Leveraging Clinical Imaging Archives for Radiomics: Reliability of Automated Methods for Brain Volume Measurement.

PubMed

Adduru, Viraj R; Michael, Andrew M; Helguera, Maria; Baum, Stefi A; Moore, Gregory J

2017-09-01

Purpose To validate the use of thick-section clinically acquired magnetic resonance (MR) imaging data for estimating total brain volume (TBV), gray matter (GM) volume (GMV), and white matter (WM) volume (WMV) by using three widely used automated toolboxes: SPM ( www.fil.ion.ucl.ac.uk/spm/ ), FreeSurfer ( surfer.nmr.mgh.harvard.edu ), and FSL (FMRIB software library; Oxford Centre for Functional MR Imaging of the Brain, Oxford, England, https://fsl.fmrib.ox.ac.uk/fsl ). Materials and Methods MR images from a clinical archive were used and data were deidentified. The three methods were applied to estimate brain volumes from thin-section research-quality brain MR images and routine thick-section clinical MR images acquired from the same 38 patients (age range, 1-71 years; mean age, 22 years; 11 women). By using these automated methods, TBV, GMV, and WMV were estimated. Thin- versus thick-section volume comparisons were made for each method by using intraclass correlation coefficients (ICCs). Results SPM exhibited excellent ICCs (0.97, 0.85, and 0.83 for TBV, GMV, and WMV, respectively). FSL exhibited ICCs of 0.69, 0.51, and 0.60 for TBV, GMV, and WMV, respectively, but they were lower than with SPM. FreeSurfer exhibited excellent ICC of 0.63 only for TBV. Application of SPM's voxel-based morphometry on the modulated images of thin-section images and interpolated thick-section images showed fair to excellent ICCs (0.37-0.98) for the majority of brain regions (88.47% [306924 of 346916 voxels] of WM and 80.35% [377 282 of 469 502 voxels] of GM). Conclusion Thick-section clinical-quality MR images can be reliably used for computing quantitative brain metrics such as TBV, GMV, and WMV by using SPM. © RSNA, 2017 Online supplemental material is available for this article.

Compensation for the phase-type spatial periodic modulation of the near-field beam at 1053 nm

NASA Astrophysics Data System (ADS)

Gao, Yaru; Liu, Dean; Yang, Aihua; Tang, Ruyu; Zhu, Jianqiang

2017-10-01

A phase-only spatial light modulator is used to provide and compensate for the spatial periodic modulation (SPM) of the near-field beam at the near infrared at 1053nm wavelength with an improved iterative weight-based method. The transmission characteristics of the incident beam has been changed by a spatial light modulator (SLM) to shape the spatial intensity of the output beam. The propagation and reverse propagation of the light in free space are two important processes in the iterative process. The based theory is the beam angular spectrum transmit formula (ASTF) and the principle of the iterative weight-based method. We have made two improvements to the originally proposed iterative weight-based method. We select the appropriate parameter by choosing the minimum value of the output beam contrast degree and use the MATLAB built-in angle function to acquire the corresponding phase of the light wave function. The required phase that compensates for the intensity distribution of the incident SPM beam is iterated by this algorithm, which can decrease the magnitude of the SPM of the intensity on the observation plane. The experimental results show that the phase-type SPM of the near-field beam is subject to a certain restriction. We have also analyzed some factors that make the results imperfect. The experiment results verifies the possible applicability of this iterative weight-based method to compensate for the SPM of the near-field beam.

Ultra-flat SPM-broadened spectra in a highly nonlinear fiber using parabolic pulses formed in a fiber Bragg grating

NASA Astrophysics Data System (ADS)

Parmigiani, Francesca; Finot, Christophe; Mukasa, Kazunori; Ibsen, Morten; Roelens, Michael A.; Petropoulos, Periklis; Richardson, David J.

2006-08-01

We propose a new method for generating flat self-phase modulation (SPM)-broadened spectra based on seeding a highly nonlinear fiber (HNLF) with chirp-free parabolic pulses generated using linear pulse shaping in a superstructured fiber Bragg grating (SSFBG). We show that the use of grating reshaped parabolic pulses allows substantially better performance in terms of the extent of SPM-based spectral broadening and flatness relative to conventional hyperbolic secant (sech) pulses. We demonstrate both numerically and experimentally the generation of SPM-broadened pulses centred at 1542 nm with 92% of the pulse energy remaining within the 29 nm 3 dB spectral bandwidth. Applications in spectra slicing and pulse compression are demonstrated.

SPM for functional identification of individual biomolecules

NASA Astrophysics Data System (ADS)

Ros, Robert; Schwesinger, Falk; Padeste, Celestino; Plueckthun, Andreas; Anselmetti, Dario; Guentherodt, Hans-Joachim; Tiefenauer, Louis

1999-06-01

The identification of specific binding molecules is of increasing interest in the context of drug development based on combinatorial libraries. Scanning Probe Microscopy (SPM) is the method of choice to image and probe individual biomolecules on a surface. Functional identification of biomolecules is a first step towards screening on a single molecule level. As a model system we use recombinant single- chain Fv fragment (scFv) antibody molecules directed against the antigen fluorescein. The scFv's are covalently immobilized on a flat gold surface via the C-terminal cysteine, resulting in a high accessibility of the binding site. The antigen is immobilized covalently via a long hydrophilic spacer to the silicon nitride SPM-tip. This arrangement allows a direct measurement of binding forces. Thus, closely related antibody molecules differing in only one amino acid at their binding site could be distinguished. A novel SPM-software has been developed which combines imaging, force spectroscopic modes, and online analysis. This is a major prerequisite for future screening methods.

A versatile technique for fabrication of SiC SPM probes

NASA Astrophysics Data System (ADS)

Therrien, Joel; Schmidt, Daniel; Barrot, Sheetal; Patel, Bhavin

2008-03-01

To date SPM probes have largely been fabricated via methods borrowed from the semiconductor industry for fabricating Micro Electro Mechanical Systems. Although these techniques have enabled SPM to see widespread use, the processes put significant limitations on what structures can be made. We report our progress on fabricating SPM cantilevers composed of Silicon Carbide using polymer molding techniques. A pre-ceramic polymer is molded into the desired probe shape and then converted to SiC via pyrolisys. We will also report on progress in using photo-sterolithography for fabrication of even more complex geometries. In addition to opening up a much larger set of probe structures, the use of SiC leads to improved wear resistance of the resulting probes. Among the potential applications, this method enables the fabrication of low spring constant, high resonant frequency cantilevers via cross sectional geometries not accessible to standard fabrication techniques. Such probes are required for high speed tapping and non-contact imaging.

Concentration of biologically active polyamines in meat and liver of sheep and lambs after slaughter and their changes in mutton during storage and cooking.

PubMed

Dadáková, Eva; Pelikánová, Tamara; Kalač, Pavel

2011-02-01

Putrescine (PUT), spermidine (SPD) and spermine (SPM) concentrations using a UPLC method, in chilled mutton, lamb and livers 24 h after slaughter were determined. PUT concentrations were quantifiable only in some samples. Mean SPD concentrations were 4-6, 13.5 and 16.8 mg kg-1 in the meats, sheep and lamb livers, respectively. The respective SPM concentrations were 17-25, 128 and 79 mg kg-1. SPD and SPM losses of about one fifth and half of the initial level, respectively, were apparent in mutton loins stored at -18°C for 6 months. Significant losses of SPD and SPM were found in mutton loins stored aerobically, vacuum-packaged or in a modified atmosphere at +2°C. Boiling and stewing of mutton legs caused SPD and SPM losses of about 40% and roasting of about 60% of the initial content. Copyright © 2010 Elsevier Ltd. All rights reserved.

A robust sebum, oil, and particulate pollution model for assessing cleansing efficacy of human skin.

PubMed

Peterson, G; Rapaka, S; Koski, N; Kearney, M; Ortblad, K; Tadlock, L

2017-06-01

With increasing concerns over the rise of atmospheric particulate pollution globally and its impact on systemic health and skin ageing, we have developed a pollution model to mimic particulate matter trapped in sebum and oils creating a robust (difficult to remove) surrogate for dirty, polluted skin. To evaluate the cleansing efficacy/protective effect of a sonic brush vs. manual cleansing against particulate pollution (trapped in grease/oil typical of human sebum). The pollution model (Sebollution; sebum pollution model; SPM) consists of atmospheric particulate matter/pollution combined with grease/oils typical of human sebum. Twenty subjects between the ages of 18-65 were enrolled in a single-centre, cleansing study comparisons between the sonic cleansing brush (normal speed) compared to manual cleansing. Equal amount of SPM was applied to the centre of each cheek (left and right). Method of cleansing (sonic vs. manual) was randomized to the side of the face (left or right) for each subject. Each side was cleansed for five-seconds using the sonic cleansing device with sensitive brush head or manually, using equal amounts of water and a gel cleanser. Photographs (VISIA-CR, Canfield Imaging, NJ, USA) were taken at baseline (before application of the SPM), after application of SPM (pre-cleansing), and following cleansing. Image analysis (ImageJ, NIH, Bethesda, MD, USA) was used to quantify colour intensity (amount of particulate pollutants on the skin) using a scale of 0 to 255 (0 = all black pixels; 255 = all white pixels). Differences between the baseline and post-cleansing values (pixels) are reported as the amount of SPM remaining following each method of cleansing. Using a robust cleansing protocol to assess removal of pollutants (SPM; atmospheric particulate matter trapped in grease/oil), the sonic brush removed significantly more SPM than manual cleansing (P < 0.001). While extreme in colour, this pollution method easily allows assessment of efficacy through image analysis. © 2016 The Authors. International Journal of Cosmetic Science published by John Wiley & Sons Ltd on behalf of Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Construction and comparative evaluation of different activity detection methods in brain FDG-PET.

PubMed

Buchholz, Hans-Georg; Wenzel, Fabian; Gartenschläger, Martin; Thiele, Frank; Young, Stewart; Reuss, Stefan; Schreckenberger, Mathias

2015-08-18

We constructed and evaluated reference brain FDG-PET databases for usage by three software programs (Computer-aided diagnosis for dementia (CAD4D), Statistical Parametric Mapping (SPM) and NEUROSTAT), which allow a user-independent detection of dementia-related hypometabolism in patients' brain FDG-PET. Thirty-seven healthy volunteers were scanned in order to construct brain FDG reference databases, which reflect the normal, age-dependent glucose consumption in human brain, using either software. Databases were compared to each other to assess the impact of different stereotactic normalization algorithms used by either software package. In addition, performance of the new reference databases in the detection of altered glucose consumption in the brains of patients was evaluated by calculating statistical maps of regional hypometabolism in FDG-PET of 20 patients with confirmed Alzheimer's dementia (AD) and of 10 non-AD patients. Extent (hypometabolic volume referred to as cluster size) and magnitude (peak z-score) of detected hypometabolism was statistically analyzed. Differences between the reference databases built by CAD4D, SPM or NEUROSTAT were observed. Due to the different normalization methods, altered spatial FDG patterns were found. When analyzing patient data with the reference databases created using CAD4D, SPM or NEUROSTAT, similar characteristic clusters of hypometabolism in the same brain regions were found in the AD group with either software. However, larger z-scores were observed with CAD4D and NEUROSTAT than those reported by SPM. Better concordance with CAD4D and NEUROSTAT was achieved using the spatially normalized images of SPM and an independent z-score calculation. The three software packages identified the peak z-scores in the same brain region in 11 of 20 AD cases, and there was concordance between CAD4D and SPM in 16 AD subjects. The clinical evaluation of brain FDG-PET of 20 AD patients with either CAD4D-, SPM- or NEUROSTAT-generated databases from an identical reference dataset showed similar patterns of hypometabolism in the brain regions known to be involved in AD. The extent of hypometabolism and peak z-score appeared to be influenced by the calculation method used in each software package rather than by different spatial normalization parameters.

Quantitative comparisons of three automated methods for estimating intracranial volume: A study of 270 longitudinal magnetic resonance images.

PubMed

Shang, Xiaoyan; Carlson, Michelle C; Tang, Xiaoying

2018-04-30

Total intracranial volume (TIV) is often used as a measure of brain size to correct for individual variability in magnetic resonance imaging (MRI) based morphometric studies. An adjustment of TIV can greatly increase the statistical power of brain morphometry methods. As such, an accurate and precise TIV estimation is of great importance in MRI studies. In this paper, we compared three automated TIV estimation methods (multi-atlas likelihood fusion (MALF), Statistical Parametric Mapping 8 (SPM8) and FreeSurfer (FS)) using longitudinal T1-weighted MR images in a cohort of 70 older participants at elevated sociodemographic risk for Alzheimer's disease. Statistical group comparisons in terms of four different metrics were performed. Furthermore, sex, education level, and intervention status were investigated separately for their impacts on the TIV estimation performance of each method. According to our experimental results, MALF was the least susceptible to atrophy, while SPM8 and FS suffered a loss in precision. In group-wise analysis, MALF was the least sensitive method to group variation, whereas SPM8 was particularly sensitive to sex and FS was unstable with respect to education level. In terms of effectiveness, both MALF and SPM8 delivered a user-friendly performance, while FS was relatively computationally intensive. Copyright © 2018 Elsevier B.V. All rights reserved.

Spontaneous Swallowing Frequency [Has Potential to] Identify Dysphagia in Acute Stroke

PubMed Central

Carnaby, Giselle D; Sia, Isaac; Khanna, Anna; Waters, Michael

2014-01-01

Background and Purpose Spontaneous swallowing frequency has been described as an index of dysphagia in various health conditions. This study evaluated the potential of spontaneous swallow frequency analysis as a screening protocol for dysphagia in acute stroke. Methods In a cohort of 63 acute stroke cases swallow frequency rates (swallows per minute: SPM) were compared to stroke and swallow severity indices, age, time from stroke to assessment, and consciousness level. Mean differences in SPM were compared between patients with vs. without clinically significant dysphagia. ROC analysis was used to identify the optimal threshold in SPM which was compared to a validated clinical dysphagia examination for identification of dysphagia cases. Time series analysis was employed to identify the minimally adequate time period to complete spontaneous swallow frequency analysis. Results SPM correlated significantly with stroke and swallow severity indices but not with age, time from stroke onset, or consciousness level. Patients with dysphagia demonstrated significantly lower SPM rates. SPM differed by dysphagia severity. ROC analysis yielded a threshold of SPM ≤ 0.40 which identified dysphagia (per the criterion referent) with 0.96 sensitivity, 0.68 specificity, and 0.96 negative predictive value. Time series analysis indicated that a 5 to 10 minute sampling window was sufficient to calculate spontaneous swallow frequency to identify dysphagia cases in acute stroke. Conclusions Spontaneous swallowing frequency presents high potential to screen for dysphagia in acute stroke without the need for trained, available personnel. PMID:24149008

Beta systems error analysis

NASA Technical Reports Server (NTRS)

1984-01-01

The atmospheric backscatter coefficient, beta, measured with an airborne CO Laser Doppler Velocimeter (LDV) system operating in a continuous wave, focussed model is discussed. The Single Particle Mode (SPM) algorithm, was developed from concept through analysis of an extensive amount of data obtained with the system on board a NASA aircraft. The SPM algorithm is intended to be employed in situations where one particle at a time appears in the sensitive volume of the LDV. In addition to giving the backscatter coefficient, the SPM algorithm also produces as intermediate results the aerosol density and the aerosol backscatter cross section distribution. A second method, which measures only the atmospheric backscatter coefficient, is called the Volume Mode (VM) and was simultaneously employed. The results of these two methods differed by slightly less than an order of magnitude. The measurement uncertainties or other errors in the results of the two methods are examined.

New Algorithm to Enable Construction and Display of 3D Structures from Scanning Probe Microscopy Images Acquired Layer-by-Layer.

PubMed

Deng, William Nanqiao; Wang, Shuo; Ventrici de Souza, Joao; Kuhl, Tonya L; Liu, Gang-Yu

2018-06-25

Scanning probe microscopy (SPM), such as atomic force microscopy (AFM), is widely known for high-resolution imaging of surface structures and nanolithography in two dimensions (2D), providing important physical insights into surface science and material science. This work reports a new algorithm to enable construction and display of layer-by-layer 3D structures from SPM images. The algorithm enables alignment of SPM images acquired during layer-by-layer deposition and removal of redundant features and faithfully constructs the deposited 3D structures. The display uses a "see-through" strategy to enable the structure of each layer to be visible. The results demonstrate high spatial accuracy as well as algorithm versatility; users can set parameters for reconstruction and display as per image quality and research needs. To the best of our knowledge, this method represents the first report to enable SPM technology for 3D imaging construction and display. The detailed algorithm is provided to facilitate usage of the same approach in any SPM software. These new capabilities support wide applications of SPM that require 3D image reconstruction and display, such as 3D nanoprinting and 3D additive and subtractive manufacturing and imaging.

[Three-dimensional reconstruction of functional brain images].

PubMed

Inoue, M; Shoji, K; Kojima, H; Hirano, S; Naito, Y; Honjo, I

1999-08-01

We consider PET (positron emission tomography) measurement with SPM (Statistical Parametric Mapping) analysis to be one of the most useful methods to identify activated areas of the brain involved in language processing. SPM is an effective analytical method that detects markedly activated areas over the whole brain. However, with the conventional presentations of these functional brain images, such as horizontal slices, three directional projection, or brain surface coloring, makes understanding and interpreting the positional relationships among various brain areas difficult. Therefore, we developed three-dimensionally reconstructed images from these functional brain images to improve the interpretation. The subjects were 12 normal volunteers. The following three types of images were constructed: 1) routine images by SPM, 2) three-dimensional static images, and 3) three-dimensional dynamic images, after PET images were analyzed by SPM during daily dialog listening. The creation of images of both the three-dimensional static and dynamic types employed the volume rendering method by VTK (The Visualization Toolkit). Since the functional brain images did not include original brain images, we synthesized SPM and MRI brain images by self-made C++ programs. The three-dimensional dynamic images were made by sequencing static images with available software. Images of both the three-dimensional static and dynamic types were processed by a personal computer system. Our newly created images showed clearer positional relationships among activated brain areas compared to the conventional method. To date, functional brain images have been employed in fields such as neurology or neurosurgery, however, these images may be useful even in the field of otorhinolaryngology, to assess hearing and speech. Exact three-dimensional images based on functional brain images are important for exact and intuitive interpretation, and may lead to new developments in brain science. Currently, the surface model is the most common method of three-dimensional display. However, the volume rendering method may be more effective for imaging regions such as the brain.

An Automated Method of Scanning Probe Microscopy (SPM) Data Analysis and Reactive Site Tracking for Mineral-Water Interface Reactions Observed at the Nanometer Scale

NASA Astrophysics Data System (ADS)

Campbell, B. D.; Higgins, S. R.

2008-12-01

Developing a method for bridging the gap between macroscopic and microscopic measurements of reaction kinetics at the mineral-water interface has important implications in geological and chemical fields. Investigating these reactions on the nanometer scale with SPM is often limited by image analysis and data extraction due to the large quantity of data usually obtained in SPM experiments. Here we present a computer algorithm for automated analysis of mineral-water interface reactions. This algorithm automates the analysis of sequential SPM images by identifying the kinetically active surface sites (i.e., step edges), and by tracking the displacement of these sites from image to image. The step edge positions in each image are readily identified and tracked through time by a standard edge detection algorithm followed by statistical analysis on the Hough Transform of the edge-mapped image. By quantifying this displacement as a function of time, the rate of step edge displacement is determined. Furthermore, the total edge length, also determined from analysis of the Hough Transform, combined with the computed step speed, yields the surface area normalized rate of the reaction. The algorithm was applied to a study of the spiral growth of the calcite(104) surface from supersaturated solutions, yielding results almost 20 times faster than performing this analysis by hand, with results being statistically similar for both analysis methods. This advance in analysis of kinetic data from SPM images will facilitate the building of experimental databases on the microscopic kinetics of mineral-water interface reactions.

Anti-Invasive and Anti-Proliferative Synergism between Docetaxel and a Polynuclear Pd-Spermine Agent

PubMed Central

Batista de Carvalho, Ana L. M.; Medeiros, Paula S. C.; Costa, Francisco M.; Ribeiro, Vanessa P.; Sousa, Joana B.; Marques, Maria P. M.

2016-01-01

The present work is aimed at evaluating the antitumour properties of a Pd(II) dinuclear complex with the biogenic polyamine spermine, by investigating: i) the anti-angiogenic and anti-migration properties of a Pd(II) dinuclear complex with spermine (Pd2Spm); ii) the anti-proliferative activity of Pd2Spm against a triple negative human breast carcinoma (MDA-MB-231); and finally iii) the putative interaction mediated by combination of Pd2Spm with Docetaxel. Anti-invasive (anti-angiogenic and anti-migratory) as well as anti-proliferative capacities were assessed, for different combination schemes and drug exposure times, using the CAM assay and VEGFR2 activity measurement, the MatrigelTM method and the SRB proliferation test. The results thus obtained evidence the ability of Pd2Spm to restrict angiogenesis and cell migration: Pd2Spm induced a marked inhibition of migration (43.8±12.2%), and a higher inhibition of angiogenesis (81.8±4.4% for total length values, at 4 μM) as compared to DTX at the clinical dosage 4x10-2 μM (26.4±14.4%; n = 4 to 11). Combination of Pd2Spm/DTX was more effective as anti-invasive and anti-proliferative than DTX or Pd2Spm in sole administration, which is compatible with the occurrence of synergism: for the anti-angiogenic effect, IC50(Pd2Spm/DTX) = 0.5/0.5x10-2 μM vs IC50(DTX) = 1.7x10-2 μM and IC50(Pd2Spm) = 1.6 μM. In conclusion, the reported effects of Pd2Spm on angiogenesis, migration and proliferation showed that this compound is a promising therapeutic agent against this type of breast cancer. Moreover, combined administration of Pd2Spm and DTX was found to trigger a substantial synergetic effect regarding angiogenesis inhibition as well as anti-migratory and anti-proliferative activities reinforcing the putative use of Pd(II) complexes in chemotherapeutic regimens. This is a significant outcome, aiming at the application of these combined strategies towards metastatic breast cancer (or other type of resistant cancers), justifying further studies that include pre-clinical trials. PMID:27880824

Characterization of microcracks by application of digital image correlation to SPM images

NASA Astrophysics Data System (ADS)

Keller, Juergen; Gollhardt, Astrid; Vogel, Dietmar; Michel, Bernd

2004-07-01

With the development of micro- and nanotechnological products such as sensors, MEMS/NEMS and their broad application in a variety of market segments new reliability issues will arise. The increasing interface-to-volume ratio in highly integrated systems and nanoparticle filled materials and unsolved questions of size effect of nanomaterials are challenges for experimental reliability evaluation. To fulfill this needs the authors developed the nanoDAC method (nano Deformation Analysis by Correlation), which allows the determination and evaluation of 2D displacement fields based on scanning probe microscopy (SPM) data. In-situ SPM scans of the analyzed object are carried out at different thermo-mechanical load states. The obtained topography-, phase- or error-images are compared utilizing grayscale cross correlation algorithms. This allows the tracking of local image patterns of the analyzed surface structure. The measurement results of the nanoDAC method are full-field displacement and strain fields. Due to the application of SPM equipment deformations in the micro-, nanometer range can be easily detected. The method can be performed on bulk materials, thin films and on devices i.e microelectronic components, sensors or MEMS/NEMS. Furthermore, the characterization and evaluation of micro- and nanocracks or defects in bulk materials, thin layers and at material interfaces can be carried out.

High reliability linear drive device for artificial hearts

NASA Astrophysics Data System (ADS)

Ji, Jinghua; Zhao, Wenxiang; Liu, Guohai; Shen, Yue; Wang, Fangqun

2012-04-01

In this paper, a new high reliability linear drive device, termed as stator-permanent-magnet tubular oscillating actuator (SPM-TOA), is proposed for artificial hearts (AHs). The key is to incorporate the concept of two independent phases into this linear AH device, hence achieving high reliability operation. The fault-tolerant teeth are employed to provide the desired decoupling phases in magnetic circuit. Also, as the magnets and the coils are located in the stator, the proposed SPM-TOA takes the definite advantages of robust mover and direct-drive capability. By using the time-stepping finite element method, the electromagnetic characteristics of the proposed SPM-TOA are analyzed, including magnetic field distributions, flux linkages, back- electromotive forces (back-EMFs) self- and mutual inductances, as well as cogging and thrust forces. The results confirm that the proposed SPM-TOA meets the dimension, weight, and force requirements of the AH drive device.

EEG and MEG data analysis in SPM8.

PubMed

Litvak, Vladimir; Mattout, Jérémie; Kiebel, Stefan; Phillips, Christophe; Henson, Richard; Kilner, James; Barnes, Gareth; Oostenveld, Robert; Daunizeau, Jean; Flandin, Guillaume; Penny, Will; Friston, Karl

2011-01-01

SPM is a free and open source software written in MATLAB (The MathWorks, Inc.). In addition to standard M/EEG preprocessing, we presently offer three main analysis tools: (i) statistical analysis of scalp-maps, time-frequency images, and volumetric 3D source reconstruction images based on the general linear model, with correction for multiple comparisons using random field theory; (ii) Bayesian M/EEG source reconstruction, including support for group studies, simultaneous EEG and MEG, and fMRI priors; (iii) dynamic causal modelling (DCM), an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses, and phase coupling. SPM8 is integrated with the FieldTrip toolbox , making it possible for users to combine a variety of standard analysis methods with new schemes implemented in SPM and build custom analysis tools using powerful graphical user interface (GUI) and batching tools.

EEG and MEG Data Analysis in SPM8

PubMed Central

Litvak, Vladimir; Mattout, Jérémie; Kiebel, Stefan; Phillips, Christophe; Henson, Richard; Kilner, James; Barnes, Gareth; Oostenveld, Robert; Daunizeau, Jean; Flandin, Guillaume; Penny, Will; Friston, Karl

2011-01-01

SPM is a free and open source software written in MATLAB (The MathWorks, Inc.). In addition to standard M/EEG preprocessing, we presently offer three main analysis tools: (i) statistical analysis of scalp-maps, time-frequency images, and volumetric 3D source reconstruction images based on the general linear model, with correction for multiple comparisons using random field theory; (ii) Bayesian M/EEG source reconstruction, including support for group studies, simultaneous EEG and MEG, and fMRI priors; (iii) dynamic causal modelling (DCM), an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses, and phase coupling. SPM8 is integrated with the FieldTrip toolbox , making it possible for users to combine a variety of standard analysis methods with new schemes implemented in SPM and build custom analysis tools using powerful graphical user interface (GUI) and batching tools. PMID:21437221

Design research of nanopositioner based on SPM and its simulation of FEM

NASA Astrophysics Data System (ADS)

Zhang, Zhenyu; Li, Hongqi; Zhou, Hongxiu; Li, Linan; Liu, Xiangjun

2006-01-01

A novel nanopositioning stage was designed according to the scanning property of SPM with flexure hinge as kinematic structure and piezoelectric ceramic as actuator. Kinetic precision and X directional area of nanopositioner are 1.55nm and 26.4 micron, respectively, which is demonstrated by kinetic analysis and finite element method FEM simulation. Designed nanopositioner based on SPM moves at 3 dimensions with nanometer scale and its motion of X, Y, and Z directions is decoupled and isotropic. Furthermore, frame of nanopositioner is simple and manufacturing is convenient, which will have broad prospect in the field of nanopositioning and nanotracing.

[Elaboration of the SPM template for the standardization of SPECT images with 123I-Ioflupane].

PubMed

García-Gómez, F J; García-Solís, D; Luis-Simón, F J; Marín-Oyaga, V A; Carrillo, F; Mir, P; Vázquez-Albertino, R J

2013-01-01

Statistical parametric mapping (SPM) is a widely used produced for normalization of functional images. This study has aimed to develop a normalization template of (123)I-Ioflupane SPECT-imaging DaTSCAN(®), GE Healthcare), not available in SPM5, and to validate it compared to other quantification methods. In order to write the template we retrospectively selected 26 subjects who had no evidence of nigrostriatal degeneration and whose age distribution was similar to that of the patients in the usual practice of our Department: 2 subjects (7.6%) were < 35 years, 9 between 35-65 years (34.6%) and 15 > 65 years (57.7%). All the studies were normalized with the T1-template available in SPM5 and an average image of the value was obtained for each voxel. For validation we analyzed 60 patients: 30 with idiopathic Parkinson's disease patients (iPD) with right involvement (66.83±12.20 years) and 30 with essential tremor patients (ET) (67.27±8.33 years). Specific uptake rates (SUR) of different striatal regions were compared after image normalization with our template and the application of a semiautomated VOIs-map created with Analyze v9.0 ((©)BIR, Mayo Clinic), against two quantification methods: a) manual adjustment of a ROIs-map drawn in Analyze, and b) semi-automated method (HERMES-BRASS) with normalization and implementation of VOIs-map. No statistically significant differences in the iPD/ET discriminatory capacity between the three methods analyzed were observed (p<0,001). The correlation of SUR after normalization with our «template» was higher than that obtained by method b) (R>0,871, p<0,001). This difference was greater in patients with PD. Our study demonstrates the efficacy of our SPM «template» for (123)I-Ioflupane SPECT-imaging, obtained from normalization with «T1-template». Copyright © 2012 Elsevier España, S.L. and SEMNIM. All rights reserved.

Spatial distribution of organic contaminants in three rivers of Southern England bound to suspended particulate material and dissolved in water.

PubMed

Wilkinson, John L; Hooda, Peter S; Swinden, Julian; Barker, James; Barton, Stephen

2017-09-01

The spatial distribution of pharmaceuticals, personal care products (PPCPs) and other emerging contaminants (ECs) such as plasticisers, perflourinated compounds (PFCs) and illicit drug metabolites in water and bound to suspended particulate material (SPM) is not well-understood. Here, we quantify levels of thirteen selected contaminants in water (n=88) and their partition to suspended particulate material (SPM, n=16) in three previously-unstudied rivers of Greater London and Southern England during a key reproduction/spawning period. Analysis was conducted using an in-house validated method for Solid Phase Extraction followed by High-Performance Liquid Chromatography-Tandem Mass-Spectrometry. Analytes were extracted from SPM using an optimised method for ultrasonic-assisted solvent extraction. Detection frequencies of contaminants dissolved in water ranged from 3% (ethinylestradiol) to 100% (bisphenol-A). Overall mean concentrations in the aqueous-phase ranged from 14.7ng/L (benzoylecgonine) to 159ng/L (bisphenol-A). Sewage treatment works (STW) effluent was the predominant source of pharmaceuticals, while plasticisers/perfluorinated compounds may additionally enter rivers via other sources. In SPM, detection frequencies ranged from 44% (PFOA) to 94% (hydroxyacetophenone). Mean quantifiable levels of analytes bound to SPM ranged from 13.5ng/g dry SPM (0.33ng bound/L water) perfluorononanoic acid to 2830ng/g dry SPM (14.3ng bound/L water) perfluorooctanesulfonic acid. Long chain (>C7) amphipathic and acidic PFCs were found to more preferentially bind to SPM than short chain PFCs and other contaminants (Kd=34.1-75.5 vs <5 respectively). Per capita daily contributions of studied contaminants entering rivers ranged from 0.157μg/person/day of benzoylecgonine (cocaine metabolite) to 58.6μg/person/day of bisphenol-A. The large sample size of this work (n=104) enabled ANOVA followed by Tukey HSD post-hoc tests to establish significant trends in PPCP/EC spatial distribution from headwaters through downstream stretches of studied rivers. Novel findings include environmental Kd calculations, the occurrence of contaminants in river headwaters, increases in contaminant metabolite concentrations downstream of STW effluents revealing possible in-river degradation or de-conjugation, the influence of polarity and acidity in the partition of contaminants to particulate-material, among others. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Sparse SPM: Group Sparse-dictionary learning in SPM framework for resting-state functional connectivity MRI analysis.

PubMed

Lee, Young-Beom; Lee, Jeonghyeon; Tak, Sungho; Lee, Kangjoo; Na, Duk L; Seo, Sang Won; Jeong, Yong; Ye, Jong Chul

2016-01-15

Recent studies of functional connectivity MR imaging have revealed that the default-mode network activity is disrupted in diseases such as Alzheimer's disease (AD). However, there is not yet a consensus on the preferred method for resting-state analysis. Because the brain is reported to have complex interconnected networks according to graph theoretical analysis, the independency assumption, as in the popular independent component analysis (ICA) approach, often does not hold. Here, rather than using the independency assumption, we present a new statistical parameter mapping (SPM)-type analysis method based on a sparse graph model where temporal dynamics at each voxel position are described as a sparse combination of global brain dynamics. In particular, a new concept of a spatially adaptive design matrix has been proposed to represent local connectivity that shares the same temporal dynamics. If we further assume that local network structures within a group are similar, the estimation problem of global and local dynamics can be solved using sparse dictionary learning for the concatenated temporal data across subjects. Moreover, under the homoscedasticity variance assumption across subjects and groups that is often used in SPM analysis, the aforementioned individual and group analyses using sparse dictionary learning can be accurately modeled by a mixed-effect model, which also facilitates a standard SPM-type group-level inference using summary statistics. Using an extensive resting fMRI data set obtained from normal, mild cognitive impairment (MCI), and Alzheimer's disease patient groups, we demonstrated that the changes in the default mode network extracted by the proposed method are more closely correlated with the progression of Alzheimer's disease. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparison between KPVT/SPM and SoHO/MDI magnetograms with an application to solar irradiance reconstructions

NASA Astrophysics Data System (ADS)

Wenzler, T.; Solanki, S. K.; Krivova, N. A.; Fluri, D. M.

2004-12-01

To be able to use both space- and ground-based solar magnetograms and construct long time series of derived parameters it is important to cross-calibrate them so that we can estimate their reliability and combine them. Using two different techniques, we compare magnetograms as well as continuum images recorded by the Spectropolarimeter (SPM) on Kitt Peak and the Michelson Doppler Interferometer (MDI) on board SoHO. We find that the result obtained depends on the method used. The method we favour gives almost identical umbral and penumbral areas and very similar total magnetic fluxes in faculae. The magnetic fluxes in umbrae and penumbrae returned by the two instruments, however, differ considerably. We also demonstrate that SPM data can be employed to reconstruct total solar irradiance variations with almost the same accuracy as recently shown for MDI data.

Optimized statistical parametric mapping for partial-volume-corrected amyloid positron emission tomography in patients with Alzheimer's disease and Lewy body dementia

NASA Astrophysics Data System (ADS)

Oh, Jungsu S.; Kim, Jae Seung; Chae, Sun Young; Oh, Minyoung; Oh, Seung Jun; Cha, Seung Nam; Chang, Ho-Jong; Lee, Chong Sik; Lee, Jae Hong

2017-03-01

We present an optimized voxelwise statistical parametric mapping (SPM) of partial-volume (PV)-corrected positron emission tomography (PET) of 11C Pittsburgh Compound B (PiB), incorporating the anatomical precision of magnetic resonance image (MRI) and amyloid β (A β) burden-specificity of PiB PET. First, we applied region-based partial-volume correction (PVC), termed the geometric transfer matrix (GTM) method, to PiB PET, creating MRI-based lobar parcels filled with mean PiB uptakes. Then, we conducted a voxelwise PVC by multiplying the original PET by the ratio of a GTM-based PV-corrected PET to a 6-mm-smoothed PV-corrected PET. Finally, we conducted spatial normalizations of the PV-corrected PETs onto the study-specific template. As such, we increased the accuracy of the SPM normalization and the tissue specificity of SPM results. Moreover, lobar smoothing (instead of whole-brain smoothing) was applied to increase the signal-to-noise ratio in the image without degrading the tissue specificity. Thereby, we could optimize a voxelwise group comparison between subjects with high and normal A β burdens (from 10 patients with Alzheimer's disease, 30 patients with Lewy body dementia, and 9 normal controls). Our SPM framework outperformed than the conventional one in terms of the accuracy of the spatial normalization (85% of maximum likelihood tissue classification volume) and the tissue specificity (larger gray matter, and smaller cerebrospinal fluid volume fraction from the SPM results). Our SPM framework optimized the SPM of a PV-corrected A β PET in terms of anatomical precision, normalization accuracy, and tissue specificity, resulting in better detection and localization of A β burdens in patients with Alzheimer's disease and Lewy body dementia.

Multi data mode method as an alternative way for SPM studies of high relief surfaces

NASA Astrophysics Data System (ADS)

Abdullayeva, S. H.; Molchanov, S. P.; Mamedov, N. T.; Alekperov, S. D.

2006-09-01

In this paper we report the results of our studies of the high relief surfaces of Al oxide-based ceramic catalyst by SPM contact mode, and by so-called Multi Data Mode (MDM) method for comparison. We failed to obtain any reasonable image of the highly-developed surfaces of above material by the first method but were successful in doing so when applied the second one. The topographic and complimentary images obtained by MDM probing with high resolution are discussed to show a full range of the applications possible using MDM.

Temporal contrast enhancement of a femtosecond fiber CPA system by filtering of SPM broadened spectra

NASA Astrophysics Data System (ADS)

Buldt, J.; Müller, M.; Klas, R.; Eidam, T.; Limpert, J.; Tünnermann, A.

2018-02-01

We present a novel approach for temporal contrast enhancement of energetic laser pulses by filtered SPM broadened spectra. A measured temporal contrast enhancement by at least 7 orders of magnitude in a simple setup has been achieved. This technique is applicable to a wide range of laser parameters and poses a highly efficient alternative to existing contrast-enhancement methods.

Characterisation of urban catchment suspended particulate matter (Auckland region, New Zealand); a comparison with non-urban SPM.

PubMed

Bibby, Rebecca L; Webster-Brown, Jenny G

2005-05-01

Suspended particulate matter (SPM) is an important transport agent for metal contaminants in streams, particularly during high flow periods such as storm events. For highly contaminated urban catchments in the greater Auckland (New Zealand) area, trace metal partitioning between the dissolved phase and SPM was determined, and SPM characterised in terms of its Si, Al, Fe, Mn, Zn, Cu, Pb, TOC, TON and PO(4) concentrations, as well as particle size, abundance, type and surface area. This data was compared to similar data from representative non-urban catchments in the Auckland region, the Kaipara River and Waikato River catchments, to identify any significant differences in the SPM and its potential trace metal adsorption capacity. Trace metal partitioning was assessed by way of a distribution coefficient: K(D)=[Me(SPM)]/[Me(DISS)]. Auckland urban SPM comprises quartz, feldspars and clay minerals, with Fe-oxides and minor Mn-oxides. No particles of anthropogenic origin, other than glass shards, were observed. No change in urban SPM particle size or SSA was observed with seasonal change in temperature, but the nature of the SPM was observed to change with flow regime. The abundance of finer particles, SSA and Al content of the SPM increased under moderate flow conditions; however, Si/Al ratios remained constant, confirming the importance of aluminosilicate detrital minerals in surface run-off. The SPM Fe content was observed to decrease with increased flow and was attributed to dilution of SPM Fe-oxide of groundwater origin. The Kaipara River SPM was found to be mineralogically, chemically and biologically similar to the urban SPM. However, major differences between urban catchment SPM and SPM from the much larger (non-urban) Waikato River were observed, and attributed to a higher abundance of diatoms. The Fe content of the Waikato River SPM was consistently lower (<5%), and the Si/Al ratio and Mn content was higher. Such differences observed between urban and non-urban SPM did not appear to affect the partitioning of Zn and Cu; however, Pb in the Kaipara and Waikato Rivers was found to be more associated with the dissolved phase. This is likely to reflect higher particulate Pb inputs to urban systems.

Complete information acquisition in scanning probe microscopy

DOE PAGES

Belianinov, Alex; Kalinin, Sergei V.; Jesse, Stephen

2015-03-13

In the last three decades, scanning probe microscopy (SPM) has emerged as a primary tool for exploring and controlling the nanoworld. A critical part of the SPM measurements is the information transfer from the tip-surface junction to a macroscopic measurement system. This process reduces the many degrees of freedom of a vibrating cantilever to relatively few parameters recorded as images. Similarly, the details of dynamic cantilever response at sub-microsecond time scales of transients, higher-order eigenmodes and harmonics are averaged out by transitioning to millisecond time scale of pixel acquisition. Hence, the amount of information available to the external observer ismore » severely limited, and its selection is biased by the chosen data processing method. Here, we report a fundamentally new approach for SPM imaging based on information theory-type analysis of the data stream from the detector. This approach allows full exploration of complex tip-surface interactions, spatial mapping of multidimensional variability of material s properties and their mutual interactions, and SPM imaging at the information channel capacity limit.« less

Modeling Electrokinetic Flows by the Smoothed Profile Method

PubMed Central

Luo, Xian; Beskok, Ali; Karniadakis, George Em

2010-01-01

We propose an efficient modeling method for electrokinetic flows based on the Smoothed Profile Method (SPM) [1–4] and spectral element discretizations. The new method allows for arbitrary differences in the electrical conductivities between the charged surfaces and the the surrounding electrolyte solution. The electrokinetic forces are included into the flow equations so that the Poisson-Boltzmann and electric charge continuity equations are cast into forms suitable for SPM. The method is validated by benchmark problems of electroosmotic flow in straight channels and electrophoresis of charged cylinders. We also present simulation results of electrophoresis of charged microtubules, and show that the simulated electrophoretic mobility and anisotropy agree with the experimental values. PMID:20352076

Mobility of the maize suppressor-mutator element in transgenic tobacco cells.

PubMed Central

Masson, P; Fedoroff, N V

1989-01-01

Maize Suppressor-mutator (Spm) transposable elements have been introduced into tobacco cells and a visual assay for Spm activity has been developed using a bacterial beta-glucuronidase gene. The Spm element is mobile in tobacco and can trans-activate excision of a transposition-defective Spm (dSpm) element either from a different site on the same transforming Ti plasmid or from a second plasmid. An Spm element expressed from the stronger cauliflower mosaic virus 35S promoter trans-activates transposition of a dSpm element earlier after its introduction into tobacco cells than an element expressed from its own promoter. Images PMID:2538837

Development of an indirect ELISA based on the recombinant Spm2 protein for detection of tropical theileriosis.

PubMed

Tian, Zhancheng; Du, Xiaoyue; Du, Junzheng; Gao, Shandian; Yu, Ruiming; Hassan, Muhammad Adeel; Liu, Guangyuan; Luo, Jianxun; Yin, Hong

2018-06-01

Tropical theileriosis, caused by Theileria annulata, is distributed worldwide and causes great economic losses in dairy. The reliable diagnostic method is critical for prevention and control of the disease. In this study, a sporozoite and macroschizont gene 2 (spm2) protein from T. annulata was used to develop an indirect ELISA for tropical theileriosis. Specificity test showed that there were no cross-reactions with antibodies raised against other bovine piroplasm species using ELISA or western blotting. The specificity and sensitivity were 98.4% and 98.7%, respectively, with a threshold of 35.5% of the specific mean antibody rate (AbR). Furthermore, a total of 196 field sera samples collected from Xinjiang and Gansu provinces were detected by the spm2 ELISA and IFA. The results obtained with the spm2 ELISA and IFA in this study had the moderate agreement. The average positive rates of T. annulata sera samples detected in the present study were close to the prevalence of previous reports in these endemic areas. This indicated that the Spm2 ELISA could be used as a reliable diagnostic tool for serological survey of T. annulata infection in areas where Theileria parva is not present. Copyright © 2018 Elsevier B.V. All rights reserved.

Spm1, a stress-activated MAP kinase that regulates morphogenesis in S.pombe.

PubMed Central

Zaitsevskaya-Carter, T; Cooper, J A

1997-01-01

A gene encoding a novel MAP kinase family member, Spm1, was isolated from the fission yeast Schizosaccharomyces pombe. Overproduction of Spm1 inhibits proliferation. Disruption of the spm1+ gene interferes with cell separation and morphogenesis. Under conditions of nutrient limitation, hypertonic stress or elevated temperature, spm1 delta cells grow as short branched filaments in which the cell walls and septa are thickened, suggesting defects in polarized growth and cell wall remodeling. At high osmolarity, spm1 delta cells fail to form colonies. The Spm1 protein is tyrosine phosphorylated and activated in response to osmotic and heat stress, consistent with a role for Spm1 in adaptation to these conditions. Two other S.pombe MAP kinases are known, Spk1, required for sexual differentiation and sporulation, and Spc1/Sty1/Phh1, which is activated in hypertonic conditions. However, the distinctive features of the spm1 delta mutant phenotype and direct biochemical assays suggest that Spm1 does not lie on other known MAP kinase pathways. Our results demonstrate the existence of a new MAP kinase pathway that regulates cell wall remodeling and cytokinesis in response to environmental stresses. PMID:9135147

One-dimensional statistical parametric mapping in Python.

PubMed

Pataky, Todd C

2012-01-01

Statistical parametric mapping (SPM) is a topological methodology for detecting field changes in smooth n-dimensional continua. Many classes of biomechanical data are smooth and contained within discrete bounds and as such are well suited to SPM analyses. The current paper accompanies release of 'SPM1D', a free and open-source Python package for conducting SPM analyses on a set of registered 1D curves. Three example applications are presented: (i) kinematics, (ii) ground reaction forces and (iii) contact pressure distribution in probabilistic finite element modelling. In addition to offering a high-level interface to a variety of common statistical tests like t tests, regression and ANOVA, SPM1D also emphasises fundamental concepts of SPM theory through stand-alone example scripts. Source code and documentation are available at: www.tpataky.net/spm1d/.

An estimate of the suspended particulate matter (SPM) transport in the southern North Sea using SeaWiFS images, in situ measurements and numerical model results

NASA Astrophysics Data System (ADS)

Fettweis, Michael; Nechad, Bouchra; Van den Eynde, Dries

2007-06-01

A study is presented where satellite images (SeaWiFS), in situ measurements (tidal cycle and snapshot) and a 2D hydrodynamic numerical model have been combined to calculate the long term SPM (Suspended Particulate Matter) transport through the Dover Strait and in the southern North Sea. The total amount of SPM supplied to the North Sea through the Dover Strait is estimated to be 31.74×10 6 t. The satellite images provide synoptic views of SPM concentration distribution but do not take away the uncertainty of SPM transport calculation. This is due to the fact that SPM concentration varies as a function of tide, wind, spring-neap tidal cycles and seasons. The short term variations (tidal, spring-neap tidal cycle) have not been found in the satellite images, however seasonal variations are clearly visible. Furthermore the SPM concentration in the satellite images is generally lower than in the in situ measurements. The representativness of SPM concentration maps derived from satellites for calculating long term transports has therefore been investigated by comparing the SPM concentration variability from the in situ measurements with those of the remote sensing data. The most important constraints of satellite images are related to the fact that satellite data is evidence of clear sky conditions, whereas in situ measurements from a vessel can be carried out also during rougher meteorological conditions and that due to the too low time resolution of the satellite images the SPM concentration peaks are often missed. It is underlined that SPM concentration measurements should be carried out during at least one tidal cycle in high turbidity areas to obtain representative values of SPM concentration.

A Mixed Prioritization Operators Strategy Using A Single Measurement Criterion For AHP Application Development

NASA Astrophysics Data System (ADS)

Yuen, Kevin Kam Fung

2009-10-01

The most appropriate prioritization method is still one of the unsettled issues of the Analytic Hierarchy Process, although many studies have been made and applied. Interestingly, many AHP applications apply only Saaty's Eigenvector method as many studies have found that this method may produce rank reversals and have proposed various prioritization methods as alternatives. Some methods have been proved to be better than the Eigenvector method. However, these methods seem not to attract the attention of researchers. In this paper, eight important prioritization methods are reviewed. A Mixed Prioritization Operators Strategy (MPOS) is developed to select a vector which is prioritized by the most appropriate prioritization operator. To verify this new method, a case study of high school selection is revised using the proposed method. The contribution is that MPOS is useful for solving prioritization problems in the AHP.

Similar survival of patients with multiple versus single primary melanomas based on Utah Surveillance, Epidemiology, and End Results data (1973-2011).

PubMed

Grossman, Douglas; Farnham, James M; Hyngstrom, John; Klapperich, Marki E; Secrest, Aaron M; Empey, Sarah; Bowen, Glen M; Wada, David; Andtbacka, Robert H I; Grossmann, Kenneth; Bowles, Tawnya L; Cannon-Albright, Lisa A

2018-03-01

Survival data are mixed comparing patients with multiple primary melanomas (MPM) to those with single primary melanomas (SPM). We compared MPM versus SPM patient survival using a matching method that avoids potential biases associated with other analytic approaches. Records of 14,138 individuals obtained from the Surveillance, Epidemiology, and End Results registry of all melanomas diagnosed or treated in Utah between 1973 and 2011 were reviewed. A single matched control patient was selected randomly from the SPM cohort for each MPM patient, with the restriction that they survived at least as long as the interval between the first and second diagnoses for the matched MPM patient. Survival curves (n = 887 for both MPM and SPM groups) without covariates showed a significant survival disadvantage for MPM patients (chi-squared 39.29, P < .001). However, a multivariate Cox proportional hazards model showed no significant survival difference (hazard ratio 1.07, P = .55). Restricting the multivariate analysis to invasive melanomas also showed no significant survival difference (hazard ratio 0.99, P = .96). Breslow depth, ulceration status, and specific cause of death were not available for all patients. Patients with MPM had similar survival times as patients with SPM. Copyright © 2018 American Academy of Dermatology, Inc. Published by Elsevier Inc. All rights reserved.

A knowledge-guided active model method of cortical structure segmentation on pediatric MR images.

PubMed

Shan, Zuyao Y; Parra, Carlos; Ji, Qing; Jain, Jinesh; Reddick, Wilburn E

2006-10-01

To develop an automated method for quantification of cortical structures on pediatric MR images. A knowledge-guided active model (KAM) approach was proposed with a novel object function similar to the Gibbs free energy function. Triangular mesh models were transformed to images of a given subject by maximizing entropy, and then actively slithered to boundaries of structures by minimizing enthalpy. Volumetric results and image similarities of 10 different cortical structures segmented by KAM were compared with those traced manually. Furthermore, the segmentation performances of KAM and SPM2, (statistical parametric mapping, a MATLAB software package) were compared. The averaged volumetric agreements between KAM- and manually-defined structures (both 0.95 for structures in healthy children and children with medulloblastoma) were higher than the volumetric agreement for SPM2 (0.90 and 0.80, respectively). The similarity measurements (kappa) between KAM- and manually-defined structures (0.95 and 0.93, respectively) were higher than those for SPM2 (both 0.86). We have developed a novel automatic algorithm, KAM, for segmentation of cortical structures on MR images of pediatric patients. Our preliminary results indicated that when segmenting cortical structures, KAM was in better agreement with manually-delineated structures than SPM2. KAM can potentially be used to segment cortical structures for conformal radiation therapy planning and for quantitative evaluation of changes in disease or abnormality. Copyright (c) 2006 Wiley-Liss, Inc.

A landmark-based 3D calibration strategy for SPM

NASA Astrophysics Data System (ADS)

Ritter, Martin; Dziomba, Thorsten; Kranzmann, Axel; Koenders, Ludger

2007-02-01

We present a new method for the complete three-dimensional (3D) calibration of scanning probe microscopes (SPM) and other high-resolution microscopes, e.g., scanning electron microscopes (SEM) and confocal laser scanning microscopes (CLSM), by applying a 3D micrometre-sized reference structure with the shape of a cascade slope-step pyramid. The 3D reference structure was produced by focused ion beam induced metal deposition. In contrast to pitch featured calibration procedures that require separate lateral and vertical reference standards such as gratings and step height structures, the new method includes the use of landmarks, which are well established in calibration and measurement tasks on a larger scale. However, the landmarks applied to the new 3D reference structures are of sub-micrometre size, the so-called 'nanomarkers'. The nanomarker coordinates are used for a geometrical calibration of the scanning process of SPM as well as of other instrument types such as SEM and CLSM. For that purpose, a parameter estimation routine involving three scale factors and three coupling factors has been developed that allows lateral and vertical calibration in only one sampling step. With this new calibration strategy, we are able to detect deviations of SPM lateral scaling errors as well as coupling effects causing, e.g., a lateral coordinate shift depending on the measured height position of the probe.

Interferometer-Controlled Optical Tweezers Constructed for Nanotechnology and Biotechnology

NASA Technical Reports Server (NTRS)

Decker, Arthur J.

2002-01-01

A new method to control microparticles was developed in-house at the NASA Glenn Research Center in support of the nanotechnology project under NASA's Aerospace Propulsion and Power Base Research Program. A prototype interferometer-controlled optical tweezers was constructed to manipulate scanning probe microscope (SPM) tips. A laser beam passed through a Mach-Zehnder interferometer, and a microscope objective then produced an optical trap from the coaxial beams. The trap levitated and generated the coarse motion of a 10-mm polystyrene sphere used to simulate a SPM tip. The interference between the beams provided fine control of the forces and moments on the sphere. The interferometer included a piezoelectric-scanned mirror to modulate the interference pattern. The 10-mm sphere was observed to oscillate about 1 mm as the mirror and fringe pattern oscillated. The prototype tweezers proved the feasibility of constructing a more sophisticated interferometer tweezers to hold and manipulate SPM tips. The SPM tips are intended to interrogate and manipulate nanostructures. A more powerful laser will be used to generate multiple traps to hold nanostructures and SPM tips. The vibrating mirror in the interferometer will be replaced with a spatial light modulator. The modulator will allow the optical phase distribution in one leg of the interferometer to be programmed independently at 640 by 480 points for detailed control of the forces and moments. The interference patterns will be monitored to measure the motion of the SPM tips. Neuralnetwork technology will provide fast analysis of the interference patterns for diagnostic purposes and for local or remote feedback control of the tips. This effort also requires theoretical and modeling support in the form of scattering calculations for twin coherent beams from nonspherical particles.

Extending Inferential Group Analysis in Type 2 Diabetic Patients with Multivariate GLM Implemented in SPM8

PubMed Central

Ferreira, Fábio S.; Pereira, João M.S.; Duarte, João V.; Castelo-Branco, Miguel

2017-01-01

Background: Although voxel based morphometry studies are still the standard for analyzing brain structure, their dependence on massive univariate inferential methods is a limiting factor. A better understanding of brain pathologies can be achieved by applying inferential multivariate methods, which allow the study of multiple dependent variables, e.g. different imaging modalities of the same subject. Objective: Given the widespread use of SPM software in the brain imaging community, the main aim of this work is the implementation of massive multivariate inferential analysis as a toolbox in this software package. applied to the use of T1 and T2 structural data from diabetic patients and controls. This implementation was compared with the traditional ANCOVA in SPM and a similar multivariate GLM toolbox (MRM). Method: We implemented the new toolbox and tested it by investigating brain alterations on a cohort of twenty-eight type 2 diabetes patients and twenty-six matched healthy controls, using information from both T1 and T2 weighted structural MRI scans, both separately – using standard univariate VBM - and simultaneously, with multivariate analyses. Results: Univariate VBM replicated predominantly bilateral changes in basal ganglia and insular regions in type 2 diabetes patients. On the other hand, multivariate analyses replicated key findings of univariate results, while also revealing the thalami as additional foci of pathology. Conclusion: While the presented algorithm must be further optimized, the proposed toolbox is the first implementation of multivariate statistics in SPM8 as a user-friendly toolbox, which shows great potential and is ready to be validated in other clinical cohorts and modalities. PMID:28761571

Analysis of riverine suspended particulate matter fluxes (Gulf of Lion, Mediterranean Sea) using a synergy of ocean color observations with a 3-D hydrodynamic sediment transport model

NASA Astrophysics Data System (ADS)

Le Fouest, Vincent; Chami, Malik; Verney, Romaric

2015-02-01

The export of riverine suspended particulate matter (SPM) in the coastal ocean has major implications for the biogeochemical cycles. In the Mediterranean Sea (France), the Rhone River inputs of SPM into the Gulf of Lion (GoL) are highly variable in time, which severely impedes the assessment of SPM fluxes. The objectives of this study are (i) to investigate the prediction of the land-to-ocean flux of SPM using the complementarity (i.e., synergy) between a hydrodynamic sediment transport model and satellite observations, and (ii) to analyze the spatial distribution of the SPM export. An original approach that combines the MARS-3D model with satellite ocean color data is proposed. Satellite-derived SPM and light penetration depth are used to initialize MARS-3D and to validate its predictions. A sensitivity analysis is performed to quantify the impact of riverine SPM size composition and settling rate on the horizontal export of SPM. The best agreement between the model and the satellite in terms of SPM spatial distribution and export is obtained for two conditions: (i) when the relative proportion of "heavy and fast" settling particles significantly increases relative to the "light and slow" ones, and (ii) when the settling rate of heavy and light SPM increases by fivefold. The synergy between MARS-3D and the satellite data improved the SPM flux predictions by 48% near the Rhone River mouth. Our results corroborate the importance of implementing satellite observations within initialization procedures of ocean models since data assimilation techniques may fail for river floods showing strong seasonal variability.

Fast and reliable method of conductive carbon nanotube-probe fabrication for scanning probe microscopy

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

Dremov, Vyacheslav, E-mail: dremov@issp.ac.ru; Fedorov, Pavel; Grebenko, Artem

2015-05-15

We demonstrate the procedure of scanning probe microscopy (SPM) conductive probe fabrication with a single multi-walled carbon nanotube (MWNT) on a silicon cantilever pyramid. The nanotube bundle reliably attached to the metal-covered pyramid is formed using dielectrophoresis technique from the MWNT suspension. It is shown that the dimpled aluminum sample can be used both for shortening/modification of the nanotube bundle by applying pulse voltage between the probe and the sample and for controlling the probe shape via atomic force microscopy imaging the sample. Carbon nanotube attached to cantilever covered with noble metal is suitable for SPM imaging in such modulationmore » regimes as capacitance contrast microscopy, Kelvin probe microscopy, and scanning gate microscopy. The majority of such probes are conductive with conductivity not degrading within hours of SPM imaging.« less

Methods for determining and processing 3D errors and uncertainties for AFM data analysis

NASA Astrophysics Data System (ADS)

Klapetek, P.; Nečas, D.; Campbellová, A.; Yacoot, A.; Koenders, L.

2011-02-01

This paper describes the processing of three-dimensional (3D) scanning probe microscopy (SPM) data. It is shown that 3D volumetric calibration error and uncertainty data can be acquired for both metrological atomic force microscope systems and commercial SPMs. These data can be used within nearly all the standard SPM data processing algorithms to determine local values of uncertainty of the scanning system. If the error function of the scanning system is determined for the whole measurement volume of an SPM, it can be converted to yield local dimensional uncertainty values that can in turn be used for evaluation of uncertainties related to the acquired data and for further data processing applications (e.g. area, ACF, roughness) within direct or statistical measurements. These have been implemented in the software package Gwyddion.

Oligodeoxyribonucleotide association with single-walled carbon nanotubes studied by SPM.

PubMed

Lahiji, Roya R; Dolash, Bridget D; Bergstrom, Donald E; Reifenberger, Ronald

2007-11-01

Studies have been performed on both as-received and chemically oxidized single-walled carbon nanotubes (SWCNTs) grown by two different growth methods to better understand the preferential association of the oligodeoxyribonucleotide T30 (ODN) with SWCNTs. Samples of T30 ODN:SWCNT were examined under ambient conditions using non-contact scanning probe microscope (SPM) techniques. The resulting images show different morphologies ranging from tangled networks of SWCNTs to individual, well-dispersed isolated SWCNTs as the sonication time is increased. SPM images of well-dispersed, as-received SWCNTs reveal isolated features that are 1.4 to 2.8 nm higher than the bare SWCNT itself. X-ray photoemission spectroscopy (XPS) confirmed these features to be T30 ODN in nature. Chemically oxidizing the SWCNTs before sonication is found to be an effective way to increase the number of T30 ODN features.

FDG-PET and CSF biomarker accuracy in prediction of conversion to different dementias in a large multicentre MCI cohort.

PubMed

Caminiti, Silvia Paola; Ballarini, Tommaso; Sala, Arianna; Cerami, Chiara; Presotto, Luca; Santangelo, Roberto; Fallanca, Federico; Vanoli, Emilia Giovanna; Gianolli, Luigi; Iannaccone, Sandro; Magnani, Giuseppe; Perani, Daniela

2018-01-01

In this multicentre study in clinical settings, we assessed the accuracy of optimized procedures for FDG-PET brain metabolism and CSF classifications in predicting or excluding the conversion to Alzheimer's disease (AD) dementia and non-AD dementias. We included 80 MCI subjects with neurological and neuropsychological assessments, FDG-PET scan and CSF measures at entry, all with clinical follow-up. FDG-PET data were analysed with a validated voxel-based SPM method. Resulting single-subject SPM maps were classified by five imaging experts according to the disease-specific patterns, as "typical-AD", "atypical-AD" (i.e. posterior cortical atrophy, asymmetric logopenic AD variant, frontal-AD variant), "non-AD" (i.e. behavioural variant FTD, corticobasal degeneration, semantic variant FTD; dementia with Lewy bodies) or "negative" patterns. To perform the statistical analyses, the individual patterns were grouped either as "AD dementia vs. non-AD dementia (all diseases)" or as "FTD vs. non-FTD (all diseases)". Aβ42, total and phosphorylated Tau CSF-levels were classified dichotomously, and using the Erlangen Score algorithm. Multivariate logistic models tested the prognostic accuracy of FDG-PET-SPM and CSF dichotomous classifications. Accuracy of Erlangen score and Erlangen Score aided by FDG-PET SPM classification was evaluated. The multivariate logistic model identified FDG-PET "AD" SPM classification (Expβ = 19.35, 95% C.I. 4.8-77.8, p < 0.001) and CSF Aβ42 (Expβ = 6.5, 95% C.I. 1.64-25.43, p < 0.05) as the best predictors of conversion from MCI to AD dementia. The "FTD" SPM pattern significantly predicted conversion to FTD dementias at follow-up (Expβ = 14, 95% C.I. 3.1-63, p < 0.001). Overall, FDG-PET-SPM classification was the most accurate biomarker, able to correctly differentiate either the MCI subjects who converted to AD or FTD dementias, and those who remained stable or reverted to normal cognition (Expβ = 17.9, 95% C.I. 4.55-70.46, p < 0.001). Our results support the relevant role of FDG-PET-SPM classification in predicting progression to different dementia conditions in prodromal MCI phase, and in the exclusion of progression, outperforming CSF biomarkers.

Potential implications of mine dusts on human health: A case study of Mukula Mine, Limpopo Province, South Africa

PubMed Central

Momoh, Abuh; E. Mhlongo, Sphiwe; Abiodun, Olukoga; Muzerengi, Confidence; Mudanalwo, Matamela

2013-01-01

Objective: The purpose of this study was to estimate the levels of Suspended Particulate Matter (SPM) in ambient air within Mukula mine and the potential risks to mineworkers and inhabitants of the adjoining Mukula community’s health. Methods : An SPM was used to measure the levels of particulate matter (PM10) in and around the mining site. One-way Analysis of Variance (ANOVA) was used to determine significance level of PM10 in ambient air. Results: Suspended particulate matter in the air ranged from 60.25 to 1820.45 µg/m3. The lowest value of SPM was more than four times the required World Health Organisation’s allowable level in ambient air, which the mine workers and locals would be inhaling. Conclusion: Continuous inhalation of mine dusts by mine workers and locals could result in pulmonary fibrosis, silicosis and lung cancer. The findings from this study support the need to have in place the necessary control measures that will drastically reduce SPM in the air. Such measure includes wet drilling and blasting, sprinkling of water on the mine roads and planting of vegetation around the mines and neighbouring communities. PMID:24550971

Potential implications of mine dusts on human health: A case study of Mukula Mine, Limpopo Province, South Africa.

PubMed

Momoh, Abuh; E Mhlongo, Sphiwe; Abiodun, Olukoga; Muzerengi, Confidence; Mudanalwo, Matamela

2013-11-01

Objective : The purpose of this study was to estimate the levels of Suspended Particulate Matter (SPM) in ambient air within Mukula mine and the potential risks to mineworkers and inhabitants of the adjoining Mukula community's health. Methods : An SPM was used to measure the levels of particulate matter (PM10) in and around the mining site. One-way Analysis of Variance (ANOVA) was used to determine significance level of PM10 in ambient air. Results : Suspended particulate matter in the air ranged from 60.25 to 1820.45 µg/m(3). The lowest value of SPM was more than four times the required World Health Organisation's allowable level in ambient air, which the mine workers and locals would be inhaling. Conclusion : Continuous inhalation of mine dusts by mine workers and locals could result in pulmonary fibrosis, silicosis and lung cancer. The findings from this study support the need to have in place the necessary control measures that will drastically reduce SPM in the air. Such measure includes wet drilling and blasting, sprinkling of water on the mine roads and planting of vegetation around the mines and neighbouring communities.

Three-dimensional nanoscale imaging by plasmonic Brownian microscopy

NASA Astrophysics Data System (ADS)

Labno, Anna; Gladden, Christopher; Kim, Jeongmin; Lu, Dylan; Yin, Xiaobo; Wang, Yuan; Liu, Zhaowei; Zhang, Xiang

2017-12-01

Three-dimensional (3D) imaging at the nanoscale is a key to understanding of nanomaterials and complex systems. While scanning probe microscopy (SPM) has been the workhorse of nanoscale metrology, its slow scanning speed by a single probe tip can limit the application of SPM to wide-field imaging of 3D complex nanostructures. Both electron microscopy and optical tomography allow 3D imaging, but are limited to the use in vacuum environment due to electron scattering and to optical resolution in micron scales, respectively. Here we demonstrate plasmonic Brownian microscopy (PBM) as a way to improve the imaging speed of SPM. Unlike photonic force microscopy where a single trapped particle is used for a serial scanning, PBM utilizes a massive number of plasmonic nanoparticles (NPs) under Brownian diffusion in solution to scan in parallel around the unlabeled sample object. The motion of NPs under an evanescent field is three-dimensionally localized to reconstruct the super-resolution topology of 3D dielectric objects. Our method allows high throughput imaging of complex 3D structures over a large field of view, even with internal structures such as cavities that cannot be accessed by conventional mechanical tips in SPM.

Support of surgical process modeling by using adaptable software user interfaces

NASA Astrophysics Data System (ADS)

Neumuth, T.; Kaschek, B.; Czygan, M.; Goldstein, D.; Strauß, G.; Meixensberger, J.; Burgert, O.

2010-03-01

Surgical Process Modeling (SPM) is a powerful method for acquiring data about the evolution of surgical procedures. Surgical Process Models are used in a variety of use cases including evaluation studies, requirements analysis and procedure optimization, surgical education, and workflow management scheme design. This work proposes the use of adaptive, situation-aware user interfaces for observation support software for SPM. We developed a method to support the modeling of the observer by using an ontological knowledge base. This is used to drive the graphical user interface for the observer to restrict the search space of terminology depending on the current situation. In the evaluation study it is shown, that the workload of the observer was decreased significantly by using adaptive user interfaces. 54 SPM observation protocols were analyzed by using the NASA Task Load Index and it was shown that the use of the adaptive user interface disburdens the observer significantly in workload criteria effort, mental demand and temporal demand, helping him to concentrate on his essential task of modeling the Surgical Process.

The application of surgical procedure manager (SPM): first experience with FESS.

PubMed

Feige, Katharina; Gollnick, Iris; Schmitz, Pia; Strauss, Gero

2017-09-01

In our hypothesis, the newly developed program SPM (surgical procedure manager) will ensure successful standardization and efficiency of the FESS (functional endoscopic sinus surgery) and therefore make a decisive contribution in terms of economization and improvement of intraoperative quality. Between 27th March 2015 and 8th October 2015, data from 259 FESS procedures were collected using the SPM. The study took place at the surgical desk, an operating room in the ACQUA clinic in Leipzig, Germany. 233 FESS (90%) of the total FESS (n = 259, 100%) were conducted entirely with SPM. 26 SPM terminations (10%) of 259 FESS remain, which are classified as actual SPM terminations-when the surgeon intentionally stops the SPM. The maximum time slot decreased clearly from 1 h 39 min (period A) to 1 h 10 min (period B). A time reduction can also be seen with the minimum duration of 13.5 min compared to 11 min. The variability of the time slot also decreases since the standard deviation is reduced by 4.5 min. On the basis of available recordings it can be postulated that the application of SPM is suitable for standardization for FESS. Standardization by means of SPM and minimal development can be recognized over a period of time. The SPM makes it possible to transfer the general advantages of mechanization on a concrete FESS and do not influence the medical processes nor even restrict the medical freedom. The users are still entirely free in the implementation of the respective procedure.

Radioprotection of Human Cell Nuclear DNA by Polyamines: Radiosensitivity of Chromatin is Influenced by Tightly Bound Spermine

NASA Technical Reports Server (NTRS)

Warters, Raymond L.; Newton, Gerald L.; Olive, Peggy L.; Fahey, Robert C.

1999-01-01

The polyamines putrescine (PUT) and spermine (SPM) were examined for their ability to protect human cell Deoxyribonucleic Acid (DNA) against the formation of radiation-induced double-strand breaks (DSBs). As observed previously, under conditions where polyamines were shown to be almost completely absent, association with nuclear matrix protein into a nucleoid, and organization into chromatin structure, protected DNA from induction of DSBs by factors of 4.5 and 95, respectively. At concentrations below 1 mM, PUT or SPM provided equivalent levels of protection to deproteinized nuclear DNA, consistent with their capacity to scavenge radiation-induced radicals. At constant ionic strength, 5 mM SPM protected deproteinized DNA and nucleoid DNA and DNA in nuclear chromatin by factors of 100 and 26, respectively. At 5 mM, SPM provided 15 times greater protection of deproteinized DNA than did PUT. Under physiologically relevant conditions, 5 mM SPM protected DNA in the intact nucleus from the induction of DSBs by a factor of 2 relative to DNA in the absence of SPM. Studies of SPM binding during cellular fractionation revealed that a significant fraction of the cellular SPM is tightly bound in the nucleus but can be removed by extended washing. Thus the association of SPM with nuclear chromatin appears to be a significant contributor to the resistance of the cell's DNA to the induction of DSBs.

Solid Propellant Microthruster Design, Fabrication, and Testing for Nanosatellites

NASA Astrophysics Data System (ADS)

Sathiyanathan, Kartheephan

This thesis describes the design, fabrication, and testing of a solid propellant microthruster (SPM), which is a two-dimensional matrix of millimeter-sized rockets each capable of delivering millinewtons of thrust and millinewton-seconds of impulse to perform fine orbit and attitude corrections. The SPM is a potential payload for nanosatellites to increase spacecraft maneuverability and is constrained by strict mass, volume, and power requirements. The dimensions of the SPM in the millimeter-scale result in a number of scaling issues that need consideration such as a low Reynolds number, high heat loss, thermal and radical quenching, and incomplete combustion. The design of the SPM, engineered to address these issues, is outlined. The SPM fabrication using low-cost commercial off-the-shelf materials and standard micromachining is presented. The selection of a suitable propellant and its customization are described. Experimental results of SPM firing to demonstrate successful ignition and sustained combustion are presented for three configurations: nozzleless, sonic nozzle, and supersonic nozzle. The SPM is tested using a ballistic pendulum thrust stand. Impulse and thrust values are calculated and presented. The performance values of the SPM are found to be consistent with existing designs.

A novel design of a scanning probe microscope integrated with an ultramicrotome for serial block-face nanotomography

NASA Astrophysics Data System (ADS)

Efimov, Anton E.; Agapov, Igor I.; Agapova, Olga I.; Oleinikov, Vladimir A.; Mezin, Alexey V.; Molinari, Michael; Nabiev, Igor; Mochalov, Konstantin E.

2017-02-01

We present a new concept of a combined scanning probe microscope (SPM)/ultramicrotome apparatus. It enables "slice-and-view" scanning probe nanotomography measurements and 3D reconstruction of the bulk sample nanostructure from series of SPM images after consecutive ultrathin sections. The sample is fixed on a flat XYZ scanning piezostage mounted on the ultramicrotome arm. The SPM measuring head with a cantilever tip and a laser-photodiode tip detection system approaches the sample for SPM measurements of the block-face surface immediately after the ultramicrotome sectioning is performed. The SPM head is moved along guides that are also fixed on the ultramicrotome arm. Thereby, relative dysfunctional displacements of the tip, the sample, and the ultramicrotome knife are minimized. The design of the SPM head enables open frontal optical access to the sample block-face adapted for high-resolution optical lenses for correlative SPM/optical microscopy applications. The new system can be used in a wide range of applications for the study of 3D nanostructures of biological objects, biomaterials, polymer nanocomposites, and nanohybrid materials in various SPM and optical microscopy measuring modes.

High speed operation of permanent magnet machines

NASA Astrophysics Data System (ADS)

El-Refaie, Ayman M.

This work proposes methods to extend the high-speed operating capabilities of both the interior PM (IPM) and surface PM (SPM) machines. For interior PM machines, this research has developed and presented the first thorough analysis of how a new bi-state magnetic material can be usefully applied to the design of IPM machines. Key elements of this contribution include identifying how the unique properties of the bi-state magnetic material can be applied most effectively in the rotor design of an IPM machine by "unmagnetizing" the magnet cavity center posts rather than the outer bridges. The importance of elevated rotor speed in making the best use of the bi-state magnetic material while recognizing its limitations has been identified. For surface PM machines, this research has provided, for the first time, a clear explanation of how fractional-slot concentrated windings can be applied to SPM machines in order to achieve the necessary conditions for optimal flux weakening. A closed-form analytical procedure for analyzing SPM machines designed with concentrated windings has been developed. Guidelines for designing SPM machines using concentrated windings in order to achieve optimum flux weakening are provided. Analytical and numerical finite element analysis (FEA) results have provided promising evidence of the scalability of the concentrated winding technique with respect to the number of poles, machine aspect ratio, and output power rating. Useful comparisons between the predicted performance characteristics of SPM machines equipped with concentrated windings and both SPM and IPM machines designed with distributed windings are included. Analytical techniques have been used to evaluate the impact of the high pole number on various converter performance metrics. Both analytical techniques and FEA have been used for evaluating the eddy-current losses in the surface magnets due to the stator winding subharmonics. Techniques for reducing these losses have been investigated. A 6kW, 36slot/30pole prototype SPM machine has been designed and built. Experimental measurements have been used to verify the analytical and FEA results. These test results have demonstrated that wide constant-power speed range can be achieved. Other important machine features such as the near-sinusoidal back-emf, high efficiency, and low cogging torque have also been demonstrated.

Automated determination of polyamines by high-performance liquid chromatography with simple sample preparation.

PubMed

van Eijk, H M; Rooyakkers, D R; Deutz, N E

1996-04-12

Recently, a new fully endcapped reversed-phase packing material, Inertsil, was introduced, especially suitable for the determination of basic compounds. We used this packing material to separate ophthaldialdehyde (OPA) derivatives of amino acid derivatives completely from the OPA derivatives of spermine (SPM), spermidine (SPD), putrescine (PUT) and cadaverine (CAD). The obtained separation made the commonly used off-line extraction procedure redundant and thus an on-line sample clean-up was introduced. This enabled automation of the procedure resulting in a better reproducibility and a more efficient use of equipment. Furthermore, no studies are required to determine the extraction recovery. The present method has a cycle time of 30 min. A linear response for each polyamine was found up to 250 pmol, with an R2 ranging from 0.9981 (SPM) to 0.9998 (CAD). The limit of detection, calculated at a signal-to-noise ratio of 3, was 0.1 pmol, corresponding to a plasma concentration of 0.1 mumol/l. The coefficient of variation (C.V.) for the peak area was below 3% and for retention times below 0.5% (n = 15). In order to evaluate the applicability of the method, three different types of sample were chromatographed, e.g. urine (obtained from healthy human volunteers), pig plasma and sulfosalicylic acid homogenates of pig intestine biopsies. Tissue homogenates and urine-specimen could easily be quantitated, while plasma concentrations were just above the limit of detection, resulting in a plasma C.V. ranging from 4.8% (SPM) to 13.6% (SPD) and a tissue C.V. ranging from 2.1% (SPM) to 8.5% (CAD), The urinary C.V.s were not determined. In conclusion, the present method provides an easy way to measure polyamine concentrations for most applications.

Comparison and validation of the aerosol optical depth obtained with the Langley plot method in the UV-B from Brewer Ozone Spectrophotometer measurements

NASA Astrophysics Data System (ADS)

Cheymol, Anne; de Backer, Hugo; Josefsson, Weine; Stübi, René

2006-08-01

The Aerosol Optical Depths (AODs) retrieved from Brewer Ozone Spectrophotometer measurements with a method previously developed (Cheymol and De Backer, 2003) are now validated by comparisons between AODs from six Brewer spectrophotometers and two CSEM SPM2000 sunphotometers: two Brewer spectrophotometers 016 and 178 at Uccle in Belgium; one Brewer spectrophotometer 128 and one sunphotometer CSEM SPM2000 at Norrköping in Sweden; and three Brewer instruments 040, 072, 156 at Arosa and one CSEM SPM2000 sunphotometer at Davos in Switzerland. The comparison between AODs from Brewer spectrophotometer 128 at 320.1 nm and sunphotometer SPM2000 at 368 nm at Norrköping shows that the AODs obtained from the Brewer measurements with the Langley Plot Method (LPM) are very accurate if the neutral density filter spectral transmittances are well known: with the measured values of these filters, the correlation coefficient, the slope, and the intercept of the regression line are 0.98, 0.85 ± 0.004, and 0.02 ± 0.0014, respectively. The bias observed is mainly owing to the wavelength difference between the two instruments. The comparison between AODs from different Brewer spectrophotometers confirm that AODs will be in very good agreement if they are measured with several Brewer instruments at the same place: At Uccle, the correlation coefficient, slope, and intercept of the regression line are 0.98, 1.02 ± 0.003, and 0.06 ± 0.001, respectively; at Arosa, the comparisons between the AODs from three Brewer spectrophotometers 040, 072, and 156 give a correlation coefficient, a slope, and an intercept of the regression line above 0.94, 0.98 and below 0.04, respectively.

Isolation and genetic characterization of metallo-β-lactamase and carbapenamase producing strains of Acinetobacter baumannii from patients at Tehran hospitals

PubMed Central

Shahcheraghi, F; Abbasalipour, M; Feizabadi, MM; Ebrahimipour, GH; Akbari, N

2011-01-01

Background and Objective Carbapenems are therapeutic choice against infections caused by gram-negative bacilli including strains of Acinetobacter baumannii. Resistance to these antibiotics is mediated by efflux pumps, porins, PBPs and ß-lactamases. The aim of this study was to determine the possibility of existence of MBLs, OXAs and GES-1 betalactamase genes among clinical isolates of Acinetobacter collected from Tehran hospitals. Material and Methods Two hundred and three Acinetobacter isolates were collected from patient at Tehran hospitals. The isolates were identified using biochemical tests. The susceptibility to different antibiotics was evaluated by disk diffusion method and MICs of imipenem were determined using Micro broth dilution method (CLSI). PCR was performed for detection of bla VIM-2, bla SPM-1, bla IMP-2, bla GES-1, bla OXA-51, bla OXA-23 betalactamase genes. Clonal relatedness was estimated by PFGE with the restriction enzyme SmaI. Results and Conclusion Of 100 isolates of imipenem resistant Acinetobacter spp. collected from Tehran hospitals in 2009 and 2010, 6 isolates produced metallo-beta-lactamases and 94 isolates produced OXA-type carbapenemase. The bla SPM-1, bla GES-1, bla OXA-51, bla OXA-23 genes were detected by PCR among 6, 2, 94 and 84 isolates of A. baumannii, respectively. The MICs of isolates to imipenem were 8–128 µg/mL. PFGE analysis of 29 bla OXA-51 and bla OXA-23-positive A. baumannii isolates gave 6 different patterns. This is the first report of SPM-1 and GES-1 beta-lactamase producing A. baumannii. Production of the OXA-23, OXA-51, GES-1 and SPM-1 enzyme presents an emerging threat of carbapenem resistance among A. baumannii in Iran. PMID:22347585

Impact of latency time on survival for adolescents and young adults with a second primary malignancy.

PubMed

Goldfarb, Melanie; Rosenberg, Aaron S; Li, Qian; Keegan, Theresa H M

2018-03-15

The adverse impact of second primary malignancies (SPMs) on survival is substantial for adolescents and young adults (AYAs; ie, those 15-39 years old). No studies have evaluated whether the latency time between the first malignancy (the primary malignancy [PM]) and the SPM affects cancer-specific survival (CSS). A multivariate Cox proportional hazards regression with Surveillance, Epidemiology, and End Results data for 13 regions from 1992 to 2008 was used to ascertain whether the latency time (1-5 vs ≥ 6 years) to the development of an SPM affected the CSS and overall survival with respect to either the PM or SPM for AYAs with common SPMs. The majority of 1515 AYAs with an SPM had their PM diagnosed between the ages of 26 and 39 years (74.2%) and an SPM diagnosed within 1 to 5 years (72.9%) of the PM's diagnosis. Overall, AYAs that developed an SPM 1 to 5 years after the diagnosis (vs ≥ 6 years) had an increased risk of death from cancer (hazard ratio [HR], 2.52; 95% confidence interval [CI], 1.92-3.29) as well as any cause (HR, 2.60; 95% CI, 2.04-3.32). Specifically, for AYAs with an SPM that was leukemia or a colorectal, breast, or central nervous system malignancy, a shorter latency time (1-5 years) from their PM diagnosis was associated with an overall significantly increased risk of death (2.6-fold) from either their PM or that particular SPM. However, latency did not appear to affect the CSS with respect to either the PM or SPM for AYA patients with a lymphoma or sarcoma SPM. Most AYAs who develop an SPM do so within 1 to 5 years of their primary cancer diagnosis, and they have an increased risk of death from cancer in comparison with AYAs with an SPM developing after longer survivorship intervals. Cancer 2018;124:1260-8. © 2017 American Cancer Society. © 2017 American Cancer Society.

Evaluating Several Hundred Predictors for Suspended Particulate Matter in the Northern Gulf of Mexico Using Inherent and Apparent Optical Properties & Considering Their Applicability for Use With Bathymetric Lidar Surveys

NASA Astrophysics Data System (ADS)

Epps, S. A.

2017-12-01

Suspended particulate matter (SPM) is an important agent in generating marine light conditions which in turn have strong influences on biogeochemical systems. SPM also behaves as a vehicle for contaminant migration and is of interest to the estimation of bulk material transport in the marine environment. The measurement of inherent optical properties (IOPs) and apparent optical properties (AOPs) is becoming increasingly important in the prediction of SPM concentration. To more fully utilize data generated in bathymetric lidar surveys, modern systems such as CZMIL (the Coastal Zone Mapping Imaging LIDAR) include a hyperspectral sensor to collect data necessary for remote sensing reflectance (Rrs), an AOP. Some IOPs can be estimated can be estimated from Rrs. Additionally, a bathymetric lidar return signal contains both absorption and backscattering components (IOPs) at 532 nm which may be utilized for SPM prediction. This research utilizes IOP measurements using AC-9, AC-S, BB-9, and LISST-100X-B sensors deployed in the Northern Gulf of Mexico concurrent with SPM collection via filtration. Concomitant Rrs values were collected using a hand held hyperspectral sensor. Several hundred linearly regressed single-parameter estimates are created to predict SPM concentration using the IOPs attenuation, total scatter, backscatter, absorption and significant amalgamations thereof. Multiple wavelengths of light are analyzed for each IOP or IOP combination. Consideration is given to the suitability of each IOP type to SPM concentration prediction. Several criteria are assessed to winnow out the best predictors. These include sensor, data, and environmental limitations. The quantitative analyses of this research assist to identify the best types of IOPs (and wavelengths) for SPM prediction. Rrs at multiple wavelengths is also considered for SPM prediction. This research is focused on the functionality of IOP and AOP based SPM concentration predictions made available from the data products of bathymetric lidar surveys. It has applications for researchers with interest in IOPs, AOPs and SPM. There are also implications for monitoring estuarine, coastal, and offshore environments using bathymetric lidar and in-situ optical sensor suites to estimate SPM.

Spermine alleviates drought stress in white clover with different resistance by influencing carbohydrate metabolism and dehydrins synthesis.

PubMed

Li, Zhou; Jing, Wen; Peng, Yan; Zhang, Xin Quan; Ma, Xiao; Huang, Lin Kai; Yan, Yan-Hong

2015-01-01

The objective of this research was to analyse whether ameliorating drought stress through exogenously applied spermine (Spm) was related to carbohydrate metabolism, dehydrins accumulation and the transcription of genes encoding dehydrins in two white clovers (drought-susceptible cv. 'Ladino' and drought-resistant cv. 'Haifa') under controlled drying conditions for 10 days. The results show that the application of Spm effectively alleviates negative effects caused by drought stress in both cultivars. Exogenous Spm led to accumulation of more water-soluble carbohydrates (WSC), sucrose, fructose and sorbitol in both cultivars under drought stress, and also significantly elevated glucose content in leaves of drought-resistant cv. 'Haifa', but had no effect on drought-susceptible cv. 'Ladino'. Accordingly, the key enzyme activities of sucrose and sorbitol metabolism changed along with the application of Spm under drought stress. Spm induced a significant increase in sucrose phosphate synthase (SPS) or sorbitol dehydrogenase (SDH) activity, but decrease in sucrose synthetase (SS) activity when two cultivars were subjected to drought. In addition, the improved accumulation of dehydrins induced by exogenous Spm coincided with three genes expression which was responsible for dehydrins synthesis. But Spm-induced transcript level of dehydrin genes increased earlier in cv. 'Ladino' than that in cv. 'Haifa'. Thus, these results suggest that ameliorating drought stress through exogenously applied Spm may be associated with increased carbohydrate accumulation and dehydrins synthesis. There are differences between drought-susceptible and -resistant white clover cultivars related to Spm regulation of WSC metabolism and dehydrins expression.

In-phase oscillation of global regulons is orchestrated by a pole-specific organizer

PubMed Central

Janakiraman, Balaganesh; Mignolet, Johann; Narayanan, Sharath; Viollier, Patrick H.

2016-01-01

Cell fate determination in the asymmetric bacterium Caulobacter crescentus (Caulobacter) is triggered by the localization of the developmental regulator SpmX to the old (stalked) cell pole during the G1→S transition. Although SpmX is required to localize and activate the cell fate-determining kinase DivJ at the stalked pole in Caulobacter, in cousins such as Asticcacaulis, SpmX directs organelle (stalk) positioning and possibly other functions. We define the conserved σ54-dependent transcriptional activator TacA as a global regulator in Caulobacter whose activation by phosphorylation is indirectly down-regulated by SpmX. Using a combination of forward genetics and cytological screening, we uncover a previously uncharacterized and polarized component (SpmY) of the TacA phosphorylation control system, and we show that SpmY function and localization are conserved. Thus, SpmX organizes a site-specific, ancestral, and multifunctional regulatory hub integrating the in-phase oscillation of two global transcriptional regulators, CtrA (the master cell cycle transcriptional regulator A) and TacA, that perform important cell cycle functions. PMID:27791133

DNA condensation by chiral alpha-methylated polyamine analogues and protection of cellular DNA from oxidative damage.

PubMed

Nayvelt, Irina; Hyvönen, Mervi T; Alhonen, Leena; Pandya, Ipsit; Thomas, Thresia; Khomutov, Alex R; Vepsäläinen, Jouko; Patel, Rajesh; Keinänen, Tuomo A; Thomas, T J

2010-01-11

Polyamines are essential molecules supporting the structure, conformation, and function of nucleic acids and proteins. We studied stereoisomers of alpha,alpha'-dimethylated spermine [(R,R)-Me(2)Spm, (S,S)-Me(2)Spm, (R,S)-Me(2)Spm] for their ability to provoke DNA condensation and protect DNA from damage. (R,R)- and (R,S)-Me(2)Spm displayed more efficient condensing ability than spermine, with significantly lower EC(50) (concentration for 50% compaction) values (p < or = 0.01). However, spermine exerted slightly more duplex stabilization than Me(2)Spm. Condensation resulted in nanoparticles with hydrodynamic radii between 39.6 and 48.4 nm, and electron microscopy showed the presence of toroids and spheroids. Natural polyamines and stereoisomers of Me(2)Spm protected DNA against DNase digestion and oxidative stress in vitro and against etoposide and oxidative stress in DU145 cells but afforded little protection against UV-C irradiation. Our findings indicate that Me(2)Spm stereoisomers are efficient DNA packaging agents with potential applications in gene delivery. Our study also reveals stereospecificity in DNA interaction and protection against cellular stress.

A Population-Based Study of Subsequent Primary Malignancies After Endometrial Cancer: Genetic, Environmental, and Treatment-Related Associations

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

Brown, Aaron P.; Neeley, E. Shannon; Werner, Theresa

2010-09-01

Purpose: To examine the risk of subsequent primary malignancies (SPMs) in women diagnosed with endometrial cancer. Methods and Materials: The National Cancer Institute's Survival, Epidemiology, and End Results database was used to determine the risk of SPM after endometrial cancer in 69,739 women diagnosed between 1973 and 2005. Standardized incidence ratios were calculated (observed/expected [O/E]) for SPM sites. Results: Median follow-up was 11.2 years, representing 757,567 person-years of follow-up. The risk of SPM was significantly increased for small intestine (O/E = 1.48; 99% confidence interval [CI], 1.03-2.05), colon (O/E = 1.16; CI, 1.09-1.24), vagina (O/E = 2.71; CI, 1.86-3.8), andmore » urinary bladder (O/E = 1.41; CI, 1.25-1.59) SPMs and decreased for oral cavity and pharynx (O/E = 0.75; CI, 0.6-0.93), lung and bronchus (O/E = 0.78; CI, 0.72-0.84), and esophagus (O/E = 0.58; CI, 0.37-0.86) SPMs. Patients receiving external-beam radiotherapy for endometrial cancer had an increased risk of colon (p < 0.001), bladder (p < 0.001), vagina (p = 0.04), and soft-tissue (p = 0.014) SPMs. Patients treated with brachytherapy had an increased risk of bladder SPM (p = 0.006). A positive bidirectional association with endometrial cancer was observed for colorectal cancer, with a negative bidirectional association for oropharyngeal and lung cancers. Conclusions: Genetic, environmental, and treatment-related factors influence SPM risk. Genetic factors may contribute to the increased risk of colorectal cancer. Smoking's negative effect on endometrial cancer risk factors might explain the decreased risk of lung and oropharyngeal cancer. Patients treated with radiotherapy likely have a small but significantly increased risk of bladder, vagina, colon, and soft-tissue SPM.« less

Evaluation of the Applicability of Solar and Lamp Radiometric Calibrations of a Precision Sun Photometer Operating Between 300 and 1025 nm

NASA Technical Reports Server (NTRS)

Schmid, Beat; Spyak, Paul R.; Biggar, Stuart F.; Joerg, Sekler; Ingold, Thomas; Maetzler, Christian; Kaempfer, Niklaus

2000-01-01

Over a period of 3 year a precision Sun photometer (SPM) operating between 300 and 1025 nm was calibrated four times at three different high-mountain sites in Switzerland, Germany, and the United States by means of the Langley-plot technique. We found that for atmospheric window wavelengths the total error (2 sigma-statistical plus systematic errors) of the calibration constants V(sub 0)(lambda), the SPM voltage in the absence of any attenuating atmosphere, can be kept below 1.60% in the UV-A and blue, 0.9% in the mid-visible, and 0.6% in the near-infra red spectral region. For SPM channels within strong water-vapor or ozone absorption bands a modified Langley-plot technique was used to determine V(sub 0)(lambda) with a lower accuracy. Within the same period of time, we calibrated the SPM five times using irradiance standard lamps in the optical labs of the Physikalisch-Meteorologisches Observatorium Davos and World Radiation Center, Switzerland, and of the Remote Sensing Group of the Optical Sciences Center, University of Arizona, Tucson, Arizona. The lab calibration method requires knowledge of the extraterrestrial spectral irradiance. When we refer the standard lamp results to the World Radiation Center extraterrestrial solar irradiance spectrum, they agree with the Langley results within 2% at 6 or 13 SPM wavelengths. The largest disagreement (4.4%) is found for the channel centered at 610 nm. The results of these intercomparisons change significantly when the lamp results are referred to two different extraterrestrial solar irradiance spectra that have become recently available.

Amine oxidase-based biosensors for spermine and spermidine determination.

PubMed

Boffi, Alberto; Favero, Gabriele; Federico, Rodolfo; Macone, Alberto; Antiochia, Riccarda; Tortolini, Cristina; Sanzó, Gabriella; Mazzei, Franco

2015-02-01

The present work describes the development and optimization of electrochemical biosensors for specific determination of the biogenic polyamine spermine (Spm) and spermidine (Spmd) whose assessment represents a novel important analytical tool in food analysis and human diagnostics. These biosensors have been prepared using novel engineered enzymes: polyamine oxidase (PAO) endowed with selectivity towards Spm and Spmd and spermine oxidase (SMO) characterized by strict specificity towards Spm. The current design entails biosensors in which the enzymes were entrapped in poly(vinyl alcohol) bearing styrylpyridinium groups (PVA-SbQ), a photocrosslinkable gel, onto an electrode surface. Screen-printed electrodes (SPEs) were used as electrochemical transducers for enzymatically produced hydrogen peroxide, operating at different potential vs Ag/AgCl according to the material of the working electrode (WE): +700 mV for graphite (GP) or -100 mV for Prussian blue (PB)-modified SPE, respectively. Biosensor performances were evaluated by means of flow injection amperometric (FIA) measurements. The modified electrodes showed good sensitivity, long-term stability and reproducibility. Under optimal conditions, the PAO biosensor showed a linear range 0.003-0.3 mM for Spm and 0.01-0.4 mM for Spmd, while with the SMO biosensor, a linear range of 0.004-0.5 mM for Spm has been obtained. The main kinetic parameters apparent Michaelis constant (K M), turnover number (K cat) and steady-state current (I max) were determined. The proposed device was then applied to the determination of biogenic amines in blood samples. The results obtained were in good agreement with those obtained with the GC-MS reference method.

Superparamagnetic nano-immunobeads toward food safety insurance

NASA Astrophysics Data System (ADS)

Liu, Xuefeng; Zhang, Lei; Zeng, Jing; Gao, Yan; Tang, Zhiyong

2013-07-01

In this work, superparamagnetic nano-immunobeads (SPM-NIBs) based on conjugation of superparamagnetic Fe3O4 nanoparticles with specific antibodies have been developed toward food safety insurance. The resultant SPM-NIBs exhibits excellent colloidal stability and reversible magnetic response. Vibrio parahaemolyticus, which is a main foodborne pathogenes from contaminated seafood, can be separated specifically and efficiently by the resultant SPM-NIBs. The results of bacteria separation demonstrate that the SPM-NIBs have a higher specific activity and sensitivity toward V. parahaemolyticus. About 80 % of V. parahaemolyticus cells can be captured when the concentration of the broth reaches 103 CFU/mL. Thus, the SPM-NIBs can effectively enhance the efficiency for target bacteria inspections by shortening the period of culture time. This work holds the promise of development of general technique to prepare effective SPM-NIBs toward food safety inspections and other bio-related applications for target analyte separation and collection.

Study of the properties of new SPM detectors

NASA Astrophysics Data System (ADS)

Stewart, A. G.; Greene-O'Sullivan, E.; Herbert, D. J.; Saveliev, V.; Quinlan, F.; Wall, L.; Hughes, P. J.; Mathewson, A.; Jackson, J. C.

2006-02-01

The operation and performance of multi-pixel, Geiger-mode APD structures referred to as Silicon Photomultiplier (SPM) are reported. The SPM is a solid state device that has emerged over the last decade as a promising alternative to vacuum PMTs. This is due to their comparable performance in addition to their lower bias operation and power consumption, insensitivity to magnetic fields and ambient light, smaller size and ruggedness. Applications for these detectors are numerous and include life sciences, nuclear medicine, particle physics, microscopy and general instrumentation. With SPM devices, many geometrical and device parameters can be adjusted to optimize their performance for a particular application. In this paper, Monte Carlo simulations and experimental results for 1mm2 SPM structures are reported. In addition, trade-offs involved in optimizing the SPM in terms of the number and size of pixels for a given light intensity, and its affect on the dynamic range are discussed.

Exogenous polyamines elicit herbivore-induced volatiles in lima bean leaves: involvement of calcium, H2O2 and Jasmonic acid.

PubMed

Ozawa, Rika; Bertea, Cinzia M; Foti, Maria; Narayana, Ravishankar; Arimura, Gen-Ichiro; Muroi, Atsushi; Horiuchi, Jun-Ichiro; Nishioka, Takaaki; Maffei, Massimo E; Takabayashi, Junji

2009-12-01

We investigated the role of polyamines (PAs) in lima bean (Phaseolus lunatus) leaves on the production of herbivorous mite (Tetranychus urticae)-induced plant volatiles that attract carnivorous natural enemies of the herbivores. To do this, we focused on the effects of the exogenous PAs [cadaverine, putrescine, spermidine and spermine (Spm)] on the production of volatiles, H(2)O(2) and jasmonic acid (JA) and the levels of defensive genes, cytosolic calcium and reactive oxygen species (ROS). Among the tested PAs, Spm was the most active in inducing the production of volatile terpenoids known to be induced by T. urticae. An increase in JA levels was also found after Spm treatment, indicating that Spm induces the biosynthesis of JA, which has been shown elsewhere to regulate the production of some volatile terpenoids. Further, treatment with JA and Spm together resulted in greater volatile emission than that with JA alone. In a Y-tube olfactometer, leaves treated with Spm + JA attracted more predatory mites (Phytoseiulus persimilis) than those treated with JA alone. After treatment with Spm + JA, no effects were found on the enzyme activity of polyamine oxidase and copper amine oxidase. However, induction of calcium influx and ROS production, and increased enzyme activities and gene expression for NADPH oxidase complex, superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase and glutathione peroxidase were found after treatment with Spm + JA. These results indicate that Spm plays an important role in the production of T. urticae-induced lima bean leaf volatiles.

Spermine Alleviates Drought Stress in White Clover with Different Resistance by Influencing Carbohydrate Metabolism and Dehydrins Synthesis

PubMed Central

Li, Zhou; Jing, Wen; Peng, Yan; Zhang, Xin Quan; Ma, Xiao; Huang, Lin Kai; Yan, Yan-hong

2015-01-01

The objective of this research was to analyse whether ameliorating drought stress through exogenously applied spermine (Spm) was related to carbohydrate metabolism, dehydrins accumulation and the transcription of genes encoding dehydrins in two white clovers (drought-susceptible cv. ‘Ladino’ and drought-resistant cv. ‘Haifa’) under controlled drying conditions for 10 days. The results show that the application of Spm effectively alleviates negative effects caused by drought stress in both cultivars. Exogenous Spm led to accumulation of more water-soluble carbohydrates (WSC), sucrose, fructose and sorbitol in both cultivars under drought stress, and also significantly elevated glucose content in leaves of drought-resistant cv. ‘Haifa’, but had no effect on drought-susceptible cv. ‘Ladino’. Accordingly, the key enzyme activities of sucrose and sorbitol metabolism changed along with the application of Spm under drought stress. Spm induced a significant increase in sucrose phosphate synthase (SPS) or sorbitol dehydrogenase (SDH) activity, but decrease in sucrose synthetase (SS) activity when two cultivars were subjected to drought. In addition, the improved accumulation of dehydrins induced by exogenous Spm coincided with three genes expression which was responsible for dehydrins synthesis. But Spm-induced transcript level of dehydrin genes increased earlier in cv. ‘Ladino’ than that in cv. ‘Haifa’. Thus, these results suggest that ameliorating drought stress through exogenously applied Spm may be associated with increased carbohydrate accumulation and dehydrins synthesis. There are differences between drought-susceptible and -resistant white clover cultivars related to Spm regulation of WSC metabolism and dehydrins expression. PMID:25835290

40 CFR 58.10 - Annual monitoring network plan and periodic network assessment.

Code of Federal Regulations, 2012 CFR

2012-07-01

... part of SLAMS, NCore stations, STN stations, State speciation stations, SPM stations, and/or, in... analysis method(s) for each measured parameter. (4) The operating schedules for each monitor. (5) Any...

40 CFR 58.10 - Annual monitoring network plan and periodic network assessment.

Code of Federal Regulations, 2013 CFR

2013-07-01

... part of SLAMS, NCore stations, STN stations, State speciation stations, SPM stations, and/or, in... and analysis method(s) for each measured parameter. (4) The operating schedules for each monitor. (5...

40 CFR 58.10 - Annual monitoring network plan and periodic network assessment.

Code of Federal Regulations, 2014 CFR

2014-07-01

... part of SLAMS, NCore stations, STN stations, State speciation stations, SPM stations, and/or, in... and analysis method(s) for each measured parameter. (4) The operating schedules for each monitor. (5...

Extending Inferential Group Analysis in Type 2 Diabetic Patients with Multivariate GLM Implemented in SPM8.

PubMed

Ferreira, Fábio S; Pereira, João M S; Duarte, João V; Castelo-Branco, Miguel

2017-01-01

Although voxel based morphometry studies are still the standard for analyzing brain structure, their dependence on massive univariate inferential methods is a limiting factor. A better understanding of brain pathologies can be achieved by applying inferential multivariate methods, which allow the study of multiple dependent variables, e.g. different imaging modalities of the same subject. Given the widespread use of SPM software in the brain imaging community, the main aim of this work is the implementation of massive multivariate inferential analysis as a toolbox in this software package. applied to the use of T1 and T2 structural data from diabetic patients and controls. This implementation was compared with the traditional ANCOVA in SPM and a similar multivariate GLM toolbox (MRM). We implemented the new toolbox and tested it by investigating brain alterations on a cohort of twenty-eight type 2 diabetes patients and twenty-six matched healthy controls, using information from both T1 and T2 weighted structural MRI scans, both separately - using standard univariate VBM - and simultaneously, with multivariate analyses. Univariate VBM replicated predominantly bilateral changes in basal ganglia and insular regions in type 2 diabetes patients. On the other hand, multivariate analyses replicated key findings of univariate results, while also revealing the thalami as additional foci of pathology. While the presented algorithm must be further optimized, the proposed toolbox is the first implementation of multivariate statistics in SPM8 as a user-friendly toolbox, which shows great potential and is ready to be validated in other clinical cohorts and modalities.

Standardization in dimensional nanometrology: development of a calibration guideline for Scanning Probe Microscopy

NASA Astrophysics Data System (ADS)

Dziomba, Thorsten; Koenders, Ludger; Wilkening, Günter

2005-10-01

The continuing miniaturization in many technologies - among them the optical systems - demands high-resolution measurements with uncertainties in the nanometre-range or even well below. A brief introduction of measurement methods used at the micro- & nanometre scale is therefore given as introduction. While a wide range of these methods are well established for the determination of various physical properties down to the nanometric scale, it is Scanning Probe Microscopy (SPM) that provides a unique direct access to topographic surface features in the size range from atomic diameters to some ten or hundred micrometres. With the increasing use of SPMs as quantitative measurement instruments, the demand for standardized calibration routines also for this type of instruments rises. However, except for a few specially designed set-ups mainly at National Metrology Institutes (e. g. PTB in Germany), measurements made with SPMs usually lack traceability to the metre definition. A number of physical transfer standards have therefore been developed and are already available commercially. While detailed knowledge of the standards' properties is a prerequisite for their practical applicability, the calibration procedure itself deserves careful consideration as well. As there is, up to now, no generally accepted concept how to perform SPM calibrations, guidelines are now being developed on various national and international levels, e. g. VDI/VDE-GMA in Germany and ISO. This papers discusses the draft of an SPM calibration guideline by focusing on several critical practical aspects of SPM calibration. The paper intends to invite the readers to take active part in guideline discussions.

Evaluating Treatment and Generalization Patterns of Two Theoretically Motivated Sentence Comprehension Therapies

PubMed Central

Des Roches, Carrie A.; Vallila-Rohter, Sofia; Villard, Sarah; Tripodis, Yorghos; Caplan, David

2016-01-01

Purpose The current study examined treatment outcomes and generalization patterns following 2 sentence comprehension therapies: object manipulation (OM) and sentence-to-picture matching (SPM). Findings were interpreted within the framework of specific deficit and resource reduction accounts, which were extended in order to examine the nature of generalization following treatment of sentence comprehension deficits in aphasia. Method Forty-eight individuals with aphasia were enrolled in 1 of 8 potential treatment assignments that varied by task (OM, SPM), complexity of trained sentences (complex, simple), and syntactic movement (noun phrase, wh-movement). Comprehension of trained and untrained sentences was probed before and after treatment using stimuli that differed from the treatment stimuli. Results Linear mixed-model analyses demonstrated that, although both OM and SPM treatments were effective, OM resulted in greater improvement than SPM. Analyses of covariance revealed main effects of complexity in generalization; generalization from complex to simple linguistically related sentences was observed both across task and across movement. Conclusions Results are consistent with the complexity account of treatment efficacy, as generalization effects were consistently observed from complex to simpler structures. Furthermore, results provide support for resource reduction accounts that suggest that generalization can extend across linguistic boundaries, such as across movement type. PMID:27997950

Decreasing trends of suspended particulate matter and PM2.5 concentrations in Tokyo, 1990-2010.

PubMed

Hara, Kunio; Homma, Junichi; Tamura, Kenji; Inoue, Mariko; Karita, Kanae; Yano, Eiji

2013-06-01

In Tokyo, the annual average suspended particulate matter (SPM) and PM2.5 concentrations have decreased in the past two decades. The present study quantitatively evaluated these decreasing trends using data from air-pollution monitoring stations. Annual SPM and PM2.5 levels at 83 monitoring stations and hourly SPM and PM2.5 levels at four monitoring stations in Tokyo, operated by the Tokyo Metropolitan Government, were used for analysis, together with levels of co-pollutants and meteorological conditions. Traffic volume in Tokyo was calculated from the total traveling distance of vehicles as reported by the Ministry of Land, Infrastructure, Transport, and Tourism. High positive correlations between SPM levels and nitrogen oxide levels, sulfur dioxide levels, and traffic volume were determined. The annual average SPM concentration declined by 62.6%from 59.4 microg/m3 in 1994 to 22.2 microg/m3 in 2010, and PM2.5 concentration also declined by 49.8% from 29.3 microg/m3 in 2001 to 14.7 microg/m3 in 2010. Likewise, the frequencies of hourly average SPM and PM2.5 concentrations exceeding the daily guideline values have significantly decreased since 2001 and the hourly average SPM or PM2.5 concentrations per traffic volume for each time period have also significantly decreased since 2001. However SPM and PM2.5 concentrations increased at some monitoring stations between 2004 and 2006 and from 2009 despite strengthened environmental regulations and improvements in vehicle engine performance. The annual average SPM and PM2.5 concentrations were positively correlated with traffic volumes and in particular with the volume of diesel trucks. These results suggest that the decreasing levels of SPM and PM2.5 in Tokyo may be attributable to decreased traffic volumes, along with the effects of stricter governmental regulation and improvements to vehicle engine performance, including the fitting of devices for exhaust emission reduction.

Mechanisms controlling the intra-annual mesoscale variability of SST and SPM in the southern North Sea

NASA Astrophysics Data System (ADS)

Pietrzak, Julie D.; de Boer, Gerben J.; Eleveld, Marieke A.

2011-04-01

Thermal and optical remote sensing data were used to investigate the spatial and temporal distribution of sea surface temperature (SST) and of suspended particulate matter (SPM) in the southern North Sea. Monthly SST composites showed pronounced seasonal warming of the southern North Sea and delineated the English coastal and continental coastal waters. The East-Anglia Plume is the dominant feature of the English coastal waters in the winter and autumn SPM composites, and the Rhine region of freshwater influence (ROFI), including the Flemish Banks, is the dominant feature of the continental waters. These mesoscale spatial structures are also influenced by the evolution of fronts, such as the seasonal front separating well-mixed water in the southern Bight, from the seasonally stratified central North Sea waters. A harmonic analysis of the SST and SPM images showed pronounced seasonal variability, as well as spring-neap variations in the level of tidal mixing in the East Anglia Plume, the Rhine ROFI and central North Sea. The harmonic analysis indicates the important role played by the local meteorology and tides in governing the SST and near-surface SPM concentrations in the southern North Sea. In the summer, thermal stratification affects the visibility of SPM to satellite sensors in the waters to the north of the Flamborough and Frisian Fronts. Haline stratification plays an important role in the visibility of SPM in the Rhine ROFI throughout the year. When stratified, both regions typically exhibit low surface SPM values. A numerical model study, together with the harmonic analysis, highlights the importance of tides and waves in controlling the stratification in the southern North Sea and hence the visibility of SPM.

Synthesis and electroplating of high resolution insulated carbon nanotube scanning probes for imaging in liquid solutions

PubMed Central

Roberts, N.A.; Noh, J.H.; Lassiter, M.G.; Guo, S.; Kalinin, S.V.; Rack, P.D.

2012-01-01

High resolution and isolated scanning probe microscopy (SPM) is in demand for continued development of energy storage and conversion systems involving chemical reactions at the nanoscale as well as an improved understanding of biological systems. Carbon nanotubes (CNTs) have large aspect ratios and, if leveraged properly, can be used to develop high resolution SPM probes. Isolation of SPM probes can be achieved by deposited a dielectric film and selectively etching at the apex of the probe. In this paper the fabrication of a high resolution and isolated SPM tip is demonstrated using electron beam induced etching of a dielectric film deposited onto an SPM tip with an attached CNT at the apex. PMID:22433664

Synthesis and electroplating of high resolution insulated carbon nanotube scanning probes for imaging in liquid solutions.

PubMed

Roberts, N A; Noh, J H; Lassiter, M G; Guo, S; Kalinin, S V; Rack, P D

2012-04-13

High resolution and isolated scanning probe microscopy (SPM) is in demand for continued development of energy storage and conversion systems involving chemical reactions at the nanoscale as well as an improved understanding of biological systems. Carbon nanotubes (CNTs) have large aspect ratios and, if leveraged properly, can be used to develop high resolution SPM probes. Isolation of SPM probes can be achieved by depositing a dielectric film and selectively etching at the apex of the probe. In this paper the fabrication of a high resolution and isolated SPM tip is demonstrated using electron beam induced etching of a dielectric film deposited onto an SPM tip with an attached CNT at the apex.

Functional recognition imaging using artificial neural networks: applications to rapid cellular identification via broadband electromechanical response

NASA Astrophysics Data System (ADS)

Nikiforov, M. P.; Reukov, V. V.; Thompson, G. L.; Vertegel, A. A.; Guo, S.; Kalinin, S. V.; Jesse, S.

2009-10-01

Functional recognition imaging in scanning probe microscopy (SPM) using artificial neural network identification is demonstrated. This approach utilizes statistical analysis of complex SPM responses at a single spatial location to identify the target behavior, which is reminiscent of associative thinking in the human brain, obviating the need for analytical models. We demonstrate, as an example of recognition imaging, rapid identification of cellular organisms using the difference in electromechanical activity over a broad frequency range. Single-pixel identification of model Micrococcus lysodeikticus and Pseudomonas fluorescens bacteria is achieved, demonstrating the viability of the method.

The Genome of S-PM2, a “Photosynthetic” T4-Type Bacteriophage That Infects Marine Synechococcus Strains

PubMed Central

Mann, Nicholas H.; Clokie, Martha R. J.; Millard, Andrew; Cook, Annabel; Wilson, William H.; Wheatley, Peter J.; Letarov, Andrey; Krisch, H. M.

2005-01-01

Bacteriophage S-PM2 infects several strains of the abundant and ecologically important marine cyanobacterium Synechococcus. A large lytic phage with an isometric icosahedral head, S-PM2 has a contractile tail and by this criterion is classified as a myovirus (1). The linear, circularly permuted, 196,280-bp double-stranded DNA genome of S-PM2 contains 37.8% G+C residues. It encodes 239 open reading frames (ORFs) and 25 tRNAs. Of these ORFs, 19 appear to encode proteins associated with the cell envelope, including a putative S-layer-associated protein. Twenty additional S-PM2 ORFs have homologues in the genomes of their cyanobacterial hosts. There is a group I self-splicing intron within the gene encoding the D1 protein. A total of 40 ORFs, organized into discrete clusters, encode homologues of T4 proteins involved in virion morphogenesis, nucleotide metabolism, gene regulation, and DNA replication and repair. The S-PM2 genome encodes a few surprisingly large (e.g., 3,779 amino acids) ORFs of unknown function. Our analysis of the S-PM2 genome suggests that many of the unknown S-PM2 functions may be involved in the adaptation of the metabolism of the host cell to the requirements of phage infection. This hypothesis originates from the identification of multiple phage-mediated modifications of the host's photosynthetic apparatus that appear to be essential for maintaining energy production during the lytic cycle. PMID:15838046

EDITORIAL: Probing the nanoworld Probing the nanoworld

NASA Astrophysics Data System (ADS)

Miles, Mervyn

2009-10-01

In nanotechnology, it is the unique properties arising from nanometre-scale structures that lead not only to their technological importance but also to a better understanding of the underlying science. Over the last twenty years, material properties at the nanoscale have been dominated by the properties of carbon in the form of the C60 molecule, single- and multi-wall carbon nanotubes, nanodiamonds, and recently graphene. During this period, research published in the journal Nanotechnology has revealed the amazing mechanical properties of such materials as well as their remarkable electronic properties with the promise of new devices. Furthermore, nanoparticles, nanotubes, nanorods, and nanowires from metals and dielectrics have been characterized for their electronic, mechanical, optical, chemical and catalytic properties. Scanning probe microscopy (SPM) has become the main characterization technique and atomic force microscopy (AFM) the most frequently used SPM. Over the past twenty years, SPM techniques that were previously experimental in nature have become routine. At the same time, investigations using AFM continue to yield impressive results that demonstrate the great potential of this powerful imaging tool, particularly in close to physiological conditions. In this special issue a collaboration of researchers in Europe report the use of AFM to provide high-resolution topographical images of individual carbon nanotubes immobilized on various biological membranes, including a nuclear membrane for the first time (Lamprecht C et al 2009 Nanotechnology 20 434001). Other SPM developments such as high-speed AFM appear to be making a transition from specialist laboratories to the mainstream, and perhaps the same may be said for non-contact AFM. Looking to the future, characterisation techniques involving SPM and spectroscopy, such as tip-enhanced Raman spectroscopy, could emerge as everyday methods. In all these advanced techniques, routinely available probes will be needed to make them mainstream methods, as was indeed the case for establishing AFM. At the same time, both transmission electron microscopy and scanning electron microscopy have undergone major developments in resolution, spectroscopic techniques, and new techniques such as tomography. It is exciting to speculate in which areas new properties of materials at the nanoscale will be discovered over the next twenty years, and how characterization methods will evolve, but it is the unimaginable and unpredictable that will bring the most dramatic changes to nanotechnology.

33 CFR 150.445 - When is oil in a single point mooring-oil transfer system (SPM-OTS) displaced with water?

Code of Federal Regulations, 2010 CFR

2010-07-01

... the pipeline end manifold must be closed whenever: (1) A storm warning forecasts weather conditions... vessel is about to depart the SPM because of storm conditions; or (3) The SPM is not scheduled for use in...

33 CFR 150.445 - When is oil in a single point mooring-oil transfer system (SPM-OTS) displaced with water?

Code of Federal Regulations, 2011 CFR

2011-07-01

... the pipeline end manifold must be closed whenever: (1) A storm warning forecasts weather conditions... vessel is about to depart the SPM because of storm conditions; or (3) The SPM is not scheduled for use in...

33 CFR 150.445 - When is oil in a single point mooring-oil transfer system (SPM-OTS) displaced with water?

Code of Federal Regulations, 2014 CFR

2014-07-01

... the pipeline end manifold must be closed whenever: (1) A storm warning forecasts weather conditions... vessel is about to depart the SPM because of storm conditions; or (3) The SPM is not scheduled for use in...

33 CFR 150.445 - When is oil in a single point mooring-oil transfer system (SPM-OTS) displaced with water?

Code of Federal Regulations, 2013 CFR

2013-07-01

... the pipeline end manifold must be closed whenever: (1) A storm warning forecasts weather conditions... vessel is about to depart the SPM because of storm conditions; or (3) The SPM is not scheduled for use in...

33 CFR 150.445 - When is oil in a single point mooring-oil transfer system (SPM-OTS) displaced with water?

Code of Federal Regulations, 2012 CFR

2012-07-01

... the pipeline end manifold must be closed whenever: (1) A storm warning forecasts weather conditions... vessel is about to depart the SPM because of storm conditions; or (3) The SPM is not scheduled for use in...

Control theory for scanning probe microscopy revisited.

PubMed

Stirling, Julian

2014-01-01

We derive a theoretical model for studying SPM feedback in the context of control theory. Previous models presented in the literature that apply standard models for proportional-integral-derivative controllers predict a highly unstable feedback environment. This model uses features specific to the SPM implementation of the proportional-integral controller to give realistic feedback behaviour. As such the stability of SPM feedback for a wide range of feedback gains can be understood. Further consideration of mechanical responses of the SPM system gives insight into the causes of exciting mechanical resonances of the scanner during feedback operation.

Comparison of remote sensing algorithms for retrieval of suspended particulate matter concentration from reflectance in coastal waters

NASA Astrophysics Data System (ADS)

Freeman, Lauren A.; Ackleson, Steven G.; Rhea, William Joseph

2017-10-01

Suspended particulate matter (SPM) is a key environmental indicator for rivers, estuaries, and coastal waters, which can be calculated from remote sensing reflectance obtained by an airborne or satellite imager. Here, algorithms from prior studies are applied to a dataset of in-situ at surface hyperspectral remote sensing reflectance, collected in three geographic regions representing different water types. These data show the optically inherent exponential nature of the relationship between reflectance and sediment concentration. However, linear models are also shown to provide a reasonable estimate of sediment concentration when utilized with care in similar conditions to those under which the algorithms were developed, particularly at lower SPM values (0 to 20 mg/L). Fifteen published SPM algorithms are tested, returning strong correlations of R2>0.7, and in most cases, R2>0.8. Very low SPM values show weaker correlation with algorithm calculated SPM that is not wavelength dependent. None of the tested algorithms performs well for high SPM values (>30 mg/L), with most algorithms underestimating SPM. A shift toward a smaller number of simple exponential or linear models relating satellite remote sensing reflectance to suspended sediment concentration with regional consideration will greatly aid larger spatiotemporal studies of suspended sediment trends.

Post traumatic brain perfusion SPECT analysis using reconstructed ROI maps of radioactive microsphere derived cerebral blood flow and statistical parametric mapping

PubMed Central

McGoron, Anthony J; Capille, Michael; Georgiou, Michael F; Sanchez, Pablo; Solano, Juan; Gonzalez-Brito, Manuel; Kuluz, John W

2008-01-01

Background Assessment of cerebral blood flow (CBF) by SPECT could be important in the management of patients with severe traumatic brain injury (TBI) because changes in regional CBF can affect outcome by promoting edema formation and intracranial pressure elevation (with cerebral hyperemia), or by causing secondary ischemic injury including post-traumatic stroke. The purpose of this study was to establish an improved method for evaluating regional CBF changes after TBI in piglets. Methods The focal effects of moderate traumatic brain injury (TBI) on cerebral blood flow (CBF) by SPECT cerebral blood perfusion (CBP) imaging in an animal model were investigated by parallelized statistical techniques. Regional CBF was measured by radioactive microspheres and by SPECT 2 hours after injury in sham-operated piglets versus those receiving severe TBI by fluid-percussion injury to the left parietal lobe. Qualitative SPECT CBP accuracy was assessed against reference radioactive microsphere regional CBF measurements by map reconstruction, registration and smoothing. Cerebral hypoperfusion in the test group was identified at the voxel level using statistical parametric mapping (SPM). Results A significant area of hypoperfusion (P < 0.01) was found as a response to the TBI. Statistical mapping of the reference microsphere CBF data confirms a focal decrease found with SPECT and SPM. Conclusion The suitability of SPM for application to the experimental model and ability to provide insight into CBF changes in response to traumatic injury was validated by the SPECT SPM result of a decrease in CBP at the left parietal region injury area of the test group. Further study and correlation of this characteristic lesion with long-term outcomes and auxiliary diagnostic modalities is critical to developing more effective critical care treatment guidelines and automated medical imaging processing techniques. PMID:18312639

Heavy metal partitioning of suspended particulate matter-water and sediment-water in the Yangtze Estuary.

PubMed

Feng, Chenghong; Guo, Xiaoyu; Yin, Su; Tian, Chenhao; Li, Yangyang; Shen, Zhenyao

2017-10-01

The partitioning of ten heavy metals (As, Cd, Co, Cr, Cu, Hg, Ni, Pb, Sb, and Zn) between the water, suspended particulate matter (SPM), and sediments in seven channel sections during three hydrologic seasons in the Yangtze Estuary was comprehensively investigated. Special attention was paid to the role of tides, influential factors (concentrations of SPM and dissolved organic carbon, and particle size), and heavy metal speciation. The SPM-water and sediment-water partition coefficients (K p ) of the heavy metals exhibited similar changes along the channel sections, though the former were larger throughout the estuary. Because of the higher salinity, the K p values of most of the metals were higher in the north branch than in the south branch. The K p values of Cd, Co, and As generally decreased from the wet season to the dry season. Both the diagonal line method and paired samples t-test showed that no specific phase transfer of heavy metals existed during the flood and ebb tides, but the sediment-water K p was more concentrated for the diagonal line method, owing to the relatively smaller tidal influences on the sediment. The partition coefficients (especially the K p for SPM-water) had negative correlations with the dissolved organic carbon (DOC) but positive correlations were noted with the particle size for most of the heavy metals in sediment. Two types of significant correlations were observed between K p and metal speciation (i.e., exchangeable, carbonate, reducible, organic, and residual fractions), which can be used to identify the dominant phase-partition mechanisms (e.g., adsorption or desorption) of heavy metals. Copyright © 2017 Elsevier Ltd. All rights reserved.

Optical Characterisation of Suspended Particles in the Mackenzie River Plume (Canadian Arctic Ocean) and Implications for Ocean Colour Remote Sensing

NASA Technical Reports Server (NTRS)

Doxaran, D.; Ehn, J.; Belanger, S.; Matsuoka, A.; Hooker, S.; Babin, M.

2012-01-01

Climate change significantly impacts Arctic shelf regions in terms of air temperature, ultraviolet radiation, melting of sea ice, precipitation, thawing of permafrost and coastal erosion. Direct consequences have been observed on the increasing Arctic river flow and a large amount of organic carbon sequestered in soils at high latitudes since the last glacial maximum can be expected to be delivered to the Arctic Ocean during the coming decade. Monitoring the fluxes and fate of this terrigenous organic carbon is problematic in such sparsely populated regions unless remote sensing techniques can be developed and proved to be operational. The main objective of this study is to develop an ocean colour algorithm to operationally monitor dynamics of suspended particulate matter (SPM) on the Mackenzie River continental shelf (Canadian Arctic Ocean) using satellite imagery. The water optical properties are documented across the study area and related to concentrations of SPM and particulate organic carbon (POC). Robust SPM and POC : SPM proxies are identified, such as the light backscattering and attenuation coefficients, and relationships are established between these optical and biogeochemical parameters. Following a semi-analytical approach, a regional SPM quantification relationship is obtained for the inversion of the water reflectance signal into SPM concentration. This relationship is reproduced based on independent field optical measurements. It is successfully applied to a selection of MODIS satellite data which allow estimating fluxes at the river mouth and monitoring the extension and dynamics of the Mackenzie River surface plume in 2009, 2010 and 2011. Good agreement is obtained with field observations representative of the whole water column in the river delta zone where terrigenous SPM is mainly constrained (out of short periods of maximum river outflow). Most of the seaward export of SPM is observed to occur within the west side of the river mouth. Future work will require the validation of the developed SPM regional algorithm based on match-ups with field measurements, then the routine application to ocean colour satellite data in order to better estimate the fluxes and fate of SPM and POC delivered by the Mackenzie River to the Arctic Ocean.

A simple method of equine limb force vector analysis and its potential applications.

PubMed

Hobbs, Sarah Jane; Robinson, Mark A; Clayton, Hilary M

2018-01-01

Ground reaction forces (GRF) measured during equine gait analysis are typically evaluated by analyzing discrete values obtained from continuous force-time data for the vertical, longitudinal and transverse GRF components. This paper describes a simple, temporo-spatial method of displaying and analyzing sagittal plane GRF vectors. In addition, the application of statistical parametric mapping (SPM) is introduced to analyse differences between contra-lateral fore and hindlimb force-time curves throughout the stance phase. The overall aim of the study was to demonstrate alternative methods of evaluating functional (a)symmetry within horses. GRF and kinematic data were collected from 10 horses trotting over a series of four force plates (120 Hz). The kinematic data were used to determine clean hoof contacts. The stance phase of each hoof was determined using a 50 N threshold. Vertical and longitudinal GRF for each stance phase were plotted both as force-time curves and as force vector diagrams in which vectors originating at the centre of pressure on the force plate were drawn at intervals of 8.3 ms for the duration of stance. Visual evaluation was facilitated by overlay of the vector diagrams for different limbs. Summary vectors representing the magnitude (VecMag) and direction (VecAng) of the mean force over the entire stance phase were superimposed on the force vector diagram. Typical measurements extracted from the force-time curves (peak forces, impulses) were compared with VecMag and VecAng using partial correlation (controlling for speed). Paired samples t -tests (left v. right diagonal pair comparison and high v. low vertical force diagonal pair comparison) were performed on discrete and vector variables using traditional methods and Hotelling's T 2 tests on normalized stance phase data using SPM. Evidence from traditional statistical tests suggested that VecMag is more influenced by the vertical force and impulse, whereas VecAng is more influenced by the longitudinal force and impulse. When used to evaluate mean data from the group of ten sound horses, SPM did not identify differences between the left and right contralateral limb pairs or between limb pairs classified according to directional asymmetry. When evaluating a single horse, three periods were identified during which differences in the forces between the left and right forelimbs exceeded the critical threshold ( p  < .01). Traditional statistical analysis of 2D GRF peak values, summary vector variables and visual evaluation of force vector diagrams gave harmonious results and both methods identified the same inter-limb asymmetries. As alpha was more tightly controlled using SPM, significance was only found in the individual horse although T 2 plots followed the same trends as discrete analysis for the group. The techniques of force vector analysis and SPM hold promise for investigations of sidedness and asymmetry in horses.

Triple primary malignancies of surface osteosarcoma of jaw, myelodysplastic syndrome and colorectal cancer as a second primary cancer detected by PET2-[18F]-fluoro-2-deoxy-D-glucose positron emission tomography: A case report.

PubMed

Maruyama, Nobuyuki; Nishihara, Kazuhide; Nakasone, Toshiyuki; Saio, Masanao; Maruyama, Tessho; Tedokon, Iori; Ohira, Tetsuya; Nimura, Fumikazu; Matayoshi, Akira; Karube, Ken-Nosuke; Yoshimi, Naoki; Arasaki, Akira

2018-06-01

Second primary malignancy (SPM) is a severe issue for cancer survivors, particularly for osteosarcoma (OS) survivors. To date, the associations between subsequent SPM and OS have been well reported. Hematogenic and solid malignancies tend to occur following OS treatment. Reportedly, 2-[ 18 F]-fluoro-2-deoxy-D-glucose positron emission tomography (FDG-PET) is mainly used in OS patients for initial cancer staging, to evaluate the response of neoadjuvant chemotherapy, and when recurrence or metastasis is clinically suspected. The present case report describes a 70-year-old man diagnosed with three primary malignancies: jaw OS, myelodysplastic syndrome and colorectal adenocarcinoma. To the best of our knowledge, this combination of malignancies has not been reported previously. Until now, there is no specific protocol of postoperative FDG-PET for OS patients. Few studies have described OS follow-up methods; therefore, there is no consensus on proper follow-up methods. In the present case report, the colorectal early-stage SPM was observed, without any symptoms, by FDG-PET/computed tomography. To avoid overlooking solid SPMs, it is suggested that FDG-PET should be performed in the long-term follow-up of OS patients.

A review of oil-suspended particulate matter aggregation--a natural process of cleansing spilled oil in the aquatic environment.

PubMed

Sun, Juan; Zheng, Xilai

2009-10-01

It has been acknowledged that following an oil spill in coastal areas where suspended particulate matter (SPM) is rich, aggregation between oil and SPM can be naturally formed. This kind of aggregation product is termed as oil-SPM aggregates (OSAs). Because OSAs are not as sticky to the shorelines as crude oil and the oil-water contact area is greatly increased due to the formation of OSAs, both oil dispersion into the water body and oil biodegration would be significantly enhanced. In this review article, the authors (1) describe in detail the mechanism of OSA formation and controlling parameters which can influence OSA formation (the parameters discussed include the oil nature and properties, sediment types and concentrations, and the environmental factors such as salinity, temperature and mixing energy); (2) briefly review qualitative and quantitative methods used for characterization of OSA formation (two main methods used for the OSA characterization are the UV epi-fluorescence microscopy and gas chromatography equipped with flame ionization detector (GC-FID); (3) elucidate the applications of OSA formation in oil spill response strategies including natural attenuation, sediment relocation, and sediment mixing; and (4) discuss research needs in the future which would further improve our understanding of OSA formation and move towards the development of adequate oil behaviour models.

Availability of feature-oriented scanning probe microscopy for remote-controlled measurements on board a space laboratory or planet exploration Rover.

PubMed

Lapshin, Rostislav V

2009-06-01

Prospects for a feature-oriented scanning (FOS) approach to investigations of sample surfaces, at the micrometer and nanometer scales, with the use of scanning probe microscopy under space laboratory or planet exploration rover conditions, are examined. The problems discussed include decreasing sensitivity of the onboard scanning probe microscope (SPM) to temperature variations, providing autonomous operation, implementing the capabilities for remote control, self-checking, self-adjustment, and self-calibration. A number of topical problems of SPM measurements in outer space or on board a planet exploration rover may be solved via the application of recently proposed FOS methods.

Brillouin Light Scattering from Magnetic Excitations in Superparamagnetic and Ferromagnetic Co-Al-O Granular Films

NASA Astrophysics Data System (ADS)

Yoshihara, Akira; Maeda, Toshiteru; Kawamura, Satoshi; Nakamura, Shintaro; Nojima, Tsutomu; Takeda, Yoshihiko; Ohnuma, Shigehiro

2018-04-01

A systematic study of Brillouin light scattering (BLS) from superparamagnetic (SPM) and ferromagnetic (FM) Co-Al-O granular films was performed under magnetic fields of up to 4.6 kOe in the standard backscattering geometry at room temperature. The SPM and FM boundary, defined as the Co composition at which the exchange field vanishes, was found to be located at xC(Co) = 59.3 ± 1.3 at. %. From FM films we observed a pair of bulk spin-wave peaks on both the positive- and negative-frequency sides and a surface localized Damon-Eshbach peak only on the positive-frequency side under the present scattering conditions. From SPM films, a pair of broader but propagative excitation peaks with asymmetric intensity were observed on both frequency sides in a spectrum. We performed a numerical analysis of the BLS spectrum by employing the theory developed by Camley and Mills (CM) while retaining dipole and exchange couplings for FM films and only dipole coupling for SPM films. The CM theory successfully reproduced the observed spectrum for both SPM and FM films. The SPM spectrum exhibits a singlet-doublet peak structure similarly to an FM SW spectrum. The SPM peak stems from the dipole-coupled larger-amplitude precession motion of the granule magnetic moment around the external-field-induced magnetization.

Statistical process management: An essential element of quality improvement

NASA Astrophysics Data System (ADS)

Buckner, M. R.

Successful quality improvement requires a balanced program involving the three elements that control quality: organization, people and technology. The focus of the SPC/SPM User's Group is to advance the technology component of Total Quality by networking within the Group and by providing an outreach within Westinghouse to foster the appropriate use of statistic techniques to achieve Total Quality. SPM encompasses the disciplines by which a process is measured against its intrinsic design capability, in the face of measurement noise and other obscuring variability. SPM tools facilitate decisions about the process that generated the data. SPM deals typically with manufacturing processes, but with some flexibility of definition and technique it accommodates many administrative processes as well. The techniques of SPM are those of Statistical Process Control, Statistical Quality Control, Measurement Control, and Experimental Design. In addition, techniques such as job and task analysis, and concurrent engineering are important elements of systematic planning and analysis that are needed early in the design process to ensure success. The SPC/SPM User's Group is endeavoring to achieve its objectives by sharing successes that have occurred within the member's own Westinghouse department as well as within other US and foreign industry. In addition, failures are reviewed to establish lessons learned in order to improve future applications. In broader terms, the Group is interested in making SPM the accepted way of doing business within Westinghouse.

40 CFR 58.20 - Special purpose monitors (SPM).

Code of Federal Regulations, 2010 CFR

2010-07-01

... Administrator will not base a NAAQS violation determination for the PM2.5 or ozone NAAQS solely on data from the... discontinuation of the monitor as a SLAMS site. (b) Any SPM data collected by an air monitoring agency using a... monitoring agency's data objectives are inconsistent with those requirements. Data collected at an SPM using...

Comparison of ASE and SFE with Soxhlet, Sonication, and Methanolic Saponification Extractions for the Determination of Organic Micropollutants in Marine Particulate Matter.

PubMed

Heemken, O P; Theobald, N; Wenclawiak, B W

1997-06-01

The methods of accelerated solvent extraction (ASE) and supercritical fluid extraction (SFE) of polycyclic aromatic hydrocarbons (PAHs), aliphatic hydrocarbons, and chlorinated hydrocarbons from marine samples were investigated. The results of extractions of a certified sediment and four samples of suspended particulate matter (SPM) were compared to classical Soxhlet (SOX), ultrasonication (USE), and methanolic saponification extraction (MSE) methods. The recovery data, including precision and systematic deviations of each method, were evaluated statistically. It was found that recoveries and precision of ASE and SFE compared well with the other methods investigated. Using SFE, the average recoveries of PAHs in three different samples ranged from 96 to 105%, for ASE the recoveries were in the range of 97-108% compared to the reference methods. Compared to the certified values of sediment HS-6, the average recoveries of SFE and ASE were 87 and 88%, most compounds being within the limits of confidence. Also, for alkanes the average recoveries by SFE and ASE were equal to the results obtained by SOX, USE, and MSE. In the case of SFE, the recoveries were in the range 93-115%, and ASE achieved recoveries of 94-107% as compared to the other methods. For ASE and SFE, the influence of water on the extraction efficiency was examined. While the natural water content of the SPM sample (56 wt %) led to insufficient recoveries in ASE and SFE, quantitative extractions were achieved in SFE after addition of anhydrous sodium sulfate to the sample. Finally, ASE was applied to SPM-loaded filter candles whereby a mixture of n-hexane/acetone as extraction solvent allowed the simultaneous determination of PAHs, alkanes, and chlorinated hydrocarbons.

In situ observations of suspended particulate matter plumes at an offshore wind farm, southern North Sea

NASA Astrophysics Data System (ADS)

Baeye, Matthias; Fettweis, Michael

2015-08-01

Suspended particulate matter (SPM) plumes associated with the monopile foundations of the Belgian offshore wind farm (OWF) Belwind I were acoustically profiled by means of a Doppler current profiler (ADCP). Together with the analysis of a bottom lander dataset of optical and acoustic backscatter sensors (OBSs and ADPs respectively), the spatiotemporal SPM plume dynamics were inferred. The fieldwork comprised (1) near-bed measurements of hydrodynamics and SPM concentrations in the direct vicinity of the wind turbines, by means of a bottom lander over a spring-neap cycle in May 2010; this dataset represents a typically tide-driven situation because there was no significant meteorological forcing during the measurement period; (2) additional vessel-based measurements conducted in May 2013 to capture the SPM plumes inside and outside the OWF over part of a tidal cycle. Both in situ datasets revealed that the SPM plumes were generated at the turbine piles, consistent with aerial and space-borne imagery. The SPM plumes are well aligned with the tidal current direction in the wake of the monopiles, concentrations being estimated to reach up to 5 times that of the background concentration of about 3 mg/l. It is suggested that the epifaunal communities colonizing the monopile surface and the protective rock collar at the base play a key role as source of the suspended matter recorded in the plumes. The organisms filter and trap fine SPM from the water column, resulting in predominant accumulation of SPM, including detritus and (pseudo-) faeces, at the base of the piles. When tidal currents exceed a certain velocity, fine particles in the near-bed fluff layer are re-suspended and transported downstream in the wake of the piles.

Holocene provenance shift of suspended particulate matter in the Amazon River basin

NASA Astrophysics Data System (ADS)

Höppner, Natalie; Lucassen, Friedrich; Chiessi, Cristiano M.; Sawakuchi, André O.; Kasemann, Simone A.

2018-06-01

The strontium (Sr), neodymium (Nd) and lead (Pb) isotope signatures of suspended particulate matter (SPM) in rivers reflect the radiogenic isotope signatures of the rivers' drainage basin. These signatures are not significantly affected by weathering, transport or depositional cycles, but document the sedimentary contributions of the respective sources. We report new Sr, Nd and Pb isotope ratios and element concentrations of modern SPM from the Brazilian Amazon River basin and document the past evolution of the basin by analyzing radiogenic isotopes of a marine sediment core from the slope off French Guiana archiving the last 40 kyr of Amazon River SPM, and the Holocene section of sediment cores raised between the Amazon River mouth and the slope off French Guiana. The composition of modern SPM confirms two main source areas, the Andes and the cratonic Shield. In the marine sediment core notable changes occurred during the second phase of Heinrich Stadial 1 (i.e. increased proportion of Shield rivers SPM) and during the last deglaciation (i.e. increased proportion of Madeira River SPM) together with elsewhere constant source contributions. Furthermore, we report a prominent offset in Sr and Nd isotopic composition between the average core value (εNd: -11.7 ± 0.9 (2SD), 87Sr/86Sr: 0.7229 ± 0.0016 (2SD)) and the average modern Amazon River SPM signal (εNd: -10.5 ± 0.5 (2SD), 87Sr/86Sr: 0.7213 ± 0.0036 (2SD)). We suggest that a permanent change in the Amazon River basin sediment supply during the late Holocene to a more Andean dominated SPM was responsible for the offset.

Secondary Primary Malignancy Risk in Patients With Cervical Cancer in Taiwan: A Nationwide Population-Based Study.

PubMed

Teng, Chung-Jen; Huon, Leh-Kiong; Hu, Yu-Wen; Yeh, Chiu-Mei; Chao, Yee; Yang, Muh-Hwa; Chen, Tzeng-Ji; Hung, Yi-Ping; Liu, Chia-Jen

2015-10-01

To evaluate the risk of secondary primary malignancy (SPM) in patients with cervical cancer using a nationwide population-based dataset.Patients newly diagnosed with cervical cancer between 1997 and 2011 were identified using Taiwan's National Health Insurance database. Patients with antecedent malignancies were excluded. Standardized incidence ratios (SIRs) for SPM were calculated by comparing with the cancer incidence in the general population. Risk factors for cancer development were analyzed using Cox proportional hazard models.During the 14-year study period (follow-up of 223,062 person-years), 2004 cancers developed in 35,175 patients with cervical cancer. The SIR for all cancers was 1.56 (95% confidence interval, 1.50-1.63, P < 0.001). SIRs for follow-up periods of >10, 5 to 10, 1 to 5, and <1 year were 1.37, 1.51, 1.34, and 2.59, respectively. After the exclusion of SPM occurring within 1 year of cervical cancer diagnosis, SIRs were significantly higher for cancers of the esophagus (2.05), stomach (1.38), colon, rectum, and anus (1.36); lung and mediastinum (2.28), bone and soft tissue (2.23), uterus (3.76), bladder (2.26), and kidneys (1.41). Multivariate analysis showed that age ≥60 was a significant SPM risk factor (hazard ratio [HR] 1.59). Different treatments for cervical cancer, including radiotherapy (HR 1.41) and chemotherapy (HR 1.27), had different impacts on SPM risk. Carboplatin and fluorouracil independently increased SPM risk in cervical cancer patients.Patients with cervical cancer are at increased risk of SPM development. Age ≥60 years, chemotherapy, and radiotherapy are independent risk factors. Carboplatin and fluorouracil also increased SPM risk independently. Close surveillance of patients at high risk should be considered for the early detection of SPMs.

Forward and inverse models of electromagnetic scattering from layered media with rough interfaces

NASA Astrophysics Data System (ADS)

Tabatabaeenejad, Seyed Alireza

This work addresses the problem of electromagnetic scattering from layered dielectric structures with rough boundaries and the associated inverse problem of retrieving the subsurface parameters of the structure using the scattered field. To this end, a forward scattering model based on the Small Perturbation Method (SPM) is developed to calculate the first-order spectral-domain bistatic scattering coefficients of a two-layer rough surface structure. SPM requires the boundaries to be slightly rough compared to the wavelength, but to understand the range of applicability of this method in scattering from two-layer rough surfaces, its region of validity is investigated by comparing its output with that of a first principle solver that does not impose roughness restrictions. The Method of Moments (MoM) is used for this purpose. Finally, for retrieval of the model parameters of the layered structure using scattered field, an inversion scheme based on the Simulated Annealing method is investigated and a strategy is proposed to address convergence to local minimum.

QSAR models for predicting octanol/water and organic carbon/water partition coefficients of polychlorinated biphenyls.

PubMed

Yu, S; Gao, S; Gan, Y; Zhang, Y; Ruan, X; Wang, Y; Yang, L; Shi, J

2016-04-01

Quantitative structure-property relationship modelling can be a valuable alternative method to replace or reduce experimental testing. In particular, some endpoints such as octanol-water (KOW) and organic carbon-water (KOC) partition coefficients of polychlorinated biphenyls (PCBs) are easier to predict and various models have been already developed. In this paper, two different methods, which are multiple linear regression based on the descriptors generated using Dragon software and hologram quantitative structure-activity relationships, were employed to predict suspended particulate matter (SPM) derived log KOC and generator column, shake flask and slow stirring method derived log KOW values of 209 PCBs. The predictive ability of the derived models was validated using a test set. The performances of all these models were compared with EPI Suite™ software. The results indicated that the proposed models were robust and satisfactory, and could provide feasible and promising tools for the rapid assessment of the SPM derived log KOC and generator column, shake flask and slow stirring method derived log KOW values of PCBs.

Evidence against involvement of the acid lysosomal sphingomyelinase in the tumor-necrosis-factor- and interleukin-1-induced sphingomyelin cycle and cell proliferation in human fibroblasts.

PubMed Central

Andrieu, N; Salvayre, R; Levade, T

1994-01-01

The hydrolysis of sphingomyelin (SPM) has been reported to mediate a number of responses to extracellular agents, including cytokines. The so-called SPM cycle may result from the activation of different types of sphingomyelinases (SPMases). We investigated the hypothetical contribution of acid lysosomal SPMase in the SPM signal-transduction pathway. We examined the ability of human skin fibroblasts with a genetic deficiency of acid lysosomal SPMase activity to respond to tumour necrosis factor alpha (TNF-alpha) or interleukin-1 beta (IL-1 beta). We report that both cytokines promoted SPM hydrolysis in fibroblasts derived from patients with Niemann-Pick disease or I-cell disease, similar to that observed in normal cells. Treatment of normal fibroblasts with cationic amphiphilic drugs resulted in inhibition of acid SPMase activity, but had no effect on cytokine-induced SPM turnover. In addition, TNF-alpha and IL-1 beta stimulated [3H]thymidine incorporation in Niemann-Pick fibroblasts, as in normal cells. Thus our results argue against a role for acid endolysosomal SPMase in mediating the cytokine-induced SPM signalling cascade. Images Figure 2 PMID:7980390

A simple method of equine limb force vector analysis and its potential applications

PubMed Central

Robinson, Mark A.; Clayton, Hilary M.

2018-01-01

Background Ground reaction forces (GRF) measured during equine gait analysis are typically evaluated by analyzing discrete values obtained from continuous force-time data for the vertical, longitudinal and transverse GRF components. This paper describes a simple, temporo-spatial method of displaying and analyzing sagittal plane GRF vectors. In addition, the application of statistical parametric mapping (SPM) is introduced to analyse differences between contra-lateral fore and hindlimb force-time curves throughout the stance phase. The overall aim of the study was to demonstrate alternative methods of evaluating functional (a)symmetry within horses. Methods GRF and kinematic data were collected from 10 horses trotting over a series of four force plates (120 Hz). The kinematic data were used to determine clean hoof contacts. The stance phase of each hoof was determined using a 50 N threshold. Vertical and longitudinal GRF for each stance phase were plotted both as force-time curves and as force vector diagrams in which vectors originating at the centre of pressure on the force plate were drawn at intervals of 8.3 ms for the duration of stance. Visual evaluation was facilitated by overlay of the vector diagrams for different limbs. Summary vectors representing the magnitude (VecMag) and direction (VecAng) of the mean force over the entire stance phase were superimposed on the force vector diagram. Typical measurements extracted from the force-time curves (peak forces, impulses) were compared with VecMag and VecAng using partial correlation (controlling for speed). Paired samples t-tests (left v. right diagonal pair comparison and high v. low vertical force diagonal pair comparison) were performed on discrete and vector variables using traditional methods and Hotelling’s T2 tests on normalized stance phase data using SPM. Results Evidence from traditional statistical tests suggested that VecMag is more influenced by the vertical force and impulse, whereas VecAng is more influenced by the longitudinal force and impulse. When used to evaluate mean data from the group of ten sound horses, SPM did not identify differences between the left and right contralateral limb pairs or between limb pairs classified according to directional asymmetry. When evaluating a single horse, three periods were identified during which differences in the forces between the left and right forelimbs exceeded the critical threshold (p < .01). Discussion Traditional statistical analysis of 2D GRF peak values, summary vector variables and visual evaluation of force vector diagrams gave harmonious results and both methods identified the same inter-limb asymmetries. As alpha was more tightly controlled using SPM, significance was only found in the individual horse although T2 plots followed the same trends as discrete analysis for the group. Conclusions The techniques of force vector analysis and SPM hold promise for investigations of sidedness and asymmetry in horses. PMID:29492341

7 CFR 1955.112 - Method of sale (housing).

Code of Federal Regulations, 2010 CFR

2010-01-01

.... Adequate and timely advertising in accordance with § 1955.146 of this subpart is of utmost importance when... Family Housing Servicing and Property Management (SFH/SPM) Division, to request authority to sell program...

Dynamic Allocation of SPM Based on Time-Slotted Cache Conflict Graph for System Optimization

NASA Astrophysics Data System (ADS)

Wu, Jianping; Ling, Ming; Zhang, Yang; Mei, Chen; Wang, Huan

This paper proposes a novel dynamic Scratch-pad Memory allocation strategy to optimize the energy consumption of the memory sub-system. Firstly, the whole program execution process is sliced into several time slots according to the temporal dimension; thereafter, a Time-Slotted Cache Conflict Graph (TSCCG) is introduced to model the behavior of Data Cache (D-Cache) conflicts within each time slot. Then, Integer Nonlinear Programming (INP) is implemented, which can avoid time-consuming linearization process, to select the most profitable data pages. Virtual Memory System (VMS) is adopted to remap those data pages, which will cause severe Cache conflicts within a time slot, to SPM. In order to minimize the swapping overhead of dynamic SPM allocation, a novel SPM controller with a tightly coupled DMA is introduced to issue the swapping operations without CPU's intervention. Last but not the least, this paper discusses the fluctuation of system energy profit based on different MMU page size as well as the Time Slot duration quantitatively. According to our design space exploration, the proposed method can optimize all of the data segments, including global data, heap and stack data in general, and reduce the total energy consumption by 27.28% on average, up to 55.22% with a marginal performance promotion. And comparing to the conventional static CCG (Cache Conflicts Graph), our approach can obtain 24.7% energy profit on average, up to 30.5% with a sight boost in performance.

Ultra low-dose CT attenuation correction in PET SPM

NASA Astrophysics Data System (ADS)

Wang, Shyh-Jen; Yang, Bang-Hung; Tsai, Chia-Jung; Yang, Ching-Ching; Lee, Jason J. S.; Wu, Tung-Hsin

2010-07-01

The use of CT images for attenuation correction (CTAC) allows significantly shorter scanning time and a high quality noise-free attenuation map compared with conventional germanium-68 transmission scan because at least 10 4 times greater of photon flux would be generated from a CT scan under standard operating condition. However, this CTAC technique would potentially introduce more radiation risk to the patients owing to the higher radiation exposure from CT scan. Statistic parameters mapping (SPM) is a prominent technique in nuclear medicine community for the analysis of brain imaging data. The purpose of this study is to assess the feasibility of low-dose CT (LDCT) and ultra low-dose CT (UDCT) in PET SPM applications. The study was divided into two parts. The first part was to evaluate of tracer uptake distribution pattern and quantity analysis by using the striatal phantom to initially assess the feasibility of AC for clinical purpose. The second part was to examine the group SPM analysis using the Hoffman brain phantom. The phantom study is to simulate the human brain and to reduce the experimental uncertainty of real subjects. The initial studies show that the results of PET SPM analysis have no significant differences between LDCT and UDCT comparing to the current used default CTAC. Moreover, the dose of the LDCT is lower than that of the default CT by a factor of 9, and UDCT can even yield a 42 times dose reduction. We have demonstrated the SPM results while using LDCT and UDCT for PET AC is comparable to those using default CT setting, suggesting their feasibility in PET SPM applications. In addition, the necessity of UDCT in PET SPM studies to avoid excess radiation dose is also evident since most of the subjects involved are non-cancer patients or children and some normal subjects are even served as a comparison group in the experiment. It is our belief that additional attempts to decrease the radiation dose would be valuable, especially for children and normal volunteers, to work towards ALARA (as low as reasonably achievable) concept for PET SPM studies.

The effects of alcohol on plasma lipid mediators of inflammation resolution in patients with Type 2 diabetes mellitus.

PubMed

Barden, Anne; Shinde, Sujata; Phillips, Michael; Beilin, Lawrence; Mas, Emilie; Hodgson, Jonathan M; Puddey, Ian; Mori, Trevor A

2018-06-01

Type 2 diabetes mellitus is characterized by peripheral insulin resistance and low-grade systemic inflammation. Inflammation resolution is recognised as an important process driven by specialised pro-resolving mediators of inflammation (SPMs) and has the potential to moderate chronic inflammation. Alcohol has the potential to affect synthesis of SPMs by altering key enzymes involved in SPM synthesis and may influence ongoing inflammation associated with Type 2 diabetes mellitus. (i) To examine the effects of alcohol consumed as red wine on plasma SPM in men and women with Type 2 diabetes in a randomised controlled trial and (ii) compare baseline plasma SPM levels in the same patients with those of healthy volunteers. Twenty-four patients with Type 2 diabetes mellitus were randomized to a three-period crossover study with men drinking red wine 300 ml/day (∼31 g alcohol/day) and women drinking red wine 230 ml/day (∼24 g alcohol/day), or equivalent volumes of dealcoholized red wine (DRW) or water, each for 4 weeks. The SPM 18-hydroxyeicosapentaenoic acid (18-HEPE), E-series resolvins (Rv) (RvE1-RvE3), 17-hydroxydocosahexaenoic acid (17-HDHA), and D-series resolvins (RvD1, 17R-RvD1, RvD2, RvD5), 14-hydroxydocosahexaenoic acid (14-HDHA) and Maresin 1 were measured at the end of each period. A baseline comparison of plasma SPM, hs CRP, lipids and glucose was made with healthy volunteers. Red wine did not differentially affect any of the SPM measured when compared with DRW or water. Baseline levels of the hs-CRP and the SPM 18-HEPE, 17-HDHA, RvD1 and 17R-RvD1 in patients with Type 2 diabetes mellitus were all significantly elevated compared with healthy controls and remained so after adjusting for age and gender. Moderate alcohol consumption as red wine does not alter plasma SPM in patients with Type 2 diabetes mellitus. The elevation of SPM levels compared with healthy volunteers may be a homeostatic response to counter ongoing inflammation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Trends of Second Primary Malignancy in Patients with Thyroid Cancer: A Population-Based Cohort Study in Israel.

PubMed

Izkhakov, Elena; Barchana, Micha; Liphshitz, Irena; Silverman, Barbara G; Stern, Naftali; Keinan-Boker, Lital

2017-06-01

Thyroid cancer (TC) is the most common endocrine malignancy. TC patients have a good prognosis and a low disease-related mortality rate. Since such patients are often young, they may be at a higher risk for a second primary malignancy (SPM). This study sought to determine the incidence, risk, and types of SPM between 1980 and 2011, and to assess SPM trends over time among Israeli TC patients. Data were derived from the Israel National Cancer Registry. Primary TC patients diagnosed during 1980-2009 were followed up for SPM incidence until December 31, 2011. Standardized incidence ratios (SIRs) of observed to expected SPM (based on the general population rates) were calculated using Poisson regression. Analyses were stratified by time period of initial TC diagnosis (1980-1995 and 1996-2009). A total of 11,538 TC patients were identified. After exclusion of 107 duplicate cases, records of 1032 patients with SPM were analyzed (an SPM incidence of 8.9%). SIRs for all-site SPMs were 1.23 [confidence interval 1.08-1.35] for males and 1.19 [confidence interval 1.10-1.27] for females. SIRs for tumors of the urinary system and prostate were significantly elevated in males, as were SIRs for tumors of the brain, urinary system, breast, and lung in females. Variables associated with increased risk of developing SPMs included a younger age at TC diagnosis, a shorter latency period, being born in Asia/Africa for both sexes, and being born in Israel for females. Compared with the general population, a subanalysis by TC diagnosis during 1980-1995 and 1996-2009 disclosed a higher SPM incidence for the latter time period in males and for both time periods, with a slightly higher SIR for the latter time period in females. The overall risk of SPM in Israeli TC patients was significantly greater for both sexes compared with the general population, thus identifying TC patients as a high-risk group and calling for caretakers to apply specific follow-up guidelines.

Shifting roles of heterotrophy and autotrophy in coral energetics under varying turbidity.

PubMed

Anthony; Fabricius

2000-09-20

Suspended particulate matter (SPM) strongly alters the trophic environment of photosymbiotic aquatic organisms. At high particles loads, phototrophic energy gains can be diminished due to light absorption by suspended particles, and stress from particle abrasion or deposition on tissues. However, energy gains are enhanced if organisms are able to use SPM as a food source. For photosymbiotic benthic suspension feeders, increases in SPM concentrations may require both phototrophic and heterotrophic acclimation to sustain a positive energy balance. This study provides an experimental analysis of the effects of contrasting light and SPM regimes on the energy budget (scope for growth) of two zooxanthellate corals (Goniastrea retiformis and Porites cylindrica). Using a factorial design in a flow-through tank system, corals were exposed for 2 months to shaded and unshaded conditions (equivalent to 3-4 m depth at 4 and 16 mg dry weight SPM l(-1), respectively) and a range of controlled SPM loads with a natural organic content ( approximately 3% w/w). In G. retiformis, rates of particle ingestion were a linear function of SPM concentration within a broad range (1-30 mg dry weight l(-1)). After 2 months of shading, photosynthetic acclimation was significant in G. retiformis, but did not compensate for the reduced light level, as daily respiration exceeded daily photosynthesis. However, in response to the prolonged shading, G. retiformis more than doubled its rate of particle feeding. At high SPM treatments (16 mg dw l(-1)), sediment feeding by this species compensated fully for the 35-47% lower phototrophy in the shaded treatment. Due to both photo- and heterotrophic plasticity, G. retiformis gained tissue and skeletal mass at all experimental levels of light and SPM. In contrast, rates of particle intake by P. cylindrica contributed <10% to the energy budget in shaded and <3% in unshaded conditions. Feeding rates of P. cylindrica were half-saturated at approximately 3 mg dry weight l(-1), and four- to eight-fold lower than those of G. retiformis. Skeletal growth was sustained, but tissue mass and lipid contents declined in shaded and high-SPM treatments, and carbon loss due to shading by SPM was not compensated for by particle feeding. Thus, due to a lack of photo- and heterotrophic plasticity, periods of high turbidity resulted in energy deficiency in P. cylindrica, and high turbidity conditions appeared physiologically unsustainable for this species. This study is the first to show heterotrophic plasticity in a symbiotic coral, and to show that such plasticity can offset stress from high particle loads. It demonstrates that changes in the trophic mode of some coral species are a mechanism for sustaining a positive energy balance in turbid environments, thereby broadening their physiological niche.

Correlated regions of cerebral blood flow with clinical parameters in Parkinson's disease; comparison using 'Anatomy' and 'Talairach Daemon' software.

PubMed

Yoon, Hyun Jin; Cheon, Sang Myung; Jeong, Young Jin; Kang, Do-Young

2012-02-01

We assign the anatomical names of functional activation regions in the brain, based on the probabilistic cyto-architectonic atlas by Anatomy 1.7 from an analysis of correlations between regional cerebral blood flow (rCBF) and clinical parameters of the non-demented Parkinson's disease (PD) patients by SPM8. We evaluated Anatomy 1.7 of SPM toolbox compared to 'Talairach Daemon' (TD) Client 2.4.2 software. One hundred and thirty-six patients (mean age 60.0 ± 9.09 years; 73 women and 63 men) with non-demented PD were selected. Tc-99m-HMPAO brain single-photon emission computed tomography (SPECT) scans were performed on the patients using a two-head gamma-camera. We analyzed the brain image of PD patients by SPM8 and found the anatomical names of correlated regions of rCBF perfusion with the clinical parameters using TD Client 2.4.2 and Anatomy 1.7. The SPM8 provided a correlation coefficient between clinical parameters and cerebral hypoperfusion by a simple regression method. To the clinical parameters were added age, duration of disease, education period, Hoehn and Yahr (H&Y) stage and Korean mini-mental state examination (K-MMSE) score. Age was correlated with cerebral perfusion in the Brodmann area (BA) 6 and BA 3b assigned by Anatomy 1.7 and BA 6 and pyramis in gray matter by TD Client 2.4.2 with p < 0.001 uncorrected. Also, assigned significant correlated regions were found in the left and right lobules VI (Hem) with duration of disease, in left and right lobules VIIa crus I (Hem) with education, in left insula (Ig2), left and right lobules VI (Hem) with H&Y, and in BA 4a and 6 with K-MMSE score with p < 0.05 uncorrected by Anatomy 1.7, respectively. Most areas of correlation were overlapped by two different anatomical labeling methods, but some correlation areas were found with different names. Age was the most significantly correlated clinical parameter with rCBF. TD Client found the exact anatomical name by the peak intensity position of the cluster while Anatomy 1.7 of SPM8 toolbox, using the cyto-architectonic probability maps, assigned the anatomical name by percentage value of the probability.

Effectiveness and Usability of the Sensory Processing Measure-Preschool Quick Tips: Data-Driven Intervention Following the Use of the SPM-Preschool in an Early Childhood, Multiple-Case Study

ERIC Educational Resources Information Center

Olson, Carol H.; Henry, Diana A.; Kliner, Ashley Peck; Kyllo, Alissa; Richter, Chelsea Munson; Charley, Jane; Whitcher, Meagan Chapman; Reinke, Katherine Roth; Tysver, Chelsay Horner; Wagner, Lacey; Walworth, Jessica

2016-01-01

This pre- and posttest multiple-case study examined the effectiveness and usability of the Sensory Processing Measure-Preschool Quick Tips (SPM-P QT) by key stakeholders (parents and teachers) for implementing data-driven intervention to address sensory processing challenges. The Sensory Processing Measure-Preschool (SPM-P) was administered as an…

Measurement Scale of the SOLIS Vector Spectromagnetograph

NASA Technical Reports Server (NTRS)

Jones, Harrison P.; Harvey, John W.; Henney, Carl J.; Keller, Christoph U.; Malanushenko, Olena M.

2004-01-01

Longitudinal magnetograms obtained with thc SOLIS Vector Spectromagnetograph (VSM) during a cross-calibration period are compared with similar data from the NASA/NSO Spectromagnetograph (SPM) at the NSO/Kitt Peak Vacuum Telescope as well as with SOHO/MDI and GONG magnetogram. The VSM began observation at the University of Arizona agricultural test site and collaborative observations were obtained with both the VSM and SPM from 2003 Aug 05 through 2003 Sep 21 where the SPM was officially retired. The VSM replaces the SPM and continues the 3O-year NSO/Kitt Peak synoptic magnetogram record. Magnetograms are compared by equating histograms and, for selected examples, by pixel-by-pixel comparison of co-registered images. The VSM was not corrected for polarization crosstalk and was operated without hast guiding. Solar activity was at best moderate during this period. Over the range of observed fields, the VSM magnetograms show greatly improved sensitivity but are otherwise virtually identical with "raw" SPM magnetogram. GONG magnetograms are also closely comparable with the SPM while MDI flux values tend to be stronger by a factor of 1.2 - 1.4. Dependence of the results on seeing will be discussed. Partial funding for this work was provided through Solar and Heliospheric Research Supporting Research and Technology grants from NASA's Office of Space Sciences.

Improvement of SPM nonlinear limit by chirped duobinary PolSK transmission

NASA Astrophysics Data System (ADS)

Yang, Lixiu; Fan, Jiayu; Wang, Lutang; Huang, Zhaoming

2005-02-01

In today's terrestrial long-haul optical fiber communication systems, high channel powers are required to obtain a large transmission distance with reasonable optical amplifier spacing. In such systems, however, the presence of nonlinear effects such as the self-phase modulation (SPM) and the fiber dispersion as well as their combined effects, called SPM-induced nonlinear limitation or SPM limit, will seriously degrade the system performances in respect of the effective transmission distance and ultimately become a limiting factor in high-speed, long-haul optical fiber transmission.In this paper, a new transmission format: chirped duobinary PolSK transmission, has been proposed to generate a pre-chirped duobianry signal with fixed polarity (either positive or negative), which is modulated by a PolSK modulator. This format is based on a transmitter setup consisting of a duobinary PolSK Modulation transmitter followed by an additional phase modulator. The chirped duobinary PolSK transmission reduces the signal degradation and spectral broadening in the nonlinear regime significantly. Thus it shifts this SPM nonlinear limit to enable more relaxed dispersion compensation at high optical power compared to the conventional duobinary schemes.The simulation results show chirped duobinary PolSK transmission enlarges the dispersion limited transmission distance, increases the dispersion tolerance and overcome the SPM nonlinear limit.

Advanced simulation model for IPM motor drive with considering phase voltage and stator inductance

NASA Astrophysics Data System (ADS)

Lee, Dong-Myung; Park, Hyun-Jong; Lee, Ju

2016-10-01

This paper proposes an advanced simulation model of driving system for Interior Permanent Magnet (IPM) BrushLess Direct Current (BLDC) motors driven by 120-degree conduction method (two-phase conduction method, TPCM) that is widely used for sensorless control of BLDC motors. BLDC motors can be classified as SPM (Surface mounted Permanent Magnet) and IPM motors. Simulation model of driving system with SPM motors is simple due to the constant stator inductance regardless of the rotor position. Simulation models of SPM motor driving system have been proposed in many researches. On the other hand, simulation models for IPM driving system by graphic-based simulation tool such as Matlab/Simulink have not been proposed. Simulation study about driving system of IPMs with TPCM is complex because stator inductances of IPM vary with the rotor position, as permanent magnets are embedded in the rotor. To develop sensorless scheme or improve control performance, development of control algorithm through simulation study is essential, and the simulation model that accurately reflects the characteristic of IPM is required. Therefore, this paper presents the advanced simulation model of IPM driving system, which takes into account the unique characteristic of IPM due to the position-dependent inductances. The validity of the proposed simulation model is validated by comparison to experimental and simulation results using IPM with TPCM control scheme.

[Substances transport in an underground river of typical karst watershed during storm events].

PubMed

Yang, Ping-Heng; Kuang, Ying-Lun; Yuan, Wen-Hao; Jia, Peng; He, Qiu-Fang; Lin, Yu-Shi

2009-11-01

Hydrologic process, turbidity, suspended particles matters (SPM), major cations and TOC concentrations during two storm events in late April 2008 were monitored at Jiangjia Spring which is the outlet of Qingmu Guan underground river system. Scanning electron microscopy (SEM) and energy disperse spectroscopy (EDS) analyses of SPM were also performed in order to investigate the transport characteristics of substances, such as SPM, turbidity and major cations in the underground river of typical karst watershed. The results show that at a single and well-developed karst conduit of Jiangjia Spring, discharge, turbidity, and concentrations of SPM, major cations and TOC respond promptly to the rainfall. The carbonate-derived cations including Ca2+, Mg2+ and Sr2+ are subject to dilution effect during the rising limb of discharge. The elevation in turbidity and SPM concentration is a result of the gradual increase of allochthonous substances (soil) flux input from the surface. Al3+, Fe, Mn, Ba2+ and TOC are concomitant substances of SPM. And their concentrations are ascending with turbid rise. The flux of SPM in diameter > 0.45 microm in the underground river is about 9.7 tons during the events. The bad water quality suggests us that the spring water is unfit to drink without purification during the period of rising and recession time of discharge at Jiangjia Spring. Thus, soil erosion and nutrient losing not only strongly destroy the fragile karst ecological environment, but also lead to non-point source pollution, and seriously threaten the drinking water safety of locals.

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

Kumar, Pragati, E-mail: pkumar.phy@gmail.com; Agarwal, Avinash; Saxena, Nupur

The influence of swift heavy ion irradiation (SHII) on surface phonon mode (SPM) and green emission in nanocrystalline CdS thin films grown by chemical bath deposition is studied. The SHII of nanocrystalline CdS thin films is carried out using 70 MeV Ni ions. The micro Raman analysis shows that asymmetry and broadening in fundamental longitudinal optical (LO) phonon mode increases systematically with increasing ion fluence. To analyze the role of phonon confinement, spatial correlation model (SCM) is fitted to the experimental data. The observed deviation of SCM to the experimental data is further investigated by fitting the micro Raman spectra usingmore » two Lorentzian line shapes. It is found that two Lorentzian functions (LFs) provide better fitting than SCM fitting and facilitate to identify the contribution of SPM in the observed distortion of LO mode. The behavior of SPM as a function of ion fluence is studied to correlate the observed asymmetry (Γ{sub a}/Γ{sub b}) and full width at half maximum of LO phonon mode and to understand the SHII induced enhancement of SPM. The ion beam induced interstitial and surface state defects in thin films, as observed by photoluminescence (PL) spectroscopy studies, may be the underlying reason for enhancement in SPM. PL studies also show enhancement in green luminescence with increase in ion fluence. PL analysis reveals that the variation in population density of surface state defects after SHII is similar to that of SPM. The correlation between SPM and luminescence and their dependence on ion irradiation fluence is explained with the help of thermal spike model.« less

Intraclonal Genome Stability of the Metallo-β-lactamase SPM-1-producing Pseudomonas aeruginosa ST277, an Endemic Clone Disseminated in Brazilian Hospitals.

PubMed

Nascimento, Ana P B; Ortiz, Mauro F; Martins, Willames M B S; Morais, Guilherme L; Fehlberg, Lorena C C; Almeida, Luiz G P; Ciapina, Luciane P; Gales, Ana C; Vasconcelos, Ana T R

2016-01-01

Carbapenems represent the mainstay therapy for the treatment of serious P. aeruginosa infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-β-lactamase has been the most common mechanism of carbapenem resistance identified in P. aeruginosa isolated from Brazilian medical centers. Interestingly, a single SPM-1-producing P. aeruginosa clone belonging to the ST277 has been widely spread within the Brazilian territory. In the current study, we performed a next-generation sequencing of six SPM-1-producing P. aeruginosa ST277 isolates. The core genome contains 5899 coding genes relative to the reference strain P. aeruginos a PAO1. A total of 26 genomic islands were detected in these isolates. We identified remarkable elements inside these genomic islands, such as copies of the bla SPM-1 gene conferring resistance to carbapenems and a type I-C CRISPR-Cas system, which is involved in protection of the chromosome against foreign DNA. In addition, we identified single nucleotide polymorphisms causing amino acid changes in antimicrobial resistance and virulence-related genes. Together, these factors could contribute to the marked resistance and persistence of the SPM-1-producing P. aeruginosa ST277 clone. A comparison of the SPM-1-producing P. aeruginosa ST277 genomes showed that their core genome has a high level nucleotide similarity and synteny conservation. The variability observed was mainly due to acquisition of genomic islands carrying several antibiotic resistance genes.

Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma.

PubMed

Finster, Kai Waldemar; Herbert, Rodney Andrew; Lomstein, Bente Aagaard

2009-04-01

Two pigmented, Gram-negative, non-motile, pleomorphic rod-shaped bacteria (strains SPM-9(T) and SPM-10(T)) were isolated from a permafrost soil collected from the Adventdalen valley, Spitsbergen, northern Norway. A third isolate (strain M5-H2) was recovered from the same soil sample after the sample had been exposed to simulated Martian environmental conditions. The three strains were characterized taxonomically by using a polyphasic approach. Phylogenetic, chemotaxonomic, physiological and morphological analyses demonstrated that the three isolates were most closely related to members of the genus Spirosoma. 16S rRNA gene sequence data indicated that the three isolates could be divided into two clusters: (i) strain SPM-9(T) and (ii) strains SPM-10(T) and M5-H2. This grouping was confirmed by DNA-DNA hybridization experiments. Strains SPM-9(T) and SPM-10(T) exhibited 92 % 16S rRNA gene sequence similarity to both Spirosoma linguale LMG 10896(T) and Spirosoma rigui WPCB 118(T). The major fatty acids present in all three isolates were summed feature 3 (comprising iso-C(15:0) 2-OH and/or C(16 : 1)omega7c; 43.0-48.2 % of the total), C(16 : 1)omega5c (19.1-21.3 %), C(16 : 0) (6.7-7.3 %), iso-C(17 : 0) 3-OH (4.7-6.0 %) and iso-C(15 : 0) (2.6-5.7 %). On the basis of their phenotypic and genotypic characteristics, the new strains are assigned to two novel species of the genus Spirosoma, for which the names Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov. are proposed. The type strain of Spirosoma spitsbergense is SPM-9(T) (=NCIMB 14407(T)=DSM 19989(T)) and the type strain of Spirosoma luteum is SPM-10(T) (=NCIMB 14406(T)=DSM 19990(T)). An emended description of the genus Spirosoma is also proposed.

Collaborative Problem Solving Methods towards Critical Thinking

ERIC Educational Resources Information Center

Yin, Khoo Yin; Abdullah, Abdul Ghani Kanesan; Alazidiyeen, Naser Jamil

2011-01-01

This research attempts to examine the collaborative problem solving methods towards critical thinking based on economy (AE) and non economy (TE) in the SPM level among students in the lower sixth form. The quasi experiment method that uses the modal of 3X2 factorial is applied. 294 lower sixth form students from ten schools are distributed…

Prioritizing sewer rehabilitation projects using AHP-PROMETHEE II ranking method.

PubMed

Kessili, Abdelhak; Benmamar, Saadia

2016-01-01

The aim of this paper is to develop a methodology for the prioritization of sewer rehabilitation projects for Algiers (Algeria) sewer networks to support the National Sanitation Office in its challenge to make decisions on prioritization of sewer rehabilitation projects. The methodology applies multiple-criteria decision making. The study includes 47 projects (collectors) and 12 criteria to evaluate them. These criteria represent the different issues considered in the prioritization of the projects, which are structural, hydraulic, environmental, financial, social and technical. The analytic hierarchy process (AHP) is used to determine weights of the criteria and the Preference Ranking Organization Method for Enrichment Evaluations (PROMETHEE II) method is used to obtain the final ranking of the projects. The model was verified using the sewer data of Algiers. The results have shown that the method can be used for prioritizing sewer rehabilitation projects.

Mining sequential patterns for protein fold recognition.

PubMed

Exarchos, Themis P; Papaloukas, Costas; Lampros, Christos; Fotiadis, Dimitrios I

2008-02-01

Protein data contain discriminative patterns that can be used in many beneficial applications if they are defined correctly. In this work sequential pattern mining (SPM) is utilized for sequence-based fold recognition. Protein classification in terms of fold recognition plays an important role in computational protein analysis, since it can contribute to the determination of the function of a protein whose structure is unknown. Specifically, one of the most efficient SPM algorithms, cSPADE, is employed for the analysis of protein sequence. A classifier uses the extracted sequential patterns to classify proteins in the appropriate fold category. For training and evaluating the proposed method we used the protein sequences from the Protein Data Bank and the annotation of the SCOP database. The method exhibited an overall accuracy of 25% in a classification problem with 36 candidate categories. The classification performance reaches up to 56% when the five most probable protein folds are considered.

Scanning proton microprobe applied to analysis of individual aerosol particles from Amazon Basin

NASA Astrophysics Data System (ADS)

Gerab, Fábio; Artaxo, Paulo; Swietlicki, Erik; Pallon, Jan

1998-03-01

The development of the Scanning Proton Microprobe (SPM) offers a new possibility for individual aerosol particle studies. The SPM joins Particle Induced X-ray Emission (PIXE) elemental analysis qualities with micrometric spatial resolution. In this work the Lund University SPM facility was used for elemental characterization of individual aerosol particles emitted to the atmosphere in the Brazilian Amazon Basin, during gold mining activities by the so-called "gold shops".

Silver behaviour along the salinity gradient of the Gironde Estuary.

PubMed

Lanceleur, Laurent; Schäfer, Jörg; Blanc, Gérard; Coynel, Alexandra; Bossy, Cécile; Baudrimont, Magalie; Glé, Corine; Larrose, Aurélie; Renault, Sophie; Strady, Emilie

2013-03-01

Dissolved and particulate Ag concentrations (Ag(D) and Ag(P), respectively) were measured in surface water and suspended particulate matter (SPM) along the salinity gradient of the Gironde Estuary, South West France, during three cruises (2008-2009) covering contrasting hydrological conditions, i.e. two cruises during intermediate and one during high freshwater discharge (~740 and ~2,300 m(3)/s). Silver distribution reflected non-conservative behaviour with 60-70 % of Ag(P) in freshwater particles being desorbed by chlorocomplexation. The amount of Ag(P) desorbed was similar to the so-called reactive, potentially bioavailable Ag(P) fraction (60 ± 4 %) extracted from river SPM by 1 M HCl. Both Ag(P) (0.22 ± 0.05 mg/kg) and Ag(P)/Th(P) (0.025-0.028) in the residual fraction of fluvial and estuarine SPM were similar to those in SPM from the estuary mouth and in coastal sediments from the shelf off the Gironde Estuary, indicating that chlorocomplexation desorbs the reactive Ag(P). The data show that desorption of reactive Ag(P) mainly occurs inside the estuary during low and intermediate discharge, whereas expulsion of partially Ag(P)-depleted SPM (Ag(P)/Th(P) ~0.040) during the flood implies ongoing desorption in the coastal ocean, e.g. in the nearby oyster production areas (Marennes-Oléron Bay). The highest Ag(D) levels (6-8 ng/L) occurred in the mid-salinity range (15-20) of the Gironde Estuary and were decoupled from freshwater discharge. In the maximum turbidity zone, Ag(D) were at minimum, showing that high SPM concentrations (a) induce Ag(D) adsorption in estuarine freshwater and (b) counterbalance Ag(P) desorption in the low salinity range (1-3). Accordingly, Ag behaviour in turbid estuaries appears to be controlled by the balance between salinity and SPM levels. The first estimates of daily Ag(D) net fluxes for the Gironde Estuary (Boyle's method) showed relatively stable theoretical Ag(D) at zero salinity (Ag (D) (0) = 25-30 ng/L) for the contrasting hydrological situations. Accordingly, Ag(D) net fluxes were very similar for the situations with intermediate discharge (1.7 and 1.6 g/day) and clearly higher during the flood (5.0 g/day) despite incomplete desorption. Applying Ag (D) (0) to the annual freshwater inputs provided an annual net Ag(D) flux (0.64-0.89 t/year in 2008 and 0.56-0.77 t/year in 2009) that was 12-50 times greater than the Ag(D) gross flux. This estimate was consistent with net Ag(D) flux estimates obtained from gross Ag(P) flux considering 60 % desorption in the estuarine salinity gradient.

Electron-beam-induced potentials in semiconductors: calculation and measurement with an SEM/SPM hybrid system

NASA Astrophysics Data System (ADS)

Thomas, Ch; Joachimsthaler, I.; Heiderhoff, R.; Balk, L. J.

2004-10-01

In this work electron-beam-induced potentials are analysed theoretically and experimentally for semiconductors. A theoretical model is developed to describe the surface potential distribution produced by an electron beam. The distribution of generated carriers is calculated using semiconductor equations. This distribution causes a local change in surface potential, which is derived with the help of quasi-Fermi energies. The potential distribution is simulated using the model developed and measured with a scanning probe microscope (SPM) built inside a scanning electron microscope (SEM), for different samples, for different beam excitations and for different cantilever voltages of SPM. In the end, some fields of application are shown where material properties can be determined using an SEM/SPM hybrid system.

An empirical comparison of SPM preprocessing parameters to the analysis of fMRI data.

PubMed

Della-Maggiore, Valeria; Chau, Wilkin; Peres-Neto, Pedro R; McIntosh, Anthony R

2002-09-01

We present the results from two sets of Monte Carlo simulations aimed at evaluating the robustness of some preprocessing parameters of SPM99 for the analysis of functional magnetic resonance imaging (fMRI). Statistical robustness was estimated by implementing parametric and nonparametric simulation approaches based on the images obtained from an event-related fMRI experiment. Simulated datasets were tested for combinations of the following parameters: basis function, global scaling, low-pass filter, high-pass filter and autoregressive modeling of serial autocorrelation. Based on single-subject SPM analysis, we derived the following conclusions that may serve as a guide for initial analysis of fMRI data using SPM99: (1) The canonical hemodynamic response function is a more reliable basis function to model the fMRI time series than HRF with time derivative. (2) Global scaling should be avoided since it may significantly decrease the power depending on the experimental design. (3) The use of a high-pass filter may be beneficial for event-related designs with fixed interstimulus intervals. (4) When dealing with fMRI time series with short interstimulus intervals (<8 s), the use of first-order autoregressive model is recommended over a low-pass filter (HRF) because it reduces the risk of inferential bias while providing a relatively good power. For datasets with interstimulus intervals longer than 8 seconds, temporal smoothing is not recommended since it decreases power. While the generalizability of our results may be limited, the methods we employed can be easily implemented by other scientists to determine the best parameter combination to analyze their data.

STM, SECPM, AFM and Electrochemistry on Single Crystalline Surfaces

PubMed Central

Wolfschmidt, Holger; Baier, Claudia; Gsell, Stefan; Fischer, Martin; Schreck, Matthias; Stimming, Ulrich

2010-01-01

Scanning probe microscopy (SPM) techniques have had a great impact on research fields of surface science and nanotechnology during the last decades. They are used to investigate surfaces with scanning ranges between several 100 μm down to atomic resolution. Depending on experimental conditions, and the interaction forces between probe and sample, different SPM techniques allow mapping of different surface properties. In this work, scanning tunneling microscopy (STM) in air and under electrochemical conditions (EC-STM), atomic force microscopy (AFM) in air and scanning electrochemical potential microscopy (SECPM) under electrochemical conditions, were used to study different single crystalline surfaces in electrochemistry. Especially SECPM offers potentially new insights into the solid-liquid interface by providing the possibility to image the potential distribution of the surface, with a resolution that is comparable to STM. In electrocatalysis, nanostructured catalysts supported on different electrode materials often show behavior different from their bulk electrodes. This was experimentally and theoretically shown for several combinations and recently on Pt on Au(111) towards fuel cell relevant reactions. For these investigations single crystals often provide accurate and well defined reference and support systems. We will show heteroepitaxially grown Ru, Ir and Rh single crystalline surface films and bulk Au single crystals with different orientations under electrochemical conditions. Image studies from all three different SPM methods will be presented and compared to electrochemical data obtained by cyclic voltammetry in acidic media. The quality of the single crystalline supports will be verified by the SPM images and the cyclic voltammograms. Furthermore, an outlook will be presented on how such supports can be used in electrocatalytic studies. PMID:28883327

Chemical determination of particulate nitrogen in San Francisco Bay. Nitrogen: chlorophyll a ratios in plankton

USGS Publications Warehouse

Hager, S.W.; Harmon, D.D.; Alpine, A.E.

1984-01-01

Particulate nitrogen (PN) and chlorophyll a (Chla) were measured in the northern reach of San Francisco Bay throughout 1980. The PN values were calculated as the differences between unfiltered and filtered (0??4 ??m) samples analyzed using the UV-catalyzed peroxide digestion method. The Chla values were measured spectrophotometrically, with corrections made for phaeopigments. The plot of all PN Chla data was found to be non-linear, and the concentration of suspended particulate matter (SPM) was found to be the best selector for linear subsets of the data. The best-fit slopes of PN Chla plots, as determined by linear regression (model II), were interpreted to be the N: Chla ratios of phytoplankton. The Y-intercepts of the regression lines were considered to represent easily-oxidizable detrital nitrogen (EDN). In clear water ( < 10 mg l-1 SPM), the N: Chla ratio was 1??07 ??g-at N per ??g Chla. It decreased to 0??60 in the 10-18 mg l-1 range and averaged 0??31 in the remaining four ranges (18-35, 35-65, 65-155, and 155-470 mg l-1). The EDN values were less than 1 ??g-at N l-1 in the clear water and increased monotonically to almost 12 ??g-at N l-1 in the highest SPM range. The N: Chla ratios for the four highest SPM ranges agree well with data for phytoplankton in light-limited cultures. In these ranges, phytoplankton-N averaged only 20% of the PN, while EDN averaged 39% and refractory-N 41%. ?? 1984.

Study on the occurrence of platinum in Xinjie CuNi sulfide deposits by a combination of SPM and NAA

NASA Astrophysics Data System (ADS)

Li, Xiaolin; Zhu, Jieqing; Lu, Rongrong; Gu, Yingmei; Wu, Xiankang; Chen, Youhong

1997-07-01

A combination of neutron-activation analysis (NAA) and scanning proton microprobe (SPM) was used to study the distribution of platinum-group elements (PGEs) in rocks and ores from Xinjie CuNi deposit. The minimum detection limits of PGEs by NAA had been much improved by means of a nickel-sulfide fire-assay technique for pre-concentration of PGEs in the ore samples. A simple and effective method was developed for true element mapping in SPM experiments. A pair of moveable absorption filters was set up in the target chamber for high sensitivities of both major and trace elements. The bulk analysis results by NNA indicated that the PGE mineralization occurred at the base of Xinjie layered intrusion in clinopyroxenite rocks and the CuNi sulfide minerals disseminated within the rocks had high abundance level of PGEs. However, the micro-PIXE analysis of the CuNi sulfide mineral grains did not find PGEs above the MDL of 6-9 ppm for Rh, Ru and Pd, and 60 ppm for Pt. The search for platinum occurrence in sulfide minerals was followed by scanning analysis of SPM when some smaller platinum enriched grains were found in the sulfide minerals. The microscopic analysis results suggested that platinum occurred in the CuNi sulfide matrix as independent arsenide mineral grains. The chemical formula of the arsenide sperrylite was PtAs 2. The information of the platinum occurrence was helpful to future mineralogical research and mineral processing and beneficiation of the CuNi deposit.

Spatial-temporal dynamics and sources of total Hg in a hydroelectric reservoir in the Western Amazon, Brazil.

PubMed

Pestana, I A; Bastos, W R; Almeida, M G; de Carvalho, D P; Rezende, C E; Souza, C M M

2016-05-01

Damming rivers to construct hydroelectric reservoirs results in a series of impacts on the biogeochemical Hg cycle. For example, modifying the hydrodynamics of a natural watercourse can result in the suspension and transport of Hg deposits in the water column, which represents an exposure risk for biota. The objective of this study was to evaluate the influences of seasonality on the dispersion of total Hg in the Hydroelectric Power Plant (HPP)-Samuel Reservoir (Porto Velho/Brazil). Sampling campaigns were performed during the three following hydrological periods characteristic of the region: low (Oct/2011), ebbing (May/2012), and high (Feb/2013) water. Sediment profiles, suspended particulate matter (SPM), and aquatic macrophytes (Eicchornia crassipes and Oryza spp.) were collected, and their Hg concentrations and isotopic and elemental C and N signatures were determined. The drainage basin significantly influenced the SPM compositions during all the periods, with a small autochthonous influence from the reservoir during the low water. The highest SPM Hg concentrations inside the reservoir were observed during the high water period, suggesting that the hydrodynamics of this environment favor the suspension of fine SPM, which has a higher Hg adsorption capacity. The Hg concentrations in the sediment profiles were ten times lower than those in the SPM, indicating that large particles with low Hg concentrations were deposited to form the bottom sediment. Hg concentrations were higher in aquatic macrophyte roots than in their leaves and appeared to contribute to the formation of SPM during the low water period. In this environment, Hg transport mainly occurs in SPM from the Jamari River drainage basin, which is the primary source of Hg in this environment.

Effect of flood events on transport of suspended sediments, organic matter and particulate metals in a forest watershed in the Basque Country (Northern Spain).

PubMed

Peraza-Castro, M; Sauvage, S; Sánchez-Pérez, J M; Ruiz-Romera, E

2016-11-01

An understanding of the processes controlling sediment, organic matter and metal export is critical to assessing and anticipating risk situations in water systems. Concentrations of suspended particulate matter (SPM), dissolved (DOC) and particulate (POC) organic carbon and metals (Cu, Ni, Pb, Cr, Zn, Mn, Fe) in dissolved and particulate phases were monitored in a forest watershed in the Basque Country (Northern Spain) (31.5km(2)) over three hydrological years (2009-2012), to evaluate the effect of flood events on the transport of these materials. Good regression was found between SPM and particulate metal concentration, making it possible to compute the load during the twenty five flood events that occurred during the study period at an annual scale. Particulate metals were exported in the following order: Fe>Mn>Zn>Cr>Pb>Cu>Ni. Annual mean loads of SPM, DOC and POC were estimated at 2267t, 104t and 57t, respectively, and the load (kg) of particulate metals at 76 (Ni), 83 (Cu), 135 (Pb), 256 (Cr), 532 (Zn), 1783 (Mn) and 95170 (Fe). Flood events constituted 91%-SPM, 65%-DOC, 71%-POC, 80%-Cu, 85%-Ni, 72%-Pb, 84%-Cr, 74%-Zn, 87%-Mn and 88%-Fe of total load exported during the three years studied. Flood events were classified into three categories according to their capacity for transporting organic carbon and particulate metals. High intensity flood events are those with high transport capacity of SPM, organic carbon and particulate metals. Most of the SPM, DOC, POC and particulate metal load was exported by this type of flood event, which contributed 59% of SPM, 45% of organic carbon and 54% of metals. Copyright © 2016 Elsevier B.V. All rights reserved.

A simple optical model to estimate suspended particulate matter in Yellow River Estuary.

PubMed

Qiu, Zhongfeng

2013-11-18

Distribution of the suspended particulate matter (SPM) concentration is a key issue for analyzing the deposition and erosion variety of the estuary and evaluating the material fluxes from river to sea. Satellite remote sensing is a useful tool to investigate the spatial variation of SPM concentration in estuarial zones. However, algorithm developments and validations of the SPM concentrations in Yellow River Estuary (YRE) have been seldom performed before and therefore our knowledge on the quality of retrieval of SPM concentration is poor. In this study, we developed a new simple optical model to estimate SPM concentration in YRE by specifying the optimal wavelength ratios (600-710 nm)/ (530-590 nm) based on observations of 5 cruises during 2004 and 2011. The simple optical model was attentively calibrated and the optimal band ratios were selected for application to multiple sensors, 678/551 for the Moderate Resolution Imaging Spectroradiometer (MODIS), 705/560 for the Medium Resolution Imaging Spectrometer (MERIS) and 680/555 for the Geostationary Ocean Color Imager (GOCI). With the simple optical model, the relative percentage difference and the mean absolute error were 35.4% and 15.6 gm(-3) respectively for MODIS, 42.2% and 16.3 gm(-3) for MERIS, and 34.2% and 14.7 gm(-3) for GOCI, based on an independent validation data set. Our results showed a good precision of estimation for SPM concentration using the new simple optical model, contrasting with the poor estimations derived from existing empirical models. Providing an available atmospheric correction scheme for satellite imagery, our simple model could be used for quantitative monitoring of SPM concentrations in YRE.

Maximum sinking velocities of suspended particulate matter in a coastal transition zone

NASA Astrophysics Data System (ADS)

Maerz, Joeran; Hofmeister, Richard; van der Lee, Eefke M.; Gräwe, Ulf; Riethmüller, Rolf; Wirtz, Kai W.

2016-09-01

Marine coastal ecosystem functioning is crucially linked to the transport and fate of suspended particulate matter (SPM). Transport of SPM is controlled by, amongst other factors, sinking velocity ws. Since the ws of cohesive SPM aggregates varies significantly with size and composition of the mineral and organic origin, ws exhibits large spatial variability along gradients of turbulence, SPM concentration (SPMC) and SPM composition. In this study, we retrieved ws for the German Bight, North Sea, by combining measured vertical turbidity profiles with simulation results for turbulent eddy diffusivity. We analyzed ws with respect to modeled prevailing dissipation rates ɛ and found that mean ws were significantly enhanced around log10(ɛ (m2 s-3)) ≈ -5.5. This ɛ region is typically found at water depths of approximately 15 to 20 m along cross-shore transects. Across this zone, SPMC declines towards the offshore waters and a change in particle composition occurs. This characterizes a transition zone with potentially enhanced vertical fluxes. Our findings contribute to the conceptual understanding of nutrient cycling in the coastal region which is as follows. Previous studies identified an estuarine circulation. Its residual landward-oriented bottom currents are loaded with SPM, particularly within the transition zone. This retains and traps fine sediments and particulate-bound nutrients in coastal waters where organic components of SPM become remineralized. Residual surface currents transport dissolved nutrients offshore, where they are again consumed by phytoplankton. Algae excrete extracellular polymeric substances which are known to mediate mineral aggregation and thus sedimentation. This probably takes place particularly in the transition zone and completes the coastal nutrient cycle. The efficiency of the transition zone for retention is thus suggested as an important mechanism that underlies the often observed nutrient gradients towards the coast.

How IPCC Science-Policy Interactions Shape Its Policymaker Summaries

NASA Astrophysics Data System (ADS)

Mach, K. J.; Freeman, P. T.; Mastrandrea, M.; Field, C. B.

2016-12-01

Government approval is a defining feature of the Intergovernmental Panel on Climate Change (IPCC) assessment process. In plenary sessions with scientist authors, IPCC member governments discuss and agree each sentence of every report's summary for policymakers (SPM). This consensus-based approval builds joint ownership of scientific knowledge by both scientists and governments. The approval process and its resulting SPM revisions have received extensive attention in published anecdotes and perspectives, but without comprehensive evaluation to date. We present the results of an in-depth analysis of IPCC SPM revisions, providing an evidence basis for understanding a complex science-policy interaction. Revisions resulting from governmental review and approval expand SPMs. SPM text lengthens by 17 to 53% in recent assessment summaries. Political sensitivities and associated failures of consensus have led to prominent exceptions resulting in SPM contractions. Contrasting recent assertions, we find IPCC SPMs to be as readable as other professionally edited assessment summaries, for multiple measures of reading ease. Across metrics, some SPMs, but not all, become more readable through the revision process. We additionally examine each revision in an SPM for which we have deep familiarity. Most of the SPM's revisions occur prior to the in-person government-approval session, and they emphasize different purposes compared to revisions made during the approval session. Revisions prior to the in-person session largely pertain to clarity, scientific rigor, and explanation, whereas the subsequent in-person government-approval revisions place more emphasis on policy relevance, comprehensiveness of examples, and nuances of expert judgment. The value added in the IPCC government-approval process emerges through multiple stages of revision and approval, as scientists and governments together navigate a complex science-policy interaction.

Secondary Primary Malignancy Risk in Patients With Ovarian Cancer in Taiwan: A Nationwide Population-Based Study.

PubMed

Hung, Yi-Ping; Liu, Chia-Jen; Hu, Yu-Wen; Chen, Min-Huang; Li, Chun-Pin; Yeh, Chiu-Mei; Chiou, Tzeon-Jye; Chen, Tzeng-Ji; Yang, Muh-Hwa; Chao, Yee

2015-09-01

To evaluate the incidence of secondary primary malignancy (SPM) in patients with ovarian cancer using a nationwide retrospective population-based dataset. Patients newly diagnosed with ovarian cancer between 1997 and 2010 were identified using Taiwan's National Health Insurance database. Patients with antecedent malignancies were excluded. Standardized incidence ratios (SIRs) for SPM were calculated and compared with the cancer incidence in the general population. Risk factors for cancer development were analyzed using Cox proportional hazard models. Effects of surgery, chemotherapy, and radiotherapy after ovarian cancer diagnosis were regarded as time-dependent variables to prevent immortal time bias. During the 14-year study period (follow-up of 56,214 person-years), 707 cancers developed in 12,127 patients with ovarian cancer. The SIR for all cancers was 2.78 (95% confidence interval 2.58-3.00). SIRs for follow-up periods of >5, 1-5, and <1 year were 1.87, 2.04, and 6.40, respectively. After the exclusion of SPM occurring within 1 year of ovarian cancer diagnosis, SIRs were significantly higher for cancers of the colon, rectum, and anus (2.14); lung and mediastinum (1.58); breast (1.68); cervix (1.65); uterus (7.96); bladder (3.17), and thyroid (2.23); as well as for leukemia (3.98) and others (3.83). Multivariate analysis showed that age ≥ 50 years was a significant SPM risk factor (hazard ratio [HR] 1.60). Different treatments for ovarian cancer, including radiotherapy (HR 2.07) and chemotherapy (HR 1.27), had different impacts on SPM risk. Patients with ovarian cancer are at increased risk of SPM development. Age ≥ 50 years, radiotherapy, and chemotherapy are independent risk factors. Close surveillance of patients at high risk should be considered for the early detection of SPM.

Big, Deep, and Smart Data in Scanning Probe Microscopy.

PubMed

Kalinin, Sergei V; Strelcov, Evgheni; Belianinov, Alex; Somnath, Suhas; Vasudevan, Rama K; Lingerfelt, Eric J; Archibald, Richard K; Chen, Chaomei; Proksch, Roger; Laanait, Nouamane; Jesse, Stephen

2016-09-27

Scanning probe microscopy (SPM) techniques have opened the door to nanoscience and nanotechnology by enabling imaging and manipulation of the structure and functionality of matter at nanometer and atomic scales. Here, we analyze the scientific discovery process in SPM by following the information flow from the tip-surface junction, to knowledge adoption by the wider scientific community. We further discuss the challenges and opportunities offered by merging SPM with advanced data mining, visual analytics, and knowledge discovery technologies.

Cotton ACAULIS5 is involved in stem elongation and the plant defense response to Verticillium dahliae through thermospermine alteration.

PubMed

Mo, Huijuan; Wang, Xingfen; Zhang, Yan; Yang, Jun; Ma, Zhiying

2015-11-01

Overexpression of GhACL5 , an ACAULIS5 from cotton, in Arabidopsis increased plant height and T-Spm level. Silencing of GhACL5 in cotton exhibited a dwarf phenotype and reduced resistance to Verticillium dahliae. The Arabidopsis thaliana gene ACAULIS5 (ACL5), for which inactivation causes a defect in stem elongation, encodes thermospermine (T-Spm) synthase. However, limited information is available about improvement in plant height by the overexpression of ACL5 gene, and the biological functions of ACL5 genes in response to biotic stress. Here, this study reports that constitutive expression of the cotton ACL5 gene (GhACL5) in Arabidopsis thaliana significantly increased plant height and elevated the level of T-Spm. Silencing of that gene in cotton reduced the amount of T-Spm and led to a severe dwarf phenotype. Expression of GhACL5 was induced upon treatment with the fungal pathogen Verticillium dahliae and plant hormones salicylic acid, jasmonic acid, and ethylene in resistant cotton plants, but gene silencing in cotton enhanced their susceptibility to V. dahliae infection. Furthermore, T-Spm exposure effectively inhibited V. dahliae growth in vitro. In summary, GhACL5 expression is related to in planta levels of T-Spm and is involved in stem elongation and defense responses against V. dahliae.

Pharmaceuticals in settleable particulate material in urban and non-urban waters.

PubMed

Lahti, Marja; Oikari, Aimo

2011-10-01

Wastewater treatment plants (WWTP) are important sources of settleable particulate material (SPM), heading to sediments with natural suspended solids. To date, there is little information about the fate of pharmaceuticals in sediment systems. In this study, the objective was to determine if pharmaceuticals are detected in SPM at locations near WWTPs or even in rural areas, thus being susceptible for sedimentation. SPM samples were collected from 10 sites in Finland, grouped as reference, rural and wastewater effluent sites. SPM collectors were placed about 35 cm above bottom for about 2 months during summer. After extraction, a set of 17 pharmaceuticals was analyzed. Several pharmaceuticals were detected in SPM accumulated at sites next to WWTPs. The concentration of citalopram was notably high (300-1350 ng g⁻¹ dw). Also bisoprolol and ciprofloxacin were detected at high concentrations (6-325 and 9-390 ng g⁻¹ dw, respectively). In contrast, none of the pharmaceuticals were detected from reference sites and only two were found from a single rural site. There is no previous information about the presence of pharmaceuticals in SPM. The results showed that pharmaceuticals are sorbed to particles in WWTP and nearby, eventually ending up in sediments. These results also indicate that pharmaceuticals are not markedly contaminating sediments of rural areas in Finland. Copyright © 2011 Elsevier Ltd. All rights reserved.

The dynamics of suspended particulate matter (SPM) and chlorophyll-a from intratidal to annual time scales in a coastal turbidity maximum

NASA Astrophysics Data System (ADS)

van der Hout, C. M.; Witbaard, R.; Bergman, M. J. N.; Duineveld, G. C. A.; Rozemeijer, M. J. C.; Gerkema, T.

2017-09-01

The analysis of 1.8 years of data gives an understanding of the response to varying forcing of suspended particulate matter (SPM) and chlorophyll-a (CHL-a) in a coastal turbidity maximum zone (TMZ). Both temporal and vertical concentration variations in the near-bed layer (0-2 m) in the shallow (11 m deep) coastal zone at 1 km off the Dutch coast are shown. Temporal variations in the concentration of both parameters are found on tidal and seasonal scales, and a marked response to episodic events (e.g. storms). The seasonal cycle in the near-bed CHL-a concentration is determined by the spring bloom. The role of the wave climate as the primary forcing in the SPM seasonal cycle is discussed. The tidal current provides a background signal, generated predominantly by local resuspension and settling and a minor role is for advection in the cross-shore and the alongshore direction. We tested the logarithmic Rouse profile to the vertical profiles of both the SPM and the CHL-a data, with respectively 84% and only 2% success. The resulting large percentage of low Rouse numbers for the SPM profiles suggest a mixed suspension is dominant in the TMZ, i.e. surface SPM concentrations are in the same order of magnitude as near-bed concentrations.

A missing link in the estuarine nitrogen cycle?: Coupled nitrification-denitrification mediated by suspended particulate matter.

PubMed

Zhu, Weijing; Wang, Cheng; Hill, Jaclyn; He, Yangyang; Tao, Bangyi; Mao, Zhihua; Wu, Weixiang

2018-02-02

In estuarine and coastal ecosystems, the majority of previous studies have considered coupled nitrification-denitrification (CND) processes to be exclusively sediment based, with little focus on suspended particulate matter (SPM) in the water column. Here, we present evidence of CND processes in the water column of Hangzhou Bay, one of the largest macrotidal embayments in the world. Spearman's correlation analysis showed that SPM was negatively correlated with nitrate (rho = -0.372, P = 0.018) and marker genes for nitrification and denitrification in the water column were detected by quantitative PCR analysis. The results showed that amoA and nir gene abundances strongly correlated with SPM (all P < 0.01) and the ratio of amoA/nir strongly correlated with nitrate (rho = -0.454, P = 0.003). Furthermore, aggregates consisting of nitrifiers and denitrifiers on SPM were also detected by fluorescence in situ hybridization. Illumina MiSeq sequencing further showed that ammonia oxidizers mainly belonged to the genus Nitrosomonas, while the potential denitrifying genera Bradyrhizobium, Comamonas, Thauera, Stenotrophomonas, Acinetobacter, Anaeromyxobacter, Sulfurimonas, Paenibacillus and Sphingobacterium showed significant correlations with SPM (all P < 0.01). This study suggests that SPM may provide a niche for CND processes to occur, which has largely been missing from our understanding of nitrogen cycling in estuarine waters.

Understanding Succession Planning and Management Efforts at Midwestern University: A Mixed Methods Study

ERIC Educational Resources Information Center

Mateso, Peter E. E.

2010-01-01

The purpose of this concurrent triangulation mixed methods study was to understand the status of succession planning and management (SPM) efforts of the subject university as perceived by the fulltime academic and fulltime administrative staff. Four research questions guided this study: (1) how do fulltime academic staff and fulltime…

Estimation of suspended particulate matter in turbid coastal waters: application to hyperspectral satellite imagery.

PubMed

Zhao, Jun; Cao, Wenxi; Xu, Zhantang; Ye, Haibin; Yang, Yuezhong; Wang, Guifen; Zhou, Wen; Sun, Zhaohua

2018-04-16

An empirical algorithm is proposed to estimate suspended particulate matter (SPM) ranging from 0.675 to 25.7 mg L -1 in the turbid Pearl River estuary (PRE). Comparisons between model predicted and in situ measured SPM resulted in R 2 s of 0.97 and 0.88 and mean absolute percentage errors (MAPEs) of 23.96% and 29.69% by using the calibration and validation data sets, respectively. The developed algorithm demonstrated the highest accuracy when compared with existing ones for turbid coastal waters. The diurnal dynamics of SPM was revealed by applying the proposed algorithm to reflectance data collected by a moored buoy in the PRE. The established algorithm was implemented to Hyperspectral Imager for the Coastal Ocean (HICO) data and the distribution pattern of SPM in the PRE was elucidated. Validation of HICO-derived reflectance data by using concurrent MODIS/Aqua data as a benchmark indicated their reliability. Factors influencing variability of SPM in the PRE were analyzed, which implicated the combined effects of wind, tide, rainfall, and circulation as the cause.

Numerical Investigation of an Oscillating Flat Plate Airfoil

NASA Astrophysics Data System (ADS)

Mohaghegh, Fazlolah; Janechek, Matthew; Buchholz, James; Udaykumar, Hs

2017-11-01

This research investigates the vortex dynamics of a plunging flat plate airfoil by analyzing the vorticity transport in 2D simulations. A horizontal airfoil is subject to a freestream flow at Re =10000. A prescribed vertical sinusoidal motion is applied to the airfoil. Smoothed Profile Method (SPM) models the fluid-structure interaction. SPM as a diffuse interface model considers a thickness for the interface and applies a smooth transition from solid to fluid. As the forces on the airfoil are highly affected by the interaction of the generated vortices from the surface, it is very important to find out whether a diffuse interface solver can model a flow dominated by vorticities. The results show that variation of lift coefficient with time agrees well with the experiment. Study of vortex evolution shows that similar to experiments, when the plate starts moving downward from top, the boundary layer is attached to the surface and the leading-edge vortex (LEV) is very small. By time, LEV grows and rolls up and a secondary vortex emerges. Meanwhile, the boundary layer starts to separate and finally LEV detaches from the surface. In overall, SPM as a diffuse interface model can predict the lift force and vortex pattern accurately.

An Approach for Integrating the Prioritization of Functional and Nonfunctional Requirements

PubMed Central

Dabbagh, Mohammad; Lee, Sai Peck

2014-01-01

Due to the budgetary deadlines and time to market constraints, it is essential to prioritize software requirements. The outcome of requirements prioritization is an ordering of requirements which need to be considered first during the software development process. To achieve a high quality software system, both functional and nonfunctional requirements must be taken into consideration during the prioritization process. Although several requirements prioritization methods have been proposed so far, no particular method or approach is presented to consider both functional and nonfunctional requirements during the prioritization stage. In this paper, we propose an approach which aims to integrate the process of prioritizing functional and nonfunctional requirements. The outcome of applying the proposed approach produces two separate prioritized lists of functional and non-functional requirements. The effectiveness of the proposed approach has been evaluated through an empirical experiment aimed at comparing the approach with the two state-of-the-art-based approaches, analytic hierarchy process (AHP) and hybrid assessment method (HAM). Results show that our proposed approach outperforms AHP and HAM in terms of actual time-consumption while preserving the quality of the results obtained by our proposed approach at a high level of agreement in comparison with the results produced by the other two approaches. PMID:24982987

An approach for integrating the prioritization of functional and nonfunctional requirements.

PubMed

Dabbagh, Mohammad; Lee, Sai Peck

2014-01-01

Due to the budgetary deadlines and time to market constraints, it is essential to prioritize software requirements. The outcome of requirements prioritization is an ordering of requirements which need to be considered first during the software development process. To achieve a high quality software system, both functional and nonfunctional requirements must be taken into consideration during the prioritization process. Although several requirements prioritization methods have been proposed so far, no particular method or approach is presented to consider both functional and nonfunctional requirements during the prioritization stage. In this paper, we propose an approach which aims to integrate the process of prioritizing functional and nonfunctional requirements. The outcome of applying the proposed approach produces two separate prioritized lists of functional and non-functional requirements. The effectiveness of the proposed approach has been evaluated through an empirical experiment aimed at comparing the approach with the two state-of-the-art-based approaches, analytic hierarchy process (AHP) and hybrid assessment method (HAM). Results show that our proposed approach outperforms AHP and HAM in terms of actual time-consumption while preserving the quality of the results obtained by our proposed approach at a high level of agreement in comparison with the results produced by the other two approaches.

Linking water quality guidelines to the natural characteristics of catchments in order to support distinct aquatic ecosystems: Water quality guidelines for suspended particulate matter

NASA Astrophysics Data System (ADS)

Bilotta, G. S.; Grove, M. K.; Harrison, C.; Joyce, C. B.; Peacock, C.

2012-12-01

The natural characteristics of a catchment provide a template that controls the background rates of geomorphological processes operating within that catchment, which in-turn determines the background physico-chemical and hydro-morphological characteristics of the catchment's surface waters. Large differences in the natural characteristics of catchments (e.g. geology, topography, climate), lead to unique physico-chemical and hydro-morphological conditions that support unique freshwater communities. However, this uniqueness is not always recognised in international water quality guidelines, which often attempt to apply blanket water-quality guidelines to 'protect' a wide range of ecosystems. In this paper we investigate the natural characteristics that control background concentrations of suspended particulate matter (SPM - including nano-scale particles to sand-sized sediments), which is a well-known cause of ecological degradation. At present, the management of SPM is hampered by a lack of understanding of the SPM conditions that water quality managers should aim to achieve in contrasting environments in order to support good ecological status. To address this, in this paper we examine the SPM preferences of contrasting biological communities that are in reference condition (minimal anthropogenic disturbance and high ecological status). We analyse historical SPM data collected on a monthly basis from a wide range of reference-condition temperate environments (638 stream/river sites comprising 42 different biological community-types). This analysis reveals that there are statistically significant differences (One-way ANOVA p < 0.001) between the background SPM concentrations observed in contrasting communities that are in reference condition. Mean background SPM concentrations for contrasting communities ranged from 1.7 to 26.2 mg L-1 (i.e. more than a 15-fold difference). We propose a model for predicting environment-specific water quality guidelines for SPM. In order to develop this model, the 638 reference-condition sites were first classified into one of five mean background SPM ranges (0.00-5.99, 6.00-11.99, 12.00-17.99, 18.00-23.99 and >24.00 mg L-1). Stepwise Multiple Discriminant Analysis (MDA) of these ranges showed that a site's SPM range can be predicted as a function of: mean annual air temperature, mean annual precipitation, mean altitude of upstream catchment, distance from source, slope to source, channel width and depth, the percentage of catchment area comprised of clay, chalk, and hard rock solid geology, and the percentage of the catchment area comprised of blown sand/landslide material as the surface (drift) material. Although the model is still being improved and developed, this research highlights the need to link water quality guidelines to the natural characteristics of catchments and the physico-chemical preferences of the biological communities that would naturally inhabit them.

Bounds on the cross-correlation functions of state m-sequences

NASA Astrophysics Data System (ADS)

Woodcock, C. F.; Davies, Phillip A.; Shaar, Ahmed A.

1987-03-01

Lower and upper bounds on the peaks of the periodic Hamming cross-correlation function for state m-sequences, which are often used in frequency-hopped spread-spectrum systems, are derived. The state position mapped (SPM) sequences of the state m-sequences are described. The use of SPM sequences for OR-channel code division multiplexing is studied. The relation between the Hamming cross-correlation function and the correlation function of SPM sequence is examined. Numerical results which support the theoretical data are presented.

Relevant Optical Issues of the SPM-Twin Telescopes

NASA Astrophysics Data System (ADS)

González, J. J.; Orlov, V.

2007-06-01

Most technical aspects of the SPM-Twin Telescopes have been basically solved by the Magellan and MMT projects. However, the Spectroscopic "Wide Field Telescope" will be the first of its kind and an optical solution based on Magellan needs to be further investigated. In addition, the requirements for adaptive optics for the Standard Field Telescope need to be worked out. In this contribution we will compare optical wide field conceptual designs and the potential scope of AO for SPM-Twin.

Spatial and temporal distribution of metals in suspended particulate matter of the Kali estuary, India

NASA Astrophysics Data System (ADS)

Suja, S.; Kessarkar, Pratima M.; Fernandes, Lina L.; Kurian, Siby; Tomer, Arti

2017-09-01

Major (Al, Fe, Mn, Ti, Mg) and trace (Cu, Zn, Pb, Cr, Ni, Co, Zr, Rb, Sr, Ba, Li, Be, Sc, V, Ga, Nb, Mo, Sn, Sb, Cs, Hf, Ta, Bi, Th, U) elements and particulate organic carbon (POC) concentrations in surface suspended particulate matter (SPM) of the Kali estuary, (central west coast of India) were studied during the pre-monsoon, monsoon and post monsoon seasons to infer estuarine processes, source of SPM and Geoaccumulation Index (Igeo) assigned pollutionIgeo levels. Distribution of SPM indicates the presence of the estuarine turbidity maximum (ETM) during all three seasons near the river mouth and a second ETM during the post monsoon time in the upstream associated with salinities gradient. The SPM during the monsoon is finer grained (avg. 53 μm), characterized by uniformly low normalized elemental concentration, whereas the post and pre monsoon are characterized by high normalized elemental concentration with coarser grain size (avg. 202 μm and 173 μm respectively) with highest ratios in the upstream estuary. The elemental composition and principal component analysis for the upstream estuary SPM support more contribution from the upstream catchment area rocks during the monsoon season; there is additional contribution from the downstream catchment area during the pre and post monsoon period due to the tidal effect. The Kali estuarine SPM has higher Al, Fe, Mn, Ti, Mg, Ni, Co, Ba, Li and V with respect to Average World River SPM (WRSPM). Igeo values for the SPM indicate Kali Estuary to be severely enriched with Mn and moderately enriched with Cu, Zn, Ni, Co, U and Mo in the upstream estuary during pre and post monsoon seasons. Seasonal changes in salinity gradient (reduced freshwater flow due to closing of the dam gates), reduced velocity at meandering region of the estuary and POC of 1.6-2.3% resulted in co-precipitation of trace elements that were further fortified by flocculation and coagulation throughout the water column resulting in metal trapping in the upstream region.

Uptake and degradation of several pyrenesphingomyelins by skin fibroblasts from control subjects and patients with Niemann-Pick disease. Effect of the structure of the fluorescent fatty acyl residue.

PubMed Central

Levade, T; Gatt, S; Salvayre, R

1991-01-01

Three fluorescent analogues of sphingomyelin (SPM), each containing pyrene in the fatty acyl residue, were synthesized and employed for the study of their mode of uptake by, and degradation within, intact cultured human skin fibroblasts. These were prepared by condensing sphingosylphosphocholine and the following fatty acids: pyrenedodecanoic acid (P12), pyrenesulphonylaminoundecanoic acid (PSA11) and pyrenepropenoic acid (P3:1). The cell association and catabolism of these SPM analogues by normal, Niemann-Pick-disease-Type-A and low-density-lipoprotein (LDL)-receptor-negative familial hypercholesterolaemia fibroblasts were investigated and compared with the metabolism of [cholinemethyl-14C]sphingomyelin. The catabolism of the fluorescent derivatives was monitored by measuring the appearance of the corresponding fluorescent ceramides. Two modes of uptake and degradation patterns were observed. Thus P12-SPM and radiolabelled SPM were taken up by LDL-receptor-mediated endocytosis when incubated with serum-containing medium, this conclusion being supported by the very low uptake by familial-hypercholesterolaemia fibroblasts, which lack the apolipoprotein-B/E receptor. After uptake, these compounds were metabolically degraded solely by the lysosomal sphingomyelinase, as evidenced by the fact that more than 98% of the SPM remained undegraded in Niemann-Pick-disease cells. By contrast, PSA11- and P3:1-SPMs were taken up by a receptor-independent endocytic pathway, as indicated by the similar rates of uptake in control and familial-hypercholesterolaemia cells in the absence or presence of fetal-calf serum in the culture medium. The degradation of PSA11-SPM and P3:1-SPM was brought about, in the main, by the lysosomal sphingomyelinase, but also by a yet uncharacterized process. The latter catabolic pathway, active in Niemann-Pick-disease-Type-A fibroblasts, seems to differ from the neutral Mg2(+)-dependent sphingomyelinase whose activity was undetectable in homogenates of skin fibroblasts. The present study emphasizes the influence of the structure of the fatty acyl moiety of SPM on its association with lipoproteins and/or cell membranes and on its intracellular routing and metabolic degradation. Images Fig. 2. PMID:2018477

Sources and distributions of branched and isoprenoid tetraether lipids on the Amazon shelf and fan: Implications for the use of GDGT-based proxies in marine sediments

NASA Astrophysics Data System (ADS)

Zell, Claudia; Kim, Jung-Hyun; Hollander, David; Lorenzoni, Laura; Baker, Paul; Silva, Cleverson Guizan; Nittrouer, Charles; Sinninghe Damsté, Jaap S.

2014-08-01

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) in river fan sediments have been used successfully to reconstruct mean annual air temperature (MAAT) and soil pH of the Congo River drainage basin. However, in a previous study of Amazon deep-sea fan sediments the reconstructed MAATs were ca. 10 °C colder than the actual MAAT of the Amazon basin. In this study we investigated this apparent offset, by comparing the concentrations and distributions of brGDGTs in Amazon River suspended particulate matter (SPM) and sediments to those in marine SPM and surface sediments. The riverine brGDGT input was evident from the elevated brGDGT concentrations in marine SPM and surface sediments close to the river mouth. The distributions of brGDGTs in marine SPM and sediments varied widely, but generally showed a higher relative abundance of methylated and cyclic brGDGTs than those in the river. Since this difference in brGDGT distribution was also found in intact polar lipid (IPL)-derived brGDGTs, which were more recently produced, the change in the marine brGDGT distribution was most likely due to marine in situ production. Consequently, the MAATs calculated based on the methylation of branched tetraethers (MBT) and the cyclisation of branched tetraethers (CBT) were lower and the CBT-derived pH values were higher than those of the Amazon basin. However, SPM and sediments from stations close to the river mouth still showed MBT/CBT values that were similar to those of the river. Therefore, we recommend caution when applying the MBT/CBT proxy, it should only be used in sediment cores that were under high river influence. The influence of riverine derived isoprenoid GDGT (isoGDGT) on the isoGDGT-based TEX86 temperature proxy was also examined in marine SPM and sediments. An input of riverine isoGDGTs from the Amazon River was apparent, but its influence on the marine TEX86 was minor since the TEX86 of SPM in the Amazon River was similar to that in the marine SPM and sediments.

Comparing diffuse optical tomography and functional magnetic resonance imaging signals during a cognitive task: pilot study

PubMed Central

Hernández-Martin, Estefania; Marcano, Francisco; Casanova, Oscar; Modroño, Cristian; Plata-Bello, Julio; González-Mora, Jose Luis

2017-01-01

Abstract. Diffuse optical tomography (DOT) measures concentration changes in both oxy- and deoxyhemoglobin providing three-dimensional images of local brain activations. A pilot study, which compares both DOT and functional magnetic resonance imaging (fMRI) volumes through t-maps given by canonical statistical parametric mapping (SPM) processing for both data modalities, is presented. The DOT series were processed using a method that is based on a Bayesian filter application on raw DOT data to remove physiological changes and minimum description length application index to select a number of singular values, which reduce the data dimensionality during image reconstruction and adaptation of DOT volume series to normalized standard space. Therefore, statistical analysis is performed with canonical SPM software in the same way as fMRI analysis is done, accepting DOT volumes as if they were fMRI volumes. The results show the reproducibility and ruggedness of the method to process DOT series on group analysis using cognitive paradigms on the prefrontal cortex. Difficulties such as the fact that scalp–brain distances vary between subjects or cerebral activations are difficult to reproduce due to strategies used by the subjects to solve arithmetic problems are considered. T-images given by fMRI and DOT volume series analyzed in SPM show that at the functional level, both DOT and fMRI measures detect the same areas, although DOT provides complementary information to fMRI signals about cerebral activity. PMID:28386575

Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods

PubMed Central

de Bresser, Jeroen; Hendrikse, Jeroen; Siero, Jeroen C. W.; Petersen, Esben T.; De Vis, Jill B.

2018-01-01

Objective In previous work we have developed a fast sequence that focusses on cerebrospinal fluid (CSF) based on the long T2 of CSF. By processing the data obtained with this CSF MRI sequence, brain parenchymal volume (BPV) and intracranial volume (ICV) can be automatically obtained. The aim of this study was to assess the precision of the BPV and ICV measurements of the CSF MRI sequence and to validate the CSF MRI sequence by comparison with 3D T1-based brain segmentation methods. Materials and methods Ten healthy volunteers (2 females; median age 28 years) were scanned (3T MRI) twice with repositioning in between. The scan protocol consisted of a low resolution (LR) CSF sequence (0:57min), a high resolution (HR) CSF sequence (3:21min) and a 3D T1-weighted sequence (6:47min). Data of the HR 3D-T1-weighted images were downsampled to obtain LR T1-weighted images (reconstructed imaging time: 1:59 min). Data of the CSF MRI sequences was automatically segmented using in-house software. The 3D T1-weighted images were segmented using FSL (5.0), SPM12 and FreeSurfer (5.3.0). Results The mean absolute differences for BPV and ICV between the first and second scan for CSF LR (BPV/ICV: 12±9/7±4cc) and CSF HR (5±5/4±2cc) were comparable to FSL HR (9±11/19±23cc), FSL LR (7±4, 6±5cc), FreeSurfer HR (5±3/14±8cc), FreeSurfer LR (9±8, 12±10cc), and SPM HR (5±3/4±7cc), and SPM LR (5±4, 5±3cc). The correlation between the measured volumes of the CSF sequences and that measured by FSL, FreeSurfer and SPM HR and LR was very good (all Pearson’s correlation coefficients >0.83, R2 .67–.97). The results from the downsampled data and the high-resolution data were similar. Conclusion Both CSF MRI sequences have a precision comparable to, and a very good correlation with established 3D T1-based automated segmentations methods for the segmentation of BPV and ICV. However, the short imaging time of the fast CSF MRI sequence is superior to the 3D T1 sequence on which segmentation with established methods is performed. PMID:29672584

Rapid inactivation of the maize transposable element En/Spm in Medicago truncatula.

PubMed

d'Erfurth, I; Cosson, V; Eschstruth, A; Rippa, S; Messinese, E; Durand, P; Trinh, H; Kondorosi, A; Ratet, P

2003-09-01

Transposable elements have been widely used as mutagens in many organisms. Among them, the maize transposable element En/Spm has been shown to transpose efficiently in several plant species including the model plant Arabidopsis, where it has been used for large-scale mutagenesis. To determine whether we could use this transposon as a mutagen in the model legume plant Medicago truncatula, we tested the activity of the autonomous element, as well as two defective elements, in this plant, and in Arabidopsis as a positive control. In agreement with previous reports, we observed efficient excision of the autonomous En/Spm element in A. thaliana. This element was also active in M. truncatula, but the transposition activity was low and was apparently restricted to the tissue culture step necessary for the production of transgenic plants. The activity of one of the defective transposable elements, dSpm, was very low in A. thaliana and even lower in M. truncatula. The use of different sources of transposases suggested that this defect in transposition was associated with the dSpm element itself. Transposition of the other defective element, I6078, was also detected in M. truncatula, but, as observed with the autonomous element, transposition events were very rare and occurred during tissue culture. These results suggest that the En/Spm element is rapidly inactivated in the regenerated plants and their progeny, and therefore is not suitable for routine insertion mutagenesis in M. truncatula.

Human Milk Proresolving Mediators Stimulate Resolution of Acute Inflammation

PubMed Central

Dalli, Jesmond; Serhan, Charles N

2015-01-01

Human milk contains nutrients and bioactive products relevant to infant development and immunological protection. Here, we investigated the pro-resolving properties of milk using human milk lipid mediator isolates (HLMI) and determined their impact on resolution programs in vivo and with human macrophages. HLMI reduced maximum neutrophil numbers (14.6±1.2×106 to 11.0±1.0×106 cells/exudate) and shortened the resolution interval (Ri; 50% neutrophil reduction) 54% compared to peritonitis. Using rigorous liquid-chromatography tandem-mass spectrometry (LC-MS-MS)-based lipid mediator (LM) metabololipidomics, we demonstrated that human milk possesses a proresolving LM-SPM signature profile, containing specialized proresolving mediators (SPM; e.g. resolvins, protectins, maresins and lipoxins) at bioactive levels (pico-nanomolar concentrations) that enhanced human macrophage efferocytosis and bacterial containment. SPM identified in human milk included D-series resolvins, (e.g. Resolvin (Rv) D1, RvD2, RvD3, AT-RvD3 and RvD4), Protectin (PD)1, Maresin (MaR)1, E-series resolvins (e.g. RvE1, RvE2 and RvE3) and lipoxins (LXA4 and LXB4). Of the SPM identified in human milk, RvD2 and MaR1 (50 ng/mouse) individually shortened Ri ~75%. Milk from mastitis gave higher LTB4 and prostanoids and lower SPM levels. Taken together, these findings provide evidence that human milk has pro-resolving actions via comprehensive LM-SPM profiling, describing a potentially novel mechanism in maternal-infant biochemical imprinting. PMID:26462421

Spontaneous swallowing frequency has potential to identify dysphagia in acute stroke.

PubMed

Crary, Michael A; Carnaby, Giselle D; Sia, Isaac; Khanna, Anna; Waters, Michael F

2013-12-01

Spontaneous swallowing frequency has been described as an index of dysphagia in various health conditions. This study evaluated the potential of spontaneous swallow frequency analysis as a screening protocol for dysphagia in acute stroke. In a cohort of 63 acute stroke cases, swallow frequency rates (swallows per minute [SPM]) were compared with stroke and swallow severity indices, age, time from stroke to assessment, and consciousness level. Mean differences in SPM were compared between patients with versus without clinically significant dysphagia. Receiver operating characteristic curve analysis was used to identify the optimal threshold in SPM, which was compared with a validated clinical dysphagia examination for identification of dysphagia cases. Time series analysis was used to identify the minimally adequate time period to complete spontaneous swallow frequency analysis. SPM correlated significantly with stroke and swallow severity indices but not with age, time from stroke onset, or consciousness level. Patients with dysphagia demonstrated significantly lower SPM rates. SPM differed by dysphagia severity. Receiver operating characteristic curve analysis yielded a threshold of SPM≤0.40 that identified dysphagia (per the criterion referent) with 0.96 sensitivity, 0.68 specificity, and 0.96 negative predictive value. Time series analysis indicated that a 5- to 10-minute sampling window was sufficient to calculate spontaneous swallow frequency to identify dysphagia cases in acute stroke. Spontaneous swallowing frequency presents high potential to screen for dysphagia in acute stroke without the need for trained, available personnel.

Effect of including sweet potato (Ipomoea batatas Lam) meal in finishing pig diets on growth performance, carcass traits and pork quality.

PubMed

Pietrosemoli, Silvana; Moron-Fuenmayor, Oneida Elizabeth; Paez, Angel; Villamide, Maria Jesús

2016-10-01

The partial replacement of a commercial concentrate at 10-20% and 15-30% (the first percentage of each dietary treatment corresponded to weeks 1-3 and the second to weeks 4-7 of the experiment, respectively) by sweet potato meal (SPM; 70% foliage: 30% roots) was evaluated for growth performance, carcass yield, instrumental and sensory pork quality using 36 commercial crossbred pigs (56.8 ± 1.3 kg initial body weight). Three dietary treatments were compared in a randomized complete block design. Most growth, carcass traits and pork quality variables were not affected by the SPM inclusion. Growth performance averaged 868 g/day and feed efficiency 0.24 kg/kg. However, feed intake increased 2.2% (P = 0.04) in pigs fed the 10-20% SPM diets, in a similar order of magnitude as the decrease in dietary energy. Despite an increase in gastrointestinal tract as a percent of hot carcass weight (+14.7%) (P = 0.03) with SPM inclusion, carcass yield averaged 69.4%. Conversely, decreases in loin yield (-4.2%) (P = 0.05), backfat thickness (-6.0%) (P < 0.01) and pork tenderness (-13%) (P = 0.02) were observed with 15-30% SPM inclusion. Results suggest that up to 20% SPM inclusion is a viable feed strategy for finishing pigs, easily replicable in small farm settings. © 2016 Japanese Society of Animal Science. © 2016 Japanese Society of Animal Science.

A multistage crucible of revision and approval shapes IPCC policymaker summaries.

PubMed

Mach, Katharine J; Freeman, Patrick T; Mastrandrea, Michael D; Field, Christopher B

2016-08-01

Intergovernmental Panel on Climate Change (IPCC) member governments approve each report's summary for policymakers (SPM) by consensus, discussing and agreeing on each sentence in a plenary session with scientist authors. A defining feature of IPCC assessment, the governmental approval process builds joint ownership of current knowledge by scientists and governments. The resulting SPM revisions have been extensively discussed in anecdotes, interviews, and perspectives, but they have not been comprehensively analyzed. We provide an in-depth evaluation of IPCC SPM revisions, establishing an evidential basis for understanding their nature. Revisions associated with governmental review and approval generally expand SPMs, with SPM text growing by 17 to 53% across recent assessment reports. Cases of high political sensitivity and failure to reach consensus are notable exceptions, resulting in SPM contractions. In contrast to recent claims, we find that IPCC SPMs are as readable, for multiple metrics of reading ease, as other professionally edited assessment summaries. Across reading-ease metrics, some SPMs become more readable through governmental review and approval, whereas others do not. In an SPM examined through the entire revision process, most revisions associated with governmental review and approval occurred before the start of the government-approval plenary session. These author revisions emphasize clarity, scientific rigor, and explanation. In contrast, the subsequent plenary revisions place greater emphasis especially on policy relevance, comprehensiveness of examples, and nuances of expert judgment. Overall, the value added by the IPCC process emerges in a multistage crucible of revision and approval, as individuals together navigate complex science-policy terrain.

A method searching for optimum fractional order and its application in self-phase modulation induced nonlinear phase noise estimation in coherent optical fiber transmission systems

NASA Astrophysics Data System (ADS)

Huang, Chuan; Guo, Peng; Yang, Aiying; Qiao, Yaojun

2018-07-01

In single channel systems, the nonlinear phase noise only comes from the channel itself through self-phase modulation (SPM). In this paper, a fast-nonlinear effect estimation method is proposed based on fractional Fourier transformation (FrFT). The nonlinear phase noise caused by Self-phase modulation effect is accurately estimated for single model 10Gbaud OOK and RZ-QPSK signals with the fiber length range of 0-200 km and the launch power range of 1-10 mW. The pulse windowing is adopted to search the optimum fractional order for the OOK and RZ-QPSK signals. Since the nonlinear phase shift caused by the SPM effect is very small, the accurate optimum fractional order of the signal cannot be found based on the traditional method. In this paper, a new method magnifying the phase shift is proposed to get the accurate optimum order and thus the nonlinear phase shift is calculated. The simulation results agree with the theoretical analysis and the method is applicable to signals whose pulse type has the similar characteristics with Gaussian pulse.

Prioritizing conservation activities using reserve site selection methods and population viability analysis.

PubMed

Newbold, Stephen C; Siikamäki, Juha

2009-10-01

In recent years a large literature on reserve site selection (RSS) has developed at the interface between ecology, operations research, and environmental economics. Reserve site selection models use numerical optimization techniques to select sites for a network of nature reserves for protecting biodiversity. In this paper, we develop a population viability analysis (PVA) model for salmon and incorporate it into an RSS framework for prioritizing conservation activities in upstream watersheds. We use spawner return data for three closely related salmon stocks in the upper Columbia River basin and estimates of the economic costs of watershed protection from NOAA to illustrate the framework. We compare the relative cost-effectiveness of five alternative watershed prioritization methods, based on various combinations of biological and economic information. Prioritization based on biological benefit-economic cost comparisons and accounting for spatial interdependencies among watersheds substantially outperforms other more heuristic methods. When using this best-performing prioritization method, spending 10% of the cost of protecting all upstream watersheds yields 79% of the biological benefits (increase in stock persistence) from protecting all watersheds, compared to between 20% and 64% for the alternative methods. We also find that prioritization based on either costs or benefits alone can lead to severe reductions in cost-effectiveness.

Associative list processing unit

DOEpatents

Hemmert, Karl Scott; Underwood, Keith D.

2013-01-29

An associative list processing unit and method comprising employing a plurality of prioritized cell blocks and permitting inserts to occur in a single clock cycle if all of the cell blocks are not full. Also, an associative list processing unit and method comprising employing a plurality of prioritized cell blocks and using a tree of prioritized multiplexers descending from the plurality of cell blocks.

Magnetic fingerprint of the sediment load in a meander bend section of the Seine River (France)

NASA Astrophysics Data System (ADS)

Kayvantash, D.; Cojan, I.; Kissel, C.; Franke, C.

2017-06-01

This study aims to evaluate the potential of magnetic methods to determine the composition of the sediment load in a cross section of an unmanaged meander in the upstream stretch of the Seine River (Marnay-sur-Seine). Suspended particulate matter (SPM) was collected based on a regular sampling scheme along a cross section of the river, at two different depth levels: during a low-water stage (May 2014) and a high-water stage (February 2015). Riverbed sediments (RBS) were collected during the low-water stage and supplementary samples were taken from the outer and inner banks. Magnetic properties of the dry bulk SPM and sieved RBS and bank sediments were analysed. After characterizing the main magnetic carrier as magnetite, hysteresis parameters were measured, giving access to the grain size and the concentration of these magnetite particles. The results combined with sedimentary grain size data were compared to the three-dimensional velocity profile of the river flow. In the RBS where the magnetic grain size is rather uniform, the concentration of magnetite is inversely proportional to the mean grain size of the total sediment indicating that magnetite is strongly associated with the fine sedimentary fraction. The same pattern is observed in the samples from the outer and inner banks. During the low-water stage, the uniformly fine SPM grain size distribution characterizes the wash load. The magnetic fraction is also relatively fine (within the pseudo single domain range) with concentration similar to that of the fine RBS fraction. During the high-water stage, SPM samples correspond to mixtures of wash load and resuspended sediment from the bedload and riverbanks. Here, the grain size distribution is heterogeneous across the section showing coarser particles compared to those in the low-water stage and more varying magnetite concentrations while the magnetic grain size is like that of the low-water stage. The magnetite concentration in the high-water SPM can be modelled based on a mixing of the magnetite concentrations of the different grain size fractions, thus quantifying the impact of resuspension in the cross section.

Priority rating : stormwater outfall prioritization scheme

DOT National Transportation Integrated Search

1996-10-01

The prioritization system, which compares the impacts of one outfall to another : and makes a determination of their overall impacts, was developed in the : Prioritization Method for Retrofitting Highways with Stormwater BMPs, prepared : by the Water...

Using SPM 12’s Second-Level Bayesian Inference Procedure for fMRI Analysis: Practical Guidelines for End Users

PubMed Central

Han, Hyemin; Park, Joonsuk

2018-01-01

Recent debates about the conventional traditional threshold used in the fields of neuroscience and psychology, namely P < 0.05, have spurred researchers to consider alternative ways to analyze fMRI data. A group of methodologists and statisticians have considered Bayesian inference as a candidate methodology. However, few previous studies have attempted to provide end users of fMRI analysis tools, such as SPM 12, with practical guidelines about how to conduct Bayesian inference. In the present study, we aim to demonstrate how to utilize Bayesian inference, Bayesian second-level inference in particular, implemented in SPM 12 by analyzing fMRI data available to public via NeuroVault. In addition, to help end users understand how Bayesian inference actually works in SPM 12, we examine outcomes from Bayesian second-level inference implemented in SPM 12 by comparing them with those from classical second-level inference. Finally, we provide practical guidelines about how to set the parameters for Bayesian inference and how to interpret the results, such as Bayes factors, from the inference. We also discuss the practical and philosophical benefits of Bayesian inference and directions for future research. PMID:29456498

Distributed Source Modeling of Language with Magnetoencephalography: Application to Patients with Intractable Epilepsy

PubMed Central

McDonald, Carrie R.; Thesen, Thomas; Hagler, Donald J.; Carlson, Chad; Devinksy, Orrin; Kuzniecky, Rubin; Barr, William; Gharapetian, Lusineh; Trongnetrpunya, Amy; Dale, Anders M.; Halgren, Eric

2009-01-01

Purpose To examine distributed patterns of language processing in healthy controls and patients with epilepsy using magnetoencephalography (MEG), and to evaluate the concordance between laterality of distributed MEG sources and language laterality as determined by the intracarotid amobarbitol procedure (IAP). Methods MEG was performed in ten healthy controls using an anatomically-constrained, noise-normalized distributed source solution (dSPM). Distributed source modeling of language was then applied to eight patients with intractable epilepsy. Average source strengths within temporoparietal and frontal lobe regions of interest (ROIs) were calculated and the laterality of activity within ROIs during discrete time windows was compared to results from the IAP. Results In healthy controls, dSPM revealed activity in visual cortex bilaterally from ~80-120ms in response to novel words and sensory control stimuli (i.e., false fonts). Activity then spread to fusiform cortex ~160-200ms, and was dominated by left hemisphere activity in response to novel words. From ~240-450ms, novel words produced activity that was left-lateralized in frontal and temporal lobe regions, including anterior and inferior temporal, temporal pole, and pars opercularis, as well as bilaterally in posterior superior temporal cortex. Analysis of patient data with dSPM demonstrated that from 350-450ms, laterality of temporoparietal sources agreed with the IAP 75% of the time, whereas laterality of frontal MEG sources agreed with the IAP in all eight patients. Discussion Our results reveal that dSPM can unveil the timing and spatial extent of language processes in patients with epilepsy and may enhance knowledge of language lateralization and localization for use in preoperative planning. PMID:19552656

Post traumatic brain perfusion SPECT analysis using reconstructed ROI maps of radioactive microsphere derived cerebral blood flow and statistical parametric mapping.

PubMed

McGoron, Anthony J; Capille, Michael; Georgiou, Michael F; Sanchez, Pablo; Solano, Juan; Gonzalez-Brito, Manuel; Kuluz, John W

2008-02-29

Assessment of cerebral blood flow (CBF) by SPECT could be important in the management of patients with severe traumatic brain injury (TBI) because changes in regional CBF can affect outcome by promoting edema formation and intracranial pressure elevation (with cerebral hyperemia), or by causing secondary ischemic injury including post-traumatic stroke. The purpose of this study was to establish an improved method for evaluating regional CBF changes after TBI in piglets. The focal effects of moderate traumatic brain injury (TBI) on cerebral blood flow (CBF) by SPECT cerebral blood perfusion (CBP) imaging in an animal model were investigated by parallelized statistical techniques. Regional CBF was measured by radioactive microspheres and by SPECT 2 hours after injury in sham-operated piglets versus those receiving severe TBI by fluid-percussion injury to the left parietal lobe. Qualitative SPECT CBP accuracy was assessed against reference radioactive microsphere regional CBF measurements by map reconstruction, registration and smoothing. Cerebral hypoperfusion in the test group was identified at the voxel level using statistical parametric mapping (SPM). A significant area of hypoperfusion (P < 0.01) was found as a response to the TBI. Statistical mapping of the reference microsphere CBF data confirms a focal decrease found with SPECT and SPM. The suitability of SPM for application to the experimental model and ability to provide insight into CBF changes in response to traumatic injury was validated by the SPECT SPM result of a decrease in CBP at the left parietal region injury area of the test group. Further study and correlation of this characteristic lesion with long-term outcomes and auxiliary diagnostic modalities is critical to developing more effective critical care treatment guidelines and automated medical imaging processing techniques.

Chemical determination of particulate nitrogen in San Francisco Bay. Nitrogen: chlorophyll a rations in plankton

USGS Publications Warehouse

Hager, S.W.; Harmon, D.D.; Alpine, A.E.

1984-01-01

Particulate nitrogen (PN) and chlorophyll a (Chla) were measured in the northern reach of San Francisco Bay throughout 1980. The PN values were calculated as the differences between unfiltered and filtered (0·4 μm) samples analyzed using the UV-catalyzed peroxide digestion method. The Chla values were measured spectrophotometrically, with corrections made for phaeopigments. The plot of all PNChla data was found to be non-linear, and the concentration of suspended particulate matter (SPM) was found to be the best selector for linear subsets of the data. The best-fit slopes of PNChla plots, as determined by linear regression (model II), were interpreted to be the N: Chla ratios of phytoplankton. The Y-intercepts of the regression lines were considered to represent easily-oxidizable detrital nitrogen (EDN). In clear water ( < 10 mg l−1 SPM), the N: Chla ratio was 1·07 μg-at N per μg Chla. It decreased to 0·60 in the 10–18 mg l−1 range and averaged 0·31 in the remaining four ranges (18–35, 35–65, 65–155, and 155–470 mg l−1). The EDN values were less than 1 μg-at N l−1 in the clear water and increased monotonically to almost 12 μg-at N l−1 in the highest SPM range. The N: Chla ratios for the four highest SPM ranges agree well with data for phytoplankton in light-limited cultures. In these ranges, phytoplankton-N averaged only 20% of the PN, while EDN averaged 39% and refractory-N 41%.

General Mode Scanning Probe Microscopy

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

Somnath, Suhas; Jesse, Stephen

A critical part of SPM measurements is the information transfer from the probe-sample junction to the measurement system. Current information transfer methods heavily compress the information-rich data stream by averaging the data over a time interval, or via heterodyne detection approaches such as lock-in amplifiers and phase-locked loops. As a consequence, highly valuable information at the sub-microsecond time scales or information from frequencies outside the measurement band is lost. We have developed a fundamentally new approach called General Mode (G-mode), where we can capture the complete information stream from the detectors in the microscope. The availability of the complete informationmore » allows the microscope operator to analyze the data via information-theory analysis or comprehensive physical models. Furthermore, the complete data stream enables advanced data-driven filtering algorithms, multi-resolution imaging, ultrafast spectroscropic imaging, spatial mapping of multidimensional variability in material properties, etc. Though we applied this approach to scanning probe microscopy, the general philosophy of G-mode can be applied to many other modes of microscopy. G-mode data is captured by completely custom software written in LabVIEW and Matlab. The software generates the waveforms to electrically, thermally, or mechanically excite the SPM probe. It handles real-time communications with the microscope software for operations such as moving the SPM probe position and also controls other instrumentation hardware. The software also controls multiple variants of high-speed data acquisition cards to excite the SPM probe with the excitation waveform and simultaneously measure multiple channels of information from the microscope detectors at sampling rates of 1-100 MHz. The software also saves the raw data to the computer and allows the microscope operator to visualize processed or filtered data during the experiment. The software performs all these features while offering a user-friendly interface.« less

SPM analysis of parametric (R)-[11C]PK11195 binding images: plasma input versus reference tissue parametric methods.

PubMed

Schuitemaker, Alie; van Berckel, Bart N M; Kropholler, Marc A; Veltman, Dick J; Scheltens, Philip; Jonker, Cees; Lammertsma, Adriaan A; Boellaard, Ronald

2007-05-01

(R)-[11C]PK11195 has been used for quantifying cerebral microglial activation in vivo. In previous studies, both plasma input and reference tissue methods have been used, usually in combination with a region of interest (ROI) approach. Definition of ROIs, however, can be labourious and prone to interobserver variation. In addition, results are only obtained for predefined areas and (unexpected) signals in undefined areas may be missed. On the other hand, standard pharmacokinetic models are too sensitive to noise to calculate (R)-[11C]PK11195 binding on a voxel-by-voxel basis. Linearised versions of both plasma input and reference tissue models have been described, and these are more suitable for parametric imaging. The purpose of this study was to compare the performance of these plasma input and reference tissue parametric methods on the outcome of statistical parametric mapping (SPM) analysis of (R)-[11C]PK11195 binding. Dynamic (R)-[11C]PK11195 PET scans with arterial blood sampling were performed in 7 younger and 11 elderly healthy subjects. Parametric images of volume of distribution (Vd) and binding potential (BP) were generated using linearised versions of plasma input (Logan) and reference tissue (Reference Parametric Mapping) models. Images were compared at the group level using SPM with a two-sample t-test per voxel, both with and without proportional scaling. Parametric BP images without scaling provided the most sensitive framework for determining differences in (R)-[11C]PK11195 binding between younger and elderly subjects. Vd images could only demonstrate differences in (R)-[11C]PK11195 binding when analysed with proportional scaling due to intersubject variation in K1/k2 (blood-brain barrier transport and non-specific binding).

Task-evoked brain functional magnetic susceptibility mapping by independent component analysis (χICA).

PubMed

Chen, Zikuan; Calhoun, Vince D

2016-03-01

Conventionally, independent component analysis (ICA) is performed on an fMRI magnitude dataset to analyze brain functional mapping (AICA). By solving the inverse problem of fMRI, we can reconstruct the brain magnetic susceptibility (χ) functional states. Upon the reconstructed χ dataspace, we propose an ICA-based brain functional χ mapping method (χICA) to extract task-evoked brain functional map. A complex division algorithm is applied to a timeseries of fMRI phase images to extract temporal phase changes (relative to an OFF-state snapshot). A computed inverse MRI (CIMRI) model is used to reconstruct a 4D brain χ response dataset. χICA is implemented by applying a spatial InfoMax ICA algorithm to the reconstructed 4D χ dataspace. With finger-tapping experiments on a 7T system, the χICA-extracted χ-depicted functional map is similar to the SPM-inferred functional χ map by a spatial correlation of 0.67 ± 0.05. In comparison, the AICA-extracted magnitude-depicted map is correlated with the SPM magnitude map by 0.81 ± 0.05. The understanding of the inferiority of χICA to AICA for task-evoked functional map is an ongoing research topic. For task-evoked brain functional mapping, we compare the data-driven ICA method with the task-correlated SPM method. In particular, we compare χICA with AICA for extracting task-correlated timecourses and functional maps. χICA can extract a χ-depicted task-evoked brain functional map from a reconstructed χ dataspace without the knowledge about brain hemodynamic responses. The χICA-extracted brain functional χ map reveals a bidirectional BOLD response pattern that is unavailable (or different) from AICA. Copyright © 2016 Elsevier B.V. All rights reserved.

Effectiveness of mathematics education in secondary schools to meet the local universities missions in producing quality engineering and science undergraduates

NASA Astrophysics Data System (ADS)

Bakar Hasan, Abu; Fatah Abdul, Abdul; Selamat, Zalilah

2018-01-01

Critical claims by certain quarters that our local undergraduates are not performing well in Mathematics, Statistics and Numerical Methods needs a serious thinking and actions. Yearly examinations results from the Sijil Pelajaran Malaysia (SPM equivalent to A-Level) and Sijil Tinggi Pelajaran Malaysia (STPM equivalent to O-Level) levels have been splendid whereby it is either increasing or decreasing in a very tight range. A good foundation in mathematics and additional mathematics will tremendously benefit these students when they enter their university education especially in engineering and science courses. This paper uses SPM results as the primary data, questionnaires as secondary, and apply the Fish Bones technique for analysis. The outcome shows that there is a clear correlation between the causes and effect.

Monolithically Integrated, Mechanically Resilient Carbon-Based Probes for Scanning Probe Microscopy

NASA Technical Reports Server (NTRS)

Kaul, Anupama B.; Megerian, Krikor G.; Jennings, Andrew T.; Greer, Julia R.

2010-01-01

Scanning probe microscopy (SPM) is an important tool for performing measurements at the nanoscale in imaging bacteria or proteins in biology, as well as in the electronics industry. An essential element of SPM is a sharp, stable tip that possesses a small radius of curvature to enhance spatial resolution. Existing techniques for forming such tips are not ideal. High-aspect-ratio, monolithically integrated, as-grown carbon nanofibers (CNFs) have been formed that show promise for SPM applications by overcoming the limitations present in wet chemical and separate substrate etching processes.

Scalar Potential Model progress

NASA Astrophysics Data System (ADS)

Hodge, John

2007-04-01

Because observations of galaxies and clusters have been found inconsistent with General Relativity (GR), the focus of effort in developing a Scalar Potential Model (SPM) has been on the examination of galaxies and clusters. The SPM has been found to be consistent with cluster cellular structure, the flow of IGM from spiral galaxies to elliptical galaxies, intergalactic redshift without an expanding universe, discrete redshift, rotation curve (RC) data without dark matter, asymmetric RCs, galaxy central mass, galaxy central velocity dispersion, and the Pioneer Anomaly. In addition, the SPM suggests a model of past expansion, past contraction, and current expansion of the universe. GR corresponds to the SPM in the limit in which a flat and static scalar potential field replaces the Sources and Sinks such as between clusters and on the solar system scale which is small relative to the distance to a Source. The papers may be viewed at http://web.infoave.net/˜scjh/ .

The Stochastic Parcel Model: A deterministic parameterization of stochastically entraining convection

DOE PAGES

Romps, David M.

2016-03-01

Convective entrainment is a process that is poorly represented in existing convective parameterizations. By many estimates, convective entrainment is the leading source of error in global climate models. As a potential remedy, an Eulerian implementation of the Stochastic Parcel Model (SPM) is presented here as a convective parameterization that treats entrainment in a physically realistic and computationally efficient way. Drawing on evidence that convecting clouds comprise air parcels subject to Poisson-process entrainment events, the SPM calculates the deterministic limit of an infinite number of such parcels. For computational efficiency, the SPM groups parcels at each height by their purity, whichmore » is a measure of their total entrainment up to that height. This reduces the calculation of convective fluxes to a sequence of matrix multiplications. The SPM is implemented in a single-column model and compared with a large-eddy simulation of deep convection.« less

Optimisation of flux calculation in rivers from discrete water quality surveys, a step towards an expert system

NASA Astrophysics Data System (ADS)

Raymond, S.; Moatar, F.; Meybeck, M.; Bustillo, V.

2009-04-01

Good estimates of fluxes of suspended particulate matter (SPM), total dissolved solids (TDS) and nutrients and contaminants are required for both Earth System science and river basin management. However, in most cases discrete sampling (weekly to monthly) is the rule. Few flux calculation methods are commonly used, yet their performances, i.e. uncertainties for given frequencies, at given stations and for each water quality variables, remain unknown. Based on a rare set of 1085 station-year of daily flux record for SPM, TDS and nutrients (dissolved and total), the performance of 9 calculations methods is explored. Discrete surveys at various frequencies (3days to 30 days) are simulated by Monte-Carlo sorting (100 runs) on which the 9 fluxes are calculated (annual and interannual). At this stage, the sub-daily variations of fluxes for the medium and large basins are not considered. The dataset for SPM corresponds to 55 stations (600 to 600 000 km2 basin area), 34 stations (700 to 1000000 km2) for TDS and for nutrients we consider 9 stations for NO3-, NH4+, PO43- and Ptot (600 to 30 000 km2). About 80% of the dataset originates from US records (USGS and Lake Erie tributaries survey) and 20% from French stations, this covering a wide range of hydrological and geochemical conditions in the temperate zone. Each sorted flux is compared to known fluxes established on daily records: percentiles of their relative errors (e10, e50 and e90) are used to determine the biases (e50) and the imprecisions (e90-e10) (Walling and Webb, 1981) which are then compared for each of the 6 water quality variables, for each flux methods and for various simulated survey frequencies. The calculation methods include 5 rating-curve approaches (linear"M1", "M2", Phillipps et al, 1999) with and without Ferguson correction (Ferguson, 1987), polynomial, truncated at discharges exceeding median annual or long-term water discharge), 2 methods based on hydrograph separation (Phillips et al, 1999) including a quadratic runoff module (Bustillo, 2005), 1 linear interpolation method and 2 discharge-weighted concentration methods ("M18", "M19", Philipps et al, 1999). As expected, based on 55 stations and 430 years, SPM fluxes are the most uncertain ones with maximum biases determined on annual fluxes (monthly sampling simulations). ranging at stations from -75% to +55% by the classical rating-curves approach ("M1", "M2") droping to -60% to +5% for the M18 method. At this frequency, biases are much less for Ptot and PO4-3 (-30% to +10%), nitrate (-5% to +10%) and are negligible for TDS. For higher frequencies, the biases are reduced: for instance for weekly surveys they drop to -25% for SPM and to -20% to 5% for Ptot for the M18 method. The river basin size is influencing the performance of calculations methods: SPM flux errors are much higher for smaller basins (103 to 104 km2) than for larger ones (> 104 km2), probably in relation with the flow duration in 2% of time which is a key control factor of flux duration in 2% of time (Moatar et al, 2006). This indicator based on daily flow (Q) records is generally available at water quality stations. Other indicators based on discrete water quality surveys are being tested to explain the performance of flux methods for each variable: concentrations (C) variability, C vs Q relationship, concentration seasonality. For each variable and each station the optimal flux calculation method will be derived from the future expert system. BUSTILLO V., Biogéochimie et hydroclimatologie appliquées à l'aménagement des bassins fluviaux .PhD Thesis, INP Toulouse,232 p+annexes (2005). FERGUSON R.I., Accuracy and precision of methods for estimating river loads. Earth Surface Processes and Landforms, vol. 12,95-104 (1987). MOATAR F., PERSON G., MEYBECK M., COYNEL A., ETCHEBER H., CROUZET P., The influence of contrasting suspended particulate matter transport regimes on the bias and precision of flux estimates Science of the Total Environment 370, 515-531 (2006). PHILLIPS. J.M., WEBB B.W., WALLING D.E., LEEKS G.J.L., Estimating the suspended sediment load of rivers in the LOIS study area using infrequent samples. Hydrol Process, 13:1035-50 (1999). WALLING D.E. et WEBB B.W., The reliability of suspended sediment load data IAHS Publ., 133, 177-94 (1981).

Imaging electron motion in graphene

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

Bhandari, Sagar; Westervelt, Robert M.

A cooled scanning probe microscope (SPM) is an ideal tool to image electronic motion in graphene: the SPM tip acts as a scanning gate, which interacts with the electron gas below. We introduce the technique using our group's previous work on imaging electron flow from a quantum point contact in a GaAs 2DEG and tuning an InAs quantum dot in an InAs/InP nanowire. Carriers in graphene have very different characteristics: electrons and holes travel at a constant speed with no bandgap, and they pass through potential barriers via Klein tunneling. In this paper, we review the extension of SPM imagingmore » techniques to graphene. We image the cyclotron orbits passing between two narrow contacts in a single-atomic-layer graphene device in a perpendicular magnetic field. Magnetic focusing produces a peak in transmission between the contacts when the cyclotron diameter is equal to the contact spacing. The charged SPM tip deflects electrons passing from one contact to the other, changing the transmission when it interrupts the flow. By displaying the change in transmission as the tip is raster scanned above the sample, an image of flow is obtained. In addition, we have developed a complementary technique to image electronic charge using a cooled scanning capacitance microscope (SCM) that uses a sensitive charge preamplifier near the SPM tip to achieve a charge noise level 0.13 e Hz -1/2 with high spatial resolution 100 nm. The cooled SPM and SCM can be used to probe the motion of electrons on the nanoscale in graphene devices.« less

Characterization of Disease-Related Covariance Topographies with SSMPCA Toolbox: Effects of Spatial Normalization and PET Scanners

PubMed Central

Peng, Shichun; Ma, Yilong; Spetsieris, Phoebe G; Mattis, Paul; Feigin, Andrew; Dhawan, Vijay; Eidelberg, David

2013-01-01

In order to generate imaging biomarkers from disease-specific brain networks, we have implemented a general toolbox to rapidly perform scaled subprofile modeling (SSM) based on principal component analysis (PCA) on brain images of patients and normals. This SSMPCA toolbox can define spatial covariance patterns whose expression in individual subjects can discriminate patients from controls or predict behavioral measures. The technique may depend on differences in spatial normalization algorithms and brain imaging systems. We have evaluated the reproducibility of characteristic metabolic patterns generated by SSMPCA in patients with Parkinson's disease (PD). We used [18F]fluorodeoxyglucose PET scans from PD patients and normal controls. Motor-related (PDRP) and cognition-related (PDCP) metabolic patterns were derived from images spatially normalized using four versions of SPM software (spm99, spm2, spm5 and spm8). Differences between these patterns and subject scores were compared across multiple independent groups of patients and control subjects. These patterns and subject scores were highly reproducible with different normalization programs in terms of disease discrimination and cognitive correlation. Subject scores were also comparable in PD patients imaged across multiple PET scanners. Our findings confirm a very high degree of consistency among brain networks and their clinical correlates in PD using images normalized in four different SPM platforms. SSMPCA toolbox can be used reliably for generating disease-specific imaging biomarkers despite the continued evolution of image preprocessing software in the neuroimaging community. Network expressions can be quantified in individual patients independent of different physical characteristics of PET cameras. PMID:23671030

Characterization of disease-related covariance topographies with SSMPCA toolbox: effects of spatial normalization and PET scanners.

PubMed

Peng, Shichun; Ma, Yilong; Spetsieris, Phoebe G; Mattis, Paul; Feigin, Andrew; Dhawan, Vijay; Eidelberg, David

2014-05-01

To generate imaging biomarkers from disease-specific brain networks, we have implemented a general toolbox to rapidly perform scaled subprofile modeling (SSM) based on principal component analysis (PCA) on brain images of patients and normals. This SSMPCA toolbox can define spatial covariance patterns whose expression in individual subjects can discriminate patients from controls or predict behavioral measures. The technique may depend on differences in spatial normalization algorithms and brain imaging systems. We have evaluated the reproducibility of characteristic metabolic patterns generated by SSMPCA in patients with Parkinson's disease (PD). We used [(18) F]fluorodeoxyglucose PET scans from patients with PD and normal controls. Motor-related (PDRP) and cognition-related (PDCP) metabolic patterns were derived from images spatially normalized using four versions of SPM software (spm99, spm2, spm5, and spm8). Differences between these patterns and subject scores were compared across multiple independent groups of patients and control subjects. These patterns and subject scores were highly reproducible with different normalization programs in terms of disease discrimination and cognitive correlation. Subject scores were also comparable in patients with PD imaged across multiple PET scanners. Our findings confirm a very high degree of consistency among brain networks and their clinical correlates in PD using images normalized in four different SPM platforms. SSMPCA toolbox can be used reliably for generating disease-specific imaging biomarkers despite the continued evolution of image preprocessing software in the neuroimaging community. Network expressions can be quantified in individual patients independent of different physical characteristics of PET cameras. Copyright © 2013 Wiley Periodicals, Inc.

Imaging electron motion in graphene

DOE PAGES

Bhandari, Sagar; Westervelt, Robert M.

2017-01-05

A cooled scanning probe microscope (SPM) is an ideal tool to image electronic motion in graphene: the SPM tip acts as a scanning gate, which interacts with the electron gas below. We introduce the technique using our group's previous work on imaging electron flow from a quantum point contact in a GaAs 2DEG and tuning an InAs quantum dot in an InAs/InP nanowire. Carriers in graphene have very different characteristics: electrons and holes travel at a constant speed with no bandgap, and they pass through potential barriers via Klein tunneling. In this paper, we review the extension of SPM imagingmore » techniques to graphene. We image the cyclotron orbits passing between two narrow contacts in a single-atomic-layer graphene device in a perpendicular magnetic field. Magnetic focusing produces a peak in transmission between the contacts when the cyclotron diameter is equal to the contact spacing. The charged SPM tip deflects electrons passing from one contact to the other, changing the transmission when it interrupts the flow. By displaying the change in transmission as the tip is raster scanned above the sample, an image of flow is obtained. In addition, we have developed a complementary technique to image electronic charge using a cooled scanning capacitance microscope (SCM) that uses a sensitive charge preamplifier near the SPM tip to achieve a charge noise level 0.13 e Hz -1/2 with high spatial resolution 100 nm. The cooled SPM and SCM can be used to probe the motion of electrons on the nanoscale in graphene devices.« less

Self-phase modulation and two-photon absorption imaging of cells and active neurons

NASA Astrophysics Data System (ADS)

Fischer, Martin C.; Liu, Henry; Piletic, Ivan R.; Ye, Tong; Yasuda, Ryohei; Warren, Warren S.

2007-02-01

Even though multi-photon fluorescence microscopy offers higher resolution and better penetration depth than traditional fluorescence microscopy, its use is restricted to the detection of molecules that fluoresce. Two-photon absorption (TPA) imaging can provide contrast in non-fluorescent molecules while retaining the high resolution and sectioning capabilities of nonlinear imaging modalities. In the long-wavelength water window, tissue TPA is dominated by the endogenous molecules melanin and hemoglobin with an almost complete absence of endogenous two-photon fluorescence. A complementary nonlinear contrast mechanism is self-phase modulation (SPM), which can provide intrinsic signatures that can depend on local tissue anisotropy, chemical environment, or other structural properties. We have developed a spectral hole refilling measurement technique for TPA and SPM measurements using shaped ultrafast laser pulses. Here we report on a microscopy setup to simultaneously acquire 3D, high-resolution TPA and SPM images. We have acquired data in mounted B16 melanoma cells with very modest laser power levels. We will also discuss the possible application of this measurement technique to neuronal imaging. Since SPM is sensitive to material structure we can expect SPM properties of neurons to change during neuronal firing. Using our hole-refilling technique we have now demonstrated strong novel intrinsic nonlinear signatures of neuronal activation in a hippocampal brain slice. The observed changes in nonlinear signal upon collective activation were up to factors of two, unlike other intrinsic optical signal changes on the percent level. These results show that TPA and SPM imaging can provide important novel functional contrast in tissue using very modest power levels suitable for in vivo applications.

Quantitative analysis of the text and graphic content in ophthalmic slide presentations.

PubMed

Ing, Edsel; Celo, Erdit; Ing, Royce; Weisbrod, Lawrence; Ing, Mercedes

2017-04-01

To determine the characteristics of ophthalmic digital slide presentations. Retrospective quantitative analysis. Slide presentations from a 2015 Canadian primary eye care conference were analyzed for their duration, character and word count, font size, words per minute (wpm), lines per slide, words per slide, slides per minute (spm), text density product (wpm × spm), proportion of graphic content, and Flesch Reading Ease (FRE) score using Microsoft PowerPoint and Word. The median audience evaluation score for the lectures was used to dichotomize the higher scoring lectures (HSL) from the lower scoring lectures (LSL). A priori we hypothesized that there would be a difference in the wpm, spm, text density product, and FRE score between HSL and LSL. Wilcoxon rank-sum tests with Bonferroni correction were utilized. The 17 lectures had medians of 2.5 spm, 20.3 words per slide, 5.0 lines per slide, 28-point sans serif font, 36% graphic content, and text density product of 136.4 words × slides/minute 2 . Although not statistically significant, the HSL had more wpm, fewer words per slide, more graphics per slide, greater text density, and higher FRE score than LSL. There was a statistically significant difference in the spm of the HSL (3.1 ± 1.0) versus the LSL (2.2 ± 1.0) at p = 0.0124. All presenters showed more than 1 slide per minute. The HSL showed more spm than the LSL. The descriptive statistics from this study may aid in the preparation of slides used for teaching and conferences. Copyright © 2017 Canadian Ophthalmological Society. Published by Elsevier Inc. All rights reserved.

PAH occurrence in chalk river systems from the Jura region (France). Pertinence of suspended particulate matter and sediment as matrices for river quality monitoring.

PubMed

Chiffre, Axelle; Degiorgi, François; Morin-Crini, Nadia; Bolard, Audrey; Chanez, Etienne; Badot, Pierre-Marie

2015-11-01

This study investigates the variations of polycyclic aromatic hydrocarbon (PAH) levels in surface water, suspended particulate matter (SPM) and sediment upstream and downstream of the discharges of two wastewater treatment plant (WWTP) effluents. Relationships between the levels of PAHs in these different matrices were also investigated. The sum of 16 US EPA PAHs ranged from 73.5 to 728.0 ng L(-1) in surface water and from 85.4 to 313.1 ng L(-1) in effluent. In SPM and sediment, ∑16PAHs ranged from 749.6 to 2,463 μg kg(-1) and from 690.7 μg kg(-1) to 3,625.6 μg kg(-1), respectively. Investigations performed upstream and downstream of both studied WWTPs showed that WWTP discharges may contribute to the overall PAH contaminations in the Loue and the Doubs rivers. Comparison between gammarid populations upstream and downstream of WWTP discharge showed that biota was impacted by the WWTP effluents. When based only on surface water samples, the assessment of freshwater quality did not provide evidence for a marked PAH contamination in either of the rivers studied. However, using SPM and sediment samples, we found PAH contents exceeding sediment quality guidelines. We conclude that sediment and SPM are relevant matrices to assess overall PAH contamination in aquatic ecosystems. Furthermore, we found a positive linear correlation between PAH contents of SPM and sediment, showing that SPM represents an integrating matrix which is able to provide meaningful data about the overall contamination over a given time span.

A multistage crucible of revision and approval shapes IPCC policymaker summaries

PubMed Central

Mach, Katharine J.; Freeman, Patrick T.; Mastrandrea, Michael D.; Field, Christopher B.

2016-01-01

Intergovernmental Panel on Climate Change (IPCC) member governments approve each report’s summary for policymakers (SPM) by consensus, discussing and agreeing on each sentence in a plenary session with scientist authors. A defining feature of IPCC assessment, the governmental approval process builds joint ownership of current knowledge by scientists and governments. The resulting SPM revisions have been extensively discussed in anecdotes, interviews, and perspectives, but they have not been comprehensively analyzed. We provide an in-depth evaluation of IPCC SPM revisions, establishing an evidential basis for understanding their nature. Revisions associated with governmental review and approval generally expand SPMs, with SPM text growing by 17 to 53% across recent assessment reports. Cases of high political sensitivity and failure to reach consensus are notable exceptions, resulting in SPM contractions. In contrast to recent claims, we find that IPCC SPMs are as readable, for multiple metrics of reading ease, as other professionally edited assessment summaries. Across reading-ease metrics, some SPMs become more readable through governmental review and approval, whereas others do not. In an SPM examined through the entire revision process, most revisions associated with governmental review and approval occurred before the start of the government-approval plenary session. These author revisions emphasize clarity, scientific rigor, and explanation. In contrast, the subsequent plenary revisions place greater emphasis especially on policy relevance, comprehensiveness of examples, and nuances of expert judgment. Overall, the value added by the IPCC process emerges in a multistage crucible of revision and approval, as individuals together navigate complex science-policy terrain. PMID:27532046

Spatial Preference Modelling for equitable infrastructure provision: an application of Sen's Capability Approach

NASA Astrophysics Data System (ADS)

Wismadi, Arif; Zuidgeest, Mark; Brussel, Mark; van Maarseveen, Martin

2014-01-01

To determine whether the inclusion of spatial neighbourhood comparison factors in Preference Modelling allows spatial decision support systems (SDSSs) to better address spatial equity, we introduce Spatial Preference Modelling (SPM). To evaluate the effectiveness of this model in addressing equity, various standardisation functions in both Non-Spatial Preference Modelling and SPM are compared. The evaluation involves applying the model to a resource location-allocation problem for transport infrastructure in the Special Province of Yogyakarta in Indonesia. We apply Amartya Sen's Capability Approach to define opportunity to mobility as a non-income indicator. Using the extended Moran's I interpretation for spatial equity, we evaluate the distribution output regarding, first, `the spatial distribution patterns of priority targeting for allocation' (SPT) and, second, `the effect of new distribution patterns after location-allocation' (ELA). The Moran's I index of the initial map and its comparison with six patterns for SPT as well as ELA consistently indicates that the SPM is more effective for addressing spatial equity. We conclude that the inclusion of spatial neighbourhood comparison factors in Preference Modelling improves the capability of SDSS to address spatial equity. This study thus proposes a new formal method for SDSS with specific attention on resource location-allocation to address spatial equity.

Experimental vitrification of human compacted morulae and early blastocysts using fine diameter plastic micropipettes.

PubMed

Cremades, N; Sousa, M; Silva, J; Viana, P; Sousa, S; Oliveira, C; Teixeira da Silva, J; Barros, A

2004-02-01

Vitrification of human blastocysts has been successfully applied using grids, straws and cryoloops. We assessed the survival rate of human compacted morulae and early blastocysts vitrified in pipette tips with a smaller inner diameter and solution volume than the previously described open pulled straw (OPS) method. Excess day 5 human embryos (n = 63) were experimentally vitrified in vessels. Embryos were incubated at 37 degrees C with sperm preparation medium (SPM) for 1 min, SPM + 7.5% ethylene glycol (EG)/dimethylsulphoxide (DMSO) for 3 min, and SPM + 16.5% EG + 16.5% DMSO + 0.67 mol/l sucrose for 25 s. They were then aspirated (0.5 microl) into a plastic micropipette tip (0.36 mm inner diameter), exposed to liquid nitrogen (LN(2)) vapour for 2 min before being placed into a pre-cooled cryotube, which was then closed and plunged into LN(2). Embryos were warmed and diluted using 0.33 mol/l and 0.2 mol/l sucrose. The survival rate for compacted morulae was 73% (22/30) and 82% (27/33) for early blastocysts. The survival rates of human compacted morulae and early blastocysts after vitrification with this simple technique are similar to those reported in the literature achieved by slow cooling and other vitrification protocols.

Cortical Thinning in Patients with Recent Onset Post-Traumatic Stress Disorder after a Single Prolonged Trauma Exposure

PubMed Central

Liu, Yang; Li, Yi-Jun; Luo, Er-Ping; Lu, Hong-Bing; Yin, Hong

2012-01-01

Most of magnetic resonance imaging (MRI) studies about post-traumatic stress disorder (PTSD) focused primarily on measuring of small brain structure volume or regional brain volume changes. There were rare reports investigating cortical thickness alterations in recent onset PTSD. Recent advances in computational analysis made it possible to measure cortical thickness in a fully automatic way, along with voxel-based morphometry (VBM) that enables an exploration of global structural changes throughout the brain by applying statistical parametric mapping (SPM) to high-resolution MRI. In this paper, Laplacian method was utilized to estimate cortical thickness after automatic segmentation of gray matter from MR images under SPM. Then thickness maps were analyzed by SPM8. Comparison between 10 survivors from a mining disaster with recent onset PTSD and 10 survivors without PTSD from the same trauma indicates cortical thinning in the left parietal lobe, right inferior frontal gyrus, and right parahippocampal gyrus. The regional cortical thickness of the right inferior frontal gyrus showed a significant negative correlation with the CAPS score in the patients with PTSD. Our study suggests that shape-related cortical thickness analysis may be more sensitive than volumetric analysis to subtle alteration at early stage of PTSD. PMID:22720021

Spontaneous Pneumomediastinum: Case Presentation to a College Student Health Clinic

ERIC Educational Resources Information Center

Spotts, P. Hunter

2017-01-01

The author describes a case of spontaneous pneumomediastinum (SPM) in a 19-year-old man presenting to a college student health clinic. The author also provides a review on SPM, including clinical manifestations, diagnostic evaluation, and management.

Regional mapping of soil parent material by machine learning based on point data

NASA Astrophysics Data System (ADS)

Lacoste, Marine; Lemercier, Blandine; Walter, Christian

2011-10-01

A machine learning system (MART) has been used to predict soil parent material (SPM) at the regional scale with a 50-m resolution. The use of point-specific soil observations as training data was tested as a replacement for the soil maps introduced in previous studies, with the aim of generating a more even distribution of training data over the study area and reducing information uncertainty. The 27,020-km 2 study area (Brittany, northwestern France) contains mainly metamorphic, igneous and sedimentary substrates. However, superficial deposits (aeolian loam, colluvial and alluvial deposits) very often represent the actual SPM and are typically under-represented in existing geological maps. In order to calibrate the predictive model, a total of 4920 point soil descriptions were used as training data along with 17 environmental predictors (terrain attributes derived from a 50-m DEM, as well as emissions of K, Th and U obtained by means of airborne gamma-ray spectrometry, geological variables at the 1:250,000 scale and land use maps obtained by remote sensing). Model predictions were then compared: i) during SPM model creation to point data not used in model calibration (internal validation), ii) to the entire point dataset (point validation), and iii) to existing detailed soil maps (external validation). The internal, point and external validation accuracy rates were 56%, 81% and 54%, respectively. Aeolian loam was one of the three most closely predicted substrates. Poor prediction results were associated with uncommon materials and areas with high geological complexity, i.e. areas where existing maps used for external validation were also imprecise. The resultant predictive map turned out to be more accurate than existing geological maps and moreover indicated surface deposits whose spatial coverage is consistent with actual knowledge of the area. This method proves quite useful in predicting SPM within areas where conventional mapping techniques might be too costly or lengthy or where soil maps are insufficient for use as training data. In addition, this method allows producing repeatable and interpretable results, whose accuracy can be assessed objectively.

Reliability evaluation of I-123 ADAM SPECT imaging using SPM software and AAL ROI methods

NASA Astrophysics Data System (ADS)

Yang, Bang-Hung; Tsai, Sung-Yi; Wang, Shyh-Jen; Su, Tung-Ping; Chou, Yuan-Hwa; Chen, Chia-Chieh; Chen, Jyh-Cheng

2011-08-01

The level of serotonin was regulated by serotonin transporter (SERT), which is a decisive protein in regulation of serotonin neurotransmission system. Many psychiatric disorders and therapies were also related to concentration of cerebral serotonin. I-123 ADAM was the novel radiopharmaceutical to image SERT in brain. The aim of this study was to measure reliability of SERT densities of healthy volunteers by automated anatomical labeling (AAL) method. Furthermore, we also used statistic parametric mapping (SPM) on a voxel by voxel analysis to find difference of cortex between test and retest of I-123 ADAM single photon emission computed tomography (SPECT) images.Twenty-one healthy volunteers were scanned twice with SPECT at 4 h after intravenous administration of 185 MBq of 123I-ADAM. The image matrix size was 128×128 and pixel size was 3.9 mm. All images were obtained through filtered back-projection (FBP) reconstruction algorithm. Region of interest (ROI) definition was performed based on the AAL brain template in PMOD version 2.95 software package. ROI demarcations were placed on midbrain, pons, striatum, and cerebellum. All images were spatially normalized to the SPECT MNI (Montreal Neurological Institute) templates supplied with SPM2. And each image was transformed into standard stereotactic space, which was matched to the Talairach and Tournoux atlas. Then differences across scans were statistically estimated on a voxel by voxel analysis using paired t-test (population main effect: 2 cond's, 1 scan/cond.), which was applied to compare concentration of SERT between the test and retest cerebral scans.The average of specific uptake ratio (SUR: target/cerebellum-1) of 123I-ADAM binding to SERT in midbrain was 1.78±0.27, pons was 1.21±0.53, and striatum was 0.79±0.13. The cronbach's α of intra-class correlation coefficient (ICC) was 0.92. Besides, there was also no significant statistical finding in cerebral area using SPM2 analysis. This finding might help us to understand reliability of I-123 ADAM SPECT imaging and further develop new strategy for the treatment of psychiatric disorders.

ProphTools: general prioritization tools for heterogeneous biological networks.

PubMed

Navarro, Carmen; Martínez, Victor; Blanco, Armando; Cano, Carlos

2017-12-01

Networks have been proven effective representations for the analysis of biological data. As such, there exist multiple methods to extract knowledge from biological networks. However, these approaches usually limit their scope to a single biological entity type of interest or they lack the flexibility to analyze user-defined data. We developed ProphTools, a flexible open-source command-line tool that performs prioritization on a heterogeneous network. ProphTools prioritization combines a Flow Propagation algorithm similar to a Random Walk with Restarts and a weighted propagation method. A flexible model for the representation of a heterogeneous network allows the user to define a prioritization problem involving an arbitrary number of entity types and their interconnections. Furthermore, ProphTools provides functionality to perform cross-validation tests, allowing users to select the best network configuration for a given problem. ProphTools core prioritization methodology has already been proven effective in gene-disease prioritization and drug repositioning. Here we make ProphTools available to the scientific community as flexible, open-source software and perform a new proof-of-concept case study on long noncoding RNAs (lncRNAs) to disease prioritization. ProphTools is robust prioritization software that provides the flexibility not present in other state-of-the-art network analysis approaches, enabling researchers to perform prioritization tasks on any user-defined heterogeneous network. Furthermore, the application to lncRNA-disease prioritization shows that ProphTools can reach the performance levels of ad hoc prioritization tools without losing its generality. © The Authors 2017. Published by Oxford University Press.

Fast CSF MRI for brain segmentation; Cross-validation by comparison with 3D T1-based brain segmentation methods.

PubMed

van der Kleij, Lisa A; de Bresser, Jeroen; Hendrikse, Jeroen; Siero, Jeroen C W; Petersen, Esben T; De Vis, Jill B

2018-01-01

In previous work we have developed a fast sequence that focusses on cerebrospinal fluid (CSF) based on the long T2 of CSF. By processing the data obtained with this CSF MRI sequence, brain parenchymal volume (BPV) and intracranial volume (ICV) can be automatically obtained. The aim of this study was to assess the precision of the BPV and ICV measurements of the CSF MRI sequence and to validate the CSF MRI sequence by comparison with 3D T1-based brain segmentation methods. Ten healthy volunteers (2 females; median age 28 years) were scanned (3T MRI) twice with repositioning in between. The scan protocol consisted of a low resolution (LR) CSF sequence (0:57min), a high resolution (HR) CSF sequence (3:21min) and a 3D T1-weighted sequence (6:47min). Data of the HR 3D-T1-weighted images were downsampled to obtain LR T1-weighted images (reconstructed imaging time: 1:59 min). Data of the CSF MRI sequences was automatically segmented using in-house software. The 3D T1-weighted images were segmented using FSL (5.0), SPM12 and FreeSurfer (5.3.0). The mean absolute differences for BPV and ICV between the first and second scan for CSF LR (BPV/ICV: 12±9/7±4cc) and CSF HR (5±5/4±2cc) were comparable to FSL HR (9±11/19±23cc), FSL LR (7±4, 6±5cc), FreeSurfer HR (5±3/14±8cc), FreeSurfer LR (9±8, 12±10cc), and SPM HR (5±3/4±7cc), and SPM LR (5±4, 5±3cc). The correlation between the measured volumes of the CSF sequences and that measured by FSL, FreeSurfer and SPM HR and LR was very good (all Pearson's correlation coefficients >0.83, R2 .67-.97). The results from the downsampled data and the high-resolution data were similar. Both CSF MRI sequences have a precision comparable to, and a very good correlation with established 3D T1-based automated segmentations methods for the segmentation of BPV and ICV. However, the short imaging time of the fast CSF MRI sequence is superior to the 3D T1 sequence on which segmentation with established methods is performed.

Design and Optimization of Nanomaterials for Sensing Applications

NASA Astrophysics Data System (ADS)

Sanderson, Robert Noboru

Nanomaterials, materials with one or more of their dimensions on the nanoscale, have emerged as an important field in the development of next-generation sensing systems. Their high surface-to-volume ratio makes them useful for sensing, but also makes them sensitive to processing defects and inherent material defects. To develop and optimize these systems, it is thus necessary to characterize these defects to understand their origin and how to work around them. Scanning probe microscopy (SPM) techniques like atomic force microscopy (AFM) and scanning tunneling microscopy (STM) are important characterization methods which can measure nanoscale topography and electronic structure. These methods are appealing in nanomaterial systems because they are non-damaging and provide local, high-resolution data, and so are capable of detecting nanoscale features such as single defect sites. There are difficulties, however, in the interpretation of SPM data. For instance, AFM-based methods are prone to experimental artifacts due to long-range interactions, such as capacitive crosstalk in Kelvin probe force microscopy (KPFM), and artifacts due to the finite size of the probe tip, such as incorrect surface tracking at steep topographical features. Mechanical characterization (via force spectroscopy) of nanomaterials with significant nanoscale variations, such as tethered lipid bilayer membranes (tLBMs), is also difficult since variations in the bulk system's mechanical behavior must be distinguished from local fluctuations. Additionally, interpretation of STM data is non-trivial due to local variations in electron density in addition to topographical variations. In this thesis we overcome some limitations of SPM methods by supplementing them with additional surface analytical methods as well as computational methods, and we characterize several nanomaterial systems. Current-carrying vapor-liquid-solid Si nanowires (useful for interdigitated-electrode-based sensors) are characterized using finite-element-method (FEM)-supplemented KPFM to retrieve useful information about processing defects, contact resistance, and the primary charge carriers. Next, a tLBM system's stiffness and the stiffness' dependence on tethering molecule concentration is measured using statistical analysis of thousands of AFM force spectra, demonstrating a biosensor-compatible system with a controllable bulk rigidity. Finally, we utilize surface analytical techniques to inform the development of a novel three-dimensional graphene system for sensing applications.

Planar-type ferromagnetic tunnel junctions fabricated by SPM local oxidation

NASA Astrophysics Data System (ADS)

Tomoda, Y.; Kayashima, S.; Ogino, T.; Motoyama, M.; Takemura, Y.; Shirakashi, J.

Nanometer-scale oxide wires were fabricated by local oxidation nanolithography using scanning probe microscope (SPM). This technique was applied to the fabrication of planar-type Ni/Ni oxide/Ni ferromagnetic tunnel junctions. In order to induce magnetic shape anisotropy, asymmetrical channel structure was patterned by conventional photolithography and wet etching processes. The magnetoresistance (MR) characteristics were clearly shown in the planar-type Ni/Ni oxide/Ni ferromagnetic tunnel junctions. MR ratio of above 100% was obtained at 17 K. This result suggests that the local oxidation nanolithography using SPM is useful for the application to planar-type ferromagnetic tunnel junctions.

Anomalous reduction in the long-time flux creep relaxation in superconducting Ca10(Pt4As8)((Fe1‑x Pt x )2As2)5 (x ≈ 0.05) single crystals

NASA Astrophysics Data System (ADS)

Haberkorn, N.; Huang, Silu; Jin, R.

2018-06-01

We report the vortex dynamics of superconducting a Ca10(Pt4As8)((Fe1‑x Pt x )2As2)5 (x ≈ 0.05) single crystal with T c = 26 K investigated by performing magnetic measurements. The field dependence of the magnetization displays a second peak (SPM), typically related to a crossover between elastic and plastic vortex relaxation in a weak pinning scenario. Long-time flux creep relaxation measurements for fields smaller that of the SPM show that the vortex dynamics can be separated in two different regions. For magnetic fields smaller than the lower end of the SPM, glassy relaxation (with a characteristic glassy exponent μ) is observed. For magnetic fields between the lower end and the SPM, the flux creep rate decreases systematically to values below to the ones predicted by the collective theory. This effect can be understood by considering a stable vortex lattice configuration. As the field position of the SPM can be adjusted by modifying the quenched potential, our results suggest that extremely low flux creep relaxation rate may be tuned in many other superconducting materials.

Harnessing Big Data for Systems Pharmacology

PubMed Central

Xie, Lei; Draizen, Eli J.; Bourne, Philip E.

2017-01-01

Systems pharmacology aims to holistically understand mechanisms of drug actions to support drug discovery and clinical practice. Systems pharmacology modeling (SPM) is data driven. It integrates an exponentially growing amount of data at multiple scales (genetic, molecular, cellular, organismal, and environmental). The goal of SPM is to develop mechanistic or predictive multiscale models that are interpretable and actionable. The current explosions in genomics and other omics data, as well as the tremendous advances in big data technologies, have already enabled biologists to generate novel hypotheses and gain new knowledge through computational models of genome-wide, heterogeneous, and dynamic data sets. More work is needed to interpret and predict a drug response phenotype, which is dependent on many known and unknown factors. To gain a comprehensive understanding of drug actions, SPM requires close collaborations between domain experts from diverse fields and integration of heterogeneous models from biophysics, mathematics, statistics, machine learning, and semantic webs. This creates challenges in model management, model integration, model translation, and knowledge integration. In this review, we discuss several emergent issues in SPM and potential solutions using big data technology and analytics. The concurrent development of high-throughput techniques, cloud computing, data science, and the semantic web will likely allow SPM to be findable, accessible, interoperable, reusable, reliable, interpretable, and actionable. PMID:27814027

Analytical Characterization of SPM Impact on XPM-Induced Degradation in Dispersion-Compensated WDM Systems

NASA Astrophysics Data System (ADS)

Luís, Ruben S.; Cartaxo, Adolfo V. T.

2005-03-01

This paper proposes the definition of a cross-phase modulation (XPM)-induced power penalty for intensity modulation/direct detection (IM-DD) systems as a function of the normalized variance of the XPM-induced IM. This allows the definition of 1-dB power penalty reference values. New expressions of the equivalent linear model transfer functions for the XPM-induced IM and phase modulation (PM) that include the influence of self-phase modulation (SPM) as well as group-velocity dispersion are derived. The new expressions allow a significant extension for higher powers and dispersion parameters of expressions derived in previous papers for single-segment and multisegment fiber systems with dispersion compensation. Good agreement between analytical results and numerical simulations is obtained. Consistency with work performed numerically and experimentally by other authors is shown, validating the proposed model. Using the proposed model, the influence of residual dispersion and SPM on the limitations imposed by XPM on the performance of dispersion-compensated systems is assessed. It is shown that inline residual dispersion may lead to performance improvement for a properly tuned total residual dispersion. The influence of SPM is shown to degrade the system performance when nonzero-dispersion-shifted fiber is used. However, systems using standard single-mode fiber may benefit from the presence of SPM.

Harnessing Big Data for Systems Pharmacology.

PubMed

Xie, Lei; Draizen, Eli J; Bourne, Philip E

2017-01-06

Systems pharmacology aims to holistically understand mechanisms of drug actions to support drug discovery and clinical practice. Systems pharmacology modeling (SPM) is data driven. It integrates an exponentially growing amount of data at multiple scales (genetic, molecular, cellular, organismal, and environmental). The goal of SPM is to develop mechanistic or predictive multiscale models that are interpretable and actionable. The current explosions in genomics and other omics data, as well as the tremendous advances in big data technologies, have already enabled biologists to generate novel hypotheses and gain new knowledge through computational models of genome-wide, heterogeneous, and dynamic data sets. More work is needed to interpret and predict a drug response phenotype, which is dependent on many known and unknown factors. To gain a comprehensive understanding of drug actions, SPM requires close collaborations between domain experts from diverse fields and integration of heterogeneous models from biophysics, mathematics, statistics, machine learning, and semantic webs. This creates challenges in model management, model integration, model translation, and knowledge integration. In this review, we discuss several emergent issues in SPM and potential solutions using big data technology and analytics. The concurrent development of high-throughput techniques, cloud computing, data science, and the semantic web will likely allow SPM to be findable, accessible, interoperable, reusable, reliable, interpretable, and actionable.

Analysis of emerging contaminants in water and solid samples using high resolution mass spectrometry with a Q Exactive orbital ion trap and estrogenic activity with YES-assay.

PubMed

Comtois-Marotte, Simon; Chappuis, Thomas; Vo Duy, Sung; Gilbert, Nicolas; Lajeunesse, André; Taktek, Salma; Desrosiers, Mélanie; Veilleux, Éloïse; Sauvé, Sébastien

2017-01-01

Trace emerging contaminants (ECs) occur in both waste and surface waters that are rich in particulates that have been found to sorb several organic contaminants. An analytical method based on off-line solid-phase extraction (SPE) followed by liquid chromatography-mass spectrometry (LC-MS) analysis was developed for the detection and quantification of 31 ECs from surface water, wastewater, suspended particulate matter (SPM) as well as sediments. Lyophilized sediments and air-dried SPM were subjected to ultrasonic extraction. Water samples and extracts were then concentrated and cleaned-up by off-line SPE. Quantification was realized using a Q Exactive mass spectrometer in both full scan (FS) and MS 2 modes. These two modes were optimized and compared to determine which one was the most suitable for each matrix studied. Yeast estrogen screen assay (YES-assay) adapted from the direct measurement of estrogenic activity without sample extraction was tested on filtered wastewater samples. An endocrine disrupting effect was detected in all effluent samples analyzed with estradiol equivalent concentrations ranging from 4.4 to 720 ng eq E2 L -1 for the WWTP-1 and 6.5-42 ng eq E2 L -1 for the WWTP-2. The analytical methods were also applied on six samples of surface water, the corresponding SPM, the sediments and thirty-nine effluent samples from two wastewater treatment plants (WWTPs) sampled over a period of five months (February to June 2014). Copyright © 2016 Elsevier Ltd. All rights reserved.

ExpoCast: Exposure Science for Prioritization and Toxicity Testing (S)

EPA Science Inventory

The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCast. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize limi...

ExpoCast: Exposure Science for Prioritization and Toxicity Testing

EPA Science Inventory

The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCastTM. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize l...

Partially supervised P300 speller adaptation for eventual stimulus timing optimization: target confidence is superior to error-related potential score as an uncertain label

NASA Astrophysics Data System (ADS)

Zeyl, Timothy; Yin, Erwei; Keightley, Michelle; Chau, Tom

2016-04-01

Objective. Error-related potentials (ErrPs) have the potential to guide classifier adaptation in BCI spellers, for addressing non-stationary performance as well as for online optimization of system parameters, by providing imperfect or partial labels. However, the usefulness of ErrP-based labels for BCI adaptation has not been established in comparison to other partially supervised methods. Our objective is to make this comparison by retraining a two-step P300 speller on a subset of confident online trials using naïve labels taken from speller output, where confidence is determined either by (i) ErrP scores, (ii) posterior target scores derived from the P300 potential, or (iii) a hybrid of these scores. We further wish to evaluate the ability of partially supervised adaptation and retraining methods to adjust to a new stimulus-onset asynchrony (SOA), a necessary step towards online SOA optimization. Approach. Eleven consenting able-bodied adults attended three online spelling sessions on separate days with feedback in which SOAs were set at 160 ms (sessions 1 and 2) and 80 ms (session 3). A post hoc offline analysis and a simulated online analysis were performed on sessions two and three to compare multiple adaptation methods. Area under the curve (AUC) and symbols spelled per minute (SPM) were the primary outcome measures. Main results. Retraining using supervised labels confirmed improvements of 0.9 percentage points (session 2, p < 0.01) and 1.9 percentage points (session 3, p < 0.05) in AUC using same-day training data over using data from a previous day, which supports classifier adaptation in general. Significance. Using posterior target score alone as a confidence measure resulted in the highest SPM of the partially supervised methods, indicating that ErrPs are not necessary to boost the performance of partially supervised adaptive classification. Partial supervision significantly improved SPM at a novel SOA, showing promise for eventual online SOA optimization.

Text Mining in Cancer Gene and Pathway Prioritization

PubMed Central

Luo, Yuan; Riedlinger, Gregory; Szolovits, Peter

2014-01-01

Prioritization of cancer implicated genes has received growing attention as an effective way to reduce wet lab cost by computational analysis that ranks candidate genes according to the likelihood that experimental verifications will succeed. A multitude of gene prioritization tools have been developed, each integrating different data sources covering gene sequences, differential expressions, function annotations, gene regulations, protein domains, protein interactions, and pathways. This review places existing gene prioritization tools against the backdrop of an integrative Omic hierarchy view toward cancer and focuses on the analysis of their text mining components. We explain the relatively slow progress of text mining in gene prioritization, identify several challenges to current text mining methods, and highlight a few directions where more effective text mining algorithms may improve the overall prioritization task and where prioritizing the pathways may be more desirable than prioritizing only genes. PMID:25392685

Text mining in cancer gene and pathway prioritization.

PubMed

Luo, Yuan; Riedlinger, Gregory; Szolovits, Peter

2014-01-01

Prioritization of cancer implicated genes has received growing attention as an effective way to reduce wet lab cost by computational analysis that ranks candidate genes according to the likelihood that experimental verifications will succeed. A multitude of gene prioritization tools have been developed, each integrating different data sources covering gene sequences, differential expressions, function annotations, gene regulations, protein domains, protein interactions, and pathways. This review places existing gene prioritization tools against the backdrop of an integrative Omic hierarchy view toward cancer and focuses on the analysis of their text mining components. We explain the relatively slow progress of text mining in gene prioritization, identify several challenges to current text mining methods, and highlight a few directions where more effective text mining algorithms may improve the overall prioritization task and where prioritizing the pathways may be more desirable than prioritizing only genes.

Suspended particulate matter determines physical speciation of Fe, Mn, and trace metals in surface waters of Loire watershed.

PubMed

Baalousha, Mohamed; Stoll, Serge; Motelica-Heino, Mikaël; Guigues, Nathalie; Braibant, Gilles; Huneau, Frédéric; Le Coustumer, Philippe

2018-02-10

This study investigates the spatiotemporal variability of major and trace elements, dissolved organic carbon (DOC), total dissolved solids (TDS), and suspended particulate matter (SPM) in surface waters of several hydrosystems of the Loire River watershed in France. In particular, this study aims to delineate the impact of the abovementioned water physicochemical parameters on natural iron and manganese physical speciation (homoaggregation/heteroaggregation) among fine colloidal and dissolved (< 10 nm), colloidal (10-450 nm) and particulate (> 450 nm) phases in Loire River watershed. Results show that the chemistry of the Loire River watershed is controlled by two end members: magmatic and metamorphic petrographic context on the upper part of the watershed; and sedimentary rocks for the middle and low part of the Loire. The percentage of particulate Fe and Mn increased downstream concurrent with the increase in SPM and major cations concentration, whereas the percentage of colloidal Fe and Mn decreased downstream. Transmission electron microscopy analyses of the colloidal and particulate fractions (from the non-filtered water sample) revealed that heteroaggregation of Fe and Mn rich natural nanoparticles and natural organic matter to the particulate phase is the dominant mechanism. The heteroaggregation controls the partitioning of Fe and Mn in the different fractions, potentially due to the increase in the ionic strength, and divalent cations concentration downstream, and SPM concentration. These findings imply that SPM concentration plays an important role in controlling the fate and behavior of Fe and Mn in various sized fractions. Graphical abstract Physical speciation by heteroaggregation of (Fe-Mn) compounds: high [SPM] → [Fe-Mn] particulate faction; low {SPM] → [Fe-Mn] colloid-dissolved fraction.

Synthesis and evaluation of the antioxidative potential of minoxidil-polyamine conjugates.

PubMed

Hadjipavlou-Litina, Dimitra; Magoulas, George E; Bariamis, Stavros E; Tsimali, Zinovia; Avgoustakis, Konstantinos; Kontogiorgis, Christos A; Athanassopoulos, Constantinos M; Papaioannou, Dionissios

2013-07-01

A series of conjugates (MNX-CO-PA) of minoxidil (MNX) with the polyamines (PAs) putrescine (PUT), spermidine (SPD) and spermine (SPM) as well as dopamine were produced through activation of MNX with N,N'-carbonyldiimidazole, followed by reaction with dopamine or selectively protected PAs and acid-mediated deprotection. These conjugates together with conjugates of the general type MNX-PA or PA-MNX-PA, readily produced using literature protocols, were tested as antioxidants. The most potent inhibitors of lipid peroxidation were the conjugates MNX-SPM (2, 94%), SPM-MNX-SPM (4, 94%) and MNX-N(4)-SPD (7, 91%) and MNX (91%). The most powerful lipoxygenase (LOX) inhibitors were MNX (IC50 = 20 μM) and the conjugates MNX-N(8)-SPD (9, IC50 = 22.1 μM), MNX-CO-dopamine (11, IC50 = 28 μM) and MNX-N(1)-SPD (8, IC50 = 30 μM). The most interesting conjugates 2, MNX-CO-PUT (5), 8 and 11 as well as MNX were generally found to exhibit weaker (22-36.5%) or no (conjugate 8) anti-inflammatory activity than indomethacin (47%) with the exception of MNX which showed almost equal potency (49%) to indomethacin. The cytocompatibility of conjugates and MNX at the highest concentration of 100 μM showed a survival percentage of 87-107%, with the exception of conjugates with SPM (compound 2) and MNX-CO-SPM (6), which showed considerable cytotoxicity (survival percentage 8-14%). Molecular docking studies were carried on conjugate 9 and the parent compound MNX and were found to be in accordance with our experimental biological results. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Colon targeted delivery systems of metronidazole based on osmotic technology: development and evaluation.

PubMed

Kumar, Pramod; Singh, Sanjay; Mishra, Brahmeshwar

2008-09-01

Colon targeted delivery systems of metronidazole (MTZ) based on osmotic technology were developed. The developed systems consisted of osmotic core (drug, osmotic agent and wicking agent), coated with semipermeable membrane (SPM) containing guar gum as pore former, coated core were then further coated with enteric coating to protect the system from acidic environment of stomach. The effect of various formulation variables namely the level of wicking agent (sodium lauryl sulphate), osmotic agent in the osmotic core, the level of pore former (guar gum) in SPM, and the thickness of SPM, were studied on physical parameters and drug release characteristics of developed formulations. MTZ release was inversely proportional to SPM thickness, but directly related to the level of pore former, wicking agent and osmotic agent. On the other hand burst strength of the exhausted shells was decreased with the increase in level of pore former in the membrane but increased with the increase in the thickness of SPM. The drug release from the developed formulations was independent of pH, and agitation intensity, but dependent on the osmotic pressure of the release media. The thickness of enteric coating could prevent formation of delivery pores before contact with simulated colonic fluid, but had no effect on drug release. Result of SEM studies showed the formation of in-situ delivery pores in the membrane from where the drug release occurred, and the number of pores formed were directly related to the initial level of pore former (guar gum) in SPM. The manufacturing procedure was found to be reproducible and formulations were found to be stable during 3 months of accelerated stability studies.

Theory of Self-Phase Modulation and Spectral Broadening

NASA Astrophysics Data System (ADS)

Shen, Y. R.; Yang, Guo-Zhen

Self-phase modulation refers to the phenomenon in which a laser beam propagating in a medium interacts with the medium and imposes a phase modulation on itself. It is one of those very fascinating effects discovered in the early days of nonlinear optics (Bloembergen and Lallemand, 1966; Brewer, 1967; Cheung et al., 1968; Lallemand, 1966; Jones and Stoicheff, 1964; Shimizu, 1967; Stoicheff, 1963). The physical origin of the phenomenon lies in the fact that the strong field of a laser beam is capable of inducing an appreciable intensity-dependent refractive index change in the medium. The medium then reacts back and inflicts a phase change on the incoming wave, resulting in self-phase modulation (SPM). Since a laser beam has a finite cross section, and hence a transverse intensity profile, SPM on the beam should have a transverse spatial dependence, equivalent to a distortion of the wave front. Consequently, the beam will appear to have self-diffracted. Such a self-diffraction action, resulting from SPM in space, is responsible for the well-known nonlinear optical phenomena of self-focusing and self-defocusing (Marburger, 1975; Shen, 1975). It can give rise to a multiple ring structure in the diffracted beam if the SPM is sufficiently strong (Durbin et al., 1981; Santamato and Shen, 1984). In the case of a pulsed laser input, the temporal variation of the laser intensity leads to an SPM in time. Since the time derivative of the phase of a wave is simply the angular frequency of the wave, SPM also appears as a frequency modulation. Thus, the output beam appears with a self-induced spectral broadening (Cheung et al., 1968; Gustafson et al., 1969; Shimizu, 1967).

The impact of missing sensor information on surgical workflow management.

PubMed

Liebmann, Philipp; Meixensberger, Jürgen; Wiedemann, Peter; Neumuth, Thomas

2013-09-01

Sensor systems in the operating room may encounter intermittent data losses that reduce the performance of surgical workflow management systems (SWFMS). Sensor data loss could impact SWFMS-based decision support, device parameterization, and information presentation. The purpose of this study was to understand the robustness of surgical process models when sensor information is partially missing. SWFMS changes caused by wrong or no data from the sensor system which tracks the progress of a surgical intervention were tested. The individual surgical process models (iSPMs) from 100 different cataract procedures of 3 ophthalmologic surgeons were used to select a randomized subset and create a generalized surgical process model (gSPM). A disjoint subset was selected from the iSPMs and used to simulate the surgical process against the gSPM. The loss of sensor data was simulated by removing some information from one task in the iSPM. The effect of missing sensor data was measured using several metrics: (a) successful relocation of the path in the gSPM, (b) the number of steps to find the converging point, and (c) the perspective with the highest occurrence of unsuccessful path findings. A gSPM built using 30% of the iSPMs successfully found the correct path in 90% of the cases. The most critical sensor data were the information regarding the instrument used by the surgeon. We found that use of a gSPM to provide input data for a SWFMS is robust and can be accurate despite missing sensor data. A surgical workflow management system can provide the surgeon with workflow guidance in the OR for most cases. Sensor systems for surgical process tracking can be evaluated based on the stability and accuracy of functional and spatial operative results.

Spatial variation and sources of polycyclic aromatic hydrocarbons influenced by intensive land use in an urbanized river network of East China.

PubMed

Bi, Chunjuan; Wang, Xueping; Jia, Jinpu; Chen, Zhenlou

2018-06-15

The concentrations and distribution of polycyclic aromatic hydrocarbons (PAHs) in urbanized river networks are strongly influenced by intensive land use, industrial activities and population density. The spatial variations and their influencing factors of 16 priority PAHs were investigated in surface water, suspended particulate matter (SPM) and sediments among areas under different intensive land uses (industrial areas, agricultural areas, inner city, suburban towns and island areas) in the Shanghai river network, East China. Source apportionment was carried out using isomer ratios of PAHs and Positive Matrix Factorization (PMF). Total concentrations of 16 PAHs ranged from 105.2 to 400.5 ng/L, 108.1 to 1058.8 ng/L and 104.4 to 19,480.0 ng/g in water, SPM and sediments, respectively. The concentrations of PAHs in SPM and sediments varied significantly among areas (p < 0.05), with the highest concentrations in inner city characterized by highly intensive land use and high population density. The PAH concentrations in sediments were positively correlated with those in SPM and were more strongly correlated with black carbon than with total organic carbon, indicating a stronger influence of prolonged anthropogenic contamination than the recent surface input in sediments. Biomass and coal combustion contributed strongly to total PAHs, followed by natural gas combustion in water and SPM, and vehicular emissions in sediments. Vehicular emissions were the strongest contributors in SPM and sediments of the inner city, indicating the strong influence of vehicular transportation to PAHs pollution in the urbanized river network. Copyright © 2018 Elsevier B.V. All rights reserved.

Whole brain analysis of postmortem density changes of grey and white matter on computed tomography by statistical parametric mapping.

PubMed

Nishiyama, Yuichi; Kanayama, Hidekazu; Mori, Hiroshi; Tada, Keiji; Yamamoto, Yasushi; Katsube, Takashi; Takeshita, Haruo; Kawakami, Kazunori; Kitagaki, Hajime

2017-06-01

This study examined the usefulness of statistical parametric mapping (SPM) for investigating postmortem changes on brain computed tomography (CT). This retrospective study included 128 patients (23 - 100 years old) without cerebral abnormalities who underwent unenhanced brain CT before and after death. The antemortem CT (AMCT) scans and postmortem CT (PMCT) scans were spatially normalized using our original brain CT template, and postmortem changes of CT values (in Hounsfield units; HU) were analysed by the SPM technique. Compared with AMCT scans, 58.6 % and 98.4 % of PMCT scans showed loss of the cerebral sulci and an unclear grey matter (GM)-white matter (WM) interface, respectively. SPM analysis revealed a significant decrease in cortical GM density within 70 min after death on PMCT scans, suggesting cytotoxic brain oedema. Furthermore, there was a significant increase in the density of the WM, lenticular nucleus and thalamus more than 120 min after death. The SPM technique demonstrated typical postmortem changes on brain CT scans, and revealed that the unclear GM-WM interface on early PMCT scans is caused by a rapid decrease in cortical GM density combined with a delayed increase in WM density. SPM may be useful for assessment of whole brain postmortem changes. • The original brain CT template achieved successful normalization of brain morphology. • Postmortem changes in the brain were independent of sex. • Cortical GM density decreased rapidly after death. • WM and deep GM densities increased following cortical GM density change. • SPM could be useful for assessment of whole brain postmortem changes.

The impact of disposal of fine-grained sediments from maintenance dredging works on SPM concentration and fluid mud in and outside the harbor of Zeebrugge

NASA Astrophysics Data System (ADS)

Fettweis, Michael; Baeye, Matthias; Cardoso, Claudio; Dujardin, Arvid; Lauwaert, Brigitte; Van den Eynde, Dries; Van Hoestenberghe, Thomas; Vanlede, Joris; Van Poucke, Luc; Velez, Carlos; Martens, Chantal

2016-11-01

The amount of sediments to be dredged and disposed depends to a large part on the suspended particulate matter (SPM) concentration. Tidal, meteorological, climatological, and seasonal forcings have an influence on the horizontal and vertical distribution of the SPM in the water column and on the bed and control the inflow of fine-grained sediments towards harbors and navigation channels. About 3 million tons (dry matter) per year of mainly fine-grained sediments is dredged in the port of Zeebrugge and is disposed on a nearby disposal site. The disposed sediments are quickly resuspended and transported away from the site. The hypothesis is that a significant part of the disposed sediments recirculates back to the dredging places and that a relocation of the disposal site to another location at equal distance to the dredging area would reduce this recirculation. In order to validate the hypothesis, a 1-year field study was set up in 2013-2014. During 1 month, the dredged material was disposed at a new site. Variations in SPM concentration were related to tides, storms, seasonal changes, and human impacts. In the high-turbidity Belgian near-shore area, the natural forcings are responsible for the major variability in the SPM concentration signal, while disposal has only a smaller influence. The conclusion from the measurements is that the SPM concentration decreases after relocation of the disposal site but indicate stronger (first half of field experiment) or weaker (second half of field experiment) effects that are, however, supported by the environmental conditions. The results of the field study may have consequences on the management of disposal operations as the effectiveness of the disposal site depends on environmental conditions, which are inherently associated with chaotic behavior.

Profiling Cholinesterase Adduction: A High-Throughput Prioritization Method for Organophosphate Exposure Samples

PubMed Central

Carter, Melissa D.; Crow, Brian S.; Pantazides, Brooke G.; Watson, Caroline M.; deCastro, B. Rey; Thomas, Jerry D.; Blake, Thomas A.; Johnson, Rudolph C.

2017-01-01

A high-throughput prioritization method was developed for use with a validated confirmatory method detecting organophosphorus nerve agent exposure by immunomagnetic separation-HPLC-MS/MS. A ballistic gradient was incorporated into this analytical method in order to profile unadducted butyrylcholinesterase (BChE) in clinical samples. With Zhang, et al. 1999’s Z′-factor of 0.88 ± 0.01 (SD) of control analytes and Z-factor of 0.25 ± 0.06 (SD) of serum samples, the assay is rated an “excellent assay” for the synthetic peptide controls used and a “double assay” when used to prioritize clinical samples. Hits, defined as samples containing BChE Ser-198 adducts or no BChE present, were analyzed in a confirmatory method for identification and quantitation of the BChE adduct, if present. The ability to prioritize samples by highest exposure for confirmatory analysis is of particular importance in an exposure to cholinesterase inhibitors such as organophosphorus nerve agents where a large number of clinical samples may be collected. In an initial blind screen, 67 out of 70 samples were accurately identified giving an assay accuracy of 96% and yielded no false negatives. The method is the first to provide a high-throughput prioritization assay for profiling adduction of Ser-198 BChE in clinical samples. PMID:23954929

High-power picosecond pulses by SPM-induced spectral compression in a fiber amplifier

NASA Astrophysics Data System (ADS)

Schreiber, T.; Liem, A.; Roeser, F.; Zellmer, H.; Tuennermann, A.; Limpert, J.; Deguil-Robin, N.; Manek-Honninger, I.; Salin, F.; Courjaud, A.; Honninger, C.; Mottay, E.

2005-04-01

The fiber based generation of nearly transform-limited 10-ps pulses with 200 kW peak power (97 W average power) based on SPM-induced spectral compression is reported. Efficient second harmonic generation applying this source is also discussed.

Innovative SPM Probes for Energy-Storage Science: MWCNT-Nanopipettes to Nanobattery Probes

NASA Astrophysics Data System (ADS)

Larson, Jonathan; Talin, Alec; Pearse, Alexander; Kozen, Alexander; Reutt-Robey, Janice

As energy-storage materials and designs continue to advance, new tools are needed to direct and explore ion insertion/de-insertion at well-defined battery materials interfaces. Scanned probe tips, assembled from actual energy-storage materials, permit SPM measures of local cathode-anode (tip-sample) interactions, including ion transfer. We present examples of ``cathode'' MWCNT-terminated STM probe tips interacting with Li(s)/Si(111) anode substrates. The MWCNT tip functions as both SPM probe and Li-nanopipette,[1] for controlled transport and manipulation of Li. Local field conditions for lithium ionization and transfer are determined and compared to electrostatic models. Additional lithium metallic and oxide tips have been prepared by thin film deposition on conventional W tips, the latter of which effectively functions as a nanobattery. We demonstrate use of these novel probe materials in the local lithiation of low-index Si anode interfaces, probing local barriers for lithium insertion. Prospects and limitations of these novel SPM probes will be discussed. U.S. Department of Energy Award Number DESC0001160.

The tetravalent organic cation spermine causes the gating of the IRK1 channel expressed in murine fibroblast cells.

PubMed Central

Ishihara, K; Hiraoka, M; Ochi, R

1996-01-01

1. The activation kinetics of the IRK1 channel stably expressed in L cells (a murine fibroblast cell line) were studied under the whole-cell voltage clamp. Without polyamines or Mg2+ in the pipettes, inward currents showed an exponential activation on hyperpolarization. The steep inward rectification of the currents around the reversal potential (Erev) could be described by the open-close transition of the channel with first-order kinetics. 2. When the tetravalent organic cation spermine (Spm) was added in the pipettes, the activation kinetics changed; this was explicable by the increase in the closing rate constant. The activation of the currents observed without Spm or Mg2+ in the pipettes was ascribed to the unblocking of the 'endogenous-Spm block'. 3. In the presence of the divalent cation putrescine (Put) or of Mg2+ in the pipettes, a different non-conductive state suppressed the outward currents on depolarization; the channels instantaneously changed to the open state on repolarization. As the depolarization was prolonged, this non-conductive state was replaced by the non-conductive state that shows an exponential activation on repolarization. This phenomenon was attributed to the redistribution of the channels from the Put- or Mg(2+)-blocked state to the 'endogenous Spm-blocked state' during depolarization. 4. In the presence of the trivalent cation spermidine (Spd) in the pipettes, two different non-conductive states occurred, showing a faster and a slower activation on repolarization. The rectification around Erev was mainly due to the non-conductive state showing a faster activation, which appeared to be the Spd-blocked state. During depolarization, redistribution of the channels to the 'endogenous Spm-blocked state' also occurred. 5. In the presence of Spd, Put or Mg2+ in the pipettes, the voltage dependence of the activation time constant reflecting the unblocking of the 'endogenous Spm' was shifted in the hyperpolarizing direction. 6. Our results suggest that the 'intrinsic gating' that shows the time-dependent activation on repolarization, and that is responsible for the inward rectification around Erev, reflects the blocking kinetics of the tetravalent Spm. PMID:8866861

Particulate matter modifies the association between airborne pollen and daily medical consultations for pollinosis in Tokyo.

PubMed

Konishi, Shoko; Ng, Chris Fook Sheng; Stickley, Andrew; Nishihata, Shinichi; Shinsugi, Chisa; Ueda, Kayo; Takami, Akinori; Watanabe, Chiho

2014-11-15

Pollen from Japanese cedar (sugi) and cypress (hinoki) trees is responsible for the growing prevalence of allergic rhinitis, especially pollinosis in Japan. Previous studies have suggested that air pollutants enhance the allergic response to pollen in susceptible individuals. We conducted a time-stratified case-crossover study to examine the potential modifying effects of PM2.5 and suspended particulate matter (SPM) on the association between pollen concentration and daily consultations for pollinosis. A total of 11,713 daily pollinosis cases (International Classification of Diseases, ICD-10, J30.1) from January to May, 2001-2011, were obtained from a clinic in Chiyoda, Tokyo. Daily pollen counts and the daily mean values of air pollutants (PM2.5, SPM, SO2, NO2, CO, and O3) were collected from monitoring stations across Tokyo. The effects of pollen were stratified by the level of PM2.5 and SPM to examine the interaction effect of pollen and particulate pollutants. We found a statistically significant interaction between pollen concentration and PM2.5/SPM. On days with a high level of PM2.5 (>95th percentile), an interquartile increase in the mean cumulative pollen count (an average of 28 pollen grains per cm(2) during lag-days 0 to 5) corresponded to a 10.30% (95%CI: 8.48%-12.16%) increase in daily new pollinosis cases, compared to 8.04% (95%CI: 7.28%-8.81%) on days with a moderate level of PM2.5 (5th-95th percentile). This interaction persisted when different percentile cut-offs were used and was robust to the inclusion of other air pollutants. A similar interaction pattern was observed between SPM and pollen when a less extreme cut-off for SPM was used to stratify the effect of pollen. Our study showed the acute effect of pollen was greater when the concentration of air particulate pollutant, specifically PM2.5 and SPM, was higher. These findings are consistent with the notion that particulate air pollution may act as an adjuvant that promotes allergic disease (i.e. pollinosis). Copyright © 2014 Elsevier B.V. All rights reserved.

Validation of the Tactical Air Force’s Decision Making Process to Prioritize Modifications Using the Analytic Hierarchy Process.

DTIC Science & Technology

1987-12-01

were presented. The second part of the thesis proposed the alternative methods of decision analysis and PROMETHEE to solve TAF’s . prioritization...of decision analysis (DA) and Preference Ranking Orqanization Method for Enrichment Evaluations ( PROMETHEE ) will be explained. First, the...dollars. However, once this task is successfully accomplished, TAF would be able to use DA to prioritize their mods. The PROMETHEE is a "new class of

A large-scale benchmark of gene prioritization methods.

PubMed

Guala, Dimitri; Sonnhammer, Erik L L

2017-04-21

In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations. The Gene Ontology(GO) contains genes clustered around annotation terms. This intrinsic property of GO can be utilized in construction of robust benchmarks, objective to the problem domain. We demonstrate how this can be achieved for network-based gene prioritization tools, utilizing the FunCoup network. We use cross-validation and a set of appropriate performance measures to compare state-of-the-art gene prioritization algorithms: three based on network diffusion, NetRank and two implementations of Random Walk with Restart, and MaxLink that utilizes network neighborhood. Our benchmark suite provides a systematic and objective way to compare the multitude of available and future gene prioritization tools, enabling researchers to select the best gene prioritization tool for the task at hand, and helping to guide the development of more accurate methods.

Decision making in prioritization of required operational capabilities

NASA Astrophysics Data System (ADS)

Andreeva, P.; Karev, M.; Kovacheva, Ts.

2015-10-01

The paper describes an expert heuristic approach to prioritization of required operational capabilities in the field of defense. Based on expert assessment and by application of the method of Analytical Hierarchical Process, a methodology for their prioritization has been developed. It has been applied to practical simulation decision making games.

SPM local oxidation nanolithography with active control of cantilever dynamics

NASA Astrophysics Data System (ADS)

Nishimura, S.; Takemura, Y.; Shirakashi, J.

2007-04-01

Local oxidation nanolithography using scanning probe microscope (SPM) has enabled us to fabricate nanometer-scale oxide wires on material surfaces. Here, we study tapping mode SPM local oxidation experiments for silicon by controlling the dynamic properties of the cantilever. Dependence of feature size of fabricated oxide wires on the amplitude of the cantilever was precisely investigated. The quality factor (Q) was fixed at a natural value of ~500. By enhancing the amplitude of the cantilever, both width and height of fabricated Si oxide wires were decreased. With the variation of the amplitude of the cantilever from 0.5 V to 3.0 V (DC voltage = 22.5 V, scanning speed = 20 nm/s), the feature size of Si oxide wires was well controlled, ranging from 40 nm to 18 nm in width and 2.3 nm to 0.6 nm in height. Standard deviation of width on Si oxide wires formed by tapping mode SPM is around 2.0 nm, which is smaller than that of contact mode Si oxide wires. Furthermore, the variation of the oscillation amplitude of the cantilever does not affect the size uniformity of the wires. These results imply that the SPM local oxidation nanolithography with active control of cantilever dynamics is a useful technique for producing higher controllability on the nanometer-scale fabrication of Si oxide wires.

Progress on Poverty? New Estimates of Historical Trends Using an Anchored Supplemental Poverty Measure.

PubMed

Wimer, Christopher; Fox, Liana; Garfinkel, Irwin; Kaushal, Neeraj; Waldfogel, Jane

2016-08-01

This study examines historical trends in poverty using an anchored version of the U.S. Census Bureau's recently developed Research Supplemental Poverty Measure (SPM) estimated back to 1967. Although the SPM is estimated each year using a quasi-relative poverty threshold that varies over time with changes in families' expenditures on a core basket of goods and services, this study explores trends in poverty using an absolute, or anchored, SPM threshold. We believe the anchored measure offers two advantages. First, setting the threshold at the SPM's 2012 levels and estimating it back to 1967, adjusted only for changes in prices, is more directly comparable to the approach taken in official poverty statistics. Second, it allows for a better accounting of the roles that social policy, the labor market, and changing demographics play in trends in poverty rates over time, given that changes in the threshold are held constant. Results indicate that unlike official statistics that have shown poverty rates to be fairly flat since the 1960s, poverty rates have dropped by 40 % when measured using a historical anchored SPM over the same period. Results obtained from comparing poverty rates using a pretax/pretransfer measure of resources versus a post-tax/post-transfer measure of resources further show that government policies, not market incomes, are driving the declines observed over time.

The Relationship between Polyamines and Hormones in the Regulation of Wheat Grain Filling

PubMed Central

Liu, Yang; Gu, Dandan; Wu, Wei; Wen, Xiaoxia; Liao, Yuncheng

2013-01-01

The grain weight of wheat is strongly influenced by filling. Polyamines (PA) are involved in regulating plant growth. However, the effects of PA on wheat grain filling and its mechanism of action are unclear. The objective of the present study was to investigate the relationship between PAs and hormones in the regulation of wheat grain filling. Three PAs, spermidine (Spd), spermine (Spm), and putrescine (Put), were exogenously applied, and the grain filling characteristics and changes in endogenous PA and hormones, i.e., indole-3-acetic acid (IAA), zeatin (Z) + zeatin riboside (ZR), abscisic acid (ABA), ethylene (ETH) and gibberellin 1+4 (GAs), were quantified during wheat grain filling. Exogenous applications of Spd and Spm significantly increased the grain filling rate and weight, but exogenous Put had no significant effects on these measures. Exogenous Spd and Spm significantly increased the endogenous Spd, Spm, Z+ZR, ABA, and IAA contents and significantly decreased ETH evolution in grains. The endogenous Spd, Spm and Z+ZR contents were positively and significantly correlated with the grain filling rate and weight of wheat, and the endogenous ETH evolution was negatively and significantly correlated with the wheat grain filling rate and weight. Based upon these results, we concluded that PAs were involved in the balance of hormones that regulated the grain filling of wheat. PMID:24205154

Micromagnet arrays for on-chip focusing, switching, and separation of superparamagnetic beads and single cells.

PubMed

Rampini, S; Kilinc, D; Li, P; Monteil, C; Gandhi, D; Lee, G U

2015-08-21

Nonlinear magnetophoresis (NLM) is a novel approach for on-chip transport and separation of superparamagnetic (SPM) beads, based on a travelling magnetic field wave generated by the combination of a micromagnet array (MMA) and an applied rotating magnetic field. Here, we present two novel MMA designs that allow SPM beads to be focused, sorted, and separated on-chip. Converging MMAs were used to rapidly collect the SPM beads from a large region of the chip and focus them into synchronised lines. We characterise the collection efficiency of the devices and demonstrate that they can facilitate on-chip analysis of populations of SPM beads using a single-point optical detector. The diverging MMAs were used to control the transport of the beads and to separate them based on their size. The separation efficiency of these devices was determined by the orientation of the magnetisation of the micromagnets relative to the external magnetic field and the size of the beads and relative to that of micromagnets. By controlling these parameters and the rotation of the external magnetic field we demonstrated the controlled transport of SPM bead-labelled single MDA-MB-231 cells. The use of these novel MMAs promises to allow magnetically-labelled cells to be efficiently isolated and then manipulated on-chip for analysis with high-resolution chemical and physical techniques.

An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods.

PubMed

Valentini, Giorgio; Paccanaro, Alberto; Caniza, Horacio; Romero, Alfonso E; Re, Matteo

2014-06-01

In the context of "network medicine", gene prioritization methods represent one of the main tools to discover candidate disease genes by exploiting the large amount of data covering different types of functional relationships between genes. Several works proposed to integrate multiple sources of data to improve disease gene prioritization, but to our knowledge no systematic studies focused on the quantitative evaluation of the impact of network integration on gene prioritization. In this paper, we aim at providing an extensive analysis of gene-disease associations not limited to genetic disorders, and a systematic comparison of different network integration methods for gene prioritization. We collected nine different functional networks representing different functional relationships between genes, and we combined them through both unweighted and weighted network integration methods. We then prioritized genes with respect to each of the considered 708 medical subject headings (MeSH) diseases by applying classical guilt-by-association, random walk and random walk with restart algorithms, and the recently proposed kernelized score functions. The results obtained with classical random walk algorithms and the best single network achieved an average area under the curve (AUC) across the 708 MeSH diseases of about 0.82, while kernelized score functions and network integration boosted the average AUC to about 0.89. Weighted integration, by exploiting the different "informativeness" embedded in different functional networks, outperforms unweighted integration at 0.01 significance level, according to the Wilcoxon signed rank sum test. For each MeSH disease we provide the top-ranked unannotated candidate genes, available for further bio-medical investigation. Network integration is necessary to boost the performances of gene prioritization methods. Moreover the methods based on kernelized score functions can further enhance disease gene ranking results, by adopting both local and global learning strategies, able to exploit the overall topology of the network. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Hesitant fuzzy linguistic multicriteria decision-making method based on generalized prioritized aggregation operator.

PubMed

Wu, Jia-ting; Wang, Jian-qiang; Wang, Jing; Zhang, Hong-yu; Chen, Xiao-hong

2014-01-01

Based on linguistic term sets and hesitant fuzzy sets, the concept of hesitant fuzzy linguistic sets was introduced. The focus of this paper is the multicriteria decision-making (MCDM) problems in which the criteria are in different priority levels and the criteria values take the form of hesitant fuzzy linguistic numbers (HFLNs). A new approach to solving these problems is proposed, which is based on the generalized prioritized aggregation operator of HFLNs. Firstly, the new operations and comparison method for HFLNs are provided and some linguistic scale functions are applied. Subsequently, two prioritized aggregation operators and a generalized prioritized aggregation operator of HFLNs are developed and applied to MCDM problems. Finally, an illustrative example is given to illustrate the effectiveness and feasibility of the proposed method, which are then compared to the existing approach.

An ensemble rank learning approach for gene prioritization.

PubMed

Lee, Po-Feng; Soo, Von-Wun

2013-01-01

Several different computational approaches have been developed to solve the gene prioritization problem. We intend to use the ensemble boosting learning techniques to combine variant computational approaches for gene prioritization in order to improve the overall performance. In particular we add a heuristic weighting function to the Rankboost algorithm according to: 1) the absolute ranks generated by the adopted methods for a certain gene, and 2) the ranking relationship between all gene-pairs from each prioritization result. We select 13 known prostate cancer genes in OMIM database as training set and protein coding gene data in HGNC database as test set. We adopt the leave-one-out strategy for the ensemble rank boosting learning. The experimental results show that our ensemble learning approach outperforms the four gene-prioritization methods in ToppGene suite in the ranking results of the 13 known genes in terms of mean average precision, ROC and AUC measures.

A continuous time delay-difference type model (CTDDM) applied to stock assessment of the southern Atlantic albacore Thunnus alalunga

NASA Astrophysics Data System (ADS)

Liao, Baochao; Liu, Qun; Zhang, Kui; Baset, Abdul; Memon, Aamir Mahmood; Memon, Khadim Hussain; Han, Yanan

2016-09-01

A continuous time delay-diff erence model (CTDDM) has been established that considers continuous time delays of biological processes. The southern Atlantic albacore ( Thunnus alalunga) stock is the one of the commercially important tuna population in the marine world. The age structured production model (ASPM) and the surplus production model (SPM) have already been used to assess the albacore stock. However, the ASPM requires detailed biological information and the SPM lacks the biological realism. In this study, we focus on applying a CTDDM to the southern Atlantic albacore ( T. alalunga) species, which provides an alternative method to assess this fishery. It is the first time that CTDDM has been provided for assessing the Atlantic albacore ( T. alalunga) fishery. CTDDM obtained the 80% confidence interval of MSY (maximum sustainable yield) of (21 510 t, 23 118t). The catch in 2011 (24 100 t) is higher than the MSY values and the relative fishing mortality ratio ( F 2011/ F MSY) is higher than 1.0. The results of CTDDM were analyzed to verify the proposed methodology and provide reference information for the sustainable management of the southern Atlantic albacore stock. The CTDDM treats the recruitment, the growth, and the mortality rates as all varying continuously over time and fills gaps between ASPM and SPM in this stock assessment.

Inorganic PM in poultry house using rice hull bedding

USDA-ARS?s Scientific Manuscript database

The persistence and long life expectancy of ammonia, odors and toxic pollutants from poultry houses may be due to the ability of suspended particulate matters (SPM) to serve as carriers for odorous compounds such as ammonium ions and volatile organic compounds. SPM is generated from the feed, anima...

Flight Model Discharge System

DTIC Science & Technology

1989-09-01

Itterconnection wiring diagram for the ESA ............................... 34 3-13 Typical gain versus total count curve for CEM...42 3-16 Calibration curve for energy bin 12 of the ion ESA ....................... 43 3-17 Flight ESA S/N001...Calibration curves for SPM S/N001 ......................................... 67 4-11 Calibration curves for SPM S/N002

A Critical Examination of Senior Executive Leadership Succession Planning and Management with Implications for Underrepresented Minorities

ERIC Educational Resources Information Center

Jackson, LeKeisha D.

2017-01-01

Guided by the research questions, this study utilized a sequential explanatory mixed methods research design to examine senior executive leadership succession planning at four-year, predominately white, doctoral universities in the state of Georgia. Utilizing the Representative Bureaucracy theory and the Mateso SPM conceptual model, this study…

Characterization of LiMn 2O 4 cathodes by electrochemical strain microscopy

DOE PAGES

Alikin, D. O.; Ievlev, A. V.; Luchkin, S. Yu.; ...

2016-03-15

Electrochemical strain microscopy (ESM) is a scanning probe microscopy(SPM) method in which the local electrodiffusion is probed via application of AC voltage to the SPM tip and registration of resulting electrochemical strain. In this study, we implemented ESM to measure local strain in bulk LiMn 2O 4 cathodes of a commercial Li-battery in different states of charge to investigate distribution of Li-ion mobility and concentration. Ramped AC ESM imaging and voltage spectroscopy were used to find the most reliable regime of measurements allowing separating and diminishing different contributions to ESM. This is not a trivial task due to complex geometrymore » of the sample and various obstacles resulting in less predictable contributions of different origins into ESM response: electrostatic tip–surface interactions, charge injection, electrostriction, and flexoelectricity. Finally, understanding and control of these contributions is an important step towards quantitative interpretation of ESM data.« less

Microfabrication of Silicon/Ceramic Hybrid Cantilever for Scanning Probe Microscope and Sensor Applications

NASA Astrophysics Data System (ADS)

Wakayama, Takayuki; Kobayashi, Toshinari; Iwata, Nobuya; Tanifuji, Nozomi; Matsuda, Yasuaki; Yamada, Syoji

2003-12-01

We present here new cantilevers for scanning probe microscopy (SPM) and sensor applications, which consist of silicon cantilever beam and ceramic pedestal. Silicon is only used to make cantilever beams and tips. Precision-machinery-made ceramics replaces silicon pedestal part. The ceramics was recently developed by Sumikin Ceramics and Quarts Co., Ltd. and can be machined precisely with end mill cutting. Many silicon beams are fabricated at once from a wafer using batch fabrication method. Therefore, SPM probes can be fabricated in high productivity and in low cost. These beams are transferred with transfer technique and are bonded on the ceramic pedestal with epoxy glue. We demonstrate here atomic force microscope (AFM) and gas sensor applications of the hybrid structure. In a gas sensor application, the ends of the cantilever are selectively modified with zeolite crystals as a sensitive layer. The bonding strength is enough for each application.

Real space mapping of ionic diffusion and electrochemical activity in energy storage and conversion materials

DOEpatents

Kalinin, Sergei V; Balke, Nina; Kumar, Amit; Dudney, Nancy J; Jesse, Stephen

2014-05-06

A method and system for probing mobile ion diffusivity and electrochemical reactivity on a nanometer length scale of a free electrochemically active surface includes a control module that biases the surface of the material. An electrical excitation signal is applied to the material and induces the movement of mobile ions. An SPM probe in contact with the surface of the material detects the displacement of mobile ions at the surface of the material. A detector measures an electromechanical strain response at the surface of the material based on the movement and reactions of the mobile ions. The use of an SPM tip to detect local deformations allows highly reproducible measurements in an ambient environment without visible changes in surface structure. The measurements illustrate effective spatial resolution comparable with defect spacing and well below characteristic grain sizes of the material.

Strain Prioritization for Natural Product Discovery by a High-Throughput Real-Time PCR Method

PubMed Central

2015-01-01

Natural products offer unmatched chemical and structural diversity compared to other small-molecule libraries, but traditional natural product discovery programs are not sustainable, demanding too much time, effort, and resources. Here we report a strain prioritization method for natural product discovery. Central to the method is the application of real-time PCR, targeting genes characteristic to the biosynthetic machinery of natural products with distinct scaffolds in a high-throughput format. The practicality and effectiveness of the method were showcased by prioritizing 1911 actinomycete strains for diterpenoid discovery. A total of 488 potential diterpenoid producers were identified, among which six were confirmed as platensimycin and platencin dual producers and one as a viguiepinol and oxaloterpin producer. While the method as described is most appropriate to prioritize strains for discovering specific natural products, variations of this method should be applicable to the discovery of other classes of natural products. Applications of genome sequencing and genome mining to the high-priority strains could essentially eliminate the chance elements from traditional discovery programs and fundamentally change how natural products are discovered. PMID:25238028

20180311 - Development of a Tool for Systematic Integration of Traditional and New Approach Methods for Prioritizing Chemical Lists (SOT)

EPA Science Inventory

Multiple chemical regulatory bodies (US EPA, ECHA, OECD, Health Canada) are currently tasked with prioritizing chemicals for in-depth risk assessments. These prioritization efforts are driven by the fact that there are many chemicals in commerce, or in the environment for which d...

Development of a Tool for Systematic Integration of Traditional and New Approach Methods for Prioritizing Chemical Lists

EPA Science Inventory

Multiple chemical regulatory bodies (US EPA, ECHA, OECD, Health Canada) are currently tasked with prioritizing chemicals for in-depth risk assessments. These prioritization efforts are driven by the fact that there are many chemicals in commerce, or in the environment for which d...

A hybrid analog-digital phase-locked loop for frequency mode non-contact scanning probe microscopy.

PubMed

Mehta, M M; Chandrasekhar, V

2014-01-01

Non-contact scanning probe microscopy (SPM) has developed into a powerful technique to image many different properties of samples. The conventional method involves monitoring the amplitude, phase, or frequency of a cantilever oscillating at or near its resonant frequency as it is scanned across the surface of a sample. For high Q factor cantilevers, monitoring the resonant frequency is the preferred method in order to obtain reasonable scan times. This can be done by using a phase-locked-loop (PLL). PLLs can be obtained as commercial integrated circuits, but these do not have the frequency resolution required for SPM. To increase the resolution, all-digital PLLs requiring sophisticated digital signal processors or field programmable gate arrays have also been implemented. We describe here a hybrid analog/digital PLL where most of the components are implemented using discrete analog integrated circuits, but the frequency resolution is provided by a direct digital synthesis chip controlled by a simple peripheral interface controller (PIC) microcontroller. The PLL has excellent frequency resolution and noise, and can be controlled and read by a computer via a universal serial bus connection.

A hybrid analog-digital phase-locked loop for frequency mode non-contact scanning probe microscopy

NASA Astrophysics Data System (ADS)

Mehta, M. M.; Chandrasekhar, V.

2014-01-01

Non-contact scanning probe microscopy (SPM) has developed into a powerful technique to image many different properties of samples. The conventional method involves monitoring the amplitude, phase, or frequency of a cantilever oscillating at or near its resonant frequency as it is scanned across the surface of a sample. For high Q factor cantilevers, monitoring the resonant frequency is the preferred method in order to obtain reasonable scan times. This can be done by using a phase-locked-loop (PLL). PLLs can be obtained as commercial integrated circuits, but these do not have the frequency resolution required for SPM. To increase the resolution, all-digital PLLs requiring sophisticated digital signal processors or field programmable gate arrays have also been implemented. We describe here a hybrid analog/digital PLL where most of the components are implemented using discrete analog integrated circuits, but the frequency resolution is provided by a direct digital synthesis chip controlled by a simple peripheral interface controller (PIC) microcontroller. The PLL has excellent frequency resolution and noise, and can be controlled and read by a computer via a universal serial bus connection.

Interaction centres of pyrimidine nucleotides: cytidine-5'-diphosphate (CDP) and cytidine-5'-triphosphate (CTP) in their reactions with tetramines and Cu(II) ions.

PubMed

Gasowska, A

2005-08-01

The interactions between pyrimidine nucleotides: cytidine-5'-diphosphate (CDP) and cytidine-5'-triphosphate (CTP) and Cu(II) ions, spermine (Spm) and 1,11-diamino-4,8-diazaundecane (3,3,3-tet) have been studied. The composition and stability constants of the complexes formed have been determined by means of the potentiometric method, while the centres of interactions in the ligands have been identified by the spectral methods (UV-Vis, Ultraviolet and Visible spectroscopy; EPR, electron spin resonance; NMR). In the systems without metal, formation of the molecular complexes nucleotide-polyamine with the interaction centres at the endocyclic nitrogen atom of purine ring N3, the oxygen atoms of the phosphate group from the nucleotide and protonated nitrogen atoms of the polyamine have been detected. Significant differences have been found in the metallation between the systems with Spm and with 3,3,3-tet. In the systems with spermine, mainly protonated species are formed with the phosphate group of the nucleotide and deprotonated nitrogen atoms of the polyamine making the coordination centres, while the donor nitrogen atom of the nucleotide N3 is involved in the intramolecular interligand interactions, additionally stabilising the complex. In the systems with 3,3,3-tet, the MLL' type species are formed in which the oxygen atoms of the phosphate group and nitrogen atoms of the polyamine are involved in metallation, whereas the N3 atom from the pyrimidine ring of the nucleotide is located outside the inner coordination sphere of copper ion. The main centre of Cu(II) interaction in the nucleotide, both in the system with Spm and 3,3,3-tet is the phosphate group of the nucleotide.

The application of statistical parametric mapping to 123I-FP-CIT SPECT in dementia with Lewy bodies, Alzheimer's disease and Parkinson's disease.

PubMed

Colloby, Sean J; O'Brien, John T; Fenwick, John D; Firbank, Michael J; Burn, David J; McKeith, Ian G; Williams, E David

2004-11-01

Dopaminergic loss can be visualised using (123)I-FP-CIT single photon emission computed tomography (SPECT) in several disorders including Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Most previous SPECT studies have adopted region of interest (ROI) methods for analysis, which are subjective and operator-dependent. The purpose of this study was to investigate differences in striatal binding of (123)I-FP-CIT SPECT using the automated technique of statistical parametric mapping (SPM99) in subjects with DLB, Alzheimer's disease (AD), PD and healthy age-matched controls. This involved spatial normalisation of each subject's image to a customised template, followed by smoothing and intensity normalisation of each image to its corresponding mean occipital count per voxel. Group differences were assessed using a two-sample t test. Applying a height threshold of P

Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model.

PubMed

Ni, Jingchao; Koyuturk, Mehmet; Tong, Hanghang; Haines, Jonathan; Xu, Rong; Zhang, Xiang

2016-11-10

Accurately prioritizing candidate disease genes is an important and challenging problem. Various network-based methods have been developed to predict potential disease genes by utilizing the disease similarity network and molecular networks such as protein interaction or gene co-expression networks. Although successful, a common limitation of the existing methods is that they assume all diseases share the same molecular network and a single generic molecular network is used to predict candidate genes for all diseases. However, different diseases tend to manifest in different tissues, and the molecular networks in different tissues are usually different. An ideal method should be able to incorporate tissue-specific molecular networks for different diseases. In this paper, we develop a robust and flexible method to integrate tissue-specific molecular networks for disease gene prioritization. Our method allows each disease to have its own tissue-specific network(s). We formulate the problem of candidate gene prioritization as an optimization problem based on network propagation. When there are multiple tissue-specific networks available for a disease, our method can automatically infer the relative importance of each tissue-specific network. Thus it is robust to the noisy and incomplete network data. To solve the optimization problem, we develop fast algorithms which have linear time complexities in the number of nodes in the molecular networks. We also provide rigorous theoretical foundations for our algorithms in terms of their optimality and convergence properties. Extensive experimental results show that our method can significantly improve the accuracy of candidate gene prioritization compared with the state-of-the-art methods. In our experiments, we compare our methods with 7 popular network-based disease gene prioritization algorithms on diseases from Online Mendelian Inheritance in Man (OMIM) database. The experimental results demonstrate that our methods recover true associations more accurately than other methods in terms of AUC values, and the performance differences are significant (with paired t-test p-values less than 0.05). This validates the importance to integrate tissue-specific molecular networks for studying disease gene prioritization and show the superiority of our network models and ranking algorithms toward this purpose. The source code and datasets are available at http://nijingchao.github.io/CRstar/ .

Radio frequency elevator for a pulsed positron beam

NASA Astrophysics Data System (ADS)

Dickmann, Marcel; Mitteneder, Johannes; Kögel, Gottfried; Egger, Werner; Sperr, Peter; Ackermann, Ulrich; Piochacz, Christian; Dollinger, Günther

2016-06-01

An elevator increases the potential energy of a particle beam with respect to ground potential without any alteration of kinetic energy and other beam parameters. This elevator is necessary for the implementation of the Munich Scanning Positron Microscope (SPM) at the intense positron source NEPOMUC at the research reactor FRM II in Munich. The principles of the rf elevator for pure electrostatically guided positrons are described. Measurements of beam quality behind the elevator are reported, which confirm that after the implementation of elevator and SPM at NEPOMUC the SPM can be operated at a considerably improved resolution (~ 0.3 μm) and event rate (~3.7 kHz) compared to the laboratory based β+-source.

Nanoscale patterning of Si surface using SPM scratching

NASA Astrophysics Data System (ADS)

Ogino, T.; Nishimura, S.; Shirakashi, J.

2008-03-01

Nanolithography of Si surface using scanning probe microscopy (SPM) scratching with a diamond-coated tip was systematically investigated at a low force regime below 9 μN. The groove patterns with controlled width and depth could be achieved by adjusting the applied force, scan direction and the number of scan cycles. There was no effect of scan speed on the groove size. The minimum groove width of 10 nm was obtained on Si surfaces. Furthermore, more complex nanostructures such as line and space patterns of 30 nm pith and dot arrays of 2.6×1010 cm-2 density were realized. SPM scratching with a diamond-coated tip allows nanoscale patterning of Si surfaces to be performed simply.

SPM oxidation and parallel writing on zirconium nitride thin films

NASA Astrophysics Data System (ADS)

Farkas, N.; Comer, J. R.; Zhang, G.; Evans, E. A.; Ramsier, R. D.; Dagata, J. A.

2005-07-01

Systematic investigation of the SPM oxidation process of sputter-deposited ZrN thin films is reported. During the intrinsic part of the oxidation, the density of the oxide increases until the total oxide thickness is approximately twice the feature height. Further oxide growth is sustainable as the system undergoes plastic flow followed by delamination from the ZrN-silicon interface keeping the oxide density constant. ZrN exhibits superdiffusive oxidation kinetics in these single tip SPM studies. We extend this work to the fabrication of parallel oxide patterns 70 nm in height covering areas in the square centimeter range. This simple, quick, and well-controlled parallel nanolithographic technique has great potential for biomedical template fabrication.

Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration

PubMed Central

Klein, Arno; Andersson, Jesper; Ardekani, Babak A.; Ashburner, John; Avants, Brian; Chiang, Ming-Chang; Christensen, Gary E.; Collins, D. Louis; Gee, James; Hellier, Pierre; Song, Joo Hyun; Jenkinson, Mark; Lepage, Claude; Rueckert, Daniel; Thompson, Paul; Vercauteren, Tom; Woods, Roger P.; Mann, J. John; Parsey, Ramin V.

2009-01-01

All fields of neuroscience that employ brain imaging need to communicate their results with reference to anatomical regions. In particular, comparative morphometry and group analysis of functional and physiological data require coregistration of brains to establish correspondences across brain structures. It is well established that linear registration of one brain to another is inadequate for aligning brain structures, so numerous algorithms have emerged to nonlinearly register brains to one another. This study is the largest evaluation of nonlinear deformation algorithms applied to brain image registration ever conducted. Fourteen algorithms from laboratories around the world are evaluated using 8 different error measures. More than 45,000 registrations between 80 manually labeled brains were performed by algorithms including: AIR, ANIMAL, ART, Diffeomorphic Demons, FNIRT, IRTK, JRD-fluid, ROMEO, SICLE, SyN, and four different SPM5 algorithms (“SPM2-type” and regular Normalization, Unified Segmentation, and the DARTEL Toolbox). All of these registrations were preceded by linear registration between the same image pairs using FLIRT. One of the most significant findings of this study is that the relative performances of the registration methods under comparison appear to be little affected by the choice of subject population, labeling protocol, and type of overlap measure. This is important because it suggests that the findings are generalizable to new subject populations that are labeled or evaluated using different labeling protocols. Furthermore, we ranked the 14 methods according to three completely independent analyses (permutation tests, one-way ANOVA tests, and indifference-zone ranking) and derived three almost identical top rankings of the methods. ART, SyN, IRTK, and SPM's DARTEL Toolbox gave the best results according to overlap and distance measures, with ART and SyN delivering the most consistently high accuracy across subjects and label sets. Updates will be published on the http://www.mindboggle.info/papers/ website. PMID:19195496

Effect of Feeding Schedule on Fractionated Particulate Matter Distribution in Rooster House

USDA-ARS?s Scientific Manuscript database

The persistence and long life expectancy of ammonia, odors and toxic pollutants from poultry houses may be due to the ability of suspended particulate matters (SPM) to serve as carriers for odorous compounds such as ammonium ions and volatile organic compounds. SPM is generated from the feed, anima...

Dysgenic Fertility, Intelligence and Family Size in Libya

ERIC Educational Resources Information Center

Al-Shahomee, Alsedig Abdalgadr; Lynn, Richard; Abdalla, Saleh El-ghmary

2013-01-01

The Standard Progressive Matrices (SPM) was administered to a sample of 592 16 year old school students in Libya. There was a small negative correlation of -0.14 between SPM scores and the number of siblings, indicating only marginal dysgenic fertility. Supplementary material giving the data is given online. (Contains 1 table.)

Experimental Evaluation of a Serious Game for Teaching Software Process Modeling

ERIC Educational Resources Information Center

Chaves, Rafael Oliveira; von Wangenheim, Christiane Gresse; Furtado, Julio Cezar Costa; Oliveira, Sandro Ronaldo Bezerra; Santos, Alex; Favero, Eloi Luiz

2015-01-01

Software process modeling (SPM) is an important area of software engineering because it provides a basis for managing, automating, and supporting software process improvement (SPI). Teaching SPM is a challenging task, mainly because it lays great emphasis on theory and offers few practical exercises. Furthermore, as yet few teaching approaches…

Trends and the effect of management on macronutrients in fractionated particulate matter in rooster house

USDA-ARS?s Scientific Manuscript database

The persistence and long life expectancy of ammonia, odors and toxic pollutants from poultry houses may be due to the ability of suspended particulate matters (SPM) to serve as carriers for odorous compounds such as ammonium ions and volatile organic compounds. SPM is generated from the feed, anima...

Visualizing Confidence Bands for Semiparametrically Estimated Nonlinear Relations among Latent Variables

ERIC Educational Resources Information Center

Pek, Jolynn; Chalmers, R. Philip; Kok, Bethany E.; Losardo, Diane

2015-01-01

Structural equation mixture models (SEMMs), when applied as a semiparametric model (SPM), can adequately recover potentially nonlinear latent relationships without their specification. This SPM is useful for exploratory analysis when the form of the latent regression is unknown. The purpose of this article is to help users familiar with structural…

Hedonic approaches based on spatial econometrics and spatial statistics: application to evaluation of project benefits

NASA Astrophysics Data System (ADS)

Tsutsumi, Morito; Seya, Hajime

2009-12-01

This study discusses the theoretical foundation of the application of spatial hedonic approaches—the hedonic approach employing spatial econometrics or/and spatial statistics—to benefits evaluation. The study highlights the limitations of the spatial econometrics approach since it uses a spatial weight matrix that is not employed by the spatial statistics approach. Further, the study presents empirical analyses by applying the Spatial Autoregressive Error Model (SAEM), which is based on the spatial econometrics approach, and the Spatial Process Model (SPM), which is based on the spatial statistics approach. SPMs are conducted based on both isotropy and anisotropy and applied to different mesh sizes. The empirical analysis reveals that the estimated benefits are quite different, especially between isotropic and anisotropic SPM and between isotropic SPM and SAEM; the estimated benefits are similar for SAEM and anisotropic SPM. The study demonstrates that the mesh size does not affect the estimated amount of benefits. Finally, the study provides a confidence interval for the estimated benefits and raises an issue with regard to benefit evaluation.

Cyclobutanone Mimics of Intermediates in Metallo-β-Lactamase Catalysis.

PubMed

Abboud, Martine I; Kosmopoulou, Magda; Krismanich, Anthony P; Johnson, Jarrod W; Hinchliffe, Philip; Brem, Jürgen; Claridge, Timothy D W; Spencer, James; Schofield, Christopher J; Dmitrienko, Gary I

2018-04-17

The most important resistance mechanism to β-lactam antibiotics involves hydrolysis by two β-lactamase categories: the nucleophilic serine and the metallo-β-lactamases (SBLs and MBLs, respectively). Cyclobutanones are hydrolytically stable β-lactam analogues with potential to inhibit both SBLs and MBLs. We describe solution and crystallographic studies on the interaction of a cyclobutanone penem analogue with the clinically important MBL SPM-1. NMR experiments using 19 F-labeled SPM-1 imply the cyclobutanone binds to SPM-1 with micromolar affinity. A crystal structure of the SPM-1:cyclobutanone complex reveals binding of the hydrated cyclobutanone through interactions with one of the zinc ions, stabilisation of the hydrate by hydrogen bonding to zinc-bound water, and hydrophobic contacts with aromatic residues. NMR analyses using a 13 C-labeled cyclobutanone support assignment of the bound species as the hydrated ketone. The results inform on how MBLs bind substrates and stabilize tetrahedral intermediates. They support further investigations on the use of transition-state and/or intermediate analogues as inhibitors of all β-lactamase classes. © 2018 Die Autoren. Veröffentlicht von Wiley-VCH Verlag GmbH & Co. KGaA.

The Absolute Proper Motion of NGC 6397 Revisited

NASA Astrophysics Data System (ADS)

Rees, Richard; Cudworth, Kyle

2018-01-01

We compare several determinations of the absolute proper motion of the Galactic globular cluster NGC 6397: (1) our own determination relative to field stars derived from scans of 38 photographic plates spanning 97 years in epoch; (2) using our proper motion membership to identify cluster stars in various catalogs in the literature (UCAC4, UCAC5, PPMXL, HSOY, Tycho-2, Hipparcos, TGAS); (3) published results from the Yale SPM Program (both tied to Hipparcos and relative to galaxies) and two from HST observations relative to galaxies. The various determinations are not in good agreement. Curiously, the Yale SPM relative to galaxies does not agree with the HST determinations, and the individual HST error ellipses are close to each other but do not overlap. The Yale SPM relative to galaxies does agree with our determination, Tycho-2, and the Yale SPM tied to Hipparcos. It is not clear which of the current determinations is most reliable; we have found evidence of systematic errors in some of them (including one of the HST determinations). This research has been partially supported by the NSF.

Molecular epidemiology of SPM-1-producing Pseudomonas aeruginosa by rep-PCR in hospitals in Parana, Brazil.

PubMed

Kalluf, K O; Arend, L N; Wuicik, T E; Pilonetto, M; Tuon, F F

2017-04-01

Infections caused by multidrug resistant microorganisms are a global health problem, and Pseudomonas aeruginosa is an important nosocomial pathogen, easily disseminated in the hospital environment. The aim of this study was to determine SPM-1 in P. aeruginosa strains in 30 Brazilian hospitals and the genetic similarity of isolates. We analyzed 161 isolates of carbapenem-resistant P. aeruginosa. Imipenem/EDTA and imipenem strip were used for phenotypic detection of MBL production; and real-time polymerase chain reaction (PCR) for genetic detection. Genetic similarity was determined by rep-PCR. We obtained 136/161 (84.5%) isolates with positive phenotypic result for metallo-β-lactamase (MBL) and the bla SPM-1 gene was identified in 41 isolates. There was a predominant profile (>95% of genetic similarity) in 92.7% of isolates. This predominant profile was widely disseminated in Paraná state. SPM-1 is the main MBL identified in carbapenem-resistant P. aeruginosa in Southern Brazil. The genetic similarity among some isolates suggests a clonal expansion. Copyright © 2016 Elsevier B.V. All rights reserved.

Concentration of biologically active polyamines in rabbit meat, liver and kidney after slaughter and their changes during meat storage and cooking.

PubMed

Dadáková, Eva; Pelikánová, Tamara; Kalač, Pavel

2012-03-01

The concentration of putrescine (PUT), spermidine (SPD) and spermine (SPM) was determined in chilled meat and kidneys of 18 rabbits and in liver of 12 animals 24h after slaughter. Very low PUT concentrations were detected only in kidneys. Mean SPD levels were 2.2, 2.2, 61.7 and 32.7mgkg(-1) in saddle, leg, liver and kidneys, respectively. The respective SPM concentrations were 14.7, 8.0, 115 and 88.4mgkg(-1). SPD and SPM losses of about one third of the initial levels were apparent in saddles stored at -18°C for 8months. Losses of both polyamines of about 15-20% of the initial concentrations were found in saddles stored aerobically at +2°C for up to 9days. Stewing of saddles caused significant SPD and SPM losses of about 20-25%, while upon roasting and pan-roasting without oil a decrease of about 50% of the initial concentration was observed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Tapping mode SPM local oxidation nanolithography with sub-10 nm resolution

NASA Astrophysics Data System (ADS)

Nishimura, S.; Ogino, T.; Takemura, Y.; Shirakashi, J.

2008-03-01

Tapping mode SPM local oxidation nanolithography with sub-10 nm resolution is investigated by optimizing the applied bias voltage (V), scanning speed (S) and the oscillation amplitude of the cantilever (A). We fabricated Si oxide wires with an average width of 9.8 nm (V = 17.5 V, S = 250 nm/s, A = 292 nm). In SPM local oxidation with tapping mode operation, it is possible to decrease the size of the water meniscus by enhancing the oscillation amplitude of cantilever. Hence, it seems that the water meniscus with sub-10 nm dimensions could be formed by precisely optimizing the oxidation conditions. Moreover, we quantitatively explain the size (width and height) of Si oxide wires with a model based on the oxidation ratio, which is defined as the oxidation time divided by the period of the cantilever oscillation. The model allows us to understand the mechanism of local oxidation in tapping mode operation with amplitude modulation. The results imply that the sub-10 nm resolution could be achieved using tapping mode SPM local oxidation technique with the optimization of the cantilever dynamics.

SPM-Twin Telescopes: Project Overview

NASA Astrophysics Data System (ADS)

González, J. J.

2007-06-01

The SPM-Twin Project is an international initiative for a pair of 6.5-m telescopes, at the San Pedro Mártir Observatory (SPM), to provide a limber, and highly competitive, platform for discovery by focusing on scientific niches technically difficult for existing or planned larger aperture telescopes, and by exploiting the superiority of the SPM site. The telescopes are based on the proven and highly efficient Magellan concept, but each with a distinct optimization to cover two complementary but mutually exclusive aspects: (a) the "Standard Field Telescope" would have a field of view of 15'- 30', capable of observing in the optical through the thermal infrared (0.4 - 24 μm) and prepared for adaptive optics, and (b) the "Wide Field Telescope" (WFT) with a field of view of 1.5° or more, capable of multi-object fiber spectroscopy, integral field unit (IFU) spectroscopy, and potentially narrow-band imaging as well. The WFT spectroscopy would extend from 0.36 to 1.8 μm, and would contain several thousand fibers. We present a general overview of the project.

Protective Action of Spermine and Spermidine against Photoinhibition of Photosystem I in Isolated Thylakoid Membranes

PubMed Central

Yaakoubi, Hnia; Hamdani, Saber; Bekalé, Laurent; Carpentier, Robert

2014-01-01

The photo-stability of photosystem I (PSI) is of high importance for the photosynthetic processes. For this reason, we studied the protective action of two biogenic polyamines (PAs) spermine (Spm) and spermidine (Spd) on PSI activity in isolated thylakoid membranes subjected to photoinhibition. Our results show that pre-loading thylakoid membranes with Spm and Spd reduced considerably the inhibition of O2 uptake rates, P700 photooxidation and the accumulation of superoxide anions (O2 −) induced by light stress. Spm seems to be more effective than Spd in preserving PSI photo-stability. The correlation of the extent of PSI protection, photosystem II (PSII) inhibition and O2 − generation with increasing Spm doses revealed that PSI photo-protection is assumed by two mechanisms depending on the PAs concentration. Given their antioxidant character, PAs scavenge directly the O2 − generated in thylakoid membranes at physiological concentration (1 mM). However, for non-physiological concentration, the ability of PAs to protect PSI is due to their inhibitory effect on PSII electron transfer. PMID:25420109

Spermine modulates the expression of two probable polyamine transporter genes and determines growth responses to cadaverine in Arabidopsis.

PubMed

Sagor, G H M; Berberich, Thomas; Kojima, Seiji; Niitsu, Masaru; Kusano, Tomonobu

2016-06-01

Two genes, LAT1 and OCT1 , are likely to be involved in polyamine transport in Arabidopsis. Endogenous spermine levels modulate their expression and determine the sensitivity to cadaverine. Arabidopsis spermine (Spm) synthase (SPMS) gene-deficient mutant was previously shown to be rather resistant to the diamine cadaverine (Cad). Furthermore, a mutant deficient in polyamine oxidase 4 gene, accumulating about twofold more of Spm than wild type plants, showed increased sensitivity to Cad. It suggests that endogenous Spm content determines growth responses to Cad in Arabidopsis thaliana. Here, we showed that Arabidopsis seedlings pretreated with Spm absorbs more Cad and has shorter root growth, and that the transgenic Arabidopsis plants overexpressing the SPMS gene are hypersensitive to Cad, further supporting the above idea. The transgenic Arabidopsis overexpressing L-Amino acid Transporter 1 (LAT1) absorbed more Cad and showed increased Cad sensitivity, suggesting that LAT1 functions as a Cad importer. Recently, other research group reported that Organic Cation Transporter 1 (OCT1) is a causal gene which determines the Cad sensitivity of various Arabidopsis accessions. Furthermore, their results suggested that OCT1 is involved in Cad efflux. Thus we monitored the expression of OCT1 and LAT1 during the above experiments. Based on the results, we proposed a model in which the level of Spm content modulates the expression of OCT1 and LAT1, and determines Cad sensitivity of Arabidopsis.

Differential growth forms of the sponge Biemna fortis govern the abundance of its associated brittle star Ophiactis modesta

NASA Astrophysics Data System (ADS)

Dahihande, Azraj S.; Thakur, Narsinh L.

2017-08-01

Marine intertidal regions are physically stressful habitats. In such an environment, facilitator species and positive interactions mitigate unfavorable conditions to the benefit of less tolerant organisms. In sponge-brittle star association, sponges effectively shelter brittle stars from biotic and abiotic stresses. The sponge, Biemna fortis (Topsent, 1897) was examined from two intertidal regions Anjuna and Mhapan along the Central West Coast of India for associated brittle star Ophiactis modesta (Brock, 1888) during 2013-2014. The study sites varied in suspended particulate matter (SPM). B. fortis at the high SPM habitat (Anjuna) had partially buried growth form and at the low SPM habitat (Mhapan) had massive growth form. O. modesta was abundantly associated with the massive growth form (50-259 individuals per 500 ml sponge) but rarely occurred in association with partially buried growth form (6-16 individuals per 500 ml sponge). In laboratory choice assay O. modesta showed equal preference to the chemical cues from both the growth forms of B. fortis. In addition, O. modesta showed significant preference to B. fortis compared to other sympatric sponges. These observations highlight the involvement of chemical cues in host recognition by O. modesta. Massive growth forms transplanted to the high SPM habitat were unable to survive but partially buried growth forms transplanted to the low SPM habitat were able to survive. Differential growth forms of the host sponge B. fortis at different abiotic stresses affect the abundance of the associated brittle star O. modesta.

Oil sands process-affected water impairs feeding by Daphnia magna.

PubMed

Lari, Ebrahim; Steinkey, Dylan; Morandi, Garrett; Rasmussen, Joseph B; Giesy, John P; Pyle, Greg G

2017-05-01

Growth in extraction of bitumen from oil sands has raised concerns about influences of this industry on surrounding environments. Water clearance rate (a surrogate of feeding rate by Daphnia magna) in water containing D. magna exposed to oil sands process-affected water (OSPW) and its principal components, dissolved component (DC) and suspended particulate matter (SPM), was reduced to 72, 29, and 59% of controls, respectively. This study also examined several possible mechanisms for the observed changes algal cell density (i.e., feeding rate). There was no change in the digestive enzymes trypsin or amylase when D. magna were exposed to DC or SPM; however, exposure to total OSPW reduced trypsin activity. Mandible rolling or post-abdominal rejections, which are indicators of feeding and palatability of food, were not affected by any exposures to OSPW. Beating of thoracic limbs, which provides water flow toward the feeding groove, was reduced by exposure to SPM or total OSPW. Peristaltic activity was reduced by exposure to DC, which then might result in reduced digestion time in D. magna exposed to DC, SPM or whole OSPW. All treatments caused an increase in numbers of intact algae cells in the hindgut and excreted material. These results suggest that both DC and SPM affect feeding of D. magna by impairing actions of the digestive system, but most probably not by reducing rates of ingestion. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Stakeholder-Informed Approach to the Identification of Criteria for the Prioritization of Zoonoses in Canada

PubMed Central

Ng, Victoria; Sargeant, Jan M.

2012-01-01

Background Zoonotic diseases account for over 60% of all communicable diseases causing illness in humans and 75% of recently emerging infectious diseases. As limited resources are available for the control and prevention of zoonotic diseases, it is necessary to prioritize diseases in order to direct resources into those with the greatest needs. The selection of criteria for prioritization has traditionally been on the basis of expert opinion; however, details of the methods used to identify criteria from expert opinion often are not published and a full range of criteria may not be captured by expert opinion. Methodology/Principal Findings This study used six focus groups to identify criteria for the prioritization of zoonotic diseases in Canada. Focus groups included people from the public, animal health professionals and human health professionals. A total of 59 criteria were identified for prioritizing zoonotic diseases. Human-related criteria accounted for the highest proportion of criteria identified (55%), followed by animal-related criteria (26%) then pathogen/disease-related criteria (19%). Similarities and differences were observed in the identification and scoring of criteria for disease prioritization between groups; the public groups were strongly influenced by the individual-level of disease burden, the responsibility of the scientific community in disease prioritization and the experiences of recent events while the professional groups were influenced by the societal- and population-level of disease burden and political and public pressure. Conclusions/Significance This was the first study to describe a mixed semi-quantitative and qualitative approach to deriving criteria for disease prioritization. This was also the first study to involve the opinion of the general public regarding disease prioritization. The number of criteria identified highlights the difficulty in prioritizing zoonotic diseases. The method presented in this paper has formulated a comprehensive list of criteria that can be used to inform future disease prioritization studies. PMID:22238648

Variability in the fractionation of stable isotopes during degradation of two intertidal red algae

NASA Astrophysics Data System (ADS)

Hill, Jaclyn M.; McQuaid, Christopher D.

2009-04-01

Macroalgae contribute to intertidal food webs primarily as detritus, with unclear implications for food web studies using stable isotope analysis. We examined differences in the thallus parts of two South African rhodophytes ( Gelidium pristoides and Hypnea spicifera) and changes in overall δ13C, δ15N signatures and C:N ratios during degradation in both the field and laboratory. We hypothesized that both degrading macroalgal tissue and macroalgal-derived suspended particulate material (SPM) would show negligible changes in δ13C, but enriched δ15N signatures and lower C:N ratios relative to healthy plants. Only C:N laboratory ratios conformed to predictions, with both species of macroalgae showing decomposition related changes in δ13C and significant depletions in δ15N in both the field and laboratory. In the laboratory, algal tissue and SPM from each species behaved similarly (though some effects were non-significant) but with differing strengths. Gelidium pristoides δ13C increased and C:N ratios decreased over time in tissue and SPM; δ15N became depleted only in SPM. Hypnea spicifera, δ13C, δ15N and C:N ratios all decreased during degradation in both SPM and algae. Over 60 days in the field, δ13C was depleted in both species (1-2‰) and in naturally senescent Gelidium pristoides fronds. δ15N was depleted in Hypnea spicifera (approx. 1‰), while C:N ratios of both species were unaffected. The two species differed in δ13C, δ15N and C:N after degradation, but only in C:N beforehand. We suggest isotope changes in the laboratory mainly reflect microbial effects, while in the field these are combined with leaching due to constant water replenishment and agitation. Differences between these two species in the isotope responses to degradation highlight the difficulty of linking the signature of SPM to its multiple sources.

Polychlorinated diphenyl ethers (PCDEs) in surface sediments, suspended particulate matter (SPM) and surface water of Chaohu Lake, China.

PubMed

Zhang, Xuesheng; Wang, Tantan; Gao, Lei; Feng, Mingbao; Qin, Li; Shi, Jiaqi; Cheng, Danru

2018-05-31

Polychlorinated diphenyl ethers (PCDEs) are typical halogenated aromatic pollutants that have shown various toxicological effects on organisms. However, the contamination status of PCDEs in the fresh water lakes of China remains poorly researched. In this study, the levels of 15 congeners of PCDEs in the sediments, suspended particulate matter (SPM) and water of Chaohu Lake were determined. The results showed that the ranges of concentrations of total PCDEs (ΣPCDEs) in the sediment, SPM and water were 0.279 ng g -1 dry weight (d.w.)-2.474 ng g -1 d.w., 0.331 ng g -1 d.w.-2.013 ng g -1 d.w. and 0.351 ng L -1 -2.021 ng L -1 , respectively. The most abundant congeners found in sediments, SPM and water were 3,3',4,4'-tetra-CDE, deca-CDE and 2,4,6-tri-CDE, with average contributive ratios of 17.36%, 15.48% and 20.63%, respectively. The medium and higher chlorinated PCDEs (e.g., penta- and deca-CDEs) were the dominant congeners in sediments and SPM. The percentages of lower chlorinated PCDEs (e.g., tri-CDEs) in the water were higher than those in the sediments. The combined input of ΣPCDEs from the eight main tributaries to Chaohu Lake was estimated at 6.94 kg y -1 . Strong linear correlations between the concentrations of ΣPCDEs and organic carbon (OC) contents in three type samples from Chaohu Lake suggested OC could influence the distribution of PCDEs in Chaohu Lake substantially. In addition, the calculated average organic carbon normalized partition coefficients (logK oc ) of 15 PCDEs between water and SPM were in the range of 4.55-5.45 mL g -1 . This study confirmed that Chaohu Lake is contaminated by PCDEs. Copyright © 2018 Elsevier Ltd. All rights reserved.

A new methodology to derive settleable particulate matter guidelines to assist policy-makers on reducing public nuisance

NASA Astrophysics Data System (ADS)

Machado, Milena; Santos, Jane Meri; Reisen, Valdério Anselmo; Reis, Neyval Costa; Mavroidis, Ilias; Lima, Ana T.

2018-06-01

Air quality standards for settleable particulate matter (SPM) are found in many countries around the world. As well known, annoyance caused by SPM can be considered a community problem even if only a small proportion of the population is bothered at rather infrequent occasions. Many authors have shown that SPM cause soiling in residential and urban environments and degradation of materials (eg, objects and surface painting) that can impair the use and enjoyment of property and alter the normal activities of society. In this context, this paper has as main contribution to propose a guidance to establish air quality standards for annoyance caused by SPM in metropolitan industrial areas. To attain this objective, a new methodology is proposed which is based on the nonlinear correlation between the perceived annoyance (qualitative variable) and particles deposition rate (quantitative variable). Since the response variable is binary (annoyed and not annoyed), the logistic regression model is used to estimate the probability of people being annoyed at different levels of particles deposition rate and to compute the odds ratio function which gives, under a specific level of particles deposition rate, the estimated expected value of the population perceived annoyance. The proposed methodology is verified in a data set measured in the metropolitan area of Great Vitória, Espirito Santo, Brazil. As a general conclusion, the estimated probability function of perceived annoyance as a function of SPM has shown that 17% of inhabitants report annoyance to very low particles deposition levels of 5 g/(m2•30 days). In addition, for an increasing of 1 g/(m2•30 days) of SPM, the smallest estimated odds ratio of perceived annoyance by a factor of 1.5, implying that the probability of occurrence is almost 2 times as large as the probability of no occurrence of annoyance.

Effect of dietary utilisation of sugarcane press mud on production performance of Muzaffarnagari lambs.

PubMed

Kumar, Ranjan; Saha, S K; Kumar, Dinesh; Mahesh, M S; Malapure, C D

2017-10-01

Sugarcane press mud (SPM) is one of the potential agro-industrial by-products available in India and research exploring its utilisation in small ruminant nutrition is scanty. In this direction, the present study evaluated the feasibility of dietary incorporation of SPM at different levels in a feeding trial lasting 180 days. A total of 21 Muzaffarnagari ram lambs were randomly distributed into three groups of seven each based on comparable body weight (11.70 ± 0.29 kg) and age (3-5 months) following a completely randomised design. The three dietary treatments were (1) SP 0 (control), concentrate mixture without SPM; (2) SP 10 , concentrate mixture comprising 10% SPM and (3) SP 20 , concentrate mixture comprising 20% SPM on air-dry basis. The experimental lambs were offered weighed quantity of designated isonitrogenous (crude protein = 20.6%) and isoenergetic (metabolisable energy = 12.1 MJ/kg) concentrate mixture (coarse mash) and along with ad libitum wheat straw (threshed to 1-2-cm length) and a 9-day metabolism trial was conducted. Results revealed no significant (P > 0.05) differences in intake and digestibility of nutrients, nitrogen balance, nutritive value of diets, average daily gain, as well as feed conversion ratio among three groups. The serum concentration of triiodothyronine and tetraiodothyronine did not differ due to treatments. Likewise, wool yield and its quality, measured in terms of fibre diameter, medullation percentage and staple length were also comparable irrespective of dietary variation. Furthermore, the cost of concentrate mixture (Rs/day) was lower (P ≤ 0.05) in SP 20 followed by SP 10 as compared to group SP 0 . These findings suggested that SPM could be safely fed up to 20% level in the concentrate mixture for lambs substituting expensive traditional feed ingredients without negatively inflicting the performance of growing lambs.

A population-based study of subsequent primary malignancies after endometrial cancer: genetic, environmental, and treatment-related associations.

PubMed

Brown, Aaron P; Neeley, E Shannon; Werner, Theresa; Soisson, Andrew Patrick; Burt, Randall W; Gaffney, David K

2010-09-01

To examine the risk of subsequent primary malignancies (SPMs) in women diagnosed with endometrial cancer. The National Cancer Institute's Survival, Epidemiology, and End Results database was used to determine the risk of SPM after endometrial cancer in 69,739 women diagnosed between 1973 and 2005. Standardized incidence ratios were calculated (observed/expected [O/E]) for SPM sites. Median follow-up was 11.2 years, representing 757,567 person-years of follow-up. The risk of SPM was significantly increased for small intestine (O/E = 1.48; 99% confidence interval [CI], 1.03-2.05), colon (O/E = 1.16; CI, 1.09-1.24), vagina (O/E = 2.71; CI, 1.86-3.8), and urinary bladder (O/E = 1.41; CI, 1.25-1.59) SPMs and decreased for oral cavity and pharynx (O/E = 0.75; CI, 0.6-0.93), lung and bronchus (O/E = 0.78; CI, 0.72-0.84), and esophagus (O/E = 0.58; CI, 0.37-0.86) SPMs. Patients receiving external-beam radiotherapy for endometrial cancer had an increased risk of colon (p < 0.001), bladder (p < 0.001), vagina (p = 0.04), and soft-tissue (p = 0.014) SPMs. Patients treated with brachytherapy had an increased risk of bladder SPM (p = 0.006). A positive bidirectional association with endometrial cancer was observed for colorectal cancer, with a negative bidirectional association for oropharyngeal and lung cancers. Genetic, environmental, and treatment-related factors influence SPM risk. Genetic factors may contribute to the increased risk of colorectal cancer. Smoking's negative effect on endometrial cancer risk factors might explain the decreased risk of lung and oropharyngeal cancer. Patients treated with radiotherapy likely have a small but significantly increased risk of bladder, vagina, colon, and soft-tissue SPM. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Catalytic reaction processes revealed by scanning probe microscopy. [corrected].

PubMed

Jiang, Peng; Bao, Xinhe; Salmeron, Miquel

2015-05-19

Heterogeneous catalysis is of great importance for modern society. About 80% of the chemicals are produced by catalytic reactions. Green energy production and utilization as well as environmental protection also need efficient catalysts. Understanding the reaction mechanisms is crucial to improve the existing catalysts and develop new ones with better activity, selectivity, and stability. Three components are involved in one catalytic reaction: reactant, product, and catalyst. The catalytic reaction process consists of a series of elementary steps: adsorption, diffusion, reaction, and desorption. During reaction, the catalyst surface can change at the atomic level, with roughening, sintering, and segregation processes occurring dynamically in response to the reaction conditions. Therefore, it is imperative to obtain atomic-scale information for understanding catalytic reactions. Scanning probe microscopy (SPM) is a very appropriate tool for catalytic research at the atomic scale because of its unique atomic-resolution capability. A distinguishing feature of SPM, compared to other surface characterization techniques, such as X-ray photoelectron spectroscopy, is that there is no intrinsic limitation for SPM to work under realistic reaction conditions (usually high temperature and high pressure). Therefore, since it was introduced in 1981, scanning tunneling microscopy (STM) has been widely used to investigate the adsorption, diffusion, reaction, and desorption processes on solid catalyst surfaces at the atomic level. STM can also monitor dynamic changes of catalyst surfaces during reactions. These invaluable microscopic insights have not only deepened the understanding of catalytic processes, but also provided important guidance for the development of new catalysts. This Account will focus on elementary reaction processes revealed by SPM. First, we will demonstrate the power of SPM to investigate the adsorption and diffusion process of reactants on catalyst surfaces at the atomic level. Then the dynamic processes, including surface reconstruction, roughening, sintering, and phase separation, studied by SPM will be discussed. Furthermore, SPM provides valuable insights toward identifying the active sites and understanding the reaction mechanisms. We also illustrate here how both ultrahigh vacuum STM and high pressure STM provide valuable information, expanding the understanding provided by traditional surface science. We conclude with highlighting remarkable recent progress in noncontact atomic force microscopy (NC-AFM) and inelastic electron tunneling spectroscopy (IETS), and their impact on single-chemical-bond level characterization for catalytic reaction processes in the future.

NDRC: A Disease-Causing Genes Prioritized Method Based on Network Diffusion and Rank Concordance.

PubMed

Fang, Minghong; Hu, Xiaohua; Wang, Yan; Zhao, Junmin; Shen, Xianjun; He, Tingting

2015-07-01

Disease-causing genes prioritization is very important to understand disease mechanisms and biomedical applications, such as design of drugs. Previous studies have shown that promising candidate genes are mostly ranked according to their relatedness to known disease genes or closely related disease genes. Therefore, a dangling gene (isolated gene) with no edges in the network can not be effectively prioritized. These approaches tend to prioritize those genes that are highly connected in the PPI network while perform poorly when they are applied to loosely connected disease genes. To address these problems, we propose a new disease-causing genes prioritization method that based on network diffusion and rank concordance (NDRC). The method is evaluated by leave-one-out cross validation on 1931 diseases in which at least one gene is known to be involved, and it is able to rank the true causal gene first in 849 of all 2542 cases. The experimental results suggest that NDRC significantly outperforms other existing methods such as RWR, VAVIEN, DADA and PRINCE on identifying loosely connected disease genes and successfully put dangling genes as potential candidate disease genes. Furthermore, we apply NDRC method to study three representative diseases, Meckel syndrome 1, Protein C deficiency and Peroxisome biogenesis disorder 1A (Zellweger). Our study has also found that certain complex disease-causing genes can be divided into several modules that are closely associated with different disease phenotype.

Suspended particulate matter flocculation in a natural tidal wetland located in the San Francisco Estuary

NASA Astrophysics Data System (ADS)

Saraceno, J.; Bergamaschi, B. A.; Wright, S. A.; Boss, E.; Downing, B. D.; Fleck, J.; Ganju, N. K.

2011-12-01

Suspended mineral and algal particles together comprise suspended particulate matter (SPM). The SPM size distribution influences the quantity and color of light penetration and the adsorption and transport of contaminants such as pesticides and metals. It is widely known that interaction with wetlands alters the size distribution and quality of particles through local primary production, differential settling and particle aggregation, however, our understanding of how tidal wetland processes affect SPM quantity and size spectra has been hampered by the difficulty of directly observing these parameters at tidal time scales. To evaluate how SPM concentration and size varied over tidal time scales and to better understand the relationship between organic matter and sediment characteristics, simultaneous measurements of dissolved organic matter, SPM concentration and organic content as well as in situ surrogates of particle concentration (turbidity, particulate attenuation, volume concentration) and particle size (laser diffraction) were carried out with measurements of current velocity (acoustic Doppler velocity meter) in the main channel of Brown's Island located in the western San Joaquin/Sacramento River Delta, CA. The study period coincided with high estuary sediment levels following a significant precipitation runoff event. In the Brown Island wetland, particle concentration and size dynamics were tied to variations in water level and velocity. Turbidity and attenuation covaried with the volume concentration of particles smaller than 33 um, which on average represented greater than 50% of particle population by volume. On average, these SPM concentration surrogates were three times higher in flood water than in ebb water; consistent with a loss of fine particles on the island. Following the highest flood tide, the decrease in fine particles was coincident with an increase in the concentration of particles larger than 130 um; a finding consistent with particle flocculation. Additionally, the timing of flocculation was coincident with periods of elevated dissolved organic matter, suggesting organic matter played a role in the formation of large aggregates. Measurements of SPM organic content in ebb water revealed that SPM was enriched in organic matter by up to 50% following interaction with the wetland. Newly formed aggregates were carried out to the estuary with the ebb tide. These results indicate that the Browns Island wetland (and presumably other similar wetlands throughout the San Francisco Bay-Delta) plays an important role in estuarine biogeochemistry and particle cycling because flocculated particles have higher settling velocities and optical properties than their component particles and will behave differently. The implications of these findings are relevant to several tidal wetland management concerns such as the maintenance of marsh elevation, the cycling and transport of contaminants, and water clarity.

Methodological systematic review identifies major limitations in prioritization processes for updating.

PubMed

Martínez García, Laura; Pardo-Hernandez, Hector; Superchi, Cecilia; Niño de Guzman, Ena; Ballesteros, Monica; Ibargoyen Roteta, Nora; McFarlane, Emma; Posso, Margarita; Roqué I Figuls, Marta; Rotaeche Del Campo, Rafael; Sanabria, Andrea Juliana; Selva, Anna; Solà, Ivan; Vernooij, Robin W M; Alonso-Coello, Pablo

2017-06-01

The aim of the study was to identify and describe strategies to prioritize the updating of systematic reviews (SRs), health technology assessments (HTAs), or clinical guidelines (CGs). We conducted an SR of studies describing one or more methods to prioritize SRs, HTAs, or CGs for updating. We searched MEDLINE (PubMed, from 1966 to August 2016) and The Cochrane Methodology Register (The Cochrane Library, Issue 8 2016). We hand searched abstract books, reviewed reference lists, and contacted experts. Two reviewers independently screened the references and extracted data. We included 14 studies. Six studies were classified as descriptive (6 of 14, 42.9%) and eight as implementation studies (8 of 14, 57.1%). Six studies reported an updating strategy (6 of 14, 42.9%), six a prioritization process (6 of 14, 42.9%), and two a prioritization criterion (2 of 14, 14.2%). Eight studies focused on SRs (8 of 14, 57.1%), six studies focused on CGs (6 of 14, 42.9%), and none were about HTAs. We identified 76 prioritization criteria that can be applied when prioritizing documents for updating. The most frequently cited criteria were as follows: available evidence (19 of 76, 25.0%), clinical relevance (10 of 76; 13.2%), and users' interest (10 of 76; 13.2%). There is wide variability and suboptimal reporting of the methods used to develop and implement processes to prioritize updating of SRs, HTAs, and CGs. Copyright © 2017 Elsevier Inc. All rights reserved.

Study of Methods for Assessing Research Topic Elicitation and pRioritization (SMARTER): Study Protocol to Compare Qualitative Research Methods and Advance Patient Engagement in Research

PubMed Central

Comstock, Bryan

2017-01-01

Background Involving patients as partners in research is a defining characteristic of patient-centered outcomes research (PCOR). While patients’ experiential knowledge of a health condition or treatment may yield research priorities not reflected by researchers and policy makers, the methods for identifying and effectively collaborating with patients are still evolving. Patient registries and crowdsourcing may offer ease of access and convenience to both researchers and patients. Surveys and focus groups, including online modalities, have been described for prioritizing research topics. However, little is known about how these different methods compare in producing consistent priorities and similar perceptions of engagement quality among participants. Objective The aims of this study are (1) to compare how different engagement methods used to elicit patient priorities for research perform as measured by rankings for priorities generated and participant satisfaction; and (2) to determine characteristics of individuals choosing to participate in research prioritization activities. Methods Participants in the Back pain Outcomes using Longitudinal Data (BOLD) patient registry, established to evaluate the natural history of back pain among individuals 65 years and older, and participants on the Amazon Mechanical Turk (MTurk) crowdsourcing platform, to provide input on priorities for research via a questionnaire, are invited. For BOLD participants, we subsequently randomize interested respondents to 1 of 3 interactive prioritization activities to further develop priorities: a Delphi panel, an online crowd voting activity, or an in-person facilitated prioritization activity using nominal group technique (NGT). Participants involved in each activity complete a survey to evaluate the quality of the experience and a subset of these participants discuss their experience further in an interview. Descriptive statistics are used to characterize the rankings produced by each method and compare the top 5 rated topics resulting from each prioritization activity. We use rank-ordered logistic regression models to identify associations of the ranked priority topics with baseline patient characteristics. We analyze responses to the evaluation using a mixed-methods approach wherein we tabulate responses to Likert-scale questions and use content analysis to enumerate themes emerging from interviews for the 3 activities. Results In Phase I, we invite approximately 3000 BOLD participants and 500 Amazon MTurk workers to complete a research topic prioritization survey. Based on these results, we include additional topics into a subsequent prioritization survey. In Phase II, we invite BOLD participants to join 1 of 3 activities: 90 participants for Delphi panel, 100 participants for crowd voting, and 60 participants for focus groups. Of the Phase II participants, 30 will be interviewed to evaluate the activities. Conclusions This study informs decisions about how to conduct outreach to patient registry participants for providing input on research priorities, how individuals 65 years and older wish to participate in engagement activities, and how different research prioritization methods compare in terms of rankings generated and participant satisfaction. PMID:28882810

Data Mining and Pattern Recognition Models for Identifying Inherited Diseases: Challenges and Implications.

PubMed

Iddamalgoda, Lahiru; Das, Partha S; Aponso, Achala; Sundararajan, Vijayaraghava S; Suravajhala, Prashanth; Valadi, Jayaraman K

2016-01-01

Data mining and pattern recognition methods reveal interesting findings in genetic studies, especially on how the genetic makeup is associated with inherited diseases. Although researchers have proposed various data mining models for biomedical approaches, there remains a challenge in accurately prioritizing the single nucleotide polymorphisms (SNP) associated with the disease. In this commentary, we review the state-of-art data mining and pattern recognition models for identifying inherited diseases and deliberate the need of binary classification- and scoring-based prioritization methods in determining causal variants. While we discuss the pros and cons associated with these methods known, we argue that the gene prioritization methods and the protein interaction (PPI) methods in conjunction with the K nearest neighbors' could be used in accurately categorizing the genetic factors in disease causation.

Development of a Theoretically Based Treatment for Sentence Comprehension Deficits in Individuals with Aphasia

ERIC Educational Resources Information Center

Kiran, Swathi; Caplan, David; Sandberg, Chaleece; Levy, Joshua; Berardino, Alex; Ascenso, Elsa; Villard, Sarah; Tripodis, Yorghos

2012-01-01

Purpose: Two new treatments, 1 based on sentence to picture matching (SPM) and the other on object manipulation (OM), that train participants on the thematic roles of sentences using pictures or by manipulating objects were piloted. Method: Using a single-subject multiple-baseline design, sentence comprehension was trained on the affected sentence…

Optimal geometry for a quartz multipurpose SPM sensor.

PubMed

Stirling, Julian

2013-01-01

We propose a geometry for a piezoelectric SPM sensor that can be used for combined AFM/LFM/STM. The sensor utilises symmetry to provide a lateral mode without the need to excite torsional modes. The symmetry allows normal and lateral motion to be completely isolated, even when introducing large tips to tune the dynamic properties to optimal values.

Polyamines and cellular metabolism in plants: Transgenic approaches reveal different responses to diamine putrescine versus higher polyamines spermidine and spermine

USDA-ARS?s Scientific Manuscript database

Distribution of biogenic amines – the diamine putrescine (Put), triamine spermidine (Spd), and tetraamine spermine (Spm) - differs between species with Put and Spd being particularly abundant and Spm the least abundant in plant cells. These amines are important for cell viability and their intracel...

A Generalized Form of Context-Dependent Psychophysiological Interactions (gPPI): A Comparison to Standard Approaches

PubMed Central

McLaren, Donald G.; Ries, Michele L.; Xu, Guofan; Johnson, Sterling C.

2012-01-01

Functional MRI (fMRI) allows one to study task-related regional responses and task-dependent connectivity analysis using psychophysiological interaction (PPI) methods. The latter affords the additional opportunity to understand how brain regions interact in a task-dependent manner. The current implementation of PPI in Statistical Parametric Mapping (SPM8) is configured primarily to assess connectivity differences between two task conditions, when in practice fMRI tasks frequently employ more than two conditions. Here we evaluate how a generalized form of context-dependent PPI (gPPI; http://www.nitrc.org/projects/gppi), which is configured to automatically accommodate more than two task conditions in the same PPI model by spanning the entire experimental space, compares to the standard implementation in SPM8. These comparisons are made using both simulations and an empirical dataset. In the simulated dataset, we compare the interaction beta estimates to their expected values and model fit using the Akaike Information Criterion (AIC). We found that interaction beta estimates in gPPI were robust to different simulated data models, were not different from the expected beta value, and had better model fits than when using standard PPI (sPPI) methods. In the empirical dataset, we compare the model fit of the gPPI approach to sPPI. We found that the gPPI approach improved model fit compared to sPPI. There were several regions that became non-significant with gPPI. These regions all showed significantly better model fits with gPPI. Also, there were several regions where task-dependent connectivity was only detected using gPPI methods, also with improved model fit. Regions that were detected with all methods had more similar model fits. These results suggest that gPPI may have greater sensitivity and specificity than standard implementation in SPM. This notion is tempered slightly as there is no gold standard; however, data simulations with a known outcome support our conclusions about gPPI. In sum, the generalized form of context-dependent PPI approach has increased flexibility of statistical modeling, and potentially improves model fit, specificity to true negative findings, and sensitivity to true positive findings. PMID:22484411

Atomic force microscopy of biological samples

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

Doktycz, Mitchel John

2010-01-01

The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate howmore » this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH).« less

Prioritizing Contaminants for Monitoring and Management

EPA Pesticide Factsheets

EPA researcher presents work to develop methods and tools that integrate chemical monitoring with pathway-based bioactivity measurements, which will help provide screening-level assessments useful to identify and prioritize emerging contaminants.

Assessment of particulate matter variation during 2011-2015 over a tropical station Agra, India

NASA Astrophysics Data System (ADS)

Gogikar, Priyanjali; Tyagi, Bhishma

2016-12-01

Air quality over Agra is deteriorating and causing a serious threat to people residing in the city as well as to World heritage site- Tajmahal. In the present study, daily average concentrations of Suspended Particulate Matter (SPM) and Respirable Suspended Particulate Matter (RSPM) were analysed over a period of 2011-2015 at four stations in Agra city, namely: Taj, Itmad-Ud-Daula, Rambagh and Nunhai. The concentrations are above threshold values when compared to specify standards for a healthy environment (by India, US, WHO, EU and China - Class I and Class II) for all the seasons except monsoon and the values are highest in the month of November and lowest in the month of August and September. Variation of RSPM and SPM were found to be positively correlated with each other with values of 0.76 (Taj), 0.72 (Itmad-Ud-Daula), 0.69 (Rambagh), 0.77 (Nunhai). The study illustrates that the levels of SPM and RSPM are not showing any decreasing trend over Agra even after closing of industries and taking other precautions inside the city by Government of India. The study clearly identifies that local control of pollution sources are not enough and pollution is being transported from nearby regions to keep the daily pollution value higher than threshold. Source regions of transported pollutants over Agra have been analysed by using Weighted Potential Source Contribution Function (WPSCF) for both SPM and RSPM. Wavelet analysis of monthly averaged values of RSPM and SPM data sets has shown the existence of semi-annual and annual periodicity over the study region.

Polyamines contribute to salinity tolerance in the symbiosis Medicago truncatula-Sinorhizobium meliloti by preventing oxidative damage.

PubMed

López-Gómez, Miguel; Hidalgo-Castellanos, Javier; Muñoz-Sánchez, J Rubén; Marín-Peña, Agustín J; Lluch, Carmen; Herrera-Cervera, José A

2017-07-01

Polyamines (PAs) such as spermidine (Spd) and spermine (Spm) are small ubiquitous polycationic compounds that contribute to plant adaptation to salt stress. The positive effect of PAs has been associated to a cross-talk with other anti-stress hormones such as brassinosteroids (BRs). In this work we have studied the effects of exogenous Spd and Spm pre-treatments in the response to salt stress of the symbiotic interaction between Medicago truncatula and Sinorhizobium meliloti by analyzing parameters related to nitrogen fixation, oxidative damage and cross-talk with BRs in the response to salinity. Exogenous PAs treatments incremented the foliar and nodular Spd and Spm content which correlated with an increment of the nodule biomass and nitrogenase activity. Exogenous Spm treatment partially prevented proline accumulation which suggests that this polyamine could replace the role of this amino acid in the salt stress response. Additionally, Spd and Spm pre-treatments reduced the levels of H 2 O 2 and lipid peroxidation under salt stress. PAs induced the expression of genes involved in BRs biosynthesis which support a cross-talk between PAs and BRs in the salt stress response of M. truncatula-S. meliloti symbiosis. In conclusion, exogenous PAs improved the response to salinity of the M. truncatula-S. meliloti symbiosis by reducing the oxidative damage induced under salt stress conditions. In addition, in this work we provide evidences of the cross-talk between PAs and BRs in the adaptive responses to salinity. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Child Poverty: Definition and Measurement.

PubMed

Short, Kathleen S

2016-04-01

This article provides a discussion of what we mean when we refer to 'child poverty.' Many images come to mind when we discuss child poverty, but when we try to measure and quantify the extent of child poverty, we often use a very narrow concept. In this article a variety of poverty measures that are used in the United States are described and some of the differences between those measures are illustrated. In this article 3 measures are explored in detail: a relative measure of poverty that is used more often in an international context, the official US poverty measure, and a new supplemental poverty measure (SPM). The new measure differs from the other 2 because it takes into account noncash benefits that are provided to poor families. These include nutrition assistance such as food stamps, subsidized housing, and home energy assistance. The SPM also takes account of necessary expenses that families face, such as taxes and expenses related to work and health care. Comparing estimates for 2012, the SPM showed lower poverty rates for children than the other 2 measures. Because noncash benefits help those in extreme poverty, there were also lower percentages of children in extreme poverty with resources below half the SPM threshold. These results suggest that 2 important measures of poverty, the relative measure used in international comparisons, and the official poverty measure, are not able to gauge the effect of government programs on the alleviation of poverty, and the SPM illustrates that noncash benefits do help families meet their basic needs. Published by Elsevier Inc.

Imaging Electron Motion in a Few Layer MoS2 Device

NASA Astrophysics Data System (ADS)

Bhandari, S.; Wang, K.; Watanabe, K.; Taniguchi, T.; Kim, P.; Westervelt, R. M.

2017-06-01

Ultrathin sheets of MoS2 are a newly discovered 2D semiconductor that holds great promise for nanoelectronics. Understanding the pattern of current flow will be crucial for developing devices. In this talk, we present images of current flow in MoS2 obtained with a Scanned Probe Microscope (SPM) cooled to 4 K. We previously used this technique to image electron trajectories in GaAs/AlGaAs heterostructures and graphene. The charged SPM tip is held just above the sample surface, creating an image charge inside the device that scatters electrons. By measuring the change in resistance ΔR while the tip is raster scanned above the sample, an image of electron flow is obtained. We present images of electron flow in an MoS2 device patterned into a hall bar geometry. A three-layer MoS2 sheet is encased by two hBN layers, top and bottom, and patterned into a hall-bar with multilayer graphene contacts. An SPM image shows the current flow pattern from the wide contact at the end of the device for a Hall density n = 1.3×1012 cm-2. The SPM tip tends to block flow, increasing the resistance R. The pattern of flow was also imaged for a narrow side contact on the sample. At density n = 5.4×1011 cm-2; the pattern seen in the SPM image is similar to the wide contact. The ability to image electron flow promises to be very useful for the development of ultrathin devices from new 2D materials.

PHIRST Trial - pharmacist consults: prioritization of HIV-patients with a referral screening tool.

PubMed

Awad, Catherine; Canneva, Arnaud; Chiasson, Charles-Olivier; Galarneau, Annie; Schnitzer, Mireille E; Sheehan, Nancy L; Wong, Alison Yj

2017-11-01

The role of pharmacists in HIV outpatient clinics has greatly increased in the past decades. Given the limited resources of the health system, the prioritization of pharmacist consults is now a main concern. This study aimed to create a scoring system allowing for standardized prioritization of pharmacist consults for patients living with HIV. Data was retrospectively collected from 200 HIV patients attending the Chronic Viral Illness Service at the McGill University Health Center. An expert panel consisting of four pharmacists working in the field of HIV prioritized each patient individually, after which a consensus was established and was considered as the gold standard. In order to create a scoring system, two different methods (Delphi, statistical) were used to assign a weight to each characteristic considered to be important in patient prioritization. A third method (equal weight to each characteristic) was also evaluated. The total score per patient for each method was then compared to the expert consensus in order to establish the score cut-offs to indicate the appropriate categories of delay in which to see the patient. All three systems failed to accurately prioritize patients into urgency categories ("less than 48 h", "less than 1 month", "less than 3 months", "no consult required") according to expert pharmacist consensus. The presence of high level interactions between patient characteristics, the limited number of patients and the low prevalence of some characteristics were hypothesized as the main causes for the results. Creating a prioritization tool for pharmacy consults in HIV outpatient clinics is a complex task and developing a decision tree algorithm may be a more appropriate approach in the future to take into account the importance of combinations of patient characteristic.

The Shortened Raven Standard Progressive Matrices: Item Response Theory-Based Psychometric Analyses and Normative Data

ERIC Educational Resources Information Center

Van der Elst, Wim; Ouwehand, Carolijn; van Rijn, Peter; Lee, Nikki; Van Boxtel, Martin; Jolles, Jelle

2013-01-01

The purpose of the present study was to evaluate the psychometric properties of a shortened version of the Raven Standard Progressive Matrices (SPM) under an item response theory framework (the one- and two-parameter logistic models). The shortened Raven SPM was administered to N = 453 cognitively healthy adults aged between 24 and 83 years. The…

Evaluating Treatment and Generalization Patterns of Two Theoretically Motivated Sentence Comprehension Therapies.

PubMed

Des Roches, Carrie A; Vallila-Rohter, Sofia; Villard, Sarah; Tripodis, Yorghos; Caplan, David; Kiran, Swathi

2016-12-01

The current study examined treatment outcomes and generalization patterns following 2 sentence comprehension therapies: object manipulation (OM) and sentence-to-picture matching (SPM). Findings were interpreted within the framework of specific deficit and resource reduction accounts, which were extended in order to examine the nature of generalization following treatment of sentence comprehension deficits in aphasia. Forty-eight individuals with aphasia were enrolled in 1 of 8 potential treatment assignments that varied by task (OM, SPM), complexity of trained sentences (complex, simple), and syntactic movement (noun phrase, wh-movement). Comprehension of trained and untrained sentences was probed before and after treatment using stimuli that differed from the treatment stimuli. Linear mixed-model analyses demonstrated that, although both OM and SPM treatments were effective, OM resulted in greater improvement than SPM. Analyses of covariance revealed main effects of complexity in generalization; generalization from complex to simple linguistically related sentences was observed both across task and across movement. Results are consistent with the complexity account of treatment efficacy, as generalization effects were consistently observed from complex to simpler structures. Furthermore, results provide support for resource reduction accounts that suggest that generalization can extend across linguistic boundaries, such as across movement type.

Exact modelling of the optical bistability in ferroelectics via two-wave mixing: A system with full nonlinearity

NASA Astrophysics Data System (ADS)

Khushaini, Muhammad Asif A.; Ibrahim, Abdel-Baset M. A.; Choudhury, P. K.

2018-05-01

In this paper, we provide a complete mathematical model of the phenomenon of optical bistability (OB) resulting from the degenerate two-wave mixing (TWM) process of laser beams interacting with a single nonlinear layer of ferroelectric material. Starting with the electromagnetic wave equation for optical wave propagating in nonlinear media, a nonlinear coupled wave (CW) system with both self-phase modulation (SPM) and cross-phase modulation (XPM) sources of nonlinearity are derived. The complete CW system with full nonlinearity is solved numerically and a comparison between both the cases of with and without SPM at various combinations of design parameters is given. Furthermore, to provide a reliable theoretical model for the OB via TWM process, the results obtained theoretically are compared with the available experimental data. We found that the nonlinear system without SPM fails to predict the bistable response at lower combinations of the input parameters. However, at relatively higher values, the solution without SPM shows a reduction in the switching contrast and period in the OB response. A comparison with the experimental results shows better agreement with the system with full nonlinearity.

Novel n-3 Immunoresolvents: Structures and Actions

PubMed Central

Dalli, Jesmond; Colas, Romain A.; Serhan, Charles N.

2013-01-01

Resolution of inflammation is now held to be an active process where autacoids promote homeostasis. Using functional-metabololipidomics and in vivo systems, herein we report that endogenous n-3 docosapentaenoic (DPA) acid is converted during inflammation-resolution in mice and by human leukocytes to novel n-3 products congenerous to D-series resolvins (Rv), protectins (PD) and maresins (MaR), termed specialized pro-resolving mediators (SPM). The new n-3 DPA structures include 7,8,17-trihydroxy-9,11,13,15E,19Z-docosapentaenoic acid (RvD1n-3 DPA), 7,14-dihydroxy-8,10,12,16Z,19Z-docosapentaenoic acid (MaR1n-3 DPA) and related bioactive products. Each n-3 DPA-SPM displayed protective actions from second organ injury and reduced systemic inflammation in ischemia-reperfusion. The n-3 DPA-SPM, including RvD1n-3 DPA and MaR1n-3 DPA, each exerted potent leukocyte directed actions in vivo. With human leukocytes each n-3 DPA-SPM reduced neutrophil chemotaxis, adhesion and enhanced macrophage phagocytosis. Together, these findings demonstrate that n-3 DPA is converted to novel immunoresolvents with actions comparable to resolvins and are likely produced in humans when n-3 DPA is elevated. PMID:23736886

Comparison of Total Solar Irradiance with NASA/NSO Spectromagnetograph Data in Solar Cycles 22 and 23

NASA Technical Reports Server (NTRS)

Jones, Harrison P.; Branston, Detrick D.; Jones, Patricia B.; Popescu, Miruna D.

2002-01-01

An earlier study compared NASA/NSO Spectromagnetograph (SPM) data with spacecraft measurements of total solar irradiance (TSI) variations over a 1.5 year period in the declining phase of solar cycle 22. This paper extends the analysis to an eight-year period which also spans the rising and early maximum phases of cycle 23. The conclusions of the earlier work appear to be robust: three factors (sunspots, strong unipolar regions, and strong mixed polarity regions) describe most of the variation in the SPM record, but only the first two are associated with TSI. Additionally, the residuals of a linear multiple regression of TSI against SPM observations over the entire eight-year period show an unexplained, increasing, linear time variation with a rate of about 0.05 W m(exp -2) per year. Separate regressions for the periods before and after 1996 January 01 show no unexplained trends but differ substantially in regression parameters. This behavior may reflect a solar source of TSI variations beyond sunspots and faculae but more plausibly results from uncompensated non-solar effects in one or both of the TSI and SPM data sets.

Cholesterol asymmetry in synaptic plasma membranes.

PubMed

Wood, W Gibson; Igbavboa, Urule; Müller, Walter E; Eckert, Gunter P

2011-03-01

Lipids are essential for the structural and functional integrity of membranes. Membrane lipids are not randomly distributed but are localized in different domains. A common characteristic of these membrane domains is their association with cholesterol. Lipid rafts and caveolae are examples of cholesterol enriched domains, which have attracted keen interest. However, two other important cholesterol domains are the exofacial and cytofacial leaflets of the plasma membrane. The two leaflets that make up the bilayer differ in their fluidity, electrical charge, lipid distribution, and active sites of certain proteins. The synaptic plasma membrane (SPM) cytofacial leaflet contains over 85% of the total SPM cholesterol as compared with the exofacial leaflet. This asymmetric distribution of cholesterol is not fixed or immobile but can be modified by different conditions in vivo: (i) chronic ethanol consumption; (ii) statins; (iii) aging; and (iv) apoE isoform. Several potential candidates have been proposed as mechanisms involved in regulation of SPM cholesterol asymmetry: apoE, low-density lipoprotein receptor, sterol carrier protein-2, fatty acid binding proteins, polyunsaturated fatty acids, P-glycoprotein and caveolin-1. This review examines cholesterol asymmetry in SPM, potential mechanisms of regulation and impact on membrane structure and function. © 2011 The Authors. Journal of Neurochemistry © 2011 International Society for Neurochemistry.

DEVELOPMENT OF EPA'S TOXCAST PROGRAM FOR PRIORITIZING THE TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS.

EPA Science Inventory

EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS)and genomic technologies to predict potential toxicity and prioritize the use of limited testing resources.

Nano-suspension coating as a technique to modulate the drug release from controlled porosity osmotic pumps for a soluble agent.

PubMed

Bahari, Leila Azharshekoufeh; Javadzadeh, Yousef; Jalali, Mohammad Barzegar; Johari, Peyvand; Nokhodchi, Ali; Shokri, Javad

2017-05-01

In controlled porosity osmotic pumps (CPOP), usually finding a single solvent with a capability to dissolve both film former (hydrophobic) and pore former (hydrophilic) is extremely challenging. Therefore, the aim of the present investigation was to tackle the issue associated with controlled porosity osmotic pump (CPOP) system using nano-suspension coating method. In the present study 4-Amino pyridine was used as a highly water soluble drug. In this method, a hydrophilic pore former (sucrose or mannitol) in nano range was suspended in polymeric coating solution using ball-mill. The performance of the prepared formulations was assessed in terms of D 12h (cumulative release percent after 12h), Dev zero (mean percent deviation of drug release from zero order kinetic), t L (lag time of the drug release) and RSQ zero . The results revealed that gelling agent amount (HPMC E 15LV ) in core and pore former concentration in SPM had crucial effect on SPM integrity. All the optimised formulations showed a burst drug release due to fast dissolving nature of the pore formers. Results obtained from scanning electron microscopy demonstrated the formation of nanopores in the membrane where the drug release takes place via these nanopores. Nano suspension coating method can be introduced as novel method in formulation of CPOPs. Copyright © 2017 Elsevier B.V. All rights reserved.

Optical Double Image Hiding in the Fractional Hartley Transform Using Structured Phase Filter and Arnold Transform

NASA Astrophysics Data System (ADS)

Yadav, Poonam Lata; Singh, Hukum

2018-06-01

To maintain the security of the image encryption and to protect the image from intruders, a new asymmetric cryptosystem based on fractional Hartley Transform (FrHT) and the Arnold transform (AT) is proposed. AT is a method of image cropping and edging in which pixels of the image are reorganized. In this cryptosystem we have used AT so as to extent the information content of the two original images onto the encrypted images so as to increase the safety of the encoded images. We have even used Structured Phase Mask (SPM) and Hybrid Mask (HM) as the encryption keys. The original image is first multiplied with the SPM and HM and then transformed with direct and inverse fractional Hartley transform so as to obtain the encrypted image. The fractional orders of the FrHT and the parameters of the AT correspond to the keys of encryption and decryption methods. If both the keys are correctly used only then the original image would be retrieved. Recommended method helps in strengthening the safety of DRPE by growing the key space and the number of parameters and the method is robust against various attacks. By using MATLAB 8.3.0.52 (R2014a) we calculate the strength of the recommended cryptosystem. A set of simulated results shows the power of the proposed asymmetric cryptosystem.

Separate Poles Mode for Large-Capacity HVDC System

NASA Astrophysics Data System (ADS)

Zhu, Lin; Gao, Qin

2017-05-01

This paper proposes a novel connection mode, separate poles mode (SPM), for large-capacity HVDC systems. The proposed mode focuses on the core issues of HVDC connection in interconnected power grids and principally aims at increasing effective electric distance between poles, which helps to mitigate the interaction problems between AC system and DC system. Receiving end of bipolar HVDC has been divided into different inverter stations under the mode, and thus significantly alleviates difficulties in power transmission and consumption of receiving-end AC grids. By investigating the changes of multi-feed short-circuit ratio (MISCR), finding that HVDC with SPM shows critical impacts upon itself and other HVDC systems with conventional connection mode, which demonstrates that SPM can make balance between MISCR increase and short-circuit current limit.

Participatory methods for research prioritization in primary care: an analysis of the World Café approach in Ireland and the USA.

PubMed

MacFarlane, Anne; Galvin, Rose; O'Sullivan, Madeleine; McInerney, Chris; Meagher, Eoghan; Burke, Daniel; LeMaster, Joseph W

2017-06-01

There are increasing imperatives for patients and members of the public to engage as partners in identifying health research priorities. The use of participatory methods to engage stakeholders in health care in research prioritization is not commonly reported. This article analyses the use of World Cafés as a participatory method for research prioritization with marginalized communities in Ireland and the USA. The principles of purposeful and snowball sampling were followed in both settings and a diverse range of community and health care stakeholders participated (n = 63 Ireland and n = 55 USA). The principles for a classic World Café were employed but there were novel features in each setting as well. Stewart et al.'s (Patients' and clinicians' research priorities. Health Expect 2011; 14: 439-48, conceptual framework for patient engagement was adapted and used to comparatively analyse the strengths and weaknesses of the World Cafés, focusing on agenda setting, engagement with research processes, interactional features and outputs. Design principles for World Cafés were found to align with high-quality patient engagement for research prioritization in both settings. They served to facilitate meaningful collaboration among stakeholder groups in research prioritization (research agenda setting) and explored research priorities (engagement with research). The café ambience, emphasis on hospitality and self-facilitation created an environment for dialogues within and across participating groups (interactional features). There was a commitment to follow-up actions with reference to possible subsequent research (outputs). The World Café is a valuable, participatory, flexible method that can be used with community and health care stakeholders for research prioritization with marginalized communities. © The Author 2016. Published by Oxford University Press.

METABOLISM OF N-ALKYLATED SPERMINE ANALOGUES BY POLYAMINE AND SPERMINE OXIDASES

PubMed Central

Häkkinen, Merja R.; Hyvönen, Mervi T.; Auriola, Seppo; Casero, Robert A.; Vepsäläinen, Jouko; Khomutov, Alex R.; Alhonen, Leena; Keinänen, Tuomo A.

2010-01-01

SUMMARY N-alkylated polyamine analogues have potential as anticancer and antiparasitic drugs. However, their metabolism in the host has remained incompletely defined thus potentially limiting their utility. Here, we have studied the degradation of three different spermine analogues N,N′-bis-(3-ethylaminopropyl)butane-1,4-diamine (DESPM), N-(3-benzyl-aminopropyl)-N'-(3-ethylaminopropyl)butane-1,4-diamine (BnEtSPM) and N,N′-bis-(3-benzylaminopropyl)butane-1,4-diamine (DBSPM) and related mono-alkylated derivatives as substrates of recombinant human polyamine oxidase (APAO) and spermine oxidase (SMO). APAO and SMO metabolized DESPM to EtSPD (Km(APAO)=10μM, kcat(APAO)=1.1s−1 and Km(SMO)=28μM, kcat(SMO)=0.8s−1, respectively), metabolized BnEtSPM to EtSPD (Km(APAO)=0.9 μM, kcat(APAO)=1.1s−1 and Km(SMO)=51μM, kcat(SMO)=0.4s−1, respectively), and metabolized DBSPM to BnSPD (Km(APAO)=5.4μM, kcat(APAO)= 2.0s−1 and Km(SMO)=33μM, kcat(SMO)=0.3s−1, respectively). Interestingly, mono-alkylated spermine derivatives were metabolized by APAO and SMO to SPD (EtSPM Km(APAO)=16μM, kcat(APAO)=1.5s−1; Km(SMO)=25μM, kcat(SMO) =8.2s−1; BnSPM Km(APAO)=6.0μM, kcat(APAO)=2.8s−1; Km(SMO)=19μM, kcat(SMO)=0.8s−1, respectively). Surprisingly, E t S P D ( Km(APAO)=37μM, kcat(APAO)=0.1s−1; Km(SMO)=48μM, kcat(SMO)=0.05s−1) and BnSPD (Km(APAO)=2.5μM, kcat(APAO)=3.5s−1; Km(SMO)=60μM, kcat(SMO)=0.54s−1) were metabolized to SPD by both the oxidases. Furthermore, we studied the degradation of DESPM, BnEtSPM or DBSPM in the DU145 prostate carcinoma cell line. The same major metabolites EtSPD and/or BnSPD were detected both in the culture medium and intracellularly after 48 hours of culture. Moreover, EtSPM and BnSPM were detected from cell samples. Present data shows that inducible SMO parallel with APAO could play an important role in polyamine based drug action, i.e. degradation of parent drug and its metabolites, having significant impact on efficiency of these drugs, and hence for the development of novel N-alkylated polyamine analogues. PMID:20012116

Second Primary Malignant Neoplasms and Survival in Adolescent and Young Adult Cancer Survivors.

PubMed

Keegan, Theresa H M; Bleyer, Archie; Rosenberg, Aaron S; Li, Qian; Goldfarb, Melanie

2017-11-01

Although the increased incidence of second primary malignant neoplasms (SPMs) is a well-known late effect after cancer, few studies have compared survival after an SPM to survival of the same cancer occurring as first primary malignant neoplasm (PM) by age. To assess the survival impact of SPMs in adolescents and young adults (AYAs) (15-39 years) compared with that of pediatric (<15 years) and older adult (≥40 years) patients with the same SPMs. This was a population-based, retrospective cohort study of patients with cancer in 13 Surveillance, Epidemiology and End Results regions in the United States diagnosed from 1992 to 2008 and followed through 2013. Data analysis was performed between June 2016 and January 2017. Five-year relative survival was calculated overall and for each cancer occurring as a PM or SPM by age at diagnosis. The impact of SPM status on cancer-specific death was examined using multivariable Cox proportional hazards regression. A total of 15 954 pediatric, 125 750 AYAs, and 878 370 older adult patients diagnosed as having 14 cancers occurring as a PM or SPM were included. Overall, 5-year survival after an SPM was 33.1% lower for children, 20.2% lower for AYAs, and 8.3% lower for older adults compared with a PM at the same age. For the most common SPMs in AYAs, the absolute difference in 5-year survival was 42% lower for secondary non-Hodgkin lymphoma, 19% for secondary breast carcinoma, 15% for secondary thyroid carcinoma, and 13% for secondary soft-tissue sarcoma. Survival by SPM status was significantly worse in younger vs older patients for thyroid, Hodgkin lymphoma, non-Hodgkin lymphoma, acute myeloid leukemia, soft-tissue sarcoma, and central nervous system cancer. Adolescents and young adults with secondary Hodgkin lymphoma (hazard ratio [95% CI], 3.5 [1.7-7.1]); soft-tissue sarcoma (2.8 [2.1-3.9]); breast carcinoma (2.1 [1.8-2.4]); acute myeloid leukemia (1.9 [1.5-2.4]); and central nervous system cancer (1.8 [1.2-2.8]) experienced worse survival compared with AYAs with the same PMs. The adverse impact of SPMs on survival is substantial for AYAs and may partially explain the relative lack of survival improvement in AYAs compared with other age groups. The impact of a particular SPM diagnosis on survival may inform age-specific prevention, screening, treatment, and survivorship recommendations.

Zinc and copper behaviour at the soil-river interface: New insights by Zn and Cu isotopes in the organic-rich Rio Negro basin

NASA Astrophysics Data System (ADS)

Guinoiseau, Damien; Gélabert, Alexandre; Allard, Thierry; Louvat, Pascale; Moreira-Turcq, Patricia; Benedetti, Marc F.

2017-09-01

The complex behaviour of Zn and Cu at the soil-river interface was investigated in soil and riverine water samples from the Rio Negro basin, a secondary tributary of the Rio Amazonas, using their stable isotope compositions. This acidic and organic river drains two types of intensely weathered terrains: podzols in its upstream part, and lateritic soils downstream. Bulk soil particles, suspended particulate matter (SPM) as well as colloidal fractions were sampled across the whole basin during low and high water stages. In the basin, Zn and Cu are mostly exported from lateritic soils and transported by organic colloids where significant losses are observed in the downstream part of the river. The use of δ66Zn and δ65Cu measurements reveals distinct stories for these two metals in suspended sediments and colloids. In the colloids, the constant δ66Zncoll across the basin is induced by the same weak association mode between Zn and organic ligands, regardless of the origin of the water. By contrast, in SPM, the speciation of Zn and thus δ66ZnSPM differ according to the type of drained soils. Zn is associated with organic complexes in particles exported with water draining podzol whereas Zn2+ is incorporated in the structure of the remaining kaolinite clays in lateritic output. The stronger reactivity of Cu than Zn with organic ligands induces its complete complexation. Copper is controlled by refractory particulate organic matter (POM) and by reactive colloidal organic matter; the latter being enriched in 65Cu due to stronger binding interactions than in POM. While the Cu content remains constant in the upstream part of the Rio Negro, downstream, the decrease of SPM and colloidal Cu fluxes is associated with a constant δ65CuSPM and with an increase of δ65Cucoll at the Rio Negro outlet. Geochemical mass balance modelling, based on SPM, Cu and Zn fluxes in SPM and their associated isotopic signatures, confirms distinct host phases for Zn and Cu, and identifies the most probable places where losses of these two metals occur. In colloids, the observed Cu isotope fractionation (from 0.24 to 0.45‰) superimposed on the significant Cucoll loss is assumed to result from a new isotopic equilibrium in a low velocity and high productivity zone: Cu-rich colloids enriched in 63Cu aggregate and settle down, whereas the remaining heavy Cu is partially complexed on strong organic ligands secreted by phytoplankton, forming new Cu-colloids.

Prioritizing removal of dams for passage of diadromous fishes on a major river system

USGS Publications Warehouse

Kocovsky, P.M.; Ross, R.M.; Dropkin, D.S.

2009-01-01

Native diadromous fishes have been extirpated from much of the Susquehanna River system for nearly a century. Recent restoration efforts have focused on removal of dams, but there are hundreds of dams and presently there is no biologically based system to assist in prioritizing their removal. We present a new method that uses existing habitat suitability index models (HSI) for American shad Alosa sapidissima, alewife A. pseudoharengus, blueback herring A. aestivalis, and American eel Anguilla rostrata to prioritize the removal of non-hydropower dams within the Susquehanna River system. We ranked HSI scores for each of the four species, association between a landscape-scale factor and HSIs, length of river opened by removing a dam, and distance from the mouth at Chesapeake Bay for each dam and then calculated a mean rank prioritization for dam removal by averaging the ranks for the seven criteria. This prioritization method is resistant to outliers, is not strongly affected by somewhat arbitrary decisions on metrics included in the analysis, and provides a biologically based prioritization for dam removal that can be easily amended to include other metrics or adapted to other river systems and that complements other social and economic considerations that must be included in decisions to remove dams.

Identifying Nanoscale Structure-Function Relationships Using Multimodal Atomic Force Microscopy, Dimensionality Reduction, and Regression Techniques.

PubMed

Kong, Jessica; Giridharagopal, Rajiv; Harrison, Jeffrey S; Ginger, David S

2018-05-31

Correlating nanoscale chemical specificity with operational physics is a long-standing goal of functional scanning probe microscopy (SPM). We employ a data analytic approach combining multiple microscopy modes, using compositional information in infrared vibrational excitation maps acquired via photoinduced force microscopy (PiFM) with electrical information from conductive atomic force microscopy. We study a model polymer blend comprising insulating poly(methyl methacrylate) (PMMA) and semiconducting poly(3-hexylthiophene) (P3HT). We show that PiFM spectra are different from FTIR spectra, but can still be used to identify local composition. We use principal component analysis to extract statistically significant principal components and principal component regression to predict local current and identify local polymer composition. In doing so, we observe evidence of semiconducting P3HT within PMMA aggregates. These methods are generalizable to correlated SPM data and provide a meaningful technique for extracting complex compositional information that are impossible to measure from any one technique.

How Well Can Young People with Asperger's Disorder Recognize Threat and Learn about Affect in Faces?: A Pilot Study

ERIC Educational Resources Information Center

Miyahara, Motohide; Ruffman, Ted; Fujita, Chikako; Tsujii, Masatsugu

2010-01-01

The abilities to identify threat and learn about affect in facial photographs were compared between a non-autistic university student group (NUS), a matched Asperger's group (MAS) on the Standard Progressive Matrices (SPM), and an unmatched Asperger's group (UAS) who scored lower on the SPM. Participants were given pairs of faces and asked which…

Polyamines and cellular metabolism in plants: transgenic approaches reveal different responses to diamine putrescine versus higher polyamines spermidine and spermine

Treesearch

Autar K. Mattoo; Subhash C. Minocha; Rakesh Minocha; Avtar K. Handa

2010-01-01

Distribution of biogenic amines--the diamine putrescine (Put), triamine spermidine (Spd), and tetraamine spermine (Spm)--differs between species with Put and Spd being particularly abundant and Spm the least abundant in plant cells. These amines are important for cell viability and their intracellular levels are tightly regulated, which have made it difficult to...

SPM Investigation of Thiolated Gold Nanoparticle Patterns Deposited on Different Self-Assembled Substrates

NASA Astrophysics Data System (ADS)

Sbrana, F.; Parodi, M. T.; Ricci, D.; Di Zitti, E.

We present the results of a Scanning Probe Microscopy (SPM) investigation of ordered nanosized metallo-organic structures. Our aim is to investigate the organization and stability of thiolated gold nanoparticles in a compact pattern when deposited onto gold substrates functionalized with self-assembled monolayers made from two molecules that differ essentially in their terminating group: 1,4-benzenedimethanethiol and 4-methylbenzylthiol.

ToxCast: Developing Predictive Signatures of Chemically Induced Toxicity (S)

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry, bioactivity profiling and toxicogenomic data to predict potential for toxicity and prioritize limited testing resour...

THE TOXCAST PROGRAM FOR PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

The United States Environmental Protection Agency (EPA) is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals...

Study of Methods for Assessing Research Topic Elicitation and pRioritization (SMARTER): Study Protocol to Compare Qualitative Research Methods and Advance Patient Engagement in Research.

PubMed

Lavallee, Danielle C; Comstock, Bryan; Scott, Mary R; Avins, Andrew L; Nerenz, David R; Edwards, Todd C; Patrick, Donald L; Lawrence, Sarah O; Bauer, Zoya; Truitt, Anjali R; Jarvik, Jeffrey G

2017-09-07

Involving patients as partners in research is a defining characteristic of patient-centered outcomes research (PCOR). While patients' experiential knowledge of a health condition or treatment may yield research priorities not reflected by researchers and policy makers, the methods for identifying and effectively collaborating with patients are still evolving. Patient registries and crowdsourcing may offer ease of access and convenience to both researchers and patients. Surveys and focus groups, including online modalities, have been described for prioritizing research topics. However, little is known about how these different methods compare in producing consistent priorities and similar perceptions of engagement quality among participants. The aims of this study are (1) to compare how different engagement methods used to elicit patient priorities for research perform as measured by rankings for priorities generated and participant satisfaction; and (2) to determine characteristics of individuals choosing to participate in research prioritization activities. Participants in the Back pain Outcomes using Longitudinal Data (BOLD) patient registry, established to evaluate the natural history of back pain among individuals 65 years and older, and participants on the Amazon Mechanical Turk (MTurk) crowdsourcing platform, to provide input on priorities for research via a questionnaire, are invited. For BOLD participants, we subsequently randomize interested respondents to 1 of 3 interactive prioritization activities to further develop priorities: a Delphi panel, an online crowd voting activity, or an in-person facilitated prioritization activity using nominal group technique (NGT). Participants involved in each activity complete a survey to evaluate the quality of the experience and a subset of these participants discuss their experience further in an interview. Descriptive statistics are used to characterize the rankings produced by each method and compare the top 5 rated topics resulting from each prioritization activity. We use rank-ordered logistic regression models to identify associations of the ranked priority topics with baseline patient characteristics. We analyze responses to the evaluation using a mixed-methods approach wherein we tabulate responses to Likert-scale questions and use content analysis to enumerate themes emerging from interviews for the 3 activities. In Phase I, we invite approximately 3000 BOLD participants and 500 Amazon MTurk workers to complete a research topic prioritization survey. Based on these results, we include additional topics into a subsequent prioritization survey. In Phase II, we invite BOLD participants to join 1 of 3 activities: 90 participants for Delphi panel, 100 participants for crowd voting, and 60 participants for focus groups. Of the Phase II participants, 30 will be interviewed to evaluate the activities. This study informs decisions about how to conduct outreach to patient registry participants for providing input on research priorities, how individuals 65 years and older wish to participate in engagement activities, and how different research prioritization methods compare in terms of rankings generated and participant satisfaction. ©Danielle C Lavallee, Bryan Comstock, Mary R Scott, Andrew L Avins, David R Nerenz, Todd C Edwards, Donald L Patrick, Sarah O Lawrence, Zoya Bauer, Anjali R Truitt, Jeffrey G Jarvik. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 07.09.2017.

Multi-temporal dynamics of suspended particulate matter in a macro-tidal river Plume (the Gironde) as observed by satellite data

NASA Astrophysics Data System (ADS)

Constantin, Sorin; Doxaran, David; Derkacheva, Anna; Novoa, Stéfani; Lavigne, Héloïse

2018-03-01

The Gironde River plume area is unique in terms of Suspended Particulate Matter (SPM) dynamics. Multiple factors contribute to the variations of SPM at multiple time scales, from river outputs to wind stress, currents and tidal cycles. The formation and evolution of the Maximum Turbidity Zone (MTZ) inside the estuary also plays a significant role. Thus, detailed analyses and monitoring of the region is important for better understanding the mechanisms governing the turbid plume dynamics, for proper future management and monitoring of SPM export from the estuary to the coastal ocean. In this study we use an unprecedented volume of satellite data to capture and better understand the dynamics of the river plume. We combine two types of satellite information in order to achieve these goals: data collected by the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Spinning Enhanced Visible and Infrared Imager (SEVIRI) sensors. The integrated information allows accounting for multiple time scales, i.e. from seasonal to diurnal cycles. We show and parameterize the overall effects of river discharge rates over the plume extension. Seasonal variations are also analyzed and an overall relationship between river discharge rates and plume magnitude is computed. For the first time, we clearly observe and explain the diurnal cycle of SPM dynamics in the river plume. Despite the limited capabilities of the SEVIRI sensor, geostationary data was successfully used to derive such information and results similar to in-situ datasets were obtained. The same patterns are observed, with significant increase in SPM plume during spring/ebb tide periods. Results from our study can be further used to refine sediment transport models and to gain a better perspective on the ecological implications of the sediment output in the continental shelf area.

Novel dextran-spermine conjugates as transfecting agents: comparing water-soluble and micellar polymers.

PubMed

Eliyahu, H; Makovitzki, A; Azzam, T; Zlotkin, A; Joseph, A; Gazit, D; Barenholz, Y; Domb, A J

2005-03-01

Recently, a novel cationic polymer, dextran-spermine (D-SPM) was developed for gene delivery. An efficient transfection was obtained using this polycation for a variety of genes and cell lines in serum-free or serum-poor medium. However, transfection using the water-soluble D-SPM-based polyplexes decreased with increasing serum concentration in cell culture in a concentration-dependent manner, reaching 95% inhibition at 50% serum in the cell growth medium. In order to overcome this obstacle, oleyl derivatives of D-SPM (which form micelles in aqueous phase) were synthesized at 1, 10, and 20 mol% of oleyl moiety to polymer epsilon-NH2 to form N-oleyl-D-SPM (ODS). Polyplexes based on ODS transfected well in medium containing 50% serum. Comparison with polyplexes based on well-established polymers (branched and linear polyethyleneimine) and with DOTAP/Cholesterol lipoplexes showed that regarding beta-galactosidase transgene expression level and cytotoxicity in tissue culture, the D-SPM and ODS compare well with the above polyplexes and lipoplexes. Intracellular trafficking using FITC-labeled ODS and Rhodamine-labeled pGeneGrip plasmid cloned with hBMP2 monitored by confocal microscopy revealed that during the transfection process the fluorescent-labeled polymer concentrates in the Golgi apparatus and around the nucleus, while the cell cytoplasm was free of fluorescent particles, suggesting that the polyplexes move in the cell toward the nucleus by vesicular transport through the cytoplasm and not by a random diffusion. We found that the plasmids penetrate the cell nucleus without the polymer. Preliminary results in zebra fish and mice demonstrate the potential of ODS to serve as an efficient nonviral vector for in vivo transfection.

Anti-ghrelin Spiegelmer inhibits exogenous ghrelin-induced increases in food intake, hoarding, and neural activation, but not food deprivation-induced increases

PubMed Central

Teubner, Brett J. W.

2013-01-01

Circulating concentrations of the stomach-derived “hunger-peptide” ghrelin increase in direct proportion to the time since the last meal. Exogenous ghrelin also increases food intake in rodents and humans, suggesting ghrelin may increase post-fast ingestive behaviors. Food intake after food deprivation is increased by laboratory rats and mice, but not by humans (despite dogma to the contrary) or by Siberian hamsters; instead, humans and Siberian hamsters increase food hoarding, suggesting the latter as a model of fasting-induced changes in human ingestive behavior. Exogenous ghrelin markedly increases food hoarding by ad libitum-fed Siberian hamsters similarly to that after food deprivation, indicating sufficiency. Here, we tested the necessity of ghrelin to increase food foraging, food hoarding, and food intake, and neural activation [c-Fos immunoreactivity (c-Fos-ir)] using anti-ghrelin Spiegelmer NOX-B11–2 (SPM), an l-oligonucleotide that specifically binds active ghrelin, inhibiting peptide-receptor interaction. SPM blocked exogenous ghrelin-induced increases in food hoarding the first 2 days after injection, and foraging and food intake at 1–2 h and 2–4 h, respectively, and inhibited hypothalamic c-Fos-ir. SPM given every 24 h across 48-h food deprivation inconsistently inhibited food hoarding after refeeding and c-Fos-ir, similarly to inabilities to do so in laboratory rats and mice. These results suggest that ghrelin may not be necessary for food deprivation-induced foraging and hoarding and neural activation. A possible compensatory response, however, may underlie these findings because SPM treatment led to marked increases in circulating ghrelin concentrations. Collectively, these results show that SPM can block exogenous ghrelin-induced ingestive behaviors, but the necessity of ghrelin for food deprivation-induced ingestive behaviors remains unclear. PMID:23804279

Co-pyrolysis of swine manure with agricultural plastic waste: laboratory-scale study.

PubMed

Ro, Kyoung S; Hunt, Patrick G; Jackson, Michael A; Compton, David L; Yates, Scott R; Cantrell, Keri; Chang, SeChin

2014-08-01

Manure-derived biochar is the solid product resulting from pyrolysis of animal manures. It has considerable potential both to improve soil quality with high levels of nutrients and to reduce contaminants in water and soil. However, the combustible gas produced from manure pyrolysis generally does not provide enough energy to sustain the pyrolysis process. Supplementing this process may be achieved with spent agricultural plastic films; these feedstocks have large amounts of available energy. Plastic films are often used in soil fumigation. They are usually disposed in landfills, which is wasteful, expensive, and environmentally unsustainable. The objective of this work was to investigate both the energetics of co-pyrolyzing swine solids with spent plastic mulch films (SPM) and the characteristics of its gas, liquid, and solid byproducts. The heating value of the product gas from co-pyrolysis was found to be much higher than that of natural gas; furthermore, the gas had no detectable toxic fumigants. Energetically, sustaining pyrolysis of the swine solids through the energy of the product gas could be achieved by co-pyrolyzing dewatered swine solids (25%m/m) with just 10% SPM. If more than 10% SPM is used, the co-pyrolysis would generate surplus energy which could be used for power generation. Biochars produced from co-pyrolyzing SPM and swine solid were similar to swine solid alone based on the surface area and the (1)H NMR spectra. The results of this study demonstrated the potential of using pyrolysis technology to manage two prominent agricultural waste streams (SPM and swine solids) while producing value-added biochar and a power source that could be used for local farm operations. Published by Elsevier Ltd.

Source apportionment of settleable particles in an impacted urban and industrialized region in Brazil.

PubMed

Santos, Jane Meri; Reis, Neyval Costa; Galvão, Elson Silva; Silveira, Alexsander; Goulart, Elisa Valentim; Lima, Ana Teresa

2017-09-01

Settleable particulate matter (SPM), especially coarser particles with diameters greater than 10 μm, has been found culprit of high deposition rates in cities affected by hinterland industrial activities. This is the case of Metropolitan Region of Vitoria (MRV), Espirito Santo, Brazil where industrial facilities are located within the urban sprawl and building constructions are intense. Frequent population complaints to the environmental protection agency (IEMA) throughout the years have triggered monitoring campaigns to determine SPM deposition rates and source apportionment. Eight different locations were monitored throughout the MRV, and SPM was quantified and chemically characterized. Sources profiles were defined either by using US EPA SPECIATE data or by experimental analysis. Atmospheric fallout in the MRV ranged between 2 and 20g/(m 2 30-day), with only one monitoring station ranging from 6-10 g/(m 2 30-day). EC, OC, Fe, Al, and Si were found the main constituents of dry deposition in the region. Source apportionment by the chemical mass balance (CMB) model determined that steel and iron ore pelletizing industries were the main contributor to one of the eight locations whereas resuspension, civil construction, and vehicular sources were also very important contributors to the other stations. Quarries and soil were also considered expressive SPM sources, but at the city periphery. CMB model could differentiate contributions from six industrial source groups: thermoelectric; iron ore, pellet, and pellet furnaces; coal coke and coke oven; sintering, blast furnace, and basic oxygen furnace; and soil, resuspension, and vehicles. However, the CMB model was unable to differentiate between iron ore and pellet stockpiles which are present in both steel and iron ore pelletizing industries. Further characterization of source and SPM might be necessary to aid local authorities in decision-making regarding these two industrial sources.

Prioritization of brain MRI volumes using medical image perception model and tumor region segmentation.

PubMed

Mehmood, Irfan; Ejaz, Naveed; Sajjad, Muhammad; Baik, Sung Wook

2013-10-01

The objective of the present study is to explore prioritization methods in diagnostic imaging modalities to automatically determine the contents of medical images. In this paper, we propose an efficient prioritization of brain MRI. First, the visual perception of the radiologists is adapted to identify salient regions. Then this saliency information is used as an automatic label for accurate segmentation of brain lesion to determine the scientific value of that image. The qualitative and quantitative results prove that the rankings generated by the proposed method are closer to the rankings created by radiologists. Copyright © 2013 Elsevier Ltd. All rights reserved.

Influence of group-delay ripple on timing jitter induced by SPM and IXPM in systems with dispersion compensated by CFBG

NASA Astrophysics Data System (ADS)

Qin, Xi; Cao, Jihong; Chen, Yong; Zhang, Feng; Jian, Shuisheng

2007-08-01

An analytical expression was proposed to analyze the influence of group-delay ripple (GDR) on timing jitter induced by self-phase modulation (SPM) and intra-channel cross-phase modulation (IXPM) in pseudo-linear transmission systems when dispersion was compensated by chirped fiber Bragg grating (CFBG). Effects of ripple amplitude, period, and phase on timing jitter were discussed by theoretical and numerical analysis in detail. The results show that the influence of GDR on timing jitter changes linearly with the amplitude of GDR and whether it decreases or increases the timing jitter relies on the ripple period and ripple phase. Timing jitter induced by SPM and IXPM could be suppressed totally by adjusting the relative phase between the center frequency of the pulse and the ripples.

Technology Alignment and Portfolio Prioritization (TAPP)

NASA Technical Reports Server (NTRS)

Funaro, Gregory V.; Alexander, Reginald A.

2015-01-01

Technology Alignment and Portfolio Prioritization (TAPP) is a method being developed by the Advanced Concepts Office, at NASA Marshall Space Flight Center. The TAPP method expands on current technology assessment methods by incorporating the technological structure underlying technology development, e.g., organizational structures and resources, institutional policy and strategy, and the factors that motivate technological change. This paper discusses the methods ACO is currently developing to better perform technology assessments while taking into consideration Strategic Alignment, Technology Forecasting, and Long Term Planning.

EPAS TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS(S).

EPA Science Inventory

EPAs National Center for Computational Toxicology is developing methods that apply computational chemistry, high-throughput screening (HTS) and genomic technologies to predict potential toxicity and prioritize the use of limited testing resources.

SPM of nonlinear surface plasmon waveguides

NASA Astrophysics Data System (ADS)

Li, Yuee; Zhang, Xiaoping

2008-10-01

Pulse propagation equation of nonlinear dispersion surface plasmon waveguide is educed strictly from wave equation. The nonlinear coefficient is defined and then used to assess and compare the nonlinear characteristic of three popular 1-D surface plasmon waveguides: the single metal-dielectric interface, the metal slab bounded by dielectric and the dielectric slab bounded by metal. SPM (self-phase modulation) of the typical surface plasmon waveguide is predicted and discussed.

Influence of cross-phase modulation in SPM-based nonlinear optical loop mirror

NASA Astrophysics Data System (ADS)

Pitois, Stéphane

2005-09-01

We study the role of cross-phase modulation (CPM) occurring between the two counter-propagating parts of a signal wave in a standard SPM-based nonlinear optical fiber loop mirror (NOLM). For pulse train with high duty-cycle, we experimentally observe the influence of cross-phase modulation on NOLM transmittivity. Finally, we propose a solution based on properly designed dispersion imbalanced NOLM to overcome undesirable CPM effects.

Specific interaction of postsynaptic densities with membrane rafts isolated from synaptic plasma membranes.

PubMed

Liu, Qian; Yao, Wei-Dong; Suzuki, Tatsuo

2013-06-01

Postsynaptic membrane rafts are believed to play important roles in synaptic signaling, plasticity, and maintenance. We recently demonstrated the presence, at the electron microscopic level, of complexes consisting of membrane rafts and postsynaptic densities (PSDs) in detergent-resistant membranes (DRMs) prepared from synaptic plasma membranes (SPMs) ( Suzuki et al., 2011 , J Neurochem, 119, 64-77). To further explore these complexes, here we investigated the nature of the binding between purified SPM-DRMs and PSDs in vitro. In binding experiments, we used SPM-DRMs prepared after treating SPMs with n-octyl-β-d-glucoside, because at concentrations of 1.0% or higher it completely separates SPM-DRMs and PSDs, providing substantially PSD-free unique SPM-DRMs as well as DRM-free PSDs. PSD binding to PSD-free DRMs was identified by mass spectrometry, Western blotting, and electron microscopy. PSD proteins were not incorporated into SPMs, and significantly less PSD proteins were incorporated into DRMs prepared from liver membranes, providing in vitro evidence that binding of PSDs to DRMs is specific and suggestion of the presence of specific interacting molecules. These specific interactions may have important roles in synaptic development, function, and plasticity in vivo. In addition, the binding system we developed may be a good tool to search for binding molecules and binding mechanisms between PSDs and rafts.

Spermine Regulates Pollen Tube Growth by Modulating Ca2+-Dependent Actin Organization and Cell Wall Structure

PubMed Central

Aloisi, Iris; Cai, Giampiero; Faleri, Claudia; Navazio, Lorella; Serafini-Fracassini, Donatella; Del Duca, Stefano

2017-01-01

Proper growth of the pollen tube depends on an elaborate mechanism that integrates several molecular and cytological sub-processes and ensures a cell shape adapted to the transport of gametes. This growth mechanism is controlled by several molecules among which cytoplasmic and apoplastic polyamines. Spermine (Spm) has been correlated with various physiological processes in pollen, including structuring of the cell wall and modulation of protein (mainly cytoskeletal) assembly. In this work, the effects of Spm on the growth of pear pollen tubes were analyzed. When exogenous Spm (100 μM) was supplied to germinating pollen, it temporarily blocked tube growth, followed by the induction of apical swelling. This reshaping of the pollen tube was maintained also after growth recovery, leading to a 30–40% increase of tube diameter. Apical swelling was also accompanied by a transient increase in cytosolic calcium concentration and alteration of pH values, which were the likely cause for major reorganization of actin filaments and cytoplasmic organelle movement. Morphological alterations of the apical and subapical region also involved changes in the deposition of pectin, cellulose, and callose in the cell wall. Thus, results point to the involvement of Spm in cell wall construction as well as cytoskeleton organization during pear pollen tube growth. PMID:29033970

Study of Intermediate Age (~10-30 Myr) Open Clusters

NASA Astrophysics Data System (ADS)

Olguin, Lorenzo; Michel, Raul; Contreras, Maria; Hernandez, Jesus; Schuster, William; Chavarria-Kleinhenn, Carlos

2013-07-01

We present the study of a sample of intermediate age open clusters (age ~ 10-30 Myr) using optical (UBVRI) and infrared photometric data. Optical photometry was obtained as part of the San Pedro Martir Open Clusters Project (SPM-OCP, Schuster et al. 2007; Michel et al. 2013). Infrared photometry was retrieved from 2MASS public data archive and WISE database. Open clusters included in the SPM-OCP were selected from catalogues presented by Dias et al. (2002) and Froebrich, Scholz & Raftery (2007). One of the main goals of the SPM-OCP is to compile a self-consistent and homogeneous set of cluster fundamental parameters such as reddening, distance, age, and metallicity whenever possible. In this work, we have analyzed a set of 25 clusters from the SPM-OCP with estimated ages between 10 and 30 Myr. Derived fundamental parameters for each cluster in the sample as well as an example of typical color-color and color-magnitude diagrams are presented. Kinematic membership was established by using proper motion data taken from the literature. Based on infrared photometry, we have searched for candidate stars to posses a circumstellar disk within each clusters. For those selected candidates a follow-up spectroscpic study is being carried out. This work was partially supported by UNAM-PAPIIT grant IN-109311.

Assessment of air quality in and around a steel industry with direct reduction iron route.

PubMed

Jena, Pradip K; Behera, Dillip K; Mishra, C S K; Mohanty, Saswat K

2011-10-01

The coal based Direct Reduced Iron (DRI) route for secondary steel production is now a preferred choice in India. Steel making is invariably associated with emission of air pollutants into the environment. Air quality monitoring was carried out in Winter, Summer and Rainy seasons of 2008 in eight monitoring stations in the work zone and five stations in the residential zone of an Integrated Steel Industry located in Orissa state, India. Four air quality parameters i.e. SPM, RSPM, SO2 and NO2 were monitored. Mean SPM and RSPM values were found to be significantly high (p < 0.01) at stations nearer to source in both work zone and residential zone .The highest average SPM and RSPM values in the work zone recorded were 4869 microg/m3 and 1420 microg/m3 and in the residential zone 294 microg/m3 and 198 microg/m3 respectively. No significant difference in the SO2 and NO2 levels was observed between the work and residential zones. In general, the values of air pollutants were highest in Winter followed by Summer and Rainy season. SPM and RSPM values exceeded the National Air Quality Standards (NAAQS) in both the residential and work zones.

Molecular detection of metallo-β-lactamase genes, bla IMP-1, bla VIM-2 and bla SPM-1 in imipenem resistant Pseudomonas aeruginosa isolated from clinical specimens in teaching hospitals of Ahvaz, Iran.

PubMed

Moosavian, Mojtaba; Rahimzadeh, Mohammad

2015-02-01

Carbapenem resistant Pseudomonas aeruginosa is a serious cause of nosocomial infections. The main purpose of the study is to determine the prevalence rate of imipenem resistant Pseudomonas aeruginosa carrying metallo-ß-lactamase (MBL) genes. 236 Pseudomonas aeruginosa isolates were collected from teaching hospitals of Ahvaz University of Medical Sciences during a period of 9 months in 2012. These strains were identified using conventional microbiological tests. The susceptibility of isolates to antibiotics were assessed using disk diffusion test. The IMP-EDTA combination disk phenotypic test was performed for detection of MBL producing strains. Finally, polymerase chain reaction (PCR) was performed to detect MBL genes, bla IMP-1, bla VIM-2 and bla SPM-1 in imipenem resistant strains. Out of 236 examined isolates, 122 isolates (51.4%) were resistant to imipenem. The IMP-EDTA combination test showed that among 122 imipenem resistant strains, 110 strains (90%) were phenotipically MBL producers. Additionally, the results of PCR method showed that 2 strains (1.6%) and 67strains (55%) of imipenem resistant Pseudomonas aeruginosa isolates contained bla VIM-2 and bla IMP-1 genes respectively. No SPM-1gene was found in the examined samples. Resistance of P. aeruginosa isolates to imipenem due to MBL enzymes is increasing in Ahavaz. Because of clinical significance of this kind of resistance, rapid detection of MBL producing strains and followed by appropriate treatment is necessary to prevent the spreading of these organisms.

An SPM12 extension for multiple sclerosis lesion segmentation

NASA Astrophysics Data System (ADS)

Roura, Eloy; Oliver, Arnau; Cabezas, Mariano; Valverde, Sergi; Pareto, Deborah; Vilanova, Joan C.; Ramió-Torrentà, Lluís.; Rovira, Àlex; Lladó, Xavier

2016-03-01

Purpose: Magnetic resonance imaging is nowadays the hallmark to diagnose multiple sclerosis (MS), characterized by white matter lesions. Several approaches have been recently presented to tackle the lesion segmentation problem, but none of them have been accepted as a standard tool in the daily clinical practice. In this work we present yet another tool able to automatically segment white matter lesions outperforming the current-state-of-the-art approaches. Methods: This work is an extension of Roura et al. [1], where external and platform dependent pre-processing libraries (brain extraction, noise reduction and intensity normalization) were required to achieve an optimal performance. Here we have updated and included all these required pre-processing steps into a single framework (SPM software). Therefore, there is no need of external tools to achieve the desired segmentation results. Besides, we have changed the working space from T1w to FLAIR, reducing interpolation errors produced in the registration process from FLAIR to T1w space. Finally a post-processing constraint based on shape and location has been added to reduce false positive detections. Results: The evaluation of the tool has been done on 24 MS patients. Qualitative and quantitative results are shown with both approaches in terms of lesion detection and segmentation. Conclusion: We have simplified both installation and implementation of the approach, providing a multiplatform tool1 integrated into the SPM software, which relies only on using T1w and FLAIR images. We have reduced with this new version the computation time of the previous approach while maintaining the performance.

Abnormal regional cerebral blood flow in systemic lupus erythematosus patients with psychiatric symptoms.

PubMed

Oda, Kenji; Matsushima, Eisuke; Okubo, Yoshiro; Ohta, Katsuya; Murata, Yuji; Koike, Ryuji; Miyasaka, Nobuyuki; Kato, Motoichiro

2005-07-01

Single-photon emission computed tomography (SPECT) studies have demonstrated decreased regional cerebral blood flow (rCBF) in systemic lupus erythematosus (SLE) patients. However, no study has done voxel-based analysis using statistical parametric mapping (SPM) that can evaluate rCBF objectively, and the relationship between rCBF and psychiatric symptoms has not been well investigated. Using L,L-ethyl cysteinate dimer (99mTc ECD) SPECT and SPM, we aimed to clarify the association of rCBF changes with psychiatric symptoms in SLE patients whose magnetic resonance imaging (MRI) showed no morphological abnormalities. Twenty SLE patients and 19 healthy volunteers underwent 99mTc ECD SPECT. Data were collected from August 2000 to March 2003. SLE was diagnosed according to American College of Rheumatology criteria, and psychiatric symptoms were diagnosed according to ICD-10 criteria. On the basis of the modified Carbotte, Denburg, and Denburg method, the patients were classified into 3 groups: a group with major psychiatric symptoms (hallucinosis, delusional disorder, and mood disorder), a group with minor psychiatric symptoms (anxiety disorder, dissociative disorder, and emotionally labile disorder), and a group without psychiatric symptoms. Gross organic lesions were ruled out by brain MRI. Group comparisons of rCBF were performed with analysis using SPM99. SLE patients without MRI lesions showed decreased rCBF in the posterior cingulate gyrus and thalamus. The reduction in rCBF was overt in patients with major psychiatric symptoms. Our study indicated that SLE patients may have dysfunction in the posterior cingulate gyrus and thalamus and that this may be associated with the severity of psychiatric symptoms.

Prioritization of Disease Susceptibility Genes Using LSM/SVD.

PubMed

Gong, Lejun; Yang, Ronggen; Yan, Qin; Sun, Xiao

2013-12-01

Understanding the role of genetics in diseases is one of the most important tasks in the postgenome era. It is generally too expensive and time consuming to perform experimental validation for all candidate genes related to disease. Computational methods play important roles for prioritizing these candidates. Herein, we propose an approach to prioritize disease genes using latent semantic mapping based on singular value decomposition. Our hypothesis is that similar functional genes are likely to cause similar diseases. Measuring the functional similarity between known disease susceptibility genes and unknown genes is to predict new disease susceptibility genes. Taking autism as an instance, the analysis results of the top ten genes prioritized demonstrate they might be autism susceptibility genes, which also indicates our approach could discover new disease susceptibility genes. The novel approach of disease gene prioritization could discover new disease susceptibility genes, and latent disease-gene relations. The prioritized results could also support the interpretive diversity and experimental views as computational evidence for disease researchers.

Integrated prioritization method for active and passive highway-rail crossings.

DOT National Transportation Integrated Search

2013-01-01

This two-year research project developed a prioritization system for highway-rail at-grade crossings that addressed the following major concerns: (1) warrants to identify low-volume, passive crossings with risk factors; (2) a broader priority index t...

ToxCast: Using high throughput screening to identify profiles of biological activity

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

Applications of high throughput screening to identify profiles of biological activity

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

Predictive In Vitro Screening of Environmental Chemicals – The ToxCast Project

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

EPA'S TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals that likely represent the greatest hazard to human ...

Development of procedures for identifying high-crash locations and prioritizing safety improvements

DOT National Transportation Integrated Search

2003-06-01

The objectives of this study were to review and analyze the current procedures for identifying high-crash locations and evaluating and prioritizing roadway safety improvements at high-crash locations, and to recommend improved methods. Several tasks ...

Development of procedures for identifying high-crash locations and prioritizing safety improvements.

DOT National Transportation Integrated Search

2003-06-01

The objectives of this study were to review and analyze the current procedures for identifying high-crash locations and evaluating and prioritizing roadway safety improvements at high-crash locations, and to recommend improved methods. Several tasks ...

Patient-tailored prioritization for a pediatric care decision support system through machine learning.

PubMed

Klann, Jeffrey G; Anand, Vibha; Downs, Stephen M

2013-12-01

Over 8 years, we have developed an innovative computer decision support system that improves appropriate delivery of pediatric screening and care. This system employs a guidelines evaluation engine using data from the electronic health record (EHR) and input from patients and caregivers. Because guideline recommendations typically exceed the scope of one visit, the engine uses a static prioritization scheme to select recommendations. Here we extend an earlier idea to create patient-tailored prioritization. We used Bayesian structure learning to build networks of association among previously collected data from our decision support system. Using area under the receiver-operating characteristic curve (AUC) as a measure of discriminability (a sine qua non for expected value calculations needed for prioritization), we performed a structural analysis of variables with high AUC on a test set. Our source data included 177 variables for 29 402 patients. The method produced a network model containing 78 screening questions and anticipatory guidance (107 variables total). Average AUC was 0.65, which is sufficient for prioritization depending on factors such as population prevalence. Structure analysis of seven highly predictive variables reveals both face-validity (related nodes are connected) and non-intuitive relationships. We demonstrate the ability of a Bayesian structure learning method to 'phenotype the population' seen in our primary care pediatric clinics. The resulting network can be used to produce patient-tailored posterior probabilities that can be used to prioritize content based on the patient's current circumstances. This study demonstrates the feasibility of EHR-driven population phenotyping for patient-tailored prioritization of pediatric preventive care services.

Evidences for Cu and Zn Isotope Fractionation in Sediments and Particulate Suspended Matter of the Scheldt Estuary

NASA Astrophysics Data System (ADS)

Petit, J.; Mattielli, N.; de Jong, J.; Chou, L.

2004-05-01

Recent developments in MC-ICP-MS technology allow high precision measurements of heavy stable isotopes, such as Cu and Zn isotopes, which have been shown to undergo biotic or abiotic fractionation (1). Application of Zn isotopes to the study of aquatic ecosystems has already shown some interesting perspectives in their potential use as biogeochemical tracers in deep ocean carbonates (2) or Fe-Mn nodules (3). However, until now no investigation of possible Cu and Zn isotopic fractionation has been carried out within estuaries that are important pathways for hydrological and geochemical cycling of metals. Cu and Zn isotope geochemistry has been studied in sandy to loamy surface sediments (top 20 cm) and in suspended particulate matter (SPM) along a transect in a strong tidal estuary, the Scheldt estuary situated in Belgium and the Netherlands (November 2002). Further to separation of Cu, Fe and Zn by one step ion-exchange chromatography, Cu and Zn isotopic ratios are measured with a "Nu-Plasma" MC-ICP-MS. Instrumental mass bias is corrected using reference materials (Zn JMC, Cu NIST SRM 976 and Ga JMC standard) by simultaneous standard-sample bracketing and external normalization (500 ppb Zn doping for Cu isotopic analyses in static mode and 250 ppb Ga doping for Zn isotopic analyses in dynamic mode), together with a Ni correction. These methods lead to long-term reproducibility (2σ at 95 % confidence level) of ± 0.07 per mil for δ 66Zn (n=100 over 7 analysis sessions) and ± 0.06 per mil for δ 65Cu (n=120 over 8 analysis sessions) for 500 ppb of reference material. Average beam intensities are 6 V/ppm. Precise and reproducible results are obtained for concentration as low as 100 ppb for Cu and Zn. Expected Cu and Zn enrichment in SPM (120 ppm and 1200 ppm respectively) and sediments (being 6 to 10 times lower than SPM) in the upper estuary and progressive decrease in metal content by mixing downstream of the maximum turbidity zone (MTZ, around 5 psu) are observed. Results show that variations in Cu and Zn isotopic composition are smaller in SPM (δ 66Zn varying from 0.35 to 0.17 and δ 65Cu from -0.13 to 0.18) than in sediments. Cu and Zn isotopic signatures of sediments show a clear trend of lighter isotopes removal from the MTZ seaward with δ 66Zn varying from 0.21 at 2 psu to 1.11 per mil at 33 psu (and δ 65Cu = -0.37 to 0.24). In contrast, Zn isotopic compositions in SPM are more homogeneous with average δ 66Zn of 0.24 ± 0.18 over all the transect. Cu isotopic composition in SPM are very constant downstream of the MTZ with average δ 65Cu =-0.06 ± 0.08 but become more scattered within MTZ (varying from -0.04 to 0.18). These preliminary results pinpoint important variations in Cu and Zn isotopic compositions within estuarine systems and contrasted isotopic signatures in Cu and Zn between SPM and sediments. Results suggest the important role of early diagenesis in the isotope geochemistry of heavy metals in estuarine environment. This study provides a stepping stone for further investigation of interacting processes involved in controlling the cycling of metals in the Scheldt estuary. (1) Zhu et al., Earth Planet. Sci. Lett. 200 (2002), 47-62 (2) Pichat et al., Earth Planet. Sci. Lett. 6598 (2003), 1-12 (3) Maréchal et al., Geochem. Geophys. Geosyt., 1 (2000), GC000029

ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

PubMed Central

2011-01-01

Background Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene candidates, the identification of disease genes among the candidates remains time-consuming and expensive. Efficient computational methods are therefore needed to prioritize genes within the list of candidates, by exploiting the wealth of information available about the genes in various databases. Results We propose ProDiGe, a novel algorithm for Prioritization of Disease Genes. ProDiGe implements a novel machine learning strategy based on learning from positive and unlabeled examples, which allows to integrate various sources of information about the genes, to share information about known disease genes across diseases, and to perform genome-wide searches for new disease genes. Experiments on real data show that ProDiGe outperforms state-of-the-art methods for the prioritization of genes in human diseases. Conclusions ProDiGe implements a new machine learning paradigm for gene prioritization, which could help the identification of new disease genes. It is freely available at http://cbio.ensmp.fr/prodige. PMID:21977986

Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks

PubMed Central

Zhang, Yihua; Li, Wan; Feng, Yuyan; Guo, Shanshan; Zhao, Xilei; Wang, Yahui; He, Yuehan; He, Weiming; Chen, Lina

2017-01-01

Chronic obstructive pulmonary disease (COPD) is a multi-factor disease, which could be caused by many factors, including disturbances of metabolism and protein-protein interactions (PPIs). In this paper, a weighted COPD-related metabolic network and a weighted COPD-related PPI network were constructed base on COPD disease genes and functional information. Candidate genes in these weighted COPD-related networks were prioritized by making use of a gene prioritization method, respectively. Literature review and functional enrichment analysis of the top 100 genes in these two networks suggested the correlation of COPD and these genes. The performance of our gene prioritization method was superior to that of ToppGene and ToppNet for genes from the COPD-related metabolic network or the COPD-related PPI network after assessing using leave-one-out cross-validation, literature validation and functional enrichment analysis. The top-ranked genes prioritized from COPD-related metabolic and PPI networks could promote the better understanding about the molecular mechanism of this disease from different perspectives. The top 100 genes in COPD-related metabolic network or COPD-related PPI network might be potential markers for the diagnosis and treatment of COPD. PMID:29262568

Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks.

PubMed

Zhang, Yihua; Li, Wan; Feng, Yuyan; Guo, Shanshan; Zhao, Xilei; Wang, Yahui; He, Yuehan; He, Weiming; Chen, Lina

2017-11-28

Chronic obstructive pulmonary disease (COPD) is a multi-factor disease, which could be caused by many factors, including disturbances of metabolism and protein-protein interactions (PPIs). In this paper, a weighted COPD-related metabolic network and a weighted COPD-related PPI network were constructed base on COPD disease genes and functional information. Candidate genes in these weighted COPD-related networks were prioritized by making use of a gene prioritization method, respectively. Literature review and functional enrichment analysis of the top 100 genes in these two networks suggested the correlation of COPD and these genes. The performance of our gene prioritization method was superior to that of ToppGene and ToppNet for genes from the COPD-related metabolic network or the COPD-related PPI network after assessing using leave-one-out cross-validation, literature validation and functional enrichment analysis. The top-ranked genes prioritized from COPD-related metabolic and PPI networks could promote the better understanding about the molecular mechanism of this disease from different perspectives. The top 100 genes in COPD-related metabolic network or COPD-related PPI network might be potential markers for the diagnosis and treatment of COPD.

Big, Deep, and Smart Data in Scanning Probe Microscopy

DOE PAGES

Kalinin, Sergei V.; Strelcov, Evgheni; Belianinov, Alex; ...

2016-09-27

Scanning probe microscopy techniques open the door to nanoscience and nanotechnology by enabling imaging and manipulation of structure and functionality of matter on nanometer and atomic scales. We analyze the discovery process by SPM in terms of information flow from tip-surface junction to the knowledge adoption by scientific community. Furthermore, we discuss the challenges and opportunities offered by merging of SPM and advanced data mining, visual analytics, and knowledge discovery technologies.

SPM analysis of fibrinogen adsorption on solid surfaces

NASA Astrophysics Data System (ADS)

Choukourov, A.; Grinevich, A.; Saito, N.; Takai, O.

2007-09-01

The adsorption kinetics, adhesion and orientation of human fibrinogen on solid surfaces have been studied by surface probe microscopy (SPM) and quartz crystal microbalance techniques (QCM). CF 3-, NH 2-terminated organo-silane self-assembled monolayers (SAM) and OH-terminated silicon dioxide have been used as model surfaces. Furthermore, the interaction of fibrinogen with nanocomposite Ti/hydrocarbon plasma polymer films (Ti/ppCH) deposited by dc magnetron sputtering has also been studied.

Real Space Imaging of the Microscopic Origins of the Ultrahigh Dielectric Constant in Polycrystalline CaCu 3Ti 4O 12

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

Kalinin, Sergei V; Shin, Junsoo; Veith, Gabriel M

2005-01-01

The origins of an ultrahigh dielectric constant in polycrystalline CaCu{sub 3}Ti{sub 4}O{sub 12} (CCTO) were studied using the combination of impedance spectroscopy, electron microscopy, and scanning probe microscopy (SPM). Impedance spectra indicate that the transport properties in the 0.1 Hz-1 MHz frequency range are dominated by a single parallel resistive-capacitive (RC) element with a characteristic relaxation frequency of 16 Hz. dc potential distributions measurements by SPM illustrate that significant potential drops occur at the grain boundaries, which thus can be unambiguously identified as the dominant RC element. High frequency ac amplitude and phase distributions illustrate very weak grain boundary contrastmore » in SPM, indicative of strong capacitive coupling across the interfaces. These results demonstrate that the ultrahigh dielectric constant reported for polycrystalline CCTO materials is related to grain-boundary behavior.« less

Influence of breast milk polyamines on suckling rat immune system maturation.

PubMed

Pérez-Cano, Francisco J; González-Castro, Ana; Castellote, Cristina; Franch, Angels; Castell, Margarida

2010-02-01

The aim of this study was to ascertain whether the supplementation of polyamines present in breast milk, i.e. spermine (SPM) and spermidine (SPD), influenced the post-natal maturation of the systemic and intestinal immune system in rats. From birth, pups daily received SPM or SPD. At 5, 11 and 18 days old, small intestine intraepithelial lymphocytes (IEL), lamina propria lymphocytes (LPL) and splenocytes were phenotypically characterized. SPM and, less evidently, SPD accelerated the maturation of CD8+ IEL, and enhanced the presence of intraepithelial NK cells and IEL related with specific immune responses on the proximal and distal small intestine, respectively. Polyamines increased the percentage of more mature CD4+ LPL and enhanced the early presence of splenic B cells and, later, that of NK cells. However, no effect on Ig-secretory function was detected. These results suggest that breast milk polyamines improve the maturation of the rat intestinal and systemic immune system.

An evaluation of a combined scanning probe and optical microscope for lunar regolith studies

NASA Astrophysics Data System (ADS)

Yang, S.; Pike, W. T.; Staufer, U.; Claus, D.; Rodenburg, J. M.

2011-12-01

The microscopic properties of the lunar regolith such as the shape, the surface texture and the size distribution are required for an understanding of both past surface processes and potential hazards for future human exploration [1]. To reveal the particle morphology at the sub micrometer scale, scanning-probe microscopy (SPM), first used on the 2008 Phoenix mission [1], is a proven approach; however, there are two main challenges for the measurement of lunar particles. Firstly, the SPM tip is liable to move particles during scanning, even when using the lower contact forces of the dynamic-mode imaging. Hence the particles need to be stabilised during imaging. Secondly, typically the AFM tip extends about 10 μm from its cantilever, so larger particles protruding more than this height above their substrates cannot be scanned completely. To immobilize particles and eliminate large particles during SPM scanning, micromachined Si substrates, which have been successfully applied in the Phoenix project for Mars investigation in 2008 [2], have been investigated for lunar analogue material. On these substrates micrometer pits are patterned and serve as traps to enhance the stability of the AFM scanning by grasping the particles. In addition, the diameter of pits can determine the size of dusts to be captured and reduce the adhesion for the larger dust and so eliminate the oversized particles. To extend the imaging range and assist in selecting scan areas for the SPM, we use a type of lensless optical imaging (LOM) which uses ptychographic diffractive imaging [3] to eliminate the restrictions and performance limitations of conventional focusing devices. As a reference, scanning electron microscopy (SEM) which minimizes particle-probe interactions and has the advantage of an extended depth of field, is employed to image the same particle fields at resolutions covering both the SPM and LOM. By comparing the differences and the similarities between SEM and LOM images, the ability of LOM for illuminating the details about the lunar particles sample, is demonstrated. The analysis of SEM and SPM images of the same particles of JSC-LunarA analogue soil reveals the potential of the SPM to obtain reliable microscopic images of lunar dusts including detailed morphology with the help of the micromachined Si substrates. [1] J. D. Carpenter, O. Angerer, M. Durante, D. Linnarson, W. T. Pike, "Life Sciences Investigations for ESA's First Lunar Lander," Earth, Moon, and Planets, Vol.107, pp. 11-23, 2010. [2] S. Vijendran, H.Sykulska, and W. T. Pike, "AFM investigation of Martian soil simulant on micromachined Si substrates," Journal of Microscopy, Vol.227, pp.236-245, Sep. 2007. [3] J.M. Rodenburg, "Ptychography and related diffractive imaging techniques," Advances in Imaging and Electron Physics, Vol.150, pp. 87-184, 2008

How much suspended particulate matter enters long-term in-channel storage?

NASA Astrophysics Data System (ADS)

Dietrich, Stephan; Kleisinger, Carmen; Kehl, Nora; Schubert, Birgit; Hillebrand, Gudrun

2017-04-01

The route of suspended particulate matter (SPM) downstream rivers strongly depends on discharge conditions and involves transport times and periods with resting times in deposits e.g. at areas with low-flow conditions near the channel bed. It is, however, difficult to estimate the contribution of SPM on the bed load. In this study, particle-bound polychlorinated biphenyls (PCB), which were released by an incident in the Elbe river (Central Europe) in spring 2015, could be used as unique tracer for transport pathways of SPM along the whole river stretch (over 700 km length), including low mountain ranges, lowlands, and the estuary. In 2015 the Elbe River was characterized by low-discharge conditions. Thus, the export of SPM on flood plains was strongly limited. The incident was monitored by concentration measurements of seven indicator PCB congeners along the inland part of the Elbe River as well as in the Elbe estuary. Data from ten monitoring stations (settling tanks) are considered. The total PCB load is calculated for all stations on the basis of monthly contaminant concentrations and daily suspended sediment concentrations. Monte-Carlo simulations assess the uncertainties of the calculated load. It is shown that the ratio of high versus low chlorinated PCB congeners is a suitable tracer to distinguish the PCB load of the incident from the long-term background signal (hereafter PCB6 ratio). We demonstrate that both the load of PCB as well as its chemical fingerprint allows the estimation of transport durations for the transport processes involved. Only a little part of the suspension has been transported via wash load. The PCB6 ratio is used to estimate mean transport velocities of the wash load fraction. A direct transport of wash load via the mean flow velocity of the water was not observed. Shortly after the incident, the PCB6 ratio was monitored 257 km downstream of the incident site in April 2015, in May first occurrence was monitored 514 km downstream of the incident site and in July it reaches the tidal weir 626 km downstream and enters the estuary. Here the transport velocity strongly decreases and the PCB6 ratio was not detected 25 km downstream the tidal weir before December 2015. The major part of the PCB-marked suspension is transported via suspended load. Interestingly, the reduction of total PCB tagged SPM load within the first 514 km downstream of the incident site indicates that roughly 75% of the annual SPM load (of the most upstream monitoring station located 43 km downstream of the incident site) is stored in the sediments of the Elbe River, suggesting that suspended sediment in transport enters storage after a relatively short distance. Once SPM settles, significant storage can occur over decadal time scales.

A Quantitative and Novel Approach to the Prioritization of Zoonotic Diseases in North America: A Public Perspective

PubMed Central

Ng, Victoria; Sargeant, Jan M.

2012-01-01

Background Zoonoses account for over half of all communicable diseases causing illness in humans. As there are limited resources available for the control and prevention of zoonotic diseases, a framework for their prioritization is necessary to ensure resources are directed into those of highest importance. Although zoonotic outbreaks are a significant burden of disease in North America, the systematic prioritization of zoonoses in this region has not been previously evaluated. Methodology/Principal Findings This study describes the novel use of a well-established quantitative method, conjoint analysis (CA), to identify the relative importance of 21 key characteristics of zoonotic diseases that can be used for their prioritization in Canada and the US. Relative importance weights from the CA were used to develop a point-scoring system to derive a recommended list of zoonoses for prioritization in Canada and the US. Over 1,500 participants from the general public were recruited to complete the online survey (761 from Canada and 778 from the US). Hierarchical Bayes models were fitted to the survey data to derive CA-weighted scores. Scores were applied to 62 zoonotic diseases of public health importance in Canada and the US to rank diseases in order of priority. Conclusions/Significance This was the first study to describe a systematic and quantitative approach to the prioritization of zoonoses in North America involving public participants. We found individuals with no prior knowledge or experience in prioritizing zoonoses were capable of producing meaningful results using CA as a novel quantitative approach to prioritization. More similarities than differences were observed between countries suggesting general agreement in disease prioritization between Canadians and Americans. We demonstrate CA as a potential tool for the prioritization of zoonoses; other prioritization exercises may also consider this approach. PMID:23133639

Applying Costs, Risks and Values Evaluation (CRAVE) methodology to Engineering Support Request (ESR) prioritization

NASA Technical Reports Server (NTRS)

Joglekar, Prafulla N.

1994-01-01

Given limited budget, the problem of prioritization among Engineering Support Requests (ESR's) with varied sizes, shapes, and colors is a difficult one. At the Kennedy Space Center (KSC), the recently developed 4-Matrix (4-M) method represents a step in the right direction as it attempts to combine the traditional criteria of technical merits only with the new concern for cost-effectiveness. However, the 4-M method was not adequately successful in the actual prioritization of ESRs for the fiscal year 1995 (FY95). This research identifies a number of design issues that should help us to develop better methods. It emphasizes that given the variety and diversity of ESR's one should not expect that a single method could help in the assessment of all ESR's. One conclusion is that a methodology such as Costs, Risks, and Values Evaluation (CRAVE) should be adopted. It also is clear that the development of methods such as 4-M requires input not only from engineers with technical expertise in ESR's but also from personnel with adequate background in the theory and practice of cost-effectiveness analysis. At KSC, ESR prioritization is one part of the Ground Support Working Teams (GSWT) Integration Process. It was discovered that the more important barriers to the incorporation of cost-effectiveness considerations in ESR prioritization lie in this process. The culture of integration, and the corresponding structure of review by a committee of peers, is not conducive to the analysis and confrontation necessary in the assessment and prioritization of ESR's. Without assistance from appropriately trained analysts charged with the responsibility to analyze and be confrontational about each ESR, the GSWT steering committee will continue to make its decisions based on incomplete understanding, inconsistent numbers, and at times, colored facts. The current organizational separation of the prioritization and the funding processes is also identified as an important barrier to the pursuit of cost-effectiveness. Perhaps the greatest barrier is that, at the working level, KSC's culture is so preoccupied with technical concerns that it seems almost oblivious to any cost concerns, let alone cost-effectiveness concerns. It is recommended that we must urgently begin to change that culture and seek a better balance between these two concerns.

Applications of high throughput screening to identify profiles of biological activity relevant to carcinogenesis

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

Updating and improving methodology for prioritizing highway project locations on the strategic intermodal system : [summary].

DOT National Transportation Integrated Search

2016-05-01

Florida International University researchers examined the existing performance measures and the project prioritization method in the CMP and updated them to better reflect the current conditions and strategic goals of FDOT. They also developed visual...

Procedures for prioritizing road improvements under the statewide highway plan : final report.

DOT National Transportation Integrated Search

1990-01-01

The road improvement prioritizing system currently utilized by the Virginia Department of Transportation is similar to the method utilized by many states: it is a sufficiency rating system that evaluates proposed projects on the basis of points assig...

A Multi-criteria Decision Analysis System for Prioritizing Sites and Types of Low Impact Development Practices

NASA Astrophysics Data System (ADS)

Song, Jae Yeol; Chung, Eun-Sung

2017-04-01

This study developed a multi-criteria decision analysis framework to prioritize sites and types of low impact development (LID) practices. This framework was systemized as a web-based system coupled with the Storm Water Management Model (SWMM) from the Environmental Protection Agency (EPA). Using the technique for order of preference by similarity to ideal solution (TOPSIS), which is a type of multi-criteria decision-making (MCDM) method, multiple types and sites of designated LID practices are prioritized. This system is named the Water Management Prioritization Module (WMPM) and is an improved version of the Water Management Analysis Module (WMAM) that automatically generates and simulates multiple scenarios of LID design and planning parameters for a single LID type. WMPM can simultaneously determine the priority of multiple LID types and sites. In this study, an infiltration trench and permeable pavement were considered for multiple sub-catchments in South Korea to demonstrate the WMPM procedures. The TOPSIS method was manually incorporated to select the vulnerable target sub-catchments and to prioritize the LID planning scenarios for multiple types and sites considering socio-economic, hydrologic and physical-geometric factors. In this application, the Delphi method and entropy theory were used to determine the subjective and objective weights, respectively. Comparing the ranks derived by this system, two sub-catchments, S16 and S4, out of 18 were considered to be the most suitable places for installing an infiltration trench and porous pavement to reduce the peak and total flow, respectively, considering both socio-economic factors and hydrological effectiveness. WMPM can help policy-makers to objectively develop urban water plans for sustainable development. Keywords: Low Impact Development, Multi-Criteria Decision Analysis, SWMM, TOPSIS, Water Management Prioritization Module (WMPM)

Endocrine Profiling and Prioritization of Environmental Chemicals Using ToxCast Data

PubMed Central

Reif, David M.; Martin, Matthew T.; Tan, Shirlee W.; Houck, Keith A.; Judson, Richard S.; Richard, Ann M.; Knudsen, Thomas B.; Dix, David J.; Kavlock, Robert J.

2010-01-01

Background The prioritization of chemicals for toxicity testing is a primary goal of the U.S. Environmental Protection Agency (EPA) ToxCast™ program. Phase I of ToxCast used a battery of 467 in vitro, high-throughput screening assays to assess 309 environmental chemicals. One important mode of action leading to toxicity is endocrine disruption, and the U.S. EPA’s Endocrine Disruptor Screening Program (EDSP) has been charged with screening pesticide chemicals and environmental contaminants for their potential to affect the endocrine systems of humans and wildlife. Objective The goal of this study was to develop a flexible method to facilitate the rational prioritization of chemicals for further evaluation and demonstrate its application as a candidate decision-support tool for EDSP. Methods Focusing on estrogen, androgen, and thyroid pathways, we defined putative endocrine profiles and derived a relative rank or score for the entire ToxCast library of 309 unique chemicals. Effects on other nuclear receptors and xenobiotic metabolizing enzymes were also considered, as were pertinent chemical descriptors and pathways relevant to endocrine-mediated signaling. Results Combining multiple data sources into an overall, weight-of-evidence Toxicological Priority Index (ToxPi) score for prioritizing further chemical testing resulted in more robust conclusions than any single data source taken alone. Conclusions Incorporating data from in vitro assays, chemical descriptors, and biological pathways in this prioritization schema provided a flexible, comprehensive visualization and ranking of each chemical’s potential endocrine activity. Importantly, ToxPi profiles provide a transparent visualization of the relative contribution of all information sources to an overall priority ranking. The method developed here is readily adaptable to diverse chemical prioritization tasks. PMID:20826373

Interactogeneous: Disease Gene Prioritization Using Heterogeneous Networks and Full Topology Scores

PubMed Central

Gonçalves, Joana P.; Francisco, Alexandre P.; Moreau, Yves; Madeira, Sara C.

2012-01-01

Disease gene prioritization aims to suggest potential implications of genes in disease susceptibility. Often accomplished in a guilt-by-association scheme, promising candidates are sorted according to their relatedness to known disease genes. Network-based methods have been successfully exploiting this concept by capturing the interaction of genes or proteins into a score. Nonetheless, most current approaches yield at least some of the following limitations: (1) networks comprise only curated physical interactions leading to poor genome coverage and density, and bias toward a particular source; (2) scores focus on adjacencies (direct links) or the most direct paths (shortest paths) within a constrained neighborhood around the disease genes, ignoring potentially informative indirect paths; (3) global clustering is widely applied to partition the network in an unsupervised manner, attributing little importance to prior knowledge; (4) confidence weights and their contribution to edge differentiation and ranking reliability are often disregarded. We hypothesize that network-based prioritization related to local clustering on graphs and considering full topology of weighted gene association networks integrating heterogeneous sources should overcome the above challenges. We term such a strategy Interactogeneous. We conducted cross-validation tests to assess the impact of network sources, alternative path inclusion and confidence weights on the prioritization of putative genes for 29 diseases. Heat diffusion ranking proved the best prioritization method overall, increasing the gap to neighborhood and shortest paths scores mostly on single source networks. Heterogeneous associations consistently delivered superior performance over single source data across the majority of methods. Results on the contribution of confidence weights were inconclusive. Finally, the best Interactogeneous strategy, heat diffusion ranking and associations from the STRING database, was used to prioritize genes for Parkinson’s disease. This method effectively recovered known genes and uncovered interesting candidates which could be linked to pathogenic mechanisms of the disease. PMID:23185389

Developing Methods Using ToxCast Data for the Classification and Prioritization of Antimicrobials and Inerts

EPA Science Inventory

Improved chemical risk management and increased efficiency of chemical prioritization, classification and assessment are major goals within EPA. Towards achieving these goals, EPA's ToxCast™ research program has been designed to rapidly screen hundreds to thousands of chemicals' ...

ToxCast: Developing Predictive Signatures of Chemically Induced Toxicity (Developing Predictive Bioactivity Signatures from ToxCasts HTS Data)

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry, bioactivity profiling and toxicogenomic data to predict potential for toxicity and prioritize limited testing resour...

Head Circumference as a Useful Surrogate for Intracranial Volume in Older Adults

PubMed Central

Hshieh, Tammy T.; Fox, Meaghan L.; Kosar, Cyrus M.; Cavallari, Michele; Guttmann, Charles R.G.; Alsop, David; Marcantonio, Edward R.; Schmitt, Eva M.; Jones, Richard N.; Inouye, Sharon K.

2015-01-01

Background Intracranial volume (ICV) has been proposed as a measure of maximum lifetime brain size. Accurate ICV measures require neuroimaging which is not always feasible for epidemiologic investigations. We examined head circumference as a useful surrogate for intracranial volume in older adults. Methods 99 older adults underwent Magnetic Resonance Imaging (MRI). ICV was measured by Statistical Parametric Mapping 8 (SPM8) software or Functional MRI of the Brain Software Library (FSL) extraction with manual editing, typically considered the gold standard. Head circumferences were determined using standardized tape measurement. We examined estimated correlation coefficients between head circumference and the two MRI-based ICV measurements. Results Head circumference and ICV by SPM8 were moderately correlated (overall r=0.73, men r=0.67, women r=0.63). Head circumference and ICV by FSL were also moderately correlated (overall r=0.69, men r=0.63, women r=0.49). Conclusions Head circumference measurement was strongly correlated with MRI-derived ICV. Our study presents a simple method to approximate ICV among older patients, which may prove useful as a surrogate for cognitive reserve in large scale epidemiologic studies of cognitive outcomes. This study also suggests the stability of head circumference correlation with ICV throughout the lifespan. PMID:26631180

PET evaluation of late cerebral effect in advanced radiation therapy techniques for cranial base tumors.

PubMed

Alongi, Pierpaolo; Iaccarino, Leonardo; Losa, Marco; Del Vecchio, Antonella; Gerevini, Simonetta; Plebani, Valentina; Di Muzio, Nadia; Mortini, Pietro; Gianolli, Luigi; Perani, Daniela

2018-05-25

Even though the benefits of radiation therapy are well established, it is important to recognize the broad spectrum of radiation-induced changes, particularly in the central nervous system. The possible damage to the brain parenchyma may have clinical consequences and in particular cognitive impairment might be one of the major complication of radiotherapy. To date, no studies have investigated the effects of focal radiation therapy on brain structure and function together with the assessment of their clinical outcomes at a long follow-up. In this prospective study, we evaluated in six patients the possible brain late effects after radiation therapy, using a standardized neuropsychological battery, MRI and 18F-FDG PET using SPM and semi-quantitative methods, in patients affected by cranial base tumors who underwent gamma knife or tomotherapy. Neuropsychological examinations showed no cognitive impairment after the treatment. In all patients, both MRI assessment and 18F-FDG-PET did not reveal any local or distant anatomical and metabolic late effects. The present study support the safety of advanced radiation therapy techniques. 18F-FDG-PET, using SPM and semi-quantitative methods, might be a valuable tool to evaluate the cerebral radiotoxicity in patients treated for brain neoplasms. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Search for Open binaries in the Southern Celestial Hemisphere using SPM4

NASA Astrophysics Data System (ADS)

Dávila, E.; Vieira, K.; Rosales, K.

2018-01-01

Open binaries' weak gravitational binding makes them vulnerable to any perturbation, turning them into excellent probes of the gravitational field where they are located. Currently there are only a few hundreds known or suspected open binaries, therefore a search for more of these systems is highly encouraging by looking for pairs of stars with common proper motions in an extensive, deep, and high quality astrometric catalog such as the SPM4 (Girard et al. 2011).

SPM and XPM crosstalk in WDM systems with DRA: Channel spacing and attenuation effects

NASA Astrophysics Data System (ADS)

Morsy, Emadeldeen; Fayed, Heba A.; Abd El Aziz, Ahmed; Aly, Moustafa H.

2018-06-01

This paper presents a theoretical analysis of a closed formula for nonlinear crosstalk due to self-phase modulation (SPM) and cross phase modulation (XPM) in wavelength division multiplexing (WDM) systems. The influence of channel spacing and attenuation on the system behavior is modeled and investigated. The system under consideration is a standard single-mode fiber (SSMF) with a single-span distributed Raman amplifier (DRA) and is operating at 100 Gbps.

Synthesis and biological characterization of novel charge-deficient spermine analogues.

PubMed

Weisell, Janne; Hyvönen, Mervi T; Häkkinen, Merja R; Grigorenko, Nikolay A; Pietilä, Marko; Lampinen, Anita; Kochetkov, Sergey N; Alhonen, Leena; Vepsäläinen, Jouko; Keinänen, Tuomo A; Khomutov, Alex R

2010-08-12

Biogenic polyamines, spermidine and spermine, are positively charged at physiological pH. They are present in all cells and essential for their growth and viability. Here we synthesized three novel derivatives of the isosteric charge-deficient spermine analogue 1,12-diamino-3,6,9-triazadodecane (SpmTrien, 5a) that are N(1)-Ac-SpmTrien (5c), N(12)-Ac-SpmTrien (5b), and N(1),N(12)-diethyl-1,12-diamino-3,6,9-triazadodecane (N(1),N(12)-Et(2)-SpmTrien, 5d). 5a and 5d readily accumulated in DU145 cells at the same concentration range as natural polyamines and moderately competed for the uptake with putrescine (1) but not with spermine (4a) or spermidine (2). 5a efficiently down-regulated ornithine decarboxylase and decreased polyamine levels, while 5d proved to be inefficient, compared with N(1),N(11)-diethylnorspermine (6). None of the tested analogues were substrates for human recombinant spermine oxidase, but those having free aminoterminus, including 1,8-diamino-3,6-diazaoctane (Trien, 3a), were acetylated by mouse recombinant spermidine/spermine N(1)-acetyltransferase. 5a was acetylated to 5c and 5b, and the latter was further metabolized by acetylpolyamine oxidase to 3a, a drug used to treat Wilson's disease. Thus, 5a is a bioactive precursor of 3a with enhanced bioavailability.

Quantitative analysis of diffusion tensor imaging (DTI) using statistical parametric mapping (SPM) for brain disorders

NASA Astrophysics Data System (ADS)

Lee, Jae-Seung; Im, In-Chul; Kang, Su-Man; Goo, Eun-Hoe; Kwak, Byung-Joon

2013-07-01

This study aimed to quantitatively analyze data from diffusion tensor imaging (DTI) using statistical parametric mapping (SPM) in patients with brain disorders and to assess its potential utility for analyzing brain function. DTI was obtained by performing 3.0-T magnetic resonance imaging for patients with Alzheimer's disease (AD) and vascular dementia (VD), and the data were analyzed using Matlab-based SPM software. The two-sample t-test was used for error analysis of the location of the activated pixels. We compared regions of white matter where the fractional anisotropy (FA) values were low and the apparent diffusion coefficients (ADCs) were increased. In the AD group, the FA values were low in the right superior temporal gyrus, right inferior temporal gyrus, right sub-lobar insula, and right occipital lingual gyrus whereas the ADCs were significantly increased in the right inferior frontal gyrus and right middle frontal gyrus. In the VD group, the FA values were low in the right superior temporal gyrus, right inferior temporal gyrus, right limbic cingulate gyrus, and right sub-lobar caudate tail whereas the ADCs were significantly increased in the left lateral globus pallidus and left medial globus pallidus. In conclusion by using DTI and SPM analysis, we were able to not only determine the structural state of the regions affected by brain disorders but also quantitatively analyze and assess brain function.

A Singular Perturbation Approach for Time-Domain Assessment of Phase Margin

NASA Technical Reports Server (NTRS)

Zhu, J. Jim; Yang, Xiaojing; Hodel, A Scottedward

2010-01-01

This paper considers the problem of time-domain assessment of the Phase Margin (PM) of a Single Input Single Output (SISO) Linear Time-Invariant (LTI) system using a singular perturbation approach, where a SISO LTI fast loop system, whose phase lag increases monotonically with frequency, is introduced into the loop as a singular perturbation with a singular perturbation (time-scale separation) parameter Epsilon. First, a bijective relationship between the Singular Perturbation Margin (SPM) max and the PM of the nominal (slow) system is established with an approximation error on the order of Epsilon(exp 2). In proving this result, relationships between the singular perturbation parameter Epsilon, PM of the perturbed system, PM and SPM of the nominal system, and the (monotonically increasing) phase of the fast system are also revealed. These results make it possible to assess the PM of the nominal system in the time-domain for SISO LTI systems using the SPM with a standardized testing system called "PM-gauge," as demonstrated by examples. PM is a widely used stability margin for LTI control system design and certification. Unfortunately, it is not applicable to Linear Time-Varying (LTV) and Nonlinear Time-Varying (NLTV) systems. The approach developed here can be used to establish a theoretical as well as practical metric of stability margin for LTV and NLTV systems using a standardized SPM that is backward compatible with PM.

Polyamines Regulate Strawberry Fruit Ripening by Abscisic Acid, Auxin, and Ethylene.

PubMed

Guo, Jiaxuan; Wang, Shufang; Yu, Xiaoyang; Dong, Rui; Li, Yuzhong; Mei, Xurong; Shen, Yuanyue

2018-05-01

Polyamines (PAs) participate in many plant growth and developmental processes, including fruit ripening. However, it is not clear whether PAs play a role in the ripening of strawberry ( Fragaria ananassa ), a model nonclimacteric plant. Here, we found that the content of the PA spermine (Spm) increased more sharply after the onset of fruit coloration than did that of the PAs putrescine (Put) or spermidine (Spd). Spm dominance in ripe fruit resulted from abundant transcripts of a strawberry S -adenosyl-l-Met decarboxylase gene ( FaSAMDC ), which encodes an enzyme that generates a residue needed for PA biosynthesis. Exogenous Spm and Spd promoted fruit coloration, while exogenous Put and a SAMDC inhibitor inhibited coloration. Based on transcriptome data, up- and down-regulation of FaSAMDC expression promoted and inhibited ripening, respectively, which coincided with changes in several physiological parameters and their corresponding gene transcripts, including firmness, anthocyanin content, sugar content, polyamine content, auxin (indole-3-acetic acid [IAA]) content, abscisic acid (ABA) content, and ethylene emission. Using isothermal titration calorimetry, we found that FaSAMDC also had a high enzymatic activity with a K d of 1.7 × 10 -3 m In conclusion, PAs, especially Spm, regulate strawberry fruit ripening in an ABA-dominated, IAA-participating, and ethylene-coordinated manner, and FaSAMDC plays an important role in ripening. © 2018 American Society of Plant Biologists. All Rights Reserved.

Progress on Poverty? New Estimates of Historical Trends Using an Anchored Supplemental Poverty Measure

PubMed Central

Wimer, Christopher; Fox, Liana; Garfinkel, Irwin; Kaushal, Neeraj; Waldfogel, Jane

2016-01-01

This study examines historical trends in poverty using an anchored version of the U.S. Census Bureau’s recently developed Research Supplemental Poverty Measure (SPM) estimated back to 1967. Although the SPM is estimated each year using a quasi-relative poverty threshold that varies over time with changes in families’ expenditures on a core basket of goods and services, this study explores trends in poverty using an absolute, or anchored, SPM threshold. We believe the anchored measure offers two advantages. First, setting the threshold at the SPM’s 2012 levels and estimating it back to 1967, adjusted only for changes in prices, is more directly comparable to the approach taken in official poverty statistics. Second, it allows for a better accounting of the roles that social policy, the labor market, and changing demographics play in trends in poverty rates over time, given that changes in the threshold are held constant. Results indicate that unlike official statistics that have shown poverty rates to be fairly flat since the 1960s, poverty rates have dropped by 40 % when measured using a historical anchored SPM over the same period. Results obtained from comparing poverty rates using a pretax/pretransfer measure of resources versus a posttax/posttransfer measure of resources further show that government policies, not market incomes, are driving the declines observed over time. PMID:27352076

High-throughput dietary exposure predictions for chemical migrants from food contact substances for use in chemical prioritization

EPA Science Inventory

Under the ExpoCast program, United States Environmental Protection Agency (EPA) researchers have developed a high-throughput (HT) framework for estimating aggregate exposures to chemicals from multiple pathways to support rapid prioritization of chemicals. Here, we present method...

Theory of CW lidar aerosol backscatter measurements and development of a 2.1 microns solid-state pulsed laser radar for aerosol backscatter profiling

NASA Technical Reports Server (NTRS)

Kavaya, Michael J.; Henderson, Sammy W.; Frehlich, R. G.

1991-01-01

The performance and calibration of a focused, continuous wave, coherent detection CO2 lidar operated for the measurement of atmospheric backscatter coefficient, B(m), was examined. This instrument functions by transmitting infrared (10 micron) light into the atmosphere and collecting the light which is scattered in the rearward direction. Two distinct modes of operation were considered. In volume mode, the scattered light energy from many aerosols is detected simultaneously, whereas in the single particle mode (SPM), the scattered light energy from a single aerosol is detected. The analysis considered possible sources of error for each of these two cases, and also considered the conditions where each technique would have superior performance. The analysis showed that, within reasonable assumptions, the value of B(m) could be accurately measured by either the VM or the SPM method. The understanding of the theory developed during the analysis was also applied to a pulsed CO2 lidar. Preliminary results of field testing of a solid state 2 micron lidar using a CW oscillator is included.

Sensory integration functions of children with cochlear implants.

PubMed

Koester, AnjaLi Carrasco; Mailloux, Zoe; Coleman, Gina Geppert; Mori, Annie Baltazar; Paul, Steven M; Blanche, Erna; Muhs, Jill A; Lim, Deborah; Cermak, Sharon A

2014-01-01

OBJECTIVE. We investigated sensory integration (SI) function in children with cochlear implants (CIs). METHOD. We analyzed deidentified records from 49 children ages 7 mo to 83 mo with CIs. Records included Sensory Integration and Praxis Tests (SIPT), Sensory Processing Measure (SPM), Sensory Profile (SP), Developmental Profile 3 (DP-3), and Peabody Developmental Motor Scales (PDMS), with scores depending on participants' ages. We compared scores with normative population mean scores and with previously identified patterns of SI dysfunction. RESULTS. One-sample t tests revealed significant differences between children with CIs and the normative population on the majority of the SIPT items associated with the vestibular and proprioceptive bilateral integration and sequencing (VPBIS) pattern. Available scores for children with CIs on the SPM, SP, DP-3, and PDMS indicated generally typical ratings. CONCLUSION. SIPT scores in a sample of children with CIs reflected the VPBIS pattern of SI dysfunction, demonstrating the need for further examination of SI functions in children with CIs during occupational therapy assessment and intervention planning. Copyright © 2014 by the American Occupational Therapy Association, Inc.

Efficient Posterior Probability Mapping Using Savage-Dickey Ratios

PubMed Central

Penny, William D.; Ridgway, Gerard R.

2013-01-01

Statistical Parametric Mapping (SPM) is the dominant paradigm for mass-univariate analysis of neuroimaging data. More recently, a Bayesian approach termed Posterior Probability Mapping (PPM) has been proposed as an alternative. PPM offers two advantages: (i) inferences can be made about effect size thus lending a precise physiological meaning to activated regions, (ii) regions can be declared inactive. This latter facility is most parsimoniously provided by PPMs based on Bayesian model comparisons. To date these comparisons have been implemented by an Independent Model Optimization (IMO) procedure which separately fits null and alternative models. This paper proposes a more computationally efficient procedure based on Savage-Dickey approximations to the Bayes factor, and Taylor-series approximations to the voxel-wise posterior covariance matrices. Simulations show the accuracy of this Savage-Dickey-Taylor (SDT) method to be comparable to that of IMO. Results on fMRI data show excellent agreement between SDT and IMO for second-level models, and reasonable agreement for first-level models. This Savage-Dickey test is a Bayesian analogue of the classical SPM-F and allows users to implement model comparison in a truly interactive manner. PMID:23533640

Properties of coarse particles in suspended particulate matter of the North Yellow Sea during summer

NASA Astrophysics Data System (ADS)

Zhang, Kainan; Wang, Zhenyan; Li, Wenjian; Yan, Jun

2018-01-01

Fine particles in seawater commonly form large porous aggregates. Aggregate density and settling velocity determine the behavior of this suspended particulate matter (SPM) within the water column. However, few studies of aggregate particles over a continental shelf have been undertaken. In our case study, properties of aggregate particles, including size and composition, over the continental shelf of the North Yellow Sea were investigated. During a scientific cruise in July 2016, in situ effective particle size distributions of SPM at 10 stations were measured, while temperature and turbidity measurements and samples of water were obtained from surface, middle, and bottom layers. Dispersed and inorganic particle size distributions were determined in the laboratory. The in situ SPM was divided into (1) small particles (<32 μm), (2) medium particles (32-256 μm) and (3) large particles (>256 μm). Large particles and medium particles dominated the total volume concentrations (VCs) of in situ SPM. After dispersion, the VCs of medium particles decreased to low values (<0.1 μL/L). The VCs of large particles in the surface and middle layers also decreased markedly, although they had higher peak values (0.1-1 μL/L). This suggests that almost all in situ medium particles and some large particles were aggregated, while other large particles were single particles. Correlation analysis showed that primary particles <32 μm influenced the formation of these aggregates. Microscopic examination revealed that these aggregates consisted of both organic and inorganic fine particles, while large particles were mucus-bound organic aggregates or individual plankton. The vertical distribution of coarser particles was clearly related to water stratification. Generally, medium aggregate particles were dominant in SPM of the bottom layer. A thermocline blocked resuspension of fine material into upper layers, yielding low VCs of medium-sized aggregate particles in the surface layer. Abundant large biogenic particles were present in both surface and middle layers.

Quantifying uncertainty in the measurement of arsenic in suspended particulate matter by Atomic Absorption Spectrometry with hydride generator

PubMed Central

2011-01-01

Arsenic is the toxic element, which creates several problems in human being specially when inhaled through air. So the accurate and precise measurement of arsenic in suspended particulate matter (SPM) is of prime importance as it gives information about the level of toxicity in the environment, and preventive measures could be taken in the effective areas. Quality assurance is equally important in the measurement of arsenic in SPM samples before making any decision. The quality and reliability of the data of such volatile elements depends upon the measurement of uncertainty of each step involved from sampling to analysis. The analytical results quantifying uncertainty gives a measure of the confidence level of the concerned laboratory. So the main objective of this study was to determine arsenic content in SPM samples with uncertainty budget and to find out various potential sources of uncertainty, which affects the results. Keeping these facts, we have selected seven diverse sites of Delhi (National Capital of India) for quantification of arsenic content in SPM samples with uncertainty budget following sampling by HVS to analysis by Atomic Absorption Spectrometer-Hydride Generator (AAS-HG). In the measurement of arsenic in SPM samples so many steps are involved from sampling to final result and we have considered various potential sources of uncertainties. The calculation of uncertainty is based on ISO/IEC17025: 2005 document and EURACHEM guideline. It has been found that the final results mostly depend on the uncertainty in measurement mainly due to repeatability, final volume prepared for analysis, weighing balance and sampling by HVS. After the analysis of data of seven diverse sites of Delhi, it has been concluded that during the period from 31st Jan. 2008 to 7th Feb. 2008 the arsenic concentration varies from 1.44 ± 0.25 to 5.58 ± 0.55 ng/m3 with 95% confidence level (k = 2). PMID:21466671

Voxel-based statistical analysis of cerebral blood flow using Tc-99m ECD brain SPECT in patients with traumatic brain injury: group and individual analyses.

PubMed

Shin, Yong Beom; Kim, Seong-Jang; Kim, In-Ju; Kim, Yong-Ki; Kim, Dong-Soo; Park, Jae Heung; Yeom, Seok-Ran

2006-06-01

Statistical parametric mapping (SPM) was applied to brain perfusion single photon emission computed tomography (SPECT) images in patients with traumatic brain injury (TBI) to investigate regional cerebral abnormalities compared to age-matched normal controls. Thirteen patients with TBI underwent brain perfusion SPECT were included in this study (10 males, three females, mean age 39.8 +/- 18.2, range 21 - 74). SPM2 software implemented in MATLAB 5.3 was used for spatial pre-processing and analysis and to determine the quantitative differences between TBI patients and age-matched normal controls. Three large voxel clusters of significantly decreased cerebral blood perfusion were found in patients with TBI. The largest clusters were area including medial frontal gyrus (voxel number 3642, peak Z-value = 4.31, 4.27, p = 0.000) in both hemispheres. The second largest clusters were areas including cingulated gyrus and anterior cingulate gyrus of left hemisphere (voxel number 381, peak Z-value = 3.67, 3.62, p = 0.000). Other clusters were parahippocampal gyrus (voxel number 173, peak Z-value = 3.40, p = 0.000) and hippocampus (voxel number 173, peak Z-value = 3.23, p = 0.001) in the left hemisphere. The false discovery rate (FDR) was less than 0.04. From this study, group and individual analyses of SPM2 could clearly identify the perfusion abnormalities of brain SPECT in patients with TBI. Group analysis of SPM2 showed hypoperfusion pattern in the areas including medial frontal gyrus of both hemispheres, cingulate gyrus, anterior cingulate gyrus, parahippocampal gyrus and hippocampus in the left hemisphere compared to age-matched normal controls. Also, left parahippocampal gyrus and left hippocampus were additional hypoperfusion areas. However, these findings deserve further investigation on a larger number of patients to be performed to allow a better validation of objective SPM analysis in patients with TBI.

Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles.

PubMed

Zhu, Jie; Qin, Yufang; Liu, Taigang; Wang, Jun; Zheng, Xiaoqi

2013-01-01

Identification of gene-phenotype relationships is a fundamental challenge in human health clinic. Based on the observation that genes causing the same or similar phenotypes tend to correlate with each other in the protein-protein interaction network, a lot of network-based approaches were proposed based on different underlying models. A recent comparative study showed that diffusion-based methods achieve the state-of-the-art predictive performance. In this paper, a new diffusion-based method was proposed to prioritize candidate disease genes. Diffusion profile of a disease was defined as the stationary distribution of candidate genes given a random walk with restart where similarities between phenotypes are incorporated. Then, candidate disease genes are prioritized by comparing their diffusion profiles with that of the disease. Finally, the effectiveness of our method was demonstrated through the leave-one-out cross-validation against control genes from artificial linkage intervals and randomly chosen genes. Comparative study showed that our method achieves improved performance compared to some classical diffusion-based methods. To further illustrate our method, we used our algorithm to predict new causing genes of 16 multifactorial diseases including Prostate cancer and Alzheimer's disease, and the top predictions were in good consistent with literature reports. Our study indicates that integration of multiple information sources, especially the phenotype similarity profile data, and introduction of global similarity measure between disease and gene diffusion profiles are helpful for prioritizing candidate disease genes. Programs and data are available upon request.

Design of a single projector multiview 3D display system

NASA Astrophysics Data System (ADS)

Geng, Jason

2014-03-01

Multiview three-dimensional (3D) display is able to provide horizontal parallax to viewers with high-resolution and fullcolor images being presented to each view. Most multiview 3D display systems are designed and implemented using multiple projectors, each generating images for one view. Although this multi-projector design strategy is conceptually straightforward, implementation of such multi-projector design often leads to a very expensive system and complicated calibration procedures. Even for a multiview system with a moderate number of projectors (e.g., 32 or 64 projectors), the cost of a multi-projector 3D display system may become prohibitive due to the cost and complexity of integrating multiple projectors. In this article, we describe an optical design technique for a class of multiview 3D display systems that use only a single projector. In this single projector multiview (SPM) system design, multiple views for the 3D display are generated in a time-multiplex fashion by the single high speed projector with specially designed optical components, a scanning mirror, and a reflective mirror array. Images of all views are generated sequentially and projected via the specially design optical system from different viewing directions towards a 3D display screen. Therefore, the single projector is able to generate equivalent number of multiview images from multiple viewing directions, thus fulfilling the tasks of multiple projectors. An obvious advantage of the proposed SPM technique is the significant reduction of cost, size, and complexity, especially when the number of views is high. The SPM strategy also alleviates the time-consuming procedures for multi-projector calibration. The design method is flexible and scalable and can accommodate systems with different number of views.

Prospective multi-centre Voxel Based Morphometry study employing scanner specific segmentations: Procedure development using CaliBrain structural MRI data

PubMed Central

2009-01-01

Background Structural Magnetic Resonance Imaging (sMRI) of the brain is employed in the assessment of a wide range of neuropsychiatric disorders. In order to improve statistical power in such studies it is desirable to pool scanning resources from multiple centres. The CaliBrain project was designed to provide for an assessment of scanner differences at three centres in Scotland, and to assess the practicality of pooling scans from multiple-centres. Methods We scanned healthy subjects twice on each of the 3 scanners in the CaliBrain project with T1-weighted sequences. The tissue classifier supplied within the Statistical Parametric Mapping (SPM5) application was used to map the grey and white tissue for each scan. We were thus able to assess within scanner variability and between scanner differences. We have sought to correct for between scanner differences by adjusting the probability mappings of tissue occupancy (tissue priors) used in SPM5 for tissue classification. The adjustment procedure resulted in separate sets of tissue priors being developed for each scanner and we refer to these as scanner specific priors. Results Voxel Based Morphometry (VBM) analyses and metric tests indicated that the use of scanner specific priors reduced tissue classification differences between scanners. However, the metric results also demonstrated that the between scanner differences were not reduced to the level of within scanner variability, the ideal for scanner harmonisation. Conclusion Our results indicate the development of scanner specific priors for SPM can assist in pooling of scan resources from different research centres. This can facilitate improvements in the statistical power of quantitative brain imaging studies. PMID:19445668

Skin protection behaviour and sex differences in melanoma location in patients with multiple primary melanomas.

PubMed

Warren, Matthew; McMeniman, Erin; Adams, Agnieszka; De'Ambrosis, Brian

2017-02-01

Previous studies have shown that sunscreen usage, sun-protection measures and self-examination rates in patients with single primary melanomas (SPM) are similar to that in the general population. This study hypothesises that these rates would be different in a population with multiple primary melanomas (MPM). We further hypothesise that there would be a sex difference in melanoma location in patients with MPM. The objectives of this study were to determine skin protection measures, self-examinations and melanoma location in a cohort of patients with MPM. A survey was conducted on 137 patients with MPM examining their sun-protection measures, skin self-examination rates and medical and phenotypic characteristics. These data were combined with a review of their medical records to examine the patients' skin cancer history. Patients with MPM had higher rates of skin self-evaluation (74% vs 22%), sunscreen usage (70% vs 45%) and other sun-protection measures (95% vs 46%) than has been published for patients with a history of a SPM. We have also shown that women have a higher risk of developing melanomas on their arms (p < 0.01) and lower legs (p < 0.05) than men. This report showed the rates of skin self-examination, sunscreen usage and other sun-protection methods in patients with MPM is higher than in studies of patients with SPM. It also highlighted sex differences in terms of melanoma location for patients with MPM. Further studies to examine the cause of the differences in these forms of protective behaviour could help improve the utilisation of these important preventative measures in all patients. © 2015 The Australasian College of Dermatologists.

Impaired Prioritization of Novel Onset Stimuli in Autism Spectrum Disorder

ERIC Educational Resources Information Center

Keehn, Brandon; Joseph, Robert M.

2008-01-01

Background: Deficiency in the adaptive allocation of attention to relevant environmental stimuli is an associated feature of autism spectrum disorder (ASD). Recent evidence suggests that individuals with ASD may be specifically impaired in attentional prioritization of novel onsets. Method: We investigated modulation of attention by novel onset…

Using County-Level Public Health Data to Prioritize Medical Education Topics

ERIC Educational Resources Information Center

Sumner, Walton, II; Schootman, Mario; Asaro, Philip; Yan, Yan; Hagen, Michael D.

2008-01-01

Introduction: Medical education topics might be locally prioritized using public health data on health outcomes and risk factors unrelated to quality of care. Methods: The Missouri Information for Community Assessment (MICA) supplied preventable hospitalization rates (PHRs) for asthma, chronic obstructive pulmonary disease (COPD), diabetes, heart…

Using Alternative Approaches to Prioritize Testing for the Universe of Chemicals with Potential for Human Exposure (WC9)

EPA Science Inventory

One use of alternative methods is to target animal use at only those chemicals and tests that are absolutely necessary. We discuss prioritization of testing based on high-throughput screening assays (HTS), QSAR modeling, high-throughput toxicokinetics (HTTK), and exposure modelin...

The utility of human ADME data for prioritizing the evaluation of pharmaceuticals in the environment.

EPA Science Inventory

To proceed in the investigation of potential effects of pharmaceuticals in the environment, a cohesive data collection strategy is paramount. Given the lack of data for aquatic species, prioritization seems a logical starting point. Several methods have been put forward, for exam...

Presence of high-risk clones of OXA-23-producing Acinetobacter baumannii (ST79) and SPM-1-producing Pseudomonas aeruginosa (ST277) in environmental water samples in Brazil.

PubMed

Turano, Helena; Gomes, Fernando; Medeiros, Micheli; Oliveira, Silvane; Fontes, Lívia C; Sato, Maria I Z; Lincopan, Nilton

2016-09-01

This study reports the presence of hospital-associated high-risk lineages of OXA-23-producing ST79 Acinetobacter baumannii and SPM-1-producing ST277 Pseudomonas aeruginosa in urban rivers in Brazil. These findings indicate that urban rivers can act as reservoirs of clinically important multidrug-resistant bacteria, which constitute a potential risk to human and animal health. Copyright © 2016 Elsevier Inc. All rights reserved.

Controlled Atmosphere High Temperature SPM for electrochemical measurements

NASA Astrophysics Data System (ADS)

Vels Hansen, K.; Sander, C.; Koch, S.; Mogensen, M.

2007-03-01

A new controlled atmosphere high temperature SPM has been designed and build for the purpose of performing electrochemical measurements on solid oxide fuel cell materials. The first tests show that images can be obtained at a surface temperature of 465°C in air with a standard AFM AC probe. The aim is to produce images at a surface temperature of 800°C with electrically conducting ceramic probes as working electrodes that can be positioned at desired locations at the surface for electrochemical measurements.

Method for analysis of psychopharmaceuticals in real industrial wastewater and groundwater with suspended organic particulate matter using solid phase extraction disks extraction and ultra-high performance liquid chromatography/time-of-flight mass spectrometry.

PubMed

Křesinová, Zdena; Linhartová, Lucie; Petrů, Klára; Krejčová, Lucie; Šrédlová, Kamila; Lhotský, Ondřej; Kameník, Zdeněk; Cajthaml, Tomáš

2016-04-01

A rapid and reliable analytical method was developed for the quantitative determination of psychopharmaceuticals, their precursors and by-products in real contaminated samples from a pharmaceutical company in Olomouc (Czech Republic), based on SPE disk extraction and detection by ultra performance liquid chromatography, combined with time-of-flight mass spectrometry. The target compounds were quantified in the real whole-water samples (water including suspended particles), both in the presence of suspended particulate matter (SPM) and high concentrations of other organic pollutants. A total of nine compounds were analyzed which consisted of three commonly used antidepressants (tricyclic antidepressants and antipsychotics), one antitussive agent and five by-products or precursors. At first, the SPE disk method was developed for the extraction of water samples (dissolved analytes, recovery 84-104%) and pressurised liquid extraction technique was verified for solid matrices (sludge samples, recovery 81-95%). In order to evaluate the SPE disk technique for whole water samples containing SPM, non contaminated groundwater samples were also loaded with different amounts (100 and 300mgL(-1)) of real contaminated sludge originating from the same locality. The recoveries from the whole-water samples obtained by SPE disk method ranged between 67 and 119% after the addition of the most contaminated sludge. The final method was applied to several real groundwater (whole-water) samples from the industrial area and high concentrations (up to 10(3)μgL(-1)) of the target compounds were detected. The results of this study document and indicate the feasibility of the SPE disk method for analysis of groundwater. Copyright © 2016 Elsevier B.V. All rights reserved.

Simulation of realistic abnormal SPECT brain perfusion images: application in semi-quantitative analysis

NASA Astrophysics Data System (ADS)

Ward, T.; Fleming, J. S.; Hoffmann, S. M. A.; Kemp, P. M.

2005-11-01

Simulation is useful in the validation of functional image analysis methods, particularly when considering the number of analysis techniques currently available lacking thorough validation. Problems exist with current simulation methods due to long run times or unrealistic results making it problematic to generate complete datasets. A method is presented for simulating known abnormalities within normal brain SPECT images using a measured point spread function (PSF), and incorporating a stereotactic atlas of the brain for anatomical positioning. This allows for the simulation of realistic images through the use of prior information regarding disease progression. SPECT images of cerebral perfusion have been generated consisting of a control database and a group of simulated abnormal subjects that are to be used in a UK audit of analysis methods. The abnormality is defined in the stereotactic space, then transformed to the individual subject space, convolved with a measured PSF and removed from the normal subject image. The dataset was analysed using SPM99 (Wellcome Department of Imaging Neuroscience, University College, London) and the MarsBaR volume of interest (VOI) analysis toolbox. The results were evaluated by comparison with the known ground truth. The analysis showed improvement when using a smoothing kernel equal to system resolution over the slightly larger kernel used routinely. Significant correlation was found between effective volume of a simulated abnormality and the detected size using SPM99. Improvements in VOI analysis sensitivity were found when using the region median over the region mean. The method and dataset provide an efficient methodology for use in the comparison and cross validation of semi-quantitative analysis methods in brain SPECT, and allow the optimization of analysis parameters.

An SPM8-based Approach for Attenuation Correction Combining Segmentation and Non-rigid Template Formation: Application to Simultaneous PET/MR Brain Imaging

PubMed Central

Izquierdo-Garcia, David; Hansen, Adam E.; Förster, Stefan; Benoit, Didier; Schachoff, Sylvia; Fürst, Sebastian; Chen, Kevin T.; Chonde, Daniel B.; Catana, Ciprian

2014-01-01

We present an approach for head MR-based attenuation correction (MR-AC) based on the Statistical Parametric Mapping (SPM8) software that combines segmentation- and atlas-based features to provide a robust technique to generate attenuation maps (µ-maps) from MR data in integrated PET/MR scanners. Methods Coregistered anatomical MR and CT images acquired in 15 glioblastoma subjects were used to generate the templates. The MR images from these subjects were first segmented into 6 tissue classes (gray and white matter, cerebro-spinal fluid, bone and soft tissue, and air), which were then non-rigidly coregistered using a diffeomorphic approach. A similar procedure was used to coregister the anatomical MR data for a new subject to the template. Finally, the CT-like images obtained by applying the inverse transformations were converted to linear attenuation coefficients (LACs) to be used for AC of PET data. The method was validated on sixteen new subjects with brain tumors (N=12) or mild cognitive impairment (N=4) who underwent CT and PET/MR scans. The µ-maps and corresponding reconstructed PET images were compared to those obtained using the gold standard CT-based approach and the Dixon-based method available on the Siemens Biograph mMR scanner. Relative change (RC) images were generated in each case and voxel- and region of interest (ROI)-based analyses were performed. Results The leave-one-out cross-validation analysis of the data from the 15 atlas-generation subjects showed small errors in brain LACs (RC=1.38%±4.52%) compared to the gold standard. Similar results (RC=1.86±4.06%) were obtained from the analysis of the atlas-validation datasets. The voxel- and ROI-based analysis of the corresponding reconstructed PET images revealed quantification errors of 3.87±5.0% and 2.74±2.28%, respectively. The Dixon-based method performed substantially worse (the mean RC values were 13.0±10.25% and 9.38±4.97%, respectively). Areas closer to skull showed the largest improvement. Conclusion We have presented an SPM8-based approach for deriving the head µ-map from MR data to be used for PET AC in integrated PET/MR scanners. Its implementation is straightforward and only requires the morphological data acquired with a single MR sequence. The method is very accurate and robust, combining the strengths of both segmentation- and atlas-based approaches while minimizing their drawbacks. PMID:25278515

SPM response to tide and river flow in the hyper-turbid Ems River

NASA Astrophysics Data System (ADS)

Winterwerp, Johan C.; Vroom, Julia; Wang, Zheng-B.; Krebs, Martin; Hendriks, Erik C. M.; van Maren, Dirk S.; Schrottke, Kerstin; Borgsmüller, Christine; Schöl, Andreas

2017-05-01

In this paper, we analyse the behaviour of fine sediments in the hyper-turbid Lower Ems River, with focus on the river's upper reaches, a stretch of about 25 km up-estuary of Terborg. Our analysis is based on long records of suspended particulate matter (SPM) from optical backscatter (OBS) measurements close to the bed at seven stations along the river, records of salinity and water level measurements at these stations, acoustic measurements on the vertical mud structure just up-estuary of Terborg and oxygen profiles in the lower 3 m of the water column close to Leerort and Terborg. Further, we use cross-sectionally averaged velocities computed with a calibrated numerical model. Distinction is made between four timescales, i.e. the semi-diurnal tidal timescale, the spring-neap tidal timescale, a timescale around an isolated peak in river flow (i.e. about 3 weeks) and a seasonal timescale. The data suggest that a pool of fluid/soft mud is present in these upper reaches, from up-estuary of Papenburg to a bit down-estuary of Terborg. Between Terborg and Gandersum, SPM values drop rapidly but remain high at a few gram per litre. The pool of fluid/soft mud is entrained/mobilized at the onset of flood, yielding SPM values of many tens gram per litre. This suspension is transported up-estuary with the flood. Around high water slack, part of the suspension settles, being remixed during ebb, while migrating down-estuary, but likely not much further than Terborg. Around low water slack, a large fraction of the sediment settles, reforming the pool of fluid mud. The rapid entrainment from the fluid mud layer after low water slack is only possible when the peak flood velocity exceeds a critical value of around 1 m/s, i.e. when the stratified water column seems to become internally supercritical. If the peak flood velocity does not reach this critical value, f.i. during neap tide, fluid mud is not entrained up to the OBS sensors. Thus, it is not classical tidal asymmetry, but the peak flood velocity itself which governs the hyper-turbid state in the Lower Ems River. The crucial role of river flow and river floods is in reducing these peak flood velocities. During elongated periods of high river flow, in e.g. wintertime, SPM concentrations reduce, and the soft mud deposits consolidate and possibly become locally armoured as well by sand washed in from the river. We have no observations that sediments are washed out of the hyper-turbid zone. Down-estuary of Terborg, where SPM values do not reach hyper-turbid conditions, the SPM dynamics are governed by classical tidal asymmetry and estuarine circulation. Hence, nowhere in the river, sediments are flushed from the upper reaches of the river into the Ems-Dollard estuary during high river flow events. However, exchange of sediment between river and estuary should occur because of tide-induced dispersion.

Antecedents and Consequences of Supplier Performance Evaluation Efficacy

DTIC Science & Technology

2016-06-30

forming groups of high and low values. These tests are contingent on the reliable and valid measure of high and low rating inflation and high and...year)? Future research could deploy a SPM system as a test case on a limited set of transactions. Using a quasi-experimental design , comparisons...single source, common method bias must be of concern. Harmon’s one -factor test showed that when latent-indicator items were forced onto a single

New positive feedback mechanism between boundary layer meteorology and secondary aerosol formation during severe haze events.

PubMed

Liu, Quan; Jia, Xingcan; Quan, Jiannong; Li, Jiayun; Li, Xia; Wu, Yongxue; Chen, Dan; Wang, Zifa; Liu, Yangang

2018-04-17

Severe haze events during which particulate matter (PM) increases quickly from tens to hundreds of microgram per cubic meter in 1-2 days frequently occur in China. Although it has been known that PM is influenced by complex interplays among emissions, meteorology, and physical and chemical processes, specific mechanisms remain elusive. Here, a new positive feedback mechanism between planetary boundary layer (PBL), relative humidity (RH), and secondary PM (SPM) formation is proposed based on a comprehensive field experiment and model simulation. The decreased PBL associated with increased PM increases RH by weakening the vertical transport of water vapor; the increased RH in turn enhances the SPM formation through heterogeneous aqueous reactions, which further enhances PM, weakens solar radiation, and decreases PBL height. This positive feedback, together with the PM-Radiation-PBL feedback, constitutes a key mechanism that links PM, radiation, PBL properties (e.g. PBL height and RH), and SPM formation, This mechanism is self-amplifying, leading to faster PM production, accumulation, and more severe haze pollution.

Seasonal changes of polycyclic aromatic hydrocarbons in response to hydrology and anthropogenic activities in the Pearl River estuary, China.

PubMed

Liu, Feng; Niu, Lixia; Chen, Hui; Li, Ping; Tian, Feng; Yang, Qingshu

2017-04-15

The behaviours of PAHs (containing 2-6 aromatic rings) in the Pearl River estuary were examined each month in 2011. This study was designed to investigate the abundance of 16 priority PAHs and their response to the seasonal dynamics of anthropogenic activities and hydrological cycles. Monthly mean concentrations of ∑ 16 PAHs in water and suspended particulate matter (SPM) were 88.31ng/L and 252.31ng/L respectively, with higher concentrations in the wet season (April to September). Heavy precipitation in the wet season resulted in relatively increased PAH input via riverine discharges and atmospheric deposition. Seasonal variations in suspended sediment concentration (SSC), temperature and salinity have considerably affected the PAH phase association. Higher SSC in the wet season contributed to higher concentration of the PAHs in SPM, and higher temperature and lower salinity facilitated desorption from SPM. The PAH sources were largely attributed to vehicular emissions, coal combustion and coke ovens. Copyright © 2017 Elsevier Ltd. All rights reserved.

High sensitivity and high resolution element 3D analysis by a combined SIMS–SPM instrument

PubMed Central

Wirtz, Tom

2015-01-01

Summary Using the recently developed SIMS–SPM prototype, secondary ion mass spectrometry (SIMS) data was combined with topographical data from the scanning probe microscopy (SPM) module for five test structures in order to obtain accurate chemical 3D maps: a polystyrene/polyvinylpyrrolidone (PS/PVP) polymer blend, a nickel-based super-alloy, a titanium carbonitride-based cermet, a reticle test structure and Mg(OH)2 nanoclusters incorporated inside a polymer matrix. The examples illustrate the potential of this combined approach to track and eliminate artefacts related to inhomogeneities of the sputter rates (caused by samples containing various materials, different phases or having a non-flat surface) and inhomogeneities of the secondary ion extraction efficiencies due to local field distortions (caused by topography with high aspect ratios). In this respect, this paper presents the measured relative sputter rates between PVP and PS as well as in between the different phases of the TiCN cermet. PMID:26171285

Approaching total absorption of graphene strips using a c-Si subwavelength periodic membrane

NASA Astrophysics Data System (ADS)

Sang, Tian; Wang, Rui; Li, Junlang; Zhou, Jianyu; Wang, Yueke

2018-04-01

Approaching total absorption of graphene strips at near infrared using a crystalline-silicon (c-Si) subwavelength periodic membrane (SPM) is presented. The absorption in graphene strips in a c-Si SPM is enhanced by a resonant tip, which is resulted from the coupling between the guided mode and the radiation mode through symmetry breaking of the structure at near-normal incidence. The enhancement of the electric field intensity is increased 1939 times and the group velocity of light is decreased to 3.55 ×10-4c at resonance, and 99.3% absorption in graphene strips can be achieved by critical coupling at the incident angle of 2°. High absorption of the graphene strips can be maintained as the etching thickness, the strip width, and the period are altered. When this type of c-Si SPM with graphene strips is used in refractive index sensors, it shows excellent sensing properties due to its stable near-unity absorption.

Potential for heavy metal (copper and zinc) removal from contaminated marine sediments using microalgae and light emitting diodes

NASA Astrophysics Data System (ADS)

Kwon, Hyeong Kyu; Jeon, Jin Young; Oh, Seok Jin

2017-03-01

The effects of monochromatic (blue, yellow and red LED) and mixed wavelengths (fluorescent lamp) on the adsorption and absorption of Cu and Zn by Phaeodactylum tricornutum, Nitzschia sp., Skeletonema sp., and Chlorella vulgaris were investigated. In addition, we confirmed the potential of microalgae for phytoremediation of these heavy metals from contaminated marine sediment by using microcosm experiments that incorporated LEDs and semipermeable membrane (SPM) tube containing microalgae. Among the four microalgae, C. vulgaris grown under red LED exhibited the highest Cu and Zn removal with values of 17.5 × 10-15 g Cu/cell and 38.3 × 10-15 g Zn/cell, respectively. Thus, C. vulgaris could be a useful species for phytoremediation. In the microcosm experiments with SPM containing C. vulgaris, the highest Cu and Zn removal from sediment and interstitial water showed under red LED. Therefore, phytoremediation using LED and SPM tube containing microalgae could be utilized as an eco-friendly technique for remediating contaminated marine sediment.

Heavy metals in particulate and colloidal matter from atmospheric deposition of urban Guangzhou, South China.

PubMed

Huang, Wen; Duan, Dandan; Zhang, Yulong; Cheng, Hefa; Ran, Yong

2014-08-30

Suspended particulate matter (SPM) and colloidal matter (COM) in annual dry and wet deposition samples in urban Guangzhou were for the first time collected, and their trace metals were investigated by using inductively coupled plasma mass spectrometry (ICP-MS). The deposition flux of SPM and of metal elements varied largely among the investigated seasons, and reached the maximum in spring. The correlation analysis indicated that significant correlations existed among some of the metal elements in the deposition samples. The enrichment factors (EF) of metals in COM in the deposition ranging from 79.66 to 130,000 were much higher than those of SPM ranging from 1.65 to 286.48, indicating the important role of COM. The factor analysis showed that emissions from street dust, non-ferrous metal production, and heavy fuel oil were major sources of the trace metals. Positive matrix factorization (PMF) model was used to quantitatively estimate anthropogenic source. Copyright © 2013 Elsevier Ltd. All rights reserved.

Humidity Effect on Nanoscale Electrochemistry in Solid Silver Ion Conductors and the Dual Nature of Its Locality

DOE PAGES

Yang, Sangmo; Strelcov, Evgheni; Paranthaman, Mariappan Parans; ...

2015-01-07

Scanning probe microscopy (SPM) is a powerful tool to investigate electrochemistry in nanoscale volumes. While most SPM-based studies have focused on reactions at the tip-surface junction, charge and mass conservation requires coupled and intrinsically non-local cathodic and anodic processes that can be significantly affected by ambient humidity. Here, we explore the role of water in both cathodic and anodic processes, associated charge transport, and topographic volume changes depending on the polarity of tip bias. The first-order reversal curve current-voltage technique combined with simultaneous detection of the sample topography, referred to as FORC-IVz, was applied to a silver solid ion conductor.more » We found that the protons generated from water affect silver ionic conduction, silver particle formation and dissolution, and mechanical integrity of the material. This work highlights the dual nature (simultaneously local and non-local) of electrochemical SPM studies, which should be considered for comprehensive understanding of nanoscale electrochemistry.« less

Versatile variable temperature and magnetic field scanning probe microscope for advanced material research

NASA Astrophysics Data System (ADS)

Jung, Jin-Oh; Choi, Seokhwan; Lee, Yeonghoon; Kim, Jinwoo; Son, Donghyeon; Lee, Jhinhwan

2017-10-01

We have built a variable temperature scanning probe microscope (SPM) that covers 4.6 K-180 K and up to 7 T whose SPM head fits in a 52 mm bore magnet. It features a temperature-controlled sample stage thermally well isolated from the SPM body in good thermal contact with the liquid helium bath. It has a 7-sample-holder storage carousel at liquid helium temperature for systematic studies using multiple samples and field emission targets intended for spin-polarized spectroscopic-imaging scanning tunneling microscopy (STM) study on samples with various compositions and doping conditions. The system is equipped with a UHV sample preparation chamber and mounted on a two-stage vibration isolation system made of a heavy concrete block and a granite table on pneumatic vibration isolators. A quartz resonator (qPlus)-based non-contact atomic force microscope (AFM) sensor is used for simultaneous STM/AFM operation for research on samples with highly insulating properties such as strongly underdoped cuprates and strongly correlated electron systems.

Humidity effect on nanoscale electrochemistry in solid silver ion conductors and the dual nature of its locality.

PubMed

Yang, Sang Mo; Strelcov, Evgheni; Paranthaman, M Parans; Tselev, Alexander; Noh, Tae Won; Kalinin, Sergei V

2015-02-11

Scanning probe microscopy (SPM) is a powerful tool to investigate electrochemistry in nanoscale volumes. While most SPM-based studies have focused on reactions at the tip-surface junction, charge and mass conservation requires coupled and intrinsically nonlocal cathodic and anodic processes that can be significantly affected by ambient humidity. Here, we explore the role of water in both cathodic and anodic processes, associated charge transport, and topographic volume changes depending on the polarity of tip bias. The first-order reversal curve current-voltage technique combined with simultaneous detection of the sample topography, referred to as FORC-IVz, was applied to a silver solid ion conductor. We found that the protons generated from water affect silver ionic conduction, silver particle formation and dissolution, and mechanical integrity of the material. This work highlights the dual nature (simultaneously local and nonlocal) of electrochemical SPM studies, which should be considered for comprehensive understanding of nanoscale electrochemistry.

Multi-phase arrival tracking using tetrahedral cells within a 3D layered titled transversely isotropic anisotropic model involving undulating topography and irregular interfaces

NASA Astrophysics Data System (ADS)

Li, Xing-Wang; Bai, Chao-Ying; Yue, Xiao-Peng; Greenhalgh, Stewart

2018-02-01

To overcome a major problem in current ray tracing methods, which are only capable of tracing first arrivals, and occasionally primary reflections (or mode conversions) in regular cell models, we extend in this paper the multistage triangular shortest-path method (SPM) into 3D titled transversely isotropic (TTI) anisotropic media. The proposed method is capable of tracking multi-phase arrivals composed of any kind of combinations of transmissions, mode conversions and reflections. In model parameterization, five elastic parameters, plus two angles defining the titled axis of symmetry of TTI media are sampled at the primary nodes of the tetrahedral cell, and velocity value at secondary node positions are linked by a tri-linear velocity interpolation function to the primary node velocity value of that of a tetrahedral cell, from which the group velocities of the three wave modes (qP, qSV and qSH) are computed. The multistage triangular SPM is used to track multi-phase arrivals. The uniform anisotropic test indicates that the numerical solution agrees well with the analytic solution, thus verifying the accuracy of the methodology. Several simulations and comparison results for heterogeneous models show that the proposed algorithm is able to efficiently and accurately approximate undulating surface topography and irregular subsurface velocity discontinuities. It is suitable for any combination of multi-phase arrival tracking in arbitrary tilt angle TTI media and can accommodate any magnitude of anisotropy.

Methods for medical device and equipment procurement and prioritization within low- and middle-income countries: findings of a systematic literature review.

PubMed

Diaconu, Karin; Chen, Yen-Fu; Cummins, Carole; Jimenez Moyao, Gabriela; Manaseki-Holland, Semira; Lilford, Richard

2017-08-18

Forty to 70 % of medical devices and equipment in low- and middle-income countries are broken, unused or unfit for purpose; this impairs service delivery to patients and results in lost resources. Undiscerning procurement processes are at the heart of this issue. We conducted a systematic review of the literature to August 2013 with no time or language restrictions to identify what product selection or prioritization methods are recommended or used for medical device and equipment procurement planning within low- and middle-income countries. We explore the factors/evidence-base proposed for consideration within such methods and identify prioritization criteria. We included 217 documents (corresponding to 250 texts) in the narrative synthesis. Of these 111 featured in the meta-summary. We identify experience and needs-based methods used to reach procurement decisions. Equipment costs (including maintenance) and health needs are the dominant issues considered. Extracted data suggest that procurement officials should prioritize devices with low- and middle-income country appropriate technical specifications - i.e. devices and equipment that can be used given available human resources, infrastructure and maintenance capacity. Suboptimal device use is directly linked to incomplete costing and inadequate consideration of maintenance services and user training during procurement planning. Accurate estimation of life-cycle costing and careful consideration of device servicing are of crucial importance.

Dancing with the Tides: Fluctuations of Coastal Phytoplankton Orchestrated by Different Oscillatory Modes of the Tidal Cycle

PubMed Central

Blauw, Anouk N.; Benincà, Elisa; Laane, Remi W. P. M.; Greenwood, Naomi; Huisman, Jef

2012-01-01

Population fluctuations are often driven by an interplay between intrinsic population processes and extrinsic environmental forcing. To investigate this interplay, we analyzed fluctuations in coastal phytoplankton concentration in relation to the tidal cycle. Time series of chlorophyll fluorescence, suspended particulate matter (SPM), salinity and temperature were obtained from an automated measuring platform in the southern North Sea, covering 9 years of data at a resolution of 12 to 30 minutes. Wavelet analysis showed that chlorophyll fluctuations were dominated by periodicities of 6 hours 12 min, 12 hours 25 min, 24 hours and 15 days, which correspond to the typical periodicities of tidal current speeds, the semidiurnal tidal cycle, the day-night cycle, and the spring-neap tidal cycle, respectively. During most of the year, chlorophyll and SPM fluctuated in phase with tidal current speed, indicative of alternating periods of sinking and vertical mixing of algal cells and SPM driven by the tidal cycle. Spring blooms slowly built up over several spring-neap tidal cycles, and subsequently expanded in late spring when a strong decline of the SPM concentration during neap tide enabled a temporary “escape” of the chlorophyll concentration from the tidal mixing regime. Our results demonstrate that the tidal cycle is a major determinant of phytoplankton fluctuations at several different time scales. These findings imply that high-resolution monitoring programs are essential to capture the natural variability of phytoplankton in coastal waters. PMID:23166639

Dancing with the tides: fluctuations of coastal phytoplankton orchestrated by different oscillatory modes of the tidal cycle.

PubMed

Blauw, Anouk N; Benincà, Elisa; Laane, Remi W P M; Greenwood, Naomi; Huisman, Jef

2012-01-01

Population fluctuations are often driven by an interplay between intrinsic population processes and extrinsic environmental forcing. To investigate this interplay, we analyzed fluctuations in coastal phytoplankton concentration in relation to the tidal cycle. Time series of chlorophyll fluorescence, suspended particulate matter (SPM), salinity and temperature were obtained from an automated measuring platform in the southern North Sea, covering 9 years of data at a resolution of 12 to 30 minutes. Wavelet analysis showed that chlorophyll fluctuations were dominated by periodicities of 6 hours 12 min, 12 hours 25 min, 24 hours and 15 days, which correspond to the typical periodicities of tidal current speeds, the semidiurnal tidal cycle, the day-night cycle, and the spring-neap tidal cycle, respectively. During most of the year, chlorophyll and SPM fluctuated in phase with tidal current speed, indicative of alternating periods of sinking and vertical mixing of algal cells and SPM driven by the tidal cycle. Spring blooms slowly built up over several spring-neap tidal cycles, and subsequently expanded in late spring when a strong decline of the SPM concentration during neap tide enabled a temporary "escape" of the chlorophyll concentration from the tidal mixing regime. Our results demonstrate that the tidal cycle is a major determinant of phytoplankton fluctuations at several different time scales. These findings imply that high-resolution monitoring programs are essential to capture the natural variability of phytoplankton in coastal waters.

fMRat: an extension of SPM for a fully automatic analysis of rodent brain functional magnetic resonance series.

PubMed

Chavarrías, Cristina; García-Vázquez, Verónica; Alemán-Gómez, Yasser; Montesinos, Paula; Pascau, Javier; Desco, Manuel

2016-05-01

The purpose of this study was to develop a multi-platform automatic software tool for full processing of fMRI rodent studies. Existing tools require the usage of several different plug-ins, a significant user interaction and/or programming skills. Based on a user-friendly interface, the tool provides statistical parametric brain maps (t and Z) and percentage of signal change for user-provided regions of interest. The tool is coded in MATLAB (MathWorks(®)) and implemented as a plug-in for SPM (Statistical Parametric Mapping, the Wellcome Trust Centre for Neuroimaging). The automatic pipeline loads default parameters that are appropriate for preclinical studies and processes multiple subjects in batch mode (from images in either Nifti or raw Bruker format). In advanced mode, all processing steps can be selected or deselected and executed independently. Processing parameters and workflow were optimized for rat studies and assessed using 460 male-rat fMRI series on which we tested five smoothing kernel sizes and three different hemodynamic models. A smoothing kernel of FWHM = 1.2 mm (four times the voxel size) yielded the highest t values at the somatosensorial primary cortex, and a boxcar response function provided the lowest residual variance after fitting. fMRat offers the features of a thorough SPM-based analysis combined with the functionality of several SPM extensions in a single automatic pipeline with a user-friendly interface. The code and sample images can be downloaded from https://github.com/HGGM-LIM/fmrat .

Scuba: scalable kernel-based gene prioritization.

PubMed

Zampieri, Guido; Tran, Dinh Van; Donini, Michele; Navarin, Nicolò; Aiolli, Fabio; Sperduti, Alessandro; Valle, Giorgio

2018-01-25

The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can help to cope with these problems. In particular, kernel-based methods are a powerful resource for the integration of heterogeneous biological knowledge, however, their practical implementation is often precluded by their limited scalability. We propose Scuba, a scalable kernel-based method for gene prioritization. It implements a novel multiple kernel learning approach, based on a semi-supervised perspective and on the optimization of the margin distribution. Scuba is optimized to cope with strongly unbalanced settings where known disease genes are few and large scale predictions are required. Importantly, it is able to efficiently deal both with a large amount of candidate genes and with an arbitrary number of data sources. As a direct consequence of scalability, Scuba integrates also a new efficient strategy to select optimal kernel parameters for each data source. We performed cross-validation experiments and simulated a realistic usage setting, showing that Scuba outperforms a wide range of state-of-the-art methods. Scuba achieves state-of-the-art performance and has enhanced scalability compared to existing kernel-based approaches for genomic data. This method can be useful to prioritize candidate genes, particularly when their number is large or when input data is highly heterogeneous. The code is freely available at https://github.com/gzampieri/Scuba .

A PROCESS OF PRIORITIZING TOPICS FOR HEALTH TECHNOLOGY ASSESSMENT IN KAZAKHSTAN.

PubMed

Kosherbayeva, Lyazzat; Hailey, David; Kurakbaev, Kural; Tabarov, Adlet; Kumar, Ainur; Gutzskaya, Gulnara; Stepkina, Elena

2016-01-01

The aim of this study was to develop criteria for the prioritization of topics for health technology assessment (HTA) in the healthcare system of Kazakhstan. Initial proposals for criteria were suggested through consultation with Ministry of Health (MoH) policy areas. These were refined through a workshop attended by HTA department staff, persons from medical universities and research institutes, and MoH policy makers. The workshop included discussion on methods used in international HTA practice. Opinions of participants on selection of criteria from those specified in a review of prioritization processes were used to define a list for inclusion in an instrument for routine use. A scoring system was established in later discussion. Selected criteria for HTA prioritization were burden of disease, availability of alternative technology, clinical effectiveness, economic efficiency, budget impact, and ethical, legal, and/or psychosocial aspects. For each criterion, a health technology under consideration is given a score from 3 (High) to 1 (Low). The total score determines whether the technology is of high to medium priority or of low priority. Determination of priorities for assessment, using the instrument, should be carried out by an expert group appointed by the MoH. The process was applied in 2014 to a selection of topics, and three health technologies were chosen for full assessments. Criteria for prioritization have evolved with development of the HTA program in Kazakhstan. A method for HTA prioritization has been developed that is easy to apply, requires comparatively few resources, and is compatible with processes required by the MoH.

How Do Teachers Prioritize the Adoption of Technology in the Classroom?

ERIC Educational Resources Information Center

Kurt, Serhat

2012-01-01

This study examined whether teachers prioritize the use of technology. More specifically, this paper focused on how Turkish teachers think about the importance of technology and technological tools for their daily routines. The research design employed both qualitative and quantitative methods. The data were collected through document analyses,…

TOXCAST, A TOOL FOR CATEGORIZATION AND PRIORITIZATION OF CHEMICAL HAZARD BASED ON MULTI-DIMENSIONAL INFORMATION DOMAINS

EPA Science Inventory

Across several EPA Program Offices (e.g., OPPTS, OW, OAR), there is a clear need to develop strategies and methods to screen large numbers of chemicals for potential toxicity, and to use the resulting information to prioritize the use of testing resources towards those entities a...

Prioritizing Sites for Protection and Restoration for Grizzly Bears (Ursus arctos) in Southwestern Alberta, Canada.

PubMed

Braid, Andrew C R; Nielsen, Scott E

2015-01-01

As the influence of human activities on natural systems continues to expand, there is a growing need to prioritize not only pristine sites for protection, but also degraded sites for restoration. We present an approach for simultaneously prioritizing sites for protection and restoration that considers landscape patterns for a threatened population of grizzly bears (Ursus arctos) in southwestern Alberta, Canada. We considered tradeoffs between bottom-up (food resource supply) and top-down (mortality risk from roads) factors affecting seasonal habitat quality for bears. Simulated annealing was used to prioritize source-like sites (high habitat productivity, low mortality risk) for protection, as well as sink-like sites (high habitat productivity, high mortality risk) for restoration. Priority source-like habitats identified key conservation areas where future developments should be limited, whereas priority sink-like habitats identified key areas for mitigating road-related mortality risk with access management. Systematic conservation planning methods can be used to complement traditional habitat-based methods for individual focal species by identifying habitats where conservation actions (both protection and restoration) have the highest potential utility.

Chapter 15: Disease Gene Prioritization

PubMed Central

Bromberg, Yana

2013-01-01

Disease-causing aberrations in the normal function of a gene define that gene as a disease gene. Proving a causal link between a gene and a disease experimentally is expensive and time-consuming. Comprehensive prioritization of candidate genes prior to experimental testing drastically reduces the associated costs. Computational gene prioritization is based on various pieces of correlative evidence that associate each gene with the given disease and suggest possible causal links. A fair amount of this evidence comes from high-throughput experimentation. Thus, well-developed methods are necessary to reliably deal with the quantity of information at hand. Existing gene prioritization techniques already significantly improve the outcomes of targeted experimental studies. Faster and more reliable techniques that account for novel data types are necessary for the development of new diagnostics, treatments, and cure for many diseases. PMID:23633938

Informing watershed connectivity barrier prioritization decisions: A synthesis

USGS Publications Warehouse

McKay, S. K.; Cooper, A. R.; Diebel, M.W.; Elkins, D.; Oldford, G.; Roghair, C.; Wieferich, Daniel J.

2017-01-01

Water resources and transportation infrastructure such as dams and culverts provide countless socio-economic benefits; however, this infrastructure can also disconnect the movement of organisms, sediment, and water through river ecosystems. Trade-offs associated with these competing costs and benefits occur globally, with applications in barrier addition (e.g. dam and road construction), reengineering (e.g. culvert repair), and removal (e.g. dam removal and aging infrastructure). Barrier prioritization provides a unique opportunity to: (i) restore and reconnect potentially large habitat patches quickly and effectively and (ii) avoid impacts prior to occurrence in line with the mitigation hierarchy (i.e. avoid then minimize then mitigate). This paper synthesizes 46 watershed-scale barrier planning studies and presents a procedure to guide barrier prioritization associated with connectivity for aquatic organisms. We focus on practical issues informing prioritization studies such as available data sets, methods, techniques, and tools. We conclude with a discussion of emerging trends and issues in barrier prioritization and key opportunities for enhancing the body of knowledge.

The dependence of estuarine turbidity on tidal intrusion length, tidal range and residence time

USGS Publications Warehouse

Uncles, R.J.; Stephens, J.A.; Smith, R.E.

2002-01-01

It is shown that there is a marked tendency for long, strongly tidal estuaries to have greater suspended particulate matter (SPM) concentrations within their high-turbidity regions than shorter estuaries with comparable tidal ranges at their mouths, or weakly tidal estuaries. Using consistently derived data from 44 estuaries in Europe and the Americas, contours of the logarithm of maximum estuarine SPM concentration are shown to be reasonably smooth when plotted against the logarithm of mean spring tidal range (at the estuary mouth) and the logarithm of estuarine tidal length. Predictions from the plot are compared with published observations made in the Delaware, Scheldt, Rio de la Plata, Gironde, Bay of Fundy, Changjiang (Yangtze), Amazon, Paros Lagoon and the Hawkesbury Estuary and it is shown that, qualitatively, there are no serious discrepancies. Short, weakly tidal estuaries are predicted to have very low 'intrinsic' SPM concentrations. High SPM concentrations in these estuaries would most likely be the result of either locally generated wave resuspension, high freshwater sediment loads due to freshets, or intruding seawater carrying suspended sediments derived from wave activity in the coastal zone. Application of a generic tidal model demonstrates that longer estuaries possess faster tidal currents for a given tidal range at their mouth and, in the presence of a supply of erodable fine sediment, therefore (by implication) produce greater concentrations of SPM that can be accumulated within a turbidity maximum. The same is true if the tidal range is increased for estuaries of a given length. These features are illustrated by comparing surveys of SPM data from two large estuaries possessing greatly different tidal ranges (the microtidal, medium turbidity Potomac and the macrotidal, highly turbid Humber-Ouse) and a third, much smaller but strongly tidal estuary (the low-turbidity Tweed). It is demonstrated that longer estuaries tend to have longer flushing times for solutes than shorter systems and that larger tides tend to reduce flushing times, although the tidal influence is secondary. Short, rapidly flushed estuaries quickly lose their erodable fine sediment to the coastal zone during freshets and during the ebbing currents of spring tides. Turbidity is therefore small during low runoff, low wave activity conditions. Very long, very slowly flushed estuaries are unlikely to lose a significant fraction of their resuspended sediments during freshets or individual ebb tides and are therefore able to accumulate large and increasing amounts of fine sediment in the long-term. Turbidity within them is therefore high during the fast currents of large spring tides. ?? 2002 Elsevier Science Ltd. All rights reserved.

The dependence of estuarine turbidity on tidal intrusion length, tidal range and residence time

USGS Publications Warehouse

Uncles, R.J.; Stephens, J.A.; Smith, R.E.

2002-01-01

It is shown that there is a marked tendency for long, strongly tidal estuaries to have greater suspended particulate matter (SPM) concentrations within their high-turbidity regions than shorter estuaries with comparable tidal ranges at their mouths, or weakly tidal estuaries. Using consistently derived data from 44 estuaries in Europe and the Americas, contours of the logarithm of maximum estuarine SPM concentration are shown to be reasonably smooth when plotted against the logarithm of mean spring tidal range (at the estuary mouth) and the logarithm of estuarine tidal length. Predictions from the plot are compared with published observations made in the Delaware, Scheldt, Rio de la Plata, Gironde, Bay of Fundy, Changjiang (Yangtze), Amazon, Patos Lagoon and the Hawkesbury Estuary and it is shown that, qualitatively, there are no serious discrepancies. Short, weakly tidal estuaries are predicted to have very low ‘intrinsic’ SPM concentrations. High SPM concentrations in these estuaries would most likely be the result of either locally generated wave resuspension, high freshwater sediment loads due to freshets, or intruding seawater carrying suspended sediments derived from wave activity in the coastal zone. Application of a generic tidal model demonstrates that longer estuaries possess faster tidal currents for a given tidal range at their mouth and, in the presence of a supply of erodable fine sediment, therefore (by implication) produce greater concentrations of SPM that can be accumulated within a turbidity maximum. The same is true if the tidal range is increased for estuaries of a given length. These features are illustrated by comparing surveys of SPM data from two large estuaries possessing greatly different tidal ranges (the microtidal, medium turbidity Potomac and the macrotidal, highly turbid Humber-Ouse) and a third, much smaller but strongly tidal estuary (the low-turbidity Tweed). It is demonstrated that longer estuaries tend to have longer flushing times for solutes than shorter systems and that larger tides tend to reduce flushing times, although the tidal influence is secondary. Short, rapidly flushed estuaries quickly lose their erodable fine sediment to the coastal zone during freshets and during the ebbing currents of spring tides. Turbidity is therefore small during low runoff, low wave activity conditions. Very long, very slowly flushed estuaries are unlikely to lose a significant fraction of their resuspended sediments during freshets or individual ebb tides and are therefore able to accumulate large and increasing amounts of fine sediment in the long-term. Turbidity within them is therefore high during the fast currents of large spring tides.

Using VIIRS/NPP and MODIS/Aqua data to provide a continuous record of suspended particulate matter in a highly turbid inland lake

NASA Astrophysics Data System (ADS)

Cao, Zhigang; Duan, Hongtao; Shen, Ming; Ma, Ronghua; Xue, Kun; Liu, Dong; Xiao, Qitao

2018-02-01

Inland lakes are generally an important source of drinking water, and information on their water quality needs to be obtained in real time. To date, Moderate-resolution imaging spectroradiometer (MODIS) data have played a critical, effective and long-term role in fulfilling this function. However, the MODIS instruments on board both the Terra and Aqua satellites have operated beyond their designed five-year mission lifespans (Terra was launched in 1999, whereas Aqua was launched in 2002), and these instruments may stop running at any time in the near future. The Visible Infrared Imager Radiometer Suite (VIIRS) on board the Suomi National Polar-Orbiting Partnership (Suomi NPP, which was launched in Oct 2011) is expected to provide a consistent, long-term data record and continue the series of observations initiated by MODIS. To date, few evaluations of the consistency between VIIRS and MODIS have been conducted for turbid inland waters. In this study, we first used synchronous MODIS/Aqua and VIIRS/NPP data (±1 h) collected during 2012-2015 to evaluate the consistency of Rayleigh-corrected reflectance (Rrc) observations over Lake Hongze (the fourth-largest freshwater lake in China), since accurate remote sensing reflectance (Rrs) values cannot be acquired over turbid inland waters. Second, we used recently developed algorithms based on Rrc in the red band to estimate the concentrations of suspended particulate matter (SPM) from MODIS/Aqua and VIIRS/NPP data. Finally, we assessed the consistency of the SPM products derived from MODIS/Aqua and VIIRS/NPP. The results show the following. (1) The differences in Rrc among the green (VIIRS 551 nm and MODIS 555 nm) and red bands (VIIRS 671 nm and MODIS 645 nm) indicate a satisfactory consistency, and the unbiased percentage difference (UPD) is <12%. Meanwhile, the results for the near infrared (NIR) band (MODIS 859 nm and VIIRS 862 nm) indicate relatively large differences (UPD = 21.84%). (2) The satellite-derived SPM products obtained using MODIS/Aqua and VIIRS/NPP have a satisfactory degree of consistency (0-150 mg/L SPM: R2 = 0.81, UPD < 16% and 0-80 mg/L SPM: R2 = 0.85, UPD < 12%, respectively). These results demonstrate that VIIRS/NPP can continue to record the SPM observations initiated by MODIS/Aqua for turbid inland waters and establish environmental datasets over long time periods to support water quality management endeavors.

Using model-based screening to help discover unknown environmental contaminants.

PubMed

McLachlan, Michael S; Kierkegaard, Amelie; Radke, Michael; Sobek, Anna; Malmvärn, Anna; Alsberg, Tomas; Arnot, Jon A; Brown, Trevor N; Wania, Frank; Breivik, Knut; Xu, Shihe

2014-07-01

Of the tens of thousands of chemicals in use, only a small fraction have been analyzed in environmental samples. To effectively identify environmental contaminants, methods to prioritize chemicals for analytical method development are required. We used a high-throughput model of chemical emissions, fate, and bioaccumulation to identify chemicals likely to have high concentrations in specific environmental media, and we prioritized these for target analysis. This model-based screening was applied to 215 organosilicon chemicals culled from industrial chemical production statistics. The model-based screening prioritized several recognized organosilicon contaminants and generated hypotheses leading to the selection of three chemicals that have not previously been identified as potential environmental contaminants for target analysis. Trace analytical methods were developed, and the chemicals were analyzed in air, sewage sludge, and sediment. All three substances were found to be environmental contaminants. Phenyl-tris(trimethylsiloxy)silane was present in all samples analyzed, with concentrations of ∼50 pg m(-3) in Stockholm air and ∼0.5 ng g(-1) dw in sediment from the Stockholm archipelago. Tris(trifluoropropyl)trimethyl-cyclotrisiloxane and tetrakis(trifluoropropyl)tetramethyl-cyclotetrasiloxane were found in sediments from Lake Mjøsa at ∼1 ng g(-1) dw. The discovery of three novel environmental contaminants shows that models can be useful for prioritizing chemicals for exploratory assessment.

Smoking Gun or Circumstantial Evidence? Comparison of Statistical Learning Methods using Functional Annotations for Prioritizing Risk Variants.

PubMed

Gagliano, Sarah A; Ravji, Reena; Barnes, Michael R; Weale, Michael E; Knight, Jo

2015-08-24

Although technology has triumphed in facilitating routine genome sequencing, new challenges have been created for the data-analyst. Genome-scale surveys of human variation generate volumes of data that far exceed capabilities for laboratory characterization. By incorporating functional annotations as predictors, statistical learning has been widely investigated for prioritizing genetic variants likely to be associated with complex disease. We compared three published prioritization procedures, which use different statistical learning algorithms and different predictors with regard to the quantity, type and coding. We also explored different combinations of algorithm and annotation set. As an application, we tested which methodology performed best for prioritizing variants using data from a large schizophrenia meta-analysis by the Psychiatric Genomics Consortium. Results suggest that all methods have considerable (and similar) predictive accuracies (AUCs 0.64-0.71) in test set data, but there is more variability in the application to the schizophrenia GWAS. In conclusion, a variety of algorithms and annotations seem to have a similar potential to effectively enrich true risk variants in genome-scale datasets, however none offer more than incremental improvement in prediction. We discuss how methods might be evolved for risk variant prediction to address the impending bottleneck of the new generation of genome re-sequencing studies.

A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis

PubMed Central

2011-01-01

Background Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches - the examination of similarities to known disease genes and/or the evaluation of functional annotation of genes. Each of these approaches has its own caveats. Here we employ a previously described method of candidate gene prioritization based mainly on gene annotation, in accompaniment with a technique based on the evaluation of pertinent sequence motifs or signatures, in an attempt to refine the gene prioritization approach. We apply this approach to X-linked mental retardation (XLMR), a group of heterogeneous disorders for which some of the underlying genetics is known. Results The gene annotation-based binary filtering method yielded a ranked list of putative XLMR candidate genes with good plausibility of being associated with the development of mental retardation. In parallel, a motif finding approach based on linear discriminatory analysis (LDA) was employed to identify short sequence patterns that may discriminate XLMR from non-XLMR genes. High rates (>80%) of correct classification was achieved, suggesting that the identification of these motifs effectively captures genomic signals associated with XLMR vs. non-XLMR genes. The computational tools developed for the motif-based LDA is integrated into the freely available genomic analysis portal Galaxy (http://main.g2.bx.psu.edu/). Nine genes (APLN, ZC4H2, MAGED4, MAGED4B, RAP2C, FAM156A, FAM156B, TBL1X, and UXT) were highlighted as highly-ranked XLMR methods. Conclusions The combination of gene annotation information and sequence motif-orientated computational candidate gene prediction methods highlight an added benefit in generating a list of plausible candidate genes, as has been demonstrated for XLMR. Reviewers: This article was reviewed by Dr Barbara Bardoni (nominated by Prof Juergen Brosius); Prof Neil Smalheiser and Dr Dustin Holloway (nominated by Prof Charles DeLisi). PMID:21668950

Prioritizing Scientific Data for Transmission

NASA Technical Reports Server (NTRS)

Castano, Rebecca; Anderson, Robert; Estlin, Tara; DeCoste, Dennis; Gaines, Daniel; Mazzoni, Dominic; Fisher, Forest; Judd, Michele

2004-01-01

A software system has been developed for prioritizing newly acquired geological data onboard a planetary rover. The system has been designed to enable efficient use of limited communication resources by transmitting the data likely to have the most scientific value. This software operates onboard a rover by analyzing collected data, identifying potential scientific targets, and then using that information to prioritize data for transmission to Earth. Currently, the system is focused on the analysis of acquired images, although the general techniques are applicable to a wide range of data modalities. Image prioritization is performed using two main steps. In the first step, the software detects features of interest from each image. In its current application, the system is focused on visual properties of rocks. Thus, rocks are located in each image and rock properties, such as shape, texture, and albedo, are extracted from the identified rocks. In the second step, the features extracted from a group of images are used to prioritize the images using three different methods: (1) identification of key target signature (finding specific rock features the scientist has identified as important), (2) novelty detection (finding rocks we haven t seen before), and (3) representative rock sampling (finding the most average sample of each rock type). These methods use techniques such as K-means unsupervised clustering and a discrimination-based kernel classifier to rank images based on their interest level.

GUIELOA: Adaptive Optics System for the 2.1-m SPM UNAM Telescope

NASA Astrophysics Data System (ADS)

Cuevas, S.; Iriarte, A.; Martínez, L. A.; Garfias, F.; Sánchez, L.; Chapa, O.; Ruelas, R. A.

2004-08-01

GUIELOA is the adaptive optics system project for the 2.1-m SPM telescope. This is a 19 sub-apertures curvature-type system. It corrects 8 Zernike terms. GUIELOA is very similar to PUEO, the CFHT adaptive optics system and compensates the atmospheric turbulence from the R band to the K band. Among the planned applications of GUIELOA are the study of OB binary systems, the detection of close binary stars, and the study of disks, jets and other phenomena associated with young stars.

Prioritization of Companion Animal Transmissible Diseases for Policy Intervention in Europe.

PubMed

Cito, F; Rijks, J; Rantsios, A T; Cunningham, A A; Baneth, G; Guardabassi, L; Kuiken, T; Giovannini, A

2016-07-01

A number of papers have been published on the prioritization of transmissible diseases in farm animals and wildlife, based either on semiquantitative or truly quantitative methods, but there is no published literature on the prioritization of transmissible diseases in companion animals. In this study, available epidemiological data for diseases transmissible from companion animals to man were analysed with the aim of developing a procedure suitable for their prioritization within a European framework. A new method and its associated questionnaire and scoring system were designed based on methods described by the World Organisation for Animal Health (OIE). Modifications were applied to allow for the paucity of specific information on companion animal transmissible diseases. The OIE method was also adapted to the subject and to the regional scope of the interprofessional network addressing zoonotic diseases transmitted via companion animals in Europe: the Companion Animals multisectoriaL interprofessionaL Interdisciplinary Strategic Think tank On zoonoses (CALLISTO). Adaptations were made based on information collected from expert groups on viral, bacterial and parasitic diseases using a structured questionnaire, in which all questions were closed-ended. The expert groups were asked to select the most appropriate answer for each question taking into account the relevance and reliability of the data available in the scientific literature. Subsequently, the scoring of the answers obtained for each disease covered by the questionnaire was analysed to obtain two final overall scores, one for human health impact and one for agricultural economic impact. The adapted method was then applied to select the 15 most important pathogens (five for each pathogen group: viral, bacterial and parasitic) on the basis of their overall impact on public health and agriculture. The result of the prioritization exercise was a joint priority list (available at www.callistoproject.eu) of relevant pathogens according to these two criteria. As the scope of CALLISTO was comprehensive in terms of geographical area, animal species involved and impact of the diseases, the list of prioritized diseases had to accommodate the realities in different European countries and the differences in biology and animal-human relationships in a wide range of species including cats and dogs, pet pigs and sheep as well as captive reptiles. The methodology presented in this paper can be used to generate accurate priority lists according to narrower and more specific objectives. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Prioritizing preferable locations for increasing urban tree canopy in New York City

Treesearch

Dexter Locke; J. Morgan Grove; Jacqueline W.T. Lu; Austin Troy; Jarlath P.M. O' Neil-Dunne; Brian Beck

2010-01-01

This paper presents a set of Geographic Information System (GIS) methods for identifying and prioritizing tree planting sites in urban environments. It uses an analytical approach created by a University of Vermont service-learning class called "GIS Analysis of New York City's Ecology" that was designed to provide research support to the MillionTreesNYC...

An SPM8-based approach for attenuation correction combining segmentation and nonrigid template formation: application to simultaneous PET/MR brain imaging.

PubMed

Izquierdo-Garcia, David; Hansen, Adam E; Förster, Stefan; Benoit, Didier; Schachoff, Sylvia; Fürst, Sebastian; Chen, Kevin T; Chonde, Daniel B; Catana, Ciprian

2014-11-01

We present an approach for head MR-based attenuation correction (AC) based on the Statistical Parametric Mapping 8 (SPM8) software, which combines segmentation- and atlas-based features to provide a robust technique to generate attenuation maps (μ maps) from MR data in integrated PET/MR scanners. Coregistered anatomic MR and CT images of 15 glioblastoma subjects were used to generate the templates. The MR images from these subjects were first segmented into 6 tissue classes (gray matter, white matter, cerebrospinal fluid, bone, soft tissue, and air), which were then nonrigidly coregistered using a diffeomorphic approach. A similar procedure was used to coregister the anatomic MR data for a new subject to the template. Finally, the CT-like images obtained by applying the inverse transformations were converted to linear attenuation coefficients to be used for AC of PET data. The method was validated on 16 new subjects with brain tumors (n = 12) or mild cognitive impairment (n = 4) who underwent CT and PET/MR scans. The μ maps and corresponding reconstructed PET images were compared with those obtained using the gold standard CT-based approach and the Dixon-based method available on the Biograph mMR scanner. Relative change (RC) images were generated in each case, and voxel- and region-of-interest-based analyses were performed. The leave-one-out cross-validation analysis of the data from the 15 atlas-generation subjects showed small errors in brain linear attenuation coefficients (RC, 1.38% ± 4.52%) compared with the gold standard. Similar results (RC, 1.86% ± 4.06%) were obtained from the analysis of the atlas-validation datasets. The voxel- and region-of-interest-based analysis of the corresponding reconstructed PET images revealed quantification errors of 3.87% ± 5.0% and 2.74% ± 2.28%, respectively. The Dixon-based method performed substantially worse (the mean RC values were 13.0% ± 10.25% and 9.38% ± 4.97%, respectively). Areas closer to the skull showed the largest improvement. We have presented an SPM8-based approach for deriving the head μ map from MR data to be used for PET AC in integrated PET/MR scanners. Its implementation is straightforward and requires only the morphologic data acquired with a single MR sequence. The method is accurate and robust, combining the strengths of both segmentation- and atlas-based approaches while minimizing their drawbacks. © 2014 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Determining procedures for simulation-based training in radiology: a nationwide needs assessment.

PubMed

Nayahangan, Leizl Joy; Nielsen, Kristina Rue; Albrecht-Beste, Elisabeth; Bachmann Nielsen, Michael; Paltved, Charlotte; Lindorff-Larsen, Karen Gilboe; Nielsen, Bjørn Ulrik; Konge, Lars

2018-06-01

New training modalities such as simulation are widely accepted in radiology; however, development of effective simulation-based training programs is challenging. They are often unstructured and based on convenience or coincidence. The study objective was to perform a nationwide needs assessment to identify and prioritize technical procedures that should be included in a simulation-based curriculum. A needs assessment using the Delphi method was completed among 91 key leaders in radiology. Round 1 identified technical procedures that radiologists should learn. Round 2 explored frequency of procedure, number of radiologists performing the procedure, risk and/or discomfort for patients, and feasibility for simulation. Round 3 was elimination and prioritization of procedures. Response rates were 67 %, 70 % and 66 %, respectively. In Round 1, 22 technical procedures were included. Round 2 resulted in pre-prioritization of procedures. In round 3, 13 procedures were included in the final prioritized list. The three highly prioritized procedures were ultrasound-guided (US) histological biopsy and fine-needle aspiration, US-guided needle puncture and catheter drainage, and basic abdominal ultrasound. A needs assessment identified and prioritized 13 technical procedures to include in a simulation-based curriculum. The list may be used as guide for development of training programs. • Simulation-based training can supplement training on patients in radiology. • Development of simulation-based training should follow a structured approach. • The CAMES Needs Assessment Formula explores needs for simulation training. • A national Delphi study identified and prioritized procedures suitable for simulation training. • The prioritized list serves as guide for development of courses in radiology.

A method to assess the population-level consequences of wind energy facilities on bird and bat species: Chapter

USGS Publications Warehouse

Diffendorfer, James E.; Beston, Julie A.; Merrill, Matthew; Stanton, Jessica C.; Corum, Margo D.; Loss, Scott R.; Thogmartin, Wayne E.; Johnson, Douglas H.; Erickson, Richard A.; Heist, Kevin W.

2016-01-01

For this study, a methodology was developed for assessing impacts of wind energy generation on populations of birds and bats at regional to national scales. The approach combines existing methods in applied ecology for prioritizing species in terms of their potential risk from wind energy facilities and estimating impacts of fatalities on population status and trend caused by collisions with wind energy infrastructure. Methods include a qualitative prioritization approach, demographic models, and potential biological removal. The approach can be used to prioritize species in need of more thorough study as well as to identify species with minimal risk. However, the components of this methodology require simplifying assumptions and the data required may be unavailable or of poor quality for some species. These issues should be carefully considered before using the methodology. The approach will increase in value as more data become available and will broaden the understanding of anthropogenic sources of mortality on bird and bat populations.

Use of Zn isotopes as a probe of anthropogenic contamination and biogeochemical processes in the Seine River, France

NASA Astrophysics Data System (ADS)

Chen, J.; Gaillardet, J.; Louvat, P.; Birck, J.

2009-05-01

Metal contamination is a major issue of human impact on the aqueous environment. River water is particularly susceptible to contamination for both dissolved and particulate loads, displaying a major challenge in understanding the dominant sources and pathways of metals in polluted drainage basins. Recent improvements in mass spectrometry allow isotopic measurements of "non-traditional" metals (Zn, Cu, Fe, etc.), making their isotopes a new potential device to investigate contamination of metals under dissolved and particulate forms in rivers. We focus here on Zn isotope geochemistry in the largely anthropized Seine River (France). A new protocol of two-column separation of Zn from dilute aqueous solution has been developed and proven to be reproducible and satisfactory for accurate measurement of Zn isotopic ratios in water samples by MC-ICP-MS (2σ = 0.04‰). Preliminary results show a total variation of 0.65‰ for δ66Zn in dissolved phases of the Seine basin, and a light isotope enrichment in anthropogenic sources compared to other water samples. The determined conservative behavior of Zn in river water makes its isotopes an effective probe of anthropogenic contamination. The natural and anthropogenic inputs were clearly identified and calculated based on Zn isotope compositions for dissolved loads. Suspended particular matters (SPM) display different Zn isotope compositions compared to dissolved loads, with a total δ66Zn variation of 0.22‰. Zn concentrations and its isotope compositions in SPM reveal inverse relationships as function of the distance from the headwater and the SPM content for geographical and temporal samples, respectively. The δ66Zn data in SPM are interpreted as reflecting the mixture of natural and anthropogenic particles. The correlation between dissolved and particulate δ66Zn shows that adsorption processes are not the dominant process making Zn enrichment in SPM. We report here for the first time systematic δ66Zn data in waters of a whole river basin, showing Zn isotopes a powerful probe to trace contamination sources and biogeochemical processes in hydrologic systems.

A sequential vesicle pool model with a single release sensor and a Ca(2+)-dependent priming catalyst effectively explains Ca(2+)-dependent properties of neurosecretion.

PubMed

Walter, Alexander M; Pinheiro, Paulo S; Verhage, Matthijs; Sørensen, Jakob B

2013-01-01

Neurotransmitter release depends on the fusion of secretory vesicles with the plasma membrane and the release of their contents. The final fusion step displays higher-order Ca(2+) dependence, but also upstream steps depend on Ca(2+). After deletion of the Ca(2+) sensor for fast release - synaptotagmin-1 - slower Ca(2+)-dependent release components persist. These findings have provoked working models involving parallel releasable vesicle pools (Parallel Pool Models, PPM) driven by alternative Ca(2+) sensors for release, but no slow release sensor acting on a parallel vesicle pool has been identified. We here propose a Sequential Pool Model (SPM), assuming a novel Ca(2+)-dependent action: a Ca(2+)-dependent catalyst that accelerates both forward and reverse priming reactions. While both models account for fast fusion from the Readily-Releasable Pool (RRP) under control of synaptotagmin-1, the origins of slow release differ. In the SPM the slow release component is attributed to the Ca(2+)-dependent refilling of the RRP from a Non-Releasable upstream Pool (NRP), whereas the PPM attributes slow release to a separate slowly-releasable vesicle pool. Using numerical integration we compared model predictions to data from mouse chromaffin cells. Like the PPM, the SPM explains biphasic release, Ca(2+)-dependence and pool sizes in mouse chromaffin cells. In addition, the SPM accounts for the rapid recovery of the fast component after strong stimulation, where the PPM fails. The SPM also predicts the simultaneous changes in release rate and amplitude seen when mutating the SNARE-complex. Finally, it can account for the loss of fast- and the persistence of slow release in the synaptotagmin-1 knockout by assuming that the RRP is depleted, leading to slow and Ca(2+)-dependent fusion from the NRP. We conclude that the elusive 'alternative Ca(2+) sensor' for slow release might be the upstream priming catalyst, and that a sequential model effectively explains Ca(2+)-dependent properties of secretion without assuming parallel pools or sensors.

Distribution and geochemical composition of suspended particulate material in the shallow embayment of northern Thermaikos Gulf, Greece

NASA Astrophysics Data System (ADS)

Tsompanoglou, K.; Anagnostou, Ch.; Krasakopoulou, E.; Pagou, K.; Karageorgis, A. P.; Pavlidou, A.; Albanakis, K.; Tsirambides, A.

2017-07-01

The distribution and the chemical composition of Suspended Particulate Matter (SPM), in the northern Thermaikos Gulf, were studied during an annual experiment, carried out from June 2004 to June 2005. Water samples were collected at three depths (1 m below surface, 10 m depth, and 2 m above bottom) and filtered to obtain SPM, particulate organic carbon (POC), total particulate nitrogen (PNtot) and particulate phosphorus (PP) concentrations. SPM and POC concentrations exhibited strong spatial and temporal variations, related to the different environmental characteristics in the study area such as river network, biological productivity, anthropogenic interferences, wind regime, and resuspension of the bottom sediments. The highest SPM concentrations were recorded at the surface (mean = 1.45 ± 0.75 mg/l, maximum value = 11.60 mg/l) and close to the bottom (mean = 1.49 ± 0.67 mg/l, maximum value = 11.72 mg/l), creating surface and bottom nepheloid layers (SNL and BNL), respectively. The maximum values were recorded close to the river mouths; the rivers are identified as the major sources of SPM. The Axios and Aliakmon rivers supplied the gulf with particulate matter, during the entire sampling period. Chemical analysis has revealed the significant correlation among the elements Al, Si, Fe, Ti, K, V, Mg and Ba suggesting the presence of terrigenous aluminosilicate minerals. Silica and Ca have terrigenous origin, but also come from autochthonous biogenic fraction. Chromium, Ni and Co, are of natural origin and derived from mafic and ultramafic rocks of the Axios and Aliakmon watersheds. Copper and Zn are correlated with each other and their distributions follow that of POC; these two metals are derived from partially treated domestic and industrial effluents. The vertical distribution of organic matter implies increased primary production within the upper layer of the water column. Phosphorus is present mainly in an organic form. During the sampling period, the water column was well-oxygenated. Early diagenesis only affected the concentrations of Mn and to a lesser extent Fe in the recently deposited seabed sediment.

Stable carbon isotope ratios of archaeal GDGTs in the marine water column and surface sediments

NASA Astrophysics Data System (ADS)

Pearson, A.; Hurley, S.; Close, H. G.; Jasper, C. E.

2016-12-01

Archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids are ubiquitous throughout the marine environment and are preserved in sediments and sedimentary rocks on million-year timescales. Variations in the number of ring-containing GDGT isomers in sediments correlate with differences in overlying sea surface temperatures, a relationship formalized in the TEX86 paleotemperature proxy. Ammonia-oxidizing Thaumarchaeota are believed to be the major sources of these GDGTs, implying that the greatest production and export of GDGTs from the water column should be associated with the maximum expression of ammonia monooxygenase (amoA) genes and maximum number of thaumarchaeal cells, both of which occur in the subsurface NO2- maximum near a depth of ca. 80-250 m. To examine the relationship between production and export of GDGTs from the water column, we measured the concentrations and δ13C values of GDGTs in suspended particulate matter (SPM) of the western South Atlantic Ocean and compared them to values from pure thaumarchaeal cultures and from available sediment core-tops from other locations. Thaumarchaeota are believed to fix the majority of their carbon directly from dissolved inorganic carbon (DIC). However, both the SPM and core-top δ13C values in some cases are moderately more 13C-depleted than would be predicted based on the 13C content of local DIC and the previously-published biosynthetic isotope fractionation (ɛ). This indicates that the average metabolism of the planktonic archaeal community either is mixotrophic (≥ 25% organic carbon assimilation) or that the published ɛ value for the model organism Nitrosopumilus maritimus may not be representative of the total autotrophic community. In addition to this offset, δ13C values of GDGTs in SPM inversely mirror DIC profiles, with lowest values in the nitrite maximum and higher values in the deeper water column, similar to the overall trends for bulk SPM. Finally, while individual GDGTs in SPM samples have similar δ13C values, in many sediments measured to date, the isotopic composition of individual GDGTs differs. This implies that multiple sources of GDGTs are required to explain core-top 13C distributions, especially on continental margins.

A Sequential Vesicle Pool Model with a Single Release Sensor and a Ca2+-Dependent Priming Catalyst Effectively Explains Ca2+-Dependent Properties of Neurosecretion

PubMed Central

Walter, Alexander M.; Pinheiro, Paulo S.; Verhage, Matthijs; Sørensen, Jakob B.

2013-01-01

Neurotransmitter release depends on the fusion of secretory vesicles with the plasma membrane and the release of their contents. The final fusion step displays higher-order Ca2+ dependence, but also upstream steps depend on Ca2+. After deletion of the Ca2+ sensor for fast release – synaptotagmin-1 – slower Ca2+-dependent release components persist. These findings have provoked working models involving parallel releasable vesicle pools (Parallel Pool Models, PPM) driven by alternative Ca2+ sensors for release, but no slow release sensor acting on a parallel vesicle pool has been identified. We here propose a Sequential Pool Model (SPM), assuming a novel Ca2+-dependent action: a Ca2+-dependent catalyst that accelerates both forward and reverse priming reactions. While both models account for fast fusion from the Readily-Releasable Pool (RRP) under control of synaptotagmin-1, the origins of slow release differ. In the SPM the slow release component is attributed to the Ca2+-dependent refilling of the RRP from a Non-Releasable upstream Pool (NRP), whereas the PPM attributes slow release to a separate slowly-releasable vesicle pool. Using numerical integration we compared model predictions to data from mouse chromaffin cells. Like the PPM, the SPM explains biphasic release, Ca2+-dependence and pool sizes in mouse chromaffin cells. In addition, the SPM accounts for the rapid recovery of the fast component after strong stimulation, where the PPM fails. The SPM also predicts the simultaneous changes in release rate and amplitude seen when mutating the SNARE-complex. Finally, it can account for the loss of fast- and the persistence of slow release in the synaptotagmin-1 knockout by assuming that the RRP is depleted, leading to slow and Ca2+-dependent fusion from the NRP. We conclude that the elusive ‘alternative Ca2+ sensor’ for slow release might be the upstream priming catalyst, and that a sequential model effectively explains Ca2+-dependent properties of secretion without assuming parallel pools or sensors. PMID:24339761

Ensuring relevance for Cochrane reviews: evaluating processes and methods for prioritizing topics for Cochrane reviews.

PubMed

Nasser, Mona; Welch, Vivian; Tugwell, Peter; Ueffing, Erin; Doyle, Jodie; Waters, Elizabeth

2013-05-01

The purpose of this study was to assess the presence and effectiveness of existing systems of prioritization for Cochrane review topics and to explore methods of improving those systems. We surveyed groups of Cochrane review authors and recorded any evidence of their use of priority-setting processes or policies. To evaluate the effectiveness of the policies we encountered, we assessed them using two frameworks from the literature: "Accountability for Reasonableness" (1) and Sibbald's 2009 framework (2) for successful priority setting. We then held two workshops with the subject groups to discuss our findings and their implications. Of the 66 groups surveyed, 29 had a system in place to inform the selection or prioritization of topics for Cochrane reviews. Fifteen groups used a more comprehensive structured approach that eventually resulted in a list of ranked priority titles for authoring, updating, or disseminating Cochrane reviews. Most groups involved researchers, practitioners, and patients in their prioritization processes. Groups within The Cochrane Collaboration currently use a range of different priority-setting systems, some of which are more detailed than others. These differences often reflect the nature of The Cochrane Collaboration itself: given the topic breadth, history, and variety of international contexts present in the organization, a single unified system would not always be appropriate. All Cochrane entities, however, should have or develop strategic plans to improve the inclusiveness and transparency of their own prioritization processes, increase the number of finished prioritized reviews, and make more effective use of feedback from end users to increase the likelihood of producing reviews that have positive effects on health outcomes. Copyright © 2013 Elsevier Inc. All rights reserved.

Topography of brain glucose hypometabolism and epileptic network in glucose transporter 1 deficiency.

PubMed

Akman, Cigdem Inan; Provenzano, Frank; Wang, Dong; Engelstad, Kristin; Hinton, Veronica; Yu, Julia; Tikofsky, Ronald; Ichese, Masonari; De Vivo, Darryl C

2015-02-01

(18)F fluorodeoxyglucose positron emission tomography ((18)F FDG-PET) facilitates examination of glucose metabolism. Previously, we described regional cerebral glucose hypometabolism using (18)F FDG-PET in patients with Glucose transporter 1 Deficiency Syndrome (Glut1 DS). We now expand this observation in Glut1 DS using quantitative image analysis to identify the epileptic network based on the regional distribution of glucose hypometabolism. (18)F FDG-PET scans of 16 Glut1 DS patients and 7 healthy participants were examined using Statistical parametric Mapping (SPM). Summed images were preprocessed for statistical analysis using MATLAB 7.1 and SPM 2 software. Region of interest (ROI) analysis was performed to validate SPM results. Visual analysis of the (18)F FDG-PET images demonstrated prominent regional glucose hypometabolism in the thalamus, neocortical regions and cerebellum bilaterally. Group comparison using SPM analysis confirmed that the regional distribution of glucose hypo-metabolism was present in thalamus, cerebellum, temporal cortex and central lobule. Two mildly affected patients without epilepsy had hypometabolism in cerebellum, inferior frontal cortex, and temporal lobe, but not thalamus. Glucose hypometabolism did not correlate with age at the time of PET imaging, head circumference, CSF glucose concentration at the time of diagnosis, RBC glucose uptake, or CNS score. Quantitative analysis of (18)F FDG-PET imaging in Glut1 DS patients confirmed that hypometabolism was present symmetrically in thalamus, cerebellum, frontal and temporal cortex. The hypometabolism in thalamus correlated with the clinical history of epilepsy. Copyright © 2014. Published by Elsevier B.V.

Tidal cycles of total particulate mercury in the Jade Bay, lower Saxonian Wadden Sea, southern North Sea.

PubMed

Jin, Huafang; Liebezeit, Gerd

2013-01-01

In this study, we evaluate the nature of the relationship between particulate matter and total mercury concentrations. For this purpose, we estimate both of the two values in water column over 12-h tidal cycles of the Jade Bay, southern North Sea. Total particulate mercury in 250 mL water samples was determined by oxygen combustion-gold amalgamation. Mercury contents varied from 63 to 259 ng/g suspended particulate matter (SPM) or 3.5-52.8 ng/L in surface waters. Total particulate mercury content (THg(p)) was positively correlated with (SPM), indicating that mercury in tidal waters is mostly associated with (SPM), and that tidal variations of total particulate mercury are mainly due to changes in (SPM) content throughout the tidal cycle. Maximum values for THg(p) were observed during mid-flood and mid-ebb, while the lowest values were determined at low tide and high tide. These data suggest that there are no mercury point sources in the Jade Bay. Moreover, the THg(p) content at low tide and high tide were significantly lower than the values recorded in the bottom sediment of the sampling site (>200 ng/g DW), while THg(p) content during the mid-flood and mid-ebb were comparable to the THg content in the surface bottom sediments. Therefore, changes in THg(p) content in the water column due to tidal forcing may have resulted from re-suspension of underlying surface sediments with relatively high mercury content.

Aerosol optical properties measurements by a CAPS single scattering albedo monitor: Comparisons between summer and winter in Beijing, China

NASA Astrophysics Data System (ADS)

Han, Tingting; Xu, Weiqi; Li, Jie; Freedman, Andrew; Zhao, Jian; Wang, Qingqing; Chen, Chen; Zhang, Yingjie; Wang, Zifa; Fu, Pingqing; Liu, Xingang; Sun, Yele

2017-02-01

Aerosol optical properties were measured in Beijing in summer and winter using a state-of-the-art cavity attenuated phase shift single scattering albedo monitor (CAPS PMssa) along with aerosol composition measurements by aerosol mass spectrometers and aethalometers. The SSA directly measured by the CAPS PMssa showed overall agreements with those derived from colocated measurements. However, substantial differences were observed during periods with low SSA values in both summer and winter, suggesting that interpretation of low SSA values needs to be cautious. The average (±σ) extinction coefficient (bext) and absorption coefficient (bap) were 336 (±343) Mm-1 and 44 (±41) Mm-1, respectively, during wintertime, which were approximately twice those observed in summer, while the average SSA was relatively similar, 0.86 (±0.06) and 0.85 (±0.04) in summer and winter, respectively. Further analysis showed that the variations in SSA can be approximately parameterized as a function of mass fraction of secondary particulate matter (fSPM), which is SSA = 0.74 + 0.19 × fSPM (fSPM > 0.3, r2 = 0.85). The contributions of aerosol species to extinction coefficients during the two seasons were also estimated. Our results showed that the light extinction was dominantly contributed by ammonium sulfate (30%) and secondary organic aerosol (22%) in summer, while organic aerosol was the largest contributor (51%) in winter. Consistently, SPM played the major role in visibility degradation in both seasons by contributing 70% of the total extinction.

Role of Ribonucleotide Reductase in Bacillus subtilis Stress-Associated Mutagenesis.

PubMed

Castro-Cerritos, Karla Viridiana; Yasbin, Ronald E; Robleto, Eduardo A; Pedraza-Reyes, Mario

2017-02-15

The Gram-positive microorganism Bacillus subtilis relies on a single class Ib ribonucleotide reductase (RNR) to generate 2'-deoxyribonucleotides (dNDPs) for DNA replication and repair. In this work, we investigated the influence of RNR levels on B. subtilis stationary-phase-associated mutagenesis (SPM). Since RNR is essential in this bacterium, we engineered a conditional mutant of strain B. subtilis YB955 (hisC952 metB5 leu427) in which expression of the nrdEF operon was modulated by isopropyl-β-d-thiogalactopyranoside (IPTG). Moreover, genetic inactivation of ytcG, predicted to encode a repressor (NrdR) of nrdEF in this strain, dramatically increased the expression levels of a transcriptional nrdE-lacZ fusion. The frequencies of mutations conferring amino acid prototrophy in three genes were measured in cultures under conditions that repressed or induced RNR-encoding genes. The results revealed that RNR was necessary for SPM and overexpression of nrdEF promoted growth-dependent mutagenesis and SPM. We also found that nrdEF expression was induced by H 2 O 2 and such induction was dependent on the master regulator PerR. These observations strongly suggest that the metabolic conditions operating in starved B. subtilis cells increase the levels of RNR, which have a direct impact on SPM. Results presented in this study support the concept that the adverse metabolic conditions prevailing in nutritionally stressed bacteria activate an oxidative stress response that disturbs ribonucleotide reductase (RNR) levels. Such an alteration of RNR levels promotes mutagenic events that allow Bacillus subtilis to escape from growth-limited conditions. Copyright © 2017 American Society for Microbiology.

Multi-matrix quantification and risk assessment of pesticides in the longest river of the Iberian peninsula.

PubMed

Cruzeiro, Catarina; Pardal, Miguel Ângelo; Rodrigues-Oliveira, Nádia; Castro, L Filipe C; Rocha, Eduardo; Rocha, Maria João

2016-12-01

The distribution of pesticides in dissolved aqueous phase (DAP), suspended particulate matter (SPM) and Scrobicularia plana soft tissues from the Tagus River estuary was determined to evaluate the chemicals pollution status and their hazard potential in this area. Samples were collected in 6 campaigns (December 2012-October 2013), from 3 strategical sites, and analysed via different extraction procedures followed by gas chromatography tandem mass spectrometry (GC-MS/MS) determination. The contamination profile among matrices (DAP, SPM, and soft tissue from bivalves (STB)) was marked by average concentrations of 345ng/L, 0.51mg/kg, and 0.02mg/kg, respectively, with several samples above the 2013/39/EU Directive of environmental quality standards (EQS); no differences were observed between sex. A wider range of pesticides was present in STB (n=53) than in SPM (n=36) and DAP (n=19) matrices. Sediment-water partition coefficient, bioaccumulation factor in both DAP and SPM fraction were estimated ranging between 2.5 and 4.4 and 0.008-2799, respectively. The spatial distribution of most pesticides and physicochemical parameters were consistent, indicating a pollution pattern primarily near the Trancão River mouth. Due to the presence of the target compounds, calculated risk quotients pointed out potential hazards for aquatic organisms, mainly to invertebrates. The estimated average daily intake, theoretical maximum daily intake, and hazard quotient of the studied pesticides-via bivalve ingestion-indicated no risk for human health, although it is important to note possible biomagnification processes that may happen along the estuarine food-chain. Copyright © 2016 Elsevier B.V. All rights reserved.

Polyamines and ethylene interact in rice grains in response to soil drying during grain filling.

PubMed

Chen, Tingting; Xu, Yunji; Wang, Jingchao; Wang, Zhiqin; Yang, Jianchang; Zhang, Jianhua

2013-05-01

This study tested the hypothesis that the interaction between polyamines and ethylene may mediate the effects of soil drying on grain filling of rice (Oryza sativa L.). Two rice cultivars were pot grown. Three treatments, well-watered, moderate soil drying (MD), and severe soil drying (SD), were imposed from 8 d post-anthesis until maturity. The endosperm cell division rate, grain-filling rate, and grain weight of earlier flowering superior spikelets showed no significant differences among the three treatments. However, those of the later flowering inferior spikelets were significantly increased under MD and significantly reduced under SD when compared with those which were well watered. The two cultivars showed the same tendencies. MD increased the contents of free spermidine (Spd) and free spermine (Spm), the activities of S-adenosyl-L-methionine decarboxylase and Spd synthase, and expression levels of polyamine synthesis genes, and decreased the ethylene evolution rate, the contents of 1-aminocylopropane-1-carboxylic acid (ACC) and hydrogen peroxide, the activities of ACC synthase, ACC oxidase, and polyamine oxidase, and the expression levels of ethylene synthesis genes in inferior spikelets. SD exhibited the opposite effects. Application of Spd, Spm, or an inhibitor of ethylene synthesis to rice panicles significantly reduced ethylene and ACC levels, but significantly increased Spd and Spm contents, grain-filling rate, and grain weight of inferior spikelets. The results were reversed when ACC or an inhibitor of Spd and Spm synthesis was applied. The results suggest that a potential metabolic interaction between polyamines and ethylene biosynthesis responds to soil drying and mediates the grain filling of inferior spikelets in rice.

A Localized Complex of Two Protein Oligomers Controls the Orientation of Cell Polarity

PubMed Central

Lasker, Keren; Ahrens, Daniel G.; Eckart, Michael R.

2017-01-01

ABSTRACT Signaling hubs at bacterial cell poles establish cell polarity in the absence of membrane-bound compartments. In the asymmetrically dividing bacterium Caulobacter crescentus, cell polarity stems from the cell cycle-regulated localization and turnover of signaling protein complexes in these hubs, and yet the mechanisms that establish the identity of the two cell poles have not been established. Here, we recapitulate the tripartite assembly of a cell fate signaling complex that forms during the G1-S transition. Using in vivo and in vitro analyses of dynamic polar protein complex formation, we show that a polymeric cell polarity protein, SpmX, serves as a direct bridge between the PopZ polymeric network and the cell fate-directing DivJ histidine kinase. We demonstrate the direct binding between these three proteins and show that a polar microdomain spontaneously assembles when the three proteins are coexpressed heterologously in an Escherichia coli test system. The relative copy numbers of these proteins are essential for complex formation, as overexpression of SpmX in Caulobacter reorganizes the polarity of the cell, generating ectopic cell poles containing PopZ and DivJ. Hierarchical formation of higher-order SpmX oligomers nucleates new PopZ microdomain assemblies at the incipient lateral cell poles, driving localized outgrowth. By comparison to self-assembling protein networks and polar cell growth mechanisms in other bacterial species, we suggest that the cooligomeric PopZ-SpmX protein complex in Caulobacter illustrates a paradigm for coupling cell cycle progression to the controlled geometry of cell pole establishment. PMID:28246363

Accurate discrimination of Alzheimer's disease from other dementia and/or normal subjects using SPECT specific volume analysis

NASA Astrophysics Data System (ADS)

Iyatomi, Hitoshi; Hashimoto, Jun; Yoshii, Fumuhito; Kazama, Toshiki; Kawada, Shuichi; Imai, Yutaka

2014-03-01

Discrimination between Alzheimer's disease and other dementia is clinically significant, however it is often difficult. In this study, we developed classification models among Alzheimer's disease (AD), other dementia (OD) and/or normal subjects (NC) using patient factors and indices obtained by brain perfusion SPECT. SPECT is commonly used to assess cerebral blood flow (CBF) and allows the evaluation of the severity of hypoperfusion by introducing statistical parametric mapping (SPM). We investigated a total of 150 cases (50 cases each for AD, OD, and NC) from Tokai University Hospital, Japan. In each case, we obtained a total of 127 candidate parameters from: (A) 2 patient factors (age and sex), (B) 12 CBF parameters and 113 SPM parameters including (C) 3 from specific volume analysis (SVA), and (D) 110 from voxel-based analysis stereotactic extraction estimation (vbSEE). We built linear classifiers with a statistical stepwise feature selection and evaluated the performance with the leave-one-out cross validation strategy. Our classifiers achieved very high classification performances with reasonable number of selected parameters. In the most significant discrimination in clinical, namely those of AD from OD, our classifier achieved both sensitivity (SE) and specificity (SP) of 96%. In a similar way, our classifiers achieved a SE of 90% and a SP of 98% in AD from NC, as well as a SE of 88% and a SP of 86% in AD from OD and NC cases. Introducing SPM indices such as SVA and vbSEE, classification performances improved around 7-15%. We confirmed that these SPM factors are quite important for diagnosing Alzheimer's disease.

Legacy and emerging halogenated flame retardants in the middle and lower stream of the Yellow River.

PubMed

Su, Xianfa; Li, Qilu; Feng, Jinglan; Guo, Liya; Sun, Jianhui

2017-12-01

Halogenated flame retardants (HFRs), mainly encompassing polybrominated diphenylethers (PBDEs), dechlorane plus (DP) and emerging bromine flame retardants (EBFRs), are widely employed nowadays in daily lives. However, limited knowledge has been gained to date on the concentrations and distributions of HFRs in particular within certain regions. In the present study, legacy and emerging HFRs were systematically measured in suspended particle matter (SPM) and sediments collected in 2014 from the middle and lower reach of the Yellow River in Henan province. The total concentrations of HFRs in SPM among the three seasons were 42.2±91.2ngg -1 , which was far higher than the corresponding values of HFRs in sediments (1.82±2.94ngg -1 ). In this study, PBDEs, DP and EBFRs in sediment almost exhibited relatively lower levels as compared to those found in other studies, where the limited usage of HFRs in the middle and lower stream of the Yellow River was probably the major impact factor. EBFR was the predominate pollutant from SPM and sediments in most of the sampling sites, suggesting that EBFRs were widely used nowadays as substitute materials of 'old' FRs. The mean concentration values of DBDPE/BDE-209 in SPM and sediments were apparently higher than those of previous studies. Furthermore, it is interesting to reveal that herein almost all of the HFR concentrations were unrelated to the population and GDP, which might be attributed to the characteristics of 'elevated stream' of the Yellow River as well as the complex river systems in Henan province. Copyright © 2017 Elsevier B.V. All rights reserved.

An integrated evaluation of some faecal indicator bacteria (FIB) and chemical markers as potential tools for monitoring sewage contamination in subtropical estuaries.

PubMed

Cabral, Ana Caroline; Stark, Jonathan S; Kolm, Hedda E; Martins, César C

2018-04-01

Sewage input and the relationship between chemical markers (linear alkylbenzenes and coprostanol) and fecal indicator bacteria (FIB, Escherichia coli and enterococci), were evaluated in order to establish thresholds values for chemical markers in suspended particulate matter (SPM) as indicators of sewage contamination in two subtropical estuaries in South Atlantic Brazil. Both chemical markers presented no linear relationship with FIB due to high spatial microbiological variability, however, microbiological water quality was related to coprostanol values when analyzed by logistic regression, indicating that linear models may not be the best representation of the relationship between both classes of indicators. Logistic regression was performed with all data and separately for two sampling seasons, using 800 and 100 MPN 100 mL -1 of E. coli and enterococci, respectively, as the microbiological limits of sewage contamination. Threshold values of coprostanol varied depending on the FIB and season, ranging between 1.00 and 2.23 μg g -1 SPM. The range of threshold values of coprostanol for SPM are relatively higher and more variable than those suggested in literature for sediments (0.10-0.50 μg g -1 ), probably due to higher concentration of coprostanol in SPM than in sediment. Temperature may affect the relationship between microbiological indicators and coprostanol, since the threshold value of coprostanol found here was similar to tropical areas, but lower than those found during winter in temperate areas, reinforcing the idea that threshold values should be calibrated for different climatic conditions. Copyright © 2018 Elsevier Ltd. All rights reserved.

High temperature spin-glass-like transition in La0.67Sr0.33MnO3 nanofibers near the Curie point.

PubMed

Lu, Ruie; Yang, Sen; Li, Yitong; Chen, Kaiyun; Jiang, Yun; Fu, Bi; Zhang, Yin; Zhou, Chao; Xu, Minwei; Zhou, Xuan

2017-06-28

The glassy transition of superparamagnetic (SPM) (r < r 0 ) nanoparticle systems usually occurs at a very low temperature that greatly limits its application to high temperatures. In this work, we report a spin-glass-like (SGL) behavior near the Curie point (T C ), i.e., T 0 = 330 K, in La 0.67 Sr 0.33 MnO 3 (LSMO) nanofibers (NFs) composed of nanoparticles beyond the SPM size (r ≫ r 0 ), resulting in a significant increase of the glass transition temperature. This SGL transition near the T C of bulk LSMO can be explained to be the scenario of locally ordered clusters embedded in a disordered host, in which the assembly of nanoparticles has a magnetic core-shell model driven by surface spin glass. The presence of a surface spin glass of nanoparticles was proved by the Almeida-Thouless line δT f ∝ H 2/3 , exchange bias, and reduced saturation magnetization of the NF system. Composite dynamics were found - that is, both the SPM and the super-spin-glass (SSG) behavior are found in such an NF system. The bifurcation of the zero-field-cooled (ZFC) and field-cooled (FC) magnetization vs. temperature curves at the ZFC peak, and the flatness of FC magnetization involve SSG, while the frequency-dependent ac susceptibility anomaly follows the Vogel-Fulcher law that implies weak dipole interactions of the SPM model. This finding can help us to find a way to search for high temperature spin glass materials.

Heavy metal contamination of a Greenland Fjord system by mine wastes

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

Loring, D.H.; Asmund, G.

Since 1973, about 500,000 tons/yr of metal-rich particulate tailings from a lead/zinc flotation mill have been discharged through a submarine outfall into a two-fjord system on the west coast of Greenland. Differential solubilization of particulate metals by seawater, seasonal water mixing, and sill exchange tailings dispersal processes have resulted in high, but seasonally variable, Zn, Cd, and Pb contamination of the water and suspended particulate matter (SPM). Chemical partition of the SPM shows that most of the Pb, but relatively low proportions of Zn and Cd are weakly bound to the SPM. Such particulate metal characteristics allow the real timemore » effects of tailings discharges and dispersal on the system to be traced even in the sediments where tailings accumulation is very slow. Fjord seaweeds and blue mussels also contain varying amounts of Zn, Pb, and Cd, depending on the metal and their location relative to the tailings outfall. They apparently responded almost instantly to the metal contamination as did the water and SPM. High Pb concentrations in the fjord mussels most likely derive from the preferential uptake of available particulate Pb, whereas the seaweeds appear to derive most of their heavy metal concentrations from the dissolved phase. The evidence from this and other sites, and from experimental work, indicates that any discharge of Pb-particles into the marine environment, either directly as mine wastes or indirectly from natural runoff from current and former lead mining sites, results in immediate lead contamination of the in situ mussel population. 20 refs., 4 figs., 5 tab.« less

Altered Polyamine Profiles in Colorectal Cancer.

PubMed

Venäläinen, Markus K; Roine, Antti N; Häkkinen, Merja R; Vepsäläinen, Jouko J; Kumpulainen, Pekka S; Kiviniemi, Mikko S; Lehtimäki, Terho; Oksala, Niku K; Rantanen, Tuomo K

2018-06-01

The declining mortality rate of patients with colorectal cancer (CRC) can be explained, at least partially, with early diagnosis. Simple diagnostic methods are needed to achieve a maximal patient participation rate in screening. Liquid chromatography electrospray tandem mass spectrometry (LC-MS/MS) was used to determine urinary polyamine (PA) profiles. In a prospective setting, 116 patients were included in the study: 57 with CRC, 13 with inflammatory bowel disease (IBD), 12 with adenoma, and 34 controls. N1,N12-diacetylspermine (DiAcSPM) level was significantly higher in patients with CRC than controls (sensitivity=78.0%, specificity=70.6%; p=0.00049). The level of diacetylated cadaverine (p=0.0068) was lower and that of diacetylated putrescine (p=0.0078) was higher in patients with CRC than in those with IBD. Cadaverine (p=0.00010) and spermine (p=0.042) levels were lower and that of DiAcSPM (p=0.018) higher in patients with CRC than in those with adenoma. The simultaneous determination of urinary PAs by means of LC-MS/MS can be used to discriminate CRC from controls and patients with benign colorectal diseases. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Head circumference as a useful surrogate for intracranial volume in older adults.

PubMed

Hshieh, Tammy T; Fox, Meaghan L; Kosar, Cyrus M; Cavallari, Michele; Guttmann, Charles R G; Alsop, David; Marcantonio, Edward R; Schmitt, Eva M; Jones, Richard N; Inouye, Sharon K

2016-01-01

Intracranial volume (ICV) has been proposed as a measure of maximum lifetime brain size. Accurate ICV measures require neuroimaging which is not always feasible for epidemiologic investigations. We examined head circumference as a useful surrogate for ICV in older adults. 99 older adults underwent Magnetic Resonance Imaging (MRI). ICV was measured by Statistical Parametric Mapping 8 (SPM8) software or Functional MRI of the Brain Software Library (FSL) extraction with manual editing, typically considered the gold standard. Head circumferences were determined using standardized tape measurement. We examined estimated correlation coefficients between head circumference and the two MRI-based ICV measurements. Head circumference and ICV by SPM8 were moderately correlated (overall r = 0.73, men r = 0.67, women r = 0.63). Head circumference and ICV by FSL were also moderately correlated (overall r = 0.69, men r = 0.63, women r = 0.49). Head circumference measurement was strongly correlated with MRI-derived ICV. Our study presents a simple method to approximate ICV among older patients, which may prove useful as a surrogate for cognitive reserve in large scale epidemiologic studies of cognitive outcomes. This study also suggests the stability of head circumference correlation with ICV throughout the lifespan.

Estimation of particulate matter from simulation and measurements

NASA Astrophysics Data System (ADS)

Nakata, Makiko; Nakano, Tomio; Okuhara, Takaaki; Sano, Itaru; Mukai, Sonoyo

2011-11-01

The particulate matter is a typical indicator of small particles in the atmosphere. In addition to providing impacts on climate and environment, these small particles can bring adverse effects on human health. Then an accurate estimation of particulate matter is an urgent subject. We set up SPM sampler attached to our AERONET (Aerosol Robotics Network) station in urban city of Higashi-Osaka in Japan. The SPM sampler provides particle information about the concentrations of various SPMs (e.g., PM10 and PM2.5) separately. The AEROENT program is world wide ground based sunphotometric observation networks by NASA and provides the spectral information about aerosol optical thickness (AOT) and Angstrom exponent (α). Simultaneous measurements show that a linear correlation definitely exists between AOT and PM2.5. These results indicate that particulate matter can be estimated from AOT. However AOT represents integrated values of column aerosol amount retrieved from optical property, while particulate matter concentration presents in-situ aerosol loading on the surface. Then simple way using linear correlation brings the discrepancy between observed and estimated particulate matter. In this work, we use cluster information about aerosol type to reduce the discrepancy. Our improved method will be useful for retrieving particulate matter from satellite measurements.

New positive feedback mechanism between boundary layer meteorology and secondary aerosol formation during severe haze events

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

Liu, Quan; Jia, Xingcan; Quan, Jiannong

Severe haze events during which particulate matter (PM) increases quickly from tens to hundreds of microgram per cubic meter in 1-2 days frequently occur in China. Although it has been known that PM is influenced by complex interplays among emissions, meteorology, and physical and chemical processes, specific mechanisms remain elusive. In this paper, a new positive feedback mechanism between planetary boundary layer (PBL), relative humidity (RH), and secondary PM (SPM) formation is proposed based on a comprehensive field experiment and model simulation. The decreased PBL associated with increased PM increases RH by weakening the vertical transport of water vapor; themore » increased RH in turn enhances the SPM formation through heterogeneous aqueous reactions, which further enhances PM, weakens solar radiation, and decreases PBL height. This positive feedback, together with the PM-Radiation-PBL feedback, constitutes a key mechanism that links PM, radiation, PBL properties (e.g. PBL height and RH), and SPM formation, This mechanism is self-amplifying, leading to faster PM production, accumulation, and more severe haze pollution.« less

Risk of second primary malignancies and survival of adult patients with polycythemia vera: A United States population-based retrospective study.

PubMed

Khanal, Nabin; Giri, Smith; Upadhyay, Smrity; Shostrom, Valerie K; Pathak, Ranjan; Bhatt, Vijaya Raj

2016-01-01

Although the median survival in polycythemia vera (PV) is 14 years, mortality is higher than in an age- and sex-matched population. This study included 3941 PV patients diagnosed between 2000-2012 from Surveillance, Epidemiology and End Results (SEER) 13 registry to determine 5-year survival and the incidence of second primary malignancies (SPM). The actuarial 5 year survival in the overall cohort was 79.5%. The cumulative incidence of SPM was 13.1% at 10 years. SPMs occurred at a standardized incidence ratio (SIR) of 1.29 (95% CI = 1.16-1.43; p < 0.001) with an absolute excess risk (AER) of 42.49 per 10 000 population. A significantly higher risk was noted for acute myeloid leukemia (SIR = 12.24; 95% CI = 8.17-17.8; p-value < 0.001) and chronic myeloid leukemia (SIR = 10.66; 95% CI = 3.75-19.6; p-value < 0.001). Patients with PV are at a high risk of SPM and leukemic transformation, which may compromise long-term survival.

Airborne particulate matter and spacecraft internal environments

NASA Technical Reports Server (NTRS)

Liu, Benjamin Y. H.; Rubow, Kenneth L.; Mcmurry, Peter H.; Kotz, Thomas J.; Russo, Dane

1991-01-01

Instrumentation, consisting of a Shuttle Particle Sampler (SPS) and a Shuttle Particle Monitor (SPM), has been developed to characterize the airborne particulate matter in the Space Shuttle cabin during orbital flight. The SPS size selectively collects particles in four size fractions (0-2.5, 2.5-10, 10-100, and greater than 100 microns) which are analyzed postflight for mass concentration and size distribution, elemental composition, and morphology. The SPM provides a continuous record of particle concentration through photometric light scattering. Measurements were performed onboard Columbia, OV-102, during the flight of STS-32 in January 1990. No significant changes were observed in the particle mass concentration, size distribution, or chemical composition in samples collected during flight-day 2 and flight-day 7. The total mass concentration was 56 microg/cu cm with approximately half of the particles larger than 100 microns. Elemental analysis showed that roughly 70 percent of the particles larger than 2.5 microns were carbonaceous with small amounts of other elements present. The SPM showed no temporal or spatial variation in particle mass concentration during the mission.

Mass-specific scattering coefficient for natural minerogenic particle populations: particle size distribution effect and closure analyses.

PubMed

Peng, Feng; Effler, Steve W

2012-05-01

The relationship between the particulate scattering coefficient (b(p)) and the concentration of suspended particulate matter (SPM), as represented by the mass-specific scattering coefficient of particulates (b(p)*=b(p)/SPM), depends on particle size distribution (PSD). This dependence is quantified for minerogenic particle populations in this paper through calculations of b(p)* for common minerals as idealized populations (monodispersed spheres); contemporaneous measurements of b(p), SPM, and light-scattering attributes of mineral particles with scanning electron microscopy interfaced with automated image and x-ray analyses (SAX), for a connected stream-reservoir system where minerogenic particles dominate b(p); and estimates of b(p) and its size dependency (through SAX results-driven Mie theory calculations), particle volume concentration, and b(p)*. Modest changes in minerogenic PSDs are shown to result in substantial variations in b(p)*. Good closure of the SAX-based estimates of b(p) and particle volume concentration with bulk measurements is demonstrated. Converging relationships between b(p)* and particle size, developed from three approaches, were well described by power law expressions.

The effects of plant growth regulators and L-phenylalanine on phenolic compounds of sweet basil.

PubMed

Koca, Nülüfer; Karaman, Şengül

2015-01-01

The effects of methyl jasmonate (MeJA), spermine (Spm), epibrassinolide (EBL) and l-phenylalanine on sweet basil (Ocimum basilicum L.) were studied to determine the amount of phenolic compounds and enzymatic activity of phenylalanine ammonia-lyase (PAL). Total phenolic and total flavonoid contents of sweet basils were determined by a spectrophotometer, and individual phenolic compounds and activity of PAL were analysed by HPLC/UV. The highest total phenolic (6.72 mg GAE/g) and total flavonoid contents (0.92 mg QE/g) obtained from 1.0 mM Spm+MeJA application. Rosmarinic acid (RA) and caffeic acid contents significantly enhanced after the applications but no such differences observed in chicoric acid content or PAL activity. RA was the main phenolic acid in all samples and its concentration varied from 1.04 to 2.70 mg/gFW. As a result the combinations of Spm+MeJA and EBL+MeJA can induce secondary metabolites effectively and those interactions play important role in the production of phytochemicals in plants. Copyright © 2014 Elsevier Ltd. All rights reserved.

Occurrence, distribution, and risk assessment of alkylphenols, bisphenol A, and tetrabromobisphenol A in surface water, suspended particulate matter, and sediment in Taihu Lake and its tributaries.

PubMed

Liu, Dan; Liu, Jining; Guo, Min; Xu, Huaizhou; Zhang, Shenghu; Shi, Lili; Yao, Cheng

2016-11-15

The occurrence and distribution of nine selected compounds were investigated in surface water, suspended particulate matter (SPM), and sediment in Taihu Lake and its tributaries. With the exception of 4-Butylphenol, all compounds were detected in at least two phases, and nonylphenol (NP) and 4-tert-Octylphenol (4-OP) were the predominant alkylphenols (APs) in the lake. A significant correlation was observed between NP and 4-OP, indicating that they may share the same source. Moreover, surface water phase was the dominant sink of Bisphenol A (BPA) in the aquatic environment. The concentrations of BPA between the surface water and SPM phases were closely related to each other. In addition, Tetrabromobisphenol A (TBBPA) exhibited relatively higher concentrations and detection frequencies in the SPM. Risk assessment revealed greater risk associated with the surface water than the sediment, indicating that the discharge of industrial wastewater and domestic sewage poses a serious threat to aquatic ecosystems. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Somnath, Suhas; Collins, Liam; Matheson, Michael A.

We develop and implement a multifrequency spectroscopy and spectroscopic imaging mode, referred to as general dynamic mode (GDM), that captures the complete spatially- and stimulus dependent information on nonlinear cantilever dynamics in scanning probe microscopy (SPM). GDM acquires the cantilever response including harmonics and mode mixing products across the entire broadband cantilever spectrum as a function of excitation frequency. GDM spectra substitute the classical measurements in SPM, e.g. amplitude and phase in lock-in detection. Here, GDM is used to investigate the response of a purely capacitively driven cantilever. We use information theory techniques to mine the data and verify themore » findings with governing equations and classical lock-in based approaches. We explore the dependence of the cantilever dynamics on the tip–sample distance, AC and DC driving bias. This approach can be applied to investigate the dynamic behavior of other systems within and beyond dynamic SPM. In conclusion, GDM is expected to be useful for separating the contribution of different physical phenomena in the cantilever response and understanding the role of cantilever dynamics in dynamic AFM techniques.« less

New positive feedback mechanism between boundary layer meteorology and secondary aerosol formation during severe haze events

DOE PAGES

Liu, Quan; Jia, Xingcan; Quan, Jiannong; ...

2018-04-17

Severe haze events during which particulate matter (PM) increases quickly from tens to hundreds of microgram per cubic meter in 1-2 days frequently occur in China. Although it has been known that PM is influenced by complex interplays among emissions, meteorology, and physical and chemical processes, specific mechanisms remain elusive. In this paper, a new positive feedback mechanism between planetary boundary layer (PBL), relative humidity (RH), and secondary PM (SPM) formation is proposed based on a comprehensive field experiment and model simulation. The decreased PBL associated with increased PM increases RH by weakening the vertical transport of water vapor; themore » increased RH in turn enhances the SPM formation through heterogeneous aqueous reactions, which further enhances PM, weakens solar radiation, and decreases PBL height. This positive feedback, together with the PM-Radiation-PBL feedback, constitutes a key mechanism that links PM, radiation, PBL properties (e.g. PBL height and RH), and SPM formation, This mechanism is self-amplifying, leading to faster PM production, accumulation, and more severe haze pollution.« less

Effect of SPM-based cleaning POR on EUV mask performance

NASA Astrophysics Data System (ADS)

Choi, Jaehyuck; Lee, Han-shin; Yoon, Jinsang; Shimomura, Takeya; Friz, Alex; Montgomery, Cecilia; Ma, Andy; Goodwin, Frank; Kang, Daehyuk; Chung, Paul; Shin, Inkyun; Cho, H.

2011-11-01

EUV masks include many different layers of various materials rarely used in optical masks, and each layer of material has a particular role in enhancing the performance of EUV lithography. Therefore, it is crucial to understand how the mask quality and patterning performance can change during mask fabrication, EUV exposure, maintenance cleaning, shipping, or storage. The fact that a pellicle is not used to protect the mask surface in EUV lithography suggests that EUV masks may have to undergo more cleaning cycles during their lifetime. More frequent cleaning, combined with the adoption of new materials for EUV masks, necessitates that mask manufacturers closely examine the performance change of EUV masks during cleaning process. We have investigated EUV mask quality and patterning performance during 30 cycles of Samsung's EUV mask SPM-based cleaning and 20 cycles of SEMATECH ADT exposure. We have observed that the quality and patterning performance of EUV masks does not significantly change during these processes except mask pattern CD change. To resolve this issue, we have developed an acid-free cleaning POR and substantially improved EUV mask film loss compared to the SPM-based cleaning POR.

Prioritizing chemicals for environmental management in China based on screening of potential risks

NASA Astrophysics Data System (ADS)

Yu, Xiangyi; Mao, Yan; Sun, Jinye; Shen, Yingwa

2014-03-01

The rapid development of China's chemical industry has created increasing pressure to improve the environmental management of chemicals. To bridge the large gap between the use and safe management of chemicals, we performed a comprehensive review of the international methods used to prioritize chemicals for environmental management. By comparing domestic and foreign methods, we confirmed the presence of this gap and identified potential solutions. Based on our literature review, we developed an appropriate screening method that accounts for the unique characteristics of chemical use within China. The proposed method is based on an evaluation using nine indices of the potential hazard posed by a chemical: three environmental hazard indices (persistence, bioaccumulation, and eco-toxicity), four health hazard indices (acute toxicity, carcinogenicity, mutagenicity, and reproductive and developmental toxicity), and two environmental exposure hazard indices (chemical amount and utilization pattern). The results of our screening agree with results of previous efforts from around the world, confirming the validity of the new system. The classification method will help decisionmakers to prioritize and identify the chemicals with the highest environmental risk, thereby providing a basis for improving chemical management in China.

Electrical Measurements and Nanomechanics Using Scanning Probe Microscopy

NASA Astrophysics Data System (ADS)

Chang, Yong

2002-10-01

In the early 1980s, G. Binnig et al. invented the Scanning Tunneling Microscopy (STM) [1], making it possible to obtain atomic resolution images of conducting surfaces. After that, many different types of Scanning Probe Microscopy (SPM) were invented and some of the most useful representatives are Atomic Force Microscopy (AFM) [2], Electrostatic Force Microscopy (EFM) [3] and Kelvin Probe Force Microscopy (KPFM) [4,5]. In 1985, G. Binnig et al. [2] invented the AFM, which now is used as a fundamental tool in many fields of research. Developed from AFM, Y. Martin et al. [3] invented EFM in 1987. The development of AC mode AFM allows the detection of weak long-range forces. EFM has also been used to study other systems and phenomena, such as thin liquid films on solid surfaces [6], electrically stressed gold nanowires [7], and spatial charge distribution in quantum wires [8]. In 1991, M. Nonnenmacher et al. [5] invented Kelvin Probe Force Microscopy. KPFM is used to study any property that affects the tip-surface Contact Potential Difference (CPD), such as voltage signals in integrated circuits (IC) [9], charged grain boundaries in polycrystalline silicon [10] and surface potential variations in multilayer semiconductor devices [11]. The aim of this poster is to discuss the application of SPM to electrical measurements. The theory of SPM was presented. The AFM was firstly introduced as it was developed before the other two. The design and theory were discussed. The force-distance curve was introduced. After this EFM was presented. EFM was developed from AC mode AFM. The technique was achieved by applying a DC voltage between the tip and the sample. The design, theory and features of it were surveyed. KPFM was also discussed. KPFM was developed from EFM. The central part of this technique is to measure the CPD. Experimental measurements of SPM were described after theory part. Research work using AFM was presented. The newest technique of AFM, UHV-AFM has been used in investigating the nano-mechanical properties of different materials. Normally common AFM has shortcomings as it has either strict limit resolution or difficulties in interpreting the data from the measurements. In order to solve these problems, Ultra High Vacuum (UHV) conditions were applied to acquire quantitative results. A typical UHV-AFM uses a cantilever whose spring constant is relatively high (>100 N/m) to obtain high-resolution image. Experimental measurements using KPFM was presented after AFM. Researchers are using KPFM to acquire the topography and measuring the CPD of semiconductor or metal surfaces. Similarly as in AFM, KPFM works best in UHV environment. A typical UHV-KPFM also uses a cantilever whose spring constant is relatively high. A UHV-KPFM may be able to achieve a high resolution in CPD images. In the past 20 years many different kinds of SPM were invented and used. AFM, EFM, and KPFM are representatives of them. Researchers are still developing new techniques. However, in recent years, they pay more attention in improving the measurement accuracy instead of trying to invent new SPM. These three SPM continue to be frequently used. The current capabilities of SPM do not satisfy us completely. We still cant measure the Electrical field directly. We actually measure the capacitance gradient. There are also some other questions. This is because the electrostatic force depends very strongly on the geometry of the probe at all length scales, so any model is subject to two big problems. First, the geometry is not known with complete accuracy; and second, the tip shape can change during an experiment due to wear. In the future, maybe the problems could be overcome by using a tip with a very well defined shape, such as a carbon nanotube, for which a realistic geometrical model could be more easily constructed, and the wear could be avoided or reduced.

Prioritizing treatment of second-growth forests using LiDAR

Treesearch

Lathrop P. Leonard; Daryl Van Dyke

2012-01-01

We used multi-return light detecting and ranging (LiDAR) to develop a costeffective method for describing forest conditions and prioritizing stands for treatment in over 14,000 ha of second-growth forests (11 to 85 years old) in Del Norte Coast Redwoods State Park (DNCRSP). DNCRSP consists primarily of redwood and Douglas-fir dominated forests with scattered tanoak...

Incorporating evolutionary measures into conservation prioritization.

PubMed

Redding, David W; Mooers, Arne Ø

2006-12-01

Conservation prioritization is dominated by the threat status of candidate species. However, species differ markedly in the shared genetic information they embody, and this information is not taken into account if species are prioritized by threat status alone. We developed a system of prioritization that incorporates both threat status and genetic information and applied it to 9546 species of birds worldwide. We devised a simple measure of a species' genetic value that takes into account the shape of the entire taxonomic tree of birds. This measure approximates the evolutionary history that each species embodies and sums to the phylogenetic diversity of the entire taxonomic tree. We then combined this genetic value with each species' probability of extinction to create a species-specific measure of expected loss of genetic information. The application of our methods to the world's avifauna showed that ranking species by expected loss of genetic information may help preserve bird evolutionary history by upgrading those threatened species with fewer close relatives. We recommend developing a mechanism to incorporate a species' genetic value into the prioritization framework.

Abundance models improve spatial and temporal prioritization of conservation resources.

PubMed

Johnston, Alison; Fink, Daniel; Reynolds, Mark D; Hochachka, Wesley M; Sullivan, Brian L; Bruns, Nicholas E; Hallstein, Eric; Merrifield, Matt S; Matsumoto, Sandi; Kelling, Steve

2015-10-01

Conservation prioritization requires knowledge about organism distribution and density. This information is often inferred from models that estimate the probability of species occurrence rather than from models that estimate species abundance, because abundance data are harder to obtain and model. However, occurrence and abundance may not display similar patterns and therefore development of robust, scalable, abundance models is critical to ensuring that scarce conservation resources are applied where they can have the greatest benefits. Motivated by a dynamic land conservation program, we develop and assess a general method for modeling relative abundance using citizen science monitoring data. Weekly estimates of relative abundance and occurrence were compared for prioritizing times and locations of conservation actions for migratory waterbird species in California, USA. We found that abundance estimates consistently provided better rankings of observed counts than occurrence estimates. Additionally, the relationship between abundance and occurrence was nonlinear and varied by species and season. Across species, locations prioritized by occurrence models had only 10-58% overlap with locations prioritized by abundance models, highlighting that occurrence models will not typically identify the locations of highest abundance that are vital for conservation of populations.

Perfluorooctane sulfonate (PFOS) contamination of fish in urban lakes: a prioritization methodology for lake management.

PubMed

Xiao, Feng; Gulliver, John S; Simcik, Matt F

2013-12-15

The contamination of urban lakes by anthropogenic pollutants such as perfluorooctane sulfonate (PFOS) is a worldwide environmental problem. Large-scale, long-term monitoring of urban lakes requires careful prioritization of available resources, focusing efforts on potentially impaired lakes. Herein, a database of PFOS concentrations in 304 fish caught from 28 urban lakes was used for development of an urban-lake prioritization framework by means of exploratory data analysis (EDA) with the aid of a geographical information system. The prioritization scheme consists of three main tiers: preliminary classification, carried out by hierarchical cluster analysis; predictor screening, fulfilled by a regression tree method; and model development by means of a neural network. The predictive performance of the newly developed model was assessed using a training/validation splitting method and determined by an external validation set. The application of the model in the U.S. state of Minnesota identified 40 urban lakes that may contain elevated levels of PFOS; these lakes were not previously considered in PFOS monitoring programs. The model results also highlight ongoing industrial/commercial activities as a principal determinant of PFOS pollution in urban lakes, and suggest vehicular traffic as an important source and surface runoff as a primary pollution carrier. In addition, the EDA approach was further compared to a spatial interpolation method (kriging), and their advantages and disadvantages were discussed. Copyright © 2013 Elsevier Ltd. All rights reserved.

Factoring economic costs into conservation planning may not improve agreement over priorities for protection.

PubMed

Armsworth, Paul R; Jackson, Heather B; Cho, Seong-Hoon; Clark, Melissa; Fargione, Joseph E; Iacona, Gwenllian D; Kim, Taeyoung; Larson, Eric R; Minney, Thomas; Sutton, Nathan A

2017-12-21

Conservation organizations must redouble efforts to protect habitat given continuing biodiversity declines. Prioritization of future areas for protection is hampered by disagreements over what the ecological targets of conservation should be. Here we test the claim that such disagreements will become less important as conservation moves away from prioritizing areas for protection based only on ecological considerations and accounts for varying costs of protection using return-on-investment (ROI) methods. We combine a simulation approach with a case study of forests in the eastern United States, paying particular attention to how covariation between ecological benefits and economic costs influences agreement levels. For many conservation goals, agreement over spatial priorities improves with ROI methods. However, we also show that a reliance on ROI-based prioritization can sometimes exacerbate disagreements over priorities. As such, accounting for costs in conservation planning does not enable society to sidestep careful consideration of the ecological goals of conservation.

Use of a modified Delphi panel to identify and weight criteria for prioritization of zoonotic diseases in Switzerland.

PubMed

Stebler, N; Schuepbach-Regula, G; Braam, P; Falzon, L C

2015-09-01

Zoonotic diseases have a significant impact on public health globally. To prevent or reduce future zoonotic outbreaks, there is a constant need to invest in research and surveillance programs while updating risk management strategies. However, given the limited resources available, disease prioritization based on the need for their control and surveillance is important. This study was performed to identify and weight disease criteria for the prioritization of zoonotic diseases in Switzerland using a semi-quantitative research method based on expert opinion. Twenty-eight criteria relevant for disease control and surveillance, classified under five domains, were selected following a thorough literature review, and these were evaluated and weighted by seven experts from the Swiss Federal Veterinary Office using a modified Delphi panel. The median scores assigned to each criterion were then used to rank 16 notifiable and/or emerging zoonoses in Switzerland. The experts weighted the majority of the criteria similarly, and the top three criteria were Severity of disease in humans, incidence and prevalence of the disease in humans and treatment in humans. Based on these weightings, the three highest ranked diseases were Avian Influenza, Bovine Spongiform Encephalitis, and Bovine Tuberculosis. Overall, this study provided a preliminary list of criteria relevant for disease prioritization in Switzerland. These were further evaluated in a companion study which involved a quantitative prioritization method and multiple stakeholders. Copyright © 2015 Elsevier B.V. All rights reserved.

Prioritizing Chemicals and Data Requirements for Screening-Level Exposure and Risk Assessment

PubMed Central

Brown, Trevor N.; Wania, Frank; Breivik, Knut; McLachlan, Michael S.

2012-01-01

Background: Scientists and regulatory agencies strive to identify chemicals that may cause harmful effects to humans and the environment; however, prioritization is challenging because of the large number of chemicals requiring evaluation and limited data and resources. Objectives: We aimed to prioritize chemicals for exposure and exposure potential and obtain a quantitative perspective on research needs to better address uncertainty in screening assessments. Methods: We used a multimedia mass balance model to prioritize > 12,000 organic chemicals using four far-field human exposure metrics. The propagation of variance (uncertainty) in key chemical information used as model input for calculating exposure metrics was quantified. Results: Modeled human concentrations and intake rates span approximately 17 and 15 orders of magnitude, respectively. Estimates of exposure potential using human concentrations and a unit emission rate span approximately 13 orders of magnitude, and intake fractions span 7 orders of magnitude. The actual chemical emission rate contributes the greatest variance (uncertainty) in exposure estimates. The human biotransformation half-life is the second greatest source of uncertainty in estimated concentrations. In general, biotransformation and biodegradation half-lives are greater sources of uncertainty in modeled exposure and exposure potential than chemical partition coefficients. Conclusions: Mechanistic exposure modeling is suitable for screening and prioritizing large numbers of chemicals. By including uncertainty analysis and uncertainty in chemical information in the exposure estimates, these methods can help identify and address the important sources of uncertainty in human exposure and risk assessment in a systematic manner. PMID:23008278

Teaching Plasmonics, Scanning Probe Microscopy and Other Useful Experiments at the Upper Level

NASA Astrophysics Data System (ADS)

Sanchez, Erik

2012-10-01

It is important to teach students concepts and experimental skills relating to modern research being performed today. Experiments that help educate students about the latest research helps them get jobs and into the doors at many great academic institutions. PSU's Advanced Experimental Class for physics undergraduates offers many novel experiments to help the students accomplish this task. Labs involving Plasmonics, thin film deposition, scanning probe microscopy (SPM) and more will be discussed. In addition, a new NSF funded project involving the building of a Do-It-Yourself (DIY) SPM will be discussed.

Protein classification using sequential pattern mining.

PubMed

Exarchos, Themis P; Papaloukas, Costas; Lampros, Christos; Fotiadis, Dimitrios I

2006-01-01

Protein classification in terms of fold recognition can be employed to determine the structural and functional properties of a newly discovered protein. In this work sequential pattern mining (SPM) is utilized for sequence-based fold recognition. One of the most efficient SPM algorithms, cSPADE, is employed for protein primary structure analysis. Then a classifier uses the extracted sequential patterns for classifying proteins of unknown structure in the appropriate fold category. The proposed methodology exhibited an overall accuracy of 36% in a multi-class problem of 17 candidate categories. The classification performance reaches up to 65% when the three most probable protein folds are considered.

Assessing Attentional Prioritization of Front-of-Pack Nutrition Labels using Change Detection

PubMed Central

Becker, Mark W.; Sundar, Raghav Prashant; Bello, Nora; Alzahabi, Reem; Weatherspoon, Lorraine; Bix, Laura

2015-01-01

We used a change detection method to evaluate attentional prioritization of nutrition information that appears in the traditional “Nutrition Facts Panel” and in front-of-pack nutrition labels. Results provide compelling evidence that front-of-pack labels attract attention more readily than the Nutrition Facts Panel, even when participants are not specifically tasked with searching for nutrition information. Further, color-coding the relative nutritional value of key nutrients within the front-of-pack label resulted in increased attentional prioritization of nutrition information, but coding using facial icons did not significantly increase attention to the label. Finally, the general pattern of attentional prioritization across front-of-pack designs was consistent across a diverse sample of participants. Our results indicate that color-coded, front-of-pack nutrition labels increase attention to the nutrition information of packaged food, a finding that has implications for current policy discussions regarding labeling change. PMID:26851468

Determining and prioritizing competencies in the undergraduate internal medicine curriculum in Saudi Arabia.

PubMed

Almoallim, H

2011-08-01

To determine knowledge and skills competencies in internal medicine for the undergraduate curriculum in Saudi Arabia, competencies were identified based on group work utilizing common textbooks. The Delphi Technique was used as a consensus method to determine and prioritize competencies in internal medicine. A group of 20 clinicians rated the identified competencies from 0-3 (0: no need to know, 1: interesting to know, 2: should know and 3: must know). After formulating the results, a second Delphi round was conducted with 5 experts in internal medicine. A total of 1513 knowledge competencies and 189 skills competencies were determined and prioritized. The competencies corresponded to the 12 systems in internal medicine. All competencies rated 2.2-3.0 were produced separately and considered core competencies for the undergraduate internal medicine curriculum. Determining and prioritizing competencies should influence the curriculum reform process.

Uses of research evidence among US state legislators who prioritize behavioral health issues

PubMed Central

Purtle, Jonathan; Dodson, Elizabeth A.; Brownson, Ross C.

2016-01-01

Objective Disseminating behavioral health (BH) research to legislators (i.e., elected policy makers) is widely acknowledged as a priority, but little is known about how research evidence is used and sought by this audience. The primary aim of this exploratory study was to identify the research dissemination preferences and research seeking practices of legislators who prioritize BH issues and describe the role research plays in determining their policy priorities. The secondary aim was to assess if these legislators differ from legislators who do not prioritize BH issues. Methods A telephone-based survey was conducted with 862 US state legislators (response rate 50%). A validated survey instrument was used to assess legislators’ priorities and the factors that determine them, research dissemination preferences, and research seeking practices. Bivariate analyses were conducted to characterize the study population and compare legislators who prioritized BH issues to legislators who did not. Results Legislators who prioritized BH issues were significantly more likely to identify research evidence as a factor that determined policy priorities than legislators who did not prioritize these issues (odds ratio=1.91, 95% CI=1.25–2.90, p=.002). Legislators who prioritized BH issues also attributed more importance to 10-of-12 features of disseminated research (e.g., research being unbiased [p=.014], research telling a story [p=.033]) and engaged in 8-of-11 research seeking and utilization practices (e.g., attending research presentations [p=.012]) more often. Conclusions Legislators who prioritize BH issues actively seek, have distinct preferences for, and are particularly influenced by research evidence. Testing legislator-focused BH research dissemination strategies is an area for future research. PMID:27364817

Multisectoral prioritization of zoonotic diseases in Uganda, 2017: A One Health perspective

PubMed Central

Bulage, Lilian; Kihembo, Christine; Nantima, Noelina; Monje, Fred; Ndumu, Deo; Sentumbwe, Juliet; Mbolanyi, Betty; Aruho, Robert; Kaboyo, Winyi; Mutonga, David; Basler, Colin; Paige, Sarah; Barton Behravesh, Casey

2018-01-01

Background Zoonotic diseases continue to be a public health burden globally. Uganda is especially vulnerable due to its location, biodiversity, and population. Given these concerns, the Ugandan government in collaboration with the Global Health Security Agenda conducted a One Health Zoonotic Disease Prioritization Workshop to identify zoonotic diseases of greatest national concern to the Ugandan government. Materials and methods The One Health Zoonotic Disease Prioritization tool, a semi-quantitative tool developed by the U.S. Centers for Disease Control and Prevention, was used for the prioritization of zoonoses. Workshop participants included voting members and observers representing multiple government and non-governmental sectors. During the workshop, criteria for prioritization were selected, and questions and weights relevant to each criterion were determined. We used a decision tree to provide a ranked list of zoonoses. Participants then established next steps for multisectoral engagement for the prioritized zoonoses. A sensitivity analysis demonstrated how criteria weights impacted disease prioritization. Results Forty-eight zoonoses were considered during the workshop. Criteria selected to prioritize zoonotic diseases were (1) severity of disease in humans in Uganda, (2) availability of effective control strategies, (3) potential to cause an epidemic or pandemic in humans or animals, (4) social and economic impacts, and (5) bioterrorism potential. Seven zoonotic diseases were identified as priorities for Uganda: anthrax, zoonotic influenza viruses, viral hemorrhagic fevers, brucellosis, African trypanosomiasis, plague, and rabies. Sensitivity analysis did not indicate significant changes in zoonotic disease prioritization based on criteria weights. Discussion One Health approaches and multisectoral collaborations are crucial to the surveillance, prevention, and control strategies for zoonotic diseases. Uganda used such an approach to identify zoonoses of national concern. Identifying these priority diseases enables Uganda’s National One Health Platform and Zoonotic Disease Coordination Office to address these zoonoses in the future with a targeted allocation of resources. PMID:29715287

FIFRA Scientific Advisory Panel Minutes No. 21015-04. A set of scientific issues being considered by the Environmental Protection Agency regarding integrated endocrine bioactivity and exposure-based prioritization & screening

USDA-ARS?s Scientific Manuscript database

On December 2-4, 2014, the US Environmental Protection Agency convened a public meeting of the FIFRA Scientific Advisory Panel (SAP) to address scientific issues associated with the agency’s “Integrated Endocrine Bioactivity and Exposure-Based Prioritization and Screening” methods. EPA is proposing ...

Functional mapping of language networks in the normal brain using a word-association task.

PubMed

Ghosh, Shantanu; Basu, Amrita; Kumaran, Senthil S; Khushu, Subash

2010-08-01

Language functions are known to be affected in diverse neurological conditions, including ischemic stroke, traumatic brain injury, and brain tumors. Because language networks are extensive, interpretation of functional data depends on the task completed during evaluation. The aim was to map the hemodynamic consequences of word association using functional magnetic resonance imaging (fMRI) in normal human subjects. Ten healthy subjects underwent fMRI scanning with a postlexical access semantic association task vs lexical processing task. The fMRI protocol involved a T2*-weighted gradient-echo echo-planar imaging (GE-EPI) sequence (TR 4523 ms, TE 64 ms, flip angle 90°) with alternate baseline and activation blocks. A total of 78 scans were taken (interscan interval = 3 s) with a total imaging time of 587 s. Functional data were processed in Statistical Parametric Mapping software (SPM2) with 8-mm Gaussian kernel by convolving the blood oxygenation level-dependent (BOLD) signal with an hemodynamic response function estimated by general linear method to generate SPM{t} and SPM{F} maps. Single subject analysis of the functional data (FWE-corrected, P≤0.001) revealed extensive activation in the frontal lobes, with overlaps among middle frontal gyrus (MFG), superior, and inferior frontal gyri. BOLD activity was also found in the medial frontal gyrus, middle occipital gyrus (MOG), anterior fusiform gyrus, superior and inferior parietal lobules, and to a smaller extent, the thalamus and right anterior cerebellum. Group analysis (FWE-corrected, P≤0.001) revealed neural recruitment of bilateral lingual gyri, left MFG, bilateral MOG, left superior occipital gyrus, left fusiform gyrus, bilateral thalami, and right cerebellar areas. Group data analysis revealed a cerebellar-occipital-fusiform-thalamic network centered around bilateral lingual gyri for word association, thereby indicating how these areas facilitate language comprehension by activating a semantic association network of words processed postlexical access. This finding is important when assessing the extent of cognitive damage and/or recovery and can be used for presurgical planning after optimization.

Nature, Origin and Transfers of SPM (Mineral, Organic, and Biological) in Hydrosystems : a New Methodological Approach by Morphogranulometry

NASA Astrophysics Data System (ADS)

Viennet, D.; Fournier, M.; Copard, Y.; Dupont, J. P.

2017-12-01

Source to sink is one of the main concepts in Earth Sciences for a better knowledge of hydrosystems dynamics. Regarding this issue, the present day challenge consists in the characterization by in-situ measurements of the nature and the origin of suspended particles matters (SPM). Few methods can fully cover such requirements and among them, the methodology using the form of particles deserves to be developed. Indeed, morphometry of particles is widely used in sedimentology to identify different sedimentary stocks, source-to-sink transport and sedimentation mechanisms. Currently, morphometry analyses are carried out by scanning electron microscope coupled to image analysis to measure various size and shape descriptors on particles like flatness, elongation, circularity, sphericity, bluntness, fractal dimension. However, complexity and time of analysis are the main limitations of this technique for a long-term monitoring of SPM transfers. Here we present an experimental morphometric approach using a morphogranulometer (a CCD camera coupled to a peristaltic pump). The camera takes pictures while the sample is circulating through a flow cell, leading to the analysis of numerous particles in a short time. The image analysis provides size and shape information discriminating various particles stocks according to their nature and origin by statistical analyses. Measurements were carried out on standard samples of particles commonly found in natural waters. The size and morphological distributions of the different mineral fractions (clay, sand, oxides etc), biologic (microalgae, pollen, etc) and organic (peat, coal, soil organic matter, etc) samples are statistically independent and can be discriminated on a 4D graph. Next step will be on field in situ measurements in a sink-spring network to understand the transfers of the particles stocks inside this simple karstic network. Such a development would be promising for the characterisation of natural hydrosystems.

C5 glycolipids of heterocystous cyanobacteria track symbiont abundance in the diatom Hemiaulus hauckii across the tropical North Atlantic

NASA Astrophysics Data System (ADS)

Bale, Nicole J.; Villareal, Tracy A.; Hopmans, Ellen C.; Brussaard, Corina P. D.; Besseling, Marc; Dorhout, Denise; Sinninghe Damsté, Jaap S.; Schouten, Stefan

2018-03-01

Diatom-diazotroph associations (DDAs) include marine heterocystous cyanobacteria found as exosymbionts and endosymbionts in multiple diatom species. Heterocysts are the site of N2 fixation and have thickened cell walls containing unique heterocyst glycolipids which maintain a low oxygen environment within the heterocyst. The endosymbiotic cyanobacterium Richelia intracellularis found in species of the diatom genus Hemiaulus and Rhizosolenia makes heterocyst glycolipids (HGs) which are composed of C30 and C32 diols and triols with pentose (C5) moieties that are distinct from limnetic cyanobacterial HGs with predominantly hexose (C6) moieties. Here we applied a method for analysis of intact polar lipids to the study of HGs in suspended particulate matter (SPM) and surface sediment from across the tropical North Atlantic. The study focused on the Amazon plume region, where DDAs are documented to form extensive surface blooms, in order to examine the utility of C5 HGs as markers for DDAs as well as their transportation to underlying sediments. C30 and C32 triols with C5 pentose moieties were detected in both marine SPM and surface sediments. We found a significant correlation between the water column concentration of these long-chain C5 HGs and DDA symbiont counts. In particular, the concentrations of both the C5 HGs (1-(O-ribose)-3,27,29-triacontanetriol (C5 HG30 triol) and 1-(O-ribose)-3,29,31-dotriacontanetriol (C5 HG32 triol)) in SPM exhibited a significant correlation with the number of Hemiaulus hauckii symbionts. This result strengthens the idea that long-chain C5 HGs can be applied as biomarkers for marine endosymbiotic heterocystous cyanobacteria. The presence of the same C5 HGs in surface sediment provides evidence that they are effectively transported to the sediment and hence have potential as biomarkers for studies of the contribution of DDAs to the paleo-marine N cycle.

Reactive oxygen species and nitric oxide are involved in polyamine-induced growth inhibition in wheat plants.

PubMed

Recalde, Laura; Vázquez, Analía; Groppa, María D; Benavides, María Patricia

2018-03-06

Polyamines (PAs) produce H 2 O 2 and nitric oxide (NO) during their normal catabolism and modulate plant growth and development. To explore the biochemical basis of PAs-induced growth inhibition in Triticum aestivum L seedlings, we examined the role of O 2 ·- , H 2 O 2 or NO in shoot and root development. Although all PA treatments resulted in a variable reduction of root and shoot elongation, spermine (Spm) caused the greater inhibition in a similar way to that observed with the NO donor, sodium nitroprusside (SNP). In both cases, O 2 ·- production was completely blocked whereas H 2 O 2 formation was high in the root apex under SNP or Spm treatments. Catalase recovered root and shoot growth in SNP but not in Spm-treated plants, revealing the involvement of H 2 O 2 in SNP-root length reduction. The addition of the NO scavenger, cPTIO, restored root length in SNP- or Spm-treated plants, respectively, and partially recovered O 2 ·- levels, compared to the plants exposed to PAs or SNP without cPTIO. A strong correlation was observed between root growth restoration and O 2 ·- accumulation after treating roots with SNP + aminoguanidine, a diamine oxidase inhibitor, and with SNP + 1,8-diaminoctane, a polyamine oxidase inhibitor, confirming the essential role of O 2 ·- formation for root growth and the importance of the origin and level of H 2 O 2 . The differential modulation of wheat growth by PAs through reactive oxygen species or NO is discussed. Graphical abstract Polyamines, nitric oxide and ROS interaction in plants during plant growth.

Inhibition of ATPase activity in rat synaptic plasma membranes by simultaneous exposure to metals.

PubMed

Carfagna, M A; Ponsler, G D; Muhoberac, B B

1996-03-08

Inhibition of Na+/K+-ATPase and Mg2+-ATPase activities by in vitro exposure to Cd2+, Pb2+ and Mn2+ was investigated in rat brain synaptic plasma membranes (SPMs). Cd2+ and Pb2+ produced a larger maximal inhibition of Na+/K+-ATPase than of Mg2+-ATPase activity. Metal concentrations causing 50% inhibition of Na+/K+-ATPase activity (IC50 values) were Cd2+ (0.6 microM) < Pb2+ (2.1 microM) < Mn2+ (approximately 3 mM), and the former two metals were substantially more potent in inhibiting SPM versus synaptosomal Na+/K+-ATPase. Dixon plots of SPM data indicated that equilibrium binding of metals occurs at sites causing enzyme inhibition. In addition, IC50 values for SPM K+-dependent p-nitrophenylphosphatase inhibition followed the same order and were Cd2+ (0.4 microM) < Pb2+ (1.2 microM) < Mn2+ (300 microM). Simultaneous exposure to the combinations Cd2+/Mn2+ or Pb2+/Mn2+ inhibited SPM Na+/K+-ATPase activity synergistically (i.e., greater than the sum of the metal-induced inhibitions assayed separately), while Cd2+/Pb2+ caused additive inhibition. Simultaneous exposure to Cd2+/Pb2+ antagonistically inhibited Mg2+-ATPase activity while Cd2+/Mn2+ or Pb2+/Mn2+ additively inhibited Mg2+-ATPase activity at low Mn2+ concentrations, but inhibited antagonistically at higher concentrations. The similar IC50 values for Cd2+ and Pb2+ versus Mn2+ inhibition of Na+/K+-ATPase and the pattern of inhibition/activation upon exposure to two metals simultaneously support similar modes of interaction of Cd2+ and Pb2+ with this enzyme, in agreement with their chemical reactivities.

Bloodstream infections caused by multi-drug resistant Proteus mirabilis: Epidemiology, risk factors and impact of multi-drug resistance.

PubMed

Korytny, Alexander; Riesenberg, Klaris; Saidel-Odes, Lisa; Schlaeffer, Fransisc; Borer, Abraham

2016-01-01

The prevalence of antimicrobial co-resistance among ESBL-producing Enterobactereaceae is extremely high in Israel. Multidrug-resistant Proteus mirabilis strains (MDR-PM), resistant to almost all antibiotic classes have been described. The aim was to determine the risk factors for bloodstream infections caused by MDR-PM and clinical outcomes. A retrospective case-control study. Adult patients with PM bacteremia during 7 years were identified retrospectively and their files reviewed for demographics, underlying diseases, Charlson Comorbidity Index, treatment and outcome. One hundred and eighty patients with PM-bloodstream infection (BSI) were included; 90 cases with MDR-PM and 90 controls with sensitive PM (S-PM). Compared to controls, cases more frequently were from nursing homes, had recurrent hospital admissions in the past year and received antibiotic therapy in the previous 3 months, were bedridden and suffered from peripheral vascular disease and peptic ulcer disease (p < 0.001). Two-thirds of the MDR-PM isolates were ESBL-producers vs 4.4% of S-PM isolates (p < 0.001, OR = 47.6, 95% CI = 15.9-142.6). In-hospital crude mortality rate of patients with MDR-PM BSI was 37.7% vs 23.3% in those with S-PM BSI (p = 0.0359, OR = 2, 95% CI = 1.4-3.81). PM bacteremia in elderly and functionally-dependent patients is likely to be caused by nearly pan-resistant PM strains in the institution; 51.8% of the patients received inappropriate empiric antibiotic treatment. The crude mortality rate of patients with MDR-PM BSI was significantly higher than that of patients with S-PM BSI.

Prescribing joint co-ordinates during model preparation to improve inverse kinematic estimates of elbow joint angles.

PubMed

Wells, D J M; Alderson, J A; Dunne, J; Elliott, B C; Donnelly, C J

2017-01-25

To appropriately use inverse kinematic (IK) modelling for the assessment of human motion, a musculoskeletal model must be prepared 1) to match participant segment lengths (scaling) and 2) to align the model׳s virtual markers positions with known, experimentally derived kinematic marker positions (marker registration). The purpose of this study was to investigate whether prescribing joint co-ordinates during the marker registration process (within the modelling framework OpenSim) will improve IK derived elbow kinematics during an overhead sporting task. To test this, the upper limb kinematics of eight cricket bowlers were recorded during two testing sessions, with a different tester each session. The bowling trials were IK modelled twice: once with an upper limb musculoskeletal model prepared with prescribed participant specific co-ordinates during marker registration - MR PC - and once with the same model prepared without prescribed co-ordinates - MR; and by an established direct kinematic (DK) upper limb model. Whilst both skeletal model preparations had strong inter-tester repeatability (MR: Statistical Parametric Mapping (SPM1D)=0% different; MR PC : SPM1D=0% different), when compared with DK model elbow FE waveform estimates, IK estimates using the MR PC model (RMSD=5.2±2.0°, SPM1D=68% different) were in closer agreement than the estimates from the MR model (RMSD=44.5±18.5°, SPM1D=100% different). Results show that prescribing participant specific joint co-ordinates during the marker registration phase of model preparation increases the accuracy and repeatability of IK solutions when modelling overhead sporting tasks in OpenSim. Copyright © 2016 Elsevier Ltd. All rights reserved.

Geochemistry of the suspended sediment in the estuaries of the Mandovi and Zuari rivers, central west coast of India.

PubMed

Kessarkar, Pratima M; Shynu, R; Rao, V Purnachandra; Chong, Feng; Narvekar, Tanuja; Zhang, Jing

2013-05-01

The geochemistry of the suspended particulate matter (SPM) collected during the monsoon was determined to identify the sources of SPM and to understand the physicochemical processes in the Mandovi and Zuari river estuaries. The concentrations of SPM decrease seaward in both estuaries, but are relatively high at bay stations. Kaolinite is the most dominant clay mineral in the upstream of both rivers. Smectite increases seaward in both estuaries and is abundant in the bay. Upstream stations of Mandovi, where ore deposits are stored on the shore, exhibit high Fe, Mn, total rare earth elements (∑REE), and middle REE- and heavy REE-enriched patterns. Channel stations of both estuaries exhibit middle REE- and light REE-enriched patterns, which gradually changed seaward to middle REE- and heavy REE-enriched patterns. Canal stations exhibit the highest concentrations of major and trace metals. High metal/Al ratios occur at stations in the upstream of Zuari and at the confluence of canals in the Mandovi estuary. Enrichment factors of metals indicate that Mn is significantly polluted while other metals are moderately polluted. The δ(13)C and δ(15)N of organic matter indicate that the terrigenous organic matter at the upstream is diluted seaward by marine organic matter. Organic matter at bay stations is largely marine and altered-type. The compositions of SPM are controlled by the particulates from ore dust, the geology of the drainage basins, and the physicochemical processes in the estuaries. Particulates resuspended from the bay are dominated by ore dust, which are advected into the channels of both estuaries during the lull periods of the monsoon.

Modeling Clinical Outcomes in Prostate Cancer: Application and Validation of the Discrete Event Simulation Approach.

PubMed

Pan, Feng; Reifsnider, Odette; Zheng, Ying; Proskorovsky, Irina; Li, Tracy; He, Jianming; Sorensen, Sonja V

2018-04-01

Treatment landscape in prostate cancer has changed dramatically with the emergence of new medicines in the past few years. The traditional survival partition model (SPM) cannot accurately predict long-term clinical outcomes because it is limited by its ability to capture the key consequences associated with this changing treatment paradigm. The objective of this study was to introduce and validate a discrete-event simulation (DES) model for prostate cancer. A DES model was developed to simulate overall survival (OS) and other clinical outcomes based on patient characteristics, treatment received, and disease progression history. We tested and validated this model with clinical trial data from the abiraterone acetate phase III trial (COU-AA-302). The model was constructed with interim data (55% death) and validated with the final data (96% death). Predicted OS values were also compared with those from the SPM. The DES model's predicted time to chemotherapy and OS are highly consistent with the final observed data. The model accurately predicts the OS hazard ratio from the final data cut (predicted: 0.74; 95% confidence interval [CI] 0.64-0.85 and final actual: 0.74; 95% CI 0.6-0.88). The log-rank test to compare the observed and predicted OS curves indicated no statistically significant difference between observed and predicted curves. However, the predictions from the SPM based on interim data deviated significantly from the final data. Our study showed that a DES model with properly developed risk equations presents considerable improvements to the more traditional SPM in flexibility and predictive accuracy of long-term outcomes. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

The Effect of Exogenous Spermidine Concentration on Polyamine Metabolism and Salt Tolerance in Zoysiagrass (Zoysia japonica Steud) Subjected to Short-Term Salinity Stress.

PubMed

Li, Shucheng; Jin, Han; Zhang, Qiang

2016-01-01

Salt stress, particularly short-term salt stress, is among the most serious abiotic factors limiting plant survival and growth in China. It has been established that exogenous spermidine (Spd) stimulates plant tolerance to salt stress. The present study utilized two zoysiagrass cultivars commonly grown in China that exhibit either sensitive (cv. Z081) or tolerant (cv. Z057) adaptation capacity to salt stress. The two cultivars were subjected to 200 mM salt stress and treated with different exogenous Spd concentrations for 8 days. Polyamine [diamine putrescine (Put), tetraamine spermine (Spm), and Spd], H2O2 and malondialdehyde (MDA) contents and polyamine metabolic (ADC, ODC, SAMDC, PAO, and DAO) and antioxidant (superoxide dismutase, catalase, and peroxidase) enzyme activities were measured. The results showed that salt stress induced increases in Spd and Spm contents and ornithine decarboxylase (ODC), S-adenosylmethionine decarboxylase (SAMDC), and diamine oxidase (DAO) activities in both cultivars. Exogenous Spd application did not alter polyamine contents via regulation of polyamine-degrading enzymes, and an increase in polyamine biosynthetic enzyme levels was observed during the experiment. Increasing the concentration of exogenous Spd resulted in a tendency of the Spd and Spm contents and ODC, SAMDC, DAO, and antioxidant enzyme activities to first increase and then decrease in both cultivars. H2O2 and MDA levels significantly decreased in both cultivars treated with Spd. Additionally, in both cultivars, positive correlations between polyamine biosynthetic enzymes (ADC, SAMDC), DAO, and antioxidant enzymes (SOD, POD, CAT), but negative correlations with H2O2 and MDA levels, and the Spd + Spm content were observed with an increase in the concentration of exogenous Spd.

The Effect of Exogenous Spermidine Concentration on Polyamine Metabolism and Salt Tolerance in Zoysiagrass (Zoysia japonica Steud) Subjected to Short-Term Salinity Stress

PubMed Central

Li, Shucheng; Jin, Han; Zhang, Qiang

2016-01-01

Salt stress, particularly short-term salt stress, is among the most serious abiotic factors limiting plant survival and growth in China. It has been established that exogenous spermidine (Spd) stimulates plant tolerance to salt stress. The present study utilized two zoysiagrass cultivars commonly grown in China that exhibit either sensitive (cv. Z081) or tolerant (cv. Z057) adaptation capacity to salt stress. The two cultivars were subjected to 200 mM salt stress and treated with different exogenous Spd concentrations for 8 days. Polyamine [diamine putrescine (Put), tetraamine spermine (Spm), and Spd], H2O2 and malondialdehyde (MDA) contents and polyamine metabolic (ADC, ODC, SAMDC, PAO, and DAO) and antioxidant (superoxide dismutase, catalase, and peroxidase) enzyme activities were measured. The results showed that salt stress induced increases in Spd and Spm contents and ornithine decarboxylase (ODC), S-adenosylmethionine decarboxylase (SAMDC), and diamine oxidase (DAO) activities in both cultivars. Exogenous Spd application did not alter polyamine contents via regulation of polyamine-degrading enzymes, and an increase in polyamine biosynthetic enzyme levels was observed during the experiment. Increasing the concentration of exogenous Spd resulted in a tendency of the Spd and Spm contents and ODC, SAMDC, DAO, and antioxidant enzyme activities to first increase and then decrease in both cultivars. H2O2 and MDA levels significantly decreased in both cultivars treated with Spd. Additionally, in both cultivars, positive correlations between polyamine biosynthetic enzymes (ADC, SAMDC), DAO, and antioxidant enzymes (SOD, POD, CAT), but negative correlations with H2O2 and MDA levels, and the Spd + Spm content were observed with an increase in the concentration of exogenous Spd. PMID:27582752

Temporal occurrence and sources of persistent organic pollutants in suspended particulate matter from the most heavily polluted river mouth of Lake Chaohu, China.

PubMed

Liu, Cheng; Zhang, Lei; Fan, Chengxin; Xu, Fuliu; Chen, Kaining; Gu, Xiaozhi

2017-05-01

The Nanfei River is by many measures the most heavily polluted tributary to Lake Chaohu. In this study, the temporal occurrence and sources of four classes of persistent organic pollutants (POPs), including polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs), polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs), in suspended particulate matter (SPM) from the river mouth were investigated monthly during 2014. Results show that concentrations of all four POPs in SPM were higher than those in the sediment of Lake Chaohu. PBDEs (26.7 ng g -1 dry weight (dw)) were originated mainly from commercial deca-BDE mixtures. PCB concentrations (1.336 ng g -1 dw) were lower than those of sediments in many other water bodies worldwide. PAHs (2597 ng g -1 dw) and OCPs (57.38 ng g -1 dw) were the most common POPs. PAHs mainly had high molecular weights and originated from pyrolytic sources, with a small proportion of petrogenic origin. The predominant OCPs were DDTs, heptachlorepoxides, dieldrin, hexachlorocyclohexanes, hexachlorobenzene, and chlordanes. Most OCPs originated from historical use, except lindane. Generally, of all the POPs studied, those of primary ecological concern should be acenaphthene, fluorene, DDTs, and chlordanes. Higher concentrations of POPs were detected during winter and spring than in summer and autumn, probably because of the high river flow during the rainy season. The high concentration of POPs in the riverine SPM and the fractionation of POPs in the water and SPM of the river should be a focal point in the future study of Lake Chaohu. Copyright © 2017 Elsevier Ltd. All rights reserved.