a predicted risk of x%. Typically, the calibration assumption is assessed graphically but in practice it is often challenging to judge whether a "disappointing" calibration plot is the consequence of a departure from the calibration assumption, or alternatively just "bad luck" due to sampling variability. We propose a graphical approach which enables the visualization of how much a calibration plot agrees with the calibration assumption to address this issue. The approach is mainly based on the idea of generating new plots which mimic the available data under the calibration assumption. The method handles the common non-trivial situations in which the data contain censored observations and occurrences of competing events. This is done by building on ideas from constrained non-parametric maximum likelihood estimation methods. Two examples from large cohort data illustrate our proposal. The 'wally' R package is provided to make the methodology easily usable.

Calibrated Passive Sampling--Multi-plot Field Measurements of NH3 Emissions with a Combination of Dynamic Tube Method and Passive Samplers.

PubMed

Pacholski, Andreas

2016-03-21

Agricultural ammonia (NH3) emissions (90% of total EU emissions) are responsible for about 45% airborne eutrophication, 31% soil acidification and 12% fine dust formation within the EU15. But NH3 emissions also mean a considerable loss of nutrients. Many studies on NH3 emission from organic and mineral fertilizer application have been performed in recent decades. Nevertheless, research related to NH3 emissions after application fertilizers is still limited in particular with respect to relationships to emissions, fertilizer type, site conditions and crop growth. Due to the variable response of crops to treatments, effects can only be validated in experimental designs including field replication for statistical testing. The dominating ammonia loss methods yielding quantitative emissions require large field areas, expensive equipment or current supply, which restricts their application in replicated field trials. This protocol describes a new methodology for the measurement of NH3 emissions on many plots linking a simple semi-quantitative measuring method used in all plots, with a quantitative method by simultaneous measurements using both methods on selected plots. As a semi-quantitative measurement method passive samplers are used. The second method is a dynamic chamber method (Dynamic Tube Method) to obtain a transfer quotient, which converts the semi-quantitative losses of the passive sampler to quantitative losses (kg nitrogen ha(-1)). The principle underlying this approach is that passive samplers placed in a homogeneous experimental field have the same NH3 absorption behavior under identical environmental conditions. Therefore, a transfer co-efficient obtained from single passive samplers can be used to scale the values of all passive samplers used in the same field trial. The method proved valid under a wide range of experimental conditions and is recommended to be used under conditions with bare soil or small canopies (<0.3 m). Results obtained from experiments with taller plants should be treated more carefully.

Calibrated Passive Sampling - Multi-plot Field Measurements of NH3 Emissions with a Combination of Dynamic Tube Method and Passive Samplers

PubMed Central

Pacholski, Andreas

2016-01-01

Agricultural ammonia (NH3) emissions (90% of total EU emissions) are responsible for about 45% airborne eutrophication, 31% soil acidification and 12% fine dust formation within the EU15. But NH3 emissions also mean a considerable loss of nutrients. Many studies on NH3 emission from organic and mineral fertilizer application have been performed in recent decades. Nevertheless, research related to NH3 emissions after application fertilizers is still limited in particular with respect to relationships to emissions, fertilizer type, site conditions and crop growth. Due to the variable response of crops to treatments, effects can only be validated in experimental designs including field replication for statistical testing. The dominating ammonia loss methods yielding quantitative emissions require large field areas, expensive equipment or current supply, which restricts their application in replicated field trials. This protocol describes a new methodology for the measurement of NH3 emissions on many plots linking a simple semi-quantitative measuring method used in all plots, with a quantitative method by simultaneous measurements using both methods on selected plots. As a semi-quantitative measurement method passive samplers are used. The second method is a dynamic chamber method (Dynamic Tube Method) to obtain a transfer quotient, which converts the semi-quantitative losses of the passive sampler to quantitative losses (kg nitrogen ha-1). The principle underlying this approach is that passive samplers placed in a homogeneous experimental field have the same NH3 absorption behavior under identical environmental conditions. Therefore, a transfer co-efficient obtained from single passive samplers can be used to scale the values of all passive samplers used in the same field trial. The method proved valid under a wide range of experimental conditions and is recommended to be used under conditions with bare soil or small canopies (<0.3 m). Results obtained from experiments with taller plants should be treated more carefully. PMID:27023010

Encounters with neighbours : current developments of concepts based on recurrence plots and their applications

NASA Astrophysics Data System (ADS)

Marwan, Norbert

2003-09-01

In this work, different aspects and applications of the recurrence plot analysis are presented. First, a comprehensive overview of recurrence plots and their quantification possibilities is given. New measures of complexity are defined by using geometrical structures of recurrence plots. These measures are capable to find chaos-chaos transitions in processes. Furthermore, a bivariate extension to cross recurrence plots is studied. Cross recurrence plots exhibit characteristic structures which can be used for the study of differences between two processes or for the alignment and search for matching sequences of two data series. The selected applications of the introduced techniques to various kind of data demonstrate their ability. Analysis of recurrence plots can be adopted to the specific problem and thus opens a wide field of potential applications. Regarding the quantification of recurrence plots, chaos-chaos transitions can be found in heart rate variability data before the onset of life threatening cardiac arrhythmias. This may be of importance for the therapy of such cardiac arrhythmias. The quantification of recurrence plots allows to study transitions in brain during cognitive experiments on the base of single trials. Traditionally, for the finding of these transitions the averaging of a collection of single trials is needed. Using cross recurrence plots, the existence of an El Niño/Southern Oscillation-like oscillation is traced in northwestern Argentina 34,000 yrs. ago. In further applications to geological data, cross recurrence plots are used for time scale alignment of different borehole data and for dating a geological profile with a reference data set. Additional examples from molecular biology and speech recognition emphasize the suitability of cross recurrence plots. Diese Arbeit beschäftigt sich mit verschiedenen Aspekten und Anwendungen von Recurrence Plots. Nach einer Übersicht über Methoden, die auf Recurrence Plots basieren, werden neue Komplexitätsmaße eingeführt, die geometrische Strukturen in den Recurrence Plots beschreiben. Diese neuen Maße erlauben die Identifikation von Chaos-Chaos-Übergängen in dynamischen Prozessen. In einem weiteren Schritt werden Cross Recurrence Plots eingeführt, mit denen zwei verschiedene Prozesse untersucht werden. Diese bivariate Analyse ermöglicht die Bewertung von Unterschieden zwischen zwei Prozessen oder das Anpassen der Zeitskalen von zwei Zeitreihen. Diese Technik kann auch genutzt werden, um ähnliche Abschnitte in zwei verschiedenen Datenreihen zu finden. Im Anschluß werden diese neuen Entwicklungen auf Daten verschiedener Art angewendet. Methoden, die auf Recurrence Plots basieren, können an die speziellen Probleme angepaßt werden, so daß viele weitere Anwendungen möglich sind. Durch die Anwendung der neu eingeführten Komplexitätsmaße können Chaos-Chaos-Übergänge in Herzschlagdaten vor dem Auftreten einer lebensbedrohlichen Herzrhythmusstörung festgestellt werden, was für die Entwicklung neuer Therapien dieser Herzrhythmusstörungen von Bedeutung sein könnte. In einem weiteren Beispiel, in dem EEG-Daten aus einem kognitiv orientierten Experiment untersucht werden, ermöglichen diese Komplexitätsmaße das Erkennen von spezifischen Reaktionen im Gehirn bereits in Einzeltests. Normalerweise können diese Reaktionen erst durch die Auswertung von vielen Einzeltests erkannt werden. Mit der Hilfe von Cross Recurrence Plots wird die Existenz einer klimatischen Zirkulation, die der heutigen El Niño/ Southern Oscillation sehr ähnlich ist, im Nordwesten Argentiniens vor etwa 34000 Jahren nachgewiesen. Außerdem können mit Cross Recurrence Plots die Zeitskalen verschiedener Bohrlochdaten aufeinander abgeglichen werden. Diese Methode kann auch dazu genutzt werden, ein geologisches Profil mit Hilfe eines Referenzprofiles mit bekannter Zeitskala zu datieren. Weitere Beispiele aus den Gebieten der Molekularbiologie und der Spracherkennung unterstreichen das Potential dieser Methode.

Serum hepcidin-25 may replace the ferritin index in the Thomas plot in assessing iron status in anemic patients.

PubMed

Thomas, C; Kobold, U; Balan, S; Roeddiger, R; Thomas, L

2011-04-01

Biochemical markers of iron deficiency do not distinguish iron-deficient anemia (IDA) from the anemia of chronic disease (ACD) and the combined state of ACD/IDA. Serum hepcidin-25 might be a marker resolving this problem. We investigated the extent to which serum hepcidin-25 enables the differentiation of the states above in comparison with the ferritin index plot, the so-called Thomas plot [soluble transferrin receptor (sTfR)/log ferritin and the reticulocyte hemoglobin content (CHr)]. Serum hepcidin-25 was determined in 155 anemic patients who were classified as having latent iron deficiency (latent ID), IDA, ACD, or ACD/IDA using the ferritin index plot (Thomas plot). Hepcidin-25 was determined using an isotope-dilution micro-HPLC-tandem mass spectrometry method. The ability to discriminate among these states based on serum hepcidin-25 alone or in combination with the CHr was evaluated in a receiver operating characteristic curve analysis and a comparison with the recently established ferritin index plot. Serum hepcidin-25 correlated with ferritin and the ferritin index. Use of a hepcidin-25 cutoff level of ≤4 nmol/l allowed the differentiation of IDA from ACD and ACD/IDA. Furthermore, the discrimination of ACD/IDA from ACD required combination with CHr in a new plot (hepcidin-25 and the CHr). The hepcidin-25 plot and the ferritin index plot showed a good correspondence in the differentiation of iron states in patients with anemia. Patients with IDA can be differentiated from ACD and ACD/IDA but not ACD from ACD/IDA based on hepcidin-25 alone. The combination of hepcidin-25 with CHr in the hepcidin-25 plot was useful for the differentiation of the states above. © 2010 Blackwell Publishing Ltd.

New User-Friendly Approach to Obtain an Eisenberg Plot and Its Use as a Practical Tool in Protein Sequence Analysis

PubMed Central

Keller, Rob C.A.

2011-01-01

The Eisenberg plot or hydrophobic moment plot methodology is one of the most frequently used methods of bioinformatics. Bioinformatics is more and more recognized as a helpful tool in Life Sciences in general, and recent developments in approaches recognizing lipid binding regions in proteins are promising in this respect. In this study a bioinformatics approach specialized in identifying lipid binding helical regions in proteins was used to obtain an Eisenberg plot. The validity of the Heliquest generated hydrophobic moment plot was checked and exemplified. This study indicates that the Eisenberg plot methodology can be transferred to another hydrophobicity scale and renders a user-friendly approach which can be utilized in routine checks in protein–lipid interaction and in protein and peptide lipid binding characterization studies. A combined approach seems to be advantageous and results in a powerful tool in the search of helical lipid-binding regions in proteins and peptides. The strength and limitations of the Eisenberg plot approach itself are discussed as well. The presented approach not only leads to a better understanding of the nature of the protein–lipid interactions but also provides a user-friendly tool for the search of lipid-binding regions in proteins and peptides. PMID:22016610

New user-friendly approach to obtain an Eisenberg plot and its use as a practical tool in protein sequence analysis.

PubMed

Keller, Rob C A

2011-01-01

The Eisenberg plot or hydrophobic moment plot methodology is one of the most frequently used methods of bioinformatics. Bioinformatics is more and more recognized as a helpful tool in Life Sciences in general, and recent developments in approaches recognizing lipid binding regions in proteins are promising in this respect. In this study a bioinformatics approach specialized in identifying lipid binding helical regions in proteins was used to obtain an Eisenberg plot. The validity of the Heliquest generated hydrophobic moment plot was checked and exemplified. This study indicates that the Eisenberg plot methodology can be transferred to another hydrophobicity scale and renders a user-friendly approach which can be utilized in routine checks in protein-lipid interaction and in protein and peptide lipid binding characterization studies. A combined approach seems to be advantageous and results in a powerful tool in the search of helical lipid-binding regions in proteins and peptides. The strength and limitations of the Eisenberg plot approach itself are discussed as well. The presented approach not only leads to a better understanding of the nature of the protein-lipid interactions but also provides a user-friendly tool for the search of lipid-binding regions in proteins and peptides.

Specifying the Probability Characteristics of Funnel Plot Control Limits: An Investigation of Three Approaches

PubMed Central

Manktelow, Bradley N.; Seaton, Sarah E.

2012-01-01

Background Emphasis is increasingly being placed on the monitoring and comparison of clinical outcomes between healthcare providers. Funnel plots have become a standard graphical methodology to identify outliers and comprise plotting an outcome summary statistic from each provider against a specified ‘target’ together with upper and lower control limits. With discrete probability distributions it is not possible to specify the exact probability that an observation from an ‘in-control’ provider will fall outside the control limits. However, general probability characteristics can be set and specified using interpolation methods. Guidelines recommend that providers falling outside such control limits should be investigated, potentially with significant consequences, so it is important that the properties of the limits are understood. Methods Control limits for funnel plots for the Standardised Mortality Ratio (SMR) based on the Poisson distribution were calculated using three proposed interpolation methods and the probability calculated of an ‘in-control’ provider falling outside of the limits. Examples using published data were shown to demonstrate the potential differences in the identification of outliers. Results The first interpolation method ensured that the probability of an observation of an ‘in control’ provider falling outside either limit was always less than a specified nominal probability (p). The second method resulted in such an observation falling outside either limit with a probability that could be either greater or less than p, depending on the expected number of events. The third method led to a probability that was always greater than, or equal to, p. Conclusion The use of different interpolation methods can lead to differences in the identification of outliers. This is particularly important when the expected number of events is small. We recommend that users of these methods be aware of the differences, and specify which interpolation method is to be used prior to any analysis. PMID:23029202

Computer user's manual for a generalized curve fit and plotting program

NASA Technical Reports Server (NTRS)

Schlagheck, R. A.; Beadle, B. D., II; Dolerhie, B. D., Jr.; Owen, J. W.

1973-01-01

A FORTRAN coded program has been developed for generating plotted output graphs on 8-1/2 by 11-inch paper. The program is designed to be used by engineers, scientists, and non-programming personnel on any IBM 1130 system that includes a 1627 plotter. The program has been written to provide a fast and efficient method of displaying plotted data without having to generate any additions. Various output options are available to the program user for displaying data in four different types of formatted plots. These options include discrete linear, continuous, and histogram graphical outputs. The manual contains information about the use and operation of this program. A mathematical description of the least squares goodness of fit test is presented. A program listing is also included.

A method for developing design diagrams for ceramic and glass materials using fatigue data

NASA Technical Reports Server (NTRS)

Heslin, T. M.; Magida, M. B.; Forrest, K. A.

1986-01-01

The service lifetime of glass and ceramic materials can be expressed as a plot of time-to-failure versus applied stress whose plot is parametric in percent probability of failure. This type of plot is called a design diagram. Confidence interval estimates for such plots depend on the type of test that is used to generate the data, on assumptions made concerning the statistical distribution of the test results, and on the type of analysis used. This report outlines the development of design diagrams for glass and ceramic materials in engineering terms using static or dynamic fatigue tests, assuming either no particular statistical distribution of test results or a Weibull distribution and using either median value or homologous ratio analysis of the test results.

External Threat Risk Assessment Algorithm (ExTRAA)

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

Powell, Troy C.

Two risk assessment algorithms and philosophies have been augmented and combined to form a new algorit hm, the External Threat Risk Assessment Algorithm (ExTRAA), that allows for effective and statistically sound analysis of external threat sources in relation to individual attack methods . In addition to the attack method use probability and the attack method employment consequence, t he concept of defining threat sources is added to the risk assessment process. Sample data is tabulated and depicted in radar plots and bar graphs for algorithm demonstration purposes. The largest success of ExTRAA is its ability to visualize the kind ofmore » r isk posed in a given situation using the radar plot method.« less

The Rectangle Target Plot: A New Approach to the Graphical Presentation of Accuracy of Systems for Self-Monitoring of Blood Glucose.

PubMed

Stephan, Peter; Schmid, Christina; Freckmann, Guido; Pleus, Stefan; Haug, Cornelia; Müller, Peter

2015-10-09

The measurement accuracy of systems for self-monitoring of blood glucose (SMBG) is usually analyzed by a method comparison in which the analysis results are displayed using difference plots or similar graphs. However, such plots become difficult to comprehend as the number of data points displayed increases. This article introduces a new approach, the rectangle target plot (RTP), which aims to provide a simplified and comprehensible visualization of accuracy data. The RTP is based on ISO 15197 accuracy evaluations of SMBG systems. Two-sided tolerance intervals for normally distributed data are calculated for absolute and relative differences at glucose concentrations <100 mg/dL and ≥100 mg/dL. These tolerance intervals provide an estimator of where a 90% proportion of results is found with a confidence level of 95%. Plotting these tolerance intervals generates a rectangle whose center indicates the systematic measurement difference of the investigated system relative to the comparison method. The size of the rectangle depends on the measurement variability. The RTP provides a means of displaying measurement accuracy data in a simple and comprehensible manner. The visualization is simplified by reducing the displayed information from typically 200 data points to just 1 rectangle. Furthermore, this allows data for several systems or several lots from 1 system to be displayed clearly and concisely in a single graph. © 2015 Diabetes Technology Society.

Nearest neighbor imputation of species-level, plot-scale forest structure attributes from LiDAR data

Treesearch

Andrew T. Hudak; Nicholas L. Crookston; Jeffrey S. Evans; David E. Hall; Michael J. Falkowski

2008-01-01

Meaningful relationships between forest structure attributes measured in representative field plots on the ground and remotely sensed data measured comprehensively across the same forested landscape facilitate the production of maps of forest attributes such as basal area (BA) and tree density (TD). Because imputation methods can efficiently predict multiple response...

SOIL-AIR PERMEABILITY MEASUREMENT WITH A TRANSIENT PRESSURE BUILDUP METHOD

EPA Science Inventory

An analytical solution for transient pressure change in a single venting well was derived from mass conservation of air, Darcy's law of flow in porous media, and the ideal gas law equation of state. Slopes of plots of Pw2 against ln (t+Δt)/Δt similar to Homer's plot were used to ...

Detection of the fracture zone by the method of recurrence plot

NASA Astrophysics Data System (ADS)

Hilarov, V. L.

2017-12-01

Recurrence plots (RPs) and recurrence quantification analysis (RQA) characteristics for the normal component of the displacement vector upon excitation of a defect steel plate by a sound pulse are analyzed. Different cases of spatial distribution of defects (uniform and normal) are considered, and a difference in the RQA parameters in these cases is revealed.

Braconid wasp (Hymenoptera: Braconidae) diversity in forest plots under different silvicultural methods

Treesearch

C.N. Lewis; J.B. Whitfield

1999-01-01

Braconid wasps were used as an indicator group to test the hypothesis that the degree of disturbance in silvicultural treatments will change the total abundance and composition of species. Wasps were collected with Malaise traps on undisturbed (control), moderately disturbed (pine single-tree selection) and highly disturbed (pine-hardwood seed-tree) research plots of...

Survivability Versus Time

NASA Technical Reports Server (NTRS)

Joyner, James J., Sr.

2014-01-01

Develop Survivability vs Time Model as a decision-evaluation tool to assess various emergency egress methods used at Launch Complex 39B (LC 39B) and in the Vehicle Assembly Building (VAB) on NASAs Kennedy Space Center. For each hazard scenario, develop probability distributions to address statistical uncertainty resulting in survivability plots over time and composite survivability plots encompassing multiple hazard scenarios.

The carbon consequences of thinning techniques: stand structure makes a difference

Treesearch

Coeli Hoover; Susan Stout

2007-01-01

Using results from a 25-year study of thinning in a northwestern Pennsylvania Allegheny hardwood stand, we assess whether and how thinning method affected carbon sequestration and merchantable volume production. Plots were thinned to similar residual relative density by removing trees from different portions of the diameter distribution. Plots that were thinned from...

Sensitivity of Equated Aggregate Scores to the Treatment of Misbehaving Common Items

ERIC Educational Resources Information Center

Michaelides, Michalis P.

2010-01-01

The delta-plot method (Angoff, 1972) is a graphical technique used in the context of test equating for identifying common items with aberrant changes in their item difficulties across administrations or alternate forms. This brief research report explores the effects on equated aggregate scores when delta-plot outliers are either retained in or…

Split-plot microarray experiments: issues of design, power and sample size.

PubMed

Tsai, Pi-Wen; Lee, Mei-Ling Ting

2005-01-01

This article focuses on microarray experiments with two or more factors in which treatment combinations of the factors corresponding to the samples paired together onto arrays are not completely random. A main effect of one (or more) factor(s) is confounded with arrays (the experimental blocks). This is called a split-plot microarray experiment. We utilise an analysis of variance (ANOVA) model to assess differentially expressed genes for between-array and within-array comparisons that are generic under a split-plot microarray experiment. Instead of standard t- or F-test statistics that rely on mean square errors of the ANOVA model, we use a robust method, referred to as 'a pooled percentile estimator', to identify genes that are differentially expressed across different treatment conditions. We illustrate the design and analysis of split-plot microarray experiments based on a case application described by Jin et al. A brief discussion of power and sample size for split-plot microarray experiments is also presented.

Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?

PubMed

Knapp, B; Frantal, S; Cibena, M; Schreiner, W; Bauer, P

2011-08-01

Molecular dynamics is a commonly used technique in computational biology. One key issue of each molecular dynamics simulation is: When does this simulation reach equilibrium state? A widely used way to determine this is the visual and intuitive inspection of root mean square deviation (RMSD) plots of the simulation. Although this technique has been criticized several times, it is still often used. Therefore, we present a study proving that this method is not reliable at all. We conducted a survey with participants from the field in which we illustrated different RMSD plots to scientists in the field of molecular dynamics. These plots were randomized and repeated, using a statistical model and different variants of the plots. We show that there is no mutual consent about the point of equilibrium. The decisions are severely biased by different parameters. Therefore, we conclude that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot.

System and process for ultrasonic characterization of deformed structures

DOEpatents

Panetta, Paul D [Williamsburg, VA; Morra, Marino [Richland, WA; Johnson, Kenneth I [Richland, WA

2011-11-22

Generally speaking, the method of the present invention is performed by making various ultrasonic scans at preselected orientations along the length of a material being tested. Data from the scans are then plotted together with various calculated parameters that are calculated from this data. Lines or curves are then fitted to the respective plotted points. Review of these plotted curves allows the location and severity of defects within these sections to be determined and quantified. With this information various other decisions related to how, when or whether repair or replacement of a particular portion of a structure can be made.

MIT solar wind plasma data from Explorer 33 and Explorer 35: July 1966 to September 1970

NASA Technical Reports Server (NTRS)

Howe, H.; Binsack, J.; Wang, C.; Clapp, E.

1971-01-01

The plasma experiments on Explorer 33 and Explorer 35 have yielded large amounts of solar wind data. This report gives a brief review of the method used to obtain the data, provides a description of the plasma parameters, and describes in detail the format of the plots and tapes which are available from the Data Center. Hourly average plots of the data are included at the end of the report. From these plots, the availability and interest of the solar wind data for any period of time may be determined.

Possibilities and limitations of the kinetic plot method in supercritical fluid chromatography.

PubMed

De Pauw, Ruben; Desmet, Gert; Broeckhoven, Ken

2013-08-30

Although supercritical fluid chromatography (SFC) is becoming a technique of increasing importance in the field of analytical chromatography, methods to compare the performance of SFC-columns and separations in an unbiased way are not fully developed. The present study uses mathematical models to investigate the possibilities and limitations of the kinetic plot method in SFC as this easily allows to investigate a wide range of operating pressures, retention and mobile phase conditions. The variable column length (L) kinetic plot method was further investigated in this work. Since the pressure history is identical for each measurement, this method gives the true kinetic performance limit in SFC. The deviations of the traditional way of measuring the performance as a function of flow rate (fixed back pressure and column length) and the isopycnic method with respect to this variable column length method were investigated under a wide range of operational conditions. It is found that using the variable L method, extrapolations towards other pressure drops are not valid in SFC (deviation of ∼15% for extrapolation from 50 to 200bar pressure drop). The isopycnic method provides the best prediction but its use is limited when operating closer towards critical point conditions. When an organic modifier is used, the predictions are improved for both methods with respect to the variable L method (e.g. deviations decreases from 20% to 2% when 20mol% of methanol is added). Copyright © 2013 Elsevier B.V. All rights reserved.

Impact of animal waste application on runoff water quality in field experimental plots.

PubMed

Hill, Dagne D; Owens, William E; Tchoounwou, Paul B

2005-08-01

Animal waste from dairy and poultry operations is an economical and commonly used fertilizer in the state of Louisiana. The application of animal waste to pasture lands not only is a source of fertilizer, but also allows for a convenient method of waste disposal. The disposal of animal wastes on land is a potential nonpoint source of water degradation. Water degradation and human health is a major concern when considering the disposal of large quantities of animal waste. The objective of this research was to determine the effect of animal waste application on biological (fecal coliform, Enterobacter spp. and Escherichia coli) and physical/chemical (temperature, pH, nitrate nitrogen, ammonia nitrogen, phosphate, copper, zinc, and sulfate) characteristics of runoff water in experimental plots. The effects of the application of animal waste have been evaluated by utilizing experimental plots and simulated rainfall events. Samples of runoff water were collected and analyzed for fecal coliforms. Fecal coliforms isolated from these samples were identified to the species level. Chemical analysis was performed following standard test protocols. An analysis of temperature, ammonia nitrogen, nitrate nitrogen, iron, copper, phosphate, potassium, sulfate, zinc and bacterial levels was performed following standard test protocols as presented in Standard Methods for the Examination of Water and Wastewater [1]. In the experimental plots, less time was required in the tilled broiler litter plots for the measured chemicals to decrease below the initial pre-treatment levels. A decrease of over 50% was noted between the first and second rainfall events for sulfate levels. This decrease was seen after only four simulated rainfall events in tilled broiler litter plots whereas broiler litter plots required eight simulated rainfall events to show this same type of reduction. A reverse trend was seen in the broiler litter plots and the tilled broiler plots for potassium. Bacteria numbers present after the simulated rainfall events were above 200/100 ml of sample water. It can be concluded that: 1) non-point source pollution has a significant effect on bacterial and nutrients levels in runoff water and in water resources; 2) land application of animal waste for soil fertilization makes a significant contribution to water pollution; 3) the use of tilling can significantly reduce the amount of nutrients available in runoff water.

Impact of Animal Waste Application on Runoff Water Quality in Field Experimental Plots

PubMed Central

Hill, Dagne D.; Owens, William E.; Tchounwou, Paul B.

2005-01-01

Animal waste from dairy and poultry operations is an economical and commonly used fertilizer in the state of Louisiana. The application of animal waste to pasture lands not only is a source of fertilizer, but also allows for a convenient method of waste disposal. The disposal of animal wastes on land is a potential nonpoint source of water degradation. Water degradation and human health is a major concern when considering the disposal of large quantities of animal waste. The objective of this research was to determine the effect of animal waste application on biological (fecal coliform, Enterobacter spp. and Escherichia coli) and physical/chemical (temperature, pH, nitrate nitrogen, ammonia nitrogen, phosphate, copper, zinc, and sulfate) characteristics of runoff water in experimental plots. The effects of the application of animal waste have been evaluated by utilizing experimental plots and simulated rainfall events. Samples of runoff water were collected and analyzed for fecal coliforms. Fecal coliforms isolated from these samples were identified to the species level. Chemical analysis was performed following standard test protocols. An analysis of temperature, ammonia nitrogen, nitrate nitrogen, iron, copper, phosphate, potassium, sulfate, zinc and bacterial levels was performed following standard test protocols as presented in Standard Methods for the Examination of Water and Wastewater [1]. In the experimental plots, less time was required in the tilled broiler litter plots for the measured chemicals to decrease below the initial pre-treatment levels. A decrease of over 50% was noted between the first and second rainfall events for sulfate levels. This decrease was seen after only four simulated rainfall events in tilled broiler litter plots whereas broiler litter plots required eight simulated rainfall events to show this same type of reduction. A reverse trend was seen in the broiler litter plots and the tilled broiler plots for potassium. Bacteria numbers present after the simulated rainfall events were above 200/100 ml of sample water. It can be concluded that: 1) non-point source pollution has a significant effect on bacterial and nutrients levels in runoff water and in water resources; 2) land application of animal waste for soil fertilization makes a significant contribution to water pollution; 3) the use of tilling can significantly reduce the amount of nutrients available in runoff water. PMID:16705834

Evaluation method for corrosion level of rebar in RC with electrical impedance measurement

NASA Astrophysics Data System (ADS)

Sasamoto, Akira

2018-04-01

The author reported that the impedance measurement using the 4-terminal method on the RC surface for diagnosing corrosion of internal rebar. The difference between the maximum value at 0.01 Hz and the minimum value around 10 Hz indicates the corrosion level of rebar in that report. This is successive report on a signal processing method for estimating the corrosion level by the measured impedance data to obtain more high accuracy. In the dielectric, a graph of frequency and dielectric constant (Cole-Cole plot diagram by KS Cole and RH Cole article of 1941) draws a shape of circle if the dielectric is independent of frequency but it draws a shape of ellipse in reality due to frequency dependency. Havriliak and Negami have also presented Havriliak-Negami model which introduced parameter into dielectric constant equation which deforms Cole-Cole plot diagram and showed that acquired dielectric data of polymer materials fit to this model with proper parameters. In this report, we first consider electric model connected with resistance and capacitance as a rough model of RC concrete. If the capacitance in this model circuit has some loss of dielectric, it is stated that graph in impedance plot is expected to take as similar deformation in the dielectric Cole-Cole plot. Then a numerical optimization computer code for obtaining parameters in the Cole-Cole plot diagram and Havriliak-Negami model is constructed, and the correlation between the deformation parameter of each model and corrosion is shown by this code. These results are feasibility study for diagnosis of corrosion level of rebar by associated parameters to a shape of impedance graph.

Redox biotransformation and delivery of anthracycline anticancer antibiotics: How interpretable structure-activity relationships of lethality using electrophilicity and the London formula for dispersion interaction work.

PubMed

Pang, Siu-Kwong

2017-03-30

Quantum chemical methods and molecular mechanics approaches face a lot of challenges in drug metabolism study because of their either insufficient accuracy or huge computational cost, or lack of clear molecular level pictures for building computational models. Low-cost QSAR methods can often be carried out even though molecular level pictures are not well defined; however, they show difficulty in identifying the mechanisms of drug metabolism and delineating the effects of chemical structures on drug toxicity because a certain amount of molecular descriptors are difficult to be interpreted. In order to make a breakthrough, it was proposed that mechanistically interpretable molecular descriptors were used to correlate with biological activity to establish structure-activity plots. The mechanistically interpretable molecular descriptors used in this study include electrophilicity and the mathematical function in the London formula for dispersion interaction, and they were calculated using quantum chemical methods. The biological activity is the lethality of anthracycline anticancer antibiotics denoted as log LD50, which were obtained by intraperitoneal injection into mice. The results reveal that the plots for electrophilicity, which can be interpreted as redox reactivity of anthracyclines, can describe oxidative degradation for detoxification and reductive bioactivation for toxicity induction. The plots for the dispersion interaction function, which represent the attraction between anthracyclines and biomolecules, can describe efflux from and influx into target cells of toxicity. The plots can also identify three structural scaffolds of anthracyclines that have different metabolic pathways, resulting in their different toxicity behavior. This structure-dependent toxicity behavior revealed in the plots can provide perspectives on design of anthracycline anticancer antibiotics. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Temporal Evolution of Non-equilibrium Gamma’ Precipitates in a Rapidly Quenched Nickel Base Superalloy (Preprint)

DTIC Science & Technology

2014-04-01

with the binomial distribution for a particular dataset. This technique is more commonly known as the Langer, Bar-on and Miller ( LBM ) method [22,23...distribution unlimited. Using the LBM method, the frequency distribution plot for a dataset corresponding to a phase separated system, exhibiting a split peak...estimated parameters (namely μ1, μ2, σ, fγ’ and fγ) obtained from the LBM plots in Fig. 5 are summarized in Table 3. The EWQ sample does not exhibit any

An Excel Macro to Plot the HFE-Diagram to Identify Sea Water Intrusion Phases.

PubMed

Giménez-Forcada, Elena; Sánchez San Román, F Javier

2015-01-01

A hydrochemical facies evolution diagram (HFE-D) is a multirectangular diagram, which is a useful tool in the interpretation of sea water intrusion processes. This method note describes a simple method for generating an HFE-D plot using the spreadsheet software package, Microsoft Excel. The code was applied to groundwater from the alluvial coastal plain of Grosseto (Tuscany, Italy), which is characterized by a complex salinization process in which sea water mixes with sulfate or bicarbonate recharge water. © 2014, National GroundWater Association.

On spectral techniques in analysis of Boolean networks

NASA Astrophysics Data System (ADS)

Kesseli, Juha; Rämö, Pauli; Yli-Harja, Olli

2005-06-01

In this work we present results that can be used for analysis of Boolean networks. The results utilize Fourier spectra of the functions in the network. An accurate formula is given for Derrida plots of networks of finite size N based on a result on Boolean functions presented in another context. Derrida plots are widely used to examine the stability issues of Boolean networks. For the limit N→∞, we give a computationally simple form that can be used as a good approximation for rather small networks as well. A formula for Derrida plots of random Boolean networks (RBNs) presented earlier in the literature is given an alternative derivation. It is shown that the information contained in the Derrida plot is equal to the average Fourier spectrum of the functions in the network. In the case of random networks the mean Derrida plot can be obtained from the mean spectrum of the functions. The method is applied to real data by using the Boolean functions found in genetic regulatory networks of eukaryotic cells in an earlier study. Conventionally, Derrida plots and stability analysis have been computed with statistical sampling resulting in poorer accuracy.

Performance of deep-rooted phreatophytic trees at a site containing total petroleum hydrocarbons.

PubMed

Ferro, Ari M; Adham, Tareq; Berra, Brett; Tsao, David

2013-01-01

Poplar and willow tree stands were installed in 2003 at a site in Raleigh, North Carolina containing total petroleum hydrocarbon - contaminated groundwater. The objective was groundwater uptake and plume control. The water table was 5 to 6 m below ground surface (bgs) and therefore methods were used to encourage deep root development. Growth rates, rooting depth and sap flow were measured for trees in Plot A located in the center of the plume and in Plot B peripheral to the plume. The trees were initially sub-irrigated with vertically installed drip-lines and by 2005 had roots 4 to 5 m bgs. Water balance calculations suggested groundwater uptake. In 2007, the average sap flow was higher for Plot B (approximately 59 L per day per tree) than for Plot A (approximately 23 L per day per tree), probably as a result of TPH-induced stress in Plot A. Nevertheless, the estimated rate of groundwater uptake for Plot A was sufficient, relative to the calculated rate of groundwater flux beneath the stand, that a high level of plume control was achieved based on MODFLOW modeling results. Down-gradient groundwater monitoring wells installed in late 2011 should provide quantitative data for plume control.

Noninvasive bi-graphical analysis for the quantification of slowly reversible radioligand binding

NASA Astrophysics Data System (ADS)

Seo, Seongho; Kim, Su Jin; Yoo, Hye Bin; Lee, Jee-Young; Kyeong Kim, Yu; Lee, Dong Soo; Zhou, Yun; Lee, Jae Sung

2016-09-01

In this paper, we presented a novel reference-region-based (noninvasive) bi-graphical analysis for the quantification of a reversible radiotracer binding that may be too slow to reach relative equilibrium (RE) state during positron emission tomography (PET) scans. The proposed method indirectly implements the noninvasive Logan plot, through arithmetic combination of the parameters of two other noninvasive methods and the apparent tissue-to-plasma efflux rate constant for the reference region (k2\\prime ). We investigated its validity and statistical properties, by performing a simulation study with various noise levels and k2\\prime values, and also evaluated its feasibility for [18F]FP-CIT PET in human brain. The results revealed that the proposed approach provides distribution volume ratio estimation comparable to the Logan plot at low noise levels while improving underestimation caused by non-RE state differently depending on k2\\prime . Furthermore, the proposed method was able to avoid noise-induced bias of the Logan plot, and the variability of its results was less dependent on k2\\prime than the Logan plot. Therefore, this approach, without issues related to arterial blood sampling given a pre-estimate of k2\\prime (e.g. population-based), could be useful in parametric image generation for slow kinetic tracers staying in a non-RE state within a PET scan.

Motion compensation for fully 4D PET reconstruction using PET superset data

NASA Astrophysics Data System (ADS)

Verhaeghe, J.; Gravel, P.; Mio, R.; Fukasawa, R.; Rosa-Neto, P.; Soucy, J.-P.; Thompson, C. J.; Reader, A. J.

2010-07-01

Fully 4D PET image reconstruction is receiving increasing research interest due to its ability to significantly reduce spatiotemporal noise in dynamic PET imaging. However, thus far in the literature, the important issue of correcting for subject head motion has not been considered. Specifically, as a direct consequence of using temporally extensive basis functions, a single instance of movement propagates to impair the reconstruction of multiple time frames, even if no further movement occurs in those frames. Existing 3D motion compensation strategies have not yet been adapted to 4D reconstruction, and as such the benefits of 4D algorithms have not yet been reaped in a clinical setting where head movement undoubtedly occurs. This work addresses this need, developing a motion compensation method suitable for fully 4D reconstruction methods which exploits an optical tracking system to measure the head motion along with PET superset data to store the motion compensated data. List-mode events are histogrammed as PET superset data according to the measured motion, and a specially devised normalization scheme for motion compensated reconstruction from the superset data is required. This work proceeds to propose the corresponding time-dependent normalization modifications which are required for a major class of fully 4D image reconstruction algorithms (those which use linear combinations of temporal basis functions). Using realistically simulated as well as real high-resolution PET data from the HRRT, we demonstrate both the detrimental impact of subject head motion in fully 4D PET reconstruction and the efficacy of our proposed modifications to 4D algorithms. Benefits are shown both for the individual PET image frames as well as for parametric images of tracer uptake and volume of distribution for 18F-FDG obtained from Patlak analysis.

Feasibility of assessing [(18)F]FDG lung metabolism with late dynamic PET imaging.

PubMed

Laffon, Eric; de Clermont, Henri; Vernejoux, Jean-Marc; Jougon, Jacques; Marthan, Roger

2011-04-01

The aim of this work was to non-invasively establish the feasibility of assessing 2-deoxy-2-[(18)F]fluoro-D-glucose ((18)F-FDG) lung metabolism with the use of a late dynamic positron emission tomograpy (PET) acquisition, i.e., beyond 2 h after injection. The present method has been probed in 11 patients without any respiratory disease, under fasting conditions, by assessing mean values of (18)F-FDG lung metabolism. A kinetic model analysis has been implemented on a simple calculation sheet. An arbitrary (population based) input function has been used in each individual, which was obtained from literature data. In the healthy lung, no (18)F-FDG release was found, and the mean values (±SD) of the (18)F-FDG uptake rate constant and of the fraction of the free tracer in blood and interstitial volume were: K = 0.0016 min(-1) (±0.0005), and F = 0.18 (±0.10), respectively. These results were in very close agreement with literature data that were obtained by both three-compartment model analysis and Patlak graphical analysis (gold standards), and that used an invasive blood sampling. Furthermore, K and the standard uptake value index have been compared. We conclude that assessing lung metabolism of (18)F-FDG in humans with the use of late dynamic PET imaging is feasible. The arbitrary input function of this non-invasive feasibility study could be replaced in further experiments by an input function obtained by arterial sampling. It is suggested that this method may prove useful to quantify (18)F-FDG lung metabolism under pathological conditions.

Motion compensation for fully 4D PET reconstruction using PET superset data.

PubMed

Verhaeghe, J; Gravel, P; Mio, R; Fukasawa, R; Rosa-Neto, P; Soucy, J-P; Thompson, C J; Reader, A J

2010-07-21

Fully 4D PET image reconstruction is receiving increasing research interest due to its ability to significantly reduce spatiotemporal noise in dynamic PET imaging. However, thus far in the literature, the important issue of correcting for subject head motion has not been considered. Specifically, as a direct consequence of using temporally extensive basis functions, a single instance of movement propagates to impair the reconstruction of multiple time frames, even if no further movement occurs in those frames. Existing 3D motion compensation strategies have not yet been adapted to 4D reconstruction, and as such the benefits of 4D algorithms have not yet been reaped in a clinical setting where head movement undoubtedly occurs. This work addresses this need, developing a motion compensation method suitable for fully 4D reconstruction methods which exploits an optical tracking system to measure the head motion along with PET superset data to store the motion compensated data. List-mode events are histogrammed as PET superset data according to the measured motion, and a specially devised normalization scheme for motion compensated reconstruction from the superset data is required. This work proceeds to propose the corresponding time-dependent normalization modifications which are required for a major class of fully 4D image reconstruction algorithms (those which use linear combinations of temporal basis functions). Using realistically simulated as well as real high-resolution PET data from the HRRT, we demonstrate both the detrimental impact of subject head motion in fully 4D PET reconstruction and the efficacy of our proposed modifications to 4D algorithms. Benefits are shown both for the individual PET image frames as well as for parametric images of tracer uptake and volume of distribution for (18)F-FDG obtained from Patlak analysis.

Strain and grain size of TiO2 nanoparticles from TEM, Raman spectroscopy and XRD: The revisiting of the Williamson-Hall plot method

NASA Astrophysics Data System (ADS)

Kibasomba, Pierre M.; Dhlamini, Simon; Maaza, Malik; Liu, Chuan-Pu; Rashad, Mohamed M.; Rayan, Diaa A.; Mwakikunga, Bonex W.

2018-06-01

The Williamson-Hall (W-H) equation, which has been used to obtain relative crystallite sizes and strains between samples since 1962, is revisited. A modified W-H equation is derived which takes into account the Scherrer equation, first published in 1918, (which traditionally gives more absolute crystallite size prediction) and strain prediction from Raman spectra. It is found that W-H crystallite sizes are on average 2.11 ± 0.01 times smaller than the sizes from Scherrer equation. Furthermore the strain from the W-H plots when compared to strain obtained from Raman spectral red-shifts yield factors whose values depend on the phases in the materials - whether anatase, rutile or brookite. Two main phases are identified in the annealing temperatures (350 °C-700 °C) chosen herein - anatase and brookite. A transition temperature of 550 °C has been found for nano-TiO2 to irreversibly transform from brookite to anatase by plotting the Raman peak shifts against the annealing temperatures. The W-H underestimation on the strain in the brookite phase gives W-H/Raman factor of 3.10 ± 0.05 whereas for the anatase phase, one gets 2.46 ± 0.03. The new βtot2cos2θ-sinθ plot and when fitted with a polynomial yield less strain but much better matching with experimental TEM crystallite sizes and the agglomerates than both the traditional Williamson-Hall and the Scherrer methods. There is greater improvement in the model when linearized - that is the βtotcos2θ-sinθ plot rather than the βtot2cos2θ-sinθ plot.

US army land condition-trend analysis (LCTA) program

NASA Astrophysics Data System (ADS)

Diersing, Victor E.; Shaw, Robert B.; Tazik, David J.

1992-05-01

The US Army Land Condition-Trend Analysis (LCTA) program is a standardized method of data collection, analysis, and reporting designed to meet multiple goals and objectives. The method utilizes vascular plant inventories, permanent field plot data, and wildlife inventories. Vascular plant inventories are used for environmental documentation, training of personnel, species identification during LCTA implementation, and as a survey for state and federal endangered or threatened species. The permanent field plot data documents the vegetational, edaphic, topographic, and disturbance characteristics of the installation. Inventory plots are allocated in a stratified random fashion across the installation utilizing a geographic information system that integrates satellite imagery and soil survey information. Ground cover, canopy cover, woody plant density, slope length, slope gradient, soil information, and disturbance data are collected at each plot. Plot data are used to: (1) describe plant communities, (2) characterize wildlife and threatened and endangered species habitat, (3) document amount and kind of military and nonmilitary disturbance, (4) determine the impact of military training on vegetation and soil resources, (5) estimate soil erosion potential, (6) classify land as to the kind and amount of use it can support, (7) determine allowable use estimates for tracked vehicle training, (8) document concealment resources, (9) identify lands that require restoration and evaluate the effectiveness of restorative techniques, and (10) evaluate potential acquisition property. Wildlife inventories survey small and midsize mammals, birds, bats, amphibians, and reptiles. Data from these surveys can be used for environmental documentation, to identify state and federal endangered and threatened species, and to evaluate the impact of military activities on wildlife populations. Short- and long-term monitoring of permanent field plots is used to evaluate and adjust land management decisions.

Easy handling of tectonic data: the programs TectonicVB for Mac and TectonicsFP for Windows™

NASA Astrophysics Data System (ADS)

Ortner, Hugo; Reiter, Franz; Acs, Peter

2002-12-01

TectonicVB for Macintosh and TectonicsFP for Windows TM operating systems are two menu-driven computer programs which allow the shared use of data on these environments. The programs can produce stereographic plots of orientation data (great circles, poles, lineations). Frequently used statistical procedures like calculation of eigenvalues and eigenvectors, calculation of mean vector with concentration parameters and confidence cone can be easily performed. Fault data can be plotted in stereographic projection (Angelier and Hoeppener plots). Sorting of datasets into homogeneous subsets and rotation of tectonic data can be performed in interactive two-diagram windows. The paleostress tensor can be calculated from fault data sets using graphical (calculation of kinematic axes and right dihedra method) or mathematical methods (direct inversion or numerical dynamical analysis). The calculations can be checked in dimensionless Mohr diagrams and fluctuation histograms.

Reliability of confidence intervals calculated by bootstrap and classical methods using the FIA 1-ha plot design

Treesearch

H. T. Schreuder; M. S. Williams

2000-01-01

In simulation sampling from forest populations using sample sizes of 20, 40, and 60 plots respectively, confidence intervals based on the bootstrap (accelerated, percentile, and t-distribution based) were calculated and compared with those based on the classical t confidence intervals for mapped populations and subdomains within those populations. A 68.1 ha mapped...

New Method for Determining the Relative Stand Density of Forest Inventory Plots

Treesearch

Christopher W. Woodall; Patrick D. Miles

2006-01-01

Determining the relative density of Forest Inventory and Analysis plots is complicated by the various species and tree size combinations in the Nation?s forested ecosystems. Stand density index (SDI), although developed for use in even-aged monocultures, has been used for stand density assessment in largescale forest inventories. To improve application of SDI in uneven...

Productivity of Populus in monoclonal and polyclonal blocks at three spacings.

Treesearch

Dean S. DeBell; Constance A. Harrington

1997-01-01

Four Populus clones were grown at three spacings (0.5, 1.0, and 1.5 m) in monoclonal plots and in polyclonal plots with all clones in intimate mixture. After the third year, many individual tree and stand traits differed significantly by clone, spacing, deployment method, and their interactions. Differences among clones in growth and stem form were...

Monitoring Finnish Owls 1982-1996: methods and results

Treesearch

Pertti Saurola

1997-01-01

In 1982, the Raptor Grid, a nation-wide program for monitoring birds of prey was started by the Finnish Ringing Centre. Voluntary banders were asked to select a 10 x 10 km study plot and find annually all active nests or at least occupied territories of birds of prey from their study plot (annual total averaged 120). Since 1986, additional...

A first look at logging residue characteristics in West Virginia

Treesearch

A. Jeff Martin

1975-01-01

In 1973 and 1974, the Forest Products Marketing Laboratory obtained some preliminary information about characteristics of logging residues in West Virginia. Sixteen 1-acre plots were measured in conjunction with a test of the line-intersect sampling method. Findings from the 16 plots showed that hardwood residue volumes ranged from 100 to 1,300 cubic feet per acre,...

Early thinning experiments established by the Fort Valley Experimental Forest (P-53)

Treesearch

Benjamin P. De Blois; Alex. J. Finkral; Andrew J. Sánchez Meador; Margaret M. Moore

2008-01-01

Between 1925 and 1936, the Fort Valley Experimental Forest (FVEF) scientists initiated a study to examine a series of forest thinning experiments in second growth ponderosa pine stands in Arizona and New Mexico. These early thinning plots furnished much of the early background for the development of methods used in forest management in the Southwest. The plots ranged...

Early thinning experiments established by the Fort Valley Experimental Forest

Treesearch

Benjamin P. De Blois; Alex. J. Finkral; Andrew J. Sanchez Meador; Margaret M. Moore

2008-01-01

Between 1925 and 1936, the Fort Valley Experimental Forest (FVEF) scientists initiated a study to examine a series of forest thinning experiments in second growth ponderosa pine stands in Arizona and New Mexico. These early thinning plots furnished much of the early background for the development of methods used in forest management in the Southwest. The plots ranged...

Quantifying allometric model uncertainty for plot-level live tree biomass stocks with a data-driven, hierarchical framework

Treesearch

Brian J. Clough; Matthew B. Russell; Grant M. Domke; Christopher W. Woodall

2016-01-01

Accurate uncertainty assessments of plot-level live tree biomass stocks are an important precursor to estimating uncertainty in annual national greenhouse gas inventories (NGHGIs) developed from forest inventory data. However, current approaches employed within the United States’ NGHGI do not specifically incorporate methods to address error in tree-scale biomass...

Comparison of the soil losses from (7)Be measurements and the monitoring data by erosion pins and runoff plots in the Three Gorges Reservoir region, China.

PubMed

Shi, Zhonglin; Wen, Anbang; Zhang, Xinbao; Yan, Dongchun

2011-10-01

The potential for using (7)Be measurements to document soil redistribution associated with a heavy rainfall was estimated using (7)Be method on a bare purple soil plot in the Three Gorges Reservoir region of China. The results were compared with direct measurement from traditional approaches of erosion pins and runoff plots. The study shows that estimation of soil losses from (7)Be are comparable with the monitoring results provided by erosion pins and runoff plots, and are also in agreement with the existing knowledge provided by 137Cs measurements. The results obtained from this study demonstrated the potential for using (7)Be technique to quantify short-term erosion rates in these areas. Copyright © 2011 Elsevier Ltd. All rights reserved.

GOplot: an R package for visually combining expression data with functional analysis.

PubMed

Walter, Wencke; Sánchez-Cabo, Fátima; Ricote, Mercedes

2015-09-01

Despite the plethora of methods available for the functional analysis of omics data, obtaining comprehensive-yet detailed understanding of the results remains challenging. This is mainly due to the lack of publicly available tools for the visualization of this type of information. Here we present an R package called GOplot, based on ggplot2, for enhanced graphical representation. Our package takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings. The R package GOplot is available via CRAN-The Comprehensive R Archive Network: http://cran.r-project.org/web/packages/GOplot. The shiny web application of the Venn diagram can be found at: https://wwalter.shinyapps.io/Venn/. A detailed manual of the package with sample figures can be found at https://wencke.github.io/ fscabo@cnic.es or mricote@cnic.es. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Diversity of Hymenoptera (Insecta) on different ages of oil palm in Lekir Plantation, Perak

NASA Astrophysics Data System (ADS)

Azhari, Muhammad Luqman Hakim; Hazmi, Izfa Riza

2018-04-01

This study was conducted to determine the diversity of Hymenoptera on the different ages of oil palm namely plot 12, 9 and 5 years old. Sampling was carried out from November 2015 to February 2016 at Ladang Lekir, Perak using Malaise traps and Window trap. A total of 3052 individuals Hymenopteran consisting of 58 morphospecies and 35 subfamilies of 17 families were successfully collected. The most abundant species recorded was the Pimplinae.sp4 with 447 individuals (relative abundance, RA=14.51%). According to the plot, plot 9 years old have the highest reading for all three Peilou Equality Index (E'=0.983), Shannon Diversity Index (H'=3.939) and Simpson Diversity Index (D'=0.9795) with 55 species have been recorded. The t-tests showed that there were no significant difference in term of the diversity index (H') between palm plots 9 years old and 12 years old, while there were significant differences between the two plot (9 years old and 12 years old) with 5 old palm plot. The species accumulation curve showed that only 5 old palm plot nearly asymptotic. This study is expected to help the management to provide basic information for future research and as well, to develop and implement tools, methods, strategies in farm management practices of the oil palm plantations in Malaysia.

Visualizing dispersive features in 2D image via minimum gradient method

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

He, Yu; Wang, Yan; Shen, Zhi -Xun

Here, we developed a minimum gradient based method to track ridge features in a 2D image plot, which is a typical data representation in many momentum resolved spectroscopy experiments. Through both analytic formulation and numerical simulation, we compare this new method with existing DC (distribution curve) based and higher order derivative based analyses. We find that the new method has good noise resilience and enhanced contrast especially for weak intensity features and meanwhile preserves the quantitative local maxima information from the raw image. An algorithm is proposed to extract 1D ridge dispersion from the 2D image plot, whose quantitative applicationmore » to angle-resolved photoemission spectroscopy measurements on high temperature superconductors is demonstrated.« less

Visualizing dispersive features in 2D image via minimum gradient method

DOE PAGES

He, Yu; Wang, Yan; Shen, Zhi -Xun

2017-07-24

Here, we developed a minimum gradient based method to track ridge features in a 2D image plot, which is a typical data representation in many momentum resolved spectroscopy experiments. Through both analytic formulation and numerical simulation, we compare this new method with existing DC (distribution curve) based and higher order derivative based analyses. We find that the new method has good noise resilience and enhanced contrast especially for weak intensity features and meanwhile preserves the quantitative local maxima information from the raw image. An algorithm is proposed to extract 1D ridge dispersion from the 2D image plot, whose quantitative applicationmore » to angle-resolved photoemission spectroscopy measurements on high temperature superconductors is demonstrated.« less

Pitfall Traps and Mini-Winkler Extractor as Complementary Methods to Sample Soil Coleoptera.

PubMed

Carneiro, A C; Batistella, D A; Battirola, L D; Marques, M I

2016-02-01

We compared abundance, species richness, and capture efficiency with pitfall traps and mini-Winkler extractors to examine their use as complementary methods for sampling soil Coleoptera during dry (2010) and high water seasons (2011) in three areas, including inundated and non-inundated regions, in the Pantanal of Poconé, Mato Grosso, Brazil. We paired treatments with two 10 × 10 m plots in inundated and non-inundated locations that were repeated three times in each location for a total of 18 plots. In each plot, we used nine pitfall traps and collected 2 m(2) of leaf litter and surface soil samples with mini-Winkler extractors. We collected a total of 4260 adult beetles comprising 36 families, 113 genera, and 505 species. Most were caught in pitfalls (69%) and the remainder in the mini-Winkler extractors (31%). Each method provided distinct information about the beetle community: 252 species were captured only in pitfall traps, 147 using only the mini-Winkler extractors, and these methods shared another 106 species. Pitfall and mini-Winkler contribute in different ways for the sampling of the soil beetle community, and so they should be considered complementary for a more thorough assessment of community diversity.

Greater resistance and lower contribution of free radicals to hypoxic neurotoxicity in immature rat brain compared to adult brain as revealed by dynamic changes in glucose metabolism.

PubMed

Maruoka, N; Murata, T; Omata, N; Fujibayashi, Y; Waki, A; Yoshimoto, M; Yano, R; Yonekura, Y; Wada, Y

2001-01-01

Seven-day-old rat brain slices were incubated at 36C in oxygenated Krebs-Ringer solution containing [(18)F]2-fluoro-2-deoxy-D-glucose ([(18)F]FDG), and serial two-dimensional time-resolved images of [(18)F]FDG uptake by the slices were obtained. The Gjedde-Patlak graphical method was applied to the image data, and the duration limit of hypoxia loading that allowed recovery of the fractional rate constant (k3*) of [(18)F]FDG (proportional to the cerebral glucose metabolic rate) after hypoxia loading to the unloaded control level was 50 min, and MK-801 as an N-methyl-D-aspartate antagonist had neuroprotective effects, but PBN as a free radical scavenger was ineffective. In our previous study in adult (7-week-old) rat brains [Murata et al., Exp Neurol 2000, 164:269-279], the limit of the hypoxia loading time was 20 min, and both MK-801 and PBN were effective. In the immature rat brains, the ratio of aerobic glucose metabolism to the total glucose metabolism was low compared with the adult rat brains, suggesting only a slight involvement of free radicals in hypoxic neurotoxicity. These data suggest that the higher resistance of immature brains to hypoxia compared to that of adult brains is attributable to a lower involvement of free radicals due to a lower aerobic glucose metabolic rate. Copyright 2002 S. Karger AG, Basel

Spatial distribution of soil moisture and hydrophobicity in the immediate period after a grassland fire in Lithuania

NASA Astrophysics Data System (ADS)

Pereira, P.; Pundyte, N.; Vaitkute, D.; Cepanko, V.; Pranskevicius, M.; Ubeda, X.; Mataix-Solera, J.; Cerda, A.

2012-04-01

Fire can affect significantly soil moisture (SM) and water repellency (WR) in the immediate period after the fire due the effect of the temperatures into soil profile and ash. This impact can be very heterogeneous, even in small distances, due to different conditions of combustion (e.g. fuel and soil moisture, fuel amount and type, distribution and connection, and geomorphological variables as aspect and slope) that influences fire temperature and severity. The aim of this work it is study the spatial distribution of SM and WR in a small plot (400 m2 with a sampling distance of 5 m) immediately after the a low severity grassland fire.. This was made in a burned but also in a control (unburned) plot as reference to can compare. In each plot we analyzed a total of 25 samples. SM was measured gravimetrically and WR with the water drop penetration time test (WDPT). Several interpolation methods were tested in order to identify the best predictor of SM and WR, as the Inverse Distance to a Weight (IDW) (with the power of 1,2,3,4 and 5), Local Polynomial with the first and second polynomial order, Polynomial Regression (PR), Radial Basis Functions (RBF) as Multilog (MTG), Natural Cubic Spline (NCS), Multiquadratic (MTQ), Inverse Multiquadratic (IMTQ) and Thin Plate Spline (TPS) and Ordinary Kriging. Interpolation accuracy was observed with the cross-validation method that is achieved by taking each observation in turn out of the sample and estimating from the remaining ones. The errors produced in each interpolation allowed us to calculate the Root Mean Square Error (RMSE). The best method is the one that showed the lower RMSE. The results showed that on average the SM in the control plot was 13.59 % (±2.83) and WR 2.9 (±1.3) seconds (s). The majority of the soils (88%) were hydrophilic (WDPT <5s). SM in the control plot showed a weak negative relationship with WR (r=-0.33, p<0.10). The coefficient of variation (CV%) of SM was 20.77% and SW of 44.62%. In the burned plot, SM was 14.17% (±2.83) and WR of 151 (±99) seconds (s). All the samples analysed were considered hydrophobic (WDPT >5s). We did not identify significant relationships among the variables (r=0.06, p>0.05) and the CV% was higher in WR (65.85%) than SM (19.96%). Overall we identified no significant changes in SM between plots, which means that fire did not had important implications on soil water content, contrary to observed in WR. The same dynamic was observed in the CV%. Among all tested methods the most accurate to interpolate SM, in the control plot IDW 1 and in the burned plot IDW 2, and this means that fire did not induce important inferences on the spatial distribution of SM. In WR, in the control plot, the best predictor was NCS and in the burned plot was IDW 1 and this means that spatial distribution WR was substantially affected by fire. In this case we observed an increase of the small scale variability in the burned area. Currently we are monitoring this burned area and observing the evaluation of the spatial variability of these two soil properties. It is important to observe their dynamic in the space and time and observe if fire will have medium and long term implications on SM and WR. Discussions about the results will be carried out during the poster session.

Research and Development for Technology Evolution Potential Forecasting System

NASA Astrophysics Data System (ADS)

Gao, Changqing; Cao, Shukun; Wang, Yuzeng; Ai, Changsheng; Ze, Xiangbo

Technology forecasting is a powerful weapon for many enterprises to gain an animate future. Evolutionary potential radar plot is a necessary step of some valuable methods to help the technology managers with right technical strategy. A software system for Technology Evolution Potential Forecasting (TEPF) with automatic radar plot drawing is introduced in this paper. The framework of the system and the date structure describing the concrete evolution pattern are illustrated in details. And the algorithm for radar plot drawing is researched. It is proved that the TEPF system is an effective tool during the technology strategy analyzing process with a referenced case study.

Evaluation of corrective reconstruction methods using a 3D cardiac-torso phantom and bull's-eye plots

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

Zhao, X.D.; Tsui, B.M.W.; Gregoriou, G.K.

The goal of the investigation was to study the effectiveness of the corrective reconstruction methods in cardiac SPECT using a realistic phantom and to qualitatively and quantitatively evaluate the reconstructed images using bull's-eye plots. A 3D mathematical phantom which realistically models the anatomical structures of the cardiac-torso region of patients was used. The phantom allows simulation of both the attenuation distribution and the uptake of radiopharmaceuticals in different organs. Also, the phantom can be easily modified to simulate different genders and variations in patient anatomy. Two-dimensional projection data were generated from the phantom and included the effects of attenuation andmore » detector response blurring. The reconstruction methods used in the study included the conventional filtered backprojection (FBP) with no attenuation compensation, and the first-order Chang algorithm, an iterative filtered backprojection algorithm (IFBP), the weighted least square conjugate gradient algorithm and the ML-EM algorithm with non-uniform attenuation compensation. The transaxial reconstructed images were rearranged into short-axis slices from which bull's-eye plots of the count density distribution in the myocardium were generated.« less

Effects of disease severity distribution on the performance of quantitative diagnostic methods and proposal of a novel 'V-plot' methodology to display accuracy values.

PubMed

Petraco, Ricardo; Dehbi, Hakim-Moulay; Howard, James P; Shun-Shin, Matthew J; Sen, Sayan; Nijjer, Sukhjinder S; Mayet, Jamil; Davies, Justin E; Francis, Darrel P

2018-01-01

Diagnostic accuracy is widely accepted by researchers and clinicians as an optimal expression of a test's performance. The aim of this study was to evaluate the effects of disease severity distribution on values of diagnostic accuracy as well as propose a sample-independent methodology to calculate and display accuracy of diagnostic tests. We evaluated the diagnostic relationship between two hypothetical methods to measure serum cholesterol (Chol rapid and Chol gold ) by generating samples with statistical software and (1) keeping the numerical relationship between methods unchanged and (2) changing the distribution of cholesterol values. Metrics of categorical agreement were calculated (accuracy, sensitivity and specificity). Finally, a novel methodology to display and calculate accuracy values was presented (the V-plot of accuracies). No single value of diagnostic accuracy can be used to describe the relationship between tests, as accuracy is a metric heavily affected by the underlying sample distribution. Our novel proposed methodology, the V-plot of accuracies, can be used as a sample-independent measure of a test performance against a reference gold standard.

Preliminary Evaluation of Methods for Classifying Forest Site Productivity Based on Species Composition in Western North Carolina

Treesearch

W. Henry McNab; F. Thomas Lloyd; David L. Loftis

2002-01-01

The species indicator approach to forest site classification was evaluated for 210 relatively undisturbed plots established by the USDA Forest Service Forest Inventory and Analysis uni (FIA) in western North Carolina. Plots were classified by low, medium, and high levels of productivity based on 10-year individual tree basal area increment data standardized for initial...

A nearest-neighbor imputation approach to mapping tree species over large areas using forest inventory plots and moderate resolution raster data

Treesearch

B. Tyler Wilson; Andrew J. Lister; Rachel I. Riemann

2012-01-01

The paper describes an efficient approach for mapping multiple individual tree species over large spatial domains. The method integrates vegetation phenology derived from MODIS imagery and raster data describing relevant environmental parameters with extensive field plot data of tree species basal area to create maps of tree species abundance and distribution at a 250-...

Growth after partial cutting of ponderosa pine on permanent sample plots in eastern Oregon.

Treesearch

Edwin L. Mowat

1961-01-01

Between the years 1913 and 1938, seven sets of permanent sample plots were established on the Whitman, Malheur, Rogue River, and Deschutes National Forests in eastern and central Oregon to study the results of various methods of selection cutting in old-growth ponderosa pine stands. This report briefly describes these studies and gives statistics on board-foot growth...

Evaluating the Limits of Network Topology Inference Via Virtualized Network Emulation

DTIC Science & Technology

2015-06-01

76 xi Figure 5.33 Hop-plot of five best reduction methods. KDD most closely matches the Internet plot...respectively, located around the world. These monitors provide locations from which to perform network measurement experiments, primarily using the ping ...International Symposium on Modeling, Analysis and Simulation of Computer Telecommunication Systems. IEEE, 2001, pp. 346–353. 90 [21] C. Jin , Q. Chen, and S

A further use for the Harvest plot: a novel method for the presentation of data synthesis.

PubMed

Crowther, Mark; Avenell, Alison; MacLennan, Graeme; Mowatt, Graham

2011-06-01

When performing a systematic review, whether or not a meta-analysis is performed, graphical displays can be useful. Data do still need to be described, ideally in graphical form. The Harvest plot has been developed to display combined data from several studies that allows demonstration of not only effect but also study quality. We describe a modification to the Harvest plot that allows the presentation of data that normally could not be included in a forest plot meta-analysis and allows extra information to be displayed. Using specific examples, we describe how the arrangement of studies, height of the bars and additional information can be used to enhance the plot. This is an important development, which by fulfilling Tufte's nine requirements for graphical presentation, allows researchers to display evidence in a flexible way. This means readers can follow an argument in a clear and efficient manner without the need for large volumes of descriptive text. Copyright © 2011 John Wiley & Sons, Ltd. Copyright © 2011 John Wiley & Sons, Ltd.

On the Mixing of Single and Opposed Rows of Jets With a Confined Crossflow

NASA Technical Reports Server (NTRS)

Holdeman, James D.; Clisset, James R.; Moder, Jeffrey P.; Lear, William E.

2006-01-01

The primary objectives of this study were 1) to demonstrate that contour plots could be made using the data interface in the NASA GRC jet-in-crossflow (JIC) spreadsheet, and 2) to investigate the suitability of using superposition for the case of opposed rows of jets with their centerlines in-line. The current report is similar to NASA/TM-2005-213137 but the "basic" effects of a confined JIC that are shown in profile plots there are shown as contour plots in this report, and profile plots for opposed rows of aligned jets are presented here using both symmetry and superposition models. Although superposition was found to be suitable for most cases of opposed rows of jets with jet centerlines in-line, the calculation procedure in the JIC spreadsheet was not changed and it still uses the symmetry method for this case, as did all previous publications of the NASA empirical model.

Examining robustness of model selection with half-normal and LASSO plots for unreplicated factorial designs

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

Jang, Dae -Heung; Anderson-Cook, Christine Michaela

When there are constraints on resources, an unreplicated factorial or fractional factorial design can allow efficient exploration of numerous factor and interaction effects. A half-normal plot is a common graphical tool used to compare the relative magnitude of effects and to identify important effects from these experiments when no estimate of error from the experiment is available. An alternative is to use a least absolute shrinkage and selection operation plot to examine the pattern of model selection terms from an experiment. We examine how both the half-normal and least absolute shrinkage and selection operation plots are impacted by the absencemore » of individual observations or an outlier, and the robustness of conclusions obtained from these 2 techniques for identifying important effects from factorial experiments. As a result, the methods are illustrated with 2 examples from the literature.« less

Examining robustness of model selection with half-normal and LASSO plots for unreplicated factorial designs

DOE PAGES

Jang, Dae -Heung; Anderson-Cook, Christine Michaela

2017-04-12

When there are constraints on resources, an unreplicated factorial or fractional factorial design can allow efficient exploration of numerous factor and interaction effects. A half-normal plot is a common graphical tool used to compare the relative magnitude of effects and to identify important effects from these experiments when no estimate of error from the experiment is available. An alternative is to use a least absolute shrinkage and selection operation plot to examine the pattern of model selection terms from an experiment. We examine how both the half-normal and least absolute shrinkage and selection operation plots are impacted by the absencemore » of individual observations or an outlier, and the robustness of conclusions obtained from these 2 techniques for identifying important effects from factorial experiments. As a result, the methods are illustrated with 2 examples from the literature.« less

Net present value probability distributions from decline curve reserves estimates

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

Simpson, D.E.; Huffman, C.H.; Thompson, R.S.

1995-12-31

This paper demonstrates how reserves probability distributions can be used to develop net present value (NPV) distributions. NPV probability distributions were developed from the rate and reserves distributions presented in SPE 28333. This real data study used practicing engineer`s evaluations of production histories. Two approaches were examined to quantify portfolio risk. The first approach, the NPV Relative Risk Plot, compares the mean NPV with the NPV relative risk ratio for the portfolio. The relative risk ratio is the NPV standard deviation (a) divided the mean ({mu}) NPV. The second approach, a Risk - Return Plot, is a plot of themore » {mu} discounted cash flow rate of return (DCFROR) versus the {sigma} for the DCFROR distribution. This plot provides a risk-return relationship for comparing various portfolios. These methods may help evaluate property acquisition and divestiture alternatives and assess the relative risk of a suite of wells or fields for bank loans.« less

LOFT data acquisition and visual display system (DAVDS) presentation program

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

Bullock, M.G.; Miyasaki, F.S.

1976-03-01

The Data Acquisition and Visual Display System (DAVDS) at the Loss-of-Fluid Test Facility (LOFT) has 742 data channel recording capability of which 576 are recorded digitally. The purpose of this computer program is to graphically present the data acquired and/or processed by the LOFT DAVDS. This program takes specially created plot data buffers of up to 1024 words and generates time history plots on the system electrostatic printer-plotter. The data can be extracted from two system input devices: Magnetic disk or digital magnetic tape. Versatility has been designed in the program by providing the user three methods of scaling plots:more » Automatic, control record, and manual. Time required to produce a plot on the system electrostatic printer-plotter varies from 30 to 90 seconds depending on the options selected. The basic computer and program details are described.« less

Stellar refraction - A tool to monitor the height of the tropopause from space

NASA Technical Reports Server (NTRS)

Schuerman, D. W.; Giovane, F.; Greenberg, J. M.

1975-01-01

Calculations of stellar refraction for a setting or rising star as viewed from a spacecraft show that the tropopause is a discernible feature in a plot of refraction vs time. The height of the tropopause is easily obtained from such a plot. Since the refraction suffered by the starlight appears to be measurable with some precision from orbital altitudes, this technique is suggested as a method for remotely monitoring the height of the tropopause. Although limited to nighttime measurements, the method is independent of supporting data or model fitting and easily lends itself to on-line data reduction.

Developing tools for the safety specification in risk management plans: lessons learned from a pilot project.

PubMed

Cooper, Andrew J P; Lettis, Sally; Chapman, Charlotte L; Evans, Stephen J W; Waller, Patrick C; Shakir, Saad; Payvandi, Nassrin; Murray, Alison B

2008-05-01

Following the adoption of the ICH E2E guideline, risk management plans (RMP) defining the cumulative safety experience and identifying limitations in safety information are now required for marketing authorisation applications (MAA). A collaborative research project was conducted to gain experience with tools for presenting and evaluating data in the safety specification. This paper presents those tools found to be useful and the lessons learned from their use. Archive data from a successful MAA were utilised. Methods were assessed for demonstrating the extent of clinical safety experience, evaluating the sensitivity of the clinical trial data to detect treatment differences and identifying safety signals from adverse event and laboratory data to define the extent of safety knowledge with the drug. The extent of clinical safety experience was demonstrated by plots of patient exposure over time. Adverse event data were presented using dot plots, which display the percentages of patients with the events of interest, the odds ratio, and 95% confidence interval. Power and confidence interval plots were utilised for evaluating the sensitivity of the clinical database to detect treatment differences. Box and whisker plots were used to display laboratory data. This project enabled us to identify new evidence-based methods for presenting and evaluating clinical safety data. These methods represent an advance in the way safety data from clinical trials can be analysed and presented. This project emphasises the importance of early and comprehensive planning of the safety package, including evaluation of the use of epidemiology data.

Comparison of methods applied in photoinduced transient spectroscopy to determining the defect center parameters: The correlation procedure and the signal analysis based on inverse Laplace transformation

NASA Astrophysics Data System (ADS)

Suproniuk, M.; Pawłowski, M.; Wierzbowski, M.; Majda-Zdancewicz, E.; Pawłowski, Ma.

2018-04-01

The procedure for determination of trap parameters by photo-induced transient spectroscopy is based on the Arrhenius plot that illustrates a thermal dependence of the emission rate. In this paper, we show that the Arrhenius plot obtained by the correlation method is shifted toward lower temperatures as compared to the one obtained with the inverse Laplace transformation. This shift is caused by the model adequacy error of the correlation method and introduces errors to a calculation procedure of defect center parameters. The effect is exemplified by comparing the results of the determination of trap parameters with both methods based on photocurrent transients for defect centers observed in tin-doped neutron-irradiated silicon crystals and in gallium arsenide grown with the Vertical Gradient Freeze method.

[Comparison of the quick Gram stain method to the B&M modified and favor methods].

PubMed

Osawa, Kayo; Kataoka, Nobumasa; Maruo, Toshio

2011-01-01

The Gram stain is an established method for bacterial identification, but the time needed to carry out this stain is 2-3 min. We attempted to shorten this time and stained a total of 70 clinical specimens isolated from using the Bartholomew & Mittwer (B&M) modified or Favor methods with a 3 s duration for washing and staining steps. Results were plotted and analyzed using a Hue Saturation Intensity (HSI) model. The range based on a plot of the two methods with the HSI model was presented as a reference interval. Our results indicated that 100% (35/35) of strains were Gram positive and 97.1% (34/35) were Gram negative for the quick B&M modified method. In the quick Favor method, 80.0% (28/35) were Gram positive and 68.6% (24/35) of strains were Gram negative. We propose that the quick B&M modified method is equivalent to the standard Gram staining method and is superior to the quick Favor method.

Noninvasive image derived heart input function for CMRglc measurements in small animal slow infusion FDG PET studies

NASA Astrophysics Data System (ADS)

Xiong, Guoming; Cumming, Paul; Todica, Andrei; Hacker, Marcus; Bartenstein, Peter; Böning, Guido

2012-12-01

Absolute quantitation of the cerebral metabolic rate for glucose (CMRglc) can be obtained in positron emission tomography (PET) studies when serial measurements of the arterial [18F]-fluoro-deoxyglucose (FDG) input are available. Since this is not always practical in PET studies of rodents, there has been considerable interest in defining an image-derived input function (IDIF) by placing a volume of interest (VOI) within the left ventricle of the heart. However, spill-in arising from trapping of FDG in the myocardium often leads to progressive contamination of the IDIF, which propagates to underestimation of the magnitude of CMRglc. We therefore developed a novel, non-invasive method for correcting the IDIF without scaling to a blood sample. To this end, we first obtained serial arterial samples and dynamic FDG-PET data of the head and heart in a group of eight anaesthetized rats. We fitted a bi-exponential function to the serial measurements of the IDIF, and then used the linear graphical Gjedde-Patlak method to describe the accumulation in myocardium. We next estimated the magnitude of myocardial spill-in reaching the left ventricle VOI by assuming a Gaussian point-spread function, and corrected the measured IDIF for this estimated spill-in. Finally, we calculated parametric maps of CMRglc using the corrected IDIF, and for the sake of comparison, relative to serial blood sampling from the femoral artery. The uncorrected IDIF resulted in 20% underestimation of the magnitude of CMRglc relative to the gold standard arterial input method. However, there was no bias with the corrected IDIF, which was robust to the variable extent of myocardial tracer uptake, such that there was a very high correlation between individual CMRglc measurements using the corrected IDIF with gold-standard arterial input results. Based on simulation, we furthermore find that electrocardiogram-gating, i.e. ECG-gating is not necessary for IDIF quantitation using our approach.

Abundance of diurnal raptors in relation to prairie dog colonies: Implications for bird-aircraft strike hazard

USGS Publications Warehouse

Merriman, J.W.; Boal, C.W.; Bashore, T.L.; Zwank, P.J.; Wester, D.B.

2007-01-01

Some diurnal raptors are frequently observed at prairie dog (Cynomys sp.) colonies. As a result, some military installations have conducted prairie dog control activities to reduce the bird-aircraft strike hazard (BASH) potential of low-flying aircraft. To evaluate the validity of this management strategy, we assessed raptor associations with prairie dog colonies at 2 short-grass prairie study areas: southern Lubbock County, Texas, USA, and Melrose Bombing and Gunnery Range in east-central New Mexico, USA. We quantified diurnal raptors (i.e., Falconiformes) at plots occupied (colony plots) and unoccupied (noncolony plots) by black-tailed prairie dogs (Cynomys ludovicianus) at both sites throughout 2002. We compared the number of individual birds of a given species at colony and noncolony plots within each study area by season. Ferruginous hawks (Buteo regalis) and northern harriers (Circus cyaneus) were more abundant at colony plots, whereas Swainson's hawks (B. swainsoni) and American kestrels (Falco sparverius) were more abundant at noncolony plots. Red-tailed hawk (B. jamaicensis) abundance did not differ between the 2 plot types. Our results suggest prairie dog control as a method of reducing BASH potential may be effective at some sites but may be ineffective or even increase the BASH potential at others. Thus, bird-avoidance models assessing the BASH potential should be conducted on a site-specific basis using information on relative and seasonal abundances of individual raptor species and the relative strike risks they pose to aircraft.

Kudzu (Pueraria montana) community responses to herbicides, burning, and high-density loblolly pine

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

T.B. Harrington; L.T. Rader-Dixon; J.W. Taylor, Jr.

Kudzu is an aggressive, nonnative vine that currently dominates an estimated 810,000 ha of mesic forest communities in the eastern United States. To test an integrated method of weed control, abundances of kudzu and other plant species were compared during 4 yr after six herbicide treatments (clopyralid, triclopyr, metsulfuron, picloram 1 2,4-D, tebuthiuron, and a nonsprayed check), in which loblolly pines were planted at three densities (0, 1, and 4 seedlings m22) to induce competition and potentially delay kudzu recovery. This split-plot design was replicated on each of the four kudzu-dominated sites near Aiken, SC. Relative light intensity (RLI) andmore » soil water content (SWC) were measured periodically to identify mechanisms of interference among plant species. Two years after treatment (1999), crown coverage of kudzu averaged , 2% in herbicide plots compared with 93% in the nonsprayed check, and these differences were maintained through 2001, except in clopyralid plots where kudzu cover increased to 15%. In 2001, pine interference was associated with 33, 56, and 67% reductions in biomass of kudzu, blackberry, and herbaceous vegetation, respectively. RLI in kudzu-dominated plots (4 to 15% of full sun) generally was less than half that of herbicide-treated plots. SWC was greatest in tebuthiuron plots, where total vegetation cover averaged 26% compared with 77 to 111% in other plots. None of the treatments eradicated kudzu, but combinations of herbicides and induced pine competition delayed its recovery.« less

A Performance Comparison on the Probability Plot Correlation Coefficient Test using Several Plotting Positions for GEV Distribution.

NASA Astrophysics Data System (ADS)

Ahn, Hyunjun; Jung, Younghun; Om, Ju-Seong; Heo, Jun-Haeng

2014-05-01

It is very important to select the probability distribution in Statistical hydrology. Goodness of fit test is a statistical method that selects an appropriate probability model for a given data. The probability plot correlation coefficient (PPCC) test as one of the goodness of fit tests was originally developed for normal distribution. Since then, this test has been widely applied to other probability models. The PPCC test is known as one of the best goodness of fit test because it shows higher rejection powers among them. In this study, we focus on the PPCC tests for the GEV distribution which is widely used in the world. For the GEV model, several plotting position formulas are suggested. However, the PPCC statistics are derived only for the plotting position formulas (Goel and De, In-na and Nguyen, and Kim et al.) in which the skewness coefficient (or shape parameter) are included. And then the regression equations are derived as a function of the shape parameter and sample size for a given significance level. In addition, the rejection powers of these formulas are compared using Monte-Carlo simulation. Keywords: Goodness-of-fit test, Probability plot correlation coefficient test, Plotting position, Monte-Carlo Simulation ACKNOWLEDGEMENTS This research was supported by a grant 'Establishing Active Disaster Management System of Flood Control Structures by using 3D BIM Technique' [NEMA-12-NH-57] from the Natural Hazard Mitigation Research Group, National Emergency Management Agency of Korea.

An analytical method to assess spruce beetle impacts on white spruce resources, Kenai Peninsula, Alaska.

Treesearch

Willem W.S. van Hees

1992-01-01

Forest inventory data collected in 1987 fTom sample plots established on the Kenai Peninsula were analyzed to provide point-in-time estimates of the trend and current status of a spruce beetle infestation. Ground plots were categorized by stage of infestation. Estimates of numbers of live and dead white spruce trees, cubic-foot volume in those trees, and areal extent...

Establishment probability in newly founded populations.

PubMed

Gusset, Markus; Müller, Michael S; Grimm, Volker

2012-06-20

Establishment success in newly founded populations relies on reaching the established phase, which is defined by characteristic fluctuations of the population's state variables. Stochastic population models can be used to quantify the establishment probability of newly founded populations; however, so far no simple but robust method for doing so existed. To determine a critical initial number of individuals that need to be released to reach the established phase, we used a novel application of the "Wissel plot", where -ln(1 - P0(t)) is plotted against time t. This plot is based on the equation P(0)t=1-c(1)e(-ω(1t)), which relates the probability of extinction by time t, P(0)(t), to two constants: c(1) describes the probability of a newly founded population to reach the established phase, whereas ω(1) describes the population's probability of extinction per short time interval once established. For illustration, we applied the method to a previously developed stochastic population model of the endangered African wild dog (Lycaon pictus). A newly founded population reaches the established phase if the intercept of the (extrapolated) linear parts of the "Wissel plot" with the y-axis, which is -ln(c(1)), is negative. For wild dogs in our model, this is the case if a critical initial number of four packs, consisting of eight individuals each, are released. The method we present to quantify the establishment probability of newly founded populations is generic and inferences thus are transferable to other systems across the field of conservation biology. In contrast to other methods, our approach disaggregates the components of a population's viability by distinguishing establishment from persistence.

Experimental study on influence of vegetation coverage on runoff in wind-water erosion crisscross region

NASA Astrophysics Data System (ADS)

Wang, Jinhua; Zhang, Ronggang; Sun, Juan

2018-02-01

Using artificial rainfall simulation method, 23 simulation experiments were carried out in water-wind erosion crisscross region in order to analyze the influence of vegetation coverage on runoff and sediment yield. The experimental plots are standard plots with a length of 20m, width of 5m and slope of 15 degrees. The simulation experiments were conducted in different vegetation coverage experimental plots based on three different rainfall intensities. According to the experimental observation data, the influence of vegetation coverage on runoff and infiltration was analyzed. Vegetation coverage has a significant impact on runoff, and the higher the vegetation coverage is, the smaller the runoff is. Under the condition of 0.6mm/min rainfall intensity, the runoff volume from the experimental plot with 18% vegetation coverage was 1.2 times of the runoff from the experimental with 30% vegetation coverage. What’s more, the difference of runoff is more obvious in higher rainfall intensity. If the rainfall intensity reaches 1.32mm/min, the runoff from the experimental plot with 11% vegetation coverage is about 2 times as large as the runoff from the experimental plot with 53%vegetation coverage. Under the condition of small rainfall intensity, the starting time of runoff in the experimental plot with higher vegetation coverage is later than that in the experimental plot with low vegetation coverage. However, under the condition of heavy rainfall intensity, there is no obvious difference in the beginning time of runoff. In addition, the higher the vegetation coverage is, the deeper the rainfall infiltration depth is.The results can provide reference for ecological construction carried out in wind erosion crisscross region with serious soil erosion.

Study of the effectiveness of several tree canopy types on roadside green belt in influencing the distribution of NO2 gas emitted from transportation

NASA Astrophysics Data System (ADS)

Desyana, R. D.; Sulistyantara, B.; Nasrullah, N.; Fatimah, I. S.

2017-03-01

Transportation is one significant factor which contributes to urban air pollution. One of the pollutants emitted from transportation which affect human’s health is NO2. Plants, especially trees, have high potential in reducing air pollutants from transportation through diffusion, absorbtion, adsorption and deposition. Purpose of this study was to analyze the effectiveness of several tree canopy types on roadside green belt in influencing distribution of NO2 gas emitted from transportation. The study conducted in three plots of tree canopy in Jagorawi Highway: Bungur (Lagerstroemia speciosa), Gmelina (Gmelina arborea) and Tanjung (Mimusops elengi). The tree canopy ability in absorbing pollutant is derived by comparing air quality on vegetated area with ambience air quality at control area (open field). Air sampling was conducted to measure NO2 concentration at elevation 1.5m, 5m and 10m at distance 0m, 10m and 30m, using Air Sampler Impinger. Concentration of NO2 was analyzed with Griess-Saltzman method. From this research, the result of ANOVA showed that tree plot (vegetated area) affected significantly to NO2 concentration. However the effect of distance from road and elevation was not significant. Among the plots, the highest NO2 concentration was found on Control plot (area without tree canopy), while the lowest NO2 concentration was found in Tanjung plot. Tanjung plot with round shape and high density canopy performed better in reducing NO2 than Bungur plot with round shape and medium density canopy, regardless the sampling elevation and distance. Gmelina plot performed the best in reducing horizontal distribution of NO2 concentration at elevation 1.5 and 5m, but the result at elevation 10m was not significant.

Predicting cotton yield of small field plots in a cotton breeding program using UAV imagery data

NASA Astrophysics Data System (ADS)

Maja, Joe Mari J.; Campbell, Todd; Camargo Neto, Joao; Astillo, Philip

2016-05-01

One of the major criteria used for advancing experimental lines in a breeding program is yield performance. Obtaining yield performance data requires machine picking each plot with a cotton picker, modified to weigh individual plots. Harvesting thousands of small field plots requires a great deal of time and resources. The efficiency of cotton breeding could be increased significantly while the cost could be decreased with the availability of accurate methods to predict yield performance. This work is investigating the feasibility of using an image processing technique using a commercial off-the-shelf (COTS) camera mounted on a small Unmanned Aerial Vehicle (sUAV) to collect normal RGB images in predicting cotton yield on small plot. An orthonormal image was generated from multiple images and used to process multiple, segmented plots. A Gaussian blur was used to eliminate the high frequency component of the images, which corresponds to the cotton pixels, and used image subtraction technique to generate high frequency pixel images. The cotton pixels were then separated using k-means cluster with 5 classes. Based on the current work, the calculated percentage cotton area was computed using the generated high frequency image (cotton pixels) divided by the total area of the plot. Preliminary results showed (five flights, 3 altitudes) that cotton cover on multiple pre-selected 227 sq. m. plots produce an average of 8% which translate to approximately 22.3 kgs. of cotton. The yield prediction equation generated from the test site was then use on a separate validation site and produced a prediction error of less than 10%. In summary, the results indicate that a COTS camera with an appropriate image processing technique can produce results that are comparable to expensive sensors.

A Review on the Nonlinear Dynamical System Analysis of Electrocardiogram Signal

PubMed Central

Mohapatra, Biswajit

2018-01-01

Electrocardiogram (ECG) signal analysis has received special attention of the researchers in the recent past because of its ability to divulge crucial information about the electrophysiology of the heart and the autonomic nervous system activity in a noninvasive manner. Analysis of the ECG signals has been explored using both linear and nonlinear methods. However, the nonlinear methods of ECG signal analysis are gaining popularity because of their robustness in feature extraction and classification. The current study presents a review of the nonlinear signal analysis methods, namely, reconstructed phase space analysis, Lyapunov exponents, correlation dimension, detrended fluctuation analysis (DFA), recurrence plot, Poincaré plot, approximate entropy, and sample entropy along with their recent applications in the ECG signal analysis. PMID:29854361

A Review on the Nonlinear Dynamical System Analysis of Electrocardiogram Signal.

PubMed

Nayak, Suraj K; Bit, Arindam; Dey, Anilesh; Mohapatra, Biswajit; Pal, Kunal

2018-01-01

Electrocardiogram (ECG) signal analysis has received special attention of the researchers in the recent past because of its ability to divulge crucial information about the electrophysiology of the heart and the autonomic nervous system activity in a noninvasive manner. Analysis of the ECG signals has been explored using both linear and nonlinear methods. However, the nonlinear methods of ECG signal analysis are gaining popularity because of their robustness in feature extraction and classification. The current study presents a review of the nonlinear signal analysis methods, namely, reconstructed phase space analysis, Lyapunov exponents, correlation dimension, detrended fluctuation analysis (DFA), recurrence plot, Poincaré plot, approximate entropy, and sample entropy along with their recent applications in the ECG signal analysis.

Towards the harmonization between National Forest Inventory and Forest Condition Monitoring. Consistency of plot allocation and effect of tree selection methods on sample statistics in Italy.

PubMed

Gasparini, Patrizia; Di Cosmo, Lucio; Cenni, Enrico; Pompei, Enrico; Ferretti, Marco

2013-07-01

In the frame of a process aiming at harmonizing National Forest Inventory (NFI) and ICP Forests Level I Forest Condition Monitoring (FCM) in Italy, we investigated (a) the long-term consistency between FCM sample points (a subsample of the first NFI, 1985, NFI_1) and recent forest area estimates (after the second NFI, 2005, NFI_2) and (b) the effect of tree selection method (tree-based or plot-based) on sample composition and defoliation statistics. The two investigations were carried out on 261 and 252 FCM sites, respectively. Results show that some individual forest categories (larch and stone pine, Norway spruce, other coniferous, beech, temperate oaks and cork oak forests) are over-represented and others (hornbeam and hophornbeam, other deciduous broadleaved and holm oak forests) are under-represented in the FCM sample. This is probably due to a change in forest cover, which has increased by 1,559,200 ha from 1985 to 2005. In case of shift from a tree-based to a plot-based selection method, 3,130 (46.7%) of the original 6,703 sample trees will be abandoned, and 1,473 new trees will be selected. The balance between exclusion of former sample trees and inclusion of new ones will be particularly unfavourable for conifers (with only 16.4% of excluded trees replaced by new ones) and less for deciduous broadleaves (with 63.5% of excluded trees replaced). The total number of tree species surveyed will not be impacted, while the number of trees per species will, and the resulting (plot-based) sample composition will have a much larger frequency of deciduous broadleaved trees. The newly selected trees have-in general-smaller diameter at breast height (DBH) and defoliation scores. Given the larger rate of turnover, the deciduous broadleaved part of the sample will be more impacted. Our results suggest that both a revision of FCM network to account for forest area change and a plot-based approach to permit statistical inference and avoid bias in the tree sample composition in terms of DBH (and likely age and structure) are desirable in Italy. As the adoption of a plot-based approach will keep a large share of the trees formerly selected, direct tree-by-tree comparison will remain possible, thus limiting the impact on the time series comparability. In addition, the plot-based design will favour the integration with NFI_2.

Soil aggregate stability and size-selective sediment transport with surface runoff as affected by organic residue amendment.

PubMed

Shi, Pu; Arter, Christian; Liu, Xingyu; Keller, Martin; Schulin, Rainer

2017-12-31

Aggregate breakdown influences the availability of soil particles for size-selective sediment transport with surface runoff during erosive rainfall events. Organic matter management is known to affect aggregate stability against breakdown, but little is known about how this translates into rainfall-induced aggregate fragmentation and sediment transport under field conditions. In this study, we performed field experiments in which artificial rainfall was applied after pre-wetting on three pairs of arable soil plots (1.5×0.75m) six weeks after incorporating a mixture of grass and wheat straw into the topsoil of one plot in each pair (OI treatment) but not on the other plot (NI treatment). Artificial rainfall was applied for approximately 2h on each pair at an intensity of 49.1mmh -1 . In both treatments, discharge and sediment concentration in the discharge were correlated and followed a similar temporal pattern after the onset of surface runoff: After a sharp increase at the beginning both approached a steady state. But the onset of runoff was more delayed on the OI plots, and the discharge and sediment concentration were in average only roughly half as high on the OI as on the NI plots. With increasing discharge the fraction of coarse sediment increased. This relationship did not differ between the two treatments. Thus, due to the lower discharge, the fraction of fine particles in the exported sediment was larger in the runoff from the OI plots than from the NI plots. The later runoff onset and lower discharge rate was related to a higher initial aggregate stability on the OI plots. Terrestrial laser scanning proved to be a very valuable method to map changes in the micro-topography of the soil surfaces. It revealed a much less profound decrease in surface roughness on the OI than on the NI plots. Copyright © 2017 Elsevier B.V. All rights reserved.

Visual evaluation of kinetic characteristics of PET probe for neuroreceptors using a two-phase graphic plot analysis.

PubMed

Ito, Hiroshi; Ikoma, Yoko; Seki, Chie; Kimura, Yasuyuki; Kawaguchi, Hiroshi; Takuwa, Hiroyuki; Ichise, Masanori; Suhara, Tetsuya; Kanno, Iwao

2017-05-01

Objectives In PET studies for neuroreceptors, tracer kinetics are described by the two-tissue compartment model (2-TCM), and binding parameters, including the total distribution volume (V T ), non-displaceable distribution volume (V ND ), and binding potential (BP ND ), can be determined from model parameters estimated by kinetic analysis. The stability of binding parameter estimates depends on the kinetic characteristics of radioligands. To describe these kinetic characteristics, we previously developed a two-phase graphic plot analysis in which V ND and V T can be estimated from the x-intercept of regression lines for early and delayed phases, respectively. In this study, we applied this graphic plot analysis to visual evaluation of the kinetic characteristics of radioligands for neuroreceptors, and investigated a relationship between the shape of these graphic plots and the stability of binding parameters estimated by the kinetic analysis with 2-TCM in simulated brain tissue time-activity curves (TACs) with various binding parameters. Methods 90-min TACs were generated with the arterial input function and assumed kinetic parameters according to 2-TCM. Graphic plot analysis was applied to these simulated TACs, and the curvature of the plot for each TAC was evaluated visually. TACs with several noise levels were also generated with various kinetic parameters, and the bias and variation of binding parameters estimated by kinetic analysis were calculated in each TAC. These bias and variation were compared with the shape of graphic plots. Results The graphic plots showed larger curvature for TACs with higher specific binding and slower dissociation of specific binding. The quartile deviations of V ND and BP ND determined by kinetic analysis were smaller for radioligands with slow dissociation. Conclusions The larger curvature of graphic plots for radioligands with slow dissociation might indicate a stable determination of V ND and BP ND by kinetic analysis. For investigation of the kinetics of radioligands, such kinetic characteristics should be considered.

Average Stand Age from Forest Inventory Plots Does Not Describe Historical Fire Regimes in Ponderosa Pine and Mixed-Conifer Forests of Western North America.

PubMed

Stevens, Jens T; Safford, Hugh D; North, Malcolm P; Fried, Jeremy S; Gray, Andrew N; Brown, Peter M; Dolanc, Christopher R; Dobrowski, Solomon Z; Falk, Donald A; Farris, Calvin A; Franklin, Jerry F; Fulé, Peter Z; Hagmann, R Keala; Knapp, Eric E; Miller, Jay D; Smith, Douglas F; Swetnam, Thomas W; Taylor, Alan H

Quantifying historical fire regimes provides important information for managing contemporary forests. Historical fire frequency and severity can be estimated using several methods; each method has strengths and weaknesses and presents challenges for interpretation and verification. Recent efforts to quantify the timing of historical high-severity fire events in forests of western North America have assumed that the "stand age" variable from the US Forest Service Forest Inventory and Analysis (FIA) program reflects the timing of historical high-severity (i.e. stand-replacing) fire in ponderosa pine and mixed-conifer forests. To test this assumption, we re-analyze the dataset used in a previous analysis, and compare information from fire history records with information from co-located FIA plots. We demonstrate that 1) the FIA stand age variable does not reflect the large range of individual tree ages in the FIA plots: older trees comprised more than 10% of pre-stand age basal area in 58% of plots analyzed and more than 30% of pre-stand age basal area in 32% of plots, and 2) recruitment events are not necessarily related to high-severity fire occurrence. Because the FIA stand age variable is estimated from a sample of tree ages within the tree size class containing a plurality of canopy trees in the plot, it does not necessarily include the oldest trees, especially in uneven-aged stands. Thus, the FIA stand age variable does not indicate whether the trees in the predominant size class established in response to severe fire, or established during the absence of fire. FIA stand age was not designed to measure the time since a stand-replacing disturbance. Quantification of historical "mixed-severity" fire regimes must be explicit about the spatial scale of high-severity fire effects, which is not possible using FIA stand age data.

Average Stand Age from Forest Inventory Plots Does Not Describe Historical Fire Regimes in Ponderosa Pine and Mixed-Conifer Forests of Western North America

PubMed Central

Stevens, Jens T.; Safford, Hugh D.; North, Malcolm P.; Fried, Jeremy S.; Gray, Andrew N.; Brown, Peter M.; Dolanc, Christopher R.; Dobrowski, Solomon Z.; Falk, Donald A.; Farris, Calvin A.; Franklin, Jerry F.; Fulé, Peter Z.; Hagmann, R. Keala; Knapp, Eric E.; Miller, Jay D.; Smith, Douglas F.; Swetnam, Thomas W.; Taylor, Alan H.

2016-01-01

Quantifying historical fire regimes provides important information for managing contemporary forests. Historical fire frequency and severity can be estimated using several methods; each method has strengths and weaknesses and presents challenges for interpretation and verification. Recent efforts to quantify the timing of historical high-severity fire events in forests of western North America have assumed that the “stand age” variable from the US Forest Service Forest Inventory and Analysis (FIA) program reflects the timing of historical high-severity (i.e. stand-replacing) fire in ponderosa pine and mixed-conifer forests. To test this assumption, we re-analyze the dataset used in a previous analysis, and compare information from fire history records with information from co-located FIA plots. We demonstrate that 1) the FIA stand age variable does not reflect the large range of individual tree ages in the FIA plots: older trees comprised more than 10% of pre-stand age basal area in 58% of plots analyzed and more than 30% of pre-stand age basal area in 32% of plots, and 2) recruitment events are not necessarily related to high-severity fire occurrence. Because the FIA stand age variable is estimated from a sample of tree ages within the tree size class containing a plurality of canopy trees in the plot, it does not necessarily include the oldest trees, especially in uneven-aged stands. Thus, the FIA stand age variable does not indicate whether the trees in the predominant size class established in response to severe fire, or established during the absence of fire. FIA stand age was not designed to measure the time since a stand-replacing disturbance. Quantification of historical “mixed-severity” fire regimes must be explicit about the spatial scale of high-severity fire effects, which is not possible using FIA stand age data. PMID:27196621

Audio feature extraction using probability distribution function

NASA Astrophysics Data System (ADS)

Suhaib, A.; Wan, Khairunizam; Aziz, Azri A.; Hazry, D.; Razlan, Zuradzman M.; Shahriman A., B.

2015-05-01

Voice recognition has been one of the popular applications in robotic field. It is also known to be recently used for biometric and multimedia information retrieval system. This technology is attained from successive research on audio feature extraction analysis. Probability Distribution Function (PDF) is a statistical method which is usually used as one of the processes in complex feature extraction methods such as GMM and PCA. In this paper, a new method for audio feature extraction is proposed which is by using only PDF as a feature extraction method itself for speech analysis purpose. Certain pre-processing techniques are performed in prior to the proposed feature extraction method. Subsequently, the PDF result values for each frame of sampled voice signals obtained from certain numbers of individuals are plotted. From the experimental results obtained, it can be seen visually from the plotted data that each individuals' voice has comparable PDF values and shapes.

Analytic modeling of aerosol size distributions

NASA Technical Reports Server (NTRS)

Deepack, A.; Box, G. P.

1979-01-01

Mathematical functions commonly used for representing aerosol size distributions are studied parametrically. Methods for obtaining best fit estimates of the parameters are described. A catalog of graphical plots depicting the parametric behavior of the functions is presented along with procedures for obtaining analytical representations of size distribution data by visual matching of the data with one of the plots. Examples of fitting the same data with equal accuracy by more than one analytic model are also given.

Confidence regions of planar cardiac vectors

NASA Technical Reports Server (NTRS)

Dubin, S.; Herr, A.; Hunt, P.

1980-01-01

A method for plotting the confidence regions of vectorial data obtained in electrocardiology is presented. The 90%, 95% and 99% confidence regions of cardiac vectors represented in a plane are obtained in the form of an ellipse centered at coordinates corresponding to the means of a sample selected at random from a bivariate normal distribution. An example of such a plot for the frontal plane QRS mean electrical axis for 80 horses is also presented.

CADDIS Volume 4. Data Analysis: Advanced Analyses - Controlling for Natural Variability: SSD Plot Diagrams

EPA Pesticide Factsheets

Methods for controlling natural variability, predicting environmental conditions from biological observations method, biological trait data, species sensitivity distributions, propensity scores, Advanced Analyses of Data Analysis references.

Recovery of heart rate variability after treadmill exercise analyzed by lagged Poincaré plot and spectral characteristics.

PubMed

Shi, Ping; Hu, Sijung; Yu, Hongliu

2018-02-01

The aim of this study was to analyze the recovery of heart rate variability (HRV) after treadmill exercise and to investigate the autonomic nervous system response after exercise. Frequency domain indices, i.e., LF(ms 2 ), HF(ms 2 ), LF(n.u.), HF(n.u.) and LF/HF, and lagged Poincaré plot width (SD1 m ) and length (SD2 m ) were introduced for comparison between the baseline period (Pre-E) before treadmill running and two periods after treadmill running (Post-E1 and Post-E2). The correlations between lagged Poincaré plot indices and frequency domain indices were applied to reveal the long-range correlation between linear and nonlinear indices during the recovery of HRV. The results suggested entirely attenuated autonomic nervous activity to the heart following the treadmill exercise. After the treadmill running, the sympathetic nerves achieved dominance and the parasympathetic activity was suppressed, which lasted for more than 4 min. The correlation coefficients between lagged Poincaré plot indices and spectral power indices could separate not only Pre-E and two sessions after the treadmill running, but also the two sessions in recovery periods, i.e., Post-E1 and Post-E2. Lagged Poincaré plot as an innovative nonlinear method showed a better performance over linear frequency domain analysis and conventional nonlinear Poincaré plot.

Unmanned aircraft system-derived crop height and normalized difference vegetation index metrics for sorghum yield and aphid stress assessment

NASA Astrophysics Data System (ADS)

Stanton, Carly; Starek, Michael J.; Elliott, Norman; Brewer, Michael; Maeda, Murilo M.; Chu, Tianxing

2017-04-01

A small, fixed-wing unmanned aircraft system (UAS) was used to survey a replicated small plot field experiment designed to estimate sorghum damage caused by an invasive aphid. Plant stress varied among 40 plots through manipulation of aphid densities. Equipped with a consumer-grade near-infrared camera, the UAS was flown on a recurring basis over the growing season. The raw imagery was processed using structure-from-motion to generate normalized difference vegetation index (NDVI) maps of the fields and three-dimensional point clouds. NDVI and plant height metrics were averaged on a per plot basis and evaluated for their ability to identify aphid-induced plant stress. Experimental soil signal filtering was performed on both metrics, and a method filtering low near-infrared values before NDVI calculation was found to be the most effective. UAS NDVI was compared with NDVI from sensors onboard a manned aircraft and a tractor. The correlation results showed dependence on the growth stage. Plot averages of NDVI and canopy height values were compared with per-plot yield at 14% moisture and aphid density. The UAS measures of plant height and NDVI were correlated to plot averages of yield and insect density. Negative correlations between aphid density and NDVI were seen near the end of the season in the most damaged crops.

Tracing Personalized Health Curves during Infections

PubMed Central

Schneider, David S.

2011-01-01

It is difficult to describe host–microbe interactions in a manner that deals well with both pathogens and mutualists. Perhaps a way can be found using an ecological definition of tolerance, where tolerance is defined as the dose response curve of health versus parasite load. To plot tolerance, individual infections are summarized by reporting the maximum parasite load and the minimum health for a population of infected individuals and the slope of the resulting curve defines the tolerance of the population. We can borrow this method of plotting health versus microbe load in a population and make it apply to individuals; instead of plotting just one point that summarizes an infection in an individual, we can plot the values at many time points over the course of an infection for one individual. This produces curves that trace the course of an infection through phase space rather than over a more typical timeline. These curves highlight relationships like recovery and point out bifurcations that are difficult to visualize with standard plotting techniques. Only nine archetypical curves are needed to describe most pathogenic and mutualistic host–microbe interactions. The technique holds promise as both a qualitative and quantitative approach to dissect host–microbe interactions of all kinds. PMID:21957398

The communities of terrestrial macrofungi in different forest types in vicinities of Khanty-Mansiysk (middle taiga zone of West Siberia).

PubMed

Filippova, Nina; Bulyonkova, Tatiana

2017-01-01

The diversity of macrofungi in the vicinities of Khanty-Mansiysk (Yugra, Russia) was surveyed using a method of permanent sampling plots. Ten plots, each consisting of a number of micro-plots, were established in several different communities ranging from old-growth mixed taiga forest to its derivatives in cutting succession and bogged areas. For more complete registration of the mycota, plots were supplemented with random walking routes directly nearby. Survey results were subjected to various quantitative analyses which allowed not only to evaluate the diversity of fungi but also to obtain valuable information on occurrence, abundance and ecology of individual species as well as community structure and its dynamics in the course of ecological succession. The paper reports the results of the first year of observations. 460 species of terrestrial macrofungi revealed in a poorly explored area in middle taiga of West Siberia. The plot-based study revealed differences between communities of terrestrial macrofungi of old coniferous forests, their after-cutting secondary formations and bogged stages. The survey allowed to reveal records of 3 species listed in the Red Data Book of Russia and 9 species listed in the Red Data Book of Yugra.

Detection of diluted contaminants on chicken carcasses using a two-dimensional scatter plot based on a two-dimensional hyperspectral correlation spectrum.

PubMed

Wu, Wei; Chen, Gui-Yun; Wu, Ming-Qing; Yu, Zhen-Wei; Chen, Kun-Jie

2017-03-20

A two-dimensional (2D) scatter plot method based on the 2D hyperspectral correlation spectrum is proposed to detect diluted blood, bile, and feces from the cecum and duodenum on chicken carcasses. First, from the collected hyperspectral data, a set of uncontaminated regions of interest (ROIs) and four sets of contaminated ROIs were selected, whose average spectra were treated as the original spectrum and influenced spectra, respectively. Then, the difference spectra were obtained and used to conduct correlation analysis, from which the 2D hyperspectral correlation spectrum was constructed using the analogy method of 2D IR correlation spectroscopy. Two maximum auto-peaks and a pair of cross peaks appeared at 656 and 474 nm. Therefore, 656 and 474 nm were selected as the characteristic bands because they were most sensitive to the spectral change induced by the contaminants. The 2D scatter plots of the contaminants, clean skin, and background in the 474- and 656-nm space were used to distinguish the contaminants from the clean skin and background. The threshold values of the 474- and 656-nm bands were determined by receiver operating characteristic (ROC) analysis. According to the ROC results, a pixel whose relative reflectance at 656 nm was greater than 0.5 and relative reflectance at 474 nm was lower than 0.3 was judged as a contaminated pixel. A region with more than 50 pixels identified was marked in the detection graph. This detection method achieved a recognition rate of up to 95.03% at the region level and 31.84% at the pixel level. The false-positive rate was only 0.82% at the pixel level. The results of this study confirm that the 2D scatter plot method based on the 2D hyperspectral correlation spectrum is an effective method for detecting diluted contaminants on chicken carcasses.

Aerial Images and Convolutional Neural Network for Cotton Bloom Detection.

PubMed

Xu, Rui; Li, Changying; Paterson, Andrew H; Jiang, Yu; Sun, Shangpeng; Robertson, Jon S

2017-01-01

Monitoring flower development can provide useful information for production management, estimating yield and selecting specific genotypes of crops. The main goal of this study was to develop a methodology to detect and count cotton flowers, or blooms, using color images acquired by an unmanned aerial system. The aerial images were collected from two test fields in 4 days. A convolutional neural network (CNN) was designed and trained to detect cotton blooms in raw images, and their 3D locations were calculated using the dense point cloud constructed from the aerial images with the structure from motion method. The quality of the dense point cloud was analyzed and plots with poor quality were excluded from data analysis. A constrained clustering algorithm was developed to register the same bloom detected from different images based on the 3D location of the bloom. The accuracy and incompleteness of the dense point cloud were analyzed because they affected the accuracy of the 3D location of the blooms and thus the accuracy of the bloom registration result. The constrained clustering algorithm was validated using simulated data, showing good efficiency and accuracy. The bloom count from the proposed method was comparable with the number counted manually with an error of -4 to 3 blooms for the field with a single plant per plot. However, more plots were underestimated in the field with multiple plants per plot due to hidden blooms that were not captured by the aerial images. The proposed methodology provides a high-throughput method to continuously monitor the flowering progress of cotton.

Influence plots for LASSO

DOE PAGES

Jang, Dae -Heung; Anderson-Cook, Christine Michaela

2016-11-22

With many predictors in regression, fitting the full model can induce multicollinearity problems. Least Absolute Shrinkage and Selection Operation (LASSO) is useful when the effects of many explanatory variables are sparse in a high-dimensional dataset. Influential points can have a disproportionate impact on the estimated values of model parameters. Here, this paper describes a new influence plot that can be used to increase understanding of the contributions of individual observations and the robustness of results. This can serve as a complement to other regression diagnostics techniques in the LASSO regression setting. Using this influence plot, we can find influential pointsmore » and their impact on shrinkage of model parameters and model selection. Lastly, we provide two examples to illustrate the methods.« less

A new method to study ferroelectrics using the remanent Henkel plots

NASA Astrophysics Data System (ADS)

Vopson, Melvin M.

2018-05-01

Analysis of experimental curves constructed from dc demagnetization and isothermal remanent magnetization known as Henkel and delta M plots, have served for over 53 years as an important tool for characterization of interactions in ferromagnets. In this article we address the question whether the same experimental technique could be applied to the study of ferroelectric systems. The successful measurement of the equivalent dc depolarisation and isothermal remanent polarization curves and the construction of the Henkel and delta P plots for ferroelectrics is reported here. Full measurement protocol is provided together with experimental examples for two ferroelectric ceramic samples. This new measurement technique is an invaluable experimental tool that could be used to further advance our understanding of ferroelectric materials and their applications.

Influence plots for LASSO

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

Jang, Dae -Heung; Anderson-Cook, Christine Michaela

With many predictors in regression, fitting the full model can induce multicollinearity problems. Least Absolute Shrinkage and Selection Operation (LASSO) is useful when the effects of many explanatory variables are sparse in a high-dimensional dataset. Influential points can have a disproportionate impact on the estimated values of model parameters. Here, this paper describes a new influence plot that can be used to increase understanding of the contributions of individual observations and the robustness of results. This can serve as a complement to other regression diagnostics techniques in the LASSO regression setting. Using this influence plot, we can find influential pointsmore » and their impact on shrinkage of model parameters and model selection. Lastly, we provide two examples to illustrate the methods.« less

Vegetation responses to natural regulation of elk in Rocky Mountain National Park

USGS Publications Warehouse

Zeigenfuss, Linda C.; Singer, Francis J.; Bowden, David

1999-01-01

Some grazing-induced responses were detected. Grazing-resistant species such as sedges (native), timothy (exotic), and club mosses increased and the amount of bare ground increased on some grazed sites. However, the changes within this sampling program alone were not alarming. The amount of bare ground increase was minor (4%), and grass and shrub cover increased in the shrub plots. The inferential power ofthis sample design was limited to the study plots only. Other factors (climate change, succession) were not controlled for using fenced plots and the sensitivity ofthe methods and plots to detect change were limited. For example, the low number oftransects in willow was not adequate to monitor conditions on the entire winter range. Lacking controls, observed changes may have been due to other factors (climate trends, beaver dam abandonment, stream channel changes), not elk herbivory alone. We recommend using a new sampling design that would include controls, pretreatment data, random site selection, and much more replication.

Fractionated irradiation of carbon beam and the isoeffect dose on acute reaction of skin

PubMed Central

Uzawa, Akiko; Hirayama, Ryoichi; Matsumoto, Yoshitaka; Koda, Kana; Koike, Sachiko; Ando, Koichi; Furusawa, Yoshiya

2014-01-01

Purpose: The aim of this study was to clear any specific LETs cause change in skin reaction. We irradiated mice feet with mono-energetic and SOBP carbon ions, to obtain dose–response of early skin reaction at different LETs. Materials and methods: Mice: C3H/HeMsNrsf female mice aged 4 months old were used for this study. The animals were produced and maintained in specific pathogen-free (SPF) facilities. Irradiation: The mice right hind legs received daily fractionated irradiation ranged from single to six fractions. Carbon ions (12C6+) were accelerated by the HIMAC synchrotron to 290 MeV/u. Irradiation was conducted using horizontal carbon-ion beams with a dose rate of ∼3 Gy/min. We chose the LETs at entrance of plateau (20keV/μm) and the SOBP (proximal: 40 keV/μm, middle: 45 keV/μm, distal: 60 keV/μm, distal-end: 80 keV/μm). The reference beam was 137Cs gamma rays with a dose rate of 1.2 Gy/min. Skin reaction: Skin reaction of the irradiated legs was scored every other day, between the14th and 35th post-irradiation days. Our scoring scale consisted of seven steps, ranging from 0.5 to 3.5 [ 1]. The skin score analyzed a result by the method that described by Ando et al. [ 2]. The Fe-plot proposed by Douglas and Fowler was used as a multifraction linear quadratic model. A plot between the reciprocal of the isoeffect dose and the dose per fraction resulted in a straight line. Results: Required isoeffect total dose increased linearly with the fraction numbers on a semi-logarithmic chart at LET 20–60 keV/µm SOBP beam. The isoeffect total dose decreased with the increase in the LET. However, no increases in isoeffect total dose were observed at few fractionations at 80 keV/µm. (data not shown) Using an Fe-plot, we analyzed the isoeffect total dose to evaluate the dependence on Carbon beam, or gamma ray. When I irradiate it by gamma ray, an Fe-plot shows linearly. But, irradiated by Carbon beam, an Fe-plot bent at low fractions (Fig. 1). Conclusion: The LQ-model-based Fe-plot could not fit skin reaction at few fractions at high-LET. Clinical Trial Registration number if required: No.Fig. 1.The reciprocal of the isoeffect dose is plotted against the dose per fraction. (i) Gamma ray: Fe-plot was linear. (ii) C-ions: Fe-plot bent at low fractions.

cp-R, an interface the R programming language for clinical laboratory method comparisons.

PubMed

Holmes, Daniel T

2015-02-01

Clinical scientists frequently need to compare two different bioanalytical methods as part of assay validation/monitoring. As a matter necessity, regression methods for quantitative comparison in clinical chemistry, hematology and other clinical laboratory disciplines must allow for error in both the x and y variables. Traditionally the methods popularized by 1) Deming and 2) Passing and Bablok have been recommended. While commercial tools exist, no simple open source tool is available. The purpose of this work was to develop and entirely open-source GUI-driven program for bioanalytical method comparisons capable of performing these regression methods and able to produce highly customized graphical output. The GUI is written in python and PyQt4 with R scripts performing regression and graphical functions. The program can be run from source code or as a pre-compiled binary executable. The software performs three forms of regression and offers weighting where applicable. Confidence bands of the regression are calculated using bootstrapping for Deming and Passing Bablok methods. Users can customize regression plots according to the tools available in R and can produced output in any of: jpg, png, tiff, bmp at any desired resolution or ps and pdf vector formats. Bland Altman plots and some regression diagnostic plots are also generated. Correctness of regression parameter estimates was confirmed against existing R packages. The program allows for rapid and highly customizable graphical output capable of conforming to the publication requirements of any clinical chemistry journal. Quick method comparisons can also be performed and cut and paste into spreadsheet or word processing applications. We present a simple and intuitive open source tool for quantitative method comparison in a clinical laboratory environment. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

An accurate and computationally efficient algorithm for ground peak identification in large footprint waveform LiDAR data

NASA Astrophysics Data System (ADS)

Zhuang, Wei; Mountrakis, Giorgos

2014-09-01

Large footprint waveform LiDAR sensors have been widely used for numerous airborne studies. Ground peak identification in a large footprint waveform is a significant bottleneck in exploring full usage of the waveform datasets. In the current study, an accurate and computationally efficient algorithm was developed for ground peak identification, called Filtering and Clustering Algorithm (FICA). The method was evaluated on Land, Vegetation, and Ice Sensor (LVIS) waveform datasets acquired over Central NY. FICA incorporates a set of multi-scale second derivative filters and a k-means clustering algorithm in order to avoid detecting false ground peaks. FICA was tested in five different land cover types (deciduous trees, coniferous trees, shrub, grass and developed area) and showed more accurate results when compared to existing algorithms. More specifically, compared with Gaussian decomposition, the RMSE ground peak identification by FICA was 2.82 m (5.29 m for GD) in deciduous plots, 3.25 m (4.57 m for GD) in coniferous plots, 2.63 m (2.83 m for GD) in shrub plots, 0.82 m (0.93 m for GD) in grass plots, and 0.70 m (0.51 m for GD) in plots of developed areas. FICA performance was also relatively consistent under various slope and canopy coverage (CC) conditions. In addition, FICA showed better computational efficiency compared to existing methods. FICA's major computational and accuracy advantage is a result of the adopted multi-scale signal processing procedures that concentrate on local portions of the signal as opposed to the Gaussian decomposition that uses a curve-fitting strategy applied in the entire signal. The FICA algorithm is a good candidate for large-scale implementation on future space-borne waveform LiDAR sensors.

Real-time complication monitoring in pediatric cardiac surgery.

PubMed

Belliveau, Daniel; Burton, Hayley J; O'Blenes, Stacy B; Warren, Andrew E; Hancock Friesen, Camille L

2012-11-01

As overall mortality rates have fallen in pediatric cardiac surgical procedures, complication monitoring is becoming an increasingly important metric of patient outcome. Currently there is no standardized method available to monitor severity-adjusted complications in congenital cardiac surgical procedures. Complications associated with pediatric cardiac surgical procedures were prospectively collected from consecutive cases in a single pediatric cardiac surgical unit from October 1, 2009 to September 31, 2011. Complications were accounted for by frequency and severity and then stratified by surgical complexity, using the Risk Adjustment for Congenital Heart Surgery (RACHS) method, giving an average morbidity burden per RACHS category. "Expected" morbidity burden for each RACHS category was derived from year 1 (2009-2010) data. Observed minus expected (O:E) plots were then generated for the entire series of complications from year 2 (2010-2011) data. Separate O:E plots were also created for 5 complication classes and monitored for increases. There were 181 index surgical procedures performed in 178 patients. Two hundred and seventeen complications occurred in 80 procedures. The frequency and severity of complications increased with surgical complexity. The overall O:E plot was flagged twice for unanticipated increases in severity-adjusted complications. When the class-specific O:E plots were monitored for increases, the overall flags were found to originate from increased rates of infections and cardiac/operative complications. The O:E plot provides a simple and effective system to monitor complication rates over time based on severity-adjusted complication data. Grouping complications into classes allows us to identify specific subsets of complications that can be focused on to improve patient outcomes. Copyright © 2012 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Estimating Mixed Broadleaves Forest Stand Volume Using Dsm Extracted from Digital Aerial Images

NASA Astrophysics Data System (ADS)

Sohrabi, H.

2012-07-01

In mixed old growth broadleaves of Hyrcanian forests, it is difficult to estimate stand volume at plot level by remotely sensed data while LiDar data is absent. In this paper, a new approach has been proposed and tested for estimating stand forest volume. The approach is based on this idea that forest volume can be estimated by variation of trees height at plots. In the other word, the more the height variation in plot, the more the stand volume would be expected. For testing this idea, 120 circular 0.1 ha sample plots with systematic random design has been collected in Tonekaon forest located in Hyrcanian zone. Digital surface model (DSM) measure the height values of the first surface on the ground including terrain features, trees, building etc, which provides a topographic model of the earth's surface. The DSMs have been extracted automatically from aerial UltraCamD images so that ground pixel size for extracted DSM varied from 1 to 10 m size by 1m span. DSMs were checked manually for probable errors. Corresponded to ground samples, standard deviation and range of DSM pixels have been calculated. For modeling, non-linear regression method was used. The results showed that standard deviation of plot pixels with 5 m resolution was the most appropriate data for modeling. Relative bias and RMSE of estimation was 5.8 and 49.8 percent, respectively. Comparing to other approaches for estimating stand volume based on passive remote sensing data in mixed broadleaves forests, these results are more encouraging. One big problem in this method occurs when trees canopy cover is totally closed. In this situation, the standard deviation of height is low while stand volume is high. In future studies, applying forest stratification could be studied.

Robust reconstruction of a signal from its unthresholded recurrence plot subject to disturbances

NASA Astrophysics Data System (ADS)

Sipers, Aloys; Borm, Paul; Peeters, Ralf

2017-02-01

To make valid inferences from recurrence plots for time-delay embedded signals, two underlying key questions are: (1) to what extent does an unthresholded recurrence (URP) plot carry the same information as the signal that generated it, and (2) how does the information change when the URP gets distorted. We studied the first question in our earlier work [1], where it was shown that the URP admits the reconstruction of the underlying signal (up to its mean and a choice of sign) if and only if an associated graph is connected. Here we refine this result and we give an explicit condition in terms of the embedding parameters and the discrete Fourier spectrum of the URP. We also develop a method for the reconstruction of the underlying signal which overcomes several drawbacks that earlier approaches had. To address the second question we investigate robustness of the proposed reconstruction method under disturbances. We carry out two simulation experiments which are characterized by a broad band and a narrow band spectrum respectively. For each experiment we choose a noise level and two different pairs of embedding parameters. The conventional binary recurrence plot (RP) is obtained from the URP by thresholding and zero-one conversion, which can be viewed as severe distortion acting on the URP. Typically the reconstruction of the underlying signal from an RP is expected to be rather inaccurate. However, by introducing the concept of a multi-level recurrence plot (MRP) we propose to bridge the information gap between the URP and the RP, while still achieving a high data compression rate. We demonstrate the working of the proposed reconstruction procedure on MRPs, indicating that MRPs with just a few discretization levels can usually capture signal properties and morphologies more accurately than conventional RPs.

Advances in the use of DNA barcodes to build a community phylogeny for tropical trees in a Puerto Rican forest dynamics plot.

PubMed

Kress, W John; Erickson, David L; Swenson, Nathan G; Thompson, Jill; Uriarte, Maria; Zimmerman, Jess K

2010-11-09

Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The phylogenetic component of diversity has been particularly difficult to quantify in species-rich tropical tree assemblages. The compilation of previously published (and often incomplete) data on evolutionary relationships of species into a composite phylogeny of the taxa in a forest, through such programs as Phylomatic, has proven useful in building community phylogenies although often of limited resolution. Recently, DNA barcodes have been used to construct a robust community phylogeny for nearly 300 tree species in a forest dynamics plot in Panama using a supermatrix method. In that study sequence data from three barcode loci were used to generate a well-resolved species-level phylogeny. Here we expand upon this earlier investigation and present results on the use of a phylogenetic constraint tree to generate a community phylogeny for a diverse, tropical forest dynamics plot in Puerto Rico. This enhanced method of phylogenetic reconstruction insures the congruence of the barcode phylogeny with broadly accepted hypotheses on the phylogeny of flowering plants (i.e., APG III) regardless of the number and taxonomic breadth of the taxa sampled. We also compare maximum parsimony versus maximum likelihood estimates of community phylogenetic relationships as well as evaluate the effectiveness of one- versus two- versus three-gene barcodes in resolving community evolutionary history. As first demonstrated in the Panamanian forest dynamics plot, the results for the Puerto Rican plot illustrate that highly resolved phylogenies derived from DNA barcode sequence data combined with a constraint tree based on APG III are particularly useful in comparative analysis of phylogenetic diversity and will enhance research on the interface between community ecology and evolution.

Monitoring larval populations of the Douglas-fir tussock moth and the western spruce budworm on permanent plots: sampling methods and statistical properties of data

Treesearch

A.R. Mason; H.G. Paul

1994-01-01

Procedures for monitoring larval populations of the Douglas-fir tussock moth and the western spruce budworm are recommended based on many years experience in sampling these species in eastern Oregon and Washington. It is shown that statistically reliable estimates of larval density can be made for a population by sampling host trees in a series of permanent plots in a...

A general method for assessing the effects of uncertainty in individual-tree volume model predictions on large-area volume estimates with a subtropical forest illustration

Treesearch

Ronald E. McRoberts; Paolo Moser; Laio Zimermann Oliveira; Alexander C. Vibrans

2015-01-01

Forest inventory estimates of tree volume for large areas are typically calculated by adding the model predictions of volumes for individual trees at the plot level, calculating the mean over plots, and expressing the result on a per unit area basis. The uncertainty in the model predictions is generally ignored, with the result that the precision of the large-area...

Field portable low temperature porous layer open tubular cryoadsorption headspace sampling and analysis part II: Applications.

PubMed

Harries, Megan; Bukovsky-Reyes, Santiago; Bruno, Thomas J

2016-01-15

This paper details the sampling methods used with the field portable porous layer open tubular cryoadsorption (PLOT-cryo) approach, described in Part I of this two-part series, applied to several analytes of interest. We conducted tests with coumarin and 2,4,6-trinitrotoluene (two solutes that were used in initial development of PLOT-cryo technology), naphthalene, aviation turbine kerosene, and diesel fuel, on a variety of matrices and test beds. We demonstrated that these analytes can be easily detected and reliably identified using the portable unit for analyte collection. By leveraging efficiency-boosting temperature control and the high flow rate multiple capillary wafer, very short collection times (as low as 3s) yielded accurate detection. For diesel fuel spiked on glass beads, we determined a method detection limit below 1 ppm. We observed greater variability among separate samples analyzed with the portable unit than previously documented in work using the laboratory-based PLOT-cryo technology. We identify three likely sources that may help explain the additional variation: the use of a compressed air source to generate suction, matrix geometry, and variability in the local vapor concentration around the sampling probe as solute depletion occurs both locally around the probe and in the test bed as a whole. This field-portable adaptation of the PLOT-cryo approach has numerous and diverse potential applications. Published by Elsevier B.V.

Field Portable Low Temperature Porous Layer Open Tubular Cryoadsorption Headspace Sampling and Analysis Part II: Applications*

PubMed Central

Harries, Megan; Bukovsky-Reyes, Santiago; Bruno, Thomas J.

2016-01-01

This paper details the sampling methods used with the field portable porous layer open tubular cryoadsorption (PLOT-cryo) approach, described in Part I of this two-part series, applied to several analytes of interest. We conducted tests with coumarin and 2,4,6-trinitrotoluene (two solutes that were used in initial development of PLOT-cryo technology), naphthalene, aviation turbine kerosene, and diesel fuel, on a variety of matrices and test beds. We demonstrated that these analytes can be easily detected and reliably identified using the portable unit for analyte collection. By leveraging efficiency-boosting temperature control and the high flow rate multiple capillary wafer, very short collection times (as low as 3 s) yielded accurate detection. For diesel fuel spiked on glass beads, we determined a method detection limit below 1 ppm. We observed greater variability among separate samples analyzed with the portable unit than previously documented in work using the laboratory-based PLOT-cryo technology. We identify three likely sources that may help explain the additional variation: the use of a compressed air source to generate suction, matrix geometry, and variability in the local vapor concentration around the sampling probe as solute depletion occurs both locally around the probe and in the test bed as a whole. This field-portable adaptation of the PLOT-cryo approach has numerous and diverse potential applications. PMID:26726934

Multi-Scale Morphological Analysis of Conductance Signals in Vertical Upward Gas-Liquid Two-Phase Flow

NASA Astrophysics Data System (ADS)

Lian, Enyang; Ren, Yingyu; Han, Yunfeng; Liu, Weixin; Jin, Ningde; Zhao, Junying

2016-11-01

The multi-scale analysis is an important method for detecting nonlinear systems. In this study, we carry out experiments and measure the fluctuation signals from a rotating electric field conductance sensor with eight electrodes. We first use a recurrence plot to recognise flow patterns in vertical upward gas-liquid two-phase pipe flow from measured signals. Then we apply a multi-scale morphological analysis based on the first-order difference scatter plot to investigate the signals captured from the vertical upward gas-liquid two-phase flow loop test. We find that the invariant scaling exponent extracted from the multi-scale first-order difference scatter plot with the bisector of the second-fourth quadrant as the reference line is sensitive to the inhomogeneous distribution characteristics of the flow structure, and the variation trend of the exponent is helpful to understand the process of breakup and coalescence of the gas phase. In addition, we explore the dynamic mechanism influencing the inhomogeneous distribution of the gas phase in terms of adaptive optimal kernel time-frequency representation. The research indicates that the system energy is a factor influencing the distribution of the gas phase and the multi-scale morphological analysis based on the first-order difference scatter plot is an effective method for indicating the inhomogeneous distribution of the gas phase in gas-liquid two-phase flow.

Quantitative Assessment of Heterogeneity in Tumor Metabolism Using FDG-PET

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

Vriens, Dennis, E-mail: d.vriens@nucmed.umcn.nl; Disselhorst, Jonathan A.; Oyen, Wim J.G.

2012-04-01

Purpose: [{sup 18}F]-fluorodeoxyglucose-positron emission tomography (FDG-PET) images are usually quantitatively analyzed in 'whole-tumor' volumes of interest. Also parameters determined with dynamic PET acquisitions, such as the Patlak glucose metabolic rate (MR{sub glc}) and pharmacokinetic rate constants of two-tissue compartment modeling, are most often derived per lesion. We propose segmentation of tumors to determine tumor heterogeneity, potentially useful for dose-painting in radiotherapy and elucidating mechanisms of FDG uptake. Methods and Materials: In 41 patients with 104 lesions, dynamic FDG-PET was performed. On MR{sub glc} images, tumors were segmented in quartiles of background subtracted maximum MR{sub glc} (0%-25%, 25%-50%, 50%-75%, and 75%-100%).more » Pharmacokinetic analysis was performed using an irreversible two-tissue compartment model in the three segments with highest MR{sub glc} to determine the rate constants of FDG metabolism. Results: From the highest to the lowest quartile, significant decreases of uptake (K{sub 1}), washout (k{sub 2}), and phosphorylation (k{sub 3}) rate constants were seen with significant increases in tissue blood volume fraction (V{sub b}). Conclusions: Tumor regions with highest MR{sub glc} are characterized by high cellular uptake and phosphorylation rate constants with relatively low blood volume fractions. In regions with less metabolic activity, the blood volume fraction increases and cellular uptake, washout, and phosphorylation rate constants decrease. These results support the hypothesis that regional tumor glucose phosphorylation rate is not dependent on the transport of nutrients (i.e., FDG) to the tumor.« less

Determination of split renal function using dynamic CT-angiography: preliminary results.

PubMed

Helck, Andreas; Schönermarck, Ulf; Habicht, Antje; Notohamiprodjo, Mike; Stangl, Manfred; Klotz, Ernst; Nikolaou, Konstantin; la Fougère, Christian; Clevert, Dirk Andrè; Reiser, Maximilian; Becker, Christoph

2014-01-01

To determine the feasibility of a dynamic CT angiography-protocol with regard to simultaneous assessment of renal anatomy and function. 7 healthy potential kidney donors (58 ± 7 years) underwent a dynamic computed tomography angiography (CTA) using a 128-slice CT-scanner with continuous bi-directional table movement, allowing the coverage of a scan range of 18 cm within 1.75 sec. Twelve scans of the kidneys (n = 14) were acquired every 3.5 seconds with the aim to simultaneously obtain CTA and renal function data. Image quality was assessed quantitatively (HU-measurements) and qualitatively (grade 1-4, 1 = best). The glomerular filtration rate (GFR) was calculated by a modified Patlak method and compared with the split renal function obtained with renal scintigraphy. Mean maximum attenuation was 464 ± 58 HU, 435 ± 48 HU and 277 ± 29 HU in the aorta, renal arteries, and renal veins, respectively. The abdominal aorta and all renal vessels were depicted excellently (grade 1.0). The image quality score for cortex differentiation was 1.6 ± 0.49, for the renal parenchyma 2.4 ± 0.49. GFR obtained from dynamic CTA correlated well with renal scintigraphy with a correlation coefficient of r = 0.84; P = 0.0002 (n = 14). The average absolute deviation was 1.6 mL/min. The average effective dose was 8.96 mSv. Comprehensive assessment of renal anatomy and function is feasible using a single dynamic CT angiography examination. The proposed protocol may help to improve management in case of asymmetric kidney function as well as to simplify evaluation of potential living kidney donors.

40 CFR 53.1 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... followed by a gravimetric mass determination, but which is not a Class I equivalent method because of... MONITORING REFERENCE AND EQUIVALENT METHODS General Provisions § 53.1 Definitions. Terms used but not defined... slope of a linear plot fitted to corresponding candidate and reference method mean measurement data...

Sample size and the detection of a hump-shaped relationship between biomass and species richness in Mediterranean wetlands

USGS Publications Warehouse

Espinar, J.L.

2006-01-01

Questions: What is the observed relationship between biomass and species richness across both spatial and temporal scales in communities of submerged annual macrophytes? Does the number of plots sampled affect detection of hump-shaped pattern? Location: Don??ana National Park, southwestern Spain. Methods: A total of 102 plots were sampled during four hydrological cycles. In each hydrological cycle, the plots were distributed randomly along an environmental flooding gradient in three contrasted microhabitats located in the transition zone just below the upper marsh. In each plot (0.5 m x 0.5 m), plant density and above- and below-ground biomass of submerged vegetation were measured. The hump-shaped model was tested by using a generalized linear model (GLM). A bootstrap procedure was used to test the effect of the number of plots on the ability to detect hump-shaped patterns. Result: The area exhibited low species density with a range of 1 - 9 species and low values of biomass with a range of 0.2 - 87.6 g-DW / 0.25 m2. When data from all years and all microhabitats were combined, the relationships between biomass and species richness showed a hump-shaped pattern. The number of plots was large enough to allow detection of the hump-shaped pattern across microhabitats but it was too small to confirm the hump-shaped pattern within each individual microhabitat. Conclusion: This study provides evidence of hump-shaped patterns across microhabitats when GLM analysis is used. In communities of submerged annual macrophytes in Mediterranean wetlands, the highest species density occurs in intermediate values of biomass. The bootstrap procedure indicates that the number of plots affects the detection of hump-shaped patterns. ?? IAVS; Opulus Press.

Conversion of sagebrush shrublands to exotic annual grasslands negatively impacts small mammal communities

USGS Publications Warehouse

Ostoja, S.M.; Schupp, E.W.

2009-01-01

Aim The exotic annual cheatgrass (Bromus tectorum) is fast replacing sagebrush (Artemisia tridentata) communities throughout the Great Basin Desert and nearby regions in the Western United States, impacting native plant communities and altering fire regimes, which contributes to the long-term persistence of this weedy species. The effect of this conversion on native faunal communities remains largely unexamined. We assess the impact of conversion from native perennial to exotic annual plant communities on desert rodent communities. Location Wyoming big sagebrush shrublands and nearby sites previously converted to cheatgrass-dominated annual grasslands in the Great Basin Desert, Utah, USA. Methods At two sites in Tooele County, Utah, USA, we investigated with Sherman live trapping whether intact sagebrush vegetation and nearby converted Bromus tectorum-dominated vegetation differed in rodent abundance, diversity and community composition. Results Rodent abundance and species richness were considerably greater in sagebrush plots than in cheatgrass-dominated plots. Nine species were captured in sagebrush plots; five of these were also trapped in cheatgrass plots, all at lower abundances than in the sagebrush. In contrast, cheatgrass-dominated plots had no species that were not found in sagebrush. In addition, the site that had been converted to cheatgrass longer had lower abundances of rodents than the site more recently converted to cheatgrass-dominated plots. Despite large differences in abundances and species richness, Simpson's D diversity and Shannon-Wiener diversity and Brillouin evenness indices did not differ between sagebrush and cheatgrass-dominated plots. Main conclusions This survey of rodent communities in native sagebrush and in converted cheatgrass-dominated vegetation suggests that the abundances and community composition of rodents may be shifting, potentially at the larger spatial scale of the entire Great Basin, where cheatgrass continues to invade and dominate more landscape at a rapid rate. ?? 2009 Blackwell Publishing Ltd.

Detecting small-study effects and funnel plot asymmetry in meta-analysis of survival data: A comparison of new and existing tests.

PubMed

Debray, Thomas P A; Moons, Karel G M; Riley, Richard D

2018-03-01

Small-study effects are a common threat in systematic reviews and may indicate publication bias. Their existence is often verified by visual inspection of the funnel plot. Formal tests to assess the presence of funnel plot asymmetry typically estimate the association between the reported effect size and their standard error, the total sample size, or the inverse of the total sample size. In this paper, we demonstrate that the application of these tests may be less appropriate in meta-analysis of survival data, where censoring influences statistical significance of the hazard ratio. We subsequently propose 2 new tests that are based on the total number of observed events and adopt a multiplicative variance component. We compare the performance of the various funnel plot asymmetry tests in an extensive simulation study where we varied the true hazard ratio (0.5 to 1), the number of published trials (N=10 to 100), the degree of censoring within trials (0% to 90%), and the mechanism leading to participant dropout (noninformative versus informative). Results demonstrate that previous well-known tests for detecting funnel plot asymmetry suffer from low power or excessive type-I error rates in meta-analysis of survival data, particularly when trials are affected by participant dropout. Because our novel test (adopting estimates of the asymptotic precision as study weights) yields reasonable power and maintains appropriate type-I error rates, we recommend its use to evaluate funnel plot asymmetry in meta-analysis of survival data. The use of funnel plot asymmetry tests should, however, be avoided when there are few trials available for any meta-analysis. © 2017 The Authors. Research Synthesis Methods Published by John Wiley & Sons, Ltd.

Poincaré plot indexes of heart rate variability detect dynamic autonomic modulation during general anesthesia induction.

PubMed

Hsu, Che-Hao; Tsai, Ming-Ya; Huang, Go-Shine; Lin, Tso-Chou; Chen, Kuen-Pao; Ho, Shung-Tai; Shyu, Liang-Yu; Li, Chi-Yuan

2012-03-01

Beat-to-beat heart rate variability (HRV) is caused by the fluctuating balance of sympathetic and parasympathetic tone. The Poincaré plot has been used to evaluate HRV. In this study, we validate that this new method may qualitatively and quantitatively assess the sympathovagal fluctuation in patients during induction of anesthesia with sevoflurane. Twenty-eight young patients were allocated for the study. The patients received a tilt test and on the next day they sustained anesthesia induced with inhaled anesthetics. Electrocardiography signals from the patients were relayed to an analogue-digital converter. The Poincaré plot is quantified by measuring SD1, SD2, and SD1/SD2. Power spectral analyses were performed and LF, HF and HF/LF were calculated. The LF power and the SD2 of the Poincaré plot increased while subjects were tilt-up from the supine position. Additionally, a significant correlation were found between LF and SD2, HF and SD1 (p < 0.05), and LF/HF and SD2/SD1 (p < 0.01). Sevoflurane inhalation for 10 minutes had no effect on heart rate, but diminished LF, total power and SD1, SD2 of the Poincaré plot respectively. However, the LF, SD2 and LF/HF increased; the HF, SD1 and SD1/SD2 ratio decreased after intubation stimulation. Poincaré plot and power spectral analysis of HRV during tilt test and sevoflurane induction significantly correlate. Poincaré plot analysis is easier and more sensitive at evaluating the sympathovagal balance and observing the beat-to-beat HRV. Copyright © 2012. Published by Elsevier B.V.

Effect of Ecological Restoration on Body Condition of a Predator

PubMed Central

González-Tokman, Daniel; Martínez-Garza, Cristina

2015-01-01

Ecological restoration attempts to recover the structure and function of ecosystems that have been degraded by human activities. A crucial test of ecosystem recovery would be to determine whether individuals in restored environments are as healthy as those in conserved environments. However, the impact of restoration on physiology of terrestrial animals has never been tested. Here, we evaluated the effect of two restoration methods on body condition measured as body size, body mass, lipid and muscle content of the spider Nephila clavipes in a tropical dry forest that has suffered chronic disturbance due to cattle grazing. We used experimental plots that had been excluded from disturbance by cattle grazing during eight years. Plots were either planted with native trees (i. e. maximal intervention), or only excluded from disturbance (i. e. minimal intervention), and were compared with control conserved (remnants of original forest) and disturbed plots (where cattle is allowed to graze). We predicted (1) better body condition in spiders of conserved and restored sites, compared to disturbed sites, and (2) better body condition in plots with maximal intervention than in plots with minimal intervention. The first prediction was not supported in males or females, and the second prediction was only supported in females: body dry mass was higher in planted than in conserved plots for spiders of both sexes and also higher that in disturbed plots for males, suggesting that plantings are providing more resources. We discuss how different life histories and environmental pressures, such as food availability, parasitism, and competition for resources can explain our contrasting findings in male and female spiders. By studying animal physiology in restoration experiments it is possible to understand the mechanistic basis of ecological and evolutionary processes that determine success of ecological restoration. PMID:26226363

Effect of Ecological Restoration on Body Condition of a Predator.

PubMed

González-Tokman, Daniel; Martínez-Garza, Cristina

2015-01-01

Ecological restoration attempts to recover the structure and function of ecosystems that have been degraded by human activities. A crucial test of ecosystem recovery would be to determine whether individuals in restored environments are as healthy as those in conserved environments. However, the impact of restoration on physiology of terrestrial animals has never been tested. Here, we evaluated the effect of two restoration methods on body condition measured as body size, body mass, lipid and muscle content of the spider Nephila clavipes in a tropical dry forest that has suffered chronic disturbance due to cattle grazing. We used experimental plots that had been excluded from disturbance by cattle grazing during eight years. Plots were either planted with native trees (i. e. maximal intervention), or only excluded from disturbance (i. e. minimal intervention), and were compared with control conserved (remnants of original forest) and disturbed plots (where cattle is allowed to graze). We predicted (1) better body condition in spiders of conserved and restored sites, compared to disturbed sites, and (2) better body condition in plots with maximal intervention than in plots with minimal intervention. The first prediction was not supported in males or females, and the second prediction was only supported in females: body dry mass was higher in planted than in conserved plots for spiders of both sexes and also higher that in disturbed plots for males, suggesting that plantings are providing more resources. We discuss how different life histories and environmental pressures, such as food availability, parasitism, and competition for resources can explain our contrasting findings in male and female spiders. By studying animal physiology in restoration experiments it is possible to understand the mechanistic basis of ecological and evolutionary processes that determine success of ecological restoration.

Funnel plots and choropleth maps in cancer risk communication: a comparison of tools for disseminating population-based incidence data to stakeholders

PubMed Central

Cusimano, Rosanna; Zarcone, Maurizio; Mazzola, Sergio; Vitale, Francesco

2017-01-01

Background Population-based cancer registries provide epidemiological cancer information, but the indicators are often too complex to be interpreted by local authorities and communities, due to numeracy and literacy limitations. The aim of this paper is to compare the commonly used visual formats to funnel plots to enable local public health authorities and communities to access valid and understandable cancer incidence data obtained at the municipal level. Methods A funnel plot representation of standardised incidence ratio (SIR) was generated for the 82 municipalities of the Palermo Province with the 2003–2011 data from the Palermo Province Cancer Registry (Sicily, Italy). The properties of the funnel plot and choropleth map methodologies were compared within the context of disseminating epidemiological data to stakeholders. Results The SIRs of all the municipalities remained within the control limits, except for Palermo city area (SIR=1.12), which was sited outside the upper control limit line of 99.8%. The Palermo Province SIRs funnel plot representation was congruent with the choropleth map generated from the same data, but the former resulted more informative as shown by the comparisons of the weaknesses and strengths of the 2 visual formats. Conclusions Funnel plot should be used as a complementary valuable tool to communicate epidemiological data of cancer registries to communities and local authorities, visually conveying an efficient and simple way to interpret cancer incidence data. PMID:28363917

Induction treatments for acute promyelocytic leukemia: a network meta-analysis

PubMed Central

Zhang, Qiaoxia; Lou, Jin; Cai, Yun; Chen, Weihong; Du, Xin

2016-01-01

Background 9 treatments for acute promyelocytic leukemia (APL) have been compared in many randomized controlled trials (RCT). The conclusions have been inconsistent and the purpose of this study is to conduct a network meta-analysis. Results Rankings of event-free survival are ATRA+RIF (81.2%), ATRA+ATO (69.6%), ATO (50.6%). Rankings of complete remission are ATRA+RIF (79.3%), ATRA+ATO (64.8%), RIF (60.3%), ATO (55.9%). Rankings of avoiding differentiation syndromes are CT (84.3%), ATO (80.3%), RIF (71.6%), ATRA+RIF (49%), ATRA+ATO (40.8%). Methods A total of 1,666 patients from 12 RCTs were enrolled. The frequentist method was used. Relative risks with 95% confidence intervals were calculated. We produced a network plot, a contribution plot, and a forest plot predictive intervals. The inconsistency factor, the surface under the cumulative ranking curve and the publication bias were evaluated. Conclusions ATRA+ATO is eligible to be the first-line treatment for APL. ATRA+RIF is a prospective alternative to the first-line treatment. RIF or ATO should be reconsidered as another option for de novo APL. PMID:27713127

Analyzing linear spatial features in ecology.

PubMed

Buettel, Jessie C; Cole, Andrew; Dickey, John M; Brook, Barry W

2018-06-01

The spatial analysis of dimensionless points (e.g., tree locations on a plot map) is common in ecology, for instance using point-process statistics to detect and compare patterns. However, the treatment of one-dimensional linear features (fiber processes) is rarely attempted. Here we appropriate the methods of vector sums and dot products, used regularly in fields like astrophysics, to analyze a data set of mapped linear features (logs) measured in 12 × 1-ha forest plots. For this demonstrative case study, we ask two deceptively simple questions: do trees tend to fall downhill, and if so, does slope gradient matter? Despite noisy data and many potential confounders, we show clearly that topography (slope direction and steepness) of forest plots does matter to treefall. More generally, these results underscore the value of mathematical methods of physics to problems in the spatial analysis of linear features, and the opportunities that interdisciplinary collaboration provides. This work provides scope for a variety of future ecological analyzes of fiber processes in space. © 2018 by the Ecological Society of America.

Influence of long-term repeated prescribed burning on mycelial communities of ectomycorrhizal fungi.

PubMed

Bastias, Brigitte A; Xu, Zhihong; Cairney, John W G

2006-01-01

To demonstrate the efficacy of direct DNA extraction from hyphal ingrowth bags for community profiling of ectomycorrhizal (ECM) mycelia in soil, we applied the method to investigate the influence of long-term repeated prescribed burning on an ECM fungal community. DNA was extracted from hyphal ingrowth bags buried in forest plots that received different prescribed burning treatments for 30 yr, and denaturing gradient gel electrophoresis (DGGE) profiles of partial fungal rDNA internal transcribed spacer (ITS) regions were compared. Restriction fragment length polymorphism (RFLP) and sequence analyses were also used to compare clone assemblages between the treatments. The majority of sequences derived from the ingrowth bags were apparently those of ECM fungi. DGGE profiles for biennially burned plots were significantly different from those of quadrennially burned and unburned control plots. Analysis of clone assemblages indicated that this reflected altered ECM fungal community composition. The results indicate that hyphal ingrowth bags represent a useful method for investigation of ECM mycelial communities, and that frequent long-term prescribed burning can influence below-ground ECM fungal communities.

Planting pattern and weed control method influence on yield production of corn (Zea mays L.)

NASA Astrophysics Data System (ADS)

Purba, E.; Nasution, D. P.

2018-02-01

Field experiment was carried out to evaluate the influence of planting patterns and weed control methods on the growth and yield of corn. The effect of the planting pattern and weed control method was studied in a split plot design. The main plots were that of planting pattern single row (25cm x 60cm), double row (25cm x 25cm x 60cm) and triangle row ( 25cm x 25cm x 25cm). Subplot was that of weed control method consisted five methods namely weed free throughout the growing season, hand weeding, sprayed with glyphosate, sprayed with paraquat, and no weeding.. Result showed that both planting pattern and weed control method did not affect the growth of corn. However, planting pattern and weed control method significantly affected yield production. Yield resulted from double row and triangle planting pattern was 14% and 41% higher, consecutively, than that of single row pattern. The triangle planting pattern combined with any weed control method produced the highest yield production of corn.

An Empirical Study of Re-sampling Techniques as a Method for Improving Error Estimates in Split-plot Designs

DTIC Science & Technology

2010-03-01

sufficient replications often lead to models that lack precision in error estimation and thus imprecision in corresponding conclusions. This work develops...v Preface This work is dedicated to all who gave and continue to give in order for me to achieve some semblance of success. Benjamin M. Lee vi...develop, examine and test methodologies for an- alyzing test results from split-plot designs. In particular, this work determines the applicability

Xylem vulnerability curves of canopy branches of mature trees from Caxiuana and Tapajos National Forests, Para, Brazil

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

Powell, Thomas; Moorcroft, Paul

Raw data for xylem vulnerability curves measured on upper canopy branches of mature trees from the Caxiuana and Tapajos National Forests, Para, Brazil. Tapajos samples were harvested from km67 transects, which is nearby the decommissioned throughfall-exclusion, drought-experiment plots. Caxiuana samples were harvested from trees growing in the throughfall-exclusion, drought-experiment plots. Data were collected in 2011 and 2012. Dataset includes: date of measurement, site ID, plot ID, tree ID (species, tree tag #), xylem pressure, percent loss of conductivity. Air injection method was used. Data reference: Powell et al. (2017) Differences in xylem cavitation resistance and leaf hydraulic traits explain differencesmore » in drought tolerance among mature Amazon rainforest trees. Global Change Biology.« less

The communities of terrestrial macrofungi in different forest types in vicinities of Khanty-Mansiysk (middle taiga zone of West Siberia)

PubMed Central

Bulyonkova, Tatiana

2017-01-01

Abstract Background The diversity of macrofungi in the vicinities of Khanty-Mansiysk (Yugra, Russia) was surveyed using a method of permanent sampling plots. Ten plots, each consisting of a number of micro-plots, were established in several different communities ranging from old-growth mixed taiga forest to its derivatives in cutting succession and bogged areas. For more complete registration of the mycota, plots were supplemented with random walking routes directly nearby. Survey results were subjected to various quantitative analyses which allowed not only to evaluate the diversity of fungi but also to obtain valuable information on occurrence, abundance and ecology of individual species as well as community structure and its dynamics in the course of ecological succession. The paper reports the results of the first year of observations. New information 460 species of terrestrial macrofungi revealed in a poorly explored area in middle taiga of West Siberia. The plot-based study revealed differences between communities of terrestrial macrofungi of old coniferous forests, their after-cutting secondary formations and bogged stages. The survey allowed to reveal records of 3 species listed in the Red Data Book of Russia and 9 species listed in the Red Data Book of Yugra. PMID:29362551

Advanced Bode Plot Techniques for Ultrasonic Transducers

NASA Astrophysics Data System (ADS)

DeAngelis, D. A.; Schulze, G. W.

The Bode plot, displayed as either impedance or admittance versus frequency, is the most basic test used by ultrasonic transducer designers. With simplicity and ease-of-use, Bode plots are ideal for baseline comparisons such as spacing of parasitic modes or impedance, but quite often the subtleties that manifest as poor process control are hard to interpret or are nonexistence. In-process testing of transducers is time consuming for quantifying statistical aberrations, and assessments made indirectly via the workpiece are difficult. This research investigates the use of advanced Bode plot techniques to compare ultrasonic transducers with known "good" and known "bad" process performance, with the goal of a-priori process assessment. These advanced techniques expand from the basic constant voltage versus frequency sweep to include constant current and constant velocity interrogated locally on transducer or tool; they also include up and down directional frequency sweeps to quantify hysteresis effects like jumping and dropping phenomena. The investigation focuses solely on the common PZT8 piezoelectric material used with welding transducers for semiconductor wire bonding. Several metrics are investigated such as impedance, displacement/current gain, velocity/current gain, displacement/voltage gain and velocity/voltage gain. The experimental and theoretical research methods include Bode plots, admittance loops, laser vibrometry and coupled-field finite element analysis.

LevelScheme: A level scheme drawing and scientific figure preparation system for Mathematica

NASA Astrophysics Data System (ADS)

Caprio, M. A.

2005-09-01

LevelScheme is a scientific figure preparation system for Mathematica. The main emphasis is upon the construction of level schemes, or level energy diagrams, as used in nuclear, atomic, molecular, and hadronic physics. LevelScheme also provides a general infrastructure for the preparation of publication-quality figures, including support for multipanel and inset plotting, customizable tick mark generation, and various drawing and labeling tasks. Coupled with Mathematica's plotting functions and powerful programming language, LevelScheme provides a flexible system for the creation of figures combining diagrams, mathematical plots, and data plots. Program summaryTitle of program:LevelScheme Catalogue identifier:ADVZ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVZ Operating systems:Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux Programming language used:Mathematica 4 Number of bytes in distributed program, including test and documentation:3 051 807 Distribution format:tar.gz Nature of problem:Creation of level scheme diagrams. Creation of publication-quality multipart figures incorporating diagrams and plots. Method of solution:A set of Mathematica packages has been developed, providing a library of level scheme drawing objects, tools for figure construction and labeling, and control code for producing the graphics.

Halo-independent direct detection analyses without mass assumptions

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

Anderson, Adam J.; Fox, Patrick J.; Kahn, Yonatan

2015-10-01

Results from direct detection experiments are typically interpreted by employing an assumption about the dark matter velocity distribution, with results presented in the m{sub χ}−σ{sub n} plane. Recently methods which are independent of the DM halo velocity distribution have been developed which present results in the v{sub min}− g-tilde plane, but these in turn require an assumption on the dark matter mass. Here we present an extension of these halo-independent methods for dark matter direct detection which does not require a fiducial choice of the dark matter mass. With a change of variables from v{sub min} to nuclear recoil momentummore » (p{sub R}), the full halo-independent content of an experimental result for any dark matter mass can be condensed into a single plot as a function of a new halo integral variable, which we call h-tilde (p{sub R}). The entire family of conventional halo-independent g-tilde (v{sub min}) plots for all DM masses are directly found from the single h-tilde (p{sub R}) plot through a simple rescaling of axes. By considering results in h-tilde (p{sub R}) space, one can determine if two experiments are inconsistent for all masses and all physically possible halos, or for what range of dark matter masses the results are inconsistent for all halos, without the necessity of multiple g-tilde (v{sub min}) plots for different DM masses. We conduct a sample analysis comparing the CDMS II Si events to the null results from LUX, XENON10, and SuperCDMS using our method and discuss how the results can be strengthened by imposing the physically reasonable requirement of a finite halo escape velocity.« less

Halo-independent direct detection analyses without mass assumptions

DOE PAGES

Anderson, Adam J.; Fox, Patrick J.; Kahn, Yonatan; ...

2015-10-06

Results from direct detection experiments are typically interpreted by employing an assumption about the dark matter velocity distribution, with results presented in the m χ – σ n plane. Recently methods which are independent of the DM halo velocity distribution have been developed which present results in the v min – g ~ plane, but these in turn require an assumption on the dark matter mass. Here we present an extension of these halo-independent methods for dark matter direct detection which does not require a fiducial choice of the dark matter mass. With a change of variables from v minmore » to nuclear recoil momentum (p R), the full halo-independent content of an experimental result for any dark matter mass can be condensed into a single plot as a function of a new halo integral variable, which we call tilde h(p R). The entire family of conventional halo-independent tilde g ~(v min) plots for all DM masses are directly found from the single tilde h ~(p R) plot through a simple rescaling of axes. By considering results in tildeh ~(p R) space, one can determine if two experiments are inconsistent for all masses and all physically possible halos, or for what range of dark matter masses the results are inconsistent for all halos, without the necessity of multiple tilde g ~(v min) plots for different DM masses. As a result, we conduct a sample analysis comparing the CDMS II Si events to the null results from LUX, XENON10, and SuperCDMS using our method and discuss how the results can be strengthened by imposing the physically reasonable requirement of a finite halo escape velocity.« less

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

Anderson, Adam J.; Fox, Patrick J.; Kahn, Yonatan

Results from direct detection experiments are typically interpreted by employing an assumption about the dark matter velocity distribution, with results presented in the m{sub χ}−σ{sub n} plane. Recently methods which are independent of the DM halo velocity distribution have been developed which present results in the v{sub min}−g-tilde plane, but these in turn require an assumption on the dark matter mass. Here we present an extension of these halo-independent methods for dark matter direct detection which does not require a fiducial choice of the dark matter mass. With a change of variables from v{sub min} to nuclear recoil momentum (p{submore » R}), the full halo-independent content of an experimental result for any dark matter mass can be condensed into a single plot as a function of a new halo integral variable, which we call h-til-tilde(p{sub R}). The entire family of conventional halo-independent g-tilde(v{sub min}) plots for all DM masses are directly found from the single h-tilde(p{sub R}) plot through a simple rescaling of axes. By considering results in h-tilde(p{sub R}) space, one can determine if two experiments are inconsistent for all masses and all physically possible halos, or for what range of dark matter masses the results are inconsistent for all halos, without the necessity of multiple g-tilde(v{sub min}) plots for different DM masses. We conduct a sample analysis comparing the CDMS II Si events to the null results from LUX, XENON10, and SuperCDMS using our method and discuss how the results can be strengthened by imposing the physically reasonable requirement of a finite halo escape velocity.« less

Correlation analysis of respiratory signals by using parallel coordinate plots.

PubMed

Saatci, Esra

2018-01-01

The understanding of the bonds and the relationships between the respiratory signals, i.e. the airflow, the mouth pressure, the relative temperature and the relative humidity during breathing may provide the improvement on the measurement methods of respiratory mechanics and sensor designs or the exploration of the several possible applications in the analysis of respiratory disorders. Therefore, the main objective of this study was to propose a new combination of methods in order to determine the relationship between respiratory signals as a multidimensional data. In order to reveal the coupling between the processes two very different methods were used: the well-known statistical correlation analysis (i.e. Pearson's correlation and cross-correlation coefficient) and parallel coordinate plots (PCPs). Curve bundling with the number intersections for the correlation analysis, Least Mean Square Time Delay Estimator (LMS-TDE) for the point delay detection and visual metrics for the recognition of the visual structures were proposed and utilized in PCP. The number of intersections was increased when the correlation coefficient changed from high positive to high negative correlation between the respiratory signals, especially if whole breath was processed. LMS-TDE coefficients plotted in PCP indicated well-matched point delay results to the findings in the correlation analysis. Visual inspection of PCB by visual metrics showed range, dispersions, entropy comparisons and linear and sinusoidal-like relationships between the respiratory signals. It is demonstrated that the basic correlation analysis together with the parallel coordinate plots perceptually motivates the visual metrics in the display and thus can be considered as an aid to the user analysis by providing meaningful views of the data. Copyright © 2017 Elsevier B.V. All rights reserved.

CI2 for creating and comparing confidence-intervals for time-series bivariate plots.

PubMed

Mullineaux, David R

2017-02-01

Currently no method exists for calculating and comparing the confidence-intervals (CI) for the time-series of a bivariate plot. The study's aim was to develop 'CI2' as a method to calculate the CI on time-series bivariate plots, and to identify if the CI between two bivariate time-series overlap. The test data were the knee and ankle angles from 10 healthy participants running on a motorised standard-treadmill and non-motorised curved-treadmill. For a recommended 10+ trials, CI2 involved calculating 95% confidence-ellipses at each time-point, then taking as the CI the points on the ellipses that were perpendicular to the direction vector between the means of two adjacent time-points. Consecutive pairs of CI created convex quadrilaterals, and any overlap of these quadrilaterals at the same time or ±1 frame as a time-lag calculated using cross-correlations, indicated where the two time-series differed. CI2 showed no group differences between left and right legs on both treadmills, but the same legs between treadmills for all participants showed differences of less knee extension on the curved-treadmill before heel-strike. To improve and standardise the use of CI2 it is recommended to remove outlier time-series, use 95% confidence-ellipses, and scale the ellipse by the fixed Chi-square value as opposed to the sample-size dependent F-value. For practical use, and to aid in standardisation or future development of CI2, Matlab code is provided. CI2 provides an effective method to quantify the CI of bivariate plots, and to explore the differences in CI between two bivariate time-series. Copyright © 2016 Elsevier B.V. All rights reserved.

A Best-Fit Line Using the Method of Averages.

ERIC Educational Resources Information Center

Hoppe, Jack

2002-01-01

Describes a method for calculating lines of best fit that is easy to understand and apply. Presents an example using the Arrhenius plot of a first-order reaction from which the energy of activation is calculated. (MM)

Methodical fitting for mathematical models of rubber-like materials

NASA Astrophysics Data System (ADS)

Destrade, Michel; Saccomandi, Giuseppe; Sgura, Ivonne

2017-02-01

A great variety of models can describe the nonlinear response of rubber to uniaxial tension. Yet an in-depth understanding of the successive stages of large extension is still lacking. We show that the response can be broken down in three steps, which we delineate by relying on a simple formatting of the data, the so-called Mooney plot transform. First, the small-to-moderate regime, where the polymeric chains unfold easily and the Mooney plot is almost linear. Second, the strain-hardening regime, where blobs of bundled chains unfold to stiffen the response in correspondence to the `upturn' of the Mooney plot. Third, the limiting-chain regime, with a sharp stiffening occurring as the chains extend towards their limit. We provide strain-energy functions with terms accounting for each stage that (i) give an accurate local and then global fitting of the data; (ii) are consistent with weak nonlinear elasticity theory and (iii) can be interpreted in the framework of statistical mechanics. We apply our method to Treloar's classical experimental data and also to some more recent data. Our method not only provides models that describe the experimental data with a very low quantitative relative error, but also shows that the theory of nonlinear elasticity is much more robust that seemed at first sight.

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

PubMed Central

Metsalu, Tauno; Vilo, Jaak

2015-01-01

The Principal Component Analysis (PCA) is a widely used method of reducing the dimensionality of high-dimensional data, often followed by visualizing two of the components on the scatterplot. Although widely used, the method is lacking an easy-to-use web interface that scientists with little programming skills could use to make plots of their own data. The same applies to creating heatmaps: it is possible to add conditional formatting for Excel cells to show colored heatmaps, but for more advanced features such as clustering and experimental annotations, more sophisticated analysis tools have to be used. We present a web tool called ClustVis that aims to have an intuitive user interface. Users can upload data from a simple delimited text file that can be created in a spreadsheet program. It is possible to modify data processing methods and the final appearance of the PCA and heatmap plots by using drop-down menus, text boxes, sliders etc. Appropriate defaults are given to reduce the time needed by the user to specify input parameters. As an output, users can download PCA plot and heatmap in one of the preferred file formats. This web server is freely available at http://biit.cs.ut.ee/clustvis/. PMID:25969447

Geophysical characterization of soil moisture spatial patterns in a tillage experiment

NASA Astrophysics Data System (ADS)

Martinez, G.; Vanderlinden, K.; Giráldez, J. V.; Muriel, J. L.

2009-04-01

Knowledge on the spatial soil moisture pattern can improve the characterisation of the hydrological response of either field-plots or small watersheds. Near-surface geophysical methods, such as electromagnetic induction (EMI), provide a means to map such patterns using non-invasive and non-destructive measurements of the soil apparent electrical conductivity (ECa. In this study ECa was measured using an EMI sensor and used to characterize spatially the hydrologic response of a cropped field to an intense shower. The study site is part of a long-term tillage experiment in Southern Spain in which Conventional Tillage (CT), Direct Drilling (DD) and Minimum Tillage (MT) are being evaluated since 1982. Soil ECa was measured before and after a rain event of 115 mm, near the soil surface and at deeper depth (ECas and ECad, respectively) using the EM38-DD EMI sensor. Simultaneously, elevation data were collected at each sampling point to generate a Digital Elevation Model (DEM). Soil moisture during the first survey was close to permanent wilting point and near field capacity during the second survey. For the first survey, both ECas and ECad, were higher in the CT and MT than in the DD plots. After the rain event, rill erosion appeared only in CT and MT plots were soil was uncovered, matching the drainage lines obtained from the DEM. Apparent electrical conductivity increased all over the field plot with higher increments in the DD plots. These plots showed the highest ECas and ECad values, in contrast to the spatial pattern found during the first sampling. Difference maps obtained from the two ECas and ECad samplings showed a clear difference between DD plots and CT and MT plots due to their distinct hydrologic response. Water infiltration was higher in the soil of the DD plots than in the MT and CT plots, as reflected by their ECad increment. Higher ECa increments were observed in the depressions of the terrain, where water and sediments accumulated. On the contrary, the most elevated places of the field showed lower ECa increments. When soil is wet topography dominates the hydrologic response of the field, while under drier conditions, hydraulic conductivity controls the soil water dynamics. These results show that when static soil properties, e.g. clay content, are spatially uniform, ECa can detect changes in dynamic properties like soil moisture content, characterizing their spatial pattern.

Does the increased air humidity affect soil respiration and carbon stocks?

NASA Astrophysics Data System (ADS)

Kukumägi, Mai; Celi, Luisella; Said-Pullicino, Daniel; Kupper, Priit; Sõber, Jaak; Lõhmus, Krista; Kutti, Sander; Ostonen, Ivika

2013-04-01

Climate manipulation experiments at ecosystem-scale enable us to simulate, investigate and predict changes in carbon balance of forest ecosystems. Considering the predicted increase in air humidity and precipitation for northern latitudes, this work aimed at investigating the effect of increased air humidity on soil respiration, distribution of soil organic matter (SOM) among pools having different turnover times, and microbial, fine root and rhizome biomass. The study was carried out in silver birch (Betula pendula Roth.) and hybrid aspen (Populus tremula L. × P. tremuloides Michx.) stands in a Free Air Humidity Manipulation (FAHM) experimental facility containing three humidified (H; on average 7% above current ambient levels since 2008) and three control (C) plots. Soil respiration rates were measured monthly during the growing season using a closed dynamic chamber method. Density fractionation was adopted to separate SOM into two light fractions (free and aggregate-occluded particulate organic matter, fPOM and oPOM respectively), and one heavy fraction (mineral-associated organic matter, MOM). The fine root and rhizome biomass and microbial data are presented for silver birch stands only. In 2011, after 4 growing seasons of humidity manipulation soil organic carbon contents were significantly higher in C plots than H plot (13.5 and 12.5 g C kg-1, respectively), while soil respiration tended to be higher in the latter. Microbial biomass and basal respiration were 13 and 14% higher in H plots than in the C plots, respectively. Twice more fine roots of trees were estimated in H plots, while the total fine root and rhizome biomass (tree + understory) was similar in C and H plots. Fine root turnover was higher for both silver birch and understory roots in H plots. Labile SOM light fractions (fPOM and oPOM) were significantly smaller in H plots with respect to C plots (silver birch and hybrid aspen stands together), whereas no differences were observed in the contents of the more stable MOM. These results strongly suggest that, apart from the predicted increase in temperature and atmospheric carbon and nitrogen concentrations, an increase in free air humidity as a result of climate change may significantly influence the complex belowground carbon cycling by affecting biomass production, soil respiration and organic matter turnover.

Atrial fibrillation detection by heart rate variability in Poincare plot.

PubMed

Park, Jinho; Lee, Sangwook; Jeon, Moongu

2009-12-11

Atrial fibrillation (AFib) is one of the prominent causes of stroke, and its risk increases with age. We need to detect AFib correctly as early as possible to avoid medical disaster because it is likely to proceed into a more serious form in short time. If we can make a portable AFib monitoring system, it will be helpful to many old people because we cannot predict when a patient will have a spasm of AFib. We analyzed heart beat variability from inter-beat intervals obtained by a wavelet-based detector. We made a Poincare plot using the inter-beat intervals. By analyzing the plot, we extracted three feature measures characterizing AFib and non-AFib: the number of clusters, mean stepping increment of inter-beat intervals, and dispersion of the points around a diagonal line in the plot. We divided distribution of the number of clusters into two and calculated mean value of the lower part by k-means clustering method. We classified data whose number of clusters is more than one and less than this mean value as non-AFib data. In the other case, we tried to discriminate AFib from non-AFib using support vector machine with the other feature measures: the mean stepping increment and dispersion of the points in the Poincare plot. We found that Poincare plot from non-AFib data showed some pattern, while the plot from AFib data showed irregularly irregular shape. In case of non-AFib data, the definite pattern in the plot manifested itself with some limited number of clusters or closely packed one cluster. In case of AFib data, the number of clusters in the plot was one or too many. We evaluated the accuracy using leave-one-out cross-validation. Mean sensitivity and mean specificity were 91.4% and 92.9% respectively. Because pulse beats of ventricles are less likely to be influenced by baseline wandering and noise, we used the inter-beat intervals to diagnose AFib. We visually displayed regularity of the inter-beat intervals by way of Poincare plot. We tried to design an automated algorithm which did not require any human intervention and any specific threshold, and could be installed in a portable AFib monitoring system.

Evaluating different methods used in ethnobotanical and ecological studies to record plant biodiversity

PubMed Central

2014-01-01

Background This study compares the efficiency of identifying the plants in an area of semi-arid Northeast Brazil by methods that a) access the local knowledge used in ethnobotanical studies using semi-structured interviews conducted within the entire community, an inventory interview conducted with two participants using the previously collected vegetation inventory, and a participatory workshop presenting exsiccates and photographs to 32 people and b) inventory the vegetation (phytosociology) in locations with different histories of disturbance using rectangular plots and quadrant points. Methods The proportion of species identified using each method was then compared with Cochran’s Q test. We calculated the use value (UV) of each species using semi-structured interviews; this quantitative index was correlated against values of the vegetation’s structural importance obtained from the sample plot method and point-centered quarter method applied in two areas with different historical usage. The analysis sought to correlate the relative importance of plants to the local community (use value - UV) with the ecological importance of the plants in the vegetation structure (importance value - IV; relative density - RD) by using different sampling methods to analyze the two areas. Results With regard to the methods used for accessing the local knowledge, a difference was observed among the ethnobotanical methods of surveying species (Q = 13.37, df = 2, p = 0.0013): 44 species were identified in the inventory interview, 38 in the participatory workshop and 33 in the semi-structured interviews with the community. There was either no correlation between the UV, relative density (RD) and importance value (IV) of some species, or this correlation was negative. Conclusion It was concluded that the inventory interview was the most efficient method for recording species and their uses, as it allowed more plants to be identified in their original environment. To optimize researchers’ time in future studies, the use of the point-centered quarter method rather than the sample plot method is recommended. PMID:24916833

Three plot correlation-based small infrared target detection in dense sun-glint environment for infrared search and track

NASA Astrophysics Data System (ADS)

Kim, Sungho; Choi, Byungin; Kim, Jieun; Kwon, Soon; Kim, Kyung-Tae

2012-05-01

This paper presents a separate spatio-temporal filter based small infrared target detection method to address the sea-based infrared search and track (IRST) problem in dense sun-glint environment. It is critical to detect small infrared targets such as sea-skimming missiles or asymmetric small ships for national defense. On the sea surface, sun-glint clutters degrade the detection performance. Furthermore, if we have to detect true targets using only three images with a low frame rate camera, then the problem is more difficult. We propose a novel three plot correlation filter and statistics based clutter reduction method to achieve robust small target detection rate in dense sun-glint environment. We validate the robust detection performance of the proposed method via real infrared test sequences including synthetic targets.

Numerical simulation of KdV equation by finite difference method

NASA Astrophysics Data System (ADS)

Yokus, A.; Bulut, H.

2018-05-01

In this study, the numerical solutions to the KdV equation with dual power nonlinearity by using the finite difference method are obtained. Discretize equation is presented in the form of finite difference operators. The numerical solutions are secured via the analytical solution to the KdV equation with dual power nonlinearity which is present in the literature. Through the Fourier-Von Neumann technique and linear stable, we have seen that the FDM is stable. Accuracy of the method is analyzed via the L2 and L_{∞} norm errors. The numerical, exact approximations and absolute error are presented in tables. We compare the numerical solutions with the exact solutions and this comparison is supported with the graphic plots. Under the choice of suitable values of parameters, the 2D and 3D surfaces for the used analytical solution are plotted.

Expanded uncertainty associated with determination of isotope enrichment factors: Comparison of two point calculation and Rayleigh-plot.

PubMed

Julien, Maxime; Gilbert, Alexis; Yamada, Keita; Robins, Richard J; Höhener, Patrick; Yoshida, Naohiro; Remaud, Gérald S

2018-01-01

The enrichment factor (ε) is a common way to express Isotope Effects (IEs) associated with a phenomenon. Many studies determine ε using a Rayleigh-plot, which needs multiple data points. More recent articles describe an alternative method using the Rayleigh equation that allows the determination of ε using only one experimental point, but this method is often subject to controversy. However, a calculation method using two points (one experimental point and one at t 0 ) should lead to the same results because the calculation is derived from the Rayleigh equation. But, it is frequently asked "what is the valid domain of use of this two point calculation?" The primary aim of the present work is a systematic comparison of results obtained with these two methodologies and the determination of the conditions required for the valid calculation of ε. In order to evaluate the efficiency of the two approaches, the expanded uncertainty (U) associated with determining ε has been calculated using experimental data from three published articles. The second objective of the present work is to describe how to determine the expanded uncertainty (U) associated with determining ε. Comparative methodologies using both Rayleigh-plot and two point calculation are detailed and it is clearly demonstrated that calculation of ε using a single data point can give the same result as a Rayleigh-plot provided one strict condition is respected: that the experimental value is measured at a small fraction of unreacted substrate (f < 30%). This study will help stable isotope users to present their results in a more rigorous expression: ε ± U and therefore to define better the significance of an experimental results prior interpretation. Capsule: Enrichment factor can be determined through two different methods and the calculation of associated expanded uncertainty allows checking its significance. Copyright © 2017 Elsevier B.V. All rights reserved.

A method to quantify FRET stoichiometry with phasor plot analysis and acceptor lifetime ingrowth.

PubMed

Chen, WeiYue; Avezov, Edward; Schlachter, Simon C; Gielen, Fabrice; Laine, Romain F; Harding, Heather P; Hollfelder, Florian; Ron, David; Kaminski, Clemens F

2015-03-10

FRET is widely used for the study of protein-protein interactions in biological samples. However, it is difficult to quantify both the FRET efficiency (E) and the affinity (Kd) of the molecular interaction from intermolecular FRET signals in samples of unknown stoichiometry. Here, we present a method for the simultaneous quantification of the complete set of interaction parameters, including fractions of bound donors and acceptors, local protein concentrations, and dissociation constants, in each image pixel. The method makes use of fluorescence lifetime information from both donor and acceptor molecules and takes advantage of the linear properties of the phasor plot approach. We demonstrate the capability of our method in vitro in a microfluidic device and also in cells, via the determination of the binding affinity between tagged versions of glutathione and glutathione S-transferase, and via the determination of competitor concentration. The potential of the method is explored with simulations. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Evaluation of Restoration Methods to Minimize Canada Thistle (Cirsium arvense) Infestation

USGS Publications Warehouse

Larson, Diane L.

2009-01-01

The National Wildlife Refuge System has an active habitat restoration program and annually seeds thousands of hectares with native plant species. The noxious weed, Canada thistle (Cirsium arvense), plagues these restorations. This study evaluates planting methodology and seed mixes with the goal of recommending optimal methods to reduce infestation of noxious weeds, especially Canada thistle, in new restorations. Three planting methods (dormant season broadcast, growing season [summer] broadcast, and growing season [summer] drill) were fully crossed with three levels of seed diversity (10, 20, and 34 species [plus a fourth level, 58 species, on the three sites in Iowa]) in a completely randomized design replicated on nine sites in Minnesota and Iowa. The propagule bank of Canada thistle was evaluated at each site. Planting occurred in winter 2004 and spring-summer 2005. Here I report on results through summer 2007. None of the planting methods or seed mix diversities consistently resulted in reduced abundance of Canada thistle. Soil texture had the strongest influence; sites with greater proportions of clay had greater frequency and cover of Canada thistle than did sandy sites. At the Minnesota study sites, the dormant broadcast planting method combined with the highest seed diversity resulted in both the greatest cover of planted species as well as the greatest richness of planted species. At the Iowa sites, planted species richness was slightly greater in the summer drill plots, but cover of planted species was greatest in the dormant broadcast plots. Richness of planted species at the Iowa sites was maximized in the high diversity plots, with the extra-high diversity seed mix resulting in significantly lower species richness. Individual species responded to planting methods idiosyncratically, which suggests that particular species could be favored by tailoring planting methods to that species.

Guide for evaluating sweetgum sites

Treesearch

W. M. Broadfoot; Roger M. Krinard

1959-01-01

Studies at the Stonevill Research Center1 have established 3 practical methods of estimating the ability of Midsouth soils to grow sweetgum (liquidambar styraciflua). The methods were developed from data collected from 104 sweetgum plots in the area mapped on the opposite page.

Apparatus and method for spectroscopic analysis of scattering media

DOEpatents

Strobl, Karlheinz; Bigio, Irving J.; Loree, Thomas R.

1994-01-01

Apparatus and method for spectroscopic analysis of scattering media. Subtle differences in materials have been found to be detectable from plots of intensity as a function of wavelength of collected emitted and scattered light versus wavelength of excitation light.

Climate Change and Ecosystem Services Output Efficiency in Southern Loblolly Pine Forests.

PubMed

Susaeta, Andres; Adams, Damian C; Carter, Douglas R; Dwivedi, Puneet

2016-09-01

Forests provide myriad ecosystem services that are vital to humanity. With climate change, we expect to see significant changes to forests that will alter the supply of these critical services and affect human well-being. To better understand the impacts of climate change on forest-based ecosystem services, we applied a data envelopment analysis method to assess plot-level efficiency in the provision of ecosystem services in Florida natural loblolly pine (Pinus taeda L.) forests. Using field data for n = 16 loblolly pine forest plots, including inputs such as site index, tree density, age, precipitation, and temperatures for each forest plot, we assessed the relative plot-level production of three ecosystem services: timber, carbon sequestered, and species richness. The results suggested that loblolly pine forests in Florida were largely inefficient in the provision of these ecosystem services under current climatic conditions. Climate change had a small negative impact on the loblolly pine forests efficiency in the provision of ecosystem services. In this context, we discussed the reduction of tree density that may not improve ecosystem services production.

Climate Change and Ecosystem Services Output Efficiency in Southern Loblolly Pine Forests

NASA Astrophysics Data System (ADS)

Susaeta, Andres; Adams, Damian C.; Carter, Douglas R.; Dwivedi, Puneet

2016-09-01

Forests provide myriad ecosystem services that are vital to humanity. With climate change, we expect to see significant changes to forests that will alter the supply of these critical services and affect human well-being. To better understand the impacts of climate change on forest-based ecosystem services, we applied a data envelopment analysis method to assess plot-level efficiency in the provision of ecosystem services in Florida natural loblolly pine ( Pinus taeda L.) forests. Using field data for n = 16 loblolly pine forest plots, including inputs such as site index, tree density, age, precipitation, and temperatures for each forest plot, we assessed the relative plot-level production of three ecosystem services: timber, carbon sequestered, and species richness. The results suggested that loblolly pine forests in Florida were largely inefficient in the provision of these ecosystem services under current climatic conditions. Climate change had a small negative impact on the loblolly pine forests efficiency in the provision of ecosystem services. In this context, we discussed the reduction of tree density that may not improve ecosystem services production.

Study of the Effect on Ionic Conductivity and Structral Morphology of the SR Doped Lanthanum Gallate Solid Electrolyte

NASA Astrophysics Data System (ADS)

Sood, Kapil; Singh, K.; Pandey, O. P.

2013-07-01

In the present study, lanthanum gallate and Sr-doped lanthanum gallate samples were prepared by conventional solid state reaction method. The phase conformation has been performed by using X-ray diffraction (XRD) study. The elemental composition has been confirmed using energy dispersive spectroscopy (EDS) analysis. Ac conductivity of the samples has been measured in the frequency range 0.1-106 Hz and from 50-800 °C. The impedance plots among real and complex impedances at particular temperature have been discussed. The behavior shows the effect of bulk and grain boundary effects of the doped sample. The impedance plots with frequency have been analyzed. The plots have been well fitted to equivalent circuit model. The conductivity shows the Arrhenius type of behavior. The activation energy has been calculated from the plots and represents that the conductivity through the material is mainly ionic. The structural morphology of the samples has been investigated using scanning electron microscope (SEM). The micrograph shows that the porosity and grain size both decreases with Sr-doping.

Segmented Poincaré plot analysis for risk stratification in patients with dilated cardiomyopathy.

PubMed

Voss, A; Fischer, C; Schroeder, R; Figulla, H R; Goernig, M

2010-01-01

The prognostic value of heart rate variability in patients with dilated cardiomyopathy (DCM) is limited and does not contribute to risk stratification although the dynamics of ventricular repolarization differs considerably between DCM patients and healthy subjects. Neither linear nor nonlinear methods of heart rate variability analysis could discriminate between patients at high and low risk for sudden cardiac death. The aim of this study was to analyze the suitability of the new developed segmented Poincaré plot analysis (SPPA) to enhance risk stratification in DCM. In contrast to the usual applied Poincaré plot analysis the SPPA retains nonlinear features from investigated beat-to-beat interval time series. Main features of SPPA are the rotation of cloud of points and their succeeded variability depended segmentation. Significant row and column probabilities were calculated from the segments and led to discrimination (up to p<0.005) between low and high risk in DCM patients. For the first time an index from Poincaré plot analysis of heart rate variability was able to contribute to risk stratification in patients suffering from DCM.

Data reduction software for LORAN-C flight test evaluation

NASA Technical Reports Server (NTRS)

Fischer, J. P.

1979-01-01

A set of programs designed to be run on an IBM 370/158 computer to read the recorded time differences from the tape produced by the LORAN data collection system, convert them to latitude/longitude and produce various plotting input files are described. The programs were written so they may be tailored easily to meet the demands of a particular data reduction job. The tape reader program is written in 370 assembler language and the remaining programs are written in standard IBM FORTRAN-IV language. The tape reader program is dependent upon the recording format used by the data collection system and on the I/O macros used at the computing facility. The other programs are generally device-independent, although the plotting routines are dependent upon the plotting method used. The data reduction programs convert the recorded data to a more readily usable form; convert the time difference (TD) numbers to latitude/longitude (lat/long), to format a printed listing of the TDs, lat/long, reference times, and other information derived from the data, and produce data files which may be used for subsequent plotting.

Patterns of space and habitat use by northern bobwhites in South Florida, USA

USGS Publications Warehouse

Singh, A.; Hines, T.C.; Hostetler, J.A.; Percival, H.F.; Oli, M.K.

2011-01-01

The manner by which animals use space and select resources can have important management consequences. We studied patterns of habitat selection by northern bobwhites (Colinus virginianus) on Babcock-Webb Wildlife Management Area, Charlotte County, Florida and evaluated factors influencing the sizes of their home ranges. A total of 1,245 radio-tagged bobwhites were monitored for 19,467 radio days during 2002-2007. The mean (?? 1 SE) annual home range size, estimated using the Kernel density method, was 88. 43 (?? 6. 16) ha and did not differ between genders. Winter home ranges of bobwhites (69. 27 ?? 4. 92 ha) were generally larger than summer home ranges (53. 90 ?? 4. 93 ha). Annual and winter home ranges were smaller for bobwhites whose ranges contained food plots compared to those that did not; however, the presence of food plots did not influence summer home ranges. We used distance-based methods to investigate habitat selection by bobwhites at two scales: selection of home ranges within the study site (second-order selection) and selection of habitats within home ranges (third-order selection). Across both scales, bobwhites generally preferred food plots and dry prairie habitat and avoided wet prairies and roads. This pattern was generally consistent between genders and across years. Our data indicate that management practices aimed at increasing and maintaining a matrix of food plots and dry prairie habitat would provide the most favorable environment for bobwhites. ?? 2010 Springer-Verlag.

Discrimination of porosity and fluid saturation using seismic velocity analysis

DOEpatents

Berryman, James G.

2001-01-01

The method of the invention is employed for determining the state of saturation in a subterranean formation using only seismic velocity measurements (e.g., shear and compressional wave velocity data). Seismic velocity data collected from a region of the formation of like solid material properties can provide relatively accurate partial saturation data derived from a well-defined triangle plotted in a (.rho./.mu., .lambda./.mu.)-plane. When the seismic velocity data are collected over a large region of a formation having both like and unlike materials, the method first distinguishes the like materials by initially plotting the seismic velocity data in a (.rho./.lambda., .mu./.lambda.)-plane to determine regions of the formation having like solid material properties and porosity.

The steady-state mosaic of disturbance and succession across an old-growth Central Amazon forest landscape.

PubMed

Chambers, Jeffrey Q; Negron-Juarez, Robinson I; Marra, Daniel Magnabosco; Di Vittorio, Alan; Tews, Joerg; Roberts, Dar; Ribeiro, Gabriel H P M; Trumbore, Susan E; Higuchi, Niro

2013-03-05

Old-growth forest ecosystems comprise a mosaic of patches in different successional stages, with the fraction of the landscape in any particular state relatively constant over large temporal and spatial scales. The size distribution and return frequency of disturbance events, and subsequent recovery processes, determine to a large extent the spatial scale over which this old-growth steady state develops. Here, we characterize this mosaic for a Central Amazon forest by integrating field plot data, remote sensing disturbance probability distribution functions, and individual-based simulation modeling. Results demonstrate that a steady state of patches of varying successional age occurs over a relatively large spatial scale, with important implications for detecting temporal trends on plots that sample a small fraction of the landscape. Long highly significant stochastic runs averaging 1.0 Mg biomass⋅ha(-1)⋅y(-1) were often punctuated by episodic disturbance events, resulting in a sawtooth time series of hectare-scale tree biomass. To maximize the detection of temporal trends for this Central Amazon site (e.g., driven by CO2 fertilization), plots larger than 10 ha would provide the greatest sensitivity. A model-based analysis of fractional mortality across all gap sizes demonstrated that 9.1-16.9% of tree mortality was missing from plot-based approaches, underscoring the need to combine plot and remote-sensing methods for estimating net landscape carbon balance. Old-growth tropical forests can exhibit complex large-scale structure driven by disturbance and recovery cycles, with ecosystem and community attributes of hectare-scale plots exhibiting continuous dynamic departures from a steady-state condition.

Introducing the fit-criteria assessment plot - A visualisation tool to assist class enumeration in group-based trajectory modelling.

PubMed

Klijn, Sven L; Weijenberg, Matty P; Lemmens, Paul; van den Brandt, Piet A; Lima Passos, Valéria

2017-10-01

Background and objective Group-based trajectory modelling is a model-based clustering technique applied for the identification of latent patterns of temporal changes. Despite its manifold applications in clinical and health sciences, potential problems of the model selection procedure are often overlooked. The choice of the number of latent trajectories (class-enumeration), for instance, is to a large degree based on statistical criteria that are not fail-safe. Moreover, the process as a whole is not transparent. To facilitate class enumeration, we introduce a graphical summary display of several fit and model adequacy criteria, the fit-criteria assessment plot. Methods An R-code that accepts universal data input is presented. The programme condenses relevant group-based trajectory modelling output information of model fit indices in automated graphical displays. Examples based on real and simulated data are provided to illustrate, assess and validate fit-criteria assessment plot's utility. Results Fit-criteria assessment plot provides an overview of fit criteria on a single page, placing users in an informed position to make a decision. Fit-criteria assessment plot does not automatically select the most appropriate model but eases the model assessment procedure. Conclusions Fit-criteria assessment plot is an exploratory, visualisation tool that can be employed to assist decisions in the initial and decisive phase of group-based trajectory modelling analysis. Considering group-based trajectory modelling's widespread resonance in medical and epidemiological sciences, a more comprehensive, easily interpretable and transparent display of the iterative process of class enumeration may foster group-based trajectory modelling's adequate use.

Visual search for tropical web spiders: the influence of plot length, sampling effort, and phase of the day on species richness.

PubMed

Pinto-Leite, C M; Rocha, P L B

2012-12-01

Empirical studies using visual search methods to investigate spider communities were conducted with different sampling protocols, including a variety of plot sizes, sampling efforts, and diurnal periods for sampling. We sampled 11 plots ranging in size from 5 by 10 m to 5 by 60 m. In each plot, we computed the total number of species detected every 10 min during 1 hr during the daytime and during the nighttime (0630 hours to 1100 hours, both a.m. and p.m.). We measured the influence of time effort on the measurement of species richness by comparing the curves produced by sample-based rarefaction and species richness estimation (first-order jackknife). We used a general linear model with repeated measures to assess whether the phase of the day during which sampling occurred and the differences in the plot lengths influenced the number of species observed and the number of species estimated. To measure the differences in species composition between the phases of the day, we used a multiresponse permutation procedure and a graphical representation based on nonmetric multidimensional scaling. After 50 min of sampling, we noted a decreased rate of species accumulation and a tendency of the estimated richness curves to reach an asymptote. We did not detect an effect of plot size on the number of species sampled. However, differences in observed species richness and species composition were found between phases of the day. Based on these results, we propose guidelines for visual search for tropical web spiders.

X-tile: a new bio-informatics tool for biomarker assessment and outcome-based cut-point optimization.

PubMed

Camp, Robert L; Dolled-Filhart, Marisa; Rimm, David L

2004-11-01

The ability to parse tumors into subsets based on biomarker expression has many clinical applications; however, there is no global way to visualize the best cut-points for creating such divisions. We have developed a graphical method, the X-tile plot that illustrates the presence of substantial tumor subpopulations and shows the robustness of the relationship between a biomarker and outcome by construction of a two dimensional projection of every possible subpopulation. We validate X-tile plots by examining the expression of several established prognostic markers (human epidermal growth factor receptor-2, estrogen receptor, p53 expression, patient age, tumor size, and node number) in cohorts of breast cancer patients and show how X-tile plots of each marker predict population subsets rooted in the known biology of their expression.

Critical behavior near the ferromagnetic phase transition in double perovskite Nd2NiMnO6

NASA Astrophysics Data System (ADS)

Ali, Anzar; Sharma, G.; Singh, Yogesh

2018-05-01

The knowledge of critical exponents plays a crucial role in trying to understand the interaction mechanism near a phase transition. In this report, we present a detailed study of the critical behaviour near the ferromagnetic (FM) transition (TC ˜ 193 K) in Nd2NiMnO6 using the temperature and magnetic field dependent isothermal magnetisation measurements. We used various analysis methods such as Arrott plot, modified Arrott plot, and Kouvel-Fisher plot to estimate the critical parameters. The magnetic critical parameters β = 0.49±0.02, γ = 1.05±0.04 and critical isothermal parameter δ = 3.05±0.02 are in excellent agreement with Widom scaling. The critical parameters analysis emphasizes that mean field interaction is the mechanism driving the FM transition in Nd2NiMnO6.

Synthesis, structural, magnetic and optical properties of Sr2CoSn based inverse Heusler alloy nanoparticles

NASA Astrophysics Data System (ADS)

Asvini, V.; Saravanan, G.; Kalaiezhily, R. K.; Ravichandran, K.

2018-05-01

The peculiar ternary full Heusler alloy Sr2CoSn nanoparticles are synthesized by co-precipitation method. X- ray diffraction pattern confirms the formation of XA or Xα structure of Sr2CoSn. Using Williamson-Hall plot (W-H plot), we are able to use the uniform deformation model and get low value of strain induced broadening. UV-Visible absorption spectrum shows sharp absorption peak at 210 nm and the estimated band gap energy of Sr2CoSn Heusler alloy nanoparticles is Eg = 4.6 eV (from Tauc plot). The presence of Sr2CoSn with the particle size of approximately 90 nm was observed using high resolution scanning electron microscopy. The magnetization measurements were carried out using VSM and studied M verses H hysteresis studies.

Common angle plots as perception-true visualizations of categorical associations.

PubMed

Hofmann, Heike; Vendettuoli, Marie

2013-12-01

Visualizations are great tools of communications-they summarize findings and quickly convey main messages to our audience. As designers of charts we have to make sure that information is shown with a minimum of distortion. We have to also consider illusions and other perceptual limitations of our audience. In this paper we discuss the effect and strength of the line width illusion, a Muller-Lyer type illusion, on designs related to displaying associations between categorical variables. Parallel sets and hammock plots are both affected by line width illusions. We introduce the common-angle plot as an alternative method for displaying categorical data in a manner that minimizes the effect from perceptual illusions. Results from user studies both highlight the need for addressing line-width illusions in displays and provide evidence that common angle charts successfully resolve this issue.

Using multi-approaches to investigate the effects of land cover on runoff and soil erosion in the Loess Plateau of China

NASA Astrophysics Data System (ADS)

Gao, G.; Fu, B.; Liu, Y.; Wang, Y.

2012-12-01

This study used the in-situ measurement, model simulation and radioisotope tracing methods to investigate the effects of land cover on runoff and soil erosion at plot and hillslope scales in the Loess Plateau of China. Three runoff plot groups covered by sparse young trees (Group 1), native shrubs (Group 2) and dense tussock (Group 3) with different revegetation time were established in the Yangjuangou catchment of Loess Plateau. Greater runoff was produced in plot groups (Group 2 and Group 3) with higher vegetation cover and longer restoration time as a result of soil compaction processes. Both of the runoff coefficient and soil loss rate decreased with increasing plot length in Group 2 and Group 3 plots. The runoff coefficient increased with plot length in Group 1 plots located at the early stage of revegetation, and the soil loss rates increased over an area threshold. Therefore, the effect of scale on runoff and soil erosion was dependent on restoration extent. The antecedent moisture condition (AMC) was explicitly incorporated in runoff production and initial abstraction of the SCS-CN model, and the direct effect of runoff on event soil loss was considered in the RUSLE model by adopting a rainfall-runoff erosivity factor. The modified SCS-CN and RUSLE models were coupled to link rainfall-runoff-erosion modeling. The modified SCS-CN model was accurate in predicting event runoff from the three plot groups with Nash-Sutcliffe model efficiency (EF) over 0.85, and the prediction accuracy of the modified RUSLE model was satisfactory with EF values being over 0.70. The 137Cs tracing technique was used to examine soil erosion under different land uses and land-use combinations. The results show that the order of erosion rate in different land uses increases sequentially from mature forest to grass to young forest to orchard to terrace crop. The land-use combinations of 'grass (6 years old) + mature forest (25 years old) + grass (25 years old)' and 'grass (6 years old) + young forest (6 years old) + mature forest (25 years old) + grass (25 years old)' are better for soil erosion control, lowering soil erosion amount by 42% compared with a mixtures of 'grass (6 years old) and shrub (6 years old)'. This study indicates that land cover type/pattern, vegetation cover, soil property, restoration time and scale effect as well as stand condition all contribute to the complex hydrological effects of restoring vegetation in the Loess Plateau. Each approach has its own advantages and limitations. Appropriate method should be chosen for specific purpose and study scale. It is better that the results from different approach can be checked with each other.

Elementary Methods for Computation of Quartiles

ERIC Educational Resources Information Center

Žerovnik, Janez; Rupnik Poklukar, Darja

2017-01-01

Quartiles are usually introduced early, often in primary school together with box-and-whisker plots. Various methods are used, and in lack of explanation in many textbooks at elementary level, this leads to unnecessary confusion. We discuss some elementary methods that are consistent with the most common definition and are also easy to understand.

A review of methods for updating forest monitoring system estimates

Treesearch

Hector Franco-Lopez; Alan R. Ek; Andrew P. Robinson

2000-01-01

Intensifying interest in forests and the development of new monitoring technologies have induced major changes in forest monitoring systems in the last few years, including major revisions in the methods used for updating. This paper describes the methods available for projecting stand- and plot-level information, emphasizing advantages and disadvantages, and the...

Cover/Frequency (CF)

Treesearch

John F. Caratti

2006-01-01

The FIREMON Cover/Frequency (CF) method is used to assess changes in plant species cover and frequency for a macroplot. This method uses multiple quadrats to sample within-plot variation and quantify statistically valid changes in plant species cover, height, and frequency over time. Because it is difficult to estimate cover in quadrats for larger plants, this method...

Assessing Grammar Teaching Methods Using a Metacognitive Framework.

ERIC Educational Resources Information Center

Burkhalter, Nancy

A study examined 3 grammar teaching methods to understand why some methods may carry over into writing better than others. E. Bialystok and E. B. Ryan's (1985) metacognitive model of language skills was adapted to plot traditional grammar, sentence combining, and the functional/inductive approach according to the amount of analyzed knowledge and…

Line Intercept (LI)

Treesearch

John F. Caratti

2006-01-01

The FIREMON Line Intercept (LI) method is used to assess changes in plant species cover for a macroplot. This method uses multiple line transects to sample within plot variation and quantify statistically valid changes in plant species cover and height over time. This method is suited for most forest and rangeland communities, but is especially useful for sampling...

Detecting gravesoil with headspace analysis with adsorption on short porous layer open tubular (PLOT) columns.

PubMed

Lovestead, Tara M; Bruno, Thomas J

2011-01-30

Victims of crimes are often buried in clandestine graves. There are several techniques for finding buried bodies or the scattered remains of a victim; however, none of these methods are very reliable or work in all scenarios. One way to detect gravesoil is to detect the biochemical changes of the surrounding soil due to cadaver decomposition, for example, the release of nitrogenous compounds. A simple and low-cost way to detect these compounds is based on the reaction of alpha amino groups with ninhydrin to form Ruhemann's purple. This test for ninhydrin-reactive nitrogen (NRN) has, to date, only been performed by direct solvent extraction of soil samples. Here, we present a method that detects trace quantities of NRN in the headspace air above gravesoil. Our method is based on an improved purge and trap method developed in our lab for sampling low volatility compounds, as well as volatile compounds at trace quantities, by applying low temperature collection on short alumina-coated porous layer open tubular (PLOT) columns. We modified this method to sample the headspace air above gravesoil with a motorized pipetter and a PLOT column at ambient temperatures. We generated gravesoil using rat cadavers and local soil. Trace quantities of NRN were successfully detected in the headspace air above gravesoil. We report the quantities of NRN recovered for buried rats, rats laid on top of soil, and blank graves (no rats) as a function of time (weeks to months). This work is the first (and thus far, only) example of a method for detecting NRN in the vapor phase, providing another tool for forensic investigators to aid in locating elusive clandestine graves. Published by Elsevier Ireland Ltd.

Toward structure prediction of cyclic peptides.

PubMed

Yu, Hongtao; Lin, Yu-Shan

2015-02-14

Cyclic peptides are a promising class of molecules that can be used to target specific protein-protein interactions. A computational method to accurately predict their structures would substantially advance the development of cyclic peptides as modulators of protein-protein interactions. Here, we develop a computational method that integrates bias-exchange metadynamics simulations, a Boltzmann reweighting scheme, dihedral principal component analysis and a modified density peak-based cluster analysis to provide a converged structural description for cyclic peptides. Using this method, we evaluate the performance of a number of popular protein force fields on a model cyclic peptide. All the tested force fields seem to over-stabilize the α-helix and PPII/β regions in the Ramachandran plot, commonly populated by linear peptides and proteins. Our findings suggest that re-parameterization of a force field that well describes the full Ramachandran plot is necessary to accurately model cyclic peptides.

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 2: Data

NASA Technical Reports Server (NTRS)

Waszak, M. R.; Schmidt, D. K.

1985-01-01

Two analysis methods are applied to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop modal analysis technique. This method considers the effect of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Both analyses indicated that dynamic aeroelastic effects caused a degradation in vehicle tracking performance, based on the evaluation of some simulation results. Volume 2 consists of the presentation of the state variable models of the flexible aircraft configurations used in the analysis applications mode shape plots for the structural modes, numerical results from the modal analysis frequency response plots from the pilot in the loop analysis and a listing of the modal analysis computer program.

Estimation of descriptive statistics for multiply censored water quality data

USGS Publications Warehouse

Helsel, Dennis R.; Cohn, Timothy A.

1988-01-01

This paper extends the work of Gilliom and Helsel (1986) on procedures for estimating descriptive statistics of water quality data that contain “less than” observations. Previously, procedures were evaluated when only one detection limit was present. Here we investigate the performance of estimators for data that have multiple detection limits. Probability plotting and maximum likelihood methods perform substantially better than simple substitution procedures now commonly in use. Therefore simple substitution procedures (e.g., substitution of the detection limit) should be avoided. Probability plotting methods are more robust than maximum likelihood methods to misspecification of the parent distribution and their use should be encouraged in the typical situation where the parent distribution is unknown. When utilized correctly, less than values frequently contain nearly as much information for estimating population moments and quantiles as would the same observations had the detection limit been below them.

PLOT3D- DRAWING THREE DIMENSIONAL SURFACES

NASA Technical Reports Server (NTRS)

Canright, R. B.

1994-01-01

PLOT3D is a package of programs to draw three-dimensional surfaces of the form z = f(x,y). The function f and the boundary values for x and y are the input to PLOT3D. The surface thus defined may be drawn after arbitrary rotations. However, it is designed to draw only functions in rectangular coordinates expressed explicitly in the above form. It cannot, for example, draw a sphere. Output is by off-line incremental plotter or online microfilm recorder. This package, unlike other packages, will plot any function of the form z = f(x,y) and portrays continuous and bounded functions of two independent variables. With curve fitting; however, it can draw experimental data and pictures which cannot be expressed in the above form. The method used is division into a uniform rectangular grid of the given x and y ranges. The values of the supplied function at the grid points (x, y) are calculated and stored; this defines the surface. The surface is portrayed by connecting successive (y,z) points with straight-line segments for each x value on the grid and, in turn, connecting successive (x,z) points for each fixed y value on the grid. These lines are then projected by parallel projection onto the fixed yz-plane for plotting. This program has been implemented on the IBM 360/67 with on-line CDC microfilm recorder.

40 CFR 61.32 - Emission standard.

Code of Federal Regulations, 2010 CFR

2010-07-01

... frequency of calibration. (b) Method of sample analysis. (c) Averaging technique for determining 30-day...) Plant and sampling area plots showing emission points and sampling sites. Topographic features...

Scaling, propagating and mapping uncertainty in spectroscopy-derived foliar traits from the leaf to the image

NASA Astrophysics Data System (ADS)

Singh, A.; Serbin, S. P.; Kingdon, C.; Townsend, P. A.

2013-12-01

A major goal of remote sensing, and imaging spectroscopy in particular, is the development of generalizable algorithms to repeatedly and accurately map ecosystem properties such as canopy chemistry across space and time. Existing methods must therefore be tested across a range of measurement approaches to identify and overcome limits to the consistent retrieval of such properties from spectroscopic imagery. Here we illustrate a general approach for the estimation of key foliar biochemical and morphological traits from spectroscopic imagery derived from the AVIRIS instrument and the propagation of errors from the leaf to the image scale using partial least squares regression (PLSR) techniques. Our method involves the integration of three types of data representing different scales of observation: At the image scale, the images were normalized for atmospheric, illumination and BRDF effects. Spectra from field plot locations were extracted from the 51AVIRIS images and were averaged when the field plot was larger than a single pixel. At the plot level, the scaling was conducted using multiple replicates (1000) derived from the leaf-level uncertainty estimates to generate plot-level estimates with their associated uncertainties. Leaf-level estimates of foliar traits (%N, %C, %Fiber, %Cellulose, %Lignin, LMA) were scaled to the canopy based on relative species composition of each plot. Image spectra were iteratively split into 50/50 randomized calibration-validation datasets and multiple (500) trait-predictive PLSR models were generated, this time sampling from within the plot-level uncertainty distribution. This allowed the propagation of uncertainty from the leaf-level dependent variables to the plot level, and finally to models built using AVIRIS image spectra. Moreover, this method allows us to generate spatially explicit maps of uncertainty in our sampled traits. Both LMA and %N PLSR models had a R2 greater than 0.8, root mean square errors (RMSEs) for both variables were less than 6% of the range of data. Fiber and lignin were predicted with R2 > 0.65 and carbon and cellulose greater than 0.5. Although R2 of these variables were lower than LMA and %N, their RMSE values were beneath 9% of the range of data. The comparatively lower R2 values for %C and cellulose in particular were related to the low amount of natural variability in these constituents. Further, coefficients from the randomized set of PLSR models were applied to imagery and aggregated to obtain pixel-wise predicted means and uncertainty estimates for each foliar trait. The resulting maps of nutritional and morphological properties together with their overall uncertainties represent a first-of-its-kind data product for examining the spatio-temporal patterns of forest functioning and nutrient cycling. These data are now being used to relate foliar traits with ecosystem processes such as streamwater nutrient export and insect herbivory. In addition, the ability to assign a retrieval uncertainty enables more efficient assimilation of these data products into ecosystem models to help constrain carbon and nutrient cycling projections.

Estimation of lattice strain in nanocrystalline RuO2 by Williamson-Hall and size-strain plot methods

NASA Astrophysics Data System (ADS)

Sivakami, R.; Dhanuskodi, S.; Karvembu, R.

2016-01-01

RuO2 nanoparticles (RuO2 NPs) have been successfully synthesized by the hydrothermal method. Structure and the particle size have been determined by X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM) and transmission electron microscopy (TEM). UV-Vis spectra reveal that the optical band gap of RuO2 nanoparticles is red shifted from 3.95 to 3.55 eV. BET measurements show a high specific surface area (SSA) of 118-133 m2/g and pore diameter (10-25 nm) has been estimated by Barret-Joyner-Halenda (BJH) method. The crystallite size and lattice strain in the samples have been investigated by Williamson-Hall (W-H) analysis assuming uniform deformation, deformation stress and deformation energy density, and the size-strain plot method. All other relevant physical parameters including stress, strain and energy density have been calculated. The average crystallite size and the lattice strain evaluated from XRD measurements are in good agreement with the results of TEM.

Thermal helium clusters at 3.2 Kelvin in classical and semiclassical simulations

NASA Astrophysics Data System (ADS)

Schulte, J.

1993-03-01

The thermodynamic stability of4He4-13 at 3.2 K is investigated with the classical Monte Carlo method, with the semiclassical path-integral Monte Carlo (PIMC) method, and with the semiclassical all-order many-body method. In the all-order many-body simulation the dipole-dipole approximation including short-range correction is used. The resulting stability plots are discussed and related to recent TOF experiments by Stephens and King. It is found that with classical Monte Carlo of course the characteristics of the measured mass spectrum cannot be resolved. With PIMC, switching on more and more quantum mechanics. by raising the number of virtual time steps results in more structure in the stability plot, but this did not lead to sufficient agreement with the TOF experiment. Only the all-order many-body method resolved the characteristic structures of the measured mass spectrum, including magic numbers. The result shows the influence of quantum statistics and quantum mechanics on the stability of small neutral helium clusters.

Non-Deterministic Dynamic Instability of Composite Shells

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Abumeri, Galib H.

2004-01-01

A computationally effective method is described to evaluate the non-deterministic dynamic instability (probabilistic dynamic buckling) of thin composite shells. The method is a judicious combination of available computer codes for finite element, composite mechanics, and probabilistic structural analysis. The solution method is incrementally updated Lagrangian. It is illustrated by applying it to thin composite cylindrical shell subjected to dynamic loads. Both deterministic and probabilistic buckling loads are evaluated to demonstrate the effectiveness of the method. A universal plot is obtained for the specific shell that can be used to approximate buckling loads for different load rates and different probability levels. Results from this plot show that the faster the rate, the higher the buckling load and the shorter the time. The lower the probability, the lower is the buckling load for a specific time. Probabilistic sensitivity results show that the ply thickness, the fiber volume ratio and the fiber longitudinal modulus, dynamic load and loading rate are the dominant uncertainties, in that order.

Dynamic Probabilistic Instability of Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

2009-01-01

A computationally effective method is described to evaluate the non-deterministic dynamic instability (probabilistic dynamic buckling) of thin composite shells. The method is a judicious combination of available computer codes for finite element, composite mechanics and probabilistic structural analysis. The solution method is incrementally updated Lagrangian. It is illustrated by applying it to thin composite cylindrical shell subjected to dynamic loads. Both deterministic and probabilistic buckling loads are evaluated to demonstrate the effectiveness of the method. A universal plot is obtained for the specific shell that can be used to approximate buckling loads for different load rates and different probability levels. Results from this plot show that the faster the rate, the higher the buckling load and the shorter the time. The lower the probability, the lower is the buckling load for a specific time. Probabilistic sensitivity results show that the ply thickness, the fiber volume ratio and the fiber longitudinal modulus, dynamic load and loading rate are the dominant uncertainties in that order.

Opportunities for Integrated Ecological Analysis across Inland Australia with Standardised Data from Ausplots Rangelands.

PubMed

Guerin, Greg R; Sparrow, Ben; Tokmakoff, Andrew; Smyth, Anita; Leitch, Emrys; Baruch, Zdravko; Lowe, Andrew J

2017-01-01

Australian rangelands ecosystems cover 81% of the continent but are understudied and continental-scale research has been limited in part by a lack of precise data that are standardised between jurisdictions. We present a new dataset from AusPlots Rangelands that enables integrative rangelands analysis due to its geographic scope and standardised methodology. The method provides data on vegetation and soils, enabling comparison of a suite of metrics including fractional vegetation cover, basal area, and species richness, diversity, and composition. Cover estimates are robust and repeatable, allowing comparisons among environments and detection of modest change. The 442 field plots presented here span a rainfall gradient of 129-1437 mm Mean annual precipitation with varying seasonality. Vegetation measurements include vouchered vascular plant species, growth form, basal area, height, cover and substrate type from 1010 point intercepts as well as systematically recorded absences, which are useful for predictive modelling and validation of remote sensing applications. Leaf and soil samples are sampled for downstream chemical and genomic analysis. We overview the sampling of vegetation parameters and environments, applying the data to the question of how species abundance distributions (SADs) vary over climatic gradients, a key question for the influence of environmental change on ecosystem processes. We found linear relationships between SAD shape and rainfall within grassland and shrubland communities, indicating more uneven abundance in deserts and suggesting relative abundance may shift as a consequence of climate change, resulting in altered diversity and ecosystem function. The standardised data of AusPlots enables such analyses at large spatial scales, and the testing of predictions through time with longitudinal sampling. In future, the AusPlots field program will be directed towards improving coverage of space, under-represented environments, vegetation types and fauna and, increasingly, re-sampling of established plots. Providing up-to-date data access methods to enhance re-use is also a priority.

Evaluating and interpreting the chemical relevance of the linear response kernel for atoms II: open shell.

PubMed

Boisdenghien, Zino; Fias, Stijn; Van Alsenoy, Christian; De Proft, Frank; Geerlings, Paul

2014-07-28

Most of the work done on the linear response kernel χ(r,r') has focussed on its atom-atom condensed form χAB. Our previous work [Boisdenghien et al., J. Chem. Theory Comput., 2013, 9, 1007] was the first effort to truly focus on the non-condensed form of this function for closed (sub)shell atoms in a systematic fashion. In this work, we extend our method to the open shell case. To simplify the plotting of our results, we average our results to a symmetrical quantity χ(r,r'). This allows us to plot the linear response kernel for all elements up to and including argon and to investigate the periodicity throughout the first three rows in the periodic table and in the different representations of χ(r,r'). Within the context of Spin Polarized Conceptual Density Functional Theory, the first two-dimensional plots of spin polarized linear response functions are presented and commented on for some selected cases on the basis of the atomic ground state electronic configurations. Using the relation between the linear response kernel and the polarizability we compare the values of the polarizability tensor calculated using our method to high-level values.

Micromechanics Analysis Code Post-Processing (MACPOST) User Guide. 1.0

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Comiskey, Michele D.; Bednarcyk, Brett A.

1999-01-01

As advanced composite materials have gained wider usage. the need for analytical models and computer codes to predict the thermomechanical deformation response of these materials has increased significantly. Recently, a micromechanics technique called the generalized method of cells (GMC) has been developed, which has the capability to fulfill this -oal. Tc provide a framework for GMC, the Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) has been developed. As MAC/GMC has been updated, significant improvements have been made to the post-processing capabilities of the code. Through the MACPOST program, which operates directly within the MSC/PATRAN graphical pre- and post-processing package, a direct link between the analysis capabilities of MAC/GMC and the post-processing capabilities of MSC/PATRAN has been established. MACPOST has simplified the production, printing. and exportation of results for unit cells analyzed by MAC/GMC. MACPOST allows different micro-level quantities to be plotted quickly and easily in contour plots. In addition, meaningful data for X-Y plots can be examined. MACPOST thus serves as an important analysis and visualization tool for the macro- and micro-level data generated by MAC/GMC. This report serves as the user's manual for the MACPOST program.

Development of the Veritas plot and its application in cardiac surgery: an evidence-synthesis graphic tool for the clinician to assess multiple meta-analyses reporting on a common outcome.

PubMed

Panesar, Sukhmeet S; Rao, Christopher; Vecht, Joshua A; Mirza, Saqeb B; Netuveli, Gopalakrishnan; Morris, Richard; Rosenthal, Joe; Darzi, Ara; Athanasiou, Thanos

2009-10-01

Meta-analyses may be prone to generating misleading results because of a paucity of experimental studies (especially in surgery); publication bias; and heterogeneity in study design, intervention and the patient population of included studies. When investigating a specific clinical or scientific question on which several relevant meta-analyses may have been published, value judgments must be applied to determine which analysis represents the most robust evidence. These value judgments should be specifically acknowledged. We designed the Veritas plot to explicitly explore important elements of quality and to facilitate decision-making by highlighting specific areas in which meta-analyses are found to be deficient. Furthermore, as a graphic tool, it may be more intuitive than when similar data are presented in a tabular or text format. The Veritas plot is an adaption of the radar plot, a graphic tool for the description of multiattribute data. Key elements of meta-analytical quality such as heterogeneity, publication bias and study design are assessed. Existing qualitative methods such as the Assessment of Multiple Systematic Reviews (AMSTAR) tool have been incorporated in addition to important considerations when interpreting surgical meta-analyses such as the year of publication and population characteristics. To demonstrate the potential of the Veritas plot to inform clinical practice, we apply the Veritas plot to the meta-analytical literature comparing the incidence of 30-day stroke in off-pump coronary artery bypass surgery and conventional coronary artery bypass surgery. We demonstrate that a visually-stimulating and practical evidence-synthesis tool can direct the clinician and scientist to a particular meta-analytical study to inform clinical practice. The Veritas plot is also cumulative and allowed us to assess the quality of evidence over time. We have presented a practical graphic application for scientists and clinicians to identify and interpret variability in meta-analyses. Although further validation of the Veritas plot is required, it may have the potential to contribute to the implementation of evidence-based practice.

Torsional Angle Driver (TorAD) System for HyperChem/Excel

NASA Astrophysics Data System (ADS)

Starkey, Ronald

1999-02-01

The torsional angle driver system for HyperChem/Excel is a package of several Excel spreadsheets and macro programs to be used with HyperChem to obtain and plot information, such as total energy, for the conformations that result from a 360° rotation about a torsional angle system in a molecule. The TorAD system also includes several HyperChem scripts to facilitate its use. TorAD was developed for use in the undergraduate organic chemistry laboratory. The results obtained with TorAD could be obtained manually with HyperChem, but it would take considerable time and would not be instructive to the students. Use of the TorAD system allows students to spend their time on the more important aspect of conformation analysisinterpretation of results. The Excel spreadsheet/macro programs in TorAD include:

· Tor_xl_a and tor_xl obtain and plot the total energy at 5° torsional-angle intervals. The calculation method, the torsional-angle restraint, and the structure to be used at each angle can be set by the user. The advanced version, tor_xl_a, which requires HyperChem 4.5 or later, also allows torsional-angle structures to be saved for later recall as individual structures or, using a HyperChem script, in a movie format. It also provides a rapid scan of the 360° rotation where only single-point calculations, rather than geometry optimizations, are performed. The tor_xl system will perform routine tasks in a manner suitable for most instructional settings. · Tor_Comp performs molecular mechanics optimizations at 5° intervals and obtains and plots four energy parameters (total, torsional, nonbonded, and bond [bend plus stretch] energy) as a function of torsional angle. The calculation method and the restraint can be specified. · TorDipol produces a plot of the total energy and the calculated dipole moment at 5° steps of the torsional angle. The default calculation is the semi-empirical AM1 method, but other methods can be used. The calculation method and the restraint can be specified. · Tor2_180 and Tor2_360 rotate two torsional angles to provide a 3D plot of the resulting total energy surface. Tor2_180 performs a 0 to 180° rotation, in 10° steps, on each of the two torsional angle systems (tor1 and tor2) selected. Tor2_360 will do a -180° to +180° (360° total) rotation of the two torsional angles in 20° steps.

Markedly divergent estimates of Amazon forest carbon density from ground plots and satellites

PubMed Central

Mitchard, Edward T A; Feldpausch, Ted R; Brienen, Roel J W; Lopez-Gonzalez, Gabriela; Monteagudo, Abel; Baker, Timothy R; Lewis, Simon L; Lloyd, Jon; Quesada, Carlos A; Gloor, Manuel; ter Steege, Hans; Meir, Patrick; Alvarez, Esteban; Araujo-Murakami, Alejandro; Aragão, Luiz E O C; Arroyo, Luzmila; Aymard, Gerardo; Banki, Olaf; Bonal, Damien; Brown, Sandra; Brown, Foster I; Cerón, Carlos E; Chama Moscoso, Victor; Chave, Jerome; Comiskey, James A; Cornejo, Fernando; Corrales Medina, Massiel; Da Costa, Lola; Costa, Flavia R C; Di Fiore, Anthony; Domingues, Tomas F; Erwin, Terry L; Frederickson, Todd; Higuchi, Niro; Honorio Coronado, Euridice N; Killeen, Tim J; Laurance, William F; Levis, Carolina; Magnusson, William E; Marimon, Beatriz S; Marimon Junior, Ben Hur; Mendoza Polo, Irina; Mishra, Piyush; Nascimento, Marcelo T; Neill, David; Núñez Vargas, Mario P; Palacios, Walter A; Parada, Alexander; Pardo Molina, Guido; Peña-Claros, Marielos; Pitman, Nigel; Peres, Carlos A; Poorter, Lourens; Prieto, Adriana; Ramirez-Angulo, Hirma; Restrepo Correa, Zorayda; Roopsind, Anand; Roucoux, Katherine H; Rudas, Agustin; Salomão, Rafael P; Schietti, Juliana; Silveira, Marcos; de Souza, Priscila F; Steininger, Marc K; Stropp, Juliana; Terborgh, John; Thomas, Raquel; Toledo, Marisol; Torres-Lezama, Armando; van Andel, Tinde R; van der Heijden, Geertje M F; Vieira, Ima C G; Vieira, Simone; Vilanova-Torre, Emilio; Vos, Vincent A; Wang, Ophelia; Zartman, Charles E; Malhi, Yadvinder; Phillips, Oliver L

2014-01-01

Aim The accurate mapping of forest carbon stocks is essential for understanding the global carbon cycle, for assessing emissions from deforestation, and for rational land-use planning. Remote sensing (RS) is currently the key tool for this purpose, but RS does not estimate vegetation biomass directly, and thus may miss significant spatial variations in forest structure. We test the stated accuracy of pantropical carbon maps using a large independent field dataset. Location Tropical forests of the Amazon basin. The permanent archive of the field plot data can be accessed at: http://dx.doi.org/10.5521/FORESTPLOTS.NET/2014_1 Methods Two recent pantropical RS maps of vegetation carbon are compared to a unique ground-plot dataset, involving tree measurements in 413 large inventory plots located in nine countries. The RS maps were compared directly to field plots, and kriging of the field data was used to allow area-based comparisons. Results The two RS carbon maps fail to capture the main gradient in Amazon forest carbon detected using 413 ground plots, from the densely wooded tall forests of the north-east, to the light-wooded, shorter forests of the south-west. The differences between plots and RS maps far exceed the uncertainties given in these studies, with whole regions over- or under-estimated by > 25%, whereas regional uncertainties for the maps were reported to be < 5%. Main conclusions Pantropical biomass maps are widely used by governments and by projects aiming to reduce deforestation using carbon offsets, but may have significant regional biases. Carbon-mapping techniques must be revised to account for the known ecological variation in tree wood density and allometry to create maps suitable for carbon accounting. The use of single relationships between tree canopy height and above-ground biomass inevitably yields large, spatially correlated errors. This presents a significant challenge to both the forest conservation and remote sensing communities, because neither wood density nor species assemblages can be reliably mapped from space. PMID:26430387

40 CFR 1065.275 - N2O measurement devices.

Code of Federal Regulations, 2012 CFR

2012-07-01

... for interpretation of infrared spectra. For example, EPA Test Method 320 is considered a valid method... uncompensated signal's bias. Examples of laser infrared analyzers are pulsed-mode high-resolution narrow band.... Examples of acceptable columns are a PLOT column consisting of bonded polystyrene-divinylbenzene or a...

Application of Classification Models to Pharyngeal High-Resolution Manometry

ERIC Educational Resources Information Center

Mielens, Jason D.; Hoffman, Matthew R.; Ciucci, Michelle R.; McCulloch, Timothy M.; Jiang, Jack J.

2012-01-01

Purpose: The authors present 3 methods of performing pattern recognition on spatiotemporal plots produced by pharyngeal high-resolution manometry (HRM). Method: Classification models, including the artificial neural networks (ANNs) multilayer perceptron (MLP) and learning vector quantization (LVQ), as well as support vector machines (SVM), were…

Flow dynamic environment data base development for the SSME

NASA Technical Reports Server (NTRS)

Sundaram, C. V.

1985-01-01

The fluid flow-induced vibration of the Space Shuttle main engine (SSME) components are being studied with a view to correlating the frequency characteristics of the pressure fluctuations in a rocket engine to its operating conditions and geometry. An overview of the data base development for SSME test firing results and the interactive computer software used to access, retrieve, and plot or print the results selectively for given thrust levels, engine numbers, etc., is presented. The various statistical methods available in the computer code for data analysis are discussed. Plots of test data, nondimensionalized using parameters such as fluid flow velocities, densities, and pressures, are presented. Results are compared with those available in the literature. Correlations between the resonant peaks observed at higher frequencies in power spectral density plots with pump geometry and operating conditions are discussed. An overview of the status of the investigation is presented and future directions are discussed.

Effects of harvesting cypress swamps on water quality and quantity

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

Ewel, K.C.

1985-09-01

The responses of cypress swamps to a spectrum of harvest techniques are being studied in the Withlacoochee State Forest, Hernando County, Florida. Among the 11 swamps in the study area, four contain plots that were harvested experimentally in 1984. Stand improvement cuts were made in plots in two large swamps. Measurements of tree biomass were made in all but two of the large swamps. The swamps were surveyed for cone production in the fall and regeneration in the spring. However, coppice was produced in all the harvested plots. These preliminary results suggest that coppice production may be a dependable regenerationmore » method, although it may not be desirable for stand improvement cuts and thinning. Evapotranspiration from three cypress swamps averaged 79 cm over a 3-year period. The purpose of this project was to determine specific impacts of harvesting on water quality and water loss rates in the study areas.« less

Crystallite size strain analysis of nanocrystalline La0.7Sr0.3MnO3 perovskite by Williamson-Hall plot method

NASA Astrophysics Data System (ADS)

Kumar, Dinesh; Verma, Narendra Kumar; Singh, Chandra Bhal; Singh, Akhilesh Kumar

2018-04-01

The nanocrystalline Sr-doped LaMnO3 (La0.7Sr0.3MnO3 = LSMO) perovskite manganites having different crystallite size were synthesized using the nitrate-glycine auto-combustion method. The phase purity of the manganites was checked by X-ray diffraction (XRD) measurement. The XRD patterns of the sample reveal that La0.7S0.3MnO3 crystallizes into rhombohedral crystal structure with space group R-3c. The size-dependence of structural lattice parameters have been investigated with the help of Rietveld refinement. The structural parameters increase as a function of crystallite size. The crystallite-size and internal strain as a function of crystallite-size have been calculated using Williamson-Hall plot.

Extracting the quark mixing phase γ from B±→K±π+π-, B0→Ksπ+π-, and B¯0→Ksπ+π-

NASA Astrophysics Data System (ADS)

Bediaga, Ignacio; Guerrer, Gabriel; de Miranda, Jussara M.

2007-10-01

We discuss some aspects of the search for CP asymmetry in the three body B decays, revealed through the interference among neighbor resonances in the Dalitz plot. We propose a competitive method to extract the CKM γ angle combining Dalitz plot amplitude analysis of B±→K±π+π- and untagged B0, B¯0→Ksπ+π-. The method also obtains the ratio and phase difference between the tree and penguin contributions from B0 and B¯0→K*±π∓ decays and the CP asymmetry between B0 and B¯0. From Monte Carlo studies of 100 K events for the neutral mesons, we show the possibility of measuring γ.

Serotonin synthesis rate and the tryptophan hydroxylase-2: G-703T polymorphism in social anxiety disorder.

PubMed

Furmark, Tomas; Marteinsdottir, Ina; Frick, Andreas; Heurling, Kerstin; Tillfors, Maria; Appel, Lieuwe; Antoni, Gunnar; Hartvig, Per; Fischer, Håkan; Långström, Bengt; Eriksson, Elias; Fredrikson, Mats

2016-10-01

It is disputed whether anxiety disorders, like social anxiety disorder, are characterized by serotonin over- or underactivity. Here, we evaluated whether our recent finding of elevated neural serotonin synthesis rate in patients with social anxiety disorder could be reproduced in a separate cohort, and whether allelic variation in the tryptophan hydroxylase-2 (TPH2) G-703T polymorphism relates to differences in serotonin synthesis assessed with positron emission tomography. Eighteen social anxiety disorder patients and six healthy controls were scanned during 60 minutes in a resting state using positron emission tomography and 5-hydroxy-L-[β -(11)C]tryptophan, [(11)C]5-HTP, a substrate of the second enzymatic step in serotonin synthesis. Parametric images were generated, using the reference Patlak method, and analysed using Statistical Parametric Mapping (SPM8). Blood samples for genotyping of the TPH2 G-703T polymorphism were obtained from 16 social anxiety disorder patients (T carriers: n=5, GG carriers: n=11). A significantly elevated [(11)C]5-HTP accumulation rate, indicative of enhanced decarboxylase activity and thereby serotonin synthesis capacity, was detected in social anxiety disorder patients compared with controls in the hippocampus and basal ganglia nuclei and, at a more lenient (uncorrected) statistical threshold, in the amygdala and anterior cingulate cortex. In patients, the serotonin synthesis rate in the amygdala and anterior cingulate cortex was significantly elevated in TPH2 T carriers in comparison with GG homozygotes. Our results support that social anxiety disorder entails an overactive presynaptic serotonergic system that, in turn, seems functionally influenced by the TPH2 G-703T polymorphism in emotionally relevant brain regions. © The Author(s) 2016.

Non-local means denoising of dynamic PET images.

PubMed

Dutta, Joyita; Leahy, Richard M; Li, Quanzheng

2013-01-01

Dynamic positron emission tomography (PET), which reveals information about both the spatial distribution and temporal kinetics of a radiotracer, enables quantitative interpretation of PET data. Model-based interpretation of dynamic PET images by means of parametric fitting, however, is often a challenging task due to high levels of noise, thus necessitating a denoising step. The objective of this paper is to develop and characterize a denoising framework for dynamic PET based on non-local means (NLM). NLM denoising computes weighted averages of voxel intensities assigning larger weights to voxels that are similar to a given voxel in terms of their local neighborhoods or patches. We introduce three key modifications to tailor the original NLM framework to dynamic PET. Firstly, we derive similarities from less noisy later time points in a typical PET acquisition to denoise the entire time series. Secondly, we use spatiotemporal patches for robust similarity computation. Finally, we use a spatially varying smoothing parameter based on a local variance approximation over each spatiotemporal patch. To assess the performance of our denoising technique, we performed a realistic simulation on a dynamic digital phantom based on the Digimouse atlas. For experimental validation, we denoised [Formula: see text] PET images from a mouse study and a hepatocellular carcinoma patient study. We compared the performance of NLM denoising with four other denoising approaches - Gaussian filtering, PCA, HYPR, and conventional NLM based on spatial patches. The simulation study revealed significant improvement in bias-variance performance achieved using our NLM technique relative to all the other methods. The experimental data analysis revealed that our technique leads to clear improvement in contrast-to-noise ratio in Patlak parametric images generated from denoised preclinical and clinical dynamic images, indicating its ability to preserve image contrast and high intensity details while lowering the background noise variance.

The International Atomic Energy Agency software package for the analysis of scintigraphic renal dynamic studies: a tool for the clinician, teacher, and researcher.

PubMed

Zaknun, John J; Rajabi, Hossein; Piepsz, Amy; Roca, Isabel; Dondi, Maurizio

2011-01-01

Under the auspices of the International Atomic Energy Agency, a new-generation, platform-independent, and x86-compatible software package was developed for the analysis of scintigraphic renal dynamic imaging studies. It provides nuclear medicine professionals cost-free access to the most recent developments in the field. The software package is a step forward towards harmonization and standardization. Embedded functionalities render it a suitable tool for education, research, and for receiving distant expert's opinions. Another objective of this effort is to allow introducing clinically useful parameters of drainage, including normalized residual activity and outflow efficiency. Furthermore, it provides an effective teaching tool for young professionals who are being introduced to dynamic kidney studies by selected teaching case studies. The software facilitates a better understanding through practically approaching different variables and settings and their effect on the numerical results. An effort was made to introduce instruments of quality assurance at the various levels of the program's execution, including visual inspection and automatic detection and correction of patient's motion, automatic placement of regions of interest around the kidneys, cortical regions, and placement of reproducible background region on both primary dynamic and on postmicturition studies. The user can calculate the differential renal function through 2 independent methods, the integral or the Rutland-Patlak approaches. Standardized digital reports, storage and retrieval of regions of interest, and built-in database operations allow the generation and tracing of full image reports and of numerical outputs. The software package is undergoing quality assurance procedures to verify the accuracy and the interuser reproducibility with the final aim of launching the program for use by professionals and teaching institutions worldwide. Copyright © 2011 Elsevier Inc. All rights reserved.

Quantification of blood-to-brain transfer rate in multiple sclerosis

PubMed Central

Taheri, Saeid; Rosenberg, Gary A.; Ford, Corey

2016-01-01

Blood–brain barrier (BBB) disruption visualized in lesions by MRI is a major biomarker of disease activity in multiple sclerosis (MS). However, in MS, destruction occurs to a variable extent in lesions as well as in gray matter (GM) and in the normal appearing white matter (NAWM). A method to quantify the BBB disruption in lesions as well as in non-lesion areas would be useful for assessment of MS progression and treatments. The objective of this study was to quantify the BBB transfer rate (Ki) in WM lesions, in the NAWM, and in the full-brain of MS patients. Thirteen MS patients with active lesions and 10 healthy controls with age and gender matching were recruited for full-brain and WM Ki studies. Dynamic contrast-enhanced MRI (DCEMRI) scans were conducted using T1 mapping with partial inversion recovery (TAPIR), a fast T1 mapping technique, following administration of a quarter-dose of the contrast agent Gadolinium-DTPA (Gd-DTPA). The Patlak modeling technique was used to derive a voxel-based map of Ki. In all patients contrast-enhanced lesions, quantified by Ki maps, were observed. Compared with controls, patients with MS exhibited an increase in mean Ki of the full-brain (P-value<0.05) but no significant difference in mean Ki of NAWM. The identified increase in full-brain Ki of MS patients suggests a global vascular involvement associated with MS disease. The lack of observed significant decrease in Ki in NAWM suggests lower involvement of WM vasculature than full-brain vasculature in MS. Ki maps constructed from time series data acquired by DCEMRI provide additional information about BBB that could be used for evaluation of vascular involvement in MS and monitoring treatment effectiveness. PMID:25877634

Chronic AMPK activity dysregulation produces myocardial insulin resistance in the human Arg302Gln-PRKAG2 glycogen storage disease mouse model

PubMed Central

2013-01-01

Background The cardiac PRKAG2 mutation in the γ2-subunit of adenosine monophosphate activated kinase (AMPK) is characterized by excessive glycogen deposition, hypertrophy, frequent arrhythmias, and progressive conduction system disease. We investigated whether myocardial glucose uptake (MGU) was augmented following insulin stimulation in a mouse model of the PRKAG2 cardiac syndrome. Methods Myocardial and skeletal muscle glucose uptake was assessed with 2-[18F]fluoro-2-deoxyglucose positron emission tomography imaging in n = 3 transgenic wildtype (TGwt) vs n = 7 PRKAG2 mutant (TGmut) mice at baseline and 1 week later, 30 min following acute insulin. Systolic function, cardiac glycogen stores, phospho-AMPK α, and insulin-receptor expression levels were analyzed to corroborate to the in vivo findings. Results TGmut Patlak Ki was reduced 56% at baseline compared to TGwt (0.3 ± 0.2 vs 0.7 ± 0.1, t test p = 0.01). MGU was augmented 71% in TGwt mice following acute insulin from baseline (0.7 ± 0.1 to 1.2 ± 0.2, t test p < 0.05). No change was observed in TGmut mice. As expected for this cardiac specific transgene, skeletal muscle was unaffected at baseline with a 33% to 38% increase (standard uptake values) for both genotypes following insulin stimulation. TGmut mice had a 47% reduction in systolic function with a fourfold increase in cardiac glycogen stores correlated with a 29% reduction in phospho-AMPK α levels. There was no difference in cardiac insulin receptor expression between mouse genotypes. Conclusions These results demonstrate a correlation between insulin resistance and AMPK activity and provide the basis for the use of this animal model for assessing metabolic therapy in the treatment of affected PRKAG2 patients. PMID:23829931

A comparison of several techniques for imputing tree level data

Treesearch

David Gartner

2002-01-01

As Forest Inventory and Analysis (FIA) changes from periodic surveys to the multipanel annual survey, new analytical methods become available. The current official statistic is the moving average. One alternative is an updated moving average. Several methods of updating plot per acre volume have been discussed previously. However, these methods may not be appropriate...

Monte Carlo approaches to sampling forested tracts with lines or points

Treesearch

Harry T. Valentine; Jeffrey H. Gove; Timothy G. Gregoire

2001-01-01

Several line- and point-based sampling methods can be employed to estimate the aggregate dimensions of trees standing on a forested tract or pieces of coarse woody debris lying on the forest floor. Line methods include line intersect sampling, horizontal line sampling, and transect relascope sampling; point methods include variable- and fixed-radius plot sampling, and...

A variable circular-plot method for estimating bird numbers

Treesearch

R. T. Reynolds; J. M. Scott; R. A. Nussbaum

1980-01-01

A bird census method is presented that is designed for tall, structurally complex vegetation types, and rugged terrain. With this method the observer counts all birds seen or heard around a station, and estimates the horizontal distance from the station to each bird. Count periods at stations vary according to the avian community and structural complexity of the...

Revisiting the Logan plot to account for non-negligible blood volume in brain tissue.

PubMed

Schain, Martin; Fazio, Patrik; Mrzljak, Ladislav; Amini, Nahid; Al-Tawil, Nabil; Fitzer-Attas, Cheryl; Bronzova, Juliana; Landwehrmeyer, Bernhard; Sampaio, Christina; Halldin, Christer; Varrone, Andrea

2017-08-18

Reference tissue-based quantification of brain PET data does not typically include correction for signal originating from blood vessels, which is known to result in biased outcome measures. The bias extent depends on the amount of radioactivity in the blood vessels. In this study, we seek to revisit the well-established Logan plot and derive alternative formulations that provide estimation of distribution volume ratios (DVRs) that are corrected for the signal originating from the vasculature. New expressions for the Logan plot based on arterial input function and reference tissue were derived, which included explicit terms for whole blood radioactivity. The new methods were evaluated using PET data acquired using [ 11 C]raclopride and [ 18 F]MNI-659. The two-tissue compartment model (2TCM), with which signal originating from blood can be explicitly modeled, was used as a gold standard. DVR values obtained for [ 11 C]raclopride using the either blood-based or reference tissue-based Logan plot were systematically underestimated compared to 2TCM, and for [ 18 F]MNI-659, a proportionality bias was observed, i.e., the bias varied across regions. The biases disappeared when optimal blood-signal correction was used for respective tracer, although for the case of [ 18 F]MNI-659 a small but systematic overestimation of DVR was still observed. The new method appears to remove the bias introduced due to absence of correction for blood volume in regular graphical analysis and can be considered in clinical studies. Further studies are however required to derive a generic mapping between plasma and whole-blood radioactivity levels.

Scale and Sampling Effects on Floristic Quality

PubMed Central

2016-01-01

Floristic Quality Assessment (FQA) is increasingly influential for making land management decisions, for directing conservation policy, and for research. But, the basic ecological properties and limitations of its metrics are ill defined and not well understood–especially those related to sample methods and scale. Nested plot data from a remnant tallgrass prairie sampled annually over a 12-year period, were used to investigate FQA properties associated with species detection rates, species misidentification rates, sample year, and sample grain/area. Plot size had no apparent effect on Mean C (an area’s average Floristic Quality level), nor did species detection levels above 65% detection. Simulated species misidentifications only affected Mean C values at greater than 10% in large plots, when the replaced species were randomly drawn from the broader county-wide species pool. Finally, FQA values were stable over the 12-year study, meaning that there was no evidence that the metrics exhibit year effects. The FQA metric Mean C is demonstrated to be robust to varied sample methodologies related to sample intensity (plot size, species detection rate), as well as sample year. These results will make FQA measures even more appealing for informing land-use decisions, policy, and research for two reasons: 1) The sampling effort needed to generate accurate and consistent site assessments with FQA measures is shown to be far lower than what has previously been assumed, and 2) the stable properties and consistent performance of metrics with respect to sample methods will allow for a remarkable level of comparability of FQA values from different sites and datasets compared to other commonly used ecological metrics. PMID:27489959

An Additional Method for Analyzing the Reversible Inhibition of an 
Enzyme Using Acid Phosphatase as a Model.

PubMed

Baumhardt, Jordan M; Dorsey, Benjamin M; McLauchlan, Craig C; Jones, Marjorie A

2015-08-01

Using wheat germ acid phosphatase and sodium orthovanadate as a competitive inhibitor, a novel method for analyzing reversible inhibition was carried out. Our alternative approach involves plotting the initial velocity at which product is formed as a function of the ratio of substrate concentration to inhibitor concentration at a constant enzyme concentration and constant assay conditions. The concept of initial concentrations driving equilibrium leads to the chosen axes. Three apparent constants can be derived from this plot: K max , K min , and K inflect . K max and K min represent the substrate to inhibitor concentration ratio for complete inhibition and minimal inhibition, respectively. K inflect represents the substrate to inhibitor concentration ratio at which the enzyme-substrate complex is equal to the inhibitory complex. These constants can be interpolated from the graph or calculated using the first and second derivative of the plot. We conclude that a steeper slope and a shift of the line to the right (increased x-axis values) would indicate a better inhibitor. Since initial velocity is not a linear function of the substrate/inhibitor ratio, this means that inhibition changes more quickly with the change in the [S]/ [I] ratio. When preincubating the enzyme with substrate before the addition of inhibitor, preincubating the enzyme with inhibitor before the addition of substrate or with concurrent addition of both substrate and inhibitor, modest changes in the slopes and y-intercepts were obtained. This plot appears useful for known competitive and non-competitive inhibitors and may have general applicability.

Automatic contouring of geologic fabric and finite strain data on the unit hyperboloid

NASA Astrophysics Data System (ADS)

Vollmer, Frederick W.

2018-06-01

Fabric and finite strain analysis, an integral part of studies of geologic structures and orogenic belts, is commonly done by the analysis of particles whose shapes can be approximated as ellipses. Given a sample of such particles, the mean and confidence intervals of particular parameters can be calculated, however, taking the extra step of plotting and contouring the density distribution can identify asymmetries or modes related to sedimentary fabrics or other factors. A common graphical strain analysis technique is to plot final ellipse ratios, Rf , versus orientations, ϕf on polar Elliott or Rf / ϕ plots to examine the density distribution. The plot may be contoured, however, it is desirable to have a contouring method that is rapid, reproducible, and based on the underlying geometry of the data. The unit hyperboloid, H2 , gives a natural parameter space for two-dimensional strain, and various projections, including equal-area and stereographic, have useful properties for examining density distributions for anisotropy. An index, Ia , is given to quantify the magnitude and direction of anisotropy. Elliott and Rf / ϕ plots can be understood by applying hyperbolic geometry and recognizing them as projections of H2 . These both distort area, however, so the equal-area projection is preferred for examining density distributions. The algorithm presented here gives fast, accurate, and reproducible contours of density distributions calculated directly on H2 . The algorithm back-projects the data onto H2 , where the density calculation is done at regular nodes using a weighting value based on the hyperboloid distribution, which is then contoured. It is implemented as an Octave compatible MATLAB function that plots ellipse data using a variety of projections, and calculates and displays contours of their density distribution on H2 .

Aquifer test interpretation using derivative analysis and diagnostic plots

NASA Astrophysics Data System (ADS)

Hernández-Espriú, Antonio; Real-Rangel, Roberto; Cortés-Salazar, Iván; Castro-Herrera, Israel; Luna-Izazaga, Gabriela; Sánchez-León, Emilio

2017-04-01

Pumping tests remain a method of choice to deduce fundamental aquifer properties and to assess well condition. In the oil and gas (O&G) industry, well testing has been the core technique in examining reservoir behavior over the last 50 years. The pressure derivative by Bourdet, it is perhaps, the most significant single development in the history of well test analysis. Recently, the so-called diagnostics plots (e.g. drawdown and drawdown derivative in a log-log plot) have been successfully tested in aquifers. However, this procedure is still underutilized by groundwater professionals. This research illustrates the applicability range, advantages and drawbacks (e.g. smoothing procedures) of diagnostic plots using field examples from a wide spectrum of tests (short/long tests, constant/variable flow rates, drawdown/buildup stages, pumping well/observation well) in dissimilar geological conditions. We analyze new and pre-existent aquifer tests in Mexico, USA, Canada, Germany, France and Saudi Arabia. In constant flow rate tests, our results show that derivative analysis is an easy, robust and powerful tool to assess near-borehole damage effects, formation heterogeneity, boundaries, flow regimes, infinite-acting radial stages, i.e., valid Theisian framework, and fracture-driven flow. In step tests, the effectiveness relies on high-frequency drawdown measurements. Moreover, we adapt O&G analytical solutions to cater for the conditions in groundwater systems. In this context, further parameters can be computed analytically from the plots, such as skin factor, head losses, wellbore storage, distance to the boundary, channel-aquifer and/or fracture zone width, among others. Therefore, diagnostic plots should be considered a mandatory tool for pumping tests analysis among hydrogeologists. This project has been supported by DGAPA (UNAM) under the research project PAPIIT IN-112815.

Visual aid tool to improve decision making in acute stroke care.

PubMed

Saposnik, Gustavo; Goyal, Mayank; Majoie, Charles; Dippel, Diederik; Roos, Yvo; Demchuk, Andrew; Menon, Bijoy; Mitchell, Peter; Campbell, Bruce; Dávalos, Antoni; Jovin, Tudor; Hill, Michael D

2016-10-01

Background Acute stroke care represents a challenge for decision makers. Recent randomized trials showed the benefits of endovascular therapy. Our goal was to provide a visual aid tool to guide clinicians in the decision process of endovascular intervention in patients with acute ischemic stroke. Methods We created visual plots (Cates' plots; www.nntonline.net ) representing benefits of standard of care vs. endovascular thrombectomy from the pooled analysis of five RCTs using stent retrievers. These plots represent the following clinically relevant outcomes (1) functionally independent state (modified Rankin scale (mRS) 0 to 2 at 90 days) (2) excellent recovery (mRS 0-1) at 90 days, (3) NIHSS 0-2 (4) early neurological recovery, and (5) revascularization at 24 h. Subgroups visually represented include time to treatment and baseline stroke severity strata. Results Overall, 1287 patients (634 assigned to endovascular thrombectomy, 653 assigned to control were included to create the visual plots. Cates' visual plots revealed that for every 100 patients with acute ischemic stroke and large vessel occlusion, 27 would achieve independence at 90 days (mRS 0-2) in the control group compared to 49 (95% CI 43-56) in the intervention group. Similarly, 21 patients would achieve early neurological recovery at 24 h compared to 54 (95% CI 45-63) out of 100 for the intervention group. Conclusion Cates' plots may assist clinicians and patients to visualize and compare potential outcomes after an acute ischemic stroke. Our results suggest that for every 100 treated individuals with an acute ischemic stroke and a large vessel occlusion, endovascular thrombectomy would provide 22 additional patients reaching independency at three months and 33 more patients achieving ENR compared to controls.

Method and apparatus for determining material structural integrity

DOEpatents

Pechersky, M.J.

1994-01-01

Disclosed are a nondestructive method and apparatus for determining the structural integrity of materials by combining laser vibrometry with damping analysis to determine the damping loss factor. The method comprises the steps of vibrating the area being tested over a known frequency range and measuring vibrational force and velocity vs time over the known frequency range. Vibrational velocity is preferably measured by a laser vibrometer. Measurement of the vibrational force depends on the vibration method: if an electromagnetic coil is used to vibrate a magnet secured to the area being tested, then the vibrational force is determined by the coil current. If a reciprocating transducer is used, the vibrational force is determined by a force gauge in the transducer. Using vibrational analysis, a plot of the drive point mobility of the material over the preselected frequency range is generated from the vibrational force and velocity data. Damping loss factor is derived from a plot of the drive point mobility over the preselected frequency range using the resonance dwell method and compared with a reference damping loss factor for structural integrity evaluation.

Iterative Boltzmann plot method for temperature and pressure determination in a xenon high pressure discharge lamp

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

Zalach, J.; Franke, St.

2013-01-28

The Boltzmann plot method allows to calculate plasma temperatures and pressures if absolutely calibrated emission coefficients of spectral lines are available. However, xenon arcs are not very well suited to be analyzed this way, as there are only a limited number of lines with atomic data available. These lines have high excitation energies in a small interval between 9.8 and 11.5 eV. Uncertainties in the experimental method and in the atomic data further limit the accuracy of the evaluation procedure. This may result in implausible values of temperature and pressure with inadmissible uncertainty. To omit these shortcomings, an iterative schememore » is proposed that is making use of additional information about the xenon fill pressure. This method is proved to be robust against noisy data and significantly reduces the uncertainties. Intentionally distorted synthetic data are used to illustrate the performance of the method, and measurements performed on a laboratory xenon high pressure discharge lamp are analyzed resulting in reasonable temperatures and pressures with significantly reduced uncertainties.« less

Astronomy, Visual Literacy, and Liberal Arts Education

NASA Astrophysics Data System (ADS)

Crider, Anthony

2016-01-01

With the exponentially growing amount of visual content that twenty-first century students will face throughout their lives, teaching them to respond to it with visual and information literacy skills should be a clear priority for liberal arts education. While visual literacy is more commonly covered within humanities curricula, I will argue that because astronomy is inherently a visual science, it is a fertile academic discipline for the teaching and learning of visual literacy. Astronomers, like many scientists, rely on three basic types of visuals to convey information: images, qualitative diagrams, and quantitative plots. In this talk, I will highlight classroom methods that can be used to teach students to "read" and "write" these three separate visuals. Examples of "reading" exercises include questioning the authorship and veracity of images, confronting the distorted scales of many diagrams published in astronomy textbooks, and extracting quantitative information from published plots. Examples of "writing" exercises include capturing astronomical images with smartphones, re-sketching textbook diagrams on whiteboards, and plotting data with Google Motion Charts or iPython notebooks. Students can be further pushed to synthesize these skills with end-of-semester slide presentations that incorporate relevant images, diagrams, and plots rather than relying solely on bulleted lists.

Diffusional falsification of kinetic constants on Lineweaver-Burk plots.

PubMed

Ghim, Y S; Chang, H N

1983-11-07

The effect of mass transfer resistances on the Lineweaver-Burk plots in immobilized enzyme systems has been investigated numerically and with analytical approximate solutions. While Hamilton, Gardner & Colton (1974) studied the effect of internal diffusion resistances in planar geometry, our study was extended to the combined effect of internal and external diffusion in cylindrical and spherical geometries as well. The variation of Lineweaver-Burk plots with respect to the geometries was minimized by modifying the Thiele modulus and the Biot number with the shape factor. Especially for a small Biot number all the three Lineweaver-Burk plots fell on a single line. As was discussed by Hamilton et al. (1974), the curvature of the line for large external diffusion resistances was small enough to be assumed linear, which was confirmed from the two approximate solutions for large and small substrate concentrations. Two methods for obtaining intrinsic kinetic constants were proposed: First, we obtained both maximum reaction rate and Michaelis constant by fitting experimental data to a straight line where external diffusion resistance was relatively large, and second, we obtained Michaelis constant from apparent Michaelis constant from the figure in case we knew maximum reaction rate a priori.

Systematic Review and Meta-analysis of the Effectiveness of Implementation Strategies for Non-communicable Disease Guidelines in Primary Health Care.

PubMed

Kovacs, Eva; Strobl, Ralf; Phillips, Amanda; Stephan, Anna-Janina; Müller, Martin; Gensichen, Jochen; Grill, Eva

2018-05-04

As clinical practice guidelines represent the most important evidence-based decision support tool, several strategies have been applied to improve their implementation into the primary health care system. This study aimed to evaluate the effect of intervention methods on the guideline adherence of primary care providers (PCPs). The studies selected through a systematic search in Medline and Embase were categorised according to intervention schemes and outcome indicator categories. Harvest plots and forest plots were applied to integrate results. The 36 studies covered six intervention schemes, with single interventions being the most effective and distribution of materials the least. The harvest plot displayed 27 groups having no effect, 14 a moderate and 21 a strong effect on the outcome indicators in the categories of knowledge transfer, diagnostic behaviour, prescription, counselling and patient-level results. The forest plot revealed a moderate overall effect size of 0.22 [0.15, 0.29] where single interventions were more effective (0.27 [0.17, 0.38]) than multifaceted interventions (0.13 [0.06, 0.19]). Guideline implementation strategies are heterogeneous. Reducing the complexity of strategies and tailoring to the local conditions and PCPs' needs may improve implementation and clinical practice.

Splatterplots: overcoming overdraw in scatter plots.

PubMed

Mayorga, Adrian; Gleicher, Michael

2013-09-01

We introduce Splatterplots, a novel presentation of scattered data that enables visualizations that scale beyond standard scatter plots. Traditional scatter plots suffer from overdraw (overlapping glyphs) as the number of points per unit area increases. Overdraw obscures outliers, hides data distributions, and makes the relationship among subgroups of the data difficult to discern. To address these issues, Splatterplots abstract away information such that the density of data shown in any unit of screen space is bounded, while allowing continuous zoom to reveal abstracted details. Abstraction automatically groups dense data points into contours and samples remaining points. We combine techniques for abstraction with perceptually based color blending to reveal the relationship between data subgroups. The resulting visualizations represent the dense regions of each subgroup of the data set as smooth closed shapes and show representative outliers explicitly. We present techniques that leverage the GPU for Splatterplot computation and rendering, enabling interaction with massive data sets. We show how Splatterplots can be an effective alternative to traditional methods of displaying scatter data communicating data trends, outliers, and data set relationships much like traditional scatter plots, but scaling to data sets of higher density and up to millions of points on the screen.

Splatterplots: Overcoming Overdraw in Scatter Plots

PubMed Central

Mayorga, Adrian; Gleicher, Michael

2014-01-01

We introduce Splatterplots, a novel presentation of scattered data that enables visualizations that scale beyond standard scatter plots. Traditional scatter plots suffer from overdraw (overlapping glyphs) as the number of points per unit area increases. Overdraw obscures outliers, hides data distributions, and makes the relationship among subgroups of the data difficult to discern. To address these issues, Splatterplots abstract away information such that the density of data shown in any unit of screen space is bounded, while allowing continuous zoom to reveal abstracted details. Abstraction automatically groups dense data points into contours and samples remaining points. We combine techniques for abstraction with with perceptually based color blending to reveal the relationship between data subgroups. The resulting visualizations represent the dense regions of each subgroup of the dataset as smooth closed shapes and show representative outliers explicitly. We present techniques that leverage the GPU for Splatterplot computation and rendering, enabling interaction with massive data sets. We show how splatterplots can be an effective alternative to traditional methods of displaying scatter data communicating data trends, outliers, and data set relationships much like traditional scatter plots, but scaling to data sets of higher density and up to millions of points on the screen. PMID:23846097

Splatterplots: Overcoming Overdraw in Scatter Plots.

PubMed

Mayorga, Adrian; Gleicher, Michael

2013-03-20

We introduce Splatterplots, a novel presentation of scattered data that enables visualizations that scale beyond standard scatter plots. Traditional scatter plots suffer from overdraw (overlapping glyphs) as the number of points per unit area increases. Overdraw obscures outliers, hides data distributions, and makes the relationship among subgroups of the data difficult to discern. To address these issues, Splatterplots abstract away information such that the density of data shown in any unit of screen space is bounded, while allowing continuous zoom to reveal abstracted details. Abstraction automatically groups dense data points into contours and samples remaining points. We combine techniques for abstraction with with perceptually based color blending to reveal the relationship between data subgroups. The resulting visualizations represent the dense regions of each subgroup of the dataset as smooth closed shapes and show representative outliers explicitly. We present techniques that leverage the GPU for Splatterplot computation and rendering, enabling interaction with massive data sets. We show how splatterplots can be an effective alternative to traditional methods of displaying scatter data communicating data trends, outliers, and data set relationships much like traditional scatter plots, but scaling to data sets of higher density and up to millions of points on the screen.

Do water-limiting conditions predispose Norway spruce to bark beetle attack?

PubMed Central

Netherer, Sigrid; Matthews, Bradley; Katzensteiner, Klaus; Blackwell, Emma; Henschke, Patrick; Hietz, Peter; Pennerstorfer, Josef; Rosner, Sabine; Kikuta, Silvia; Schume, Helmut; Schopf, Axel

2015-01-01

Drought is considered to enhance susceptibility of Norway spruce (Picea abies) to infestations by the Eurasian spruce bark beetle (Ips typographus, Coleoptera: Curculionidae), although empirical evidence is scarce. We studied the impact of experimentally induced drought on tree water status and constitutive resin flow, and how physiological stress affects host acceptance and resistance. We established rain-out shelters to induce both severe (two full-cover plots) and moderate (two semi-cover plots) drought stress. In total, 18 sample trees, which were divided equally between the above treatment plots and two control plots, were investigated. Infestation was controlled experimentally using a novel ‘attack box’ method. Treatments influenced the ratios of successful and defended attacks, but predisposition of trees to infestation appeared to be mainly driven by variations in stress status of the individual trees over time. With increasingly negative twig water potentials and decreasing resin exudation, the defence capability of the spruce trees decreased. We provide empirical evidence that water-limiting conditions impair Norway spruce resistance to bark beetle attack. Yet, at the same time our data point to reduced host acceptance byI. typographus with more extreme drought stress, indicated by strongly negative pre-dawn twig water potentials. PMID:25417785

Effects of observers using different methods upon the total population estimates of two resident island birds

Treesearch

Sheila Conant; Mark S. Collins; C. John Ralph

1981-01-01

During a 5-week study of the Nihoa Millerbird and Nihoa Finch, we censused birds using these techniques: two line transect methods, a variable-distance circular plot method, and spot-mapping of territories (millerbirds only). Densities derived from these methods varied greatly. Due to differences in behavior, it appeared that the two species reacted differently to the...

Density (DE)

Treesearch

John F. Caratti

2006-01-01

The FIREMON Density (DE) method is used to assess changes in plant species density and height for a macroplot. This method uses multiple quadrats and belt transects (transects having a width) to sample within plot variation and quantify statistically valid changes in plant species density and height over time. Herbaceous plant species are sampled with quadrats while...

Acid Rain Analysis by Standard Addition Titration.

ERIC Educational Resources Information Center

Ophardt, Charles E.

1985-01-01

The standard addition titration is a precise and rapid method for the determination of the acidity in rain or snow samples. The method requires use of a standard buret, a pH meter, and Gran's plot to determine the equivalence point. Experimental procedures used and typical results obtained are presented. (JN)

Field Guide for Evaluating Cottonwood Sites

Treesearch

W.M. Broadfoot

1960-01-01

Two field methods have been developed at the Stoneville Research Center for estimating the capability of Midsouth soils to grow eastern cottonwood (Populus deltoides Bartr.). Data for establishing the procedures were collected from 155 plots* at the locations indicated in Figure 1.The methods give site index-that is, tree-growing...

Multivariate Approaches for Simultaneous Determination of Avanafil and Dapoxetine by UV Chemometrics and HPLC-QbD in Binary Mixtures and Pharmaceutical Product.

PubMed

2016-04-07

Multivariate UV-spectrophotometric methods and Quality by Design (QbD) HPLC are described for concurrent estimation of avanafil (AV) and dapoxetine (DP) in the binary mixture and in the dosage form. Chemometric methods have been developed, including classical least-squares, principal component regression, partial least-squares, and multiway partial least-squares. Analytical figures of merit, such as sensitivity, selectivity, analytical sensitivity, LOD, and LOQ were determined. QbD consists of three steps, starting with the screening approach to determine the critical process parameter and response variables. This is followed by understanding of factors and levels, and lastly the application of a Box-Behnken design containing four critical factors that affect the method. From an Ishikawa diagram and a risk assessment tool, four main factors were selected for optimization. Design optimization, statistical calculation, and final-condition optimization of all the reactions were Carried out. Twenty-five experiments were done, and a quadratic model was used for all response variables. Desirability plot, surface plot, design space, and three-dimensional plots were calculated. In the optimized condition, HPLC separation was achieved on Phenomenex Gemini C18 column (250 × 4.6 mm, 5 μm) using acetonitrile-buffer (ammonium acetate buffer at pH 3.7 with acetic acid) as a mobile phase at flow rate of 0.7 mL/min. Quantification was done at 239 nm, and temperature was set at 20°C. The developed methods were validated and successfully applied for simultaneous determination of AV and DP in the dosage form.

Estimating vegetation biomass and cover across large plots in shrub and grass dominated drylands using terrestrial lidar and machine learning

USGS Publications Warehouse

Anderson, Kyle E.; Glenn, Nancy F.; Spaete, Lucas P.; Shinneman, Douglas; Pilliod, David S.; Arkle, Robert; McIlroy, Susan; Derryberry, DeWayne R.

2018-01-01

Terrestrial laser scanning (TLS) has been shown to enable an efficient, precise, and non-destructive inventory of vegetation structure at ranges up to hundreds of meters. We developed a method that leverages TLS collections with machine learning techniques to model and map canopy cover and biomass of several classes of short-stature vegetation across large plots. We collected high-definition TLS scans of 26 1-ha plots in desert grasslands and big sagebrush shrublands in southwest Idaho, USA. We used the Random Forests machine learning algorithm to develop decision tree models predicting the biomass and canopy cover of several vegetation classes from statistical descriptors of the aboveground heights of TLS points. Manual measurements of vegetation characteristics collected within each plot served as training and validation data. Models based on five or fewer TLS descriptors of vegetation heights were developed to predict the canopy cover fraction of shrubs (R2 = 0.77, RMSE = 7%), annual grasses (R2 = 0.70, RMSE = 21%), perennial grasses (R2 = 0.36, RMSE = 12%), forbs (R2 = 0.52, RMSE = 6%), bare earth or litter (R2 = 0.49, RMSE = 19%), and the biomass of shrubs (R2 = 0.71, RMSE = 175 g) and herbaceous vegetation (R2 = 0.61, RMSE = 99 g) (all values reported are out-of-bag). Our models explained much of the variability between predictions and manual measurements, and yet we expect that future applications could produce even better results by reducing some of the methodological sources of error that we encountered. Our work demonstrates how TLS can be used efficiently to extend manual measurement of vegetation characteristics from small to large plots in grasslands and shrublands, with potential application to other similarly structured ecosystems. Our method shows that vegetation structural characteristics can be modeled without classifying and delineating individual plants, a challenging and time-consuming step common in previous methods applying TLS to vegetation inventory. Improving application of TLS to studies of shrub-steppe ecosystems will serve immediate management needs by enhancing vegetation inventories, environmental modeling studies, and the ability to train broader datasets collected from air and space.

[Impact of tillage and nutrient management practices on the spring weed community in a winter wheat-summer maize rotation farmland].

PubMed

Wang, Neng Wei; Ge, Xiu Li; Li, Sheng Dong

2017-03-18

Conservation tillage and the weed diversity are two hot issues in the modern ecological agriculture. Although it is known that the diversity of weed would increase slightly in the farmland under conservation tillage, the interaction effects between the tillage and the nutrient management on the weed community are not clear. In this study, one wheat-maize rotation field located in Ji'nan, Shandong Province, was selected as the studying site. Different tillage methods (no-tillage, deep subsoiling, rotary tillage, deep tillage) and different nutrient managements (farmers routine, 480 kg N hm -2 per year; high production and efficiency, 360 kg N hm -2 per year; optimal management, 300 kg N hm -2 per year) were carried out for 3 years. The characteristics of the spring weed communities under different managements were investigated and compared. The results showed that there were 15 species in the spring weed communities in the test filed and Digitaria sanguinalis and Echinochloa crusgalli were the dominant species. The plots under no-tillage or deep subsoiling had higher weed densities compared with those under the deep tillage or rotary tillage. In terms of the effect of tillage on the weed community diversity, both species richness index and species evenness index were lowest but the community dominance index was highest in the plots under deep tillage. In terms of the effect of the nutrient management, with the increase of fertilizer application, both species richness and evenness index increased under the different tillage methods. The community dominance increased with the increasing fertilizer application under deep tillage or rotary tillage and vice versa under no-tillage, deep subsoiling. In terms of weed biomass, the plots under no-tillage or deep subsoiling had significantly higher weed biomass than those under the other two tillage methods. The plots under routine nutrient management had higher weed biomass than those under the other two nutrient managements. Among all these treatments, the plots under the combination treatment of no-tillage and routine nutrient management had the highest weed biomass. According to these results, it was implied that no-tillage and fertilization would improve species richness index, species evenness index, and the productivity of spring weed community in the wheat-maize farmland.

True versus perturbed forest inventory plot locations for modeling: a simulation study

Treesearch

John W. Coulston; Kurt H. Riitters; Ronald E. McRoberts; William D. Smith

2006-01-01

USDA Forest Service Forest Inventory and Analysis plot information is widely used for timber inventories, forest health assessments, and environmental risk analyses. With few exceptions, true plot locations are not revealed; the plot coordinates are manipulated to obscure the location of field plots and thereby preserve plot integrity. The influence of perturbed plot...

Automated mesostructural analyses using GIS, Beta test: Paleozoic structures from the New Jersey Great Valley region

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

Herman, G.C.; French, M.A.; Monteverde, D.H.

1993-03-01

An automated method has been developed for representing outcrop data on geologic structures on maps. Using a MS-DOS custom database management system in conjunction with the ARC/INFO Geographic Information System (GIS), trends of geologic structures are plotted with user-specific symbols. The length of structural symbols can be frequency-weighted based on collective values from structural domains. The PC-based data manager is the NJGS Field data Management System (FMS) Version 2.0 which includes sort, output, and analysis functions for structural data input in either azimuth or quadrant form. Program options include lineament sorting, data output to other data management and analysis software,more » and a circular histogram (rose diagram) routine for trend frequency analysis. Trends can be displayed with either half-or full-rose diagrams using either 10[degree] sectors or one degree spikes for strike, trend, or dip azimuth readings. Scalar and vector statistics are both included. For the mesostructural analysis, ASCII files containing the station number, structural trend and inclination, and plot-symbol-length value are downloaded from FMS and uploaded into an ARC/INFO macro which sequentially plots the information. Plots can be generated in conjunction with any complimentary GIS coverage for various types of spatial analyses. Mesostructural plots can be used for regional tectonic analyses, for hydrogeologic analysis of fractured bedrock aquifers, or for ground-truthing data from fracture-trace or lineament analyses.« less

Seeding method influences warm-season grass abundance and distribution but not local diversity in grassland restoration

USGS Publications Warehouse

Yurkonis, Kathryn A.; Wilsey, Brian J.; Moloney, Kirk A.; Drobney, Pauline; Larson, Diane L.

2010-01-01

Ecological theory predicts that the arrangement of seedlings in newly restored communities may influence future species diversity and composition. We test the prediction that smaller distances between neighboring seeds in drill seeded grassland plantings would result in lower species diversity, greater weed abundance, and larger conspecific patch sizes than otherwise similar broadcast seeded plantings. A diverse grassland seed mix was either drill seeded, which places seeds in equally spaced rows, or broadcast seeded, which spreads seeds across the ground surface, into 24 plots in each of three sites in 2005. In summer 2007, we measured species abundance in a 1 m2 quadrat in each plot and mapped common species within the quadrat by recording the most abundant species in each of 64 cells. Quadrat-scale diversity and weed abundance were similar between drilled and broadcast plots, suggesting that processes that limited establishment and controlled invasion were not affected by such fine-scale seed distribution. However, native warm-season (C4) grasses were more abundant and occurred in less compact patches in drilled plots. This difference in C4 grass abundance and distribution may result from increased germination or vegetative propagation of C4 grasses in drilled plots. Our findings suggest that local plant density may control fine-scale heterogeneity and species composition in restored grasslands, processes that need to be further investigated to determine whether seed distributions can be manipulated to increase diversity in restored grasslands.

Seeding Method Influences Warm-Season Grass Abundance and Distribution but not Local Diversity in Grassland Restoration

USGS Publications Warehouse

Yurkonis, K.A.; Wilsey, B.J.; Moloney, K.A.; Drobney, P.; Larson, D.L.

2010-01-01

Ecological theory predicts that the arrangement of seedlings in newly restored communities may influence future species diversity and composition. We test the prediction that smaller distances between neighboring seeds in drill seeded grassland plantings would result in lower species diversity, greater weed abundance, and larger conspecific patch sizes than otherwise similar broadcast seeded plantings. A diverse grassland seed mix was either drill seeded, which places seeds in equally spaced rows, or broadcast seeded, which spreads seeds across the ground surface, into 24 plots in each of three sites in 2005. In summer 2007, we measured species abundance in a 1 m2 quadrat in each plot and mapped common species within the quadrat by recording the most abundant species in each of 64 cells. Quadrat-scale diversity and weed abundance were similar between drilled and broadcast plots, suggesting that processes that limited establishment and controlled invasion were not affected by such fine-scale seed distribution. However, native warm-season (C4) grasses were more abundant and occurred in less compact patches in drilled plots. This difference in C4 grass abundance and distribution may result from increased germination or vegetative propagation of C4 grasses in drilled plots. Our findings suggest that local plant density may control fine-scale heterogeneity and species composition in restored grasslands, processes that need to be further investigated to determine whether seed distributions can be manipulated to increase diversity in restored grasslands. ?? 2010 Society for Ecological Restoration International.

Poincaré plot width, morning urine norepinephrine levels, and autonomic imbalance in children with obstructive sleep apnea.

PubMed

Chaidas, Konstantinos; Tsaoussoglou, Marina; Theodorou, Emmanouel; Lianou, Loukia; Chrousos, George; Kaditis, Athanasios G

2014-08-01

Obstructive sleep apnea (OSA) in childhood is accompanied by sympathetic overflow unopposed by the parasympathetic tone. Complex methods like power spectral analysis of heart rate variability have been applied to study this imbalance. In this report, width of Poincaré scattergram of the R-R interval (parasympathetic tone) and morning urine norepinephrine concentration (sympathetic activity) were used to assess autonomic imbalance. Poincaré plot was obtained from the electrocardiographic channel of nocturnal polysomnography and its width was measured, and norepinephrine-to-creatinine concentration ratio was calculated in morning urine specimen. Twenty children with obstructive sleep apnea and moderate-to-severe nocturnal hypoxemia (oxygen saturation of hemoglobin [SpO(2)] nadir <90%), 24 subjects with mild hypoxemia (SpO(2) nadir ≥90%), and 11 control subjects were recruited. Children with obstructive sleep apnea and moderate-to-severe hypoxemia had significantly narrower Poincaré plot width (318.7 ± 139.3 ms) and higher ln-transformed urine norepinephrine-to-creatinine ratio (4.5 ± 0.6) than control subjects (484.2 ± 104.4 ms and 3.8 ± 0.4, respectively; P < 0.05). Ln-transformed urine norepinephrine levels were inversely related to Poincaré plot width (P = 0.02). Subjects with obstructive sleep apnea and moderate-to-severe nocturnal hypoxemia have enhanced sympathetic activity and reduced parasympathetic drive. Poincaré plot width and urine norepinephrine levels are simple measures of autonomic imbalance in pediatric obstructive sleep apnea. Copyright © 2014 Elsevier Inc. All rights reserved.

Polar plot representation of time-resolved fluorescence.

PubMed

Eichorst, John Paul; Wen Teng, Kai; Clegg, Robert M

2014-01-01

Measuring changes in a molecule's fluorescence emission is a common technique to study complex biological systems such as cells and tissues. Although the steady-state fluorescence intensity is frequently used, measuring the average amount of time that a molecule spends in the excited state (the fluorescence lifetime) reveals more detailed information about its local environment. The lifetime is measured in the time domain by detecting directly the decay of fluorescence following excitation by short pulse of light. The lifetime can also be measured in the frequency domain by recording the phase and amplitude of oscillation in the emitted fluorescence of the sample in response to repetitively modulated excitation light. In either the time or frequency domain, the analysis of data to extract lifetimes can be computationally intensive. For example, a variety of iterative fitting algorithms already exist to determine lifetimes from samples that contain multiple fluorescing species. However, recently a method of analysis referred to as the polar plot (or phasor plot) is a graphical tool that projects the time-dependent features of the sample's fluorescence in either the time or frequency domain into the Cartesian plane to characterize the sample's lifetime. The coordinate transformations of the polar plot require only the raw data, and hence, there are no uncertainties from extensive corrections or time-consuming fitting in this analysis. In this chapter, the history and mathematical background of the polar plot will be presented along with examples that highlight how it can be used in both cuvette-based and imaging applications.

Weed manipulation for insect pest management in corn

NASA Astrophysics Data System (ADS)

Altieri, M. A.; Whitcomb, W. H.

1980-11-01

Populations of insect pests and associated predaceous arthropods were sampled by direct observation and other relative methods in simple and diversified corn habitats at two sites in north Florida during 1978 and 1979. Through various cultural manipulations, characteristic weed communities were established selectively in alternate rows within corn plots. Fall armyworm ( Spodoptera frugiperda J. E. Smith) incidence was consistently higher in the weed-free habitats than in the corn habitats containing natural weed complexes or selected weed associations. Corn earworm ( Heliothis zea Boddie) damage was similar in all weed-free and weedy treatments, suggesting that this insect is not affected greatly by weed diversity. Only the diversification of corn with a strip of soybean significantly reduced corn earworm damage. In one site, distance between plots was reduced. Because predators moved freely between habitats, it was difficult to identify between-treatment differences in the composition of predator communities. In the other site, increased distances between plots minimized such migrations, resulting in greater population densities and diversity of common foliage insect predators in the weed-manipulated corn systems than in the weed-free plots. Trophic relationships in the weedy habitats were more complex than food webs in monocultures. Predator diversity (measured as mean number of species per area) and predator density was higher in com plots surrounded by mature, complex vegetation than at those surrounded by annual crops. This suggests that diverse adjacent areas to crops provide refuge for predators, thus acting as colonization sources.

Earth science research

NASA Technical Reports Server (NTRS)

Botkin, Daniel B.

1987-01-01

The analysis of ground-truth data from the boreal forest plots in the Superior National Forest, Minnesota, was completed. Development of statistical methods was completed for dimension analysis (equations to estimate the biomass of trees from measurements of diameter and height). The dimension-analysis equations were applied to the data obtained from ground-truth plots, to estimate the biomass. Classification and analyses of remote sensing images of the Superior National Forest were done as a test of the technique to determine forest biomass and ecological state by remote sensing. Data was archived on diskette and tape and transferred to UCSB to be used in subsequent research.

High Precision 2-D Grating Groove Density Measurement

NASA Astrophysics Data System (ADS)

Zhang, Ningxiao; McEntaffer, Randall; Tedesco, Ross

2017-08-01

Our research group at Penn State University is working on producing X-ray reflection gratings with high spectral resolving power and high diffraction efficiency. To estimate our fabrication accuracy, we apply a precise 2-D grating groove density measurement to plot groove density distributions of gratings on 6-inch wafers. In addition to plotting a fixed groove density distribution, this method is also sensitive to measuring the variation of the groove density simultaneously. This system can reach a measuring accuracy (ΔN/N) of 10-3. Here we present this groove density measurement and some applications.

Food Gardeners’ Productivity in Laramie, Wyoming: More Than a Hobby

PubMed Central

Conk, Shannon J.

2016-01-01

Objectives. We quantified the productivity of food gardens in Laramie, Wyoming, over 3 growing seasons. Methods. From 2012 to 2014, 33 participating gardening households weighed and recorded each harvest. Academic partners measured plot sizes and converted reported harvest weights to volume in cups. Results. The yield of the average 253-square-foot plot was enough to supply an adult with the daily US Department of Agriculture–recommended amount of vegetables for 9 months. Conclusions. Gardeners produced nutritionally meaningful quantities of food; thus, food gardening offers promise as an effective public health intervention for improving food security and nutritional health. PMID:26985621

Metal alloy identifier

DOEpatents

Riley, William D.; Brown, Jr., Robert D.

1987-01-01

To identify the composition of a metal alloy, sparks generated from the alloy are optically observed and spectrographically analyzed. The spectrographic data, in the form of a full-spectrum plot of intensity versus wavelength, provide the "signature" of the metal alloy. This signature can be compared with similar plots for alloys of known composition to establish the unknown composition by a positive match with a known alloy. An alternative method is to form intensity ratios for pairs of predetermined wavelengths within the observed spectrum and to then compare the values of such ratios with similar values for known alloy compositions, thereby to positively identify the unknown alloy composition.

The kinship2 R package for pedigree data.

PubMed

Sinnwell, Jason P; Therneau, Terry M; Schaid, Daniel J

2014-01-01

The kinship2 package is restructured from the previous kinship package. Existing features are now enhanced and new features added for handling pedigree objects. Pedigree plotting features have been updated to display features on complex pedigrees while adhering to pedigree plotting standards. Kinship matrices can now be calculated for the X chromosome. Other methods have been added to subset and trim pedigrees while maintaining the pedigree structure. We make the kinship2 package available for R on the Contributed R Archives Network (CRAN), where data management is built-in and other packages can use the pedigree object.

MEGA16 - Computer program for analysis and extrapolation of stress-rupture data

NASA Technical Reports Server (NTRS)

Ensign, C. R.

1981-01-01

The computerized form of the minimum commitment method of interpolating and extrapolating stress versus time to failure data, MEGA16, is described. Examples are given of its many plots and tabular outputs for a typical set of data. The program assumes a specific model equation and then provides a family of predicted isothermals for any set of data with at least 12 stress-rupture results from three different temperatures spread over reasonable stress and time ranges. It is written in FORTRAN 4 using IBM plotting subroutines and its runs on an IBM 370 time sharing system.

Accuracy and precision of two indirect methods for estimating canopy fuels

Treesearch

Abran Steele-Feldman; Elizabeth Reinhardt; Russell A. Parsons

2006-01-01

We compared the accuracy and precision of digital hemispherical photography and the LI-COR LAI-2000 plant canopy analyzer as predictors of canopy fuels. We collected data on 12 plots in western Montana under a variety of lighting and sky conditions, and used a variety of processing methods to compute estimates. Repeated measurements from each method displayed...

Electrostatics of a Point Charge between Intersecting Planes: Exact Solutions and Method of Images

ERIC Educational Resources Information Center

Mei, W. N.; Holloway, A.

2005-01-01

In this work, the authors present a commonly used example in electrostatics that could be solved exactly in a conventional manner, yet expressed in a compact form, and simultaneously work out special cases using the method of images. Then, by plotting the potentials and electric fields obtained from these two methods, the authors demonstrate that…

Using Horn's Parallel Analysis Method in Exploratory Factor Analysis for Determining the Number of Factors

ERIC Educational Resources Information Center

Çokluk, Ömay; Koçak, Duygu

2016-01-01

In this study, the number of factors obtained from parallel analysis, a method used for determining the number of factors in exploratory factor analysis, was compared to that of the factors obtained from eigenvalue and scree plot--two traditional methods for determining the number of factors--in terms of consistency. Parallel analysis is based on…

A review of contemporary methods for the presentation of scientific uncertainty.

PubMed

Makinson, K A; Hamby, D M; Edwards, J A

2012-12-01

Graphic methods for displaying uncertainty are often the most concise and informative way to communicate abstract concepts. Presentation methods currently in use for the display and interpretation of scientific uncertainty are reviewed. Numerous subjective and objective uncertainty display methods are presented, including qualitative assessments, node and arrow diagrams, standard statistical methods, box-and-whisker plots,robustness and opportunity functions, contribution indexes, probability density functions, cumulative distribution functions, and graphical likelihood functions.

Kinematic analysis of conically scanned environmental properties

NASA Technical Reports Server (NTRS)

Wilkerson, Thomas D. (Inventor); Sanders, Jason A. (Inventor); Andrus, Ionio Q. (Inventor)

2003-01-01

A method for determining the velocity of features such as wind. The method preferably includes producing sensor signals and projecting the sensor signals sequentially along lines lying on the surface of a cone. The sensor signals may be in the form of lidar, radar or sonar for example. As the sensor signals are transmitted, the signals contact objects and are backscattered. The backscattered sensor signals are received to determine the location of objects as they pass through the transmission path. The speed and direction the object is moving may be calculated using the backscattered data. The data may be plotted in a two dimensional array with a scan angle on one axis and a scan time on the other axis. The prominent curves that appear in the plot may be analyzed to determine the speed and direction the object is traveling.

Method of determining the optimal dilution ratio for fluorescence fingerprint of food constituents.

PubMed

Trivittayasil, Vipavee; Tsuta, Mizuki; Kokawa, Mito; Yoshimura, Masatoshi; Sugiyama, Junichi; Fujita, Kaori; Shibata, Mario

2015-01-01

Quantitative determination by fluorescence spectroscopy is possible because of the linear relationship between the intensity of emitted fluorescence and the fluorophore concentration. However, concentration quenching may cause the relationship to become nonlinear, and thus, the optimal dilution ratio has to be determined. In the case of fluorescence fingerprint (FF) measurement, fluorescence is measured under multiple wavelength conditions and a method of determining the optimal dilution ratio for multivariate data such as FFs has not been reported. In this study, the FFs of mixed solutions of tryptophan and epicatechin of different concentrations and composition ratios were measured. Principal component analysis was applied, and the resulting loading plots were found to contain useful information about each constituent. The optimal concentration ranges could be determined by identifying the linear region of the PC score plotted against total concentration.

Analysis of YBCO high temperature superconductor doped with silver nanoparticles and carbon nanotubes using Williamson-Hall and size-strain plot

NASA Astrophysics Data System (ADS)

Dadras, Sedigheh; Davoudiniya, Masoumeh

2018-05-01

This paper sets out to investigate and compare the effects of Ag nanoparticles and carbon nanotubes (CNTs) doping on the mechanical properties of Y1Ba2Cu3O7-δ (YBCO) high temperature superconductor. For this purpose, the pure and doped YBCO samples were synthesized by sol-gel method. The microstructural analysis of the samples is performed using X-ray diffraction (XRD). The crystalline size, lattice strain and stress of the pure and doped YBCO samples were estimated by modified forms of Williamson-Hall analysis (W-H), namely, uniform deformation model (UDM), uniform deformation stress model (UDSM) and the size-strain plot method (SSP). These results show that the crystalline size, lattice strain and stress of the YBCO samples declined by Ag nanoparticles and CNTs doping.

VORTAB - A data-tablet method of developing input data for the VORLAX program

NASA Technical Reports Server (NTRS)

Denn, F. M.

1979-01-01

A method of developing an input data file for use in the aerodynamic analysis of a complete airplane with the VORLAX computer program is described. The hardware consists of an interactive graphics terminal equipped with a graphics tablet. Software includes graphics routines from the Tektronix PLOT 10 package as well as the VORTAB program described. The user determines the size and location of each of the major panels for the aircraft before using the program. Data is entered both from the terminal keyboard and the graphics tablet. The size of the resulting data file is dependent on the complexity of the model and can vary from ten to several hundred card images. After the data are entered, two programs READB and PLOTB, are executed which plot the configuration allowing visual inspection of the model.

Development of Poincare Software to Predict Arrythmias

NASA Technical Reports Server (NTRS)

Maaliki, Samer

2003-01-01

The most distressing types of heart malfunction occur because of an abnormal rhythm of the heart. Cardiac arrythmias can be caused by abnormal rhythmicity of the pacemaker, electrolyte disturbances, blockage of the transmission of the electric impulse through the heart, and other abnormalities. There is strong evidence that space flight is associated with decreased cardiac electrical stability that may pose a life threatening risk to astronauts. For example, during the Skylab missions, a crewmember had a five beat run of ventricular tachycardia during lower body negative pressure. Also, analysis of nine 24-hour Holter monitor recordings obtained during long term spaceflight on Mir revealed one 14-beat run of ventricular tachycardia. A Mir cosmonaut was replaced in 1986 because of cardiac dysrhythmias. Most recently, in July of 1997, a Mir commander was unable to participate in the Spektr module repair due to complaints of an irregular heart rhythm. Despite these examples, possible mechanisms of arrhythmias and countermeasure strategies have barely been addressed. The Poincare method has been proposed as a technique that might potentially predict life-threatening arrhythmias before they occur. According to this method, each RR interval obtained from an EKG recording is plotted sequentially vs. the previous RR interval. Several studies using the method have demonstrated a strong correlation between the shape of the Poincare plot and ventricular arrhythmia. Our purpose was to develop an automated software program that detects the R peaks from an EKG recording while simultaneously displaying the Poincare plot and other related parameters.

An Interactive Excel Program for Tracking a Single Droplet in Crossflow Computation

NASA Technical Reports Server (NTRS)

Urip, E.; Yang, S. L.; Marek, C. J.

2002-01-01

Spray jet in crossflow has been a subject of research because of its wide application in systems involving pollutant dispersion, jet mixing in the dilution zone of combustors, and fuel injection strategies. The focus of this work is to investigate dispersion of a 2-dimensional atomized spray jet into a 2-dimensional crossflow. A quick computational method is developed using available software. The spreadsheet can be used for any 2D droplet trajectory problem where the drop is injected into the free stream eventually coming to the free stream conditions. During the transverse injection of a spray into high velocity airflow, the droplets (carried along and deflected by a gaseous stream of co-flowing air) are subjected to forces that affect their motion in the flow field. Based on the Newton's Second Law of motion, four ordinary differential equations were used. These equations were then solved by a fourth-order Runge-Kutta method using Excel software. Visual basic programming and Excel macrocode to produce the data facilitate Excel software to plot graphs describing the droplet's motion in the flow field. This program computes and plots the data sequentially without forcing users to open other types of plotting programs. A user's manual on how to use the program is also included in this report.

Lagged segmented Poincaré plot analysis for risk stratification in patients with dilated cardiomyopathy.

PubMed

Voss, Andreas; Fischer, Claudia; Schroeder, Rico; Figulla, Hans R; Goernig, Matthias

2012-07-01

The objectives of this study were to introduce a new type of heart-rate variability analysis improving risk stratification in patients with idiopathic dilated cardiomyopathy (DCM) and to provide additional information about impaired heart beat generation in these patients. Beat-to-beat intervals (BBI) of 30-min ECGs recorded from 91 DCM patients and 21 healthy subjects were analyzed applying the lagged segmented Poincaré plot analysis (LSPPA) method. LSPPA includes the Poincaré plot reconstruction with lags of 1-100, rotating the cloud of points, its normalized segmentation adapted to their standard deviations, and finally, a frequency-dependent clustering. The lags were combined into eight different clusters representing specific frequency bands within 0.012-1.153 Hz. Statistical differences between low- and high-risk DCM could be found within the clusters II-VIII (e.g., cluster IV: 0.033-0.038 Hz; p = 0.0002; sensitivity = 85.7 %; specificity = 71.4 %). The multivariate statistics led to a sensitivity of 92.9 %, specificity of 85.7 % and an area under the curve of 92.1 % discriminating these patient groups. We introduced the LSPPA method to investigate time correlations in BBI time series. We found that LSPPA contributes considerably to risk stratification in DCM and yields the highest discriminant power in the low and very low-frequency bands.

Application of Mixed H2/H Infinity Optimization

DTIC Science & Technology

1991-11-01

Standard Form .................. . 29 4.4 a-Plot of the Open Loop System .. ......... .. 31 4.5 o-Plot of the H2 & H. Optimal Td ........... . 32 4.6 o...o.34 4.9 o-Plot of Mixed SolutiCo,,, Te.. .......... 35 4.10 a-Plot of H. Central Solution Td ........ 36 4.11 a-Plot of the Mixed Controllers...norm = 3.7) .. .. ......... 41 4.18 a3-Plot of Ted (V-norm 2.8) .......... o.42 v 4.19 a-Plot of Td (ac-norm = 2.5) . . . . . .. 0 42 4.20 a-Plot

Generalized ISAR--part II: interferometric techniques for three-dimensional location of scatterers.

PubMed

Given, James A; Schmidt, William R

2005-11-01

This paper is the second part of a study dedicated to optimizing diagnostic inverse synthetic aperture radar (ISAR) studies of large naval vessels. The method developed here provides accurate determination of the position of important radio-frequency scatterers by combining accurate knowledge of ship position and orientation with specialized signal processing. The method allows for the simultaneous presence of substantial Doppler returns from both change of roll angle and change of aspect angle by introducing generalized ISAR ates. The first paper provides two modes of interpreting ISAR plots, one valid when roll Doppler is dominant, the other valid when the aspect angle Doppler is dominant. Here, we provide, for each type of ISAR plot technique, a corresponding interferometric ISAR (InSAR) technique. The former, aspect-angle dominated InSAR, is a generalization of standard InSAR; the latter, roll-angle dominated InSAR, seems to be new to this work. Both methods are shown to be efficient at identifying localized scatterers under simulation conditions.

A Computational Observer For Performing Contrast-Detail Analysis Of Ultrasound Images

NASA Astrophysics Data System (ADS)

Lopez, H.; Loew, M. H.

1988-06-01

Contrast-Detail (C/D) analysis allows the quantitative determination of an imaging system's ability to display a range of varying-size targets as a function of contrast. Using this technique, a contrast-detail plot is obtained which can, in theory, be used to compare image quality from one imaging system to another. The C/D plot, however, is usually obtained by using data from human observer readings. We have shown earlier(7) that the performance of human observers in the task of threshold detection of simulated lesions embedded in random ultrasound noise is highly inaccurate and non-reproducible for untrained observers. We present an objective, computational method for the determination of the C/D curve for ultrasound images. This method utilizes digital images of the C/D phantom developed at CDRH, and lesion-detection algorithms that simulate the Bayesian approach using the likelihood function for an ideal observer. We present the results of this method, and discuss the relationship to the human observer and to the comparability of image quality between systems.

Measuring carbon in forests: current status and future challenges.

PubMed

Brown, Sandra

2002-01-01

To accurately and precisely measure the carbon in forests is gaining global attention as countries seek to comply with agreements under the UN Framework Convention on Climate Change. Established methods for measuring carbon in forests exist, and are best based on permanent sample plots laid out in a statistically sound design. Measurements on trees in these plots can be readily converted to aboveground biomass using either biomass expansion factors or allometric regression equations. A compilation of existing root biomass data for upland forests of the world generated a significant regression equation that can be used to predict root biomass based on aboveground biomass only. Methods for measuring coarse dead wood have been tested in many forest types, but the methods could be improved if a non-destructive tool for measuring the density of dead wood was developed. Future measurements of carbon storage in forests may rely more on remote sensing data, and new remote data collection technologies are in development.

An Examination of Alternative Multidimensional Scaling Techniques

ERIC Educational Resources Information Center

Papazoglou, Sofia; Mylonas, Kostas

2017-01-01

The purpose of this study is to compare alternative multidimensional scaling (MDS) methods for constraining the stimuli on the circumference of a circle and on the surface of a sphere. Specifically, the existing MDS-T method for plotting the stimuli on the circumference of a circle is applied, and its extension is proposed for constraining the…

EVALUATION OF A MEASUREMENT METHOD FOR FOREST VEGETATION IN A LARGE-SCALE ECOLOGICAL SURVEY

EPA Science Inventory

We evaluate a field method for determining species richness and canopy cover of vascular plants for the Forest Health Monitoring Program (FHM), an ecological survey of U.S. forests. Measurements are taken within 12 1-m2 quadrats on 1/15 ha plots in FHM. Species richness and cover...

Point Intercept (PO)

Treesearch

John F. Caratti

2006-01-01

The FIREMON Point Intercept (PO) method is used to assess changes in plant species cover or ground cover for a macroplot. This method uses a narrow diameter sampling pole or sampling pins, placed at systematic intervals along line transects to sample within plot variation and quantify statistically valid changes in plant species cover and height over time. Plant...

Selecting a sampling method to aid in vegetation management decisions in loblolly pine plantations

Treesearch

David R. Weise; Glenn R. Glover

1993-01-01

Objective methods to evaluate hardwood competition in young loblolly pine (Pinustaeda L.) plantations are not widely used in the southeastern United States. Ability of common sampling rules to accurately estimate hardwood rootstock attributes at low sampling intensities and across varying rootstock spatial distributions is unknown. Fixed area plot...

HYDRUS-1D Modeling of an Irrigated Agricultural Plot with Application to Aquifer Recharge Estimation

USDA-ARS?s Scientific Manuscript database

A variety of methods are available for estimating aquifer recharge in semi-arid regions, each with advantages and disadvantages. We are investigating a procedure for estimating recharge in an irrigated basin. The method involves computing irrigation return flows based on HYDRUS-1D modeling of root z...