retention time alignment: Topics by Science.gov

Sample records for retention time alignment

Feature Based Retention Time Alignment for Improved HDX MS Analysis

NASA Astrophysics Data System (ADS)

Venable, John D.; Scuba, William; Brock, Ansgar

2013-04-01

An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.
High-speed peak matching algorithm for retention time alignment of gas chromatographic data for chemometric analysis.

PubMed

Johnson, Kevin J; Wright, Bob W; Jarman, Kristin H; Synovec, Robert E

2003-05-09

A rapid retention time alignment algorithm was developed as a preprocessing utility to be used prior to chemometric analysis of large datasets of diesel fuel profiles obtained using gas chromatography (GC). Retention time variation from chromatogram-to-chromatogram has been a significant impediment against the use of chemometric techniques in the analysis of chromatographic data due to the inability of current chemometric techniques to correctly model information that shifts from variable to variable within a dataset. The alignment algorithm developed is shown to increase the efficacy of pattern recognition methods applied to diesel fuel chromatograms by retaining chemical selectivity while reducing chromatogram-to-chromatogram retention time variations and to do so on a time scale that makes analysis of large sets of chromatographic data practical. Two sets of diesel fuel gas chromatograms were studied using the novel alignment algorithm followed by principal component analysis (PCA). In the first study, retention times for corresponding chromatographic peaks in 60 chromatograms varied by as much as 300 ms between chromatograms before alignment. In the second study of 42 chromatograms, the retention time shifting exhibited was on the order of 10 s between corresponding chromatographic peaks, and required a coarse retention time correction prior to alignment with the algorithm. In both cases, an increase in retention time precision afforded by the algorithm was clearly visible in plots of overlaid chromatograms before and then after applying the retention time alignment algorithm. Using the alignment algorithm, the standard deviation for corresponding peak retention times following alignment was 17 ms throughout a given chromatogram, corresponding to a relative standard deviation of 0.003% at an average retention time of 8 min. This level of retention time precision is a 5-fold improvement over the retention time precision initially provided by a state-of-the-art GC instrument equipped with electronic pressure control and was critical to the performance of the chemometric analysis. This increase in retention time precision does not come at the expense of chemical selectivity, since the PCA results suggest that essentially all of the chemical selectivity is preserved. Cluster resolution between dissimilar groups of diesel fuel chromatograms in a two-dimensional scores space generated with PCA is shown to substantially increase after alignment. The alignment method is robust against missing or extra peaks relative to a target chromatogram used in the alignment, and operates at high speed, requiring roughly 1 s of computation time per GC chromatogram.
Retention time alignment of LC/MS data by a divide-and-conquer algorithm.

PubMed

Zhang, Zhongqi

2012-04-01

Liquid chromatography-mass spectrometry (LC/MS) has become the method of choice for characterizing complex mixtures. These analyses often involve quantitative comparison of components in multiple samples. To achieve automated sample comparison, the components of interest must be detected and identified, and their retention times aligned and peak areas calculated. This article describes a simple pairwise iterative retention time alignment algorithm, based on the divide-and-conquer approach, for alignment of ion features detected in LC/MS experiments. In this iterative algorithm, ion features in the sample run are first aligned with features in the reference run by applying a single constant shift of retention time. The sample chromatogram is then divided into two shorter chromatograms, which are aligned to the reference chromatogram the same way. Each shorter chromatogram is further divided into even shorter chromatograms. This process continues until each chromatogram is sufficiently narrow so that ion features within it have a similar retention time shift. In six pairwise LC/MS alignment examples containing a total of 6507 confirmed true corresponding feature pairs with retention time shifts up to five peak widths, the algorithm successfully aligned these features with an error rate of 0.2%. The alignment algorithm is demonstrated to be fast, robust, fully automatic, and superior to other algorithms. After alignment and gap-filling of detected ion features, their abundances can be tabulated for direct comparison between samples.
Unsupervised parameter optimization for automated retention time alignment of severely shifted gas chromatographic data using the piecework alignment algorithm.

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

Pierce, Karisa M.; Wright, Bob W.; Synovec, Robert E.

2007-02-02

First, simulated chromatographic separations with declining retention time precision were used to study the performance of the piecewise retention time alignment algorithm and to demonstrate an unsupervised parameter optimization method. The average correlation coefficient between the first chromatogram and every other chromatogram in the data set was used to optimize the alignment parameters. This correlation method does not require a training set, so it is unsupervised and automated. This frees the user from needing to provide class information and makes the alignment algorithm more generally applicable to classifying completely unknown data sets. For a data set of simulated chromatograms wheremore » the average chromatographic peak was shifted past two neighboring peaks between runs, the average correlation coefficient of the raw data was 0.46 ± 0.25. After automated, optimized piecewise alignment, the average correlation coefficient was 0.93 ± 0.02. Additionally, a relative shift metric and principal component analysis (PCA) were used to independently quantify and categorize the alignment performance, respectively. The relative shift metric was defined as four times the standard deviation of a given peak’s retention time in all of the chromatograms, divided by the peak-width-at-base. The raw simulated data sets that were studied contained peaks with average relative shifts ranging between 0.3 and 3.0. Second, a “real” data set of gasoline separations was gathered using three different GC methods to induce severe retention time shifting. In these gasoline separations, retention time precision improved ~8 fold following alignment. Finally, piecewise alignment and the unsupervised correlation optimization method were applied to severely shifted GC separations of reformate distillation fractions. The effect of piecewise alignment on peak heights and peak areas is also reported. Piecewise alignment either did not change the peak height, or caused it to slightly decrease. The average relative difference in peak height after piecewise alignment was –0.20%. Piecewise alignment caused the peak areas to either stay the same, slightly increase, or slightly decrease. The average absolute relative difference in area after piecewise alignment was 0.15%.« less
A Comprehensive Two-Dimensional Retention Time Alignment Algorithm To Enhance Chemometric Analysis of Comprehensive Two-Dimensional Separation Data

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

Pierce, Karisa M.; Wood, Lianna F.; Wright, Bob W.

2005-12-01

A comprehensive two-dimensional (2D) retention time alignment algorithm was developed using a novel indexing scheme. The algorithm is termed comprehensive because it functions to correct the entire chromatogram in both dimensions and it preserves the separation information in both dimensions. Although the algorithm is demonstrated by correcting comprehensive two-dimensional gas chromatography (GC x GC) data, the algorithm is designed to correct shifting in all forms of 2D separations, such as LC x LC, LC x CE, CE x CE, and LC x GC. This 2D alignment algorithm was applied to three different data sets composed of replicate GC x GCmore » separations of (1) three 22-component control mixtures, (2) three gasoline samples, and (3) three diesel samples. The three data sets were collected using slightly different temperature or pressure programs to engender significant retention time shifting in the raw data and then demonstrate subsequent corrections of that shifting upon comprehensive 2D alignment of the data sets. Thirty 12-min GC x GC separations from three 22-component control mixtures were used to evaluate the 2D alignment performance (10 runs/mixture). The average standard deviation of the first column retention time improved 5-fold from 0.020 min (before alignment) to 0.004 min (after alignment). Concurrently, the average standard deviation of second column retention time improved 4-fold from 3.5 ms (before alignment) to 0.8 ms (after alignment). Alignment of the 30 control mixture chromatograms took 20 min. The quantitative integrity of the GC x GC data following 2D alignment was also investigated. The mean integrated signal was determined for all components in the three 22-component mixtures for all 30 replicates. The average percent difference in the integrated signal for each component before and after alignment was 2.6%. Singular value decomposition (SVD) was applied to the 22-component control mixture data before and after alignment to show the restoration of trilinearity to the data, since trilinearity benefits chemometric analysis. By applying comprehensive 2D retention time alignment to all three data sets (control mixtures, gasoline samples, and diesel samples), classification by principal component analysis (PCA) substantially improved, resulting in 100% accurate scores clustering.« less
DISCO: Distance and Spectrum Correlation Optimization Alignment for Two Dimensional Gas Chromatography Time-of-Flight Mass Spectrometry-based Metabolomics

PubMed Central

Wang, Bing; Fang, Aiqin; Heim, John; Bogdanov, Bogdan; Pugh, Scott; Libardoni, Mark; Zhang, Xiang

2010-01-01

A novel peak alignment algorithm using a distance and spectrum correlation optimization (DISCO) method has been developed for two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) based metabolomics. This algorithm uses the output of the instrument control software, ChromaTOF, as its input data. It detects and merges multiple peak entries of the same metabolite into one peak entry in each input peak list. After a z-score transformation of metabolite retention times, DISCO selects landmark peaks from all samples based on both two-dimensional retention times and mass spectrum similarity of fragment ions measured by Pearson’s correlation coefficient. A local linear fitting method is employed in the original two-dimensional retention time space to correct retention time shifts. A progressive retention time map searching method is used to align metabolite peaks in all samples together based on optimization of the Euclidean distance and mass spectrum similarity. The effectiveness of the DISCO algorithm is demonstrated using data sets acquired under different experiment conditions and a spiked-in experiment. PMID:20476746
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.

PubMed

Hoffmann, Nils; Stoye, Jens

2009-08-15

We describe ChromA, a web-based alignment tool for chromatography-mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location.
ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

PubMed Central

Hoffmann, Nils; Stoye, Jens

2009-01-01

Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location. Contact: stoye@techfak.uni-bielefeld.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19505941
Robust algorithm for aligning two-dimensional chromatograms.

PubMed

Gros, Jonas; Nabi, Deedar; Dimitriou-Christidis, Petros; Rutler, Rebecca; Arey, J Samuel

2012-11-06

Comprehensive two-dimensional gas chromatography (GC × GC) chromatograms typically exhibit run-to-run retention time variability. Chromatogram alignment is often a desirable step prior to further analysis of the data, for example, in studies of environmental forensics or weathering of complex mixtures. We present a new algorithm for aligning whole GC × GC chromatograms. This technique is based on alignment points that have locations indicated by the user both in a target chromatogram and in a reference chromatogram. We applied the algorithm to two sets of samples. First, we aligned the chromatograms of twelve compositionally distinct oil spill samples, all analyzed using the same instrument parameters. Second, we applied the algorithm to two compositionally distinct wastewater extracts analyzed using two different instrument temperature programs, thus involving larger retention time shifts than the first sample set. For both sample sets, the new algorithm performed favorably compared to two other available alignment algorithms: that of Pierce, K. M.; Wood, Lianna F.; Wright, B. W.; Synovec, R. E. Anal. Chem.2005, 77, 7735-7743 and 2-D COW from Zhang, D.; Huang, X.; Regnier, F. E.; Zhang, M. Anal. Chem.2008, 80, 2664-2671. The new algorithm achieves the best matches of retention times for test analytes, avoids some artifacts which result from the other alignment algorithms, and incurs the least modification of quantitative signal information.
A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.

PubMed

Robinson, Mark D; De Souza, David P; Keen, Woon Wai; Saunders, Eleanor C; McConville, Malcolm J; Speed, Terence P; Likić, Vladimir A

2007-10-29

Gas chromatography-mass spectrometry (GC-MS) is a robust platform for the profiling of certain classes of small molecules in biological samples. When multiple samples are profiled, including replicates of the same sample and/or different sample states, one needs to account for retention time drifts between experiments. This can be achieved either by the alignment of chromatographic profiles prior to peak detection, or by matching signal peaks after they have been extracted from chromatogram data matrices. Automated retention time correction is particularly important in non-targeted profiling studies. A new approach for matching signal peaks based on dynamic programming is presented. The proposed approach relies on both peak retention times and mass spectra. The alignment of more than two peak lists involves three steps: (1) all possible pairs of peak lists are aligned, and similarity of each pair of peak lists is estimated; (2) the guide tree is built based on the similarity between the peak lists; (3) peak lists are progressively aligned starting with the two most similar peak lists, following the guide tree until all peak lists are exhausted. When two or more experiments are performed on different sample states and each consisting of multiple replicates, peak lists within each set of replicate experiments are aligned first (within-state alignment), and subsequently the resulting alignments are aligned themselves (between-state alignment). When more than two sets of replicate experiments are present, the between-state alignment also employs the guide tree. We demonstrate the usefulness of this approach on GC-MS metabolic profiling experiments acquired on wild-type and mutant Leishmania mexicana parasites. We propose a progressive method to match signal peaks across multiple GC-MS experiments based on dynamic programming. A sensitive peak similarity function is proposed to balance peak retention time and peak mass spectra similarities. This approach can produce the optimal alignment between an arbitrary number of peak lists, and models explicitly within-state and between-state peak alignment. The accuracy of the proposed method was close to the accuracy of manually-curated peak matching, which required tens of man-hours for the analyzed data sets. The proposed approach may offer significant advantages for processing of high-throughput metabolomics data, especially when large numbers of experimental replicates and multiple sample states are analyzed.
High-speed peak matching algorithm for retention time alignment of gas chromatographic data for chemometric analysis

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

Johnson, Kevin J.; Wright, Bob W.; Jarman, Kristin H.

2003-05-09

A rapid retention time alignment algorithm was developed as a preprocessing utility to be used prior to chemometric analysis of large datasets of diesel fuel gas chromatographic profiles. Retention time variation from chromatogram-to-chromatogram has been a significant impediment against the use of chemometric techniques in the analysis of chromatographic data due to the inability of current multivariate techniques to correctly model information that shifts from variable to variable within a dataset. The algorithm developed is shown to increase the efficacy of pattern recognition methods applied to a set of diesel fuel chromatograms by retaining chemical selectivity while reducing chromatogram-to-chromatogram retentionmore » time variations and to do so on a time scale that makes analysis of large sets of chromatographic data practical.« less
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets.

PubMed

Hoffmann, Nils; Keck, Matthias; Neuweger, Heiko; Wilhelm, Mathias; Högy, Petra; Niehaus, Karsten; Stoye, Jens

2012-08-27

Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to allow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features. In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE) and center-star multiple alignment by pairwise partitioned dynamic time warping (CeMAPP-DTW). We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CeMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum). We have shown that BIPACE achieves very high precision and recall and a very low number of false positive peak assignments on both evaluation datasets. CeMAPP-DTW finds a high number of true positives when executed on its own, but achieves even better results when BIPACE is used to constrain its search space. The source code of both algorithms is included in the OpenSource software framework Maltcms, which is available from http://maltcms.sf.net. The evaluation scripts of the present study are available from the same source.
Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets

PubMed Central

2012-01-01

Background Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to allow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features. Results In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE) and center-star multiple alignment by pairwise partitioned dynamic time warping (CeMAPP-DTW). We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CeMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum). Conclusions We have shown that BIPACE achieves very high precision and recall and a very low number of false positive peak assignments on both evaluation datasets. CeMAPP-DTW finds a high number of true positives when executed on its own, but achieves even better results when BIPACE is used to constrain its search space. The source code of both algorithms is included in the OpenSource software framework Maltcms, which is available from http://maltcms.sf.net. The evaluation scripts of the present study are available from the same source. PMID:22920415
Chromaligner: a web server for chromatogram alignment.

PubMed

Wang, San-Yuan; Ho, Tsung-Jung; Kuo, Ching-Hua; Tseng, Yufeng J

2010-09-15

Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such as high performance liquid chromatography and capillary electrophoresis for metabolomics works. Chromaligner resolves peak shifts by a constrained chromatogram alignment. For a collection of chromatograms and a set of defined peaks, Chromaligner aligns the chromatograms on defined peaks using correlation warping (COW). Chromaligner is faster than the original COW algorithm by k(2) times, where k is the number of defined peaks in a chromatogram. It also provides alignments based on known component peaks to reach the best results for further chemometric analysis. Chromaligner is freely accessible at http://cmdd.csie.ntu.edu.tw/~chromaligner.
Robust alignment of chromatograms by statistically analyzing the shifts matrix generated by moving window fast Fourier transform cross-correlation.

PubMed

Zhang, Mingjing; Wen, Ming; Zhang, Zhi-Min; Lu, Hongmei; Liang, Yizeng; Zhan, Dejian

2015-03-01

Retention time shift is one of the most challenging problems during the preprocessing of massive chromatographic datasets. Here, an improved version of the moving window fast Fourier transform cross-correlation algorithm is presented to perform nonlinear and robust alignment of chromatograms by analyzing the shifts matrix generated by moving window procedure. The shifts matrix in retention time can be estimated by fast Fourier transform cross-correlation with a moving window procedure. The refined shift of each scan point can be obtained by calculating the mode of corresponding column of the shifts matrix. This version is simple, but more effective and robust than the previously published moving window fast Fourier transform cross-correlation method. It can handle nonlinear retention time shift robustly if proper window size has been selected. The window size is the only one parameter needed to adjust and optimize. The properties of the proposed method are investigated by comparison with the previous moving window fast Fourier transform cross-correlation and recursive alignment by fast Fourier transform using chromatographic datasets. The pattern recognition results of a gas chromatography mass spectrometry dataset of metabolic syndrome can be improved significantly after preprocessing by this method. Furthermore, the proposed method is available as an open source package at https://github.com/zmzhang/MWFFT2. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
BiPACE 2D--graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry.

PubMed

Hoffmann, Nils; Wilhelm, Mathias; Doebbe, Anja; Niehaus, Karsten; Stoye, Jens

2014-04-01

Comprehensive 2D gas chromatography-mass spectrometry is an established method for the analysis of complex mixtures in analytical chemistry and metabolomics. It produces large amounts of data that require semiautomatic, but preferably automatic handling. This involves the location of significant signals (peaks) and their matching and alignment across different measurements. To date, there exist only a few openly available algorithms for the retention time alignment of peaks originating from such experiments that scale well with increasing sample and peak numbers, while providing reliable alignment results. We describe BiPACE 2D, an automated algorithm for retention time alignment of peaks from 2D gas chromatography-mass spectrometry experiments and evaluate it on three previously published datasets against the mSPA, SWPA and Guineu algorithms. We also provide a fourth dataset from an experiment studying the H2 production of two different strains of Chlamydomonas reinhardtii that is available from the MetaboLights database together with the experimental protocol, peak-detection results and manually curated multiple peak alignment for future comparability with newly developed algorithms. BiPACE 2D is contained in the freely available Maltcms framework, version 1.3, hosted at http://maltcms.sf.net, under the terms of the L-GPL v3 or Eclipse Open Source licenses. The software used for the evaluation along with the underlying datasets is available at the same location. The C.reinhardtii dataset is freely available at http://www.ebi.ac.uk/metabolights/MTBLS37.
Data preprocessing method for liquid chromatography-mass spectrometry based metabolomics.

PubMed

Wei, Xiaoli; Shi, Xue; Kim, Seongho; Zhang, Li; Patrick, Jeffrey S; Binkley, Joe; McClain, Craig; Zhang, Xiang

2012-09-18

A set of data preprocessing algorithms for peak detection and peak list alignment are reported for analysis of liquid chromatography-mass spectrometry (LC-MS)-based metabolomics data. For spectrum deconvolution, peak picking is achieved at the selected ion chromatogram (XIC) level. To estimate and remove the noise in XICs, each XIC is first segmented into several peak groups based on the continuity of scan number, and the noise level is estimated by all the XIC signals, except the regions potentially with presence of metabolite ion peaks. After removing noise, the peaks of molecular ions are detected using both the first and the second derivatives, followed by an efficient exponentially modified Gaussian-based peak deconvolution method for peak fitting. A two-stage alignment algorithm is also developed, where the retention times of all peaks are first transferred into the z-score domain and the peaks are aligned based on the measure of their mixture scores after retention time correction using a partial linear regression. Analysis of a set of spike-in LC-MS data from three groups of samples containing 16 metabolite standards mixed with metabolite extract from mouse livers demonstrates that the developed data preprocessing method performs better than two of the existing popular data analysis packages, MZmine2.6 and XCMS(2), for peak picking, peak list alignment, and quantification.
A Data Pre-processing Method for Liquid Chromatography Mass Spectrometry-based Metabolomics

PubMed Central

Wei, Xiaoli; Shi, Xue; Kim, Seongho; Zhang, Li; Patrick, Jeffrey S.; Binkley, Joe; McClain, Craig; Zhang, Xiang

2012-01-01

A set of data pre-processing algorithms for peak detection and peak list alignment are reported for analysis of LC-MS based metabolomics data. For spectrum deconvolution, peak picking is achieved at selected ion chromatogram (XIC) level. To estimate and remove the noise in XICs, each XIC is first segmented into several peak groups based on the continuity of scan number, and the noise level is estimated by all the XIC signals, except the regions potentially with presence of metabolite ion peaks. After removing noise, the peaks of molecular ions are detected using both the first and the second derivatives, followed by an efficient exponentially modified Gaussian-based peak deconvolution method for peak fitting. A two-stage alignment algorithm is also developed, where the retention times of all peaks are first transferred into z-score domain and the peaks are aligned based on the measure of their mixture scores after retention time correction using a partial linear regression. Analysis of a set of spike-in LC-MS data from three groups of samples containing 16 metabolite standards mixed with metabolite extract from mouse livers, demonstrates that the developed data pre-processing methods performs better than two of the existing popular data analysis packages, MZmine2.6 and XCMS2, for peak picking, peak list alignment and quantification. PMID:22931487
MetMatch: A Semi-Automated Software Tool for the Comparison and Alignment of LC-HRMS Data from Different Metabolomics Experiments

PubMed Central

Koch, Stefan; Bueschl, Christoph; Doppler, Maria; Simader, Alexandra; Meng-Reiterer, Jacqueline; Lemmens, Marc; Schuhmacher, Rainer

2016-01-01

Due to its unsurpassed sensitivity and selectivity, LC-HRMS is one of the major analytical techniques in metabolomics research. However, limited stability of experimental and instrument parameters may cause shifts and drifts of retention time and mass accuracy or the formation of different ion species, thus complicating conclusive interpretation of the raw data, especially when generated in different analytical batches. Here, a novel software tool for the semi-automated alignment of different measurement sequences is presented. The tool is implemented in the Java programming language, it features an intuitive user interface and its main goal is to facilitate the comparison of data obtained from different metabolomics experiments. Based on a feature list (i.e., processed LC-HRMS chromatograms with mass-to-charge ratio (m/z) values and retention times) that serves as a reference, the tool recognizes both m/z and retention time shifts of single or multiple analytical datafiles/batches of interest. MetMatch is also designed to account for differently formed ion species of detected metabolites. Corresponding ions and metabolites are matched and chromatographic peak areas, m/z values and retention times are combined into a single data matrix. The convenient user interface allows for easy manipulation of processing results and graphical illustration of the raw data as well as the automatically matched ions and metabolites. The software tool is exemplified with LC-HRMS data from untargeted metabolomics experiments investigating phenylalanine-derived metabolites in wheat and T-2 toxin/HT-2 toxin detoxification products in barley. PMID:27827849
MetMatch: A Semi-Automated Software Tool for the Comparison and Alignment of LC-HRMS Data from Different Metabolomics Experiments.

PubMed

Koch, Stefan; Bueschl, Christoph; Doppler, Maria; Simader, Alexandra; Meng-Reiterer, Jacqueline; Lemmens, Marc; Schuhmacher, Rainer

2016-11-02

Due to its unsurpassed sensitivity and selectivity, LC-HRMS is one of the major analytical techniques in metabolomics research. However, limited stability of experimental and instrument parameters may cause shifts and drifts of retention time and mass accuracy or the formation of different ion species, thus complicating conclusive interpretation of the raw data, especially when generated in different analytical batches. Here, a novel software tool for the semi-automated alignment of different measurement sequences is presented. The tool is implemented in the Java programming language, it features an intuitive user interface and its main goal is to facilitate the comparison of data obtained from different metabolomics experiments. Based on a feature list (i.e., processed LC-HRMS chromatograms with mass-to-charge ratio ( m / z ) values and retention times) that serves as a reference, the tool recognizes both m / z and retention time shifts of single or multiple analytical datafiles/batches of interest. MetMatch is also designed to account for differently formed ion species of detected metabolites. Corresponding ions and metabolites are matched and chromatographic peak areas, m / z values and retention times are combined into a single data matrix. The convenient user interface allows for easy manipulation of processing results and graphical illustration of the raw data as well as the automatically matched ions and metabolites. The software tool is exemplified with LC-HRMS data from untargeted metabolomics experiments investigating phenylalanine-derived metabolites in wheat and T-2 toxin/HT-2 toxin detoxification products in barley.

Unifying expression scale for peptide hydrophobicity in proteomic reversed phase high-pressure liquid chromatography experiments.

PubMed

Grigoryan, Marine; Shamshurin, Dmitry; Spicer, Victor; Krokhin, Oleg V

2013-11-19

As an initial step in our efforts to unify the expression of peptide retention times in proteomic liquid chromatography-mass spectrometry (LC-MS) experiments, we aligned the chromatographic properties of a number of peptide retention standards against a collection of peptides commonly observed in proteomic experiments. The standard peptide mixtures and tryptic digests of samples of different origins were separated under the identical chromatographic condition most commonly employed in proteomics: 100 Å C18 sorbent with 0.1% formic acid as an ion-pairing modifier. Following our original approach (Krokhin, O. V.; Spicer, V. Anal. Chem. 2009, 81, 9522-9530) the retention characteristics of these standards and collection of tryptic peptides were mapped into hydrophobicity index (HI) or acetonitrile percentage units. This scale allows for direct visualization of the chromatographic outcome of LC-MS acquisitions, monitors the performance of the gradient LC system, and simplifies method development and interlaboratory data alignment. Wide adoption of this approach would significantly aid understanding the basic principles of gradient peptide RP-HPLC and solidify our collective efforts in acquiring confident peptide retention libraries, a key component in the development of targeted proteomic approaches.
Chemometric Analysis of Gas Chromatography – Mass Spectrometry Data using Fast Retention Time Alignment via a Total Ion Current Shift Function

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

Nadeau, Jeremy S.; Wright, Bob W.; Synovec, Robert E.

2010-04-15

A critical comparison of methods for correcting severely retention time shifted gas chromatography-mass spectrometry (GC-MS) data is presented. The method reported herein is an adaptation to the Piecewise Alignment Algorithm to quickly align severely shifted one-dimensional (1D) total ion current (TIC) data, then applying these shifts to broadly align all mass channels throughout the separation, referred to as a TIC shift function (SF). The maximum shift varied from (-) 5 s in the beginning of the chromatographic separation to (+) 20 s toward the end of the separation, equivalent to a maximum shift of over 5 peak widths. Implementing themore » TIC shift function (TIC SF) prior to Fisher Ratio (F-Ratio) feature selection and then principal component analysis (PCA) was found to be a viable approach to classify complex chromatograms, that in this study were obtained from GC-MS separations of three gasoline samples serving as complex test mixtures, referred to as types C, M and S. The reported alignment algorithm via the TIC SF approach corrects for large dynamic shifting in the data as well as subtle peak-to-peak shifts. The benefits of the overall TIC SF alignment and feature selection approach were quantified using the degree-of-class separation (DCS) metric of the PCA scores plots using the type C and M samples, since they were the most similar, and thus the most challenging samples to properly classify. The DCS values showed an increase from an initial value of essentially zero for the unaligned GC-TIC data to a value of 7.9 following alignment; however, the DCS was unchanged by feature selection using F-Ratios for the GC-TIC data. The full mass spectral data provided an increase to a final DCS of 13.7 after alignment and two-dimensional (2D) F-Ratio feature selection.« less
GCALIGNER 1.0: an alignment program to compute a multiple sample comparison data matrix from large eco-chemical datasets obtained by GC.

PubMed

Dellicour, Simon; Lecocq, Thomas

2013-10-01

GCALIGNER 1.0 is a computer program designed to perform a preliminary data comparison matrix of chemical data obtained by GC without MS information. The alignment algorithm is based on the comparison between the retention times of each detected compound in a sample. In this paper, we test the GCALIGNER efficiency on three datasets of the chemical secretions of bumble bees. The algorithm performs the alignment with a low error rate (<3%). GCALIGNER 1.0 is a useful, simple and free program based on an algorithm that enables the alignment of table-type data from GC. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Authentication of organically and conventionally grown basils by gas chromatograpy/mass spectrometry chemical profiles

USDA-ARS?s Scientific Manuscript database

Basil plants cultivated by organic and conventional farming practices were differentiated using gas chromatography/mass spectrometry (GC/MS) and chemometric methods. The two-way GC/MS data sets were baseline-corrected and retention time-aligned prior to data processing. Two self-devised fuzzy clas...
U.S. Marine Corps Enlisted Retention: An Analysis of Stakeholder Incentives for the Retention of Tier 1 First-Term Marines

DTIC Science & Technology

2014-03-01

ERTF Enlisted Retention Task Force FFM fast filling military occupational specialty FTAP first-term alignment plan FY fiscal year GT general...Planning military ( FFM ) occupational specialties that are processed through boards to ensure the retention of highly qualified Marines. Fast-filling
Hydrophilic Channel Alignment of Perfluoronated Sulfonic-Acid Ionomers for Vanadium Redox Flow Batteries.

PubMed

So, Soonyong; Cha, Min Suc; Jo, Sang-Woo; Kim, Tae-Ho; Lee, Jang Yong; Hong, Young Taik

2018-06-13

It is known that uniaxially drawn perfluoronated sulfonic-acid ionomers (PFSAs) show diffusion anisotropy because of the aligned water channels along the deformation direction. We apply the uniaxially stretched membranes to vanadium redox flow batteries (VRFBs) to suppress the permeation of active species, vanadium ions through the transverse directions. The aligned water channels render much lower vanadium permeability, resulting in higher Coulombic efficiency (>98%) and longer self-discharge time (>250 h). Similar to vanadium ions, proton conduction through the membranes also decreases as the stretching ratio increases, but the thinned membranes show the enhanced voltage and energy efficiencies over the range of current density, 50-100 mA/cm 2 . Hydrophilic channel alignment of PFSAs is also beneficial for long-term cycling of VRFBs in terms of capacity retention and cell performances. This simple pretreatment of membranes offers an effective and facile way to overcome high vanadium permeability of PFSAs for VRFBs.
Application of fast Fourier transform cross-correlation and mass spectrometry data for accurate alignment of chromatograms.

PubMed

Zheng, Yi-Bao; Zhang, Zhi-Min; Liang, Yi-Zeng; Zhan, De-Jian; Huang, Jian-Hua; Yun, Yong-Huan; Xie, Hua-Lin

2013-04-19

Chromatography has been established as one of the most important analytical methods in the modern analytical laboratory. However, preprocessing of the chromatograms, especially peak alignment, is usually a time-consuming task prior to extracting useful information from the datasets because of the small unavoidable differences in the experimental conditions caused by minor changes and drift. Most of the alignment algorithms are performed on reduced datasets using only the detected peaks in the chromatograms, which means a loss of data and introduces the problem of extraction of peak data from the chromatographic profiles. These disadvantages can be overcome by using the full chromatographic information that is generated from hyphenated chromatographic instruments. A new alignment algorithm called CAMS (Chromatogram Alignment via Mass Spectra) is present here to correct the retention time shifts among chromatograms accurately and rapidly. In this report, peaks of each chromatogram were detected based on Continuous Wavelet Transform (CWT) with Haar wavelet and were aligned against the reference chromatogram via the correlation of mass spectra. The aligning procedure was accelerated by Fast Fourier Transform cross correlation (FFT cross correlation). This approach has been compared with several well-known alignment methods on real chromatographic datasets, which demonstrates that CAMS can preserve the shape of peaks and achieve a high quality alignment result. Furthermore, the CAMS method was implemented in the Matlab language and available as an open source package at http://www.github.com/matchcoder/CAMS. Copyright © 2013. Published by Elsevier B.V.
Academic Libraries and High-Impact Practices for Student Retention: Library Deans' Perspectives

ERIC Educational Resources Information Center

Murray, Adam

2015-01-01

Numerous studies on retention have highlighted the role of student engagement in influencing students' withdrawal decisions. This study seeks to address how academic libraries affect student retention by examining the perception of academic library deans or directors on the alignment between library services and resources with ten nationally…
Factors Influencing Registered Nurses' Perceptions of Their Professional Identity: An Integrative Literature Review.

PubMed

Rasmussen, Philippa; Henderson, Ann; Andrew, Nicky; Conroy, Tiffany

2018-05-01

This review synthesizes contemporary research investigating the factors influencing RNs' perceptions of their professional identity. The method used was an integrative literature review. Factors influencing RNs' perceptions of their professional identity were synthesized into three categories: the self, the role, and the context. The self is the nurse who enacts the role in practice, and the context is the practice setting. Poor alignment of these categories leads to stress, tension, and uncertainty affecting work-force retention. Strong alignment leads to satisfaction with the nursing role, increased staff retention, and improved quality of care and patient outcomes. These three categories should be considered when planning nursing professional development activities. This integrative review identified a lack of research addressing how nurses' perceptions of their professional identity change over time. A deeper understanding of their perspective is needed to establish whether career longevity and continued professional development are influences. J Contin Educ Nurs. 2018;49(5):225-232. Copyright 2018, SLACK Incorporated.
Retention system and method for the blades of a rotary machine

DOEpatents

Pedersen, Poul D.; Glynn, Christopher C.; Walker, Roger C.

2002-01-01

A retention system and method for the blades of a rotary machine for preventing forward or aft axial movement of the rotor blades includes a circumferential hub slot formed about a circumference of the machine hub. The rotor blades have machined therein a blade retention slot which is aligned with the circumferential hub slot when the blades are received in correspondingly shaped openings in the hub. At least one ring segment is secured in the blade retention slots and the circumferential hub slot to retain the blades from axial movement. A key assembly is used to secure the ring segments in the aligned slots via a hook portion receiving the ring segments and a threaded portion that is driven radially outwardly by a nut. A cap may be provided to provide a redundant back-up load path for the centrifugal loads on the key. Alternatively, the key assembly may be formed in the blade dovetail.
The Curriculum-Faculty-Reinforcement Alignment and Its Effect on Learning Retention of Core Marketing Concepts of Marketing Capstone Students

ERIC Educational Resources Information Center

Raska, David; Keller, Eileen Weisenbach; Shaw, Doris

2014-01-01

Curriculum-Faculty-Reinforcement (CFR) alignment is an alignment between fundamental marketing concepts that are integral to the mastery of knowledge expected of our marketing graduates, their perceived importance by the faculty, and their level of reinforcement throughout core marketing courses required to obtain a marketing degree. This research…
LC-MSsim – a simulation software for liquid chromatography mass spectrometry data

PubMed Central

Schulz-Trieglaff, Ole; Pfeifer, Nico; Gröpl, Clemens; Kohlbacher, Oliver; Reinert, Knut

2008-01-01

Background Mass Spectrometry coupled to Liquid Chromatography (LC-MS) is commonly used to analyze the protein content of biological samples in large scale studies. The data resulting from an LC-MS experiment is huge, highly complex and noisy. Accordingly, it has sparked new developments in Bioinformatics, especially in the fields of algorithm development, statistics and software engineering. In a quantitative label-free mass spectrometry experiment, crucial steps are the detection of peptide features in the mass spectra and the alignment of samples by correcting for shifts in retention time. At the moment, it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists only for peptide identification algorithms but no data that represents a ground truth for the evaluation of feature detection, alignment and filtering algorithms. Results We present LC-MSsim, a simulation software for LC-ESI-MS experiments. It simulates ESI spectra on the MS level. It reads a list of proteins from a FASTA file and digests the protein mixture using a user-defined enzyme. The software creates an LC-MS data set using a predictor for the retention time of the peptides and a model for peak shapes and elution profiles of the mass spectral peaks. Our software also offers the possibility to add contaminants, to change the background noise level and includes a model for the detectability of peptides in mass spectra. After the simulation, LC-MSsim writes the simulated data to mzData, a public XML format. The software also stores the positions (monoisotopic m/z and retention time) and ion counts of the simulated ions in separate files. Conclusion LC-MSsim generates simulated LC-MS data sets and incorporates models for peak shapes and contaminations. Algorithm developers can match the results of feature detection and alignment algorithms against the simulated ion lists and meaningful error rates can be computed. We anticipate that LC-MSsim will be useful to the wider community to perform benchmark studies and comparisons between computational tools. PMID:18842122
PROCAL: A Set of 40 Peptide Standards for Retention Time Indexing, Column Performance Monitoring, and Collision Energy Calibration.

PubMed

Zolg, Daniel Paul; Wilhelm, Mathias; Yu, Peng; Knaute, Tobias; Zerweck, Johannes; Wenschuh, Holger; Reimer, Ulf; Schnatbaum, Karsten; Kuster, Bernhard

2017-11-01

Beyond specific applications, such as the relative or absolute quantification of peptides in targeted proteomic experiments, synthetic spike-in peptides are not yet systematically used as internal standards in bottom-up proteomics. A number of retention time standards have been reported that enable chromatographic aligning of multiple LC-MS/MS experiments. However, only few peptides are typically included in such sets limiting the analytical parameters that can be monitored. Here, we describe PROCAL (ProteomeTools Calibration Standard), a set of 40 synthetic peptides that span the entire hydrophobicity range of tryptic digests, enabling not only accurate determination of retention time indices but also monitoring of chromatographic separation performance over time. The fragmentation characteristics of the peptides can also be used to calibrate and compare collision energies between mass spectrometers. The sequences of all selected peptides do not occur in any natural protein, thus eliminating the need for stable isotope labeling. We anticipate that this set of peptides will be useful for multiple purposes in individual laboratories but also aiding the transfer of data acquisition and analysis methods between laboratories, notably the use of spectral libraries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Association of the canine guidance angle with maxillary and mandibular intercanine widths and anterior alignment relapse: Extraction vs nonextraction treatment.

PubMed

Heiser, Wolfgang; Richter, Martin; Niederwanger, Andreas; Neunteufel, Nikolaus; Kulmer, Siegfried

2008-05-01

Long-term stability is an important measure of the success of orthodontic treatment. Research in the 1970s suggested that premolar extraction treatment had poor stability over the long term. The purpose of this prospective follow-up study was to investigate changes in intercanine widths and the irregularity index during the postretention phase in patients treated with and without extractions. Associations between the maxillary canine guidance angle and the mandibular intercanine widths and the mandibular irregularity index were also examined. Two groups of 30 patients each, with and without premolar extractions, were studied and the results compared. Records were taken at pretreatment, at bracket removal, at the end of retention, and out of retention. The times out of retention were 6.3 years for the nonextraction group and 6.5 years for the extraction group. Stone casts were mounted on an articulator with an anatomical facebow and a central wax record. The measurements were made with a 3-dimensional digitizer. Maxillary and mandibular intercanine distances behaved differently. The mandibular intercanine distance showed a net decrease between pretreatment and follow-up, whereas the maxillary arch had a net increase. The maxillary canine guidance angle at the end of retention, measured to the axis-orbital plane, was highly associated with relapse of mandibular anterior alignment and change of the mandibular intercanine distance. Methods are needed that consider the anatomical configuration of the teeth for bracket selection before treatment. Individualized brackets (torque) should then be coordinated with the guidance angle of the maxillary teeth.
Perspective: The missing link in academic career planning and development: pursuit of meaningful and aligned work.

PubMed

Lieff, Susan J

2009-10-01

Retention of faculty in academic medicine is a growing challenge. It has been suggested that inattention to the humanistic values of the faculty is contributing to this problem. Professional development should consider faculty members' search for meaning, purpose, and professional fulfillment and should support the development of an ability to reflect on these issues. Ensuring the alignment of academic physicians' inner direction with their outer context is critical to professional fulfillment and effectiveness. Personal reflection on the synergy of one's strengths, passions, and values can help faculty members define meaningful work so as to enable clearer career decision making. The premise of this article is that an awareness of and the pursuit of meaningful work and its alignment with the academic context are important considerations in the professional fulfillment and retention of academic faculty. A conceptual framework for understanding meaningful work and alignment and ways in which that framework can be applied and taught in development programs are presented and discussed.
Factors Influencing Faculty Participation & Retention in Online & Blended Education

ERIC Educational Resources Information Center

Betts, Kristen

2014-01-01

Faculty members play a central role in the development, implementation, and long-term sustainability of online and blended education programs. Therefore, faculty recruitment and retention strategies for these programs must align with the needs of the faculty. This article highlights the results of an institutional study conducted at a public…
Maui-VIA: A User-Friendly Software for Visual Identification, Alignment, Correction, and Quantification of Gas Chromatography–Mass Spectrometry Data

PubMed Central

Kuich, P. Henning J. L.; Hoffmann, Nils; Kempa, Stefan

2015-01-01

A current bottleneck in GC–MS metabolomics is the processing of raw machine data into a final datamatrix that contains the quantities of identified metabolites in each sample. While there are many bioinformatics tools available to aid the initial steps of the process, their use requires both significant technical expertise and a subsequent manual validation of identifications and alignments if high data quality is desired. The manual validation is tedious and time consuming, becoming prohibitively so as sample numbers increase. We have, therefore, developed Maui-VIA, a solution based on a visual interface that allows experts and non-experts to simultaneously and quickly process, inspect, and correct large numbers of GC–MS samples. It allows for the visual inspection of identifications and alignments, facilitating a unique and, due to its visualization and keyboard shortcuts, very fast interaction with the data. Therefore, Maui-Via fills an important niche by (1) providing functionality that optimizes the component of data processing that is currently most labor intensive to save time and (2) lowering the threshold of expertise required to process GC–MS data. Maui-VIA projects are initiated with baseline-corrected raw data, peaklists, and a database of metabolite spectra and retention indices used for identification. It provides functionality for retention index calculation, a targeted library search, the visual annotation, alignment, correction interface, and metabolite quantification, as well as the export of the final datamatrix. The high quality of data produced by Maui-VIA is illustrated by its comparison to data attained manually by an expert using vendor software on a previously published dataset concerning the response of Chlamydomonas reinhardtii to salt stress. In conclusion, Maui-VIA provides the opportunity for fast, confident, and high-quality data processing validation of large numbers of GC–MS samples by non-experts. PMID:25654076
Diagnosing Causes of Teacher Retention, Mobility and Turnover: Guidelines for TIF Grantees

ERIC Educational Resources Information Center

Finster, Matthew

2015-01-01

To effectively address teacher turnover, Teacher Incentive Fund (TIF) grantees need to follow an approach that entails aligning the tracking, diagnosing, and intervening processes. Unfortunately, too often retention strategies are implemented without regard to the various types of teacher turnover and specific data about the causes of turnover.…
Profile-Based LC-MS Data Alignment—A Bayesian Approach

PubMed Central

Tsai, Tsung-Heng; Tadesse, Mahlet G.; Wang, Yue; Ressom, Habtom W.

2014-01-01

A Bayesian alignment model (BAM) is proposed for alignment of liquid chromatography-mass spectrometry (LC-MS) data. BAM belongs to the category of profile-based approaches, which are composed of two major components: a prototype function and a set of mapping functions. Appropriate estimation of these functions is crucial for good alignment results. BAM uses Markov chain Monte Carlo (MCMC) methods to draw inference on the model parameters and improves on existing MCMC-based alignment methods through 1) the implementation of an efficient MCMC sampler and 2) an adaptive selection of knots. A block Metropolis-Hastings algorithm that mitigates the problem of the MCMC sampler getting stuck at local modes of the posterior distribution is used for the update of the mapping function coefficients. In addition, a stochastic search variable selection (SSVS) methodology is used to determine the number and positions of knots. We applied BAM to a simulated data set, an LC-MS proteomic data set, and two LC-MS metabolomic data sets, and compared its performance with the Bayesian hierarchical curve registration (BHCR) model, the dynamic time-warping (DTW) model, and the continuous profile model (CPM). The advantage of applying appropriate profile-based retention time correction prior to performing a feature-based approach is also demonstrated through the metabolomic data sets. PMID:23929872
Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards

PubMed Central

Tsai, Tsung-Heng; Tadesse, Mahlet G.; Di Poto, Cristina; Pannell, Lewis K.; Mechref, Yehia; Wang, Yue; Ressom, Habtom W.

2013-01-01

Motivation: Liquid chromatography-mass spectrometry (LC-MS) has been widely used for profiling expression levels of biomolecules in various ‘-omic’ studies including proteomics, metabolomics and glycomics. Appropriate LC-MS data preprocessing steps are needed to detect true differences between biological groups. Retention time (RT) alignment, which is required to ensure that ion intensity measurements among multiple LC-MS runs are comparable, is one of the most important yet challenging preprocessing steps. Current alignment approaches estimate RT variability using either single chromatograms or detected peaks, but do not simultaneously take into account the complementary information embedded in the entire LC-MS data. Results: We propose a Bayesian alignment model for LC-MS data analysis. The alignment model provides estimates of the RT variability along with uncertainty measures. The model enables integration of multiple sources of information including internal standards and clustered chromatograms in a mathematically rigorous framework. We apply the model to LC-MS metabolomic, proteomic and glycomic data. The performance of the model is evaluated based on ground-truth data, by measuring correlation of variation, RT difference across runs and peak-matching performance. We demonstrate that Bayesian alignment model improves significantly the RT alignment performance through appropriate integration of relevant information. Availability and implementation: MATLAB code, raw and preprocessed LC-MS data are available at http://omics.georgetown.edu/alignLCMS.html Contact: hwr@georgetown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24013927

Retention Models for STEM Majors and Alignment to Community Colleges: A Review of the Literature

ERIC Educational Resources Information Center

Snyder, Jennifer; Cudney, Elizabeth A.

2017-01-01

During the last decade, there have been numerous reports detailing the importance of increasing science, technology, engineering, and math (STEM) majors in the United States. Simultaneously, an increasing number of studies are being developed to predict a student's success and completion of a STEM degree, recognizing that retention is a…
Exploring How Age, Accession Source, Childbearing and the SWO Career Path Influence Female SWO Retention

DTIC Science & Technology

2017-03-01

OCW from ages 25–30 based on the 2015 U.S. Department of Health and Human Services Report and the Navy’s biennial Pregnancy and Parenthood Survey ... Survey , adds the 83 optimal childbearing window (OCW) to illustrate how pregnancy timing would align between ages 25–30 on each SWO career path. Each...U.S. Department of Health and Human Services report and the biennial U.S. Navy Pregnancy and Parenthood Survey , a majority of women are having
Scalable high-power redox capacitors with aligned nanoforests of crystalline MnO₂ nanorods by high voltage electrophoretic deposition.

PubMed

Santhanagopalan, Sunand; Balram, Anirudh; Meng, Dennis Desheng

2013-03-26

It is commonly perceived that reduction-oxidation (redox) capacitors have to sacrifice power density to achieve higher energy density than carbon-based electric double layer capacitors. In this work, we report the synergetic advantages of combining the high crystallinity of hydrothermally synthesized α-MnO2 nanorods with alignment for high performance redox capacitors. Such an approach is enabled by high voltage electrophoretic deposition (HVEPD) technology which can obtain vertically aligned nanoforests with great process versatility. The scalable nanomanufacturing process is demonstrated by roll-printing an aligned forest of α-MnO2 nanorods on a large flexible substrate (1 inch by 1 foot). The electrodes show very high power density (340 kW/kg at an energy density of 4.7 Wh/kg) and excellent cyclability (over 92% capacitance retention over 2000 cycles). Pretreatment of the substrate and use of a conductive holding layer have also been shown to significantly reduce the contact resistance between the aligned nanoforests and the substrates. High areal specific capacitances of around 8500 μF/cm(2) have been obtained for each electrode with a two-electrode device configuration. Over 93% capacitance retention was observed when the cycling current densities were increased from 0.25 to 10 mA/cm(2), indicating high rate capabilities of the fabricated electrodes and resulting in the very high attainable power density. The high performance of the electrodes is attributed to the crystallographic structure, 1D morphology, aligned orientation, and low contact resistance.
A GC Instrument Simulator

NASA Astrophysics Data System (ADS)

Armitage, D. Bruce

1999-02-01

This simulator was developed to help students beginning the study of gas chromatographic instruments to understand their operation. It is not meant to teach chromatographic theory. The instrument simulator is divided into 5 sections. One is for sample preparation. Another is used to manage carrier gases and choose a detector and column. The third sets the conditions for either isothermal or programmed temperature operation. A fourth section models manual injections, and the fifth is the autosampler. The operator has a choice among 6 columns of differing diameters and packing polarities and a choice of either isothermal or simple one-stage temperature programming. The simulator can be operated in either single-sample mode or as a 10-sample autosampler. The integrator has two modes of operation, a "dumb" mode in which only the retention time, area of the peak, and percentage area are listed and a "smart" mode that also lists the components' identities. The identities are obtained from a list of names and retention times created by the operator. Without this list only the percentages and areas are listed. The percentages are based on the areas obtained from the chromatogram and not on the actual percentages assigned during sample preparation. The data files for the compounds used in the simulator are ASCII files and can be edited easily to add more compounds than the 11 included with the simulator. A maximum of 10 components can be used in any one sample. Sample mixtures can be made on a percent-by-volume basis, but not by mass of sample per volume of solvent. A maximum of 30 compounds can be present in any one file, but the number of files is limited only by the operating system. (I suggest that not more than 20 compounds be used in any one file, as scrolling through large numbers of compounds is annoying to say the least.) File construction and layout are discussed in detail in the User's Manual. Chromatograms are generated by calculating a retention time based on the difference between the boiling point of the component and the temperature of the column. The polarity difference between the column packing and the component is also used to modify the retention time. The retention time decreases as the difference between the boiling point of the component and the temperature of the column increases, and retention time increases as the polarity of the component approaches the polarity of the column. If the temperature of the column is too low, a warning message is given and the chromatogram does not show that component. There is no "carry-over" to the next chromatogram, as might be the case for an actual instrument. Carrier-gas flow rate is fixed and is not part of the retention-time calculation. Because of this latter condition and the method used to determine retention time, this simulator is not useful for gas chromatography method development and is not intended for such use. The purpose of the simulator is to give a beginning student experience in what happens as column temperature is varied, why one might need temperature programming, why an autosampler might be useful, and the pitfalls of "smart" integrators. When students make mistakes in instrument setup with the simulator the consequences are not damaging to the simulator but might cause serious problems with a real instrument. Hardware and Software Requirements Hardware and software requirements for A GC Instrument Simulator are shown in Table 1.
Shown (right to left) are the main instrument control window and the manual injection window from A GC Instrument Simulator.
Analysis of the low molecular weight fraction of serum by LC-dual ESI-FT-ICR mass spectrometry: precision of retention time, mass, and ion abundance.

PubMed

Johnson, Kenneth L; Mason, Christopher J; Muddiman, David C; Eckel, Jeanette E

2004-09-01

This study quantifies the experimental uncertainty for LC retention time, mass measurement precision, and ion abundance obtained from replicate nLC-dual ESI-FT-ICR analyses of the low molecular weight fraction of serum. We used ultrafiltration to enrich the < 10-kDa fraction of components from the high-abundance proteins in a pooled serum sample derived from ovarian cancer patients. The THRASH algorithm for isotope cluster detection was applied to five replicate nLC-dual ESI-FT-ICR chromatograms. A simple two-level grouping algorithm was applied to the more than 7000 isotope clusters found in each replicate and identified 497 molecular species that appeared in at least four of the replicates. In addition, a representative set of 231 isotope clusters, corresponding to 188 unique molecular species, were manually interpreted to verify the automated algorithm and to set its tolerances. For nLC retention time reproducibility, 95% of the 497 species had a 95% confidence interval of the mean of +/- 0.9 min or less without the use of chromatographic alignment procedures. Furthermore, 95% of the 497 species had a mass measurement precision of < or = 3.2 and < or = 6.3 ppm for internally and externally calibrated spectra, respectively. Moreover, 95% of replicate ion abundance measurements, covering an ion abundance range of approximately 3 orders of magnitude, had a coefficient of variation of less than 62% without using any normalization functions. The variability of ion abundance was independent of LC retention time, mass, and ion abundance quartile. These measures of analytical reproducibility establish a statistical rationale for differentiating healthy and disease patient populations for the elucidation of biomarkers in the low molecular fraction of serum. Copyright 2004 American Chemical Society
Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning.

PubMed

Jain, Tushar; Boland, Todd; Lilov, Asparouh; Burnina, Irina; Brown, Michael; Xu, Yingda; Vásquez, Maximiliano

2017-12-01

The hydrophobicity of a monoclonal antibody is an important biophysical property relevant for its developability into a therapeutic. In addition to characterizing heterogeneity, Hydrophobic Interaction Chromatography (HIC) is an assay that is often used to quantify the hydrophobicity of an antibody to assess downstream risks. Earlier studies have shown that retention times in this assay can be correlated to amino-acid or atomic propensities weighted by the surface areas obtained from protein 3-dimensional structures. The goal of this study is to develop models to enable prediction of delayed HIC retention times directly from sequence. We utilize the randomforest machine learning approach to estimate the surface exposure of amino-acid side-chains in the variable region directly from the antibody sequence. We obtain mean-absolute errors of 4.6% for the prediction of surface exposure. Using experimental HIC data along with the estimated surface areas, we derive an amino-acid propensity scale that enables prediction of antibodies likely to have delayed retention times in the assay. We achieve a cross-validation Area Under Curve of 0.85 for the Receiver Operating Characteristic curve of our model. The low computational expense and high accuracy of this approach enables real-time assessment of hydrophobic character to enable prioritization of antibodies during the discovery process and rational engineering to reduce hydrophobic liabilities. Structure data, aligned sequences, experimental data and prediction scores for test-cases, and R scripts used in this work are provided as part of the Supplementary Material. tushar.jain@adimab.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
Relapse of incisor crowding: a visit to the Prince of Salina.

PubMed

López-Areal, Luis; Gandía, Jose-Luis

2013-03-01

The management of the retention period after comprehensive orthodontic treatment is of great importance, as a primary goal of clinician. Considerable controversy still surrounds the problem of stability after the retention period. Many studies analyze factors associated to the presence of crowding or incisor irregularity and find predictive features on its relapse. Most studies have reported little o no correlation between the treatment changes in the biological parameters - clinical, biometric (irregularity index, intermolar width, intercanine width, arch length, overjet, overbite), or cephalometric variables- that ocurred and the posttretament and postretention changes that may predict their future development. This article provides a bibliographical overview on the relapse of dental alignment in treated cases. In a brief historical introduction, the first studies on the long-term stability of orthodontic results are analysed. The article then goes on to assess studies that focus attention on anteroinferior alignment before finally studying relapse of upper crowding. It concludes by making some final comments in the light of the bibliography provided and the differents schools regarding retention needs and methods.
Dramatic improvement in water retention and proton conductivity in electrically aligned functionalized CNT/SPEEK nanohybrid PEM.

PubMed

Gahlot, Swati; Kulshrestha, Vaibhav

2015-01-14

Nanohybrid membranes of electrically aligned functionalized carbon nanotube f CNT with sulfonated poly ether ether ketone (SPEEK) have been successfully prepared by solution casting. Functionalization of CNTs was done through a carboxylation and sulfonation route. Further, a constant electric field (500 V·cm(-2)) has been applied to align CNTs in the same direction during the membrane drying process. All the membranes are characterized chemically, thermally, and mechanically by the means of FTIR, DSC, DMA, UTM, SEM, TEM, and AFM techniques. Intermolecular interactions between the components in hybrid membranes are established by FTIR. Physicochemical measurements were done to analyze membrane stability. Membranes are evaluated for proton conductivity (30-90 °C) and methanol crossover resistance to reveal their potential for direct methanol fuel cell application. Incorporation of f CNT reasonably increases the ion-exchange capacity, water retention, and proton conductivity while it reduces the methanol permeability. The maximum proton conductivity has been found in the S-sCNT-5 nanohybrid PEM with higher methanol crossover resistance. The prepared membranes can be also used for electrode material for fuel cells and batteries.
High-performance Supercapacitors Based on Electrochemical-induced Vertical-aligned Carbon Nanotubes and Polyaniline Nanocomposite Electrodes

NASA Astrophysics Data System (ADS)

Wu, Guan; Tan, Pengfeng; Wang, Dongxing; Li, Zhe; Peng, Lu; Hu, Ying; Wang, Caifeng; Zhu, Wei; Chen, Su; Chen, Wei

2017-03-01

Supercapacitors, which store electrical energy through reversible ion on the surface of conductive electrodes have gained enormous attention for variously portable energy storage devices. Since the capacitive performance is mainly determined by the structural and electrochemical properties of electrodes, the electrodes become more crucial to higher performance. However, due to the disordered microstructure and low electrochemical activity of electrode for ion tortuous migration and accumulation, the supercapacitors present relatively low capacitance and energy density. Here we report a high-performance supercapacitor based on polyaniline/vertical-aligned carbon nanotubes (PANI/VA-CNTs) nanocomposite electrodes where the vertical-aligned-structure is formed by the electrochemical-induction (0.75 V). The supercapacitor displays large specific capacitance of 403.3 F g-1, which is 6 times higher than disordered CNTs in HClO4 electrolyte. Additionally, the supercapacitor can also present high specific capacitance (314.6 F g-1), excellent cycling stability (90.2% retention after 3000 cycles at 4 A g-1) and high energy density (98.1 Wh kg-1) in EMIBF4 organic electrolyte. The key to high-performance lies in the vertical-aligned-structure providing direct path channel for ion faster diffusion and high electrochemical capacitance of polyaniline for ion more accommodation.
Evaluation of peak picking quality in LC-MS metabolomics data.

PubMed

Brodsky, Leonid; Moussaieff, Arieh; Shahaf, Nir; Aharoni, Asaph; Rogachev, Ilana

2010-11-15

The output of LC-MS metabolomics experiments consists of mass-peak intensities identified through a peak-picking/alignment procedure. Besides imperfections in biological samples and instrumentation, data accuracy is highly dependent on the applied algorithms and their parameters. Consequently, quality control (QC) is essential for further data analysis. Here, we present a QC approach that is based on discrepancies between replicate samples. First, the quantile normalization of per-sample log-signal distributions is applied to each group of biologically homogeneous samples. Next, the overall quality of each replicate group is characterized by the Z-transformed correlation coefficients between samples. This general QC allows a tuning of the procedure's parameters which minimizes the inter-replicate discrepancies in the generated output. Subsequently, an in-depth QC measure detects local neighborhoods on a template of aligned chromatograms that are enriched by divergences between intensity profiles of replicate samples. These neighborhoods are determined through a segmentation algorithm. The retention time (RT)-m/z positions of the neighborhoods with local divergences are indicative of either: incorrect alignment of chromatographic features, technical problems in the chromatograms, or to a true biological discrepancy between replicates for particular metabolites. We expect this method to aid in the accurate analysis of metabolomics data and in the development of new peak-picking/alignment procedures.
High-performance Supercapacitors Based on Electrochemical-induced Vertical-aligned Carbon Nanotubes and Polyaniline Nanocomposite Electrodes.

PubMed

Wu, Guan; Tan, Pengfeng; Wang, Dongxing; Li, Zhe; Peng, Lu; Hu, Ying; Wang, Caifeng; Zhu, Wei; Chen, Su; Chen, Wei

2017-03-08

Supercapacitors, which store electrical energy through reversible ion on the surface of conductive electrodes have gained enormous attention for variously portable energy storage devices. Since the capacitive performance is mainly determined by the structural and electrochemical properties of electrodes, the electrodes become more crucial to higher performance. However, due to the disordered microstructure and low electrochemical activity of electrode for ion tortuous migration and accumulation, the supercapacitors present relatively low capacitance and energy density. Here we report a high-performance supercapacitor based on polyaniline/vertical-aligned carbon nanotubes (PANI/VA-CNTs) nanocomposite electrodes where the vertical-aligned-structure is formed by the electrochemical-induction (0.75 V). The supercapacitor displays large specific capacitance of 403.3 F g -1 , which is 6 times higher than disordered CNTs in HClO 4 electrolyte. Additionally, the supercapacitor can also present high specific capacitance (314.6 F g -1 ), excellent cycling stability (90.2% retention after 3000 cycles at 4 A g -1 ) and high energy density (98.1 Wh kg -1 ) in EMIBF 4 organic electrolyte. The key to high-performance lies in the vertical-aligned-structure providing direct path channel for ion faster diffusion and high electrochemical capacitance of polyaniline for ion more accommodation.
High-performance Supercapacitors Based on Electrochemical-induced Vertical-aligned Carbon Nanotubes and Polyaniline Nanocomposite Electrodes

PubMed Central

Wu, Guan; Tan, Pengfeng; Wang, Dongxing; Li, Zhe; Peng, Lu; Hu, Ying; Wang, Caifeng; Zhu, Wei; Chen, Su; Chen, Wei

2017-01-01

Supercapacitors, which store electrical energy through reversible ion on the surface of conductive electrodes have gained enormous attention for variously portable energy storage devices. Since the capacitive performance is mainly determined by the structural and electrochemical properties of electrodes, the electrodes become more crucial to higher performance. However, due to the disordered microstructure and low electrochemical activity of electrode for ion tortuous migration and accumulation, the supercapacitors present relatively low capacitance and energy density. Here we report a high-performance supercapacitor based on polyaniline/vertical-aligned carbon nanotubes (PANI/VA-CNTs) nanocomposite electrodes where the vertical-aligned-structure is formed by the electrochemical-induction (0.75 V). The supercapacitor displays large specific capacitance of 403.3 F g−1, which is 6 times higher than disordered CNTs in HClO4 electrolyte. Additionally, the supercapacitor can also present high specific capacitance (314.6 F g−1), excellent cycling stability (90.2% retention after 3000 cycles at 4 A g−1) and high energy density (98.1 Wh kg−1) in EMIBF4 organic electrolyte. The key to high-performance lies in the vertical-aligned-structure providing direct path channel for ion faster diffusion and high electrochemical capacitance of polyaniline for ion more accommodation. PMID:28272474
New nurse transition: success through aligning multiple identities.

PubMed

Leong, Yee Mun Jessica; Crossman, Joanna

2015-01-01

The purpose of this paper is to explore the perceptions of new nurses in Singapore of their experiences of role transition and to examine the implications for managers in terms of employee training, development and retention. This qualitative study was conducted using a constructivist grounded theory approach. In total 26 novice nurses and five preceptors (n=31) from five different hospitals participated in the study. Data were collected from semi-structured interviews and reflective journal entries and analysed using the constant comparative method. The findings revealed that novice nurses remained emotionally and physically challenged when experiencing role transition. Two major constructs appear to play an important part in the transition process; learning how to Fit in and aligning personal with professional and organisational identities. The findings highlight factors that facilitate or impede Fitting in and aligning these identities. Although the concept of Fitting in and its relation to the attrition of novice nurses has been explored in global studies, that relationship has not yet been theorised as the dynamic alignment of multiple identities. Also, whilst most research around Fitting in, identity and retention has been conducted in western countries, little is known about these issues and their interrelationship in the context of Singapore. The study should inform decision making by healthcare organisations, nurse managers and nursing training institutions with respect to improving the transition experience of novice nurses.
Conformal Fe3O4 sheath on aligned carbon nanotube scaffolds as high-performance anodes for lithium ion batteries.

PubMed

Wu, Yang; Wei, Yang; Wang, Jiaping; Jiang, Kaili; Fan, Shoushan

2013-02-13

A uniform Fe(3)O(4) sheath is magnetron sputtered onto aligned carbon nanotube (CNT) scaffolds that are directly drawn from CNT arrays. The Fe(3)O(4)-CNT composite electrode, with the size of Fe(3)O(4) confined to 5-7 nm, exhibits a high reversible capacity over 800 mAh g(-1) based on the total electrode mass, remarkable capacity retention, as well as high rate capability. The excellent performance is attributable to the superior electrical conductivity of CNTs, the uniform loading of Fe(3)O(4) sheath, and the structural retention of the composite anode on cycling. As Fe(3)O(4) is inexpensive and environmentally friendly, and the synthesis of Fe(3)O(4)-CNT is free of chemical wastes, this composite anode material holds considerable promise for high-performance lithium ion batteries.
Retention-error patterns in complex alphanumeric serial-recall tasks.

PubMed

Mathy, Fabien; Varré, Jean-Stéphane

2013-01-01

We propose a new method based on an algorithm usually dedicated to DNA sequence alignment in order to both reliably score short-term memory performance on immediate serial-recall tasks and analyse retention-error patterns. There can be considerable confusion on how performance on immediate serial list recall tasks is scored, especially when the to-be-remembered items are sampled with replacement. We discuss the utility of sequence-alignment algorithms to compare the stimuli to the participants' responses. The idea is that deletion, substitution, translocation, and insertion errors, which are typical in DNA, are also typical putative errors in short-term memory (respectively omission, confusion, permutation, and intrusion errors). We analyse four data sets in which alphanumeric lists included a few (or many) repetitions. After examining the method on two simple data sets, we show that sequence alignment offers 1) a compelling method for measuring capacity in terms of chunks when many regularities are introduced in the material (third data set) and 2) a reliable estimator of individual differences in short-term memory capacity. This study illustrates the difficulty of arriving at a good measure of short-term memory performance, and also attempts to characterise the primary factors underpinning remembering and forgetting.
Degree of value alignment - a grounded theory of rural nurse resignations.

PubMed

Bragg, S M; Bonner, A

2014-01-01

The shortage of nurses willing to work in rural Australian healthcare settings continues to worsen. Australian rural areas have a lower retention rate of nurses than metropolitan counterparts, with more remote communities experiencing an even higher turnover of nursing staff. When retention rates are lower, patient outcomes are known to be poorer. This article reports a study that sought to explore the reasons why registered nurses resign from rural hospitals in the state of New South Wales, Australia. Using grounded theory methods, this study explored the reasons why registered nurses resigned from New South Wales rural hospitals. Data were collected from 12 participants using semi-structured interviews; each participant was a registered nurse who had resigned from a rural hospital. Nurses who had resigned due to retirement, relocation or maternity leave were excluded. Interviews were transcribed verbatim and imported into NVivo software. The constant comparative method of data collection and analysis was followed until a core category emerged. Nurses resigned from rural hospitals when their personal value of how nursing should occur conflicted with the hospital's organisational values driving the practice of nursing. These conflicting values led to a change in the degree of value alignment between the nurse and hospital. The degree of value alignment occurred in three dynamic stages that nurses moved through prior to resigning. The first stage, sharing values, was a time when a nurse and a hospital shared similar values. The second stage was conceding values where, due to perceived changes in a hospital's values, a nurse felt that patient care became compromised and this led to a divergence of values. The final stage was resigning, a stage where a nurse 'gave up' as they felt that their professional integrity was severely compromised. The findings revealed that when a nurse and organisational values were not aligned, conflict was created for a nurse about how they could perform nursing that aligned with their internalised professional values and integrity. Resignation occurred when nurses were unable to realign their personal values to changed organisational values - the organisational values changed due to rural area health service restructures, centralisation of budgets and resources, cumbersome hierarchies and management structures that inhibited communication and decision making, out-dated and ineffective operating systems, insufficient and inexperienced staff, bullying, and a lack of connectedness and shared vision. To fully comprehend rural nurse resignations, this study identified three stages that nurses move through prior to resignation. Effective retention strategies for the nursing workforce should address contributors to a decrease in value alignment and work towards encouraging the coalescence of nurses' and hospitals' values. It is imperative that strategies enable nurses to provide high quality patient care and promote a sense of connectedness and a shared vision between nurse and hospital. Senior managers need to have clear ways to articulate and imbue organisational values and be explicit in how these values accommodate nurses' values. Ward-level nurse managers have a significant responsibility to ensure that a hospital's values (both explicit and implicit) are incorporated into ward culture.
Ash leaf metabolomes reveal differences between trees tolerant and susceptible to ash dieback disease.

PubMed

Sambles, Christine M; Salmon, Deborah L; Florance, Hannah; Howard, Thomas P; Smirnoff, Nicholas; Nielsen, Lene R; McKinney, Lea V; Kjær, Erik D; Buggs, Richard J A; Studholme, David J; Grant, Murray

2017-12-19

European common ash, Fraxinus excelsior, is currently threatened by Ash dieback (ADB) caused by the fungus, Hymenoscyphus fraxineus. To detect and identify metabolites that may be products of pathways important in contributing to resistance against H. fraxineus, we performed untargeted metabolomic profiling on leaves from five high-susceptibility and five low-susceptibility F. excelsior individuals identified during Danish field trials. We describe in this study, two datasets. The first is untargeted LC-MS metabolomics raw data from ash leaves with high-susceptibility and low-susceptibility to ADB in positive and negative mode. These data allow the application of peak picking, alignment, gap-filling and retention-time correlation analyses to be performed in alternative ways. The second, a processed dataset containing abundances of aligned features across all samples enables further mining of the data. Here we illustrate the utility of this dataset which has previously been used to identify putative iridoid glycosides, well known anti-herbivory terpenoid derivatives, and show differential abundance in tolerant and susceptible ash samples.
Ash leaf metabolomes reveal differences between trees tolerant and susceptible to ash dieback disease

PubMed Central

Sambles, Christine M.; Salmon, Deborah L.; Florance, Hannah; Howard, Thomas P.; Smirnoff, Nicholas; Nielsen, Lene R.; McKinney, Lea V.; Kjær, Erik D.; Buggs, Richard J. A.; Studholme, David J.; Grant, Murray

2017-01-01

European common ash, Fraxinus excelsior, is currently threatened by Ash dieback (ADB) caused by the fungus, Hymenoscyphus fraxineus. To detect and identify metabolites that may be products of pathways important in contributing to resistance against H. fraxineus, we performed untargeted metabolomic profiling on leaves from five high-susceptibility and five low-susceptibility F. excelsior individuals identified during Danish field trials. We describe in this study, two datasets. The first is untargeted LC-MS metabolomics raw data from ash leaves with high-susceptibility and low-susceptibility to ADB in positive and negative mode. These data allow the application of peak picking, alignment, gap-filling and retention-time correlation analyses to be performed in alternative ways. The second, a processed dataset containing abundances of aligned features across all samples enables further mining of the data. Here we illustrate the utility of this dataset which has previously been used to identify putative iridoid glycosides, well known anti-herbivory terpenoid derivatives, and show differential abundance in tolerant and susceptible ash samples. PMID:29257137
Floating nut retention system

NASA Technical Reports Server (NTRS)

Charles, J. F.; Theakston, H. A. (Inventor)

1980-01-01

A floating nut retention system includes a nut with a central aperture. An inner retainer plate has an opening which is fixedly aligned with the nut aperture. An outer retainer member is formed of a base plate having an opening and a surface adjacent to a surface of the inner retainer plate. The outer retainer member includes a securing mechanism for retaining the inner retainer plate adjacent to the outer retainer member. The securing mechanism enables the inner retainer plate to float with respect to the outer retainer number, while simultaneously forming a bearing surface for inner retainer plate.
76 FR 24089 - Credit Risk Retention

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-29

... Resecuritization Transactions D. Additional Exemptions E. Safe Harbor for Certain Foreign-Related Transactions VII..., when incentives are not properly aligned and there is a lack of discipline in the origination process... incentive problems among various parties involved in the process.\\8\\ \\7\\ Securitization may reduce the cost...

Web Server for Peak Detection, Baseline Correction, and Alignment in Two-Dimensional Gas Chromatography Mass Spectrometry-Based Metabolomics Data.

PubMed

Tian, Tze-Feng; Wang, San-Yuan; Kuo, Tien-Chueh; Tan, Cheng-En; Chen, Guan-Yuan; Kuo, Ching-Hua; Chen, Chi-Hsin Sally; Chan, Chang-Chuan; Lin, Olivia A; Tseng, Y Jane

2016-11-01

Two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) is superior for chromatographic separation and provides great sensitivity for complex biological fluid analysis in metabolomics. However, GC×GC/TOF-MS data processing is currently limited to vendor software and typically requires several preprocessing steps. In this work, we implement a web-based platform, which we call GC 2 MS, to facilitate the application of recent advances in GC×GC/TOF-MS, especially for metabolomics studies. The core processing workflow of GC 2 MS consists of blob/peak detection, baseline correction, and blob alignment. GC 2 MS treats GC×GC/TOF-MS data as pictures and clusters the pixels as blobs according to the brightness of each pixel to generate a blob table. GC 2 MS then aligns the blobs of two GC×GC/TOF-MS data sets according to their distance and similarity. The blob distance and similarity are the Euclidean distance of the first and second retention times of two blobs and the Pearson's correlation coefficient of the two mass spectra, respectively. GC 2 MS also directly corrects the raw data baseline. The analytical performance of GC 2 MS was evaluated using GC×GC/TOF-MS data sets of Angelica sinensis compounds acquired under different experimental conditions and of human plasma samples. The results show that GC 2 MS is an easy-to-use tool for detecting peaks and correcting baselines, and GC 2 MS is able to align GC×GC/TOF-MS data sets acquired under different experimental conditions. GC 2 MS is freely accessible at http://gc2ms.web.cmdm.tw .
A Guideline to Univariate Statistical Analysis for LC/MS-Based Untargeted Metabolomics-Derived Data

PubMed Central

Vinaixa, Maria; Samino, Sara; Saez, Isabel; Duran, Jordi; Guinovart, Joan J.; Yanes, Oscar

2012-01-01

Several metabolomic software programs provide methods for peak picking, retention time alignment and quantification of metabolite features in LC/MS-based metabolomics. Statistical analysis, however, is needed in order to discover those features significantly altered between samples. By comparing the retention time and MS/MS data of a model compound to that from the altered feature of interest in the research sample, metabolites can be then unequivocally identified. This paper reports on a comprehensive overview of a workflow for statistical analysis to rank relevant metabolite features that will be selected for further MS/MS experiments. We focus on univariate data analysis applied in parallel on all detected features. Characteristics and challenges of this analysis are discussed and illustrated using four different real LC/MS untargeted metabolomic datasets. We demonstrate the influence of considering or violating mathematical assumptions on which univariate statistical test rely, using high-dimensional LC/MS datasets. Issues in data analysis such as determination of sample size, analytical variation, assumption of normality and homocedasticity, or correction for multiple testing are discussed and illustrated in the context of our four untargeted LC/MS working examples. PMID:24957762
A Guideline to Univariate Statistical Analysis for LC/MS-Based Untargeted Metabolomics-Derived Data.

PubMed

Vinaixa, Maria; Samino, Sara; Saez, Isabel; Duran, Jordi; Guinovart, Joan J; Yanes, Oscar

2012-10-18

Several metabolomic software programs provide methods for peak picking, retention time alignment and quantification of metabolite features in LC/MS-based metabolomics. Statistical analysis, however, is needed in order to discover those features significantly altered between samples. By comparing the retention time and MS/MS data of a model compound to that from the altered feature of interest in the research sample, metabolites can be then unequivocally identified. This paper reports on a comprehensive overview of a workflow for statistical analysis to rank relevant metabolite features that will be selected for further MS/MS experiments. We focus on univariate data analysis applied in parallel on all detected features. Characteristics and challenges of this analysis are discussed and illustrated using four different real LC/MS untargeted metabolomic datasets. We demonstrate the influence of considering or violating mathematical assumptions on which univariate statistical test rely, using high-dimensional LC/MS datasets. Issues in data analysis such as determination of sample size, analytical variation, assumption of normality and homocedasticity, or correction for multiple testing are discussed and illustrated in the context of our four untargeted LC/MS working examples.
Embedding Multiple Literacies into STEM Curricula

ERIC Educational Resources Information Center

Soules, Aline; Nielsen, Sarah; LeDuc, Danika; Inouye, Caron; Singley, Jason; Wildy, Erica; Seitz, Jeff

2014-01-01

In fall 2012, an interdisciplinary team of science, English, and library faculty embedded reading, writing, and information literacy strategies in Science, Technology, Engineering, and Mathematics (STEM) curricula as a first step in improving student learning and retention in science courses and aligning them with the Next Generation Science and…
Aligned ovine diaphragmatic myoblasts overexpressing human connexin-43 seeded on poly (L-lactic acid) scaffolds for potential use in cardiac regeneration.

PubMed

Giménez, Carlos Sebastián; Locatelli, Paola; Montini Ballarin, Florencia; Orlowski, Alejandro; Dewey, Ricardo A; Pena, Milagros; Abraham, Gustavo Abel; Aiello, Ernesto Alejandro; Bauzá, María Del Rosario; Cuniberti, Luis; Olea, Fernanda Daniela; Crottogini, Alberto

2018-04-01

Diaphragmatic myoblasts (DMs) are precursors of type-1 muscle cells displaying high exhaustion threshold on account that they contract and relax 20 times/min over a lifespan, making them potentially useful in cardiac regeneration strategies. Besides, it has been shown that biomaterials for stem cell delivery improve cell retention and viability in the target organ. In the present study, we aimed at developing a novel approach based on the use of poly (L-lactic acid) (PLLA) scaffolds seeded with DMs overexpressing connexin-43 (cx43), a gap junction protein that promotes inter-cell connectivity. DMs isolated from ovine diaphragm biopsies were characterized by immunohistochemistry and ability to differentiate into myotubes (MTs) and transduced with a lentiviral vector encoding cx43. After confirming cx43 expression (RT-qPCR and Western blot) and its effect on inter-cell connectivity (fluorescence recovery after photobleaching), DMs were grown on fiber-aligned or random PLLA scaffolds. DMs were successfully isolated and characterized. Cx43 mRNA and protein were overexpressed and favored inter-cell connectivity. Alignment of the scaffold fibers not only aligned but also elongated the cells, increasing the contact surface between them. This novel approach is feasible and combines the advantages of bioresorbable scaffolds as delivery method and a cell type that on account of its features may be suitable for cardiac regeneration. Future studies on animal models of myocardial infarction are needed to establish its usefulness on scar reduction and cardiac function.
Interactions between Skeletal Muscle Myoblasts and their Extracellular Matrix Revealed by a Serum Free Culture System.

PubMed

Chaturvedi, Vishal; Dye, Danielle E; Kinnear, Beverley F; van Kuppevelt, Toin H; Grounds, Miranda D; Coombe, Deirdre R

2015-01-01

Decellularisation of skeletal muscle provides a system to study the interactions of myoblasts with muscle extracellular matrix (ECM). This study describes the efficient decellularisation of quadriceps muscle with the retention of matrix components and the use of this matrix for myoblast proliferation and differentiation under serum free culture conditions. Three decellularisation approaches were examined; the most effective was phospholipase A2 treatment, which removed cellular material while maximizing the retention of ECM components. Decellularised muscle matrices were then solubilized and used as substrates for C2C12 mouse myoblast serum free cultures. The muscle matrix supported myoblast proliferation and differentiation equally as well as collagen and fibronectin. Immunofluorescence analyses revealed that myoblasts seeded on muscle matrix and fibronectin differentiated to form long, well-aligned myotubes, while myoblasts seeded on collagen were less organized. qPCR analyses showed a time dependent increase in genes involved in skeletal muscle differentiation and suggested that muscle-derived matrix may stimulate an increased rate of differentiation compared to collagen and fibronectin. Decellularized whole muscle three-dimensional scaffolds also supported cell adhesion and spreading, with myoblasts aligning along specific tracts of matrix proteins within the scaffolds. Thus, under serum free conditions, intact acellular muscle matrices provided cues to direct myoblast adhesion and migration. In addition, myoblasts were shown to rapidly secrete and organise their own matrix glycoproteins to create a localized ECM microenvironment. This serum free culture system has revealed that the correct muscle ECM facilitates more rapid cell organisation and differentiation than single matrix glycoprotein substrates.
Braided and Stacked Electrospun Nanofibrous Scaffolds for Tendon and Ligament Tissue Engineering

PubMed Central

Rothrauff, Benjamin B.; Lauro, Brian B.; Yang, Guang; Debski, Richard E.; Musahl, Volker

2017-01-01

Tendon and ligament injuries are a persistent orthopedic challenge given their poor innate healing capacity. Nonwoven electrospun nanofibrous scaffolds composed of polyesters have been used to mimic the mechanics and topographical cues of native tendons and ligaments. However, nonwoven nanofibers have several limitations that prevent broader clinical application, including poor cell infiltration, as well as tensile and suture-retention strengths that are inferior to native tissues. In this study, multilayered scaffolds of aligned electrospun nanofibers of two designs–stacked or braided–were fabricated. Mechanical properties, including structural and mechanical properties and suture-retention strength, were determined using acellular scaffolds. Human bone marrow-derived mesenchymal stem cells (MSCs) were seeded on scaffolds for up to 28 days, and assays for tenogenic differentiation, histology, and biochemical composition were performed. Braided scaffolds exhibited improved tensile and suture-retention strengths, but reduced moduli. Both scaffold designs supported expression of tenogenic markers, although the effect was greater on braided scaffolds. Conversely, cell infiltration was superior in stacked constructs, resulting in enhanced cell number, total collagen content, and total sulfated glycosaminoglycan content. However, when normalized against cell number, both designs modulated extracellular matrix protein deposition to a similar degree. Taken together, this study demonstrates that multilayered scaffolds of aligned electrospun nanofibers supported tenogenic differentiation of seeded MSCs, but the macroarchitecture is an important consideration for applications of tendon and ligament tissue engineering. PMID:28071988
Braided and Stacked Electrospun Nanofibrous Scaffolds for Tendon and Ligament Tissue Engineering.

PubMed

Rothrauff, Benjamin B; Lauro, Brian B; Yang, Guang; Debski, Richard E; Musahl, Volker; Tuan, Rocky S

2017-05-01

Tendon and ligament injuries are a persistent orthopedic challenge given their poor innate healing capacity. Nonwoven electrospun nanofibrous scaffolds composed of polyesters have been used to mimic the mechanics and topographical cues of native tendons and ligaments. However, nonwoven nanofibers have several limitations that prevent broader clinical application, including poor cell infiltration, as well as tensile and suture-retention strengths that are inferior to native tissues. In this study, multilayered scaffolds of aligned electrospun nanofibers of two designs-stacked or braided-were fabricated. Mechanical properties, including structural and mechanical properties and suture-retention strength, were determined using acellular scaffolds. Human bone marrow-derived mesenchymal stem cells (MSCs) were seeded on scaffolds for up to 28 days, and assays for tenogenic differentiation, histology, and biochemical composition were performed. Braided scaffolds exhibited improved tensile and suture-retention strengths, but reduced moduli. Both scaffold designs supported expression of tenogenic markers, although the effect was greater on braided scaffolds. Conversely, cell infiltration was superior in stacked constructs, resulting in enhanced cell number, total collagen content, and total sulfated glycosaminoglycan content. However, when normalized against cell number, both designs modulated extracellular matrix protein deposition to a similar degree. Taken together, this study demonstrates that multilayered scaffolds of aligned electrospun nanofibers supported tenogenic differentiation of seeded MSCs, but the macroarchitecture is an important consideration for applications of tendon and ligament tissue engineering.
Dipeptide Sequence Determination: Analyzing Phenylthiohydantoin Amino Acids by HPLC

NASA Astrophysics Data System (ADS)

Barton, Janice S.; Tang, Chung-Fei; Reed, Steven S.

2000-02-01

Amino acid composition and sequence determination, important techniques for characterizing peptides and proteins, are essential for predicting conformation and studying sequence alignment. This experiment presents improved, fundamental methods of sequence analysis for an upper-division biochemistry laboratory. Working in pairs, students use the Edman reagent to prepare phenylthiohydantoin derivatives of amino acids for determination of the sequence of an unknown dipeptide. With a single HPLC technique, students identify both the N-terminal amino acid and the composition of the dipeptide. This method yields good precision of retention times and allows use of a broad range of amino acids as components of the dipeptide. Students learn fundamental principles and techniques of sequence analysis and HPLC.
Student Perspectives on Transfer and Articulation: Implications for Teacher Education Pedagogy and Practice

ERIC Educational Resources Information Center

Kates, Laura R.

2010-01-01

This study introduces students' perspectives into the knowledge base on community college teacher education and transfer to the four-year college. There is currently widespread agreement that community colleges are an essential resource for diversifying the teaching force and improving teacher retention. While data on enrollment, alignment, and…
Talent Management in the Private and Education Sectors: A Literature Review

ERIC Educational Resources Information Center

Behrstock, Ellen

2010-01-01

Although teacher recruitment and retention have been policy concerns for many years, the strategic alignment of educator talent management initiatives has only recently begun to gain momentum. The adoption of a more comprehensive and strategic approach to securing a sufficient number of effective teachers is evidenced by the creation of human…
Curriculum Alignment with Vision and Change Improves Student Scientific Literacy

PubMed Central

Auerbach, Anna Jo; Schussler, Elisabeth E.

2017-01-01

The Vision and Change in Undergraduate Biology Education final report challenged institutions to reform their biology courses to focus on process skills and student active learning, among other recommendations. A large southeastern university implemented curricular changes to its majors’ introductory biology sequence in alignment with these recommendations. Discussion sections focused on developing student process skills were added to both lectures and a lab, and one semester of lab was removed. This curriculum was implemented using active-learning techniques paired with student collaboration. This study determined whether these changes resulted in a higher gain of student scientific literacy by conducting pre/posttesting of scientific literacy for two cohorts: students experiencing the unreformed curriculum and students experiencing the reformed curriculum. Retention of student scientific literacy for each cohort was also assessed 4 months later. At the end of the academic year, scientific literacy gains were significantly higher for students in the reformed curriculum (p = 0.005), with those students having double the scientific literacy gains of the cohort in the unreformed curriculum. Retention of scientific literacy did not differ between the cohorts. PMID:28495933
The combined use of computer-guided, minimally invasive, flapless corticotomy and clear aligners as a novel approach to moderate crowding: A case report

PubMed Central

Cassetta, Michele; Altieri, Federica; Pandolfi, Stefano; Giansanti, Matteo

2017-01-01

The aim of this case report was to describe an innovative orthodontic treatment method that combined surgical and orthodontic techniques. The novel method was used to achieve a positive result in a case of moderate crowding by employing a computer-guided piezocision procedure followed by the use of clear aligners. A 23-year-old woman had a malocclusion with moderate crowding. Her periodontal indices, oral health-related quality of life (OHRQoL), and treatment time were evaluated. The treatment included interproximal corticotomy cuts extending through the entire thickness of the cortical layer, without a full-thickness flap reflection. This was achieved with a three-dimensionally printed surgical guide using computer-aided design and computer-aided manufacturing. Orthodontic force was applied to the teeth immediately after surgery by using clear appliances for better control of tooth movement. The total treatment time was 8 months. The periodontal indices improved after crowding correction, but the oral health impact profile showed a slight deterioration of OHRQoL during the 3 days following surgery. At the 2-year retention follow-up, the stability of treatment was excellent. The reduction in surgical time and patient discomfort, increased periodontal safety and patient acceptability, and accurate control of orthodontic movement without the risk of losing anchorage may encourage the use of this combined technique in appropriate cases. PMID:28337422
The combined use of computer-guided, minimally invasive, flapless corticotomy and clear aligners as a novel approach to moderate crowding: A case report.

PubMed

Cassetta, Michele; Altieri, Federica; Pandolfi, Stefano; Giansanti, Matteo

2017-03-01

The aim of this case report was to describe an innovative orthodontic treatment method that combined surgical and orthodontic techniques. The novel method was used to achieve a positive result in a case of moderate crowding by employing a computer-guided piezocision procedure followed by the use of clear aligners. A 23-year-old woman had a malocclusion with moderate crowding. Her periodontal indices, oral health-related quality of life (OHRQoL), and treatment time were evaluated. The treatment included interproximal corticotomy cuts extending through the entire thickness of the cortical layer, without a full-thickness flap reflection. This was achieved with a three-dimensionally printed surgical guide using computer-aided design and computer-aided manufacturing. Orthodontic force was applied to the teeth immediately after surgery by using clear appliances for better control of tooth movement. The total treatment time was 8 months. The periodontal indices improved after crowding correction, but the oral health impact profile showed a slight deterioration of OHRQoL during the 3 days following surgery. At the 2-year retention follow-up, the stability of treatment was excellent. The reduction in surgical time and patient discomfort, increased periodontal safety and patient acceptability, and accurate control of orthodontic movement without the risk of losing anchorage may encourage the use of this combined technique in appropriate cases.
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

PubMed Central

Röst, Hannes L.; Liu, Yansheng; D’Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C.; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi

2016-01-01

Large scale, quantitative proteomic studies have become essential for the analysis of clinical cohorts, large perturbation experiments and systems biology studies. While next-generation mass spectrometric techniques such as SWATH-MS have substantially increased throughput and reproducibility, ensuring consistent quantification of thousands of peptide analytes across multiple LC-MS/MS runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we have developed the TRIC software which utilizes fragment ion data to perform cross-run alignment, consistent peak-picking and quantification for high throughput targeted proteomics. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate peak elution information from all LC-MS/MS runs acquired in a study. When compared to state-of-the-art SWATH-MS data analysis, the algorithm was able to reduce the identification error by more than 3-fold at constant recall, while correcting for highly non-linear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem (iPS) cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups and substantially increased the quantitative completeness and biological information in the data, providing insights into protein dynamics of iPS cells. Overall, this study demonstrates the importance of consistent quantification in highly challenging experimental setups, and proposes an algorithm to automate this task, constituting the last missing piece in a pipeline for automated analysis of massively parallel targeted proteomics datasets. PMID:27479329
NASA's Potential Contributions for Remediation of Retention Ponds Using Solar Ultraviolet Radiation and Photocatalysis

NASA Technical Reports Server (NTRS)

Underwood, Lauren W.; Ryan, Robert E.

2007-01-01

This Candidate Solution uses NASA Earth science research on atmospheric ozone and aerosols data (1) to help improve the prediction capabilities of water runoff models that are used to estimate runoff pollution from retention ponds, and (2) to understand the pollutant removal contribution and potential of photocatalytically coated materials that could be used in these ponds. Models (the EPA's SWMM and the USGS SLAMM) exist that estimate the release of pollutants into the environment from storm-water-related retention pond runoff. UV irradiance data acquired from the satellite mission Aura and from the OMI Surface UV algorithm will be incorporated into these models to enhance their capabilities, not only by increasing the general understanding of retention pond function (both the efficacy and efficiency) but additionally by adding photocatalytic materials to these retention ponds, augmenting their performance. State and local officials who run pollution protection programs could then develop and implement photocatalytic technologies for water pollution control in retention ponds and use them in conjunction with existing runoff models. More effective decisions about water pollution protection programs could be made, the persistence and toxicity of waste generated could be minimized, and subsequently our natural water resources would be improved. This Candidate Solution is in alignment with the Water Management and Public Health National Applications.
Investigation of interpolation techniques for the reconstruction of the first dimension of comprehensive two-dimensional liquid chromatography-diode array detector data.

PubMed

Allen, Robert C; Rutan, Sarah C

2011-10-31

Simulated and experimental data were used to measure the effectiveness of common interpolation techniques during chromatographic alignment of comprehensive two-dimensional liquid chromatography-diode array detector (LC×LC-DAD) data. Interpolation was used to generate a sufficient number of data points in the sampled first chromatographic dimension to allow for alignment of retention times from different injections. Five different interpolation methods, linear interpolation followed by cross correlation, piecewise cubic Hermite interpolating polynomial, cubic spline, Fourier zero-filling, and Gaussian fitting, were investigated. The fully aligned chromatograms, in both the first and second chromatographic dimensions, were analyzed by parallel factor analysis to determine the relative area for each peak in each injection. A calibration curve was generated for the simulated data set. The standard error of prediction and percent relative standard deviation were calculated for the simulated peak for each technique. The Gaussian fitting interpolation technique resulted in the lowest standard error of prediction and average relative standard deviation for the simulated data. However, upon applying the interpolation techniques to the experimental data, most of the interpolation methods were not found to produce statistically different relative peak areas from each other. While most of the techniques were not statistically different, the performance was improved relative to the PARAFAC results obtained when analyzing the unaligned data. Copyright © 2011 Elsevier B.V. All rights reserved.
Cycle stability of the electrochemical capacitors patterned with vertically aligned carbon nanotubes in an LiPF6-based electrolyte.

PubMed

Chiou, Yi-Deng; Tsai, Dah-Shyang; Lam, Hoa Hung; Chang, Chuan-hua; Lee, Kuei-Yi; Huang, Ying-Sheng

2013-09-07

The miniature ultracapacitors, with interdigitated electrodes of vertically aligned carbon nanotubes (VACNTs) and an inter-electrode gap of 20 μm, have been prepared in the LiPF6 organic electrolyte with and without PVdF-HFP gel. PVdF-HFP between two opposing electrodes enhances the device reliability, but lessens its power performance because of the extra diffusion resistance. Also noteworthy are the gel influences on the cycle stability. When the applied voltage is 2.0 or 2.5 V, both the LiPF6 and the gel capacitors exhibit excellent stability, typified by a retention ratio of ≥95% after 10,000 cycles. Their coulombic efficiencies quickly rise up, and hold steady at 100%. Nonetheless, when the applied voltage is 3.5 or 4.0 V, the cycle stability deteriorates, since the negative electrode potential descends below 0.9 V (vs. Li), leading to electrolyte decomposition and SEI formation. For the LiPF6 capacitor, its retention ratio could be around 60% after 10,000 cycles and the coulombic efficiency of 100% is difficult to reach throughout its cycle life. On the other hand, the gel capacitor cycles energy with a much higher retention ratio, >80% after 10,000 cycles, and a better coulombic efficiency, even though electrolyte decomposition still occurs. We attribute the superior stability of the gel capacitor to its extra diffusion resistance which slows down the performance deterioration.
Pseudocapacitive Electrodes Produced by Oxidant-Free Polymerization of Pyrrole between the Layers of 2D Titanium Carbide (MXene)

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

Boota, Muhammad; Anasori, Babak; Voigt, Cooper

Heterocyclic pyrrole molecules are in situ aligned and polymerized in the absence of an oxidant between layers of the 2D Ti3C2Tx (MXene), resulting in high volumetric and gravimetric capacitances with capacitance retention of 92% after 25 000 cycles at a 100 mV s-1 scan rate.
Development and Validation of a Qualitative Method for Target Screening of 448 Pesticide Residues in Fruits and Vegetables Using UHPLC/ESI Q-Orbitrap Based on Data-Independent Acquisition and Compound Database.

PubMed

Wang, Jian; Chow, Willis; Chang, James; Wong, Jon W

2017-01-18

A semiautomated qualitative method for target screening of 448 pesticide residues in fruits and vegetables was developed and validated using ultrahigh-performance liquid chromatography coupled with electrospray ionization quadrupole Orbitrap high-resolution mass spectrometry (UHPLC/ESI Q-Orbitrap). The Q-Orbitrap Full MS/dd-MS 2 (data dependent acquisition) was used to acquire product-ion spectra of individual pesticides to build a compound database or an MS library, while its Full MS/DIA (data independent acquisition) was utilized for sample data acquisition from fruit and vegetable matrices fortified with pesticides at 10 and 100 μg/kg for target screening purpose. Accurate mass, retention time and response threshold were three key parameters in a compound database that were used to detect incurred pesticide residues in samples. The concepts and practical aspects of in-spectrum mass correction or solvent background lock-mass correction, retention time alignment and response threshold adjustment are discussed while building a functional and working compound database for target screening. The validated target screening method is capable of screening at least 94% and 99% of 448 pesticides at 10 and 100 μg/kg, respectively, in fruits and vegetables without having to evaluate every compound manually during data processing, which significantly reduced the workload in routine practice.

MRM-DIFF: data processing strategy for differential analysis in large scale MRM-based lipidomics studies.

PubMed

Tsugawa, Hiroshi; Ohta, Erika; Izumi, Yoshihiro; Ogiwara, Atsushi; Yukihira, Daichi; Bamba, Takeshi; Fukusaki, Eiichiro; Arita, Masanori

2014-01-01

Based on theoretically calculated comprehensive lipid libraries, in lipidomics as many as 1000 multiple reaction monitoring (MRM) transitions can be monitored for each single run. On the other hand, lipid analysis from each MRM chromatogram requires tremendous manual efforts to identify and quantify lipid species. Isotopic peaks differing by up to a few atomic masses further complicate analysis. To accelerate the identification and quantification process we developed novel software, MRM-DIFF, for the differential analysis of large-scale MRM assays. It supports a correlation optimized warping (COW) algorithm to align MRM chromatograms and utilizes quality control (QC) sample datasets to automatically adjust the alignment parameters. Moreover, user-defined reference libraries that include the molecular formula, retention time, and MRM transition can be used to identify target lipids and to correct peak abundances by considering isotopic peaks. Here, we demonstrate the software pipeline and introduce key points for MRM-based lipidomics research to reduce the mis-identification and overestimation of lipid profiles. The MRM-DIFF program, example data set and the tutorials are downloadable at the "Standalone software" section of the PRIMe (Platform for RIKEN Metabolomics, http://prime.psc.riken.jp/) database website.
MRM-DIFF: data processing strategy for differential analysis in large scale MRM-based lipidomics studies

PubMed Central

Tsugawa, Hiroshi; Ohta, Erika; Izumi, Yoshihiro; Ogiwara, Atsushi; Yukihira, Daichi; Bamba, Takeshi; Fukusaki, Eiichiro; Arita, Masanori

2015-01-01

Based on theoretically calculated comprehensive lipid libraries, in lipidomics as many as 1000 multiple reaction monitoring (MRM) transitions can be monitored for each single run. On the other hand, lipid analysis from each MRM chromatogram requires tremendous manual efforts to identify and quantify lipid species. Isotopic peaks differing by up to a few atomic masses further complicate analysis. To accelerate the identification and quantification process we developed novel software, MRM-DIFF, for the differential analysis of large-scale MRM assays. It supports a correlation optimized warping (COW) algorithm to align MRM chromatograms and utilizes quality control (QC) sample datasets to automatically adjust the alignment parameters. Moreover, user-defined reference libraries that include the molecular formula, retention time, and MRM transition can be used to identify target lipids and to correct peak abundances by considering isotopic peaks. Here, we demonstrate the software pipeline and introduce key points for MRM-based lipidomics research to reduce the mis-identification and overestimation of lipid profiles. The MRM-DIFF program, example data set and the tutorials are downloadable at the “Standalone software” section of the PRIMe (Platform for RIKEN Metabolomics, http://prime.psc.riken.jp/) database website. PMID:25688256
Effects of posttreatment skeletal maturity measured with the cervical vertebral maturation method on incisor alignment relapse.

PubMed

Fudalej, Piotr; Rothe, Laura E; Bollen, Anne-Marie

2008-08-01

Our aim was to test the hypothesis that relapse of incisor alignment is associated with skeletal maturity at the end of treatment, as assessed with the cervical vertebral maturation (CVM) method. This was a case-control study with information from the postretention database at the University of Washington. Mandibular incisor irregularity (II) at least 10 years out of retention (T3) was used to define the subjects (II >6 mm, relapse group) and the controls (II <3.5 mm, stable group). The following model measurements were made: II at pretreatment (T1), II at posttreatment (T2), and intercanine width at T1 and T2. On cephalograms taken T2, the CVM status was determined. Logistic regression analyses were used to determine the association between relapse and CVM status after treatment. The models were adjusted for potentially confounding variables (II at pretreatment and posttreatment, intercanine width change during treatment, sex, age at T2, and treatment alternatives). No association between CVM stage at T2 and relapse was found (P = 0.89). Both groups had similar distributions of the CVM stages (P >0.05). Pretreatment II and postretention time were found to be correlated with long-term incisor stability (P = 0.007 and 0.034, respectively). Sex was not related to relapse (P = 0.33). Maturity of craniofacial structures at the end of treatment evaluated with the CVM method is not associated with long-term stability of incisor alignment.
Lead-free epitaxial ferroelectric material integration on semiconducting (100) Nb-doped SrTiO3 for low-power non-volatile memory and efficient ultraviolet ray detection

PubMed Central

Kundu, Souvik; Clavel, Michael; Biswas, Pranab; Chen, Bo; Song, Hyun-Cheol; Kumar, Prashant; Halder, Nripendra N.; Hudait, Mantu K.; Banerji, Pallab; Sanghadasa, Mohan; Priya, Shashank

2015-01-01

We report lead-free ferroelectric based resistive switching non-volatile memory (NVM) devices with epitaxial (1-x)BaTiO3-xBiFeO3 (x = 0.725) (BT-BFO) film integrated on semiconducting (100) Nb (0.7%) doped SrTiO3 (Nb:STO) substrates. The piezoelectric force microscopy (PFM) measurement at room temperature demonstrated ferroelectricity in the BT-BFO thin film. PFM results also reveal the repeatable polarization inversion by poling, manifesting its potential for read-write operation in NVM devices. The electroforming-free and ferroelectric polarization coupled electrical behaviour demonstrated excellent resistive switching with high retention time, cyclic endurance, and low set/reset voltages. X-ray photoelectron spectroscopy was utilized to determine the band alignment at the BT-BFO and Nb:STO heterojunction, and it exhibited staggered band alignment. This heterojunction is found to behave as an efficient ultraviolet photo-detector with low rise and fall time. The architecture also demonstrates half-wave rectification under low and high input signal frequencies, where the output distortion is minimal. The results provide avenue for an electrical switch that can regulate the pixels in low or high frequency images. Combined this work paves the pathway towards designing future generation low-power ferroelectric based microelectronic devices by merging both electrical and photovoltaic properties of BT-BFO materials. PMID:26202946
Lead-free epitaxial ferroelectric material integration on semiconducting (100) Nb-doped SrTiO3 for low-power non-volatile memory and efficient ultraviolet ray detection.

PubMed

Kundu, Souvik; Clavel, Michael; Biswas, Pranab; Chen, Bo; Song, Hyun-Cheol; Kumar, Prashant; Halder, Nripendra N; Hudait, Mantu K; Banerji, Pallab; Sanghadasa, Mohan; Priya, Shashank

2015-07-23

We report lead-free ferroelectric based resistive switching non-volatile memory (NVM) devices with epitaxial (1-x)BaTiO3-xBiFeO3 (x = 0.725) (BT-BFO) film integrated on semiconducting (100) Nb (0.7%) doped SrTiO3 (Nb:STO) substrates. The piezoelectric force microscopy (PFM) measurement at room temperature demonstrated ferroelectricity in the BT-BFO thin film. PFM results also reveal the repeatable polarization inversion by poling, manifesting its potential for read-write operation in NVM devices. The electroforming-free and ferroelectric polarization coupled electrical behaviour demonstrated excellent resistive switching with high retention time, cyclic endurance, and low set/reset voltages. X-ray photoelectron spectroscopy was utilized to determine the band alignment at the BT-BFO and Nb:STO heterojunction, and it exhibited staggered band alignment. This heterojunction is found to behave as an efficient ultraviolet photo-detector with low rise and fall time. The architecture also demonstrates half-wave rectification under low and high input signal frequencies, where the output distortion is minimal. The results provide avenue for an electrical switch that can regulate the pixels in low or high frequency images. Combined this work paves the pathway towards designing future generation low-power ferroelectric based microelectronic devices by merging both electrical and photovoltaic properties of BT-BFO materials.
Plasma-assisted nitrogen doping of VACNTs for efficiently enhancing the supercapacitor performance

NASA Astrophysics Data System (ADS)

Mashayekhi, Alireza; Hosseini, Seyed Mahmoud; Hassanpour Amiri, Morteza; Namdar, Naser; Sanaee, Zeinab

2016-06-01

Nitrogen doping of vertically aligned carbon nanotubes (VACNTs) using plasma-enhanced chemical vapour deposition has been investigated to improve the supercapacitance performance of CNTs. Incorporating electrochemical measurements on the open-ended nitrogen-doped CNTs, showed the achievement of 6 times improvement in the capacitance value. For nitrogen-doped CNTs on silicon substrate, specific capacitance of 60 F g-1 was obtained in 0.5 M KCl solution, with capacity retention ratio above 90 % after cycled at 0.1 A g-1 for 5000 cycles. Using this sample, a symmetric supercapacitance was fabricated which showed the power density of 37.5 kW kg-1. The facile fabrication approach and its excellent capacitance improvement, propose it as an efficient technique for enhancing the supercapacitance performance of the carbon-based electrodes.
Understanding the Behavioral Determinants of Retention in HIV Care: A Qualitative Evaluation of a Situated Information, Motivation, Behavioral Skills Model of Care Initiation and Maintenance

PubMed Central

Fisher, Jeffrey D.; Cunningham, Chinazo O.; Amico, K. Rivet

2012-01-01

Abstract The current study provides a qualitative test of a recently proposed application of an Information, Motivation, Behavioral Skills (IMB) model of health behavior situated to the social-environmental, structural, cognitive-affective, and behavioral demands of retention in HIV care. Mixed-methods qualitative analysis was used to identify the content and context of critical theory-based determinants of retention in HIV care, and to evaluate the relative fit of the model to the qualitative data collected via in-depth semi-structured interviews with a sample of inner-city patients accessing traditional and nontraditional HIV care services in the Bronx, NY. The sample reflected a diverse marginalized patient population who commonly experienced comorbid chronic conditions (e.g., psychiatric disorders, substance abuse disorders, diabetes, hepatitis C). Through deductive content coding, situated IMB model-based content was identified in all but 7.1% of statements discussing facilitators or barriers to retention in HIV care. Inductive emergent theme identification yielded a number of important themes influencing retention in HIV care (e.g., acceptance of diagnosis, stigma, HIV cognitive/physical impairments, and global constructs of self-care). Multiple elements of these themes strongly aligned with the model's IMB constructs. The convergence of the results from both sets of analysis demonstrate that participants' experiences map well onto the content and structure of the situated IMB model, providing a systematic classification of important theoretical and contextual determinants of retention in care. Future intervention efforts to enhance retention in HIV care should address these multiple determinants (i.e., information, motivation, behavioral skills) of self-directed retention in HIV care. PMID:22612447
Understanding the behavioral determinants of retention in HIV care: a qualitative evaluation of a situated information, motivation, behavioral skills model of care initiation and maintenance.

PubMed

Smith, Laramie R; Fisher, Jeffrey D; Cunningham, Chinazo O; Amico, K Rivet

2012-06-01

The current study provides a qualitative test of a recently proposed application of an Information, Motivation, Behavioral Skills (IMB) model of health behavior situated to the social-environmental, structural, cognitive-affective, and behavioral demands of retention in HIV care. Mixed-methods qualitative analysis was used to identify the content and context of critical theory-based determinants of retention in HIV care, and to evaluate the relative fit of the model to the qualitative data collected via in-depth semi-structured interviews with a sample of inner-city patients accessing traditional and nontraditional HIV care services in the Bronx, NY. The sample reflected a diverse marginalized patient population who commonly experienced comorbid chronic conditions (e.g., psychiatric disorders, substance abuse disorders, diabetes, hepatitis C). Through deductive content coding, situated IMB model-based content was identified in all but 7.1% of statements discussing facilitators or barriers to retention in HIV care. Inductive emergent theme identification yielded a number of important themes influencing retention in HIV care (e.g., acceptance of diagnosis, stigma, HIV cognitive/physical impairments, and global constructs of self-care). Multiple elements of these themes strongly aligned with the model's IMB constructs. The convergence of the results from both sets of analysis demonstrate that participants' experiences map well onto the content and structure of the situated IMB model, providing a systematic classification of important theoretical and contextual determinants of retention in care. Future intervention efforts to enhance retention in HIV care should address these multiple determinants (i.e., information, motivation, behavioral skills) of self-directed retention in HIV care.
Self-supported Zn3P2 nanowire arrays grafted on carbon fabrics as an advanced integrated anode for flexible lithium ion batteries

NASA Astrophysics Data System (ADS)

Li, Wenwu; Gan, Lin; Guo, Kai; Ke, Linbo; Wei, Yaqing; Li, Huiqiao; Shen, Guozhen; Zhai, Tianyou

2016-04-01

We, for the first time, successfully grafted well-aligned binary lithium-reactive zinc phosphide (Zn3P2) nanowire arrays on carbon fabric cloth by a facile CVD method. When applied as a novel self-supported binder-free anode for lithium ion batteries (LIBs), the hierarchical three-dimensional (3D) integrated anode shows excellent electrochemical performances: a highly reversible initial lithium storage capacity of ca. 1200 mA h g-1 with a coulombic efficiency of up to 88%, a long lifespan of over 200 cycles without obvious decay, and a high rate capability of ca. 400 mA h g-1 capacity retention at an ultrahigh rate of 15 A g-1. More interestingly, a flexible LIB full cell is assembled based on the as-synthesized integrated anode and the commercial LiFePO4 cathode, and shows striking lithium storage performances very close to the half cells: a large reversible capacity over 1000 mA h g-1, a long cycle life of over 200 cycles without obvious decay, and an ultrahigh rate performance of ca. 300 mA h g-1 even at 20 A g-1. Considering the excellent lithium storage performances of coin-type half cells as well as flexible full cells, the as-prepared carbon cloth grafted well-aligned Zn3P2 nanowire arrays would be a promising integrated anode for flexible LIB full cell devices.We, for the first time, successfully grafted well-aligned binary lithium-reactive zinc phosphide (Zn3P2) nanowire arrays on carbon fabric cloth by a facile CVD method. When applied as a novel self-supported binder-free anode for lithium ion batteries (LIBs), the hierarchical three-dimensional (3D) integrated anode shows excellent electrochemical performances: a highly reversible initial lithium storage capacity of ca. 1200 mA h g-1 with a coulombic efficiency of up to 88%, a long lifespan of over 200 cycles without obvious decay, and a high rate capability of ca. 400 mA h g-1 capacity retention at an ultrahigh rate of 15 A g-1. More interestingly, a flexible LIB full cell is assembled based on the as-synthesized integrated anode and the commercial LiFePO4 cathode, and shows striking lithium storage performances very close to the half cells: a large reversible capacity over 1000 mA h g-1, a long cycle life of over 200 cycles without obvious decay, and an ultrahigh rate performance of ca. 300 mA h g-1 even at 20 A g-1. Considering the excellent lithium storage performances of coin-type half cells as well as flexible full cells, the as-prepared carbon cloth grafted well-aligned Zn3P2 nanowire arrays would be a promising integrated anode for flexible LIB full cell devices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08467a
Angiogenesis in mucous retention cyst: a human in vivo-like model of endothelial cell differentiation in mucous substrate.

PubMed

Swelam, Wael; Ida-Yonemochi, Hiroko; Saku, Takashi

2005-01-01

Mucous retention cysts contain a mucous pool in the lumina, in which pure angiogenic processes are occasionally observed. By using this unique human material, our aim was to understand the in vivo angiogenic process. Fifteen surgical tissue samples of mucous retention cysts of the lip were examined for expression of vascular endothelial markers and extracellular matrix molecules by immunohistochemistry and in situ hybridization (ISH). Endothelial cells forming new vascular channels showed immunopositivities for CD31, CD34, vascular endothelial growth factor (VEGF), and von Willebrand factor (vWF). These newly formed capillaries were surrounded by tenascin-positive matrices and further by a dense infiltration of CD68-positive cells with foamy to epitheloid appearances. Some of these cells were simultaneously positive for CD34, VEGF, and one of its receptors, Flk-1, and they showed definite mRNA as well as protein signals for tenascin. In addition, these cells often tended to be aligned, which suggested tubule formation. The results suggest that monocyte/macrophage lineage cells are a major source for endothelial cells at least in mucous retention cysts and that tenascin produced by those cells plays an important role in differentiation of endothelial cells.
Simulation and validation of larval sucker dispersal and retention through the restored Williamson River Delta and Upper Klamath Lake system, Oregon

USGS Publications Warehouse

Wood, Tamara M.; Hendrixson, Heather A.; Markle, Douglas F.; Erdman, Charles S.; Burdick, Summer M.; Ellsworth, Craig M.

2014-01-01

A hydrodynamic model with particle tracking was used to create individual-based simulations to describe larval fish dispersal through the restored Williamson River Delta and into Upper Klamath Lake, Oregon. The model was verified by converting particle ages to larval lengths and comparing these lengths to lengths of larvae in net catches. Correlations of simulated lengths with field data were moderate and suggested a species-specific difference in model performance. Particle trajectories through the delta were affected by wind speed and direction, lake elevation, and shoreline configuration. Once particles entered the lake, transport was a function of current speed and whether behavior enhanced transport (swimming aligned with currents) or countered transport through greater dispersal (faster random swimming). We tested sensitivity to swim speed (higher speeds led to greater dispersal and more retention), shoreline configuration (restoration increased retention relative to pre-restoration conditions), and lake elevation (retention was maximized at an intermediate elevation). The simulations also highlight additional biological questions, such as the extent to which spatially heterogeneous mortality or fish behavior and environmental cues could interact with wind-driven currents and contribute to patterns of dispersal.
Computer-assisted revision total knee replacement.

PubMed

Sikorski, J M

2004-05-01

A technique for performing allograft-augmented revision total knee replacement (TKR) using computer assistance is described, on the basis of the results in 14 patients. Bone deficits were made up with impaction grafting. Femoral grafting was made possible by the construction of a retaining wall or dam which allowed pressurisation and retention of the graft. Tibial grafting used a mixture of corticocancellous and morsellised allograft. The position of the implants was monitored by the computer system and adjusted while the cement was setting. The outcome was determined using a six-parameter, quantitative technique (the Perth CT protocol) which measured the alignment of the prosthesis and provided an objective score. The final outcomes were not perfect with errors being made in femoral rotation and in producing a mismatch between the femoral and tibial components. In spite of the shortcomings the alignments were comparable in accuracy with those after primary TKR. Computer assistance shows considerable promise in producing accurate alignment in revision TKR with bone deficits.
Patient with oligodontia treated with a miniscrew for unilateral mesial movement of the maxillary molars and alignment of an impacted third molar.

PubMed

Maeda, Aya; Sakoguchi, Yoko; Miyawaki, Shouichi

2013-09-01

This report describes the treatment of a 20-year-old woman with a dental midline deviation and 7 congenitally missing premolars. She had retained a maxillary right deciduous canine and 4 deciduous second molars, and she had an impacted maxillary right third molar. The maxillary right deciduous second molar was extracted, and the space was nearly closed by mesial movement of the maxillary right molars using an edgewise appliance and a miniscrew for absolute anchorage. The miniscrew was removed, and the extraction space of the maxillary right deciduous canine was closed, correcting the dental midline deviation. After the mesial movement of the maxillary right molars, the impacted right third molar was aligned. To prevent root resorption, the retained left deciduous second molars were not aligned by the edgewise appliance. The occlusal contact area and the maximum occlusal force increased over the 2 years of retention. The miniscrew was useful for absolute anchorage for unilateral mesial movement of the maxillary molars and for the creation of eruption space and alignment of the impacted third molar in a patient with oligodontia. Copyright © 2013 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.
A modified multiscale peak alignment method combined with trilinear decomposition to study the volatile/heat-labile components in Ligusticum chuanxiong Hort - Cyperus rotundus rhizomes by HS-SPME-GC/MS.

PubMed

He, Min; Yan, Pan; Yang, Zhi-Yu; Zhang, Zhi-Min; Yang, Tian-Biao; Hong, Liang

2018-03-15

Head Space/Solid Phase Micro-Extraction (HS-SPME) coupled with Gas Chromatography/Mass Spectrometer (GC/MS) was used to determine the volatile/heat-labile components in Ligusticum chuanxiong Hort - Cyperus rotundus rhizomes. Facing co-eluting peaks in k samples, a trilinear structure was reconstructed to obtain the second-order advantage. The retention time (RT) shift with multi-channel detection signals for different samples has been vital in maintaining the trilinear structure, thus a modified multiscale peak alignment (mMSPA) method was proposed in this paper. The peak position and peak width of representative ion profile were firstly detected by mMSPA using Continuous Wavelet Transform with Haar wavelet as the mother wavelet (Haar CWT). Then, the raw shift was confirmed by Fast Fourier Transform (FFT) cross correlation calculation. To obtain the optimal shift, Haar CWT was again used to detect the subtle deviations and be amalgamated in calculation. Here, to ensure there is no peaks shape alternation, the alignment was performed in local domains of data matrices, and all data points in the peak zone were moved via linear interpolation in non-peak parts. Finally, chemical components of interest in Ligusticum chuanxiong Hort - Cyperus rotundus rhizomes were analyzed by HS-SPME-GCMS and mMSPA-alternating trilinear decomposition (ATLD) resolution. As a result, the concentration variation between herbs and their pharmaceutical products can provide a scientific basic for the quality standard establishment of traditional Chinese medicines. Copyright © 2018 Elsevier B.V. All rights reserved.
Cluster analysis of commercial samples of Bauhinia spp. using HPLC-UV/PDA and MCR-ALS/PCA without peak alignment procedure.

PubMed

Ardila, Jorge Armando; Funari, Cristiano Soleo; Andrade, André Marques; Cavalheiro, Alberto José; Carneiro, Renato Lajarim

2015-01-01

Bauhinia forficata Link. is recognised by the Brazilian Health Ministry as a treatment of hypoglycemia and diabetes. Analytical methods are useful to assess the plant identity due the similarities found in plants from Bauhinia spp. HPLC-UV/PDA in combination with chemometric tools is an alternative widely used and suitable for authentication of plant material, however, the shifts of retention times for similar compounds in different samples is a problem. To perform comparisons between the authentic medicinal plant (Bauhinia forficata Link.) and samples commercially available in drugstores claiming to be "Bauhinia spp. to treat diabetes" and to evaluate the performance of multivariate curve resolution - alternating least squares (MCR-ALS) associated to principal component analysis (PCA) when compared to pure PCA. HPLC-UV/PDA data obtained from extracts of leaves were evaluated employing a combination of MCR-ALS and PCA, which allowed the use of the full chromatographic and spectrometric information without the need of peak alignment procedures. The use of MCR-ALS/PCA showed better results than the conventional PCA using only one wavelength. Only two of nine commercial samples presented characteristics similar to the authentic Bauhinia forficata spp., considering the full HPLC-UV/PDA data. The combination of MCR-ALS and PCA is very useful when applied to a group of samples where a general alignment procedure could not be applied due to the different chromatographic profiles. This work also demonstrates the need of more strict control from the health authorities regarding herbal products available on the market. Copyright © 2015 John Wiley & Sons, Ltd.
Environmental Chemistry Compound Identification Using High ...

EPA Pesticide Factsheets

There is a growing need for rapid chemical screening and prioritization to inform regulatory decision-making on thousands of chemicals in the environment. We have previously used high-resolution mass spectrometry to examine household vacuum dust samples using liquid chromatography time-of-flight mass spectrometry (LC-TOF/MS). Using a combination of exact mass, isotope distribution, and isotope spacing, molecular features were matched with a list of chemical formulas from the EPA’s Distributed Structure-Searchable Toxicity (DSSTox) database. This has further developed our understanding of how openly available chemical databases, together with the appropriate searches, could be used for the purpose of compound identification. We report here on the utility of the EPA’s iCSS Chemistry Dashboard for the purpose of compound identification using searches against a database of over 720,000 chemicals. We also examine the benefits of QSAR prediction for the purpose of retention time prediction to allow for alignment of both chromatographic and mass spectral properties. This abstract does not reflect U.S. EPA policy presentation at the Eastern Analytical Symposium.
Adaptive collective foraging in groups with conflicting nutritional needs

PubMed Central

Senior, Alistair M.; Lihoreau, Mathieu; Charleston, Michael A.; Buhl, Jerome; Raubenheimer, David; Simpson, Stephen J.

2016-01-01

Collective foraging, based on positive feedback and quorum responses, is believed to improve the foraging efficiency of animals. Nutritional models suggest that social information transfer increases the ability of foragers with closely aligned nutritional needs to find nutrients and maintain a balanced diet. However, whether or not collective foraging is adaptive in a heterogeneous group composed of individuals with differing nutritional needs is virtually unexplored. Here we develop an evolutionary agent-based model using concepts of nutritional ecology to address this knowledge gap. Our aim was to evaluate how collective foraging, mediated by social retention on foods, can improve nutrient balancing in individuals with different requirements. The model suggests that in groups where inter-individual nutritional needs are unimodally distributed, high levels of collective foraging yield optimal individual fitness by reducing search times that result from moving between nutritionally imbalanced foods. However, where nutritional needs are highly bimodal (e.g. where the requirements of males and females differ) collective foraging is selected against, leading to group fission. In this case, additional mechanisms such as assortative interactions can coevolve to allow collective foraging by subgroups of individuals with aligned requirements. Our findings indicate that collective foraging is an efficient strategy for nutrient regulation in animals inhabiting complex nutritional environments and exhibiting a range of social forms. PMID:27152206
Aligning clinical compensation with clinical productivity: design and implementation of the financial value unit (FVU) system in an academic department of internal medicine.

PubMed

Stites, Steven; Steffen, Patrick; Turner, Scott; Pingleton, Susan

2013-07-01

A new metric was developed and implemented at the University of Kansas School of Medicine Department of Internal Medicine, the financial value unit (FVU). This metric analyzes faculty clinical compensation compared with clinical work productivity as a transparent means to decrease the physician compensation variability and compensate faculty equitably for clinical work.The FVU is the ratio of individual faculty clinical compensation compared with their total work relative value units (wRVUs) generated divided by Medical Group Management Association (MGMA) salary to wRVUs of a similar MGMA physician.The closer the FVU ratio is to 1.0, the closer clinical compensation is to that of an MGMA physician with similar clinical productivity. Using FVU metrics to calculate a faculty salary gap compared with MGMA median salary and wRVU productivity, a divisional production payment was established annually.From FY 2006 to FY 2011, both total faculty numbers and overall clinical activity increased. With the implementation of the FVU, both clinical productivity and compensation increased while, at the same time, physician retention rates remained high. Variability in physician compensation decreased. Dramatic clinical growth was associated with the alignment of clinical work and clinical compensation in a transparent and equable process.
Decoupling the effects of primary production and residence time variation on nitrogen retention in a tidally-influenced spring run

NASA Astrophysics Data System (ADS)

Hensley, R. T.; Cohen, M. J.; Korhnak, L. V.

2013-12-01

Models of nitrogen (N) retention in river networks suggest biogeochemical as well as hydraulic properties exert considerable control on reach scale nutrient retention rates. Freshwater tidally influenced rivers provide a model system for decoupling metabolic vs. hydraulic controls on retention. The clear diurnal N retention signal in response to assimilatory uptake observed in other rivers becomes convoluted as the solar day moves in and out of phase with the semi-diurnal (~12.5 hr) tidal cycle. We used an upstream-downstream mass balance approach to estimate N retention at 15 minute intervals over an entire lunar month in Manatee Springs, a tidally varying, spring-fed stream in North Florida. Retention rates varied markedly with tidal forcing. Contrary to our expectations, higher retention rates and shorter uptake lengths were observed at low tide, corresponding to the shortest residence times, which varied between 22 and 71 minutes in this 350m reach. By profiling a continuously injected conservative tracer under both high and low tide conditions, we determined this was not the result of variation in lateral inflow (e.g., dilution from denitrified hyporheic porewater at lower channel stage). This increased retention at shorter residence times (and hence higher velocity) may be the result of greater turbulent mixing, which drives river water into the benthic reactive zone where the principal retention pathway, denitrification, occurs. After controlling for residence time effects, the residual retention signal exhibited a strong diel pattern. This assimilatory N retention was highly correlated with daily primary production (using the diel oxygen method), and estimated ecosystem molar C:N ratios (8.55×0.83:1) were comparable to observed tissue stoichiometry of the dominant autotrophs (9:1). N retention (blue) and residence time (red) calculated at 15 minute intervals. Note the inverse correlation; highest retention rates occur at the shortest residence times. N retention versus residence time separated into daytime (yellow) and nighttime (blue) data points. Note the daytime data points generally lie above the nighttime regression as a result of higher daytime retention due to assimilatory uptake.
[Systematic evaluation of retention behavior of carbohydrates in hydrophilic interaction liquid chromatography].

PubMed

Fu, Qing; Wang, Jun; Liang, Tu; Xu, Xiaoyong; Jin, Yu

2013-11-01

A systematic evaluation of retention behavior of carbohydrates in hydrophilic interaction liquid chromatography (HILIC) was performed. The influences of mobile phase, stationary phase and buffer salt on the retention of carbohydrates were investigated. According to the results, the retention time of carbohydrates decreased as the proportion of acetonitrile in mobile phase decreased. Increased time of carbohydrates was observed as the concentration of buffer salt in mobile phase increased. The retention behavior of carbohydrates was also affected by organic solvent and HILIC stationary phase. Furthermore, an appropriate retention equation was used in HILIC mode. The retention equation lnk = a + blnC(B) + cC(B) could quantitatively describe the retention factors of carbohydrates of plant origin with good accuracy: the relative error of the predicted time to actual time was less than 0.3%. The evaluation results could provide guidance for carbohydrates to optimize the experimental conditions in HILIC method development especially for carbohydrate separation

3D patterned substrates for bioartificial blood vessels - The effect of hydrogels on aligned cells on a biomaterial surface.

PubMed

Zhao, Xinxin; Irvine, Scott Alexander; Agrawal, Animesh; Cao, Ye; Lim, Pei Qi; Tan, Si Ying; Venkatraman, Subbu S

2015-10-01

The optimal bio-artificial blood vessel construct is one that has a compliant tubular core with circumferentially aligned smooth muscle cells (SMCs). Obtaining this well-aligned pattern of SMCs on a scaffold is highly beneficial as this cellular orientation preserves the SMC contractile phenotype. We used 3D patterning to create channels on a polycaprolactone (PCL) scaffold; SMCs were then found to be aligned within the microchannels. To preserve this alignment, and to provide a protective coating that could further incorporate cells, we evaluated the use of two hydrogels, one based on poly(ethylene glycol) diacrylate (PEGDA) and the other based on gelatin. Hydrogels were either physically coated on the PCL surfaces or covalently linked via suitable surface modification of PCL. For covalent immobilization of PEGDA hydrogel, alkene groups were introduced on PCL, while for gelatin covalent linkage, serum proteins were introduced. It is, however, crucial that the hydrogel coating does not disrupt the cellular patterning and distribution. We show in this work that both the process of coating as well as the nature of the coating are critical to preservation of the aligned SMCs. The covalent coating methods involving the crosslinking of hydrogels with the surface of PCL films promoted hydrogel retention time on the film as compared with physical deposition. Furthermore, subsequent hydrogel degradation is affected by the components of the cell culture medium, hinting at a possible route to in vivo biodegradation. Surface features control cellular orientation and subsequently influence their functionality, a useful effect for cellularized biomedical devices. Such devices also can benefit from protective and cell friendly hydrogel coatings. However, literature is lacking on the fate of cells that have endured hydrogel coating whilst orientated on a biomaterial surface. In particular, elucidation of the cells ability to remain adherent and orientated post hydrogel addition. Coating requires two procedures that may be deleterious to the orientated cells: the surface pretreatment for gel binding and the hydrogel crosslinking reaction. We compare transglutaminase gelatin crosslinking and UV initiated PEGDA crosslinking, coated onto smooth muscle cells orientated on patterned PCL surfaces. This original study will be of considerable use to the wider biomaterials community. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Examining Part-Time Faculty Utilization and Its Impact on Student Retention at a Public Research University

ERIC Educational Resources Information Center

Johnson, Iryna Y.

2006-01-01

The important concern surrounding growing reliance on part-time faculty is its effect on student retention. Existing studies explored the relationship between part-time faculty utilization and retention of entering cohorts. The study herein assesses retention of the entire population of degree-seeking undergraduates at a single institution. The…
TagFinder for the quantitative analysis of gas chromatography--mass spectrometry (GC-MS)-based metabolite profiling experiments.

PubMed

Luedemann, Alexander; Strassburg, Katrin; Erban, Alexander; Kopka, Joachim

2008-03-01

Typical GC-MS-based metabolite profiling experiments may comprise hundreds of chromatogram files, which each contain up to 1000 mass spectral tags (MSTs). MSTs are the characteristic patterns of approximately 25-250 fragment ions and respective isotopomers, which are generated after gas chromatography (GC) by electron impact ionization (EI) of the separated chemical molecules. These fragment ions are subsequently detected by time-of-flight (TOF) mass spectrometry (MS). MSTs of profiling experiments are typically reported as a list of ions, which are characterized by mass, chromatographic retention index (RI) or retention time (RT), and arbitrary abundance. The first two parameters allow the identification, the later the quantification of the represented chemical compounds. Many software tools have been reported for the pre-processing, the so-called curve resolution and deconvolution, of GC-(EI-TOF)-MS files. Pre-processing tools generate numerical data matrices, which contain all aligned MSTs and samples of an experiment. This process, however, is error prone mainly due to (i) the imprecise RI or RT alignment of MSTs and (ii) the high complexity of biological samples. This complexity causes co-elution of compounds and as a consequence non-selective, in other words impure MSTs. The selection and validation of optimal fragment ions for the specific and selective quantification of simultaneously eluting compounds is, therefore, mandatory. Currently validation is performed in most laboratories under human supervision. So far no software tool supports the non-targeted and user-independent quality assessment of the data matrices prior to statistical analysis. TagFinder may fill this gap. TagFinder facilitates the analysis of all fragment ions, which are observed in GC-(EI-TOF)-MS profiling experiments. The non-targeted approach allows the discovery of novel and unexpected compounds. In addition, mass isotopomer resolution is maintained by TagFinder processing. This feature is essential for metabolic flux analyses and highly useful, but not required for metabolite profiling. Whenever possible, TagFinder gives precedence to chemical means of standardization, for example, the use of internal reference compounds for retention time calibration or quantitative standardization. In addition, external standardization is supported for both compound identification and calibration. The workflow of TagFinder comprises, (i) the import of fragment ion data, namely mass, time and arbitrary abundance (intensity), from a chromatography file interchange format or from peak lists provided by other chromatogram pre-processing software, (ii) the annotation of sample information and grouping of samples into classes, (iii) the RI calculation, (iv) the binning of observed fragment ions of equal mass from different chromatograms into RI windows, (v) the combination of these bins, so-called mass tags, into time groups of co-eluting fragment ions, (vi) the test of time groups for intensity correlated mass tags, (vii) the data matrix generation and (viii) the extraction of selective mass tags supported by compound identification. Thus, TagFinder supports both non-targeted fingerprinting analyses and metabolite targeted profiling. Exemplary TagFinder workspaces and test data sets are made available upon request to the contact authors. TagFinder is made freely available for academic use from http://www-en.mpimp-golm.mpg.de/03-research/researchGroups/01-dept1/Root_Metabolism/smp/TagFinder/index.html.
Tough and flexible CNT-polymeric hybrid scaffolds for engineering cardiac constructs.

PubMed

Kharaziha, Mahshid; Shin, Su Ryon; Nikkhah, Mehdi; Topkaya, Seda Nur; Masoumi, Nafiseh; Annabi, Nasim; Dokmeci, Mehmet R; Khademhosseini, Ali

2014-08-01

In the past few years, a considerable amount of effort has been devoted toward the development of biomimetic scaffolds for cardiac tissue engineering. However, most of the previous scaffolds have been electrically insulating or lacked the structural and mechanical robustness to engineer cardiac tissue constructs with suitable electrophysiological functions. Here, we developed tough and flexible hybrid scaffolds with enhanced electrical properties composed of carbon nanotubes (CNTs) embedded aligned poly(glycerol sebacate):gelatin (PG) electrospun nanofibers. Incorporation of varying concentrations of CNTs from 0 to 1.5% within the PG nanofibrous scaffolds (CNT-PG scaffolds) notably enhanced fiber alignment and improved the electrical conductivity and toughness of the scaffolds while maintaining the viability, retention, alignment, and contractile activities of cardiomyocytes (CMs) seeded on the scaffolds. The resulting CNT-PG scaffolds resulted in stronger spontaneous and synchronous beating behavior (3.5-fold lower excitation threshold and 2.8-fold higher maximum capture rate) compared to those cultured on PG scaffold. Overall, our findings demonstrated that aligned CNT-PG scaffold exhibited superior mechanical properties with enhanced CM beating properties. It is envisioned that the proposed hybrid scaffolds can be useful for generating cardiac tissue constructs with improved organization and maturation. Copyright © 2014 Elsevier Ltd. All rights reserved.
Engineering muscle cell alignment through 3D bioprinting.

PubMed

Mozetic, Pamela; Giannitelli, Sara Maria; Gori, Manuele; Trombetta, Marcella; Rainer, Alberto

2017-09-01

Processing of hydrogels represents a main challenge for the prospective application of additive manufacturing (AM) to soft tissue engineering. Furthermore, direct manufacturing of tissue precursors with a cell density similar to native tissues has the potential to overcome the extensive in vitro culture required for conventional cell-seeded scaffolds seeking to fabricate constructs with tailored structural and functional properties. In this work, we present a simple AM methodology that exploits the thermoresponsive behavior of a block copolymer (Pluronic ® ) as a means to obtain good shape retention at physiological conditions and to induce cellular alignment. Pluronic/alginate blends have been investigated as a model system for the processing of C2C12 murine myoblast cell line. Interestingly, C2C12 cell model demonstrated cell alignment along the deposition direction, potentially representing a new avenue to tailor the resulting cell histoarchitecture during AM process. Furthermore, the fabricated constructs exhibited high cell viability, as well as a significantly improved expression of myogenic genes vs. conventional 2D cultures. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2582-2588, 2017. © 2017 Wiley Periodicals, Inc.
Effects of Bioreactor Retention Time on Aerobic Microbial Decomposition of CELSS Crop Residues

NASA Technical Reports Server (NTRS)

Strayer, R. F.; Finger, B. W.; Alazraki, M. P.

1997-01-01

The focus of resource recovery research at the KSC-CELSS Breadboard Project has been the evaluation of microbiologically mediated biodegradation of crop residues by manipulation of bioreactor process and environmental variables. We will present results from over 3 years of studies that used laboratory- and breadboard-scale (8 and 120 L working volumes, respectively) aerobic, fed-batch, continuous stirred tank reactors (CSTR) for recovery of carbon and minerals from breadboard grown wheat and white potato residues. The paper will focus on the effects of a key process variable, bioreactor retention time, on response variables indicative of bioreactor performance. The goal is to determine the shortest retention time that is feasible for processing CELSS crop residues, thereby reducing bioreactor volume and weight requirements. Pushing the lower limits of bioreactor retention times will provide useful data for engineers who need to compare biological and physicochemical components. Bioreactor retention times were manipulated to range between 0.25 and 48 days. Results indicate that increases in retention time lead to a 4-fold increase in crop residue biodegradation, as measured by both dry weight losses and CO2 production. A similar overall trend was also observed for crop residue fiber (cellulose and hemicellulose), with a noticeable jump in cellulose degradation between the 5.3 day and 10.7 day retention times. Water-soluble organic compounds (measured as soluble TOC) were appreciably reduced by more than 4-fold at all retention times tested. Results from a study of even shorter retention times (down to 0.25 days), in progress, will also be presented.
PASS2: an automated database of protein alignments organised as structural superfamilies.

PubMed

Bhaduri, Anirban; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

2004-04-02

The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2) database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of the family members. The search engine has been improved for simpler browsing of the database. The database resolves alignments among the structural domains consisting of evolutionarily diverged set of sequences. Availability of reliable sequence alignments of distantly related proteins despite poor sequence identity and single-member superfamilies permit better sampling of structures in libraries for fold recognition of new sequences and for the understanding of protein structure-function relationships of individual superfamilies. PASS2 is accessible at http://www.ncbs.res.in/~faculty/mini/campass/pass2.html
Highly Stretchable Supercapacitors Based on Aligned Carbon Nanotube/Molybdenum Disulfide Composites.

PubMed

Lv, Tian; Yao, Yao; Li, Ning; Chen, Tao

2016-08-01

Stretchable supercapacitors that can sustain their performance under unpredictable tensile force are important elements for practical applications of various portable and wearable electronics. However, the stretchability of most reported supercapacitors was often lower than 100 % because of the limitation of the electrodes used. Herein we developed all-solid-state supercapacitors with a stretchability as high as 240 % by using aligned carbon nanotube composites with compact structure as electrodes. By combined with pseudocapacitive molybdenum disulfide nanosheets, the newly developed supercapacitor showed a specific capacitance of 13.16 F cm(-3) , and also showed excellent cycling retention (98 %) after 10 000 charge-discharge cycles. This work also presents a general and effective approach in developing high-performance electrodes for flexible and stretchable electronics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Prediction of gradient retention data for hydrophilic interaction liquid chromatographic separation of native and fluorescently labeled oligosaccharides.

PubMed

Vaňková, Nikola; Česla, Petr

2017-02-17

In this work, we have investigated the predictive properties of mixed-mode retention model and oligomeric mixed-mode model, taking into account the contribution of monomeric units to the retention, in hydrophilic interaction liquid chromatography. The gradient retention times of native maltooligosaccharides and their fluorescent derivatives were predicted in the oligomeric series with number of monomeric glucose units in the range from two to seven. The maltooligosaccharides were separated on a packed column with carbamoyl-bonded silica stationary phase and 15 gradient profiles with different initial and final mobile phase composition were used with the gradient times 5; 7.5 and 10min. The predicted gradient retention times were compared for calculations based on isocratic retention data and gradient retention data, which provided better accuracy of the results. By comparing two different mobile phase additives, the more accurate retention times were predicted in mobile phases containing ammonium acetate. The acidic derivatives, prepared by reaction of an oligosaccharide with 2-aminobenzoic acid or 8-aminonaphthalene-1,3,6-trisulfonic acid, provided more accurate predictions of the retention data in comparison to native oligosaccharides or their neutral derivatives. The oligomeric mixed-mode model allowed prediction of gradient retention times using only one gradient profile, which significantly speeded-up the method development. Copyright © 2017 Elsevier B.V. All rights reserved.
Latency-information theory and applications: Part III. On the discovery of the space dual of the laws of motion in physics

NASA Astrophysics Data System (ADS)

Feria, Erlan H.

2008-04-01

In this third of a multi-paper series the discovery of a space dual for the laws of motion is reported and named the laws of retention. This space-time duality in physics is found to inherently surface from a latency-information theory (LIT) that is treated in the first two papers of this multi-paper series. A motion-coder and a retention-coder are fundamental elements of a LIT's recognition-communication system. While a LIT's motion-coder addresses motion-time issues of knowledge motion, a LIT's retention-coder addresses retention-space issues of knowledge retention. For the design of a motion-coder, such as a modulation-antenna system, the laws of motion in physics are used while for the design of a retention-coder, such as a write/read memory, the newly advanced laws of retention can be used. Furthermore, while the laws of motion reflect a configuration of space certainty, the laws of retention reflect a passing of time uncertainty. Since the retention duals of motion concepts are too many to cover in a single publication, the discussion will be centered on the retention duals for Newton's Principia and the gravitational law, Coulomb's electrical law, Maxwell's equations, Einstein's relativity theory, quantum mechanics, and the uncertainty principle. Furthermore the retention duals will be illustrated with an uncharged and non-rotating black hole (UNBH). A UNBH is the retention dual of a vacuum since the UNBH and vacuum offer, from a theoretical perspective, the least resistance to knowledge retention and motion, respectively. Using this space-time duality insight it will be shown that the speed of light in a vacuum of c M=2.9979 x 10 8 meters/sec has a retention dual, herein called the pace of dark in a UNBH of c R=6.1123 x 10 63 secs/m 3 where 'pace' refers to the expected retention-time per retention-space for the 'dark' knowledge residing in a black hole.
Transit time affects the community stability of Lactobacillus and Bifidobacterium species in an in vitro model of human colonic microbiotia.

PubMed

Rodes, Laetitia; Paul, Arghya; Coussa-Charley, Michael; Al-Salami, Hani; Tomaro-Duchesneau, Catherine; Fakhoury, Marc; Prakash, Satya

2011-12-01

Retention time, which is analogous to transit time, is an index for bacterial stability in the intestine. Its consideration is of particular importance to optimize the delivery of probiotic bacteria in order to improve treatment efficacy. This study aims to investigate the effect of retention time on Lactobacilli and Bifidobacteria stability using an established in vitro human colon model. Three retention times were used: 72, 96, and 144 h. The effect of retention time on cell viability of different bacterial populations was analyzed with bacterial plate counts and PCR. The proportions of intestinal Bifidobacteria, Lactobacilli, Enterococci, Staphylococci and Clostridia populations, analyzed by plate counts, were found to be the same as that in human colonic microbiota. Retention time in the human colon affected the stability of Lactobacilli and Bifidobacteria communities, with maximum stability observed at 144 h. Therefore, retention time is an important parameter that influences bacterial stability in the colonic microbiota. Future clinical studies on probiotic bacteria formulations should take into consideration gastrointestinal transit parameters to improve treatment efficacy.
An Analysis of the Effect the Enlisted Grade Structure Review Has Upon First Term Alignment Plan Retention Requirements

DTIC Science & Technology

2003-03-01

9 Labor force participation rate equates to the labor force divided by the population. 10 Ehrenberg and Smith, “Modern Labor Economics .” 27...Econometrica 66 (1998): 249. 12 Ehrenbrg, Ronald G. and Robert S. Smith. “Modern Labor Economics : Theory and Public Policy.” Addison Wesley...whs.osd.mil/mid/military/miltop.htm> Ehrenbrg, Ronald G. and Robert S. Smith. “Modern Labor Economics : Theory and Public Policy.” Addison Wesley
High performance carbon nanotube-Si core-shell wires with a rationally structured core for lithium ion battery anodes.

PubMed

Fan, Yu; Zhang, Qing; Lu, Congxiang; Xiao, Qizhen; Wang, Xinghui; Tay, Beng Kang

2013-02-21

Core-shell Si nanowires are very promising anode materials. Here, we synthesize vertically aligned carbon nanotubes (CNTs) with relatively large diameters and large inter-wire spacing as core wires and demonstrate a CNT-Si core-shell wire composite as a lithium ion battery (LIB) anode. Owing to the rationally engineered core structure, the composite shows good capacity retention and rate performance. The excellent performance is superior to most core-shell nanowires previously reported.
Biochemical passive reactors for treatment of acid mine drainage: Effect of hydraulic retention time on changes in efficiency, composition of reactive mixture, and microbial activity.

PubMed

Vasquez, Yaneth; Escobar, Maria C; Neculita, Carmen M; Arbeli, Ziv; Roldan, Fabio

2016-06-01

Biochemical passive treatment represents a promising option for the remediation of acid mine drainage. This study determined the effect of three hydraulic retention times (1, 2, and 4 days) on changes in system efficiency, reactive mixture, and microbial activity in bioreactors under upward flow conditions. Bioreactors were sacrificed in the weeks 8, 17 and 36, and the reactive mixture was sampled at the bottom, middle, and top layers. Physicochemical analyses were performed on reactive mixture post-treatment and correlated with sulfate-reducing bacteria and cellulolytic and dehydrogenase activity. All hydraulic retention times were efficient at increasing pH and alkalinity and removing sulfate (>60%) and metals (85-99% for Fe(2+) and 70-100% for Zn(2+)), except for Mn(2+). The longest hydraulic retention time (4 days) increased residual sulfides, deteriorated the quality of treated effluent and negatively impacted sulfate-reducing bacteria. Shortest hydraulic retention time (1 day) washed out biomass and increased input of dissolved oxygen in the reactors, leading to higher redox potential and decreasing metal removal efficiency. Concentrations of iron, zinc and metal sulfides were high in the bottom layer, especially with 2 day of hydraulic retention time. Sulfate-reducing bacteria, cellulolytic and dehydrogenase activity were higher in the middle layer at 4 days of hydraulic retention time. Hydraulic retention time had a strong influence on overall performance of passive reactors. Copyright © 2016 Elsevier Ltd. All rights reserved.
Living nanofiber yarn-based woven biotextiles for tendon tissue engineering using cell tri-culture and mechanical stimulation.

PubMed

Wu, Shaohua; Wang, Ying; Streubel, Philipp N; Duan, Bin

2017-10-15

Non-woven nanofibrous scaffolds have been developed for tendon graft application by using electrospinning strategies. However, electrospun nanofibrous scaffolds face some obstacles and limitations, including suboptimal scaffold structure, weak tensile and suture-retention strengths, and compact structure for cell infiltration. In this work, a novel nanofibrous, woven biotextile, fabricated based on electrospun nanofiber yarns, was implemented as a tissue engineered tendon scaffold. Based on our modified electrospinning setup, polycaprolactone (PCL) nanofiber yarns were fabricated with reproducible quality, and were further processed into plain-weaving fabrics interlaced with polylactic acid (PLA) multifilaments. Nonwoven nanofibrous PCL meshes with random or aligned fiber structures were generated using typical electrospinning as comparative counterparts. The woven fabrics contained 3D aligned microstructures with significantly larger pore size and obviously enhanced tensile mechanical properties than their nonwoven counterparts. The biological results revealed that cell proliferation and infiltration, along with the expression of tendon-specific genes by human adipose derived mesenchymal stem cells (HADMSC) and human tenocytes (HT), were significantly enhanced on the woven fabrics compared with those on randomly-oriented or aligned nanofiber meshes. Co-cultures of HADMSC with HT or human umbilical vein endothelial cells (HUVEC) on woven fabrics significantly upregulated the functional expression of most tenogenic markers. HADMSC/HT/HUVEC tri-culture on woven fabrics showed the highest upregulation of most tendon-associated markers than all the other mono- and co-culture groups. Furthermore, we conditioned the tri-cultured constructs with dynamic conditioning and demonstrated that dynamic stretch promoted total collagen secretion and tenogenic differentiation. Our nanofiber yarn-based biotextiles have significant potential to be used as engineered scaffolds to synergize the multiple cell interaction and mechanical stimulation for promoting tendon regeneration. Tendon grafts are essential for the treatment of various tendon-related conditions due to the inherently poor healing capacity of native tendon tissues. In this study, we combined electrospun nanofiber yarns with textile manufacturing strategies to fabricate nanofibrous woven biotextiles with hierarchical features, aligned fibrous topography, and sufficient mechanical properties as tendon tissue engineered scaffolds. Comparing to traditional electrospun random or aligned meshes, our novel nanofibrous woven fabrics possess strong tensile and suture-retention strengths and larger pore size. We also demonstrated that the incorporation of tendon cells and vascular cells promoted the tenogenic differentiation of the engineered tendon constructs, especially under dynamic stretch. This study not only presents a novel tissue engineered tendon scaffold fabrication technique but also provides a useful strategy to promote tendon differentiation and regeneration. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Overcoming the drawback of lower sense margin in tunnel FET based dynamic memory along with enhanced charge retention and scalability

NASA Astrophysics Data System (ADS)

Navlakha, Nupur; Kranti, Abhinav

2017-11-01

The work reports on the use of a planar tri-gate tunnel field effect transistor (TFET) to operate as dynamic memory at 85 °C with an enhanced sense margin (SM). Two symmetric gates (G1) aligned to the source at a partial region of intrinsic film result into better electrostatic control that regulates the read mechanism based on band-to-band tunneling, while the other gate (G2), positioned adjacent to the first front gate is responsible for charge storage and sustenance. The proposed architecture results in an enhanced SM of ˜1.2 μA μm-1 along with a longer retention time (RT) of ˜1.8 s at 85 °C, for a total length of 600 nm. The double gate architecture towards the source increases the tunneling current and also reduces short channel effects, enhancing SM and scalability, thereby overcoming the critical bottleneck faced by TFET based dynamic memories. The work also discusses the impact of overlap/underlap and interface charges on the performance of TFET based dynamic memory. Insights into device operation demonstrate that the choice of appropriate architecture and biases not only limit the trade-off between SM and RT, but also result in improved scalability with drain voltage and total length being scaled down to 0.8 V and 115 nm, respectively.
Thermoplastic-based conductive composites containing multi-wall carbon nanotubes aligned under the application of external electric fields

NASA Astrophysics Data System (ADS)

Osazuwa, Osayuki

The objective of this thesis is to prepare thermoplastic/multi-wall carbon nanotubes (MWCNTs) and to apply external alternating current (AC) electric fields to achieve enhanced conductivity and dielectric properties. The first part of the thesis focuses on preparing polyolefin-based composites containing welldispersed MWCNTs. MWCNTs are functionalized with a hyperbranched polyethylene (HBPE) using a non-covalent, non-specific functionalization approach and melt compounded with an ethylene-octene copolymer (EOC) matrix. The improved filler dispersion in the functionalized EOC/MWCNT composite results in higher elongation at break compared to the non-functionalized composite. However, the electrical percolation threshold and the ultimate conductivity of the composites are not affected considerably, suggesting that this functionalization approach leaves the inherent properties of the nanotubes intact. EOC/HBPE-functionalized MWCNT composites are further subjected to external AC electric fields (35 -- 212 kV/m), which induce the formation of aligned columnar structures, as evidenced by Scanning Electron Microscopy. Experimentally acquired resistivity data are used to derive correlations between the characteristic insulator-to-conductor transition times of the composites and the electric field strength (E), polymer viscosity (eta) and MWCNT volume fraction (φ). A criterion for the selection of (eta, E, φ) conditions that enable MWCNT assembly under an electric field controlled regime (minimal Brownian motion-driven aggregation effects) is developed. The dielectric properties of the solidified aligned EOC/MWCNT composites are further studied using dielectric spectroscopy. Annealing of the composites at 160 °C results in the formation of interconnected structures, whereas electrification, using AC field of 71 and 212 kV/m induces the formation of aligned columnar structures. The electrified and annealed composites have increased real and imaginary permittivity compared to the as-compounded composite, resulting in improved conductivity and storage capacity. An equivalent circuit model is fitted to the experimentally obtained impedance data in order to correlate the effects of electric field and processing time to the dielectric characteristics of the treated composites. Finally poly(ethylene succinate) (PESu) composites containing well-dispersed MWCNT were prepared by an in-situ polymerization method. Composite electrification results in improvements in the electrical conductivity by up to 12 orders of magnitude, and a retention of high conductivity in the solidified state.
Optimal methods for fitting probability distributions to propagule retention time in studies of zoochorous dispersal.

PubMed

Viana, Duarte S; Santamaría, Luis; Figuerola, Jordi

2016-02-01

Propagule retention time is a key factor in determining propagule dispersal distance and the shape of "seed shadows". Propagules dispersed by animal vectors are either ingested and retained in the gut until defecation or attached externally to the body until detachment. Retention time is a continuous variable, but it is commonly measured at discrete time points, according to pre-established sampling time-intervals. Although parametric continuous distributions have been widely fitted to these interval-censored data, the performance of different fitting methods has not been evaluated. To investigate the performance of five different fitting methods, we fitted parametric probability distributions to typical discretized retention-time data with known distribution using as data-points either the lower, mid or upper bounds of sampling intervals, as well as the cumulative distribution of observed values (using either maximum likelihood or non-linear least squares for parameter estimation); then compared the estimated and original distributions to assess the accuracy of each method. We also assessed the robustness of these methods to variations in the sampling procedure (sample size and length of sampling time-intervals). Fittings to the cumulative distribution performed better for all types of parametric distributions (lognormal, gamma and Weibull distributions) and were more robust to variations in sample size and sampling time-intervals. These estimated distributions had negligible deviations of up to 0.045 in cumulative probability of retention times (according to the Kolmogorov-Smirnov statistic) in relation to original distributions from which propagule retention time was simulated, supporting the overall accuracy of this fitting method. In contrast, fitting the sampling-interval bounds resulted in greater deviations that ranged from 0.058 to 0.273 in cumulative probability of retention times, which may introduce considerable biases in parameter estimates. We recommend the use of cumulative probability to fit parametric probability distributions to propagule retention time, specifically using maximum likelihood for parameter estimation. Furthermore, the experimental design for an optimal characterization of unimodal propagule retention time should contemplate at least 500 recovered propagules and sampling time-intervals not larger than the time peak of propagule retrieval, except in the tail of the distribution where broader sampling time-intervals may also produce accurate fits.
Photoresist thin-film effects on alignment process capability

NASA Astrophysics Data System (ADS)

Flores, Gary E.; Flack, Warren W.

1993-08-01

Two photoresists were selected for alignment characterization based on their dissimilar coating properties and observed differences on alignment capability. The materials are Dynachem OFPR-800 and Shipley System 8. Both photoresists were examined on two challenging alignment levels in a submicron CMOS process, a nitride level and a planarized second level metal. An Ultratech Stepper model 1500 which features a darkfield alignment system with a broadband green light for alignment signal detection was used for this project. Initially, statistically designed linear screening experiments were performed to examine six process factors for each photoresist: viscosity, spin acceleration, spin speed, spin time, softbake time, and softbake temperature. Using the results derived from the screening experiments, a more thorough examination of the statistically significant process factors was performed. A full quadratic experimental design was conducted to examine viscosity, spin speed, and spin time coating properties on alignment. This included a characterization of both intra and inter wafer alignment control and alignment process capability. Insight to the different alignment behavior is analyzed in terms of photoresist material properties and the physical nature of the alignment detection system.
Automated MicroSPECT/MicroCT Image Analysis of the Mouse Thyroid Gland.

PubMed

Cheng, Peng; Hollingsworth, Brynn; Scarberry, Daniel; Shen, Daniel H; Powell, Kimerly; Smart, Sean C; Beech, John; Sheng, Xiaochao; Kirschner, Lawrence S; Menq, Chia-Hsiang; Jhiang, Sissy M

2017-11-01

The ability of thyroid follicular cells to take up iodine enables the use of radioactive iodine (RAI) for imaging and targeted killing of RAI-avid thyroid cancer following thyroidectomy. To facilitate identifying novel strategies to improve 131 I therapeutic efficacy for patients with RAI refractory disease, it is desired to optimize image acquisition and analysis for preclinical mouse models of thyroid cancer. A customized mouse cradle was designed and used for microSPECT/CT image acquisition at 1 hour (t1) and 24 hours (t24) post injection of 123 I, which mainly reflect RAI influx/efflux equilibrium and RAI retention in the thyroid, respectively. FVB/N mice with normal thyroid glands and TgBRAF V600E mice with thyroid tumors were imaged. In-house CTViewer software was developed to streamline image analysis with new capabilities, along with display of 3D voxel-based 123 I gamma photon intensity in MATLAB. The customized mouse cradle facilitates consistent tissue configuration among image acquisitions such that rigid body registration can be applied to align serial images of the same mouse via the in-house CTViewer software. CTViewer is designed specifically to streamline SPECT/CT image analysis with functions tailored to quantify thyroid radioiodine uptake. Automatic segmentation of thyroid volumes of interest (VOI) from adjacent salivary glands in t1 images is enabled by superimposing the thyroid VOI from the t24 image onto the corresponding aligned t1 image. The extent of heterogeneity in 123 I accumulation within thyroid VOIs can be visualized by 3D display of voxel-based 123 I gamma photon intensity. MicroSPECT/CT image acquisition and analysis for thyroidal RAI uptake is greatly improved by the cradle and the CTViewer software, respectively. Furthermore, the approach of superimposing thyroid VOIs from t24 images to select thyroid VOIs on corresponding aligned t1 images can be applied to studies in which the target tissue has differential radiotracer retention from surrounding tissues.

A general strategy for performing temperature-programming in high performance liquid chromatography--prediction of segmented temperature gradients.

PubMed

Wiese, Steffen; Teutenberg, Thorsten; Schmidt, Torsten C

2011-09-28

In the present work it is shown that the linear elution strength (LES) model which was adapted from temperature-programming gas chromatography (GC) can also be employed to predict retention times for segmented-temperature gradients based on temperature-gradient input data in liquid chromatography (LC) with high accuracy. The LES model assumes that retention times for isothermal separations can be predicted based on two temperature gradients and is employed to calculate the retention factor of an analyte when changing the start temperature of the temperature gradient. In this study it was investigated whether this approach can also be employed in LC. It was shown that this approximation cannot be transferred to temperature-programmed LC where a temperature range from 60°C up to 180°C is investigated. Major relative errors up to 169.6% were observed for isothermal retention factor predictions. In order to predict retention times for temperature gradients with different start temperatures in LC, another relationship is required to describe the influence of temperature on retention. Therefore, retention times for isothermal separations based on isothermal input runs were predicted using a plot of the natural logarithm of the retention factor vs. the inverse temperature and a plot of the natural logarithm of the retention factor vs. temperature. It could be shown that a plot of lnk vs. T yields more reliable isothermal/isocratic retention time predictions than a plot of lnk vs. 1/T which is usually employed. Hence, in order to predict retention times for temperature-gradients with different start temperatures in LC, two temperature gradient and two isothermal measurements have been employed. In this case, retention times can be predicted with a maximal relative error of 5.5% (average relative error: 2.9%). In comparison, if the start temperature of the simulated temperature gradient is equal to the start temperature of the input data, only two temperature-gradient measurements are required. Under these conditions, retention times can be predicted with a maximal relative error of 4.3% (average relative error: 2.2%). As an example, the systematic method development for an isothermal as well as a temperature gradient separation of selected sulfonamides by means of the adapted LES model is demonstrated using a pure water mobile phase. Both methods are compared and it is shown that the temperature-gradient separation provides some advantages over the isothermal separation in terms of limits of detection and analysis time. Copyright © 2011 Elsevier B.V. All rights reserved.
The role of nursing leadership in creating a mentoring culture in acute care environments.

PubMed

Bally, Jill M G

2007-01-01

High rates of retirement among older nurses and horizontal violence among younger nurses heighten the importance of mentoring in the context of overall organizational stability and performance. Viewing the essentials of mentoring in the context of organizational culture and leadership as a long-term commitment and solution rather than a short-term task will lead to improved staff retention, satisfaction, and, ultimately, patient outcomes. Using Bass's four leadership initiatives, a culture for mentoring can be achieved through inspirational motivation, individualized consideration, idealized influence, and intellectual stimulation. Alignment of organizational and mentoring goals is essential to a successful approach given that the qualities associated with leadership and mentorship are closely aligned. Mentoring cultures also depend upon elements of a stable infrastructure such as managerial and executive support, scheduling flexibility, incentives, and recognition. Transformational leadership practices are key to achieving the sustainable effects of mentoring programs that are rooted deeply in organizational culture.
Cultural and ethnic differences in content validation responses.

PubMed

Evans, Bronwynne C

2004-04-01

Eight instruments to evaluate grant interventions aimed at increasing recruitment and retention of Hispanic/Latino and American Indian nurses were developed for a Nursing Workforce Diversity Grant. This article compares expert reviewer responses during content validation of these instruments with (a) current literature and (b) seven filmed intervals of Hispanic/Latino and American Indian nurses speaking about their educational experiences. White reviewers responded differently to certain items than did Hispanic/Latino and American Indian reviewers (or reviewers closely affiliated with such persons). Responses of Hispanic/Latino and American Indian experts were aligned with one another but not aligned with the responses of White experts, who also agreed with one another, prompting literature and film comparisons with their responses. Faculty development may be needed to help teachers uncover their assumptions about students of color, acquire knowledge about cultural perspectives, recognize institutional racism, and attain the skills necessary to develop and implement a curriculum of inclusion.
Internal dispersal of seeds by waterfowl: effect of seed size on gut passage time and germination patterns

NASA Astrophysics Data System (ADS)

Figuerola, Jordi; Charalambidou, Iris; Santamaria, Luis; Green, Andy J.

2010-06-01

Long distance dispersal may have important consequences for gene flow and community structure. The dispersal of many plants depends on transport by vertebrate seed dispersers. The shapes of seed shadows produced by vertebrates depend both on movement patterns of the dispersers and on the dynamics and effects of passage through the disperser’s gut (i.e. the retention time, survival and germination of ingested seeds). A combination of experiments with captive waterbirds and aquatic plant seeds was used to analyse the following: (a) the effects of inter- and intra-specific variation in seed size and duck species on seed retention time in the gut and (b) the relationship between retention time and the percent germination and germination rates of seeds. Among the three Scirpus species used, those with smaller seeds showed higher survival after ingestion by birds and longer retention times inside their guts than those with larger seeds. For Potamogeton pectinatus, only seeds from the smaller size class (<8 mg) survived ingestion. Retention time affected the percent germination and germination rate of Scirpus seeds but in a manner that varied for the different plant and bird species studied. We recorded both linear and non-linear effects of retention time on percent germination. In addition, germination rate was positively correlated with retention time in Scirpus litoralis but negatively correlated in Scirpus lacustris. Small seed size can favour dispersal over larger distances. However, the effects of retention time on percent germination can modify the seed shadows produced by birds due to higher percent germination of seeds retained for short or intermediate periods. The changes in dispersal quality associated with dispersal distance (which is expected to be positively related to retention time) will affect the probability of seedling establishment over longer distances and, thus, the spatial characteristics of the effective seed shadow.
Calculation of Retention Time Tolerance Windows with Absolute Confidence from Shared Liquid Chromatographic Retention Data

PubMed Central

Boswell, Paul G.; Abate-Pella, Daniel; Hewitt, Joshua T.

2015-01-01

Compound identification by liquid chromatography-mass spectrometry (LC-MS) is a tedious process, mainly because authentic standards must be run on a user’s system to be able to confidently reject a potential identity from its retention time and mass spectral properties. Instead, it would be preferable to use shared retention time/index data to narrow down the identity, but shared data cannot be used to reject candidates with an absolute level of confidence because the data are strongly affected by differences between HPLC systems and experimental conditions. However, a technique called “retention projection” was recently shown to account for many of the differences. In this manuscript, we discuss an approach to calculate appropriate retention time tolerance windows for projected retention times, potentially making it possible to exclude candidates with an absolute level of confidence, without needing to have authentic standards of each candidate on hand. In a range of multi-segment gradients and flow rates run among seven different labs, the new approach calculated tolerance windows that were significantly more appropriate for each retention projection than global tolerance windows calculated for retention projections or linear retention indices. Though there were still some small differences between the labs that evidently were not taken into account, the calculated tolerance windows only needed to be relaxed by 50% to make them appropriate for all labs. Even then, 42% of the tolerance windows calculated in this study without standards were narrower than those required by WADA for positive identification, where standards must be run contemporaneously. PMID:26292624
Calculation of retention time tolerance windows with absolute confidence from shared liquid chromatographic retention data.

PubMed

Boswell, Paul G; Abate-Pella, Daniel; Hewitt, Joshua T

2015-09-18

Compound identification by liquid chromatography-mass spectrometry (LC-MS) is a tedious process, mainly because authentic standards must be run on a user's system to be able to confidently reject a potential identity from its retention time and mass spectral properties. Instead, it would be preferable to use shared retention time/index data to narrow down the identity, but shared data cannot be used to reject candidates with an absolute level of confidence because the data are strongly affected by differences between HPLC systems and experimental conditions. However, a technique called "retention projection" was recently shown to account for many of the differences. In this manuscript, we discuss an approach to calculate appropriate retention time tolerance windows for projected retention times, potentially making it possible to exclude candidates with an absolute level of confidence, without needing to have authentic standards of each candidate on hand. In a range of multi-segment gradients and flow rates run among seven different labs, the new approach calculated tolerance windows that were significantly more appropriate for each retention projection than global tolerance windows calculated for retention projections or linear retention indices. Though there were still some small differences between the labs that evidently were not taken into account, the calculated tolerance windows only needed to be relaxed by 50% to make them appropriate for all labs. Even then, 42% of the tolerance windows calculated in this study without standards were narrower than those required by WADA for positive identification, where standards must be run contemporaneously. Copyright © 2015 Elsevier B.V. All rights reserved.
Reversible optical switching memristors with tunable STDP synaptic plasticity: a route to hierarchical control in artificial intelligent systems.

PubMed

Jaafar, Ayoub H; Gray, Robert J; Verrelli, Emanuele; O'Neill, Mary; Kelly, Stephen M; Kemp, Neil T

2017-11-09

Optical control of memristors opens the route to new applications in optoelectronic switching and neuromorphic computing. Motivated by the need for reversible and latched optical switching we report on the development of a memristor with electronic properties tunable and switchable by wavelength and polarization specific light. The device consists of an optically active azobenzene polymer, poly(disperse red 1 acrylate), overlaying a forest of vertically aligned ZnO nanorods. Illumination induces trans-cis isomerization of the azobenzene molecules, which expands or contracts the polymer layer and alters the resistance of the off/on states, their ratio and retention time. The reversible optical effect enables dynamic control of a memristor's learning properties including control of synaptic potentiation and depression, optical switching between short-term and long-term memory and optical modulation of the synaptic efficacy via spike timing dependent plasticity. The work opens the route to the dynamic patterning of memristor networks both spatially and temporally by light, thus allowing the development of new optically reconfigurable neural networks and adaptive electronic circuits.
Predicting Factors of Perceived Organizational Support by Full-Time and Part-Time Community College Faculty as Relates to Student Retention Rates

ERIC Educational Resources Information Center

Nichols, Sarah K.

2012-01-01

Student retention is socially, politically, and financially important to educational institutions. This quantitative study explored the gap in research regarding the relationship between employment of part-time in lieu of full-time faculty and student retention. The campus climate exchange model (CCEM), served as the conceptual framework in this…
A regression model for calculating the second dimension retention index in comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry.

PubMed

Wang, Bing; Shen, Hao; Fang, Aiqin; Huang, De-Shuang; Jiang, Changjun; Zhang, Jun; Chen, Peng

2016-06-17

Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) system has become a key analytical technology in high-throughput analysis. Retention index has been approved to be helpful for compound identification in one-dimensional gas chromatography, which is also true for two-dimensional gas chromatography. In this work, a novel regression model was proposed for calculating the second dimension retention index of target components where n-alkanes were used as reference compounds. This model was developed to depict the relationship among adjusted second dimension retention time, temperature of the second dimension column and carbon number of n-alkanes by an exponential nonlinear function with only five parameters. Three different criteria were introduced to find the optimal values of parameters. The performance of this model was evaluated using experimental data of n-alkanes (C7-C31) at 24 temperatures which can cover all 0-6s adjusted retention time area. The experimental results show that the mean relative error between predicted adjusted retention time and experimental data of n-alkanes was only 2%. Furthermore, our proposed model demonstrates a good extrapolation capability for predicting adjusted retention time of target compounds which located out of the range of the reference compounds in the second dimension adjusted retention time space. Our work shows the deviation was less than 9 retention index units (iu) while the number of alkanes were added up to 5. The performance of our proposed model has also been demonstrated by analyzing a mixture of compounds in temperature programmed experiments. Copyright © 2016 Elsevier B.V. All rights reserved.
Neck-band retention for Canada geese in the Mississippi (USA) flyway

USGS Publications Warehouse

Samuel, M.D.; Weiss, N.T.; Rusch, D.H.; Craven, S.R.; Trost, R.E.; Caswell, F.D.

1990-01-01

We used capture, harvest, and observation histories of Canada geese (Branta canadensis) banded in the Mississippi flyway, 1974-88, to examine the problem of neck-band retention. Methods for the analysis of survival data were used to estimate rates of neck-band retention and to evaluate factors associated with neck-band loss. Sex, age of bird at banding, rivet use, and neck-band type significantly influenced neck-band retention. For most of the resulting cohorts (e.g., sex, age, rivet, and neck-band type categories), neck-band retention rates decreased through time. We caution against using small samples or data collected during short-term studies to determine retention rates. We suggest that observation data be used in neck-band retention studies to increase the efficiency of estimating retention time.
Curriculum Alignment with Vision and Change Improves Student Scientific Literacy.

PubMed

Auerbach, Anna Jo; Schussler, Elisabeth E

2017-01-01

The Vision and Change in Undergraduate Biology Education final report challenged institutions to reform their biology courses to focus on process skills and student active learning, among other recommendations. A large southeastern university implemented curricular changes to its majors' introductory biology sequence in alignment with these recommendations. Discussion sections focused on developing student process skills were added to both lectures and a lab, and one semester of lab was removed. This curriculum was implemented using active-learning techniques paired with student collaboration. This study determined whether these changes resulted in a higher gain of student scientific literacy by conducting pre/posttesting of scientific literacy for two cohorts: students experiencing the unreformed curriculum and students experiencing the reformed curriculum. Retention of student scientific literacy for each cohort was also assessed 4 months later. At the end of the academic year, scientific literacy gains were significantly higher for students in the reformed curriculum ( p = 0.005), with those students having double the scientific literacy gains of the cohort in the unreformed curriculum. Retention of scientific literacy did not differ between the cohorts. © 2017 A. J. Auerbach and E. E. Schussler. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).
Alignment displacements of the solar optical telescope primary mirror

NASA Technical Reports Server (NTRS)

Medenica, W. V.

1978-01-01

Solar optical telescope is a space shuttle payload which is at the present time (1978) being planned. The selected alignment method for the telescope's primary mirror is such that the six inclined legs supporting the mirror are at the same time motorized alignment actuators, changing their own length according to the alignment requirement and command. The alignment displacements were described, including circumvention of some apparent NASTRAN limitations.
Halo Intrinsic Alignment: Dependence on Mass, Formation Time, and Environment

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

Xia, Qianli; Kang, Xi; Wang, Peng

In this paper we use high-resolution cosmological simulations to study halo intrinsic alignment and its dependence on mass, formation time, and large-scale environment. In agreement with previous studies using N -body simulations, it is found that massive halos have stronger alignment. For the first time, we find that for a given halo mass older halos have stronger alignment and halos in cluster regions also have stronger alignment than those in filaments. To model these dependencies, we extend the linear alignment model with inclusion of halo bias and find that the halo alignment with its mass and formation time dependence canmore » be explained by halo bias. However, the model cannot account for the environment dependence, as it is found that halo bias is lower in clusters and higher in filaments. Our results suggest that halo bias and environment are independent factors in determining halo alignment. We also study the halo alignment correlation function and find that halos are strongly clustered along their major axes and less clustered along the minor axes. The correlated halo alignment can extend to scales as large as 100 h {sup −1} Mpc, where its feature is mainly driven by the baryon acoustic oscillation effect.« less
Analysis of the Postoperative Displacement of Trochanteric Fractures on Lateral View Radiographs.

PubMed

Furui, Atsuo; Terada, Nobuki

2017-08-01

Achieving sufficient support of the anterior cortex of the femoral neck is a fundamental goal of the reduction of trochanteric fractures. However, anterior-cortex support is often lost after the fracture reduction. Our aim was to analyze factors contributing to the postoperative displacement of an acceptably reduced trochanteric fracture. The cases of 40 patients with a post-reduction Ikuta subtype N fracture alignment were reviewed. All fractures were fixed with 135° free-sliding plates. On postoperative day 14, patients were classified into two groups: those with retention of the Ikuta subtype N alignment, and those with progression to Ikuta subtype P alignment. The clinical and radiological factors were evaluated between the groups. In addition, to define one of the factors, i.e., the postoperative rotational displacement between the proximal and distal fragments, the relationship between radiographic findings and computed tomography image measurements was assessed in 15 of the 40 patients. Angulation at the fracture site on lateral view radiographs was defined as postoperative rotational displacement, and unstable trochanteric fractures and postoperative rotational displacement were identified as significant risk factors for the postoperative displacement. Therefore, cautious and careful follow-up is warranted for patients with unstable trochanteric fractures or fractures having rotational displacement.
The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention

PubMed Central

Akhund-Zade, Jamilla; Bergland, Alan O.; Crowe, Sarah O.; Unckless, Robert L.

2017-01-01

Drosophila melanogaster is able to thrive in harsh northern climates through adaptations in life-history traits and physiological mechanisms that allow for survival through the winter. We examined the genetic basis of natural variation in one such trait, female virgin egg retention, which was previously shown to vary clinally and seasonally. To further our understanding of the genetic basis and evolution of virgin egg retention, we performed a genome-wide association study (GWAS) using the previously sequenced Drosophila Genetic Reference Panel (DGRP) mapping population. We found 29 single nucleotide polymorphisms (SNPs) associated with virgin egg retention and assayed 6 available mutant lines, each harboring a mutation in a candidate gene, for effects on egg retention time. We found that four out of the six mutant lines had defects in egg retention time as compared with the respective controls: mun, T48, Mes-4, and Klp67A. Surprisingly, none of these genes has a recognized role in ovulation control, but three of the four genes have known effects on fertility or have high expression in the ovaries. We also found that the SNP set associated with egg retention time was enriched for clinal SNPs. The majority of clinal SNPs had alleles associated with longer egg retention present at higher frequencies in higher latitudes. Our results support previous studies that show higher frequency of long retention times at higher latitude, providing evidence for the adaptive value of virgin egg-retention. PMID:28042107
Factors Affecting Retention of First-Time, Full-Time Freshmen Students at Higher Education Institutions within the Appalachian College Association

ERIC Educational Resources Information Center

Swafford, Stacy James

2017-01-01

This study examined factors that may affect the retention of first-time, full-time college freshmen to sophomore year. Institutions in the Appalachian College Association (ACA) were invited to participate, and nine of the 35 member schools provided data. The research questions were (1) Is there a relationship between retention for students'…
Towards a chromatographic similarity index to establish localised quantitative structure-retention relationships for retention prediction. II Use of Tanimoto similarity index in ion chromatography.

PubMed

Park, Soo Hyun; Talebi, Mohammad; Amos, Ruth I J; Tyteca, Eva; Haddad, Paul R; Szucs, Roman; Pohl, Christopher A; Dolan, John W

2017-11-10

Quantitative Structure-Retention Relationships (QSRR) are used to predict retention times of compounds based only on their chemical structures encoded by molecular descriptors. The main concern in QSRR modelling is to build models with high predictive power, allowing reliable retention prediction for the unknown compounds across the chromatographic space. With the aim of enhancing the prediction power of the models, in this work, our previously proposed QSRR modelling approach called "federation of local models" is extended in ion chromatography to predict retention times of unknown ions, where a local model for each target ion (unknown) is created using only structurally similar ions from the dataset. A Tanimoto similarity (TS) score was utilised as a measure of structural similarity and training sets were developed by including ions that were similar to the target ion, as defined by a threshold value. The prediction of retention parameters (a- and b-values) in the linear solvent strength (LSS) model in ion chromatography, log k=a - blog[eluent], allows the prediction of retention times under all eluent concentrations. The QSRR models for a- and b-values were developed by a genetic algorithm-partial least squares method using the retention data of inorganic and small organic anions and larger organic cations (molecular mass up to 507) on four Thermo Fisher Scientific columns (AS20, AS19, AS11HC and CS17). The corresponding predicted retention times were calculated by fitting the predicted a- and b-values of the models into the LSS model equation. The predicted retention times were also plotted against the experimental values to evaluate the goodness of fit and the predictive power of the models. The application of a TS threshold of 0.6 was found to successfully produce predictive and reliable QSRR models (Q ext(F2) 2 >0.8 and Mean Absolute Error<0.1), and hence accurate retention time predictions with an average Mean Absolute Error of 0.2min. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.
Diffusion-limited retention of porous particles at density interfaces

PubMed Central

Kindler, Kolja; Khalili, Arzhang; Stocker, Roman

2010-01-01

Downward carbon flux in the ocean is largely governed by particle settling. Most marine particles settle at low Reynolds numbers and are highly porous, yet the fluid dynamics of this regime have remained unexplored. We present results of an experimental investigation of porous particles settling through a density interface at Reynolds numbers between 0.1 and 1. We tracked 100 to 500 μm hydrogel spheres with 95.5% porosity and negligible permeability. We found that a small negative initial excess density relative to the lower (denser) fluid layer, a common scenario in the ocean, results in long retention times of particles at the interface. We hypothesized that the retention time was determined by the diffusive exchange of the stratifying agent between interstitial and ambient fluid, which increases excess density of particles that have stalled at the interface, enabling their settling to resume. This hypothesis was confirmed by observations, which revealed a quadratic dependence of retention time on particle size, consistent with diffusive exchange. These results demonstrate that porosity can control retention times and therefore accumulation of particles at density interfaces, a mechanism that could underpin the formation of particle layers frequently observed at pycnoclines in the ocean. We estimate retention times of 3 min to 3.3 d for the characteristic size range of marine particles. This enhancement in retention time can affect carbon transformation through increased microbial colonization and utilization of particles and release of dissolved organics. The observed size dependence of the retention time could further contribute to improve quantifications of vertical carbon flux. PMID:21135242
Chloride retention and release in a boreal forest soil: effects of soil water residence time and nitrogen and chloride loads.

PubMed

Bastviken, David; Sandén, Per; Svensson, Teresia; Ståhlberg, A Carina; Magounakis, Malin; Oberg, Gunilla

2006-05-01

The common assumption that chloride (Cl-) is conservative in soils and can be used as a groundwater tracer is currently being questioned, and an increasing number of studies indicate that Cl- can be retained in soils. We performed lysimeter experiments with soil from a coniferous forest in southeast Sweden to determine whether pore water residence time and nitrogen and Cl- loads affected Cl- retention. Over the first 42 days there was a net retention of Cl- with retention rates averaging 3.1 mg CI- m(-2) d(-1) (68% of the added Cl- retained over 42 days). Thereafter, a net release of Cl- at similar rates was observed for the remaining experimental period (85 d). Longer soil water residence time and higher Cl- load gave higher initial retention and subsequent release rates than shorter residence time and lower Cl- load did. Nitrogen load did not affect Cl transformation rates. This study indicates that simultaneous retention and release of Cl- can occur in soils, and that rates may be considerable relative to the load. The retention of Cl- observed was probably due to chlorination of soil organic matter or ion exchange. The cause of the shift between net retention and net release is unclear, but we hypothesize that the presence of O2 or the presence of microbially available organic matter regulates Cl- retention and release rates.
Critical evaluation of a simple retention time predictor based on LogKow as a complementary tool in the identification of emerging contaminants in water.

PubMed

Bade, Richard; Bijlsma, Lubertus; Sancho, Juan V; Hernández, Felix

2015-07-01

There has been great interest in environmental analytical chemistry in developing screening methods based on liquid chromatography-high resolution mass spectrometry (LC-HRMS) for emerging contaminants. Using HRMS, compound identification relies on the high mass resolving power and mass accuracy attainable by these analyzers. When dealing with wide-scope screening, retention time prediction can be a complementary tool for the identification of compounds, and can also reduce tedious data processing when several peaks appear in the extracted ion chromatograms. There are many in silico, Quantitative Structure-Retention Relationship methods available for the prediction of retention time for LC. However, most of these methods use commercial software to predict retention time based on various molecular descriptors. This paper explores the applicability and makes a critical discussion on a far simpler and cheaper approach to predict retention times by using LogKow. The predictor was based on a database of 595 compounds, their respective LogKow values and a chromatographic run time of 18min. Approximately 95% of the compounds were found within 4.0min of their actual retention times, and 70% within 2.0min. A predictor based purely on pesticides was also made, enabling 80% of these compounds to be found within 2.0min of their actual retention times. To demonstrate the utility of the predictors, they were successfully used as an additional tool in the identification of 30 commonly found emerging contaminants in water. Furthermore, a comparison was made by using different mass extraction windows to minimize the number of false positives obtained. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantifying Long-Term Retention of Excised Fat Grafts: A Longitudinal, Retrospective Cohort Study of 108 Patients Followed for Up to 8.4 Years.

PubMed

Herly, Mikkel; Ørholt, Mathias; Glovinski, Peter V; Pipper, Christian B; Broholm, Helle; Poulsgaard, Lars; Fugleholm, Kåre; Thomsen, Carsten; Drzewiecki, Krzysztof T

2017-05-01

Predicting the degree of fat graft retention is essential when planning reconstruction or augmentation with free fat grafting. Most surgeons observe volume loss over time after fat grafting; however, the portion lost to resorption after surgery is still poorly defined, and the time to reach steady state is unknown. The authors compiled a retrospective, longitudinal cohort of patients with vestibular schwannoma who had undergone ablative surgery and reconstruction with excised fat between the years 2006 and 2015. Fat volume retention was quantified by computed tomography and magnetic resonance imaging and used to model a graft retention trajectory and determine the volumetric steady state. In addition, the authors evaluated the association between graft retention and secondary characteristics, such as sex and transplant volume. A total of 108 patients were included. The average baseline graft volume was 18.1 ± 4.8 ml. The average time to reach steady state was 806 days after transplantation. By this time, the average fat graft retention was 50.6 percent (95 percent CI, 46.4 to 54.7 percent). No statistically significant association was found between baseline graft volume and retention. Fat graft retention over time was significantly higher in men than in women (57.7 percent versus 44.5 percent; p < 0.001). The authors' data provide evidence that the time to reach fat graft volumetric steady state is considerably longer than previously expected. Fat grafts continue to shrink long after the initial hypoxia-induced tissue necrosis has been cleared, thus indicating that factors other than blood supply may be more influential for fat graft retention. Therapeutic, IV.
Optimization of Ozonation Process for the Reduction of Excess Sludge Production from Activated Sludge Process of Sago Industry Wastewater Using Central Composite Design

PubMed Central

Subha, B.; Muthukumar, M.

2012-01-01

Sago industries effluent containing large amounts of organic content produced excess sludge which is a serious problem in wastewater treatment. In this study ozonation has been employed for the reduction of excess sludge production in activated sludge process. Central composite design is used to study the effect of ozone treatment for the reduction of excess sludge production in sago effluent and to optimise the variables such as pH, ozonation time, and retention time. ANOVA showed that the coefficient determination value (R 2) of VSS and COD reduction were 0.9689 and 0.8838, respectively. VSS reduction (81%) was achieved at acidic pH 6.9, 12 minutes ozonation, and retention time of 10 days. COD reduction (87%) was achieved at acidic pH 6.7, 8 minutes of ozonation time, and retention time of 6 days. Low ozonation time and high retention time influence maximum sludge reduction, whereas low ozonation time with low retention time was effective for COD reduction. PMID:22593666
ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

PubMed

Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

2006-12-15

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.
Reverse alignment "mirror image" visualization as a laparoscopic training tool improves task performance.

PubMed

Dunnican, Ward J; Singh, T Paul; Ata, Ashar; Bendana, Emma E; Conlee, Thomas D; Dolce, Charles J; Ramakrishnan, Rakesh

2010-06-01

Reverse alignment (mirror image) visualization is a disconcerting situation occasionally faced during laparoscopic operations. This occurs when the camera faces back at the surgeon in the opposite direction from which the surgeon's body and instruments are facing. Most surgeons will attempt to optimize trocar and camera placement to avoid this situation. The authors' objective was to determine whether the intentional use of reverse alignment visualization during laparoscopic training would improve performance. A standard box trainer was configured for reverse alignment, and 34 medical students and junior surgical residents were randomized to train with either forward alignment (DIRECT) or reverse alignment (MIRROR) visualization. Enrollees were tested on both modalities before and after a 4-week structured training program specific to their modality. Student's t test was used to determine differences in task performance between the 2 groups. Twenty-one participants completed the study (10 DIRECT, 11 MIRROR). There were no significant differences in performance time between DIRECT or MIRROR participants during forward or reverse alignment initial testing. At final testing, DIRECT participants had improved times only in forward alignment performance; they demonstrated no significant improvement in reverse alignment performance. MIRROR participants had significant time improvement in both forward and reverse alignment performance at final testing. Reverse alignment imaging for laparoscopic training improves task performance for both reverse alignment and forward alignment tasks. This may be translated into improved performance in the operating room when faced with reverse alignment situations. Minimal lab training can account for drastic adaptation to this environment.
Caveat Emptor: Is There a Relationship between Part-Time Faculty Utilization and Student Learning Outcomes and Retention? Professional File. Number 91, Spring 2004

ERIC Educational Resources Information Center

Schibik, Timothy; Harrington, Charles

2004-01-01

One important factor neglected in the literature involves an investigation into whether the increased utilization of part-time faculty impacts student retention. Are part-time faculty, who are employed primarily to teach introductory courses, having an adverse affect on student retention? Are universities recognizing and studying the potential…
Effect of hydraulic retention time on inorganic nutrient recovery and biodegradable organics removal in a biofilm reactor treating plant biomass leachate

NASA Technical Reports Server (NTRS)

Krumins, Valdis; Hummerick, Mary; Levine, Lanfang; Strayer, Richard; Adams, Jennifer L.; Bauer, Jan

2002-01-01

A fixed-film (biofilm) reactor was designed and its performance was determined at various retention times. The goal was to find the optimal retention time for recycling plant nutrients in an advanced life support system, to minimize the size, mass, and volume (hold-up) of a production model. The prototype reactor was tested with aqueous leachate from wheat crop residue at 24, 12, 6, and 3 h hydraulic retention times (HRTs). Biochemical oxygen demand (BOD), nitrates and other plant nutrients, carbohydrates, total phenolics, and microbial counts were monitored to characterize reactor performance. BOD removal decreased significantly from 92% at the 24 h HRT to 73% at 3 h. Removal of phenolics was 62% at the 24 h retention time, but 37% at 3 h. Dissolved oxygen concentrations, nitric acid consumption, and calcium and magnesium removals were also affected by HRT. Carbohydrate removals, carbon dioxide (CO2) productions, denitrification, potassium concentrations, and microbial counts were not affected by different retention times. A 6 h HRT will be used in future studies to determine the suitability of the bioreactor effluent for hydroponic plant production.
European Board of Orthodontics case report: severe skeletal discrepancy.

PubMed

Paduano, Sergio

2009-01-01

The 10.3 year-old patient presented a sagittal skeletal and dental Class II division I malocclusion with a severe overjet in the mixed dentition. The convex profile aesthetically improved with the mandibular advancement (positive Frankel manoeuvre). No signs or symptoms of TMJ disorders were present. Oral mucosa and gingiva conditions were good notwithstanding a scanty oral hygiene. The treatment plan included: a) Bass appliance to improve the retruded profile and, partially, OVJ; b) upper and lower arch fixed appliance for alignment, levelling and correction of the malocclusion c) posttreatment retention.
A simplified implementation of edge detection in MATLAB is faster and more sensitive than fast fourier transform for actin fiber alignment quantification.

PubMed

Kemeny, Steven Frank; Clyne, Alisa Morss

2011-04-01

Fiber alignment plays a critical role in the structure and function of cells and tissues. While fiber alignment quantification is important to experimental analysis and several different methods for quantifying fiber alignment exist, many studies focus on qualitative rather than quantitative analysis perhaps due to the complexity of current fiber alignment methods. Speed and sensitivity were compared in edge detection and fast Fourier transform (FFT) for measuring actin fiber alignment in cells exposed to shear stress. While edge detection using matrix multiplication was consistently more sensitive than FFT, image processing time was significantly longer. However, when MATLAB functions were used to implement edge detection, MATLAB's efficient element-by-element calculations and fast filtering techniques reduced computation cost 100 times compared to the matrix multiplication edge detection method. The new computation time was comparable to the FFT method, and MATLAB edge detection produced well-distributed fiber angle distributions that statistically distinguished aligned and unaligned fibers in half as many sample images. When the FFT sensitivity was improved by dividing images into smaller subsections, processing time grew larger than the time required for MATLAB edge detection. Implementation of edge detection in MATLAB is simpler, faster, and more sensitive than FFT for fiber alignment quantification.
The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention.

PubMed

Akhund-Zade, Jamilla; Bergland, Alan O; Crowe, Sarah O; Unckless, Robert L

2017-01-01

Drosophila melanogaster is able to thrive in harsh northern climates through adaptations in life-history traits and physiological mechanisms that allow for survival through the winter. We examined the genetic basis of natural variation in one such trait, female virgin egg retention, which was previously shown to vary clinally and seasonally. To further our understanding of the genetic basis and evolution of virgin egg retention, we performed a genome-wide association study (GWAS) using the previously sequenced Drosophila Genetic Reference Panel (DGRP) mapping population. We found 29 single nucleotide polymorphisms (SNPs) associated with virgin egg retention and assayed 6 available mutant lines, each harboring a mutation in a candidate gene, for effects on egg retention time. We found that four out of the six mutant lines had defects in egg retention time as compared with the respective controls: mun, T48, Mes-4, and Klp67A Surprisingly, none of these genes has a recognized role in ovulation control, but three of the four genes have known effects on fertility or have high expression in the ovaries. We also found that the SNP set associated with egg retention time was enriched for clinal SNPs. The majority of clinal SNPs had alleles associated with longer egg retention present at higher frequencies in higher latitudes. Our results support previous studies that show higher frequency of long retention times at higher latitude, providing evidence for the adaptive value of virgin egg-retention. © The Author 2017. Published by Oxford University Press on behalf of the Entomological Society of America.
Second-order standard addition for deconvolution and quantification of fatty acids of fish oil using GC-MS.

PubMed

Vosough, Maryam; Salemi, Amir

2007-08-15

In the present work two second-order calibration methods, generalized rank annihilation method (GRAM) and multivariate curve resolution-alternating least square (MCR-ALS) have been applied on standard addition data matrices obtained by gas chromatography-mass spectrometry (GC-MS) to characterize and quantify four unsaturated fatty acids cis-9-hexadecenoic acid (C16:1omega7c), cis-9-octadecenoic acid (C18:1omega9c), cis-11-eicosenoic acid (C20:1omega9) and cis-13-docosenoic acid (C22:1omega9) in fish oil considering matrix interferences. With these methods, the area does not need to be directly measured and predictions are more accurate. Because of non-trilinear conditions of GC-MS data matrices, at first MCR-ALS and GRAM have been used on uncorrected data matrices. In comparison to MCR-ALS, biased and imprecise concentrations (%R.S.D.=27.3) were obtained using GRAM without correcting the retention time-shift. As trilinearity is the essential requirement for implementing GRAM, the data need to be corrected. Multivariate rank alignment objectively corrects the run-to-run retention time variations between sample GC-MS data matrix and a standard addition GC-MS data matrix. Then, two second-order algorithms have been compared with each other. The above algorithms provided similar mean predictions, pure concentrations and spectral profiles. The results validated using standard mass spectra of target compounds. In addition, some of the quantification results were compared with the concentration values obtained using the selected mass chromatograms. As in the case of strong peak-overlap and the matrix effect, the classical univariate method of determination of the area of the peaks of the analytes will fail, the "second-order advantage" has solved this problem successfully.
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

PubMed

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-08-01

RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time). Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. © The Author 2015. Published by Oxford University Press.
Evaluating sedimentation problems in activated sludge treatment plants operating at complete sludge retention time.

PubMed

Amanatidou, Elisavet; Samiotis, Georgios; Trikoilidou, Eleni; Pekridis, George; Taousanidis, Nikolaos

2015-02-01

Zero net sludge growth can be achieved by complete retention of solids in activated sludge wastewater treatment, especially in high strength and biodegradable wastewaters. When increasing the solids retention time, MLSS and MLVSS concentrations reach a plateau phase and observed growth yields values tend to zero (Yobs ≈ 0). In this work, in order to evaluate sedimentation problems arised due to high MLSS concentrations and complete sludge retention operational conditions, two identical innovative slaughterhouse wastewater treatment plants were studied. Measurements of wastewaters' quality characteristics, treatment plant's operational conditions, sludge microscopic analysis and state point analysis were conducted. Results have shown that low COD/Nitrogen ratios increase sludge bulking and flotation phenomena due to accidental denitrification in clarifiers. High return activated sludge rate is essential in complete retention systems as it reduces sludge condensation and hydraulic retention time in the clarifiers. Under certain operational conditions sludge loading rates can greatly exceed literature limit values. The presented methodology is a useful tool for estimation of sedimentation problems encountered in activated sludge wastewater treatment plants with complete retention time. Copyright © 2014 Elsevier Ltd. All rights reserved.
41 CFR 101-27.304-2 - Factors affecting the economic retention limit.

Code of Federal Regulations, 2010 CFR

2010-07-01

... economic retention limit. 101-27.304-2 Section 101-27.304-2 Public Contracts and Property Management... economic retention limit. (a) The economic retention limit may be increased where: (1) The item is of... economic retention time limit; or (2) Costs incident to holding an additional quantity are insignificant...
41 CFR 101-27.304-2 - Factors affecting the economic retention limit.

Code of Federal Regulations, 2011 CFR

2011-07-01

... economic retention limit. 101-27.304-2 Section 101-27.304-2 Public Contracts and Property Management... economic retention limit. (a) The economic retention limit may be increased where: (1) The item is of... economic retention time limit; or (2) Costs incident to holding an additional quantity are insignificant...
41 CFR 101-27.304-2 - Factors affecting the economic retention limit.

Code of Federal Regulations, 2013 CFR

2013-07-01

... economic retention limit. 101-27.304-2 Section 101-27.304-2 Public Contracts and Property Management... economic retention limit. (a) The economic retention limit may be increased where: (1) The item is of... economic retention time limit; or (2) Costs incident to holding an additional quantity are insignificant...
41 CFR 101-27.304-2 - Factors affecting the economic retention limit.

Code of Federal Regulations, 2012 CFR

2012-07-01

... economic retention limit. 101-27.304-2 Section 101-27.304-2 Public Contracts and Property Management... economic retention limit. (a) The economic retention limit may be increased where: (1) The item is of... economic retention time limit; or (2) Costs incident to holding an additional quantity are insignificant...
41 CFR 101-27.304-2 - Factors affecting the economic retention limit.

Code of Federal Regulations, 2014 CFR

2014-07-01

... economic retention limit. 101-27.304-2 Section 101-27.304-2 Public Contracts and Property Management... economic retention limit. (a) The economic retention limit may be increased where: (1) The item is of... economic retention time limit; or (2) Costs incident to holding an additional quantity are insignificant...
Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines.

PubMed

Oliveira, Francisco P M; Tavares, João Manuel R S

2013-03-01

This article presents an enhanced methodology to align plantar pressure image sequences simultaneously in time and space. The temporal alignment of the sequences is accomplished using B-splines in the time modeling, and the spatial alignment can be attained using several geometric transformation models. The methodology was tested on a dataset of 156 real plantar pressure image sequences (3 sequences for each foot of the 26 subjects) that was acquired using a common commercial plate during barefoot walking. In the alignment of image sequences that were synthetically deformed both in time and space, an outstanding accuracy was achieved with the cubic B-splines. This accuracy was significantly better (p < 0.001) than the one obtained using the best solution proposed in our previous work. When applied to align real image sequences with unknown transformation involved, the alignment based on cubic B-splines also achieved superior results than our previous methodology (p < 0.001). The consequences of the temporal alignment on the dynamic center of pressure (COP) displacement was also assessed by computing the intraclass correlation coefficients (ICC) before and after the temporal alignment of the three image sequence trials of each foot of the associated subject at six time instants. The results showed that, generally, the ICCs related to the medio-lateral COP displacement were greater when the sequences were temporally aligned than the ICCs of the original sequences. Based on the experimental findings, one can conclude that the cubic B-splines are a remarkable solution for the temporal alignment of plantar pressure image sequences. These findings also show that the temporal alignment can increase the consistency of the COP displacement on related acquired plantar pressure image sequences.
Survival Analysis of Faculty Retention and Promotion in the Social Sciences by Gender.

PubMed

Box-Steffensmeier, Janet M; Cunha, Raphael C; Varbanov, Roumen A; Hoh, Yee Shwen; Knisley, Margaret L; Holmes, Mary Alice

2015-01-01

Recruitment and retention of talent is central to the research performance of universities. Existing research shows that, while men are more likely than women to be promoted at the different stages of the academic career, no such difference is found when it comes to faculty retention rates. Current research on faculty retention, however, focuses on careers in science, technology, engineering, and mathematics (STEM). We extend this line of inquiry to the social sciences. We follow 2,218 tenure-track assistant professors hired since 1990 in seven social science disciplines at nineteen U.S. universities from time of hire to time of departure. We also track their time to promotion to associate and full professor. Using survival analysis, we examine gender differences in time to departure and time to promotion. Our methods account for censoring and unobserved heterogeneity, as well as effect heterogeneity across disciplines and cohorts. We find no statistically significant differences between genders in faculty retention. However, we do find that men are more likely to be granted tenure than women. When it comes to promotion to full professor, the results are less conclusive, as the effect of gender is sensitive to model specification. The results corroborate previous findings about gender patterns in faculty retention and promotion. They suggest that advances have been made when it comes to gender equality in retention and promotion, but important differences still persist.
Orthodontic treatment stability predictors: A retrospective longitudinal study.

PubMed

de Bernabé, Paloma González-Gil; Montiel-Company, José María; Paredes-Gallardo, Vanessa; Gandía-Franco, Jose Luis; Bellot-Arcís, Carlos

2017-03-01

To examine medium- to long-term orthodontic treatment stability and its possible association with certain variables. In a retrospective longitudinal study of 70 postretention patients, the Peer Assessment Rating (PAR) index was measured at the start (T1) and end (T2) of treatment and between 4 and 10 years afterwards (T3). The stability was considered absolute when the T2 and T3 values were identical and relative when the difference was within the ±5 range. Among the 70 patients, 65.8% were female and 34.2% were male. Their mean age was 14.5 years. The mean treatment length was 2.4 years. The mean retention phase was 3.3 years. The mean pre- and posttreatment PAR scores were 29.8 (T1) and 6.3 (T2). The mean T1-T2 difference was 23.6. The mean T2-T3 difference was -0.39. Within the study, 7.1% presented absolute stability and 68.6% presented relative stability. Lower anterior segment alignment and overbite were the most unstable occlusal features and tended to worsen. Fixed retainer (odds ratio [OR] 0.31; 95% confidence interval [CI] 0.10-0.98) as a protective factor and years without retention (OR 1.32; 95% CI 1.03-1.68) as a risk factor are predictor variables of instability in the case of lower anterior segment alignment. The PAR value at the end of treatment (OR 1.29; 95% CI 1.08-1.54) and extractions (OR 4.76; 95% CI 1.05-21.6) before treatment are predictors for midline instability.

Recovery of resources for advanced life support space applications: effect of retention time on biodegradation of two crop residues in a fed-batch, continuous stirred tank reactor.

PubMed

Strayer, R F; Finger, B W; Alazraki, M P; Cook, K; Garland, J L

2002-09-01

Bioreactor retention time is a key process variable that will influence costs that are relevant to long distance space travel or long duration space habitation. However. little is known about the effects of this parameter on the microbiological treatment options that are being proposed for Advanced Life Support (ALS) systems. Two bioreactor studies were designed to examine this variable. In the first one, six retention times ranging from 1.3 to 21.3 days--were run in duplicate, 81 working-volume continuous stirred tank reactors (CSTR) that were fed ALS wheat residues. Ash-free dry weight loss, carbon mineralization, soluble TOC reduction, changes in fiber content (cellulose, hemicellulose, and lignin), bacterial numbers, and mineral recoveries were monitored. At short retention times--1.33 days--biodegradation was poor (total: 16-20%, cellulose - 12%, hemicellulose - 28%) but soluble TOC was decreased by 75-80% and recovery of major crop inorganic nutrients was adequate, except for phosphorus. A high proportion of the total bacteria (ca. 83%) was actively respiring. At the longest retention time tested, 21.3 days, biodegradation was good (total: 55-60%, cellulose ca. 70%, hemicellulose - ca. 55%) and soluble TOC was decreased by 80%. Recovery of major nutrients, except phosphorus, remained adequate. A very low proportion of total bacteria was actively respiring (ca. 16%). The second bioreactor study used potato residue to determine if even shorter retention times could be used (range 0.25-2.0 days). Although overall biodegradation deteriorated, the degradation of soluble TOC continued to be ca. 75%. We conclude that if the goal of ALS bioprocessing is maximal degradation of crop residues, including cellulose, then retention times of 10 days or longer will be needed. If the goal is to provide inorganic nutrients with the smallest volume/weight bioreactor possible, then a retention time of 1 day (or less) is sufficient.
Recovery of resources for advanced life support space applications: effect of retention time on biodegradation of two crop residues in a fed-batch, continuous stirred tank reactor

NASA Technical Reports Server (NTRS)

Strayer, R. F.; Finger, B. W.; Alazraki, M. P.; Cook, K.; Garland, J. L.

2002-01-01

Bioreactor retention time is a key process variable that will influence costs that are relevant to long distance space travel or long duration space habitation. However. little is known about the effects of this parameter on the microbiological treatment options that are being proposed for Advanced Life Support (ALS) systems. Two bioreactor studies were designed to examine this variable. In the first one, six retention times ranging from 1.3 to 21.3 days--were run in duplicate, 81 working-volume continuous stirred tank reactors (CSTR) that were fed ALS wheat residues. Ash-free dry weight loss, carbon mineralization, soluble TOC reduction, changes in fiber content (cellulose, hemicellulose, and lignin), bacterial numbers, and mineral recoveries were monitored. At short retention times--1.33 days--biodegradation was poor (total: 16-20%, cellulose - 12%, hemicellulose - 28%) but soluble TOC was decreased by 75-80% and recovery of major crop inorganic nutrients was adequate, except for phosphorus. A high proportion of the total bacteria (ca. 83%) was actively respiring. At the longest retention time tested, 21.3 days, biodegradation was good (total: 55-60%, cellulose ca. 70%, hemicellulose - ca. 55%) and soluble TOC was decreased by 80%. Recovery of major nutrients, except phosphorus, remained adequate. A very low proportion of total bacteria was actively respiring (ca. 16%). The second bioreactor study used potato residue to determine if even shorter retention times could be used (range 0.25-2.0 days). Although overall biodegradation deteriorated, the degradation of soluble TOC continued to be ca. 75%. We conclude that if the goal of ALS bioprocessing is maximal degradation of crop residues, including cellulose, then retention times of 10 days or longer will be needed. If the goal is to provide inorganic nutrients with the smallest volume/weight bioreactor possible, then a retention time of 1 day (or less) is sufficient.
Ultrasonography to investigate the effect of supplementing whole milk with complex carbohydrates and specific amino acids on curd retention in the abomasum of dairy calves.

PubMed

Singh, K; Leath, S R; Henderson, H V; Molenaar, A J; Watson, T J; Pacheco, D; McMahon, C D

2016-09-01

To determine whether the retention time of curd in the abomasum of calves was influenced by supplementing milk with a plant-derived carbohydrate and amino acid supplement, evaluated non-invasively using ultrasonography. Female dairy calves aged between 2-6 days of age were sourced from a commercial farm in March 2013. All calves were fed whole milk until weaning (4 L per day); 21 calves were supplemented with a probiotic until 18 days of age, and thereafter with a plant-derived complex carbohydrate and amino acid supplement until weaning, and 22 calves were just fed whole milk. Treatment groups were balanced for age, weight and breed. At 9-14, 24-29 and 52-57 days of age, the abomasum of each calf was examined using ultrasonography immediately before and after feeding, 1 and 2 hours after feeding, and then at 30 minute intervals until curd was no longer visible in the abomasum. Abomasal volume and curd size were recorded to assess retention time of curd in the abomasum. At 9-14 days of age, mean retention time of curd in the abomasum was similar (4.6 hours) in both groups. At 24-29 days of age, when the supplemented calves had been receiving the supplement for approximately 10 days, mean curd retention time was longer by 1.4 (SE 0.28) hours in supplemented compared with unsupplemented calves (p<0.001). At 52-57 days of age, mean retention time was longer by 0.7 (SE 0.34) hours compared to unsupplemented calves (p=0.05). Using ultrasonography, changes in abomasal content could be followed non-invasively over time and it was demonstrated that the plant-derived complex carbohydrate supplement increased the curd retention time in the abomasum. We speculate that the increased retention time enables an increased availability of nutrients following a more complete digestion of milk, thereby improving animal performance.
DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors.

PubMed

Schmollinger, Martin; Nieselt, Kay; Kaufmann, Michael; Morgenstern, Burkhard

2004-09-09

Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a) pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b) For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.
Synthesis of Superabsorbent Polymer via Inverse Suspension Method: Effect of Carbon Filler

NASA Astrophysics Data System (ADS)

Zakaria, Munirah Ezzah Tuan; Shima Jamari, Saidatul; Ling, Yeong Yi; Ghazali, Suriati

2017-05-01

This paper studies on the effect of the addition of carbon filler towards the performance of superabsorbent polymer composite (SAPc). In this work, the SAPc was synthesized using inverse suspension polymerization method. The process involved two different solutions; dispersed phase which contains partially neutralized acrylic acid, acrylamide, APS and NN-Methylenebisacrylamide, and continuous phase which contains cyclohexane, span-80 and carbon filler (at different weight percent). The optimum SAPs and filler ratio was measured in terms of water retention in soil and characterized by Mastersizer, FTIR and SEM. Biodegradability of the polymer was determined by soil burial test and SAPc with 0.02% carbon has highest biodegradability rate. SAPc with 0.04wt% carbon showed the optimal water retention percentage among all the samples. The synthesized SAPc producing spherical shapes with parallel alignment due to the addition of carbon fiber. It can be concluded that the addition of carbon fiber able to enhance the performance of the SAP composite (SAPc).
Magnetic field effect for cellulose nanofiber alignment

NASA Astrophysics Data System (ADS)

Kim, Jaehwan; Chen, Yi; Kang, Kwang-Sun; Park, Young-Bin; Schwartz, Mark

2008-11-01

Regenerated cellulose formed into cellulose nanofibers under strong magnetic field and aligned perpendicularly to the magnetic field. Well-aligned microfibrils were found as the exposure time of the magnetic field increased. Better alignment and more crystalline structure of the cellulose resulted in the increased decomposition temperature of the material. X-ray crystallograms showed that crystallinity index of the cellulose increased as the exposure time of the magnetic field increased.
Background or Experience? Using Logistic Regression to Predict College Retention

ERIC Educational Resources Information Center

Synco, Tracee M.

2012-01-01

Tinto, Astin and countless others have researched the retention and attrition of students from college for more than thirty years. However, the six year graduation rate for all first-time full-time freshmen for the 2002 cohort was 57%. This study sought to determine the retention variables that predicted continued enrollment of entering freshmen…
31 CFR 103.38 - Nature of records and retention period.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Nature of records and retention... § 103.38 Nature of records and retention period. (a) Wherever it is required that there be retained... reasonable period of time, taking into consideration the nature of the record, and the amount of time expired...
High-Performance Flexible All-Solid-State Asymmetric Supercapacitors Based on Vertically Aligned CuSe@Co(OH) 2 Nanosheet Arrays

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

Gong, Jiangfeng; Tian, Yazhou; Yang, Ziyuan

The developments of electrode active materials provide the opportunities for next-generation energy storage devices. The arrangement of electrode materials on the substrate has recently emerged as a promising strategy for preparing high-performance supercapacitors. In this paper, we demonstrate a novel vertically aligned CuSe@Co(OH) 2 nanosheet arrays electrode for supercapacitor application. The materials are thoroughly characterized by structural and spectroscopic techniques. Electrochemical performance of CuSe@Co(OH) 2 nanosheet arrays are investigated in detail, which exhibit a specific capacitance as much as 1180 F g -1 at a current density of 1 A g -1. A flexible asymmetric all-solid-state supercapacitor is fabricated usingmore » CuSe@Co(OH) 2 nanosheet arrays as the positive electrode and activated carbon as the negative electrode. The device delivers a volumetric capacitance of 441.4 mF cm -3 with maximum energy density and maximum power density is 0.17 and 62.1 mW cm -3, as well as robust cycling stability (~80.4% capacitance retention after 10 000 cycles), excellent flexibility, and mechanical stability. Finally, the excellent electrochemical performance can be attributed to its unique vertically aligned configuration.« less
High-Performance Flexible All-Solid-State Asymmetric Supercapacitors Based on Vertically Aligned CuSe@Co(OH) 2 Nanosheet Arrays

DOE PAGES

Gong, Jiangfeng; Tian, Yazhou; Yang, Ziyuan; ...

2018-01-04

The developments of electrode active materials provide the opportunities for next-generation energy storage devices. The arrangement of electrode materials on the substrate has recently emerged as a promising strategy for preparing high-performance supercapacitors. In this paper, we demonstrate a novel vertically aligned CuSe@Co(OH) 2 nanosheet arrays electrode for supercapacitor application. The materials are thoroughly characterized by structural and spectroscopic techniques. Electrochemical performance of CuSe@Co(OH) 2 nanosheet arrays are investigated in detail, which exhibit a specific capacitance as much as 1180 F g -1 at a current density of 1 A g -1. A flexible asymmetric all-solid-state supercapacitor is fabricated usingmore » CuSe@Co(OH) 2 nanosheet arrays as the positive electrode and activated carbon as the negative electrode. The device delivers a volumetric capacitance of 441.4 mF cm -3 with maximum energy density and maximum power density is 0.17 and 62.1 mW cm -3, as well as robust cycling stability (~80.4% capacitance retention after 10 000 cycles), excellent flexibility, and mechanical stability. Finally, the excellent electrochemical performance can be attributed to its unique vertically aligned configuration.« less
“Retention Projection” Enables Reliable Use of Shared Gas Chromatographic Retention Data Across Labs, Instruments, and Methods

PubMed Central

Barnes, Brian B.; Wilson, Michael B.; Carr, Peter W.; Vitha, Mark F.; Broeckling, Corey D.; Heuberger, Adam L.; Prenni, Jessica; Janis, Gregory C.; Corcoran, Henry; Snow, Nicholas H.; Chopra, Shilpi; Dhandapani, Ramkumar; Tawfall, Amanda; Sumner, Lloyd W.; Boswell, Paul G.

2014-01-01

Gas chromatography-mass spectrometry (GC-MS) is a primary tool used to identify compounds in complex samples. Both mass spectra and GC retention times are matched to those of standards, but it is often impractical to have standards on hand for every compound of interest, so we must rely on shared databases of MS data and GC retention information. Unfortunately, retention databases (e.g. linear retention index libraries) are experimentally restrictive, notoriously unreliable, and strongly instrument dependent, relegating GC retention information to a minor, often negligible role in compound identification despite its potential power. A new methodology called “retention projection” has great potential to overcome the limitations of shared chromatographic databases. In this work, we tested the reliability of the methodology in five independent laboratories. We found that even when each lab ran nominally the same method, the methodology was 3-fold more accurate than retention indexing because it properly accounted for unintentional differences between the GC-MS systems. When the labs used different methods of their own choosing, retention projections were 4- to 165-fold more accurate. More importantly, the distribution of error in the retention projections was predictable across different methods and labs, thus enabling automatic calculation of retention time tolerance windows. Tolerance windows at 99% confidence were generally narrower than those widely used even when physical standards are on hand to measure their retention. With its high accuracy and reliability, the new retention projection methodology makes GC retention a reliable, precise tool for compound identification, even when standards are not available to the user. PMID:24205931
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

PubMed Central

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-01-01

Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25838465
Accurate prediction of retention in hydrophilic interaction chromatography by back calculation of high pressure liquid chromatography gradient profiles.

PubMed

Wang, Nu; Boswell, Paul G

2017-10-20

Gradient retention times are difficult to project from the underlying retention factor (k) vs. solvent composition (φ) relationships. A major reason for this difficulty is that gradients produced by HPLC pumps are imperfect - gradient delay, gradient dispersion, and solvent mis-proportioning are all difficult to account for in calculations. However, we recently showed that a gradient "back-calculation" methodology can measure these imperfections and take them into account. In RPLC, when the back-calculation methodology was used, error in projected gradient retention times is as low as could be expected based on repeatability in the k vs. φ relationships. HILIC, however, presents a new challenge: the selectivity of HILIC columns drift strongly over time. Retention is repeatable in short time, but selectivity frequently drifts over the course of weeks. In this study, we set out to understand if the issue of selectivity drift can be avoid by doing our experiments quickly, and if there any other factors that make it difficult to predict gradient retention times from isocratic k vs. φ relationships when gradient imperfections are taken into account with the back-calculation methodology. While in past reports, the accuracy of retention projections was >5%, the back-calculation methodology brought our error down to ∼1%. This result was 6-43 times more accurate than projections made using ideal gradients and 3-5 times more accurate than the same retention projections made using offset gradients (i.e., gradients that only took gradient delay into account). Still, the error remained higher in our HILIC projections than in RPLC. Based on the shape of the back-calculated gradients, we suspect the higher error is a result of prominent gradient distortion caused by strong, preferential water uptake from the mobile phase into the stationary phase during the gradient - a factor our model did not properly take into account. It appears that, at least with the stationary phase we used, column distortion is an important factor to take into account in retention projection in HILIC that is not usually important in RPLC. Copyright © 2017 Elsevier B.V. All rights reserved.
Stemming the Revolving Door: Teacher Retention and Attrition in Arctic Alaska Schools

ERIC Educational Resources Information Center

Kaden, Ute; Patterson, Philip P.; Healy, Joanne; Adams, Barbara L.

2016-01-01

Limited research is available concerning teacher retention and teacher attrition in Arctic Alaska. This paper reports survey research findings, which identify factors related to teacher retention and attrition in Alaskan Arctic Native communities. Teacher retention rates (2009-2013) vary widely over time showing no significant trends. Results…
Langmuirian blocking of irreversible colloid retention: analytical solution, moments, and setback distance

USDA-ARS?s Scientific Manuscript database

Soil and aquifer materials have a finite capacity for colloid 20 retention. Blocking of the limited number of available retention sites further decreases the rate of retention over time and enhances risks (e.g., pathogens or colloid associated contaminants) or benefits (e.g., remediation by microorg...
Retention time and flow patterns in Lake Marion, South Carolina, 1984

USGS Publications Warehouse

Patterson, G.G.; Harvey, R.M.

1995-01-01

In 1984, six dye tracer tests were made on Lake Marion to determine flow patterns and retention times under conditions of high and low flow. During the high-flow tests, with an average inflow of about 29,000 cubic feet per second, the approximate travel time through the lake for the peak tracer concentration was 14 days. The retention time was about 20 days. During the low-flow tests, with an average inflow of about 9,000 cubic feet per second, the approximate travel time was 41 days, and the retention time was about 60 days. The primary factors controlling movement of water in the lake are lake inflow and outflow. The tracer cloud moved consistently downstream, slowing as the lake widened. Flow patterns in most of the coves, and in some areas along the northeastern shore, are influenced more by tributary inflow than by factors attributable to water from the main body of the lake.
Uniaxially aligned electrospun cellulose acetate nanofibers for thin layer chromatographic screening of hydroquinone and retinoic acid adulterated in cosmetics.

PubMed

Tidjarat, Siripran; Winotapun, Weerapath; Opanasopit, Praneet; Ngawhirunpat, Tanasait; Rojanarata, Theerasak

2014-11-07

Uniaxially aligned cellulose acetate (CA) nanofibers were successfully fabricated by electrospinning and applied to use as stationary phase for thin layer chromatography. The control of alignment was achieved by using a drum collector rotating at a high speed of 6000 rpm. Spin time of 6h was used to produce the fiber thickness of about 10 μm which was adequate for good separation. Without any chemical modification after the electrospinning process, CA nanofibers could be readily devised for screening hydroquinone (HQ) and retinoic acid (RA) adulterated in cosmetics using the mobile phase consisting of 65:35:2.5 methanol/water/acetic acid. It was found that the separation run on the aligned nanofibers over a distance of 5 cm took less than 15 min which was two to three times faster than that on the non-aligned ones. On the aligned nanofibers, the masses of HQ and RA which could be visualized were 10 and 25 ng, respectively, which were two times lower than those on the non-aligned CA fibers and five times lower than those on conventional silica plates due to the appearance of darker and sharper of spots on the aligned nanofibers. Furthermore, the proposed method efficiently resolved HQ from RA and ingredients commonly found in cosmetic creams. Due to the satisfactory analytical performance, facile and inexpensive production process, uniaxially aligned electrospun CA nanofibers are promising alternative media for planar chromatography. Copyright © 2014 Elsevier B.V. All rights reserved.
Survival Analysis of Faculty Retention and Promotion in the Social Sciences by Gender

PubMed Central

Varbanov, Roumen A.; Hoh, Yee Shwen; Knisley, Margaret L.; Holmes, Mary Alice

2015-01-01

Background Recruitment and retention of talent is central to the research performance of universities. Existing research shows that, while men are more likely than women to be promoted at the different stages of the academic career, no such difference is found when it comes to faculty retention rates. Current research on faculty retention, however, focuses on careers in science, technology, engineering, and mathematics (STEM). We extend this line of inquiry to the social sciences. Methods We follow 2,218 tenure-track assistant professors hired since 1990 in seven social science disciplines at nineteen U.S. universities from time of hire to time of departure. We also track their time to promotion to associate and full professor. Using survival analysis, we examine gender differences in time to departure and time to promotion. Our methods account for censoring and unobserved heterogeneity, as well as effect heterogeneity across disciplines and cohorts. Results We find no statistically significant differences between genders in faculty retention. However, we do find that men are more likely to be granted tenure than women. When it comes to promotion to full professor, the results are less conclusive, as the effect of gender is sensitive to model specification. Conclusions The results corroborate previous findings about gender patterns in faculty retention and promotion. They suggest that advances have been made when it comes to gender equality in retention and promotion, but important differences still persist. PMID:26580565
Quantitative structure-retention relationship models for the prediction of the reversed-phase HPLC gradient retention based on the heuristic method and support vector machine.

PubMed

Du, Hongying; Wang, Jie; Yao, Xiaojun; Hu, Zhide

2009-01-01

The heuristic method (HM) and support vector machine (SVM) were used to construct quantitative structure-retention relationship models by a series of compounds to predict the gradient retention times of reversed-phase high-performance liquid chromatography (HPLC) in three different columns. The aims of this investigation were to predict the retention times of multifarious compounds, to find the main properties of the three columns, and to indicate the theory of separation procedures. In our method, we correlated the retention times of many diverse structural analytes in three columns (Symmetry C18, Chromolith, and SG-MIX) with their representative molecular descriptors, calculated from the molecular structures alone. HM was used to select the most important molecular descriptors and build linear regression models. Furthermore, non-linear regression models were built using the SVM method; the performance of the SVM models were better than that of the HM models, and the prediction results were in good agreement with the experimental values. This paper could give some insights into the factors that were likely to govern the gradient retention process of the three investigated HPLC columns, which could theoretically supervise the practical experiment.
Predicting the chromatographic retention of polymers: poly(methyl methacrylate)s and polyacryate blends.

PubMed

Bashir, Mubasher A; Radke, Wolfgang

2007-09-07

The suitability of a retention model especially designed for polymers is investigated to describe and predict the chromatographic retention behavior of poly(methyl methacrylate)s as a function of mobile phase composition and gradient steepness. It is found that three simple yet rationally chosen chromatographic experiments suffice to extract the analyte specific model parameters necessary to calculate the retention volumes. This allows predicting accurate retention volumes based on a minimum number of initial experiments. Therefore, methods for polymer separations can be developed in relatively short time. The suitability of the virtual chromatography approach to predict the separation of polymer blend is demonstrated for the first time using a blend of different polyacrylates.

A biologically relevant method for considering patterns of oceanic retention in the Southern Ocean

NASA Astrophysics Data System (ADS)

Mori, Mao; Corney, Stuart P.; Melbourne-Thomas, Jessica; Klocker, Andreas; Sumner, Michael; Constable, Andrew

2017-12-01

Many marine species have planktonic forms - either during a larval stage or throughout their lifecycle - that move passively or are strongly influenced by ocean currents. Understanding these patterns of movement is important for informing marine ecosystem management and for understanding ecological processes generally. Retention of biological particles in a particular area due to ocean currents has received less attention than transport pathways, particularly for the Southern Ocean. We present a method for modelling retention time, based on the half-life for particles in a particular region, that is relevant for biological processes. This method uses geostrophic velocities at the ocean surface, derived from 23 years of satellite altimetry data (1993-2016), to simulate the advection of passive particles during the Southern Hemisphere summer season (from December to March). We assess spatial patterns in the retention time of passive particles and evaluate the processes affecting these patterns for the Indian sector of the Southern Ocean. Our results indicate that the distribution of retention time is related to bathymetric features and the resulting ocean dynamics. Our analysis also reveals a moderate level of consistency between spatial patterns of retention time and observations of Antarctic krill (Euphausia superba) distribution.
Keeping the wisdom at work.

PubMed

Simons, Sherri Lee

2007-01-01

There is a looming shortage of nurses with a diminishing pool of talent to staff the nation's NICUs. One critical strategy is to retain the talent and experience base of the older nurse. The replacement of experienced nurses is very costly to the unit and negatively impacts quality of care, patient safety, productivity, and unit cohesion. Older nurses can, do, and will make choices about where they work. Organizations have a responsibility to respond to their needs and align strategies aimed at their retention. Understanding the needs of older nurses will enable managers to better retain the staff they lead.
Remediation of bromate-contaminated groundwater in an ex situ fixed-film bioreactor.

PubMed

Butler, R; Ehrenberg, S; Godley, A R; Lake, R; Lytton, L; Cartmell, E

2006-07-31

Use of a pilot-scale fixed-film bioreactor was investigated for remediation of bromate contamination within groundwater. Bromate reduction with stoichiometric production of bromide was observed, providing supporting evidence for complete reduction of bromate with no production of stable intermediates. Reduction of 87-90% bromate from an influent concentration of 1.1 mg L(-1) was observed with retention times of 40-80 h. Lower retention times led to decreases in bromate reduction capability, with 11.5% removal at a 10 h retention time. Nitrate reduction of 76-99% from a 30.7 mg L(-1) as NO(3)(-) influent was observed at retention times of 10-80 h, although an increase in nitrite production to 2.7 mg L(-1) occurred with a 10 h retention time. Backwashing was not required, with the large plastic packing media able to accommodate biomass accumulation without decreases in operational efficiency. This study has provided proof of concept and demonstrated the potential of biological bromate reduction by fixed-film processes for remediation of a bromate contaminated groundwater source.
SU-F-J-44: Development of a Room Laser Based Real-Time Alignment Monitoring System Using An Array of Photodiodes

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

Noh, Y; Kim, T; Kang, S

2016-06-15

Purpose: To develop a real-time alignment monitoring system (RAMS) to compensate for the limitations of the conventional room laser based alignment system, and to verify the feasibility of the RAMS. Methods: The RAMS was composed of a room laser sensing array (RLSA), an analog-todigital converter, and a control PC. In the RLSA, seven photodiodes (each in 1 mm width) are arranged in a pattern that the RAMS provides alignment in 1 mm resolution. It works based on detecting laser light aligned on one of photodiodes. When misaligned, the laser would match with different photodiode(s) giving signal at unexpected location. Thus,more » how much displaced can be determined. To verify the reproducibility of the system with respect to time as well as repeated set-ups, temporal reproducibility and repeatability test was conducted. The accuracy of the system was tested by obtaining detection signals with varying laser-match positions. Results: The signal of the RAMS was found to be stable with respect to time. The repeatability test resulted in a maximum coefficient of variance of 1.14%, suggesting that the signal of the RAMS was stable over repeated set-ups. In the accuracy test, signals between when the laser was aligned and notaligned with any of sensors could be distinguished by signal intensity. The signals of not-aligned sensors were always below 75% of the signal of the aligned sensor. It was confirmed that the system could detect 1 mm of movement by monitoring the pattern of signals, and could observe the movement of the system in real-time. Conclusion: We developed a room laser based alignment monitoring system. The feasibility test verified that the system is capable of quantitative alignment monitoring in real time. The system is relatively simple, not expensive, and considered to be easily incorporated into conventional room laser systems for real-time alignment monitoring. This research was supported by the Mid-career Researcher Program through NRF funded by the Ministry of Science, ICT & Future Planning of Korea (NRF-2014R1A2A1A10050270) and by the Radiation Technology R&D program through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning (No. 2013M2A2A7038291)« less
Total knee arthroplasty with a computer-navigated saw: a pilot study.

PubMed

Garvin, Kevin L; Barrera, Andres; Mahoney, Craig R; Hartman, Curtis W; Haider, Hani

2013-01-01

Computer-aided surgery aims to improve implant alignment in TKA but has only been adopted by a minority for routine use. A novel approach, navigated freehand bone cutting (NFC), is intended to achieve wider acceptance by eliminating the need for cumbersome, implant-specific mechanical jigs and avoiding the expense of navigation. We determined cutting time, surface quality, implant fit, and implant alignment after NFC of synthetic femoral specimens and the feasibility and alignment of a complete TKA performed with NFC technology in cadaveric specimens. Seven surgeons prepared six synthetic femoral specimens each, using our custom NFC system. Cutting times, quality of bone cuts, and implant fit and alignment were assessed quantitatively by CT surface scanning and computational measurements. Additionally, a single surgeon performed a complete TKA on two cadaveric specimens using the NFC system, with cutting time and implant alignment analyzed through plain radiographs and CT. For the synthetic specimens, femoral coronal alignment was within ± 2° of neutral in 94% of the specimens. Sagittal alignment was within 0° to 5° of flexion in all specimens. Rotation was within ± 1° of the epicondylar axis in 97% of the specimens. The mean time to make cuts improved from 13 minutes for the first specimen to 9 minutes for the fourth specimen. TKA was performed in two cadaveric specimens without complications and implants were well aligned. TKA is feasible with NFC, which eliminates the need for implant-specific instruments. We observed a fast learning curve. NFC has the potential to improve TKA alignment, reduce operative time, and reduce the number of instruments in surgery. Fewer instruments and less sterilization could reduce costs associated with TKA.
Precision wood particle feedstocks

DOEpatents

Dooley, James H; Lanning, David N

2013-07-30

Wood particles having fibers aligned in a grain, wherein: the wood particles are characterized by a length dimension (L) aligned substantially parallel to the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L; the L.times.H dimensions define two side surfaces characterized by substantially intact longitudinally arrayed fibers; the W.times.H dimensions define two cross-grain end surfaces characterized individually as aligned either normal to the grain or oblique to the grain; the L.times.W dimensions define two substantially parallel top and bottom surfaces; and, a majority of the W.times.H surfaces in the mixture of wood particles have end checking.
A novel approach to multiple sequence alignment using hadoop data grids.

PubMed

Sudha Sadasivam, G; Baktavatchalam, G

2010-01-01

Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.
28 CFR 345.67 - Retention of benefits.

Code of Federal Regulations, 2010 CFR

2010-07-01

... INDUSTRIES (FPI) INMATE WORK PROGRAMS Inmate Pay and Benefits § 345.67 Retention of benefits. (a) Job retention. Ordinarily, when an inmate is absent from the job for a significant period of time, the SOI will... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Retention of benefits. 345.67 Section 345...
The influence of decreased hydraulic retention time on the performance and stability of co-digestion of sewage sludge with grease trap sludge and organic fraction of municipal waste.

PubMed

Grosser, Anna

2017-12-01

The effect of hydraulic retention time ranging from 12 to 20 d on process performance and stability was investigated in two anaerobic completely stirred tank reactors with a working liquid volume equal to 6 litres. The reactors were fed with mixtures containing (on volatile solids basis): 40% of sewage sludge, 30% of organic fraction of municipal waste and 30% of grease trap sludge. The change of hydraulic retention time did not significantly affect process stability. However, methane yields as well as volatile solids removal decreased from 0.54 to 0.47 l per kg of added volatile solids and 65% to 60% respectively, with the decrease of hydraulic retention time. Despite the fact that the best process performance was achieved for hydraulic retention time of 20 days, the obtained results showed that it is also possible to carry out the co-digestion process at shorter hydraulic retention times with good results. Furthermore, gas production rate as well as biogas production at the shortest hydraulic retention time were approximately 46% higher in comparison to results obtained at the longest hydraulic retention time. In this context, the proposed solution seems to be an interesting option, because it provides an unique opportunity for wastewater treatment plants to improve their profitability by enhancing energy recovery from sludge as well as full utilisation of the existing infrastructure and hence creates a new potential place for alternative treatment of organic industrial waste such as: fat-rich materials or food waste. However, implementation of the solution at wastewater treatment plants is still a big challenge and needs studies including identification of optimal digesting conditions, information about substrate pumping, inhibition thresholds and processing properties. Additionally, due to the characteristics of both co-substrates their introduction to the full-scale digester should be carefully planned due to a potential risk of overloading of the digester. For this reason, a gradual increase of the share of these wastes in the co-digestion mixture is highly recommended, because it will allow for the acclimatization of bacteria as well as prevent overloading. The results of this study show the importance of gradual acclimatization of microorganisms to the changing environmental conditions. It was found that concentration of long chain fatty acids in effluents increased with the reduction of hydraulic retention time, but this phenomenon did not significantly influence the performance and stability of the process probably due to changes hydraulic retention time being gradual. Although for palmitic acid a moderate negative correlation with volatile solids removal was observed. Copyright © 2017 Elsevier Ltd. All rights reserved.
Timing Calibration in PET Using a Time Alignment Probe

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

Moses, William W.; Thompson, Christopher J.

2006-05-05

We evaluate the Scanwell Time Alignment Probe for performing the timing calibration for the LBNL Prostate-Specific PET Camera. We calibrate the time delay correction factors for each detector module in the camera using two methods--using the Time Alignment Probe (which measures the time difference between the probe and each detector module) and using the conventional method (which measures the timing difference between all module-module combinations in the camera). These correction factors, which are quantized in 2 ns steps, are compared on a module-by-module basis. The values are in excellent agreement--of the 80 correction factors, 62 agree exactly, 17 differ bymore » 1 step, and 1 differs by 2 steps. We also measure on-time and off-time counting rates when the two sets of calibration factors are loaded into the camera and find that they agree within statistical error. We conclude that the performance using the Time Alignment Probe and conventional methods are equivalent.« less
Novel Technologies for Next Generation Memory

DTIC Science & Technology

2013-07-25

charge in the capacitor) eventually fades unless the capacitor charge is refreshed , so the memory cells must be periodically refreshed (rewritten). The...reliability issues (such as poor data retention problem and refresh failure). In order to avoid those problems, a 3-dimensional channel structure...states during the refresh cycle (retention time). When the channel length is scaled down, it is difficult to guarantee sufficient retention time
[Clinical investigation of formula feeding in extremely low birth weight infants].

PubMed

Liang, Zhiqiang; Lu, Lu; Zhou, Yingchun; Chen, Shangqin; Huang, Yumei; Lin, Zhenlang

2014-01-01

To explore the relationship between gastric retention and full enteral feeding during the course of feeding in extremely low birth weight (ELBW, birth weight <1 000 g) infants. A total of 43 ELBW infants were fed with formula according to the strategy for premature infants feeding of Canadian Society of Neonatology. The information such as gastric retention, the time they finish full enteral feeding and sucking spontaneously and complication were recorded. These infants had transition to full enteral feeding step by step since initiating formula feeding on the second day of life. The volume of gastric retention and the duration of gastric retention was analyzed with the time of attaining full enteral feeding and sucking spontaneously by linear regression. Forty-one infants finished the course, the remaining 2 infants got necrotizing enterocolitis (NEC) and were rescued by surgery. The incidence was 4.6%. In 18 infants full enteral feeding could not be initiated successfully on the second day of life, the incidence was 43.9%. The peak duration of gastric retention was the first week of feeding. The average time of attaining enteral feeding was (26.71 ± 12.24) days. The proportion of different residual contents was simlar, the major content was milky content after 3 weeks of feeding. The gastric retention time had a significant effect of on the time of attaining full enteral feeding (β = 1.045, P = 0.001) and sucking well (β = 0.787, P = 0.034) . The course of formula feeding ELBW infants to attaining full enteral feeding was a long period, in the early stage of formula feeding the occurrence of gastric retention was high; the amount of formula during the first week of feeding should be slowly increased as compared to the second week; the present strategy and aggressive strategy should be done 2 weeks later. The time of attaining full enteral feeding can be predicted by the duration of gastric retention.
Roll-to-Roll Continuous Manufacturing Multifunctional Nanocomposites by Electric-Field-Assisted "Z" Direction Alignment of Graphite Flakes in Poly(dimethylsiloxane).

PubMed

Guo, Yuanhao; Chen, Yuwei; Wang, Enmin; Cakmak, Miko

2017-01-11

A roll-to-roll continuous process was developed to manufacture large-scale multifunctional poly(dimethylsiloxane) (PDMS) films embedded with thickness direction ("Z" direction) aligned graphite nanoparticles by application of electric field. The kinetics of particle "Z" alignment and chain formation was studied by tracking the real-time change of optical light transmission through film thickness direction. Benefiting from the anisotropic structure of aligned particle chains, the electrical and thermal properties of the nanocomposites were dramatically enhanced through the thickness direction as compared to those of the nanocomposites containing the same particle loading without electrical field alignment. With 5 vol % graphite loading, 250 times higher electrical conductivity, 43 times higher dielectric permittivity, and 1.5 times higher thermal conductivity was achieved in the film thickness direction after the particles were aligned under electrical field. Moreover, the aligned nanocomposites with merely 2 vol % graphite particles exhibit even higher electric conductivity and dielectric permittivity than those of the nonaligned nanocomposites at random percolation threshold (10 vol % particles), as the "electric-field-directed" percolation threshold concentration is substantially decreased using this process. As the graphite loading increases to 20 vol %, the aligned nanocomposites exhibit thermal conductivity as high as 6.05 W/m·K, which is 35 times the thermal conductivity of pure matrix. This roll-to-roll electric field continuous process provides a simple, low-cost, and commercially viable method to manufacture multifunctional nanocomposites for applications as embedded capacitor, electromagnetic (EM) shielding, and thermal interface materials.
Enzyme activity assays within microstructured optical fibers enabled by automated alignment.

PubMed

Warren-Smith, Stephen C; Nie, Guiying; Schartner, Erik P; Salamonsen, Lois A; Monro, Tanya M

2012-12-01

A fluorescence-based enzyme activity assay has been demonstrated within a small-core microstructured optical fiber (MOF) for the first time. To achieve this, a reflection-based automated alignment system has been developed, which uses feedback and piezoelectric actuators to maintain optical alignment. The auto-alignment system provides optical stability for the time required to perform an activity assay. The chosen assay is based on the enzyme proprotein convertase 5/6 (PC6) and has important applications in women's health.
Oxygen plasma immersion ion implantation treatment to enhance data retention of tungsten nanocrystal nonvolatile memory

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

Wang, Jer-Chyi, E-mail: jcwang@mail.cgu.edu.tw; Chang, Wei-Cheng; Lai, Chao-Sung, E-mail: cslai@mail.cgu.edu.tw

Data retention characteristics of tungsten nanocrystal (W-NC) memory devices using an oxygen plasma immersion ion implantation (PIII) treatment are investigated. With an increase of oxygen PIII bias voltage and treatment time, the capacitance–voltage hysteresis memory window is increased but the data retention characteristics become degraded. High-resolution transmission electron microscopy images show that this poor data retention is a result of plasma damage on the tunneling oxide layer, which can be prevented by lowering the bias voltage to 7 kV. In addition, by using the elevated temperature retention measurement technique, the effective charge trapping level of the WO{sub 3} film surrounding themore » W-NCs can be extracted. This measurement reveals that a higher oxygen PIII bias voltage and treatment time induces more shallow traps within the WO{sub 3} film, degrading the retention behavior of the W-NC memory.« less
Student Perceptions of Support Services and the Influence of Targeted Interventions on Retention in Distance Education

ERIC Educational Resources Information Center

Nichols, Mark

2010-01-01

To improve student retention in distance education, Simpson suggested in 2003 that institutions analyse their own retention characteristics and "spot the leaks." In 2008 the Centre for Distance Learning at Laidlaw College, New Zealand, employed two part-time academic support coordinators in an effort to improve student retention and…
High Retention of Minority and International Faculty through a Formal Mentoring Program

ERIC Educational Resources Information Center

Phillips, Susan L.; Dennison, Susan T.; Davenport, Mark A.

2016-01-01

In these economic times, retention of new faculty, particularly minority and international faculty, is a high priority. In this study, retention of new faculty from 2006 to 2013 was compared for participants and nonparticipants in a formal mentoring program. Retention was 92% for participating faculty and 58% for nonparticipating new faculty. For…
GABA[subscript A] Receptors Determine the Temporal Dynamics of Memory Retention

ERIC Educational Resources Information Center

McNally, Gavan P.; Augustyn, Katarzyna A.; Richardson, Rick

2008-01-01

Four experiments studied the role of GABA[subscript A] receptors in the temporal dynamics of memory retention. Memory for an active avoidance response was a nonmonotonic function of the retention interval. When rats were tested shortly (2 min) or some time (24 h) after training, retention was excellent, but when they were tested at intermediate…
Drug Retention Times

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

Center for Human Reliability Studies

The purpose of this monograph is to provide information on drug retention times in the human body. The information provided is based on plausible illegal drug use activities that might be engaged in by a recreational drug user.
Transit ridership, reliability, and retention.

DOT National Transportation Integrated Search

2008-10-01

This project explores two major components that affect transit ridership: travel time reliability and rider : retention. It has been recognized that transit travel time reliability may have a significant impact on : attractiveness of transit to many ...

Optimizing the performance of a reactor by reducing the retention time and addition of glycerin for anaerobically digesting manure

PubMed Central

Timmerman, Maikel; Schuman, Els; van Eekert, Miriam; van Riel, Johan

2015-01-01

Anaerobic digestion of manure is a widely accepted technology for energy production. However, only a minimal portion of the manure production in the EU is anaerobically digested and occurs predominantly in codigestion plants. There is substantial potential for biogas plants that primarily operate on manure (>90%); however, the methane yields of manure are less compared to coproducts, which is one of the reasons for manure-based biogas plants often being economically non-viable. Therefore, it is essential to begin increasing the efficiency of these biogas plants. This study investigated the effect of decreasing retention time and introducing a moderate amount of glycerin on the biogas production as methods to improve efficiency. An experiment has been conducted with two different manure types in four biogas reactors. The results of the study demonstrated that, first, it was possible to decrease the retention time to 10–15 days; however, the effect on biogas production varied per manure type. Secondly, the biogas production almost triples at a retention time of 15.6 days with an addition of 4% glycerin. The relative production-enhancing effect of glycerin did not vary significantly with both manure types. However, the absolute production-enhancing effect of glycerin differed per manure type since the biogas production per gram VS differed per manure type. Thirdly, the positive effect of the glycerin input declines with shorter retention times. Therefore, the effect of glycerin addition depends on the manure type and retention time. PMID:25401272
Optimizing the performance of a reactor by reducing the retention time and addition of glycerin for anaerobically digesting manure.

PubMed

Timmerman, Maikel; Schuman, Els; van Eekert, Miriam; van Riel, Johan

2015-01-01

Anaerobic digestion of manure is a widely accepted technology for energy production. However, only a minimal portion of the manure production in the EU is anaerobically digested and occurs predominantly in codigestion plants. There is substantial potential for biogas plants that primarily operate on manure (>90%); however, the methane yields of manure are less compared to coproducts, which is one of the reasons for manure-based biogas plants often being economically non-viable. Therefore, it is essential to begin increasing the efficiency of these biogas plants. This study investigated the effect of decreasing retention time and introducing a moderate amount of glycerin on the biogas production as methods to improve efficiency. An experiment has been conducted with two different manure types in four biogas reactors. The results of the study demonstrated that, first, it was possible to decrease the retention time to 10-15 days; however, the effect on biogas production varied per manure type. Secondly, the biogas production almost triples at a retention time of 15.6 days with an addition of 4% glycerin. The relative production-enhancing effect of glycerin did not vary significantly with both manure types. However, the absolute production-enhancing effect of glycerin differed per manure type since the biogas production per gram VS differed per manure type. Thirdly, the positive effect of the glycerin input declines with shorter retention times. Therefore, the effect of glycerin addition depends on the manure type and retention time.
Optical control of ground-state atomic orbital alignment: Cl(2P3/2) atoms from HCl(v=2,J=1) photodissociation.

PubMed

Sofikitis, Dimitris; Rubio-Lago, Luis; Martin, Marion R; Ankeny Brown, Davida J; Bartlett, Nathaniel C-M; Alexander, Andrew J; Zare, Richard N; Rakitzis, T Peter

2007-10-14

H(35)Cl(v=0,J=0) molecules in a supersonic expansion were excited to the H(35)Cl(v=2,J=1,M=0) state with linearly polarized laser pulses at about 1.7 microm. These rotationally aligned J=1 molecules were then selectively photodissociated with a linearly polarized laser pulse at 220 nm after a time delay, and the velocity-dependent alignment of the (35)Cl((2)P(32)) photofragments was measured using 2+1 REMPI and time-of-flight mass spectrometry. The (35)Cl((2)P(32)) atoms are aligned by two mechanisms: (1) the time-dependent transfer of rotational polarization of the H(35)Cl(v=2,J=1,M=0) molecule to the (35)Cl((2)P(32)) nuclear spin [which is conserved during the photodissociation and thus contributes to the total (35)Cl((2)P(32)) photofragment atomic polarization] and (2) the alignment of the (35)Cl((2)P(32)) electronic polarization resulting from the photoexcitation and dissociation process. The total alignment of the (35)Cl((2)P(32)) photofragments from these two mechanisms was found to vary as a function of time delay between the excitation and the photolysis laser pulses, in agreement with theoretical predictions. We show that the alignment of the ground-state (35)Cl((2)P(32)) atoms, with respect to the photodissociation recoil direction, can be controlled optically. Potential applications include the study of alignment-dependent collision effects.
Family physician clinical compensation in an academic environment: moving away from the relative value unit

PubMed Central

Lochner, Jennifer; Trowbridge, Elizabeth; Kamnetz, Sandra; Pandhi, Nancy

2016-01-01

Background and Objectives Primary care physician compensation structures have remained largely volume-based, lagging behind changes in reimbursement that increasingly include population approaches such as capitation, bundled payments, and care management fees. We describe a population health-based physician compensation plan developed for two departmental family medicine faculty groups (residency teaching clinic faculty and community clinic faculty) along with outcomes before and after the plan’s implementation. Methods An observational study was conducted. A pre-post email survey assessed satisfaction with the plan, salary, and salary equity. Physician retention, panel size, and relative value unit (RVU) productivity metrics also were assessed before and after the plan’s implementation. Results Before implementation of the new plan, 18% of residency faculty and 33% of community faculty were satisfied or very satisfied with compensation structure. After implementation, those numbers rose to 47% for residency physicians and 74% for community physicians (p<0.01). Satisfaction with the amount of compensation also rose from 33% to 68% for residency faculty and from 26% to 87% for community faculty (p<0.01). For both groups, panel size per clinical full-time equivalent increased and RVUs moved closer to national benchmarks. RVUs decreased for residency faculty and increased for community faculty. Conclusions Aligning a compensation plan with population health delivery by moving rewards away from RVU productivity and towards panel management resulted in improved physician satisfaction and retention, as well as larger panel sizes. RVU changes were less predictable. Physician compensation is an important component of care model redesign that emphasizes population health. PMID:27272423
Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series

PubMed Central

2011-01-01

Background Comparing biological time series data across different conditions, or different specimens, is a common but still challenging task. Algorithms aligning two time series represent a valuable tool for such comparisons. While many powerful computation tools for time series alignment have been developed, they do not provide significance estimates for time shift measurements. Results Here, we present an extended version of the original DTW algorithm that allows us to determine the significance of time shift estimates in time series alignments, the DTW-Significance (DTW-S) algorithm. The DTW-S combines important properties of the original algorithm and other published time series alignment tools: DTW-S calculates the optimal alignment for each time point of each gene, it uses interpolated time points for time shift estimation, and it does not require alignment of the time-series end points. As a new feature, we implement a simulation procedure based on parameters estimated from real time series data, on a series-by-series basis, allowing us to determine the false positive rate (FPR) and the significance of the estimated time shift values. We assess the performance of our method using simulation data and real expression time series from two published primate brain expression datasets. Our results show that this method can provide accurate and robust time shift estimates for each time point on a gene-by-gene basis. Using these estimates, we are able to uncover novel features of the biological processes underlying human brain development and maturation. Conclusions The DTW-S provides a convenient tool for calculating accurate and robust time shift estimates at each time point for each gene, based on time series data. The estimates can be used to uncover novel biological features of the system being studied. The DTW-S is freely available as an R package TimeShift at http://www.picb.ac.cn/Comparative/data.html. PMID:21851598
Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series.

PubMed

Yuan, Yuan; Chen, Yi-Ping Phoebe; Ni, Shengyu; Xu, Augix Guohua; Tang, Lin; Vingron, Martin; Somel, Mehmet; Khaitovich, Philipp

2011-08-18

Comparing biological time series data across different conditions, or different specimens, is a common but still challenging task. Algorithms aligning two time series represent a valuable tool for such comparisons. While many powerful computation tools for time series alignment have been developed, they do not provide significance estimates for time shift measurements. Here, we present an extended version of the original DTW algorithm that allows us to determine the significance of time shift estimates in time series alignments, the DTW-Significance (DTW-S) algorithm. The DTW-S combines important properties of the original algorithm and other published time series alignment tools: DTW-S calculates the optimal alignment for each time point of each gene, it uses interpolated time points for time shift estimation, and it does not require alignment of the time-series end points. As a new feature, we implement a simulation procedure based on parameters estimated from real time series data, on a series-by-series basis, allowing us to determine the false positive rate (FPR) and the significance of the estimated time shift values. We assess the performance of our method using simulation data and real expression time series from two published primate brain expression datasets. Our results show that this method can provide accurate and robust time shift estimates for each time point on a gene-by-gene basis. Using these estimates, we are able to uncover novel features of the biological processes underlying human brain development and maturation. The DTW-S provides a convenient tool for calculating accurate and robust time shift estimates at each time point for each gene, based on time series data. The estimates can be used to uncover novel biological features of the system being studied. The DTW-S is freely available as an R package TimeShift at http://www.picb.ac.cn/Comparative/data.html.
Improving Retention and Enrollment Forecasting in Part-Time Programs

ERIC Educational Resources Information Center

Shapiro, Joel; Bray, Christopher

2011-01-01

This article describes a model that can be used to analyze student enrollment data and can give insights for improving retention of part-time students and refining institutional budgeting and planning efforts. Adult higher-education programs are often challenged in that part-time students take courses less reliably than full-time students. For…
Retention of Implicit Sequence Learning in Persons who Stutter and Persons with Parkinson's Disease

PubMed Central

Smits-Bandstra, Sarah; Gracco, Vincent

2014-01-01

This study investigated the retention of implicit sequence learning in 14 persons with Parkinson's disease (PPD), 14 persons who stutter (PWS) and 14 control participants. Participants completed a nonsense syllable serial reaction time task in a 120-minute session. Participants named aloud four syllables in response to four visual stimuli. The syllables formed a repeating 8-item sequence not made known to participants. After one week, participants completed a 60-minute retention session that included an explicit learning questionnaire and a sequence generation task. PPD showed retention of general learning equivalent to controls but PWS's reaction times were significantly slower on early trials of the retention test relative to other groups. Controls showed implicit learning during the initial session that was retained on the retention test. In contrast, PPD and PWS did not demonstrate significant implicit learning until the retention test suggesting intact, but delayed, learning and retention of implicit sequencing skills. All groups demonstrated similar limited explicit sequence knowledge. Performance differences between PWS and PPD relative to controls during the initial session and on early retention trials indicated possible dysfunction of the cortico-striato-thalamo-cortical loop. The etiological implications for stuttering, and clinical implications for both populations, of this dysfunction are discussed. PMID:23844763
2.5-Year-Olds' Retention and Generalization of Novel Words across Short and Long Delays

ERIC Educational Resources Information Center

Wojcik, Erica H.

2017-01-01

Two experiments investigated two-year-olds' retention and generalization of novel words across short and long time delays. Specifically, retention of newly learned words and generalization to novel exemplars or novel contexts were tested 1 min or 1 week after learning. Experiment 1 revealed successful retention as well as successful generalization…
Retention of Esperanto Is Affected by Delay-Interval Task and Item Closure: A Partial Resolution of the Delay-Retention Effect

ERIC Educational Resources Information Center

Brosvic, Gary M.; Epstein, Michael L.; Dihoff, Roberta E.; Cook, Michael L.

2006-01-01

The present studies were undertaken to examine the effects of manipulating delay-interval task (Study 1) and timing of feedback (Study 2) on acquisition and retention. Participants completed a 100-item cumulative final examination, which included 50 items from each laboratory examination, plus 50 entirely new items. Acquisition and retention were…
SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

PubMed

Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

2015-01-01

In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.
Knowledge retention after an online tutorial: a randomized educational experiment among resident physicians.

PubMed

Bell, Douglas S; Harless, Charles E; Higa, Jerilyn K; Bjork, Elizabeth L; Bjork, Robert A; Bazargan, Mohsen; Mangione, Carol M

2008-08-01

The time course of physicians' knowledge retention after learning activities has not been well characterized. Understanding the time course of retention is critical to optimizing the reinforcement of knowledge. Educational follow-up experiment with knowledge retention measured at 1 of 6 randomly assigned time intervals (0-55 days) after an online tutorial covering 2 American Diabetes Association guidelines. Internal and family medicine residents. Multiple-choice knowledge tests, subject characteristics including critical appraisal skills, and learner satisfaction. Of 197 residents invited, 91 (46%) completed the tutorial and were randomized; of these, 87 (96%) provided complete follow-up data. Ninety-two percent of the subjects rated the tutorial as "very good" or "excellent." Mean knowledge scores increased from 50% before the tutorial to 76% among those tested immediately afterward. Score gains were only half as great at 3-8 days and no significant retention was measurable at 55 days. The shape of the retention curve corresponded with a 1/4-power transformation of the delay interval. In multivariate analyses, critical appraisal skills and participant age were associated with greater initial learning, but no participant characteristic significantly modified the rate of decline in retention. Education that appears successful from immediate posttests and learner evaluations can result in knowledge that is mostly lost to recall over the ensuing days and weeks. To achieve longer-term retention, physicians should review or otherwise reinforce new learning after as little as 1 week.
How to improve patient retention in an antiretroviral treatment program in Ethiopia: a mixed-methods study

PubMed Central

2014-01-01

Background Patient retention, defined as continuous engagement of patients in care, is one of the crucial indicators for monitoring and evaluating the performance of antiretroviral treatment (ART) programs. It has been identified that suboptimal patient retention in care is one of the challenges of ART programs in many settings. ART programs have, therefore, been striving hard to identify and implement interventions that improve their suboptimal levels of retention. The objective of this study was to develop a framework for improving patient retention in care based on interventions implemented in health facilities that have achieved higher levels of retention in care. Methods A mixed-methods study, based on the positive deviance approach, was conducted in Ethiopia in 2011/12. Quantitative data were collected to estimate and compare the levels of retention in care in nine health facilities. Key informant interviews and focus group discussions were conducted to identify a package of interventions implemented in the health facilities with relatively higher or improving levels of retention. Results Retention in care in the Ethiopian ART program was found to be variable across health facilities. Among hospitals, the poorest performer had 0.46 (0.35, 0.60) times less retention than the reference; among health centers, the poorest performers had 0.44 (0.28, 0.70) times less retention than the reference. Health facilities with higher and improving patient retention were found to implement a comprehensive package of interventions: (1) retention promoting activities by health facilities, (2) retention promoting activities by community-based organizations, (3) coordination of these activities by case manager(s), and (4) patient information systems by data clerk(s). On the contrary, such interventions were either poorly implemented or did not exist in health facilities with lower retention in care. A framework to improve retention in care was developed based on the evidence found by applying the positive deviance approach. Conclusion A framework for improving retention in care of patients on ART was developed. We recommend that health facilities implement the framework, monitor and evaluate their levels of retention in care, and, if necessary, adapt the framework to their own contexts. PMID:24475889
Randomized Trial of a Health Coaching Intervention to Enhance Retention in Care: California Collaborative Treatment Group 594.

PubMed

Corado, Katya; Jain, Sonia; Morris, Sheldon; Dube, Michael P; Daar, Eric S; He, Feng; Aldous, Jeannette L; Sitapati, Amy; Haubrich, Richard; Milam, Joel; Karris, Maile Young

2018-05-03

Poor linkage, engagement and retention remain significant barriers in achieving HIV treatment goals in the US. HIV-infected persons entering or re-entering care across three Southern California academic HIV clinics, were randomized (1:1) to an Active, Linkage, Engagement, Retention and Treatment (ALERT) specialist for outreach and health coaching, or standard of care (SOC). The primary outcome of time to loss to follow up (LTFU) was compared using Cox proportional hazards regression modeling. No differences in the median time to LTFU (81.7 for ALERT versus 93.6 weeks for SOC; HR 1.27; p = 0.40), or time to ART initiation was observed (N = 116). Although, ALERT participants demonstrated worsening depressive symptomatology from baseline to week 48 compared to SOC (p = 0.02). The ALERT intervention did not improve engagement and retention in HIV care over SOC. Further studies are needed to determine how best to apply resources to improve retention and engagement.
Precision wood particle feedstocks with retained moisture contents of greater than 30% dry basis

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

Dooley, James H; Lanning, David N

Wood particles having fibers aligned in a grain, wherein: the wood particles are characterized by a length dimension (L) aligned substantially parallel to the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L; the L.times.H dimensions define two side surfaces characterized by substantially intact longitudinally arrayed fibers; the W.times.H dimensions define two cross-grain end surfaces characterized individually as aligned either normal to the grain or oblique to the grain; the L.times.W dimensions define two substantially parallel top and bottom surfaces; and, a majority of the W.times.H surfacesmore » in the mixture of wood particles have end checking.« less
Alignment of time-resolved data from high throughput experiments.

PubMed

Abidi, Nada; Franke, Raimo; Findeisen, Peter; Klawonn, Frank

2016-12-01

To better understand the dynamics of the underlying processes in cells, it is necessary to take measurements over a time course. Modern high-throughput technologies are often used for this purpose to measure the behavior of cell products like metabolites, peptides, proteins, [Formula: see text]RNA or mRNA at different points in time. Compared to classical time series, the number of time points is usually very limited and the measurements are taken at irregular time intervals. The main reasons for this are the costs of the experiments and the fact that the dynamic behavior usually shows a strong reaction and fast changes shortly after a stimulus and then slowly converges to a certain stable state. Another reason might simply be missing values. It is common to repeat the experiments and to have replicates in order to carry out a more reliable analysis. The ideal assumptions that the initial stimulus really started exactly at the same time for all replicates and that the replicates are perfectly synchronized are seldom satisfied. Therefore, there is a need to first adjust or align the time-resolved data before further analysis is carried out. Dynamic time warping (DTW) is considered as one of the common alignment techniques for time series data with equidistant time points. In this paper, we modified the DTW algorithm so that it can align sequences with measurements at different, non-equidistant time points with large gaps in between. This type of data is usually known as time-resolved data characterized by irregular time intervals between measurements as well as non-identical time points for different replicates. This new algorithm can be easily used to align time-resolved data from high-throughput experiments and to come across existing problems such as time scarcity and existing noise in the measurements. We propose a modified method of DTW to adapt requirements imposed by time-resolved data by use of monotone cubic interpolation splines. Our presented approach provides a nonlinear alignment of two sequences that neither need to have equi-distant time points nor measurements at identical time points. The proposed method is evaluated with artificial as well as real data. The software is available as an R package tra (Time-Resolved data Alignment) which is freely available at: http://public.ostfalia.de/klawonn/tra.zip .
Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

PubMed Central

Filichkin, Sergei A.; Hamilton, Michael; Dharmawardhana, Palitha D.; Singh, Sunil K.; Sullivan, Christopher; Ben-Hur, Asa; Reddy, Anireddy S. N.; Jaiswal, Pankaj

2018-01-01

Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns – a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super stress-responsive DIR events showed persisting fluctuations in the degree of IR across all treatments and tissue types. To investigate coordinated dynamics of intron-containing transcripts in the study we quantified absolute copy number of isoforms of two conserved transcription factors (TFs) using Droplet Digital PCR. This case study suggests that stress treatments can be associated with coordinated switches in relative ratios between fully spliced and intron-retaining isoforms and may play a role in adjusting transcriptome to abiotic stresses. PMID:29483921
Patient and Nurse Experiences in a Rural Chronic Disease Management Program: A Qualitative Evaluation.

PubMed

Davisson, Erica A; Swanson, Elizabeth A

Rural status confounds chronic disease self-management. The purpose of this qualitative, descriptive study was to evaluate the nurse-led "Living Well" chronic disease management program reporting patient recruitment and retention issues since program initiation in 2013. The Chronic Care Model (CCM) was the guiding framework used to reinforce that interdisciplinary teams must have productive patient interactions for their program(s) to be sustainable. A rural, Midwest county clinic's chronic disease management program. Observations, interviews, and within- and across-case coding were used. Patients' responses were analyzed to identify (1) reasons for recruitment and retention problems and (2) program elements that were viewed as successful or needing improvement. A convenience sample of 6 rural, English-speaking adults (65 years or older, with no severe cognitive impairment) with at least one chronic condition was recruited and interviewed. Themes emerged related to nurse knowledge, availability, and value; peer support; overcoming barriers; adherence enhancement; and family/friends' involvement. Patients reported engagement in self-management activities because of program elements such as support groups and productive nurse-patient interactions. Interdisciplinary communication, commitment, and patient referral processes were identified as reasons for recruitment and retention issues. Findings substantiated that certain elements must be present and improved upon for future rural programs to be successful. Interdisciplinary communication may need to be improved to address recruitment and retention problems. It was clear from patient interviews that the nurse coordinators played a major role in patients' self-management adherence and overall satisfaction with the program. This is important to case management because results revealed the need for programs of this nature that incorporate the vital role of nurse coordinators and align with the CCM value of providing a supportive community health care resource for patients with chronic disease.
Retention in a Computer-based Outreach Intervention For Chronically Ill Rural Women

PubMed Central

Weinert, Clarann; Cudney, Shirley; Hill, Wade G.

2009-01-01

The study's purpose was to examine retention factors in a computer intervention with 158 chronically ill rural women. After a 22 week intervention, 18.9 percent of the women had dropped out. A Cox regression survival analysis was performed to assess the effects of selected covariates on retention. Reasons for dropping were tallied and categorized. Major reasons for dropping were: lack of time; decline in health status, and non-participation in study activities. Four covariates predicted survival time: level of computer skills, marital status, work outside of home, and impact of social events on participants' lives. Retention-enhancing strategies are suggested for implementation. PMID:18226760
Transfer Alignment Error Compensator Design Based on Robust State Estimation

NASA Astrophysics Data System (ADS)

Lyou, Joon; Lim, You-Chol

This paper examines the transfer alignment problem of the StrapDown Inertial Navigation System (SDINS), which is subject to the ship’s roll and pitch. Major error sources for velocity and attitude matching are lever arm effect, measurement time delay and ship-body flexure. To reduce these alignment errors, an error compensation method based on state augmentation and robust state estimation is devised. A linearized error model for the velocity and attitude matching transfer alignment system is derived first by linearizing the nonlinear measurement equation with respect to its time delay and dominant Y-axis flexure, and by augmenting the delay state and flexure state into conventional linear state equations. Then an H∞ filter is introduced to account for modeling uncertainties of time delay and the ship-body flexure. The simulation results show that this method considerably decreases azimuth alignment errors considerably.

Assessing Chemical Retention Process Controls in Ponds

NASA Astrophysics Data System (ADS)

Torgersen, T.; Branco, B.; John, B.

2002-05-01

Small ponds are a ubiquitous component of the landscape and have earned a reputation as effective chemical retention devices. The most common characterization of pond chemical retention is the retention coefficient, Ri= ([Ci]inflow-[Ci] outflow)/[Ci]inflow. However, this parameter varies widely in one pond with time and among ponds. We have re-evaluated literature reported (Borden et al., 1998) monthly average retention coefficients for two ponds in North Carolina. Employing a simple first order model that includes water residence time, the first order process responsible for species removal have been separated from the water residence time over which it acts. Assuming the rate constant for species removal is constant within the pond (arguable at least), the annual average rate constant for species removal is generated. Using the annual mean rate constant for species removal and monthly water residence times results in a significantly enhanced predictive capability for Davis Pond during most months of the year. Predictive ability remains poor in Davis Pond during winter/unstratified periods when internal loading of P and N results in low to negative chemical retention. Predictive ability for Piedmont Pond (which has numerous negative chemical retention periods) is improved but not to the same extent as Davis Pond. In Davis Pond, the rate constant for sediment removal (each month) is faster than the rate constant for water and explains the good predictability for sediment retention. However, the removal rate constant for P and N is slower than the removal rate constant for sediment (longer water column residence time for P,N than for sediment). Thus sedimentation is not an overall control on nutrient retention. Additionally, the removal rate constant for P is slower than for TOC (TOC is not the dominate removal process for P) and N is removed slower than P (different in pond controls). For Piedmont Pond, sediment removal rate constants are slower than the removal rate constant for water indicating significant sediment resuspension episodes. It appears that these sediment resuspension events are aperiodic and control the loading and the chemical retention capability of Piedmont Pond for N,P,TOC. These calculated rate constants reflect the differing internal loading processes for each component and suggest means and mechanisms for the use of ponds in water quality management.
Prediction of retention times in comprehensive two-dimensional gas chromatography using thermodynamic models.

PubMed

McGinitie, Teague M; Harynuk, James J

2012-09-14

A method was developed to accurately predict both the primary and secondary retention times for a series of alkanes, ketones and alcohols in a flow-modulated GC×GC system. This was accomplished through the use of a three-parameter thermodynamic model where ΔH, ΔS, and ΔC(p) for an analyte's interaction with the stationary phases in both dimensions are known. Coupling this thermodynamic model with a time summation calculation it was possible to accurately predict both (1)t(r) and (2)t(r) for all analytes. The model was able to predict retention times regardless of the temperature ramp used, with an average error of only 0.64% for (1)t(r) and an average error of only 2.22% for (2)t(r). The model shows promise for the accurate prediction of retention times in GC×GC for a wide range of compounds and is able to utilize data collected from 1D experiments. Copyright © 2012 Elsevier B.V. All rights reserved.
[The design of removable appliances for tooth movement and tooth migration].

PubMed

Voss, H

1989-06-01

Removable/functional appliance therapy can still be further expanded and developed. Retentive elements in the anterior region increase anchorage. Thereby, active forces can be utilised without anchorage loss. Functional appliances are indicated following extraction, to maximise on tooth migration. In first molar extraction cases, treatment with activators is relatively straightforward. When considering premolar extraction cases with possible need for extraction later of the third molars as well, then one should consider extraction of the first permanent molars. With correct use of the appliance, it is possible to optimally align the second molar teeth as well as favourably influencing the soft tissue profile.
Ambulatory Voice Biofeedback: Relative Frequency and Summary Feedback Effects on Performance and Retention of Reduced Vocal Intensity in the Daily Lives of Participants With Normal Voices

PubMed Central

Mehta, Daryush D.; Sternad, Dagmar; Petit, Robert; Hillman, Robert E.

2017-01-01

Purpose Ambulatory voice biofeedback has the potential to significantly improve voice therapy effectiveness by targeting carryover of desired behaviors outside the therapy session (i.e., retention). This study applies motor learning concepts (reduced frequency and delayed, summary feedback) that demonstrate increased retention to ambulatory voice monitoring for training nurses to talk softer during work hours. Method Forty-eight nurses with normal voices wore the Voice Health Monitor (Mehta, Zañartu, Feng, Cheyne, & Hillman, 2012) for 6 days: 3 baseline days, 1 biofeedback day, 1 short-term retention day, and 1 long-term retention day. Participants were block-randomized into 3 different biofeedback groups: 100%, 25%, and Summary. Performance was measured in terms of compliance time below a participant-specific vocal intensity threshold. Results All participants exhibited a significant increase in compliance time (Cohen's d = 4.5) during biofeedback days compared with baseline days. The Summary feedback group exhibited statistically smaller performance reduction during both short-term (d = 1.14) and long-term (d = 1.04) retention days compared with the 100% feedback group. Conclusions These findings suggest that modifications in feedback frequency and timing affect retention of a modified vocal behavior in daily life. Future work calls for studying the potential beneficial impact of ambulatory voice biofeedback in participants with behaviorally based voice disorders. PMID:28329366
A Comprehensive Strategy to Construct In-house Database for Accurate and Batch Identification of Small Molecular Metabolites.

PubMed

Zhao, Xinjie; Zeng, Zhongda; Chen, Aiming; Lu, Xin; Zhao, Chunxia; Hu, Chunxiu; Zhou, Lina; Liu, Xinyu; Wang, Xiaolin; Hou, Xiaoli; Ye, Yaorui; Xu, Guowang

2018-05-29

Identification of the metabolites is an essential step in metabolomics study to interpret regulatory mechanism of pathological and physiological processes. However, it is still a big headache in LC-MSn-based studies because of the complexity of mass spectrometry, chemical diversity of metabolites, and deficiency of standards database. In this work, a comprehensive strategy is developed for accurate and batch metabolite identification in non-targeted metabolomics studies. First, a well defined procedure was applied to generate reliable and standard LC-MS2 data including tR, MS1 and MS2 information at a standard operational procedure (SOP). An in-house database including about 2000 metabolites was constructed and used to identify the metabolites in non-targeted metabolic profiling by retention time calibration using internal standards, precursor ion alignment and ion fusion, auto-MS2 information extraction and selection, and database batch searching and scoring. As an application example, a pooled serum sample was analyzed to deliver the strategy, 202 metabolites were identified in the positive ion mode. It shows our strategy is useful for LC-MSn-based non-targeted metabolomics study.
Reproductive mode and the shifting arenas of evolutionary conflict.

PubMed

Furness, Andrew I; Morrison, Keenan R; Orr, Teri J; Arendt, Jeff D; Reznick, David N

2015-12-01

In sexually reproducing organisms, the genetic interests of individuals are not perfectly aligned. Conflicts among family members are prevalent since interactions involve the transfer of limited resources between interdependent players. Intrafamilial conflict has traditionally been considered along three major axes: between the sexes, between parents and offspring, and between siblings. In these interactions, conflict is expected over traits in which the resulting phenotypic value is determined by multiple family members who have only partially overlapping fitness optima. We focus on four major categories of animal reproductive mode (broadcast spawning, egg laying, live bearing, and live bearing with matrotrophy) and identify the shared phenotypes or traits over which conflict is expected, and then review the empirical literature for evidence of their occurrence. Major transitions among reproductive mode, such as a shift from external to internal fertilization, an increase in egg-retention time, modifications of embryos and mothers for nutrient transfer, the evolution of postnatal parental care, and increased interaction with the kin network, mark key shifts that both change and expand the arenas in which conflict is played out. © 2015 New York Academy of Sciences.
Non-volatile spin bistability based on ferromagnet-semiconductor quantum dot hybrid nanostructure

NASA Astrophysics Data System (ADS)

Semenov, Yuriy; Enaya, Hani; Zavada, John; Kim, Ki Wook

2008-03-01

Electrical manipulation of a memory cell based on bistability effect in a nanostructure consisting of a semiconductor quantum dot (QD) adjoining on opposite sides with a dielectric ferromagnetic layer (DFL) and a reservoir of itinerant holes is investigated theoretically. The operating principle is based on the interplay between the exchange field of the holes Bh acting on the magnetization vector of the DFL M perpendicular to structure plane and the anisotropy field Ba which aligns M along the plane. At low hole population of the QD (Bh<Ba), the subsequent M rotation will decrease the hole energy in the QD; hence the high hole population state is sustained (second stable state ``1'') under a fixed electro-chemical potential set by the reservoir even after bias is removed. The analysis of bit retention time of the proposed memory demonstrates the feasibility of the device with lateral QD size at least 30 nm under room temperature operation. Another advantage is the extremely small dissipative energy for Write/Erase operations.
Episodes of care: is emergency medicine ready?

PubMed

Wiler, Jennifer L; Beck, Dennis; Asplin, Brent R; Granovsky, Michael; Moorhead, John; Pilgrim, Randy; Schuur, Jeremiah D

2012-05-01

Optimizing resource use, eliminating waste, aligning provider incentives, reducing overall costs, and coordinating the delivery of quality care while improving outcomes have been major themes of health care reform initiatives. Recent legislation contains several provisions designed to move away from the current fee-for-service payment mechanism toward a model that reimburses providers for caring for a population of patients over time while shifting more financial risk to providers. In this article, we review current approaches to episode of care development and reimbursement. We describe the challenges of incorporating emergency medicine into the episode of care approach and the uncertain influence this delivery model will have on emergency medicine care, including quality outcomes. We discuss the limitations of the episode of care payment model for emergency services and advocate retention of the current fee-for-service payment model, as well as identify research gaps that, if addressed, could be used to inform future policy decisions of emergency medicine health policy leaders. We then describe a meaningful role for emergency medicine in an episode of care setting. Copyright © 2011. Published by Mosby, Inc.
An examination of undergraduate engineering students' stereotype of scientists and their career intentions

NASA Astrophysics Data System (ADS)

Stara, Michelle M.

The US Government Accountability Office (GAO) (2013) has acknowledged that additional graduates are needed in engineering and related STEM fields. However, the GAO has also noted that it is difficult to determine if the additional graduates will align with employer demand at the time of entry into the workforce. This research study attempts to examine undergraduate engineering students' perceptions of scientists and if they were related to students' intentions to pursue science by examining the constructs of Stereotypes of Scientists (SOS) and Career Intentions in Science (CIS). While results of data analysis were not significant, patterns were seen that provided valuable information with regard to the variability of undergraduate engineering students and the complexity of what goes into stereotype formation and career choice. As a practitioner, there were pertinent applications that could be implemented from the results of this and related studies. From the perspective of practitioners, the findings may be used to target recruitment, retention, and specific teaching strategies to increase enrollment and graduate numbers in the lesser known engineering and STEM fields.
Right time, right place: improving access to health service through effective retention and distribution of health workers

PubMed Central

2013-01-01

This editorial introduces the 'Right time, Right place: improving access to health service through effective retention and distribution of health workers’ thematic series. This series draws from studies in a range of countries and provides new insights into what can be done to improve access to health through more effective human resources policies, planning and management. The primary focus is on health workforce distribution and retention. PMID:24274820
Associations among hypothalamus-pituitary-adrenal axis function, novelty seeking, and retention in methadone maintenance therapy for heroin dependency.

PubMed

Lin, Shih-Hsien; Chen, Wei Tseng; Chen, Kao Chin; Lee, Sheng-Yu; Lee, I Hui; Chen, Po See; Yeh, Tzung Lieh; Lu, Ru-Band; Yang, Yen Kuang

2013-01-01

The efficacy of methadone maintenance therapy for heroin dependence is compromised by the low retention rate. Hypothalamus-pituitary-adrenal (HPA) axis function, which is associated with stress response, and novelty seeking (NS), a personality trait associated with low dopaminergic activity, may play roles in retention. We conducted a prospective study in which HPA axis function and NS were assessed by the dexamethasone suppression test and the Tridimensional Personality Questionnaire at baseline, respectively. The retention rate was assessed at the half- and 1-year points of methadone maintenance therapy. A low suppression rate of dexamethasone suppression test (D%) was associated with a high level of NS. A low D% was associated with half-year dropout, whereas a high level of NS was associated with 1-year dropout. Survival analysis confirmed that D% and NS were significant time-dependent covariates for retention. The findings showed that HPA axis function and NA were associated with retention at different time points.
Investing the effectiveness of retention performance in a non-volatile floating gate memory device with a core-shell structure of CdSe nanoparticles

NASA Astrophysics Data System (ADS)

Lee, Dong-Hoon; Kim, Jung-Min; Lim, Ki-Tae; Cho, Hyeong Jun; Bang, Jin Ho; Kim, Yong-Sang

2016-03-01

In this paper, we empirically investigate the retention performance of organic non-volatile floating gate memory devices with CdSe nanoparticles (NPs) as charge trapping elements. Core-structured CdSe NPs or core-shell-structured ZnS/CdSe NPs were mixed in PMMA and their performance in pentacene based device was compared. The NPs and self-organized thin tunneling PMMA inside the devices exhibited hysteresis by trapping hole during capacitance-voltage characterization. Despite of core-structured NPs showing a larger memory window, the retention time was too short to be adopted by an industry. By contrast core-shell structured NPs showed an improved retention time of >10000 seconds than core-structure NCs. Based on these results and the energy band structure, we propose the retention mechanism of each NPs. This investigation of retention performance provides a comparative and systematic study of the charging/discharging behaviors of NPs based memory devices. [Figure not available: see fulltext.
Fast 3-T MR-guided transrectal prostate biopsy using an in-room tablet device for needle guide alignment: a feasibility study.

PubMed

Overduin, Christiaan G; Heidkamp, Jan; Rothgang, Eva; Barentsz, Jelle O; de Lange, Frank; Fütterer, Jurgen J

2018-05-22

To assess the feasibility of adding a tablet device inside the scanner room to assist needle-guide alignment during magnetic resonance (MR)-guided transrectal prostate biopsy. Twenty patients with one cancer-suspicious region (CSR) with PI-RADS score ≥ 4 on diagnostic multiparametric MRI were prospectively enrolled. Two orthogonal scan planes of an MR fluoroscopy sequence (~3 images/s) were aligned to the CSR and needle-guide pivoting point. Targeting was achieved by manipulating the needle-guide under MR fluoroscopy feedback on the in-room tablet device. Technical feasibility and targeting success were assessed. Complications and biopsy procedure times were also recorded. Needle-guide alignment with the in-room tablet device was technically successful in all patients and allowed sampling after a single alignment step in 19/20 (95%) CSRs (median size 14 mm, range: 4-45). Biopsy cores contained cancer in 18/20 patients. There were no per-procedural or post-biopsy complications. Using the tablet device, the mean time to first biopsy was 5.8 ± 1.0 min and the mean total procedure time was 23.7 ± 4.1 min. Use of an in-room tablet device to assist needle-guide alignment was feasible and safe during MR-guided transrectal prostate biopsy. Initial experience indicates potential for procedure time reduction. • Performing MR-guided prostate biopsy using an in-room tablet device is feasible. • CSRs could be sampled after a single alignment step in 19/20 patients. • The mean procedure time for biopsy with the tablet device was 23.7 min.
Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

Kim, Changhoon; Tai, Chin-Hsien; Lee, Byungkook

2009-01-01

Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. Results RSE uses SE (Seed Extension) in its core, which is an algorithm that we reported recently for obtaining a sequence alignment from two superimposed structures. The RSE procedure was evaluated by comparing the correctly aligned fractions of residues before and after the refinement of the structure-based sequence alignments produced by popular programs. CE, DaliLite, FAST, LOCK2, MATRAS, MATT, TM-align, SHEBA and VAST were included in this analysis and the NCBI's CDD root node set was used as the reference alignments. RSE improved the average accuracy of sequence alignments for all programs tested when no shift error was allowed. The amount of improvement varied depending on the program. The average improvements were small for DaliLite and MATRAS but about 5% for CE and VAST. More substantial improvements have been seen in many individual cases. The additional computation times required for the refinements were negligible compared to the times taken by the structure alignment programs. Conclusion RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional iterative refinement procedures based on residue-level dynamic programming algorithm in many structure alignment programs. PMID:19589133
Assessing the statistical robustness of inter- and intra-basinal carbon isotope chemostratigraphic correlation

NASA Astrophysics Data System (ADS)

Hay, C.; Creveling, J. R.; Huybers, P. J.

2016-12-01

Excursions in the stable carbon isotopic composition of carbonate rocks (δ13Ccarb) can facilitate correlation of Precambrian and Phanerozoic sedimentary successions at a higher temporal resolution than radiometric and biostratigraphic frameworks typically afford. Within the bounds of litho- and biostratigraphic constraints, stratigraphers often correlate isotopic patterns between distant stratigraphic sections through visual alignment of local maxima and minima of isotopic values. The reproducibility of this method can prove challenging and, thus, evaluating the statistical robustness of intrabasinal composite carbon isotope curves, and global correlations to these reference curves, remains difficult. To assess the reproducibility of stratigraphic alignment of δ13Ccarb data, and correlations between carbon isotope excursions, we employ a numerical dynamic time warping methodology that stretches and squeezes the time axis of a record to obtain an optimal correlation (in a least-squares sense) between time-uncertain series of data. In particular, we assess various alignments between series of Early Cambrian δ13Ccarb data with respect to plausible matches. We first show that an alignment of these records obtained visually, and published previously, is broadly reproducible using dynamic time warping. Alternative alignments with similar goodness of fits are also obtainable, and their stratigraphic plausibility are discussed. This approach should be generalizable to an algorithm for the purposes of developing a library of plausible alignments between multiple time-uncertain stratigraphic records.
Continuous ethanol production from cheese whey fermentation by Candida pseudotropicalis

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

Ghaly, A.E.; El-Taweel, A.A.

1997-12-01

Three pilot-scale continuous mix reactors of 5-L volume each were used to study the effects of retention time (18--42 hours) and initial substrate concentration (50--150 g/L) on the cell yield, lactose consumption, and maximum ethanol concentration during continuous fermentation of cheese whey using the yeast Candida pseudotropicalis. A microaeration rate of 480 mL/min and a nutrient supplement (yeast extract) concentration of 0.1% vol/vol were used. The results indicated that the dissolved oxygen concentration, temperature, cell concentration, lactose utilization rate, and ethanol concentration were affected by hydraulic retention time and initial substrate concentration. The highest cell concentration of 5.46 g/L andmore » the highest ethanol concentration of 57.96 g/L (with a maximum ethanol yield of 99.6% from the theoretical yield) were achieved at the 42-hour hydraulic retention time and the 150 g/L initial substrate concentration, whereas the highest cell yield was observed at the 50 g/L initial substrate concentration and the 36-hour hydraulic retention time. Lactose utilizations of 98, 91, and 83% were obtained with 50, 100, and 150 g/L initial substrate concentrations at the 42-hour hydraulic retention time. A pH control system was found unnecessary.« less
Warp-averaging event-related potentials.

PubMed

Wang, K; Begleiter, H; Porjesz, B

2001-10-01

To align the repeated single trials of the event-related potential (ERP) in order to get an improved estimate of the ERP. A new implementation of the dynamic time warping is applied to compute a warp-average of the single trials. The trilinear modeling method is applied to filter the single trials prior to alignment. Alignment is based on normalized signals and their estimated derivatives. These features reduce the misalignment due to aligning the random alpha waves, explaining amplitude differences in latency differences, or the seemingly small amplitudes of some components. Simulations and applications to visually evoked potentials show significant improvement over some commonly used methods. The new implementation of the dynamic time warping can be used to align the major components (P1, N1, P2, N2, P3) of the repeated single trials. The average of the aligned single trials is an improved estimate of the ERP. This could lead to more accurate results in subsequent analysis.
Multiple DNA and protein sequence alignment on a workstation and a supercomputer.

PubMed

Tajima, K

1988-11-01

This paper describes a multiple alignment method using a workstation and supercomputer. The method is based on the alignment of a set of aligned sequences with the new sequence, and uses a recursive procedure of such alignment. The alignment is executed in a reasonable computation time on diverse levels from a workstation to a supercomputer, from the viewpoint of alignment results and computational speed by parallel processing. The application of the algorithm is illustrated by several examples of multiple alignment of 12 amino acid and DNA sequences of HIV (human immunodeficiency virus) env genes. Colour graphic programs on a workstation and parallel processing on a supercomputer are discussed.
Experimental designs for modeling retention patterns and separation efficiency in analysis of fatty acid methyl esters by gas chromatography-mass spectrometry.

PubMed

Skartland, Liv Kjersti; Mjøs, Svein A; Grung, Bjørn

2011-09-23

The retention behavior of components analyzed by chromatography varies with instrumental settings. Being able to predict how changes in these settings alter the elution pattern is useful, both with regards to component identification, as well as with regards to optimization of the chromatographic system. In this work, it is shown how experimental designs can be used for this purpose. Different experimental designs for response surface modeling of the separation of fatty acid methyl esters (FAME) as function of chromatographic conditions in GC have been evaluated. Full factorial, central composite, Doehlert and Box-Behnken designs were applied. A mixture of 38 FAMEs was separated on a polar cyanopropyl substituted polysilphenylene-siloxane phase capillary column. The temperature gradient, the start temperature of the gradient, and the carrier gas velocity were varied in the experiments. The modeled responses, as functions of chromatographic conditions, were retention time, retention indices, peak widths, separation efficiency and resolution between selected peak pairs. The designs that allowed inclusion of quadratic terms among the predictors performed significantly better than factorial design. Box-Behnken design provided the best results for prediction of retention, but the differences between the central composite, Doehlert and Box-Behnken designs were small. Retention indices could be modeled with much better accuracy than retention times. However, because the errors of predicted tR of closely eluting peaks were highly correlated, models of resolution (Rs) that were based on retention time had errors in the same range as corresponding models based on ECL. Copyright © 2011 Elsevier B.V. All rights reserved.
A novel approach to transforming a non-targeted metabolic profiling method to a pseudo-targeted method using the retention time locking gas chromatography/mass spectrometry-selected ions monitoring.

PubMed

Li, Yong; Ruan, Qiang; Li, Yanli; Ye, Guozhu; Lu, Xin; Lin, Xiaohui; Xu, Guowang

2012-09-14

Non-targeted metabolic profiling is the most widely used method for metabolomics. In this paper, a novel approach was established to transform a non-targeted metabolic profiling method to a pseudo-targeted method using the retention time locking gas chromatography/mass spectrometry-selected ion monitoring (RTL-GC/MS-SIM). To achieve this transformation, an algorithm based on the automated mass spectral deconvolution and identification system (AMDIS), GC/MS raw data and a bi-Gaussian chromatographic peak model was developed. The established GC/MS-SIM method was compared with GC/MS-full scan (the total ion current and extracted ion current, TIC and EIC) methods, it was found that for a typical tobacco leaf extract, 93% components had their relative standard deviations (RSDs) of relative peak areas less than 20% by the SIM method, while 88% by the EIC method and 81% by the TIC method. 47.3% components had their linear correlation coefficient higher than 0.99, compared with 5.0% by the EIC and 6.2% by TIC methods. Multivariate analysis showed the pooled quality control samples clustered more tightly using the developed method than using GC/MS-full scan methods, indicating a better data quality. With the analysis of the variance of the tobacco samples from three different planting regions, 167 differential components (p<0.05) were screened out using the RTL-GC/MS-SIM method, but 151 and 131 by the EIC and TIC methods, respectively. The results show that the developed method not only has a higher sensitivity, better linearity and data quality, but also does not need complicated peak alignment among different samples. It is especially suitable for the screening of differential components in the metabolic profiling investigation. Copyright © 2012 Elsevier B.V. All rights reserved.

5 CFR 536.303 - Geographic conversion.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Geographic conversion. 536.303 Section... PAY RETENTION Pay Retention § 536.303 Geographic conversion. (a) Geographic conversion at time of... basic pay resulting from this geographic conversion is not a basis for entitlement to pay retention. The...
5 CFR 536.303 - Geographic conversion.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false Geographic conversion. 536.303 Section... PAY RETENTION Pay Retention § 536.303 Geographic conversion. (a) Geographic conversion at time of... basic pay resulting from this geographic conversion is not a basis for entitlement to pay retention. The...
Optimization and performance evaluation for nutrient removal from palm oil mill effluent wastewater using microalgae

NASA Astrophysics Data System (ADS)

Ibrahim, Raheek I.; Wong, Z. H.; Mohammad, A. W.

2015-04-01

Palm oil mill effluent (POME) wastewater was produced in huge amounts in Malaysia, and if it discharged into the environment, it causes a serious problem regarding its high content of nutrients. This study was devoted to POME wastewater treatment with microalgae. The main objective was to find the optimum conditions (retention time, and pH) in the microalgae treatment of POME wastewater considering retention time as a most important parameter in algae treatment, since after the optimum conditions there is a diverse effect of time and pH and so, the process becomes costly. According to our knowledge, there is no existing study optimized the retention time and pH with % removal of nutrients (ammonia nitrogen NH3-N, and orthophosphorous PO43-) for microalgae treatment of POME wastewater. In order to achieve with optimization, a central composite rotatable design with a second order polynomial model was used, regression coefficients and goodness of fit results in removal percentages of nutrients (NH3-N, and PO43-) were estimated.WinQSB technique was used to optimize the surface response objective functionfor the developed model. Also experiments were done to validate the model results.The optimum conditions were found to be 18 day retention time for ammonia nitrogen, and pH of 9.22, while for orthophosphorous, 15 days were indicated as the optimum retention time with a pH value of 9.2.
Physics of self-aligned assembly at room temperature

NASA Astrophysics Data System (ADS)

Dubey, V.; Beyne, E.; Derakhshandeh, J.; De Wolf, I.

2018-01-01

Self-aligned assembly, making use of capillary forces, is considered as an alternative to active alignment during thermo-compression bonding of Si chips in the 3D heterogeneous integration process. Various process parameters affect the alignment accuracy of the chip over the patterned binding site on a substrate/carrier wafer. This paper discusses the chip motion due to wetting and capillary force using a transient coupled physics model for the two regimes (that is, wetting regime and damped oscillatory regime) in the temporal domain. Using the transient model, the effect of the volume of the liquid and the placement accuracy of the chip on the alignment force is studied. The capillary time (that is, the time it takes for the chip to reach its mean position) for the chip is directly proportional to the placement offset and inversely proportional to the viscosity. The time constant of the harmonic oscillations is directly proportional to the gap between the chips due to the volume of the fluid. The predicted behavior from transient simulations is next experimentally validated and it is confirmed that the liquid volume and the initial placement affect the final alignment accuracy of the top chip on the bottom substrate. With statistical experimental data, we demonstrate an alignment accuracy reaching <1 μm.
Officer Overexecution: Analysis and Solutions (Technical Background)

DTIC Science & Technology

2015-08-01

the shorter time period, as is generally reported, the retention of men is greater than that of women , and the retention of conventional SWOs is...greater than that of SWO(N)s. Table 1. Rates of retention for SWOs Rate or number Conventional SWO(N) Men Women All Men Women All Retention (MSR-1 to...the 0.001 level. Table 5. OOE and the retention of SWO(N)s OOE by paygrade Men Women O1 OOE -1 0.6 (0.7) (1) 0 0 O2 OOE 0.6 4.1*** (0.7
Fluorescein thiocarbamyl amino acids as internal standards for migration time correction in capillary sieving electrophoresis

PubMed Central

Pugsley, Haley R.; Swearingen, Kristian E.; Dovichi, Norman J.

2009-01-01

A number of algorithms have been developed to correct for migration time drift in capillary electrophoresis. Those algorithms require identification of common components in each run. However, not all components may be present or resolved in separations of complex samples, which can confound attempts for alignment. This paper reports the use of fluorescein thiocarbamyl derivatives of amino acids as internal standards for alignment of 3-(2-furoyl)quinoline-2-carboxaldehyde (FQ)-labeled proteins in capillary sieving electrophoresis. The fluorescein thiocarbamyl derivative of aspartic acid migrates before FQ-labeled proteins and the fluorescein thiocarbamyl derivative of arginine migrates after the FQ-labeled proteins. These compounds were used as internal standards to correct for variations in migration time over a two-week period in the separation of a cellular homogenate. The experimental conditions were deliberately manipulated by varying electric field and sample preparation conditions. Three components of the homogenate were used to evaluate the alignment efficiency. Before alignment, the average relative standard deviation in migration time for these components was 13.3%. After alignment, the average relative standard deviation in migration time for these components was reduced to 0.5%. PMID:19249052
The Effect of Graduate Education Timing on the Retention of Surface Warfare Officers

DTIC Science & Technology

2016-03-01

DATES COVERED Master’s thesis 4 . TITLE AND SUBTITLE THE EFFECT OF GRADUATE EDUCATION TIMING ON THE RETENTION OF SURFACE WARFARE OFFICERS 5. FUNDING...of graduated education attainment on retention to the tenth, eleventh, and twelfth year of service as well as promotion to O- 4 . The findings show...Department Heads earning a master’s degree at any point within their careers are more likely to promote to O- 4 , compared with those who had not
Ability and Motivation: Assessing Individual Factors that Contribute to University Retention

ERIC Educational Resources Information Center

Alarcon, Gene M.; Edwards, Jean M.

2013-01-01

The current study explored individual differences in ability and motivation factors of retention in first-year college students. We used discrete-time survival mixture analysis to model university retention. Parents' education, gender, American College Test (ACT) scores, conscientiousness, and trait affectivity were explored as predictors of…
Distributed Revisiting: An Analytic for Retention of Coherent Science Learning

ERIC Educational Resources Information Center

Svihla, Vanessa; Wester, Michael J.; Linn, Marcia C.

2015-01-01

Designing learning experiences that support the development of coherent understanding of complex scientific phenomena is challenging. We sought to identify analytics that can also guide such designs to support retention of coherent understanding. Based on prior research that distributing study of material over time supports retention, we explored…
A pin-assisted retention technique for resin-bonded restorations.

PubMed

Miara, P; Touati, B

1992-09-01

The value of pins for auxiliary retention has been demonstrated many times. The use of pins with resin-bonded restorations allows for improved aesthetics and less tooth reduction while increasing resistance to dislodging forces. Clinical and technical procedures for resin-bonded bridges with pin-assisted retention are presented.
Success and Interactive Learning: Sailing toward Student Achievement

ERIC Educational Resources Information Center

Midcap, Richard; Seitzer, Joan; Holliday, Randy; Childs, Amy; Bowser, Dana

2008-01-01

Success and Interactive Learning's (SAIL) front-loaded retention activities and unique financial incentives have combined to improve retention, persistence, and success of first-time college students. Its effectiveness has been validated through a comparison of retention rates and aggregate quality-point averages of SAIL cohorts with those rates…
Retention of Community College Students: Related Student and Institutional Characteristics

ERIC Educational Resources Information Center

Craig, Alfred J.; Ward, Cynthia V. L.

2008-01-01

Public community colleges were established to improve access to higher education. However, access for all often results in low student retention and in the loss of effort, time, and money for students and institutions. This institutional specific retention study, which examined student factors, both demographic and academic, and institutional…
A general strategy for performing temperature-programming in high performance liquid chromatography--further improvements in the accuracy of retention time predictions of segmented temperature gradients.

PubMed

Wiese, Steffen; Teutenberg, Thorsten; Schmidt, Torsten C

2012-01-27

In the present work it is shown that the linear elution strength (LES) model which was adapted from temperature-programming gas chromatography (GC) can also be employed for systematic method development in high-temperature liquid chromatography (HT-HPLC). The ability to predict isothermal retention times based on temperature-gradient as well as isothermal input data was investigated. For a small temperature interval of ΔT=40°C, both approaches result in very similar predictions. Average relative errors of predicted retention times of 2.7% and 1.9% were observed for simulations based on isothermal and temperature-gradient measurements, respectively. Concurrently, it was investigated whether the accuracy of retention time predictions of segmented temperature gradients can be further improved by temperature dependent calculation of the parameter S(T) of the LES relationship. It was found that the accuracy of retention time predictions of multi-step temperature gradients can be improved to around 1.5%, if S(T) was also calculated temperature dependent. The adjusted experimental design making use of four temperature-gradient measurements was applied for systematic method development of selected food additives by high-temperature liquid chromatography. Method development was performed within a temperature interval from 40°C to 180°C using water as mobile phase. Two separation methods were established where selected food additives were baseline separated. In addition, a good agreement between simulation and experiment was observed, because an average relative error of predicted retention times of complex segmented temperature gradients less than 5% was observed. Finally, a schedule of recommendations to assist the practitioner during systematic method development in high-temperature liquid chromatography was established. Copyright © 2011 Elsevier B.V. All rights reserved.
Cooperative ordering and kinetics of cellulose nanocrystal alignment in a magnetic field

DOE PAGES

De France, Kevin J.; Yager, Kevin G.; Hoare, Todd; ...

2016-07-13

Cellulose nanocrystals (CNCs) are emerging nanomaterials that form chiral nematic liquid crystals above a critical concentration (C*) and additionally orient within electromagnetic fields. The control over CNC alignment is significant for materials processing and end use; to date, magnetic alignment has been demonstrated using only strong fields over extended or arbitrary time scales. This work investigates the effects of comparatively weak magnetic fields (0–1.2 T) and CNC concentration (1.65–8.25 wt %) on the kinetics and degree of CNC ordering using small-angle X-ray scattering. Interparticle spacing, correlation length, and orientation order parameters (η and S) increased with time and field strengthmore » following a sigmoidal profile. In a 1.2 T magnetic field for CNC suspensions above C*, partial alignment occurred in under 2 min followed by slower cooperative ordering to achieve nearly perfect alignment in under 200 min (S = –0.499 where S = –0.5 indicates perfect antialignment). At 0.56 T, nearly perfect alignment was also achieved, yet the ordering was 36% slower. Outside of a magnetic field, the order parameter plateaued at 52% alignment (S = –0.26) after 5 h, showcasing the drastic effects of relatively weak magnetic fields on CNC alignment. For suspensions below C*, no magnetic alignment was detected.« less
MEMS Integrated Submount Alignment for Optoelectronics

NASA Astrophysics Data System (ADS)

Shakespeare, W. Jeffrey; Pearson, Raymond A.; Grenestedt, Joachim L.; Hutapea, Parsaoran; Gupta, Vikas

2005-02-01

One of the most expensive and time-consuming production processes for single-mode fiber-optic components is the alignment of the photonic chip or waveguide to the fiber. The alignment equipment is capital intensive and usually requires trained technicians to achieve desired results. Current technology requires active alignment since tolerances are only ~0.2 μ m or less for a typical laser diode. This is accomplished using piezoelectric actuated stages and active optical feedback. Joining technologies such as soldering, epoxy bonding, or laser welding may contribute significant postbond shift, and final coupling efficiencies are often less than 80%. This paper presents a method of adaptive optical alignment to freeze in place directly on an optical submount using a microelectromechanical system (MEMS) shape memory alloy (SMA) actuation technology. Postbond shift is eliminated since the phase change is the alignment actuation. This technology is not limited to optical alignment but can be applied to a variety of MEMS actuations, including nano-actuation and nano-alignment for biomedical applications. Experimental proof-of-concept results are discussed, and a simple analytical model is proposed to predict the stress strain behavior of the optical submount. Optical coupling efficiencies and alignment times are compared with traditional processes. The feasibility of this technique in high-volume production is discussed.
Current distribution and ac susceptibility response of a thin superconducting disc in an axial field: a theoretical approach

NASA Astrophysics Data System (ADS)

Aruna, S. A.; Zhang, P.; Lin, F. Y.; Ding, S. Y.; Yao, X. X.

2000-04-01

Within the framework of the thermally activated process of the flux line or flux line bundles, and by time integration of the 1D equation of motion of the circulating current density icons/Journals/Common/vecJ" ALT="vecJ" ALIGN="TOP"/> (icons/Journals/Common/rho" ALT="rho" ALIGN="TOP"/> ,t ), which is suitable for thin superconducting films (R >>d ,icons/Journals/Common/le" ALT="le" ALIGN="TOP"/> icons/Journals/Common/lambda" ALT="lambda" ALIGN="TOP"/> ), we present numerical calculations of the current profiles, magnetization hysteresis loops and ac susceptibility icons/Journals/Common/chi" ALT="chi" ALIGN="TOP"/> n = icons/Journals/Common/chi" ALT="chi" ALIGN="TOP"/> ´n +iicons/Journals/Common/chi" ALT="chi" ALIGN="TOP"/> ´´n for n = 1, 3 and 5 of a thin disc immersed in an axial time-dependent external magnetic field Ba (t ) = Bdc +Bac cos(2icons/Journals/Common/pi" ALT="pi" ALIGN="TOP"/> icons/Journals/Common/nu" ALT="nu" ALIGN="TOP"/> t ). Our calculated results are compared with those of the critical state model (CSM) and found to prove the approximate validity of the CSM below the irreversibility field. The differences between our computed results and those of the CSM are also discussed.
The effect of tibiotalar alignment on coronal plane mechanics following total ankle replacement.

PubMed

Grier, A Jordan; Schmitt, Abigail C; Adams, Samuel B; Queen, Robin M

2016-07-01

Gait mechanics following total ankle replacement (TAR) have reported improved ankle motion following surgery. However, no studies have addressed the impact of preoperative radiographic tibiotalar alignment on post-TAR gait mechanics. We therefore investigated whether preoperative tibiotalar alignment (varus, valgus, or neutral) resulted in significantly different coronal plane mechanics or ground reaction forces post-TAR. We conducted a non-randomized study of 93 consecutive end-stage ankle arthritis patients. Standard weight-bearing radiographs were obtained preoperatively to categorize patients as having neutral (±4°), varus (≥5° of varus), or valgus (≥5° of valgus) coronal plane tibiotalar alignment. All patients underwent a standard walking assessment including three-dimensional lower extremity kinetics and kinematics preoperatively, 12 and 24 months postoperatively. A significant group by time interaction was observed for the propulsive vertical ground reaction force (vGRF), coronal plane hip range of motion (ROM) and the peak hip abduction moment. The valgus group demonstrated an increase in the peak knee adduction angle and knee adduction angle at heel strike when compared to the other groups. Coronal plane ankle ROM, knee and hip angles at heel strike, and the peak hip angle exhibited significant increases across time. Peak ankle inversion moment, peak knee abduction moment and the weight acceptance vGRF also exhibited significant increases across time. Neutral ankle alignment was achieved for all patients by 2 years following TAR. Restoration of neutral ankle alignment at the time of TAR in patients with preoperative varus or valgus tibiotalar alignment resulted in biomechanics similar to those of patients with neutral preoperative tibiotalar alignment by 24-month follow-up. Copyright © 2016 Elsevier B.V. All rights reserved.
Time-Extended Policies in Mult-Agent Reinforcement Learning

NASA Technical Reports Server (NTRS)

Tumer, Kagan; Agogino, Adrian K.

2004-01-01

Reinforcement learning methods perform well in many domains where a single agent needs to take a sequence of actions to perform a task. These methods use sequences of single-time-step rewards to create a policy that tries to maximize a time-extended utility, which is a (possibly discounted) sum of these rewards. In this paper we build on our previous work showing how these methods can be extended to a multi-agent environment where each agent creates its own policy that works towards maximizing a time-extended global utility over all agents actions. We show improved methods for creating time-extended utilities for the agents that are both "aligned" with the global utility and "learnable." We then show how to crate single-time-step rewards while avoiding the pi fall of having rewards aligned with the global reward leading to utilities not aligned with the global utility. Finally, we apply these reward functions to the multi-agent Gridworld problem. We explicitly quantify a utility's learnability and alignment, and show that reinforcement learning agents using the prescribed reward functions successfully tradeoff learnability and alignment. As a result they outperform both global (e.g., team games ) and local (e.g., "perfectly learnable" ) reinforcement learning solutions by as much as an order of magnitude.
Ultrasound-guided interventional therapy for recurrent ovarian chocolate cysts.

PubMed

Wang, Lu-Lu; Dong, Xiao-Qiu; Shao, Xiao-Hui; Wang, Si-Ming

2011-10-01

The aim of this study was to determine the effectiveness of ultrasound-guided interventional therapy in the treatment of postoperative recurrent chocolate cysts. The 198 patients enrolled in this study were divided into three groups. In group 1, the saline washing group, the cavity of the cyst was washed thoroughly with warm saline. In group 2, the ethanol short-time retention group, after washing with saline, the cyst was injected with 95% ethanol with a volume of half of the fluid aspirated from the cyst. Ten minutes later, the rest of the ethanol was aspirated. In group 3, the ethanol retention group, the procedures were the same as with the ethanol short-time retention group, except that 95% of the ethanol was retained in the cyst. An ultrasound examination was performed in the third, sixth and 12th months after therapy. The chocolate cyst cure rate was significantly higher in the ethanol retention group (96%, 66/69) than in the ethanol short-time retention group (82%, 56/68) and no case was cured in the first group (saline washing). We conclude that ultrasound-guided injection and 95% ethanol retention are an effective therapy for the treatment of postoperative recurrent chocolate cysts. Copyright © 2011 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.
[Separation of p-aminobenzenearsonic acid and its oxide by ion-pair reversed-phase high performance liquid chromatography].

PubMed

Kang, J; Ma, X; Meng, L; Ma, D

1999-05-01

To study the separation of p-aminobenzenearsonic acid (PABAA) and its oxide, p-aminophenylarsine oxide (PAPAO), both the absorption spectra were scanned at the wavelengths from 200 nm to 380 nm. PABAA had absorption maximum at 254 nm and PAPAO 258 nm. The effects of salt concentration, column temperature, methanol and ion-pair agent concentrations on the capacity factor were investigated. Compounds of high polarity showed almost no retention on reversed-phase column; as the volume fraction of the methanol decreased from 90% to 10%, the retention time of PABAA gradually increased with broad peak, and partially eluted when methanol volume fraction being below 20%. With temperature rising, the retention time of PABAA was decreased. But PABAA capacity factor can be increased by selecting an appropriate salt concentration for the mobile phase. The cetyltrimethyl and tetrabutyl ammonium ions were separately added as ion-pair agents to the mobile phase containing methanol in phosphate buffer of 10 mmol/L, the changes of retention time were observed. The mechanism of retention based on reversed phase ion-pair model is proposed. Besides, the retention behaviour is also influenced by size exclusion in stationary phase as well as polar interactions with residual silanol group on the silica surface.

Application of the artificial neural network in quantitative structure-gradient elution retention relationship of phenylthiocarbamyl amino acids derivatives.

PubMed

Tham, S Y; Agatonovic-Kustrin, S

2002-05-15

Quantitative structure-retention relationship(QSRR) method was used to model reversed-phase high-performance liquid chromatography (RP-HPLC) separation of 18 selected amino acids. Retention data for phenylthiocarbamyl (PTC) amino acids derivatives were obtained using gradient elution on ODS column with mobile phase of varying acetonitrile, acetate buffer and containing 0.5 ml/l of triethylamine (TEA). Molecular structure of each amino acid was encoded with 36 calculated molecular descriptors. The correlation between the molecular descriptors and the retention time of the compounds in the calibration set was established using the genetic neural network method. A genetic algorithm (GA) was used to select important molecular descriptors and supervised artificial neural network (ANN) was used to correlate mobile phase composition and selected descriptors with the experimentally derived retention times. Retention time values were used as the network's output and calculated molecular descriptors and mobile phase composition as the inputs. The best model with five input descriptors was chosen, and the significance of the selected descriptors for amino acid separation was examined. Results confirmed the dominant role of the organic modifier in such chromatographic systems in addition to lipophilicity (log P) and molecular size and shape (topological indices) of investigated solutes.
Training for long duration space missions

NASA Technical Reports Server (NTRS)

Goldberg, Joseph H.

1987-01-01

The successful completion of an extended duration manned mission to Mars will require renewed research effort in the areas of crew training and skill retention techniques. The current estimate of inflight transit time is about nine months each way, with a six month surface visit, an order of magnitude beyond previous U.S. space missions. Concerns arise when considering the level of skill retention required for highly critical, one time operations such as an emergency procedure or a Mars orbit injection. The factors responsible for the level of complex skill retention are reviewed, optimal ways of refreshing degraded skills are suggested, and a conceptual crew training design for a Mars mission is outlined. Currently proposed crew activities during a Mars mission were reviewed to identify the spectrum of skills which must be retained over a long time period. Skill retention literature was reviewed to identify those factors which must be considered in deciding when and which tasks need retraining. Task, training, and retention interval factors were identified. These factors were then interpreted in light of the current state of spaceflight and adaptive training systems.
Retention modeling for ultra-thin density of Cu-based conductive bridge random access memory (CBRAM)

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

Aga, Fekadu Gochole; Woo, Jiyong; Lee, Sangheon

We investigate the effect of Cu concentration On-state resistance retention characteristics of W/Cu/Ti/HfO{sub 2}/Pt memory cell. The development of RRAM device for application depends on the understanding of the failure mechanism and the key parameters for device optimization. In this study, we develop analytical expression for cations (Cu{sup +}) diffusion model using Gaussian distribution for detailed analysis of data retention time at high temperature. It is found that the improvement of data retention time depends not only on the conductive filament (CF) size but also on Cu atoms concentration density in the CF. Based on the simulation result, better datamore » retention time is observed for electron wave function associated with Cu{sup +} overlap and an extended state formation. This can be verified by analytical calculation of Cu atom defects inside the filament, based on Cu{sup +} diffusion model. The importance of Cu diffusion for the device reliability and the corresponding local temperature of the filament were analyzed by COMSOL Multiphysics simulation.« less
Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW.

PubMed

Oliver, Tim; Schmidt, Bertil; Nathan, Darran; Clemens, Ralf; Maskell, Douglas

2005-08-15

Aligning hundreds of sequences using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. We present a new approach to compute multiple sequence alignments in far shorter time using reconfigurable hardware. This results in an implementation of ClustalW with significant runtime savings on a standard off-the-shelf FPGA.
Minimap2: pairwise alignment for nucleotide sequences.

PubMed

Li, Heng

2018-05-10

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥ 100bp in length, ≥1kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads, and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions (INDELs) and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. https://github.com/lh3/minimap2. hengli@broadinstitute.org.
Negative Impact of Employment on Engineering Student Time Management, Time to Degree, and Retention: Faculty, Administrator, and Staff Perspectives

ERIC Educational Resources Information Center

Tyson, Will

2012-01-01

Interviews with faculty, administrators, staff, and students at four engineering programs reveal the role of undergraduate student employment on retention and timely degree completion among engineering students. Dueling narratives reveal how student approaches to earning an engineering degree differ greatly from faculty, administrator, and staff…
A modelling study of long term green roof retention performance.

PubMed

Stovin, Virginia; Poë, Simon; Berretta, Christian

2013-12-15

This paper outlines the development of a conceptual hydrological flux model for the long term continuous simulation of runoff and drought risk for green roof systems. A green roof's retention capacity depends upon its physical configuration, but it is also strongly influenced by local climatic controls, including the rainfall characteristics and the restoration of retention capacity associated with evapotranspiration during dry weather periods. The model includes a function that links evapotranspiration rates to substrate moisture content, and is validated against observed runoff data. The model's application to typical extensive green roof configurations is demonstrated with reference to four UK locations characterised by contrasting climatic regimes, using 30-year rainfall time-series inputs at hourly simulation time steps. It is shown that retention performance is dependent upon local climatic conditions. Volumetric retention ranges from 0.19 (cool, wet climate) to 0.59 (warm, dry climate). Per event retention is also considered, and it is demonstrated that retention performance decreases significantly when high return period events are considered in isolation. For example, in Sheffield the median per-event retention is 1.00 (many small events), but the median retention for events exceeding a 1 in 1 yr return period threshold is only 0.10. The simulation tool also provides useful information about the likelihood of drought periods, for which irrigation may be required. A sensitivity study suggests that green roofs with reduced moisture-holding capacity and/or low evapotranspiration rates will tend to offer reduced levels of retention, whilst high moisture-holding capacity and low evapotranspiration rates offer the strongest drought resistance. Copyright © 2013 Elsevier Ltd. All rights reserved.
A standardized method for the calibration of thermodynamic data for the prediction of gas chromatographic retention times.

PubMed

McGinitie, Teague M; Ebrahimi-Najafabadi, Heshmatollah; Harynuk, James J

2014-02-21

A new method for calibrating thermodynamic data to be used in the prediction of analyte retention times is presented. The method allows thermodynamic data collected on one column to be used in making predictions across columns of the same stationary phase but with varying geometries. This calibration is essential as slight variances in the column inner diameter and stationary phase film thickness between columns or as a column ages will adversely affect the accuracy of predictions. The calibration technique uses a Grob standard mixture along with a Nelder-Mead simplex algorithm and a previously developed model of GC retention times based on a three-parameter thermodynamic model to estimate both inner diameter and stationary phase film thickness. The calibration method is highly successful with the predicted retention times for a set of alkanes, ketones and alcohols having an average error of 1.6s across three columns. Copyright © 2014 Elsevier B.V. All rights reserved.
Interface traps and quantum size effects on the retention time in nanoscale memory devices

PubMed Central

2013-01-01

Based on the analysis of Poisson equation, an analytical surface potential model including interface charge density for nanocrystalline (NC) germanium (Ge) memory devices with p-type silicon substrate has been proposed. Thus, the effects of Pb defects at Si(110)/SiO2, Si(111)/SiO2, and Si(100)/SiO2 interfaces on the retention time have been calculated after quantum size effects have been considered. The results show that the interface trap density has a large effect on the electric field across the tunneling oxide layer and leakage current. This letter demonstrates that the retention time firstly increases with the decrease in diameter of NC Ge and then rapidly decreases with the diameter when it is a few nanometers. This implies that the interface defects, its energy distribution, and the NC size should be seriously considered in the aim to improve the retention time from different technological processes. The experimental data reported in the literature support the theoretical expectation. PMID:23984827
Functional models for colloid retention in porous media at the triple line.

PubMed

Dathe, Annette; Zevi, Yuniati; Richards, Brian K; Gao, Bin; Parlange, J-Yves; Steenhuis, Tammo S

2014-01-01

Spectral confocal microscope visualizations of microsphere movement in unsaturated porous media showed that attachment at the Air Water Solid (AWS) interface was an important retention mechanism. These visualizations can aid in resolving the functional form of retention rates of colloids at the AWS interface. In this study, soil adsorption isotherm equations were adapted by replacing the chemical concentration in the water as independent variable by the cumulative colloids passing by. In order of increasing number of fitted parameters, the functions tested were the Langmuir adsorption isotherm, the Logistic distribution, and the Weibull distribution. The functions were fitted against colloid concentrations obtained from time series of images acquired with a spectral confocal microscope for three experiments performed where either plain or carboxylated polystyrene latex microspheres were pulsed in a small flow chamber filled with cleaned quartz sand. Both moving and retained colloids were quantified over time. In fitting the models to the data, the agreement improved with increasing number of model parameters. The Weibull distribution gave overall the best fit. The logistic distribution did not fit the initial retention of microspheres well but otherwise the fit was good. The Langmuir isotherm only fitted the longest time series well. The results can be explained that initially when colloids are first introduced the rate of retention is low. Once colloids are at the AWS interface they act as anchor point for other colloids to attach and thereby increasing the retention rate as clusters form. Once the available attachment sites diminish, the retention rate decreases.
A simple approximation for larval retention around reefs

NASA Astrophysics Data System (ADS)

Cetina-Heredia, Paulina; Connolly, Sean R.

2011-09-01

Estimating larval retention at individual reefs by local scale three-dimensional flows is a significant problem for understanding, and predicting, larval dispersal. Determining larval dispersal commonly involves the use of computationally demanding and expensively calibrated/validated hydrodynamic models that resolve reef wake eddies. This study models variation in larval retention times for a range of reef shapes and circulation regimes, using a reef-scale three-dimensional hydrodynamic model. It also explores how well larval retention time can be estimated based on the "Island Wake Parameter", a measure of the degree of flow turbulence in the wake of reefs that is a simple function of flow speed, reef dimension, and vertical diffusion. The mean residence times found in the present study (0.48-5.64 days) indicate substantial potential for self-recruitment of species whose larvae are passive, or weak swimmers, for the first several days after release. Results also reveal strong and significant relationships between the Island Wake Parameter and mean residence time, explaining 81-92% of the variability in retention among reefs across a range of unidirectional flow speeds and tidal regimes. These findings suggest that good estimates of larval retention may be obtained from relatively coarse-scale characteristics of the flow, and basic features of reef geomorphology. Such approximations may be a valuable tool for modeling connectivity and meta-population dynamics over large spatial scales, where explicitly characterizing fine-scale flows around reef requires a prohibitive amount of computation and extensive model calibration.
Electric-field-induced flow-aligning state in a nematic liquid crystal.

PubMed

Fatriansyah, Jaka Fajar; Orihara, Hiroshi

2015-04-01

The response of shear stress to a weak ac electric field as a probe is measured in a nematic liquid crystal under shear flow and dc electric fields. Two states with different responses are clearly observed when the dc electric field is changed at a constant shear rate: the flow aligning and non-flow aligning states. The director lies in the shear plane in the flow aligning state and out of the plane in the non-flow aligning state. Through application of dc electric field, the non-flow aligning state can be changed to the flow aligning state. In the transition from the flow aligning state to the non-flow aligning state, it is found that the response increases and the relaxation time becomes longer. Here, the experimental results in the flow aligning state are discussed on the basis of the Ericksen-Leslie theory.
Evaluation of automated sample preparation, retention time locked gas chromatography-mass spectrometry and data analysis methods for the metabolomic study of Arabidopsis species.

PubMed

Gu, Qun; David, Frank; Lynen, Frédéric; Rumpel, Klaus; Dugardeyn, Jasper; Van Der Straeten, Dominique; Xu, Guowang; Sandra, Pat

2011-05-27

In this paper, automated sample preparation, retention time locked gas chromatography-mass spectrometry (GC-MS) and data analysis methods for the metabolomics study were evaluated. A miniaturized and automated derivatisation method using sequential oximation and silylation was applied to a polar extract of 4 types (2 types×2 ages) of Arabidopsis thaliana, a popular model organism often used in plant sciences and genetics. Automation of the derivatisation process offers excellent repeatability, and the time between sample preparation and analysis was short and constant, reducing artifact formation. Retention time locked (RTL) gas chromatography-mass spectrometry was used, resulting in reproducible retention times and GC-MS profiles. Two approaches were used for data analysis. XCMS followed by principal component analysis (approach 1) and AMDIS deconvolution combined with a commercially available program (Mass Profiler Professional) followed by principal component analysis (approach 2) were compared. Several features that were up- or down-regulated in the different types were detected. Copyright © 2011 Elsevier B.V. All rights reserved.
A Novel Adaptive H∞ Filtering Method with Delay Compensation for the Transfer Alignment of Strapdown Inertial Navigation Systems.

PubMed

Lyu, Weiwei; Cheng, Xianghong

2017-11-28

Transfer alignment is always a key technology in a strapdown inertial navigation system (SINS) because of its rapidity and accuracy. In this paper a transfer alignment model is established, which contains the SINS error model and the measurement model. The time delay in the process of transfer alignment is analyzed, and an H∞ filtering method with delay compensation is presented. Then the H∞ filtering theory and the robust mechanism of H∞ filter are deduced and analyzed in detail. In order to improve the transfer alignment accuracy in SINS with time delay, an adaptive H∞ filtering method with delay compensation is proposed. Since the robustness factor plays an important role in the filtering process and has effect on the filtering accuracy, the adaptive H∞ filter with delay compensation can adjust the value of robustness factor adaptively according to the dynamic external environment. The vehicle transfer alignment experiment indicates that by using the adaptive H∞ filtering method with delay compensation, the transfer alignment accuracy and the pure inertial navigation accuracy can be dramatically improved, which demonstrates the superiority of the proposed filtering method.
X-ray microprobe of orbital alignment in strong-field ionized atoms.

PubMed

Young, L; Arms, D A; Dufresne, E M; Dunford, R W; Ederer, D L; Höhr, C; Kanter, E P; Krässig, B; Landahl, E C; Peterson, E R; Rudati, J; Santra, R; Southworth, S H

2006-08-25

We have developed a synchrotron-based, time-resolved x-ray microprobe to investigate optical strong-field processes at intermediate intensities (10(14) - 10(15) W/cm2). This quantum-state specific probe has enabled the direct observation of orbital alignment in the residual ion produced by strong-field ionization of krypton atoms via resonant, polarized x-ray absorption. We found strong alignment to persist for a period long compared to the spin-orbit coupling time scale (6.2 fs). The observed degree of alignment can be explained by models that incorporate spin-orbit coupling. The methodology is applicable to a wide range of problems.
Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment.

PubMed

Ranwez, Vincent

2016-01-01

Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeatedly required and is time consuming. Given an alignment of n sequences and L sites, I introduce here optimized solutions reaching O(nL) time complexity for affine gap cost, instead of O(n2L), which are easy to implement.
Real-time high-resolution measurement of collagen alignment in dynamically loaded soft tissue.

PubMed

York, Timothy; Kahan, Lindsey; Lake, Spencer P; Gruev, Viktor

2014-06-01

A technique for creating maps of the direction and strength of fiber alignment in collagenous soft tissues is presented. The method uses a division of focal plane polarimeter to measure circularly polarized light transmitted through the tissue. The architecture of the sensor allows measurement of the retardance and fiber alignment at the full frame rate of the sensor without any moving optics. The technique compares favorably to the standard method of using a rotating polarizer. How the new technique enables real-time capture of the full angular spread of fiber alignment and retardance under various cyclic loading conditions is illustrated.
Knowledge Retention after an Online Tutorial: A Randomized Educational Experiment among Resident Physicians

PubMed Central

Harless, Charles E.; Higa, Jerilyn K.; Bjork, Elizabeth L.; Bjork, Robert A.; Bazargan, Mohsen; Mangione, Carol M.

2008-01-01

BACKGROUND The time course of physicians’ knowledge retention after learning activities has not been well characterized. Understanding the time course of retention is critical to optimizing the reinforcement of knowledge. DESIGN Educational follow-up experiment with knowledge retention measured at 1 of 6 randomly assigned time intervals (0–55 days) after an online tutorial covering 2 American Diabetes Association guidelines. PARTICIPANTS Internal and family medicine residents. MEASUREMENTS Multiple-choice knowledge tests, subject characteristics including critical appraisal skills, and learner satisfaction. RESULTS Of 197 residents invited, 91 (46%) completed the tutorial and were randomized; of these, 87 (96%) provided complete follow-up data. Ninety-two percent of the subjects rated the tutorial as “very good” or “excellent.” Mean knowledge scores increased from 50% before the tutorial to 76% among those tested immediately afterward. Score gains were only half as great at 3–8 days and no significant retention was measurable at 55 days. The shape of the retention curve corresponded with a 1/4-power transformation of the delay interval. In multivariate analyses, critical appraisal skills and participant age were associated with greater initial learning, but no participant characteristic significantly modified the rate of decline in retention. CONCLUSIONS Education that appears successful from immediate posttests and learner evaluations can result in knowledge that is mostly lost to recall over the ensuing days and weeks. To achieve longer-term retention, physicians should review or otherwise reinforce new learning after as little as 1 week. Electronic supplementary material The online version of this article (doi:10.1007/s11606-008-0604-2) contains supplementary material, which is available to authorized users. PMID:18446414
Impact of solids retention time on dissolved organic nitrogen and its biodegradability in treated wastewater

USDA-ARS?s Scientific Manuscript database

Dissolved organic nitrogen (DON) and its biodegradability in treated wastewater have recently gained attention because DON potentially causes oxygen depletion and/or eutrophication in receiving waters. Laboratory scale chemostat experiments were conducted at 9 different solids retention times (SRTs)...
Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment

PubMed Central

2013-01-01

Background Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. Results In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Conclusion Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA. PMID:24564200

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

PubMed

Nagar, Anurag; Hahsler, Michael

2013-01-01

Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA.
49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2011 CFR

2011-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2011-10-01 2011-10-01 false Retention of samples and additional testing. 199...
49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2013 CFR

2013-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2013-10-01 2013-10-01 false Retention of samples and additional testing. 199...
49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2012 CFR

2012-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2012-10-01 2012-10-01 false Retention of samples and additional testing. 199...
49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2010 CFR

2010-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2010-10-01 2010-10-01 false Retention of samples and additional testing. 199...
49 CFR 199.111 - Retention of samples and additional testing.

Code of Federal Regulations, 2014 CFR

2014-10-01

... SAFETY DRUG AND ALCOHOL TESTING Drug Testing § 199.111 Retention of samples and additional testing. (a... other than the unauthorized use of a prohibited drug, and if timely additional testing is requested by... 49 Transportation 3 2014-10-01 2014-10-01 false Retention of samples and additional testing. 199...
Scout-MRM: Multiplexed Targeted Mass Spectrometry-Based Assay without Retention Time Scheduling Exemplified by Dickeya dadantii Proteomic Analysis during Plant Infection.

PubMed

Rougemont, Blandine; Bontemps Gallo, Sébastien; Ayciriex, Sophie; Carrière, Romain; Hondermarck, Hubert; Lacroix, Jean Marie; Le Blanc, J C Yves; Lemoine, Jérôme

2017-02-07

Targeted mass spectrometry of a surrogate peptide panel is a powerful method to study the dynamics of protein networks, but chromatographic time scheduling remains a major limitation for dissemination and implementation of robust and large multiplexed assays. We unveil a Multiple Reaction Monitoring method (Scout-MRM) where the use of spiked scout peptides triggers complex transition lists, regardless of the retention time of targeted surrogate peptides. The interest of Scout-MRM method regarding the retention time independency, multiplexing capability, reproducibility, and putative interest in facilitating method transfer was illustrated by a 782-peptide-plex relative assay targeting 445 proteins of the phytopathogen Dickeya dadantii during plant infection.
The Impact of a Junior Faculty Fellowship Award on Academic Advancement and Retention.

PubMed

Connelly, Maureen T; Sullivan, Amy M; Chinchilla, Manuel; Dale, Margaret L; Emans, S Jean; Nadelson, Carol Cooperman; Notman, Malkah Tolpin; Tarbell, Nancy J; Zigler, Corwin M; Shore, Eleanor G

2017-08-01

Academic faculty experience barriers to career development and promotion. In 1996, Harvard Medical School (HMS) initiated an intramural junior faculty fellowship to address these obstacles. The authors sought to understand whether receiving a fellowship was associated with more rapid academic promotion and retention. Junior faculty fellowship recipients and all other instructor and assistant professors at HMS between 1996 and 2011 were identified. Using propensity score modeling, the authors created a matched comparison group for the fellowship recipients based on educational background, training, academic rank, department, hospital affiliation, and demographics. Time to promotion and time to leaving were assessed by Kaplan-Meier curves. A total of 622 junior faculty received fellowships. Faculty who received fellowships while instructors (n = 480) had shorter times to promotion to assistant professor (P < .0001) and longer retention times (P < .0001) than matched controls. There were no significant differences in time to promotion for assistant professors who received fellowships (n = 142) compared with matched controls, but assistant professor fellowship recipients were significantly more likely to remain longer on the faculty (P = .0005). Women instructors advanced more quickly than matched controls, while male instructors' rates of promotions did not differ. Fellowships to support junior faculty were associated with shorter times to promotion for instructors and more sustained faculty retention for both instructors and assistant professors. This suggests that relatively small amounts of funding early in faculty careers can play a critical role in supporting academic advancement and retention.
Drifty shifty deluxe.m

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

Josh Sugar, Dave Robinson

2014-01-24

Performs a cross-correlation calculation to align images. This is particularly useful for aligning frames of a movie so that an object of interest does not spatially drift. For in situ microscopy experiments. Movies are collected where an object changes with time. At the same time, the object usually drifts too. This shifts the movie frames so that the object is aligned from frame to frame. Then it is easy to see the object changes without the added complication of it moving too.
Optimal Alignment of Structures for Finite and Periodic Systems.

PubMed

Griffiths, Matthew; Niblett, Samuel P; Wales, David J

2017-10-10

Finding the optimal alignment between two structures is important for identifying the minimum root-mean-square distance (RMSD) between them and as a starting point for calculating pathways. Most current algorithms for aligning structures are stochastic, scale exponentially with the size of structure, and the performance can be unreliable. We present two complementary methods for aligning structures corresponding to isolated clusters of atoms and to condensed matter described by a periodic cubic supercell. The first method (Go-PERMDIST), a branch and bound algorithm, locates the global minimum RMSD deterministically in polynomial time. The run time increases for larger RMSDs. The second method (FASTOVERLAP) is a heuristic algorithm that aligns structures by finding the global maximum kernel correlation between them using fast Fourier transforms (FFTs) and fast SO(3) transforms (SOFTs). For periodic systems, FASTOVERLAP scales with the square of the number of identical atoms in the system, reliably finds the best alignment between structures that are not too distant, and shows significantly better performance than existing algorithms. The expected run time for Go-PERMDIST is longer than FASTOVERLAP for periodic systems. For finite clusters, the FASTOVERLAP algorithm is competitive with existing algorithms. The expected run time for Go-PERMDIST to find the global RMSD between two structures deterministically is generally longer than for existing stochastic algorithms. However, with an earlier exit condition, Go-PERMDIST exhibits similar or better performance.
Approximate matching of regular expressions.

PubMed

Myers, E W; Miller, W

1989-01-01

Given a sequence A and regular expression R, the approximate regular expression matching problem is to find a sequence matching R whose optimal alignment with A is the highest scoring of all such sequences. This paper develops an algorithm to solve the problem in time O(MN), where M and N are the lengths of A and R. Thus, the time requirement is asymptotically no worse than for the simpler problem of aligning two fixed sequences. Our method is superior to an earlier algorithm by Wagner and Seiferas in several ways. First, it treats real-valued costs, in addition to integer costs, with no loss of asymptotic efficiency. Second, it requires only O(N) space to deliver just the score of the best alignment. Finally, its structure permits implementation techniques that make it extremely fast in practice. We extend the method to accommodate gap penalties, as required for typical applications in molecular biology, and further refine it to search for sub-strings of A that strongly align with a sequence in R, as required for typical data base searches. We also show how to deliver an optimal alignment between A and R in only O(N + log M) space using O(MN log M) time. Finally, an O(MN(M + N) + N2log N) time algorithm is presented for alignment scoring schemes where the cost of a gap is an arbitrary increasing function of its length.
Continuous Retention and Viral Suppression Provide Further Insights Into the HIV Care Continuum Compared to the Cross-sectional HIV Care Cascade.

PubMed

Colasanti, Jonathan; Kelly, Jane; Pennisi, Eugene; Hu, Yi-Juan; Root, Christin; Hughes, Denise; Del Rio, Carlos; Armstrong, Wendy S

2016-03-01

The human immunodeficiency virus (HIV) care continuum has become an important tool for evaluating HIV care. Current depictions of the care continuum are often cross-sectional and evaluate retention and viral suppression (VS) in a single year, yet the National HIV/AIDS Strategy calls for programs with long-lasting outcomes. Retrospective chart review of HIV-infected patients enrolled in a large, urban clinic in 2010 followed longitudinally for 36 months. McNemar comparisons and logistic regression analyses were conducted to evaluate covariate association with continuous retention and VS. Generalized estimating equation log-linear models were used to integrate time into the model. Among 655 patients (77% male, 83% black, 54% men who have sex with men (MSM), 78% uninsured) continuous retention/VS at 12 months (84%/64%), 24 months (60%/48%), and 36 months (49%/39%) showed significant attrition (P < .0001) over time. Continuous retention was associated with prevalent VS at the end of 36 months (adjusted prevalence ratio 3.12; 95% confidence interval [CI], 2.40, 4.07). 12-month retention for black (84%) and nonblack (85%) patients was equivalent, yet fewer blacks (46%) than nonblacks (63%) achieved 36-month continuous retention due to a significant interaction between race and time (aOR 0.75, 95% CI, .59, .95). Continuous retention is a critically important measure of long-term success in HIV treatment and the crucial component of successful treatment-as-prevention but is infrequently evaluated. Single cross-sections may overestimate successful retention and virologic outcomes. A longitudinal HIV care continuum provides greater insight into long-term outcomes and exposes disparities not evident with traditional cross-sectional care continua. © The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.
Rapid shear alignment of sub-10 nm cylinder-forming block copolymer films based on thermal expansion mismatch

NASA Astrophysics Data System (ADS)

Nicaise, Samuel M.; Gadelrab, Karim R.; G, Amir Tavakkoli K.; Ross, Caroline A.; Alexander-Katz, Alfredo; Berggren, Karl K.

2018-01-01

Directed self-assembly of block copolymers (BCPs) provided by shear-stress can produce aligned sub-10 nm structures over large areas for applications in integrated circuits, next-generation data storage, and plasmonic structures. In this work, we present a fast, versatile BCP shear-alignment process based on coefficient of thermal expansion mismatch of the BCP film, a rigid top coat and a substrate. Monolayer and bilayer cylindrical microdomains of poly(styrene-b-dimethylsiloxane) aligned preferentially in-plane and orthogonal to naturally-forming or engineered cracks in the top coat film, allowing for orientation control over 1 cm2 substrates. Annealing temperatures, up to 275 °C, provided low-defect alignment up to 2 mm away from cracks for rapid (<1 min) annealing times. Finite-element simulations of the stress as a function of annealing time, annealing temperature, and distance from cracks showed that shear stress during the cooling phase of the thermal annealing was critical for the observed microdomain alignment.
Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.

PubMed

Rahn, René; Budach, Stefan; Costanza, Pascal; Ehrhardt, Marcel; Hancox, Jonny; Reinert, Knut

2018-05-03

Pairwise sequence alignment is undoubtedly a central tool in many bioinformatics analyses. In this paper, we present a generically accelerated module for pairwise sequence alignments applicable for a broad range of applications. In our module, we unified the standard dynamic programming kernel used for pairwise sequence alignments and extended it with a generalized inter-sequence vectorization layout, such that many alignments can be computed simultaneously by exploiting SIMD (Single Instruction Multiple Data) instructions of modern processors. We then extended the module by adding two layers of thread-level parallelization, where we a) distribute many independent alignments on multiple threads and b) inherently parallelize a single alignment computation using a work stealing approach producing a dynamic wavefront progressing along the minor diagonal. We evaluated our alignment vectorization and parallelization on different processors, including the newest Intel® Xeon® (Skylake) and Intel® Xeon Phi™ (KNL) processors, and use cases. The instruction set AVX512-BW (Byte and Word), available on Skylake processors, can genuinely improve the performance of vectorized alignments. We could run single alignments 1600 times faster on the Xeon Phi™ and 1400 times faster on the Xeon® than executing them with our previous sequential alignment module. The module is programmed in C++ using the SeqAn (Reinert et al., 2017) library and distributed with version 2.4. under the BSD license. We support SSE4, AVX2, AVX512 instructions and included UME::SIMD, a SIMD-instruction wrapper library, to extend our module for further instruction sets. We thoroughly test all alignment components with all major C++ compilers on various platforms. rene.rahn@fu-berlin.de.
Circadian Rhythms in Human Memory.

ERIC Educational Resources Information Center

Folkard, Simon; Monk, Timothy H.

1980-01-01

Two experiments are described that examined the influence of time-of-day of presentation on immediate and delayed retention and its potential effects on retrieval from long-term memory. Time of presentation was found to influence both immediate and delayed (28 day) retention, but not retrieval from long-term memory. (Author/SJL)
Five Help Desk Tips To Increase Retention Rates, Learner Satisfaction and Revenues.

ERIC Educational Resources Information Center

Feldberg, Jeffrey

2001-01-01

Discusses the necessity of a good help desk available around the clock for students of online courses to ensure a higher retention rate. Recommends a mission that emphasizes student success as the main focus, full time employees, proper training, and short response times. (LRW)
A closed-loop time-alignment system for baseband combining

NASA Technical Reports Server (NTRS)

Feria, Y.

1994-01-01

In baseband combining, the key element is the time alignment of the baseband signals. This article describes a closed-loop time-alignment system that estimates and adjusts the relative delay between two baseband signals received from two different antennas for the signals to be coherently combined. This system automatically determines which signal is advanced and delays it accordingly with a resolution of a sample period. The performance of the loop is analyzed, and the analysis is verified through simulation. The variance of the delay estimates and the signal-to-noise ratio degradation in the simulations agree with the theoretical calculations.
Improved alignment and operating room efficiency with patient-specific instrumentation for TKA.

PubMed

Renson, Luc; Poilvache, Pascal; Van den Wyngaert, Hans

2014-12-01

Achieving accurate alignment in total knee arthroplasty (TKA) remains a concern. Patient-specific instrumentation (PSI) produced using preoperative 3D models was developed to offer surgeons a simplified, reliable, efficient and customised TKA procedure. In this prospective study, 60 patients underwent TKA with conventional instrumentation and 71 patients were operated on using PSI. The primary endpoint was surgical time. Secondary endpoints included operating room (OR) time, the number of instrument trays used and postoperative radiographic limb alignment. Compared to conventional instrumentation, PSI significantly reduced total surgical time by 8.9 ± 3.3 min (p=0.038), OR time by 8.6 ± 4.2 min (p=0.043), and the number of instrument trays by six trays (p<0.001). Mechanical axis malalignment of the lower limb of >3° was observed in 13% of PSI patients versus 29% with conventional instrumentation (p=0.043). PSI predicted the size of the femoral and tibial components actually used in 85.9% and 78.9% of cases, respectively. PSI improves alignment, surgical and OR time, reduces the number of instruments trays used compared to conventional instrumentation in patients undergoing TKA and results in fewer outliers in overall mechanical alignment in the coronal plane. Prospective comparative therapeutic study. Copyright © 2014 Elsevier B.V. All rights reserved.
Novel Real-time Alignment and Calibration of the LHCb detector in Run2

NASA Astrophysics Data System (ADS)

Martinelli, Maurizio; LHCb Collaboration

2017-10-01

LHCb has introduced a novel real-time detector alignment and calibration strategy for LHC Run2. Data collected at the start of the fill are processed in a few minutes and used to update the alignment parameters, while the calibration constants are evaluated for each run. This procedure improves the quality of the online reconstruction. For example, the vertex locator is retracted and reinserted for stable beam conditions in each fill to be centred on the primary vertex position in the transverse plane. Consequently its position changes on a fill-by-fill basis. Critically, this new real-time alignment and calibration procedure allows identical constants to be used in the online and offline reconstruction, thus improving the correlation between triggered and offline-selected events. This offers the opportunity to optimise the event selection in the trigger by applying stronger constraints. The required computing time constraints are met thanks to a new dedicated framework using the multi-core farm infrastructure for the trigger. The motivation for a real-time alignment and calibration of the LHCb detector is discussed from both the operational and physics performance points of view. Specific challenges of this novel configuration are discussed, as well as the working procedures of the framework and its performance.
Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

PubMed

Robinson, Kelly M; Hawkins, Aziah S; Santana-Cruz, Ivette; Adkins, Ricky S; Shetty, Amol C; Nagaraj, Sushma; Sadzewicz, Lisa; Tallon, Luke J; Rasko, David A; Fraser, Claire M; Mahurkar, Anup; Silva, Joana C; Dunning Hotopp, Julie C

2017-09-01

As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i.e. Plasmodium falciparum or Brugia malayi ) and one minority member (i.e. human or the Wolbachia endosymbiont w Bm) of the sequence data. Increasing bwa-mem seed length from the default value reduced the number of read pairs from the majority sequence member that incorrectly aligned to the reference genome of the minority sequence member. Combining both source genomes into a single reference genome increased the specificity of mapping, while also reducing the central processing unit (CPU) time. In Plasmodium , at a seed length of 18 nt, 24.1 % of reads mapped to the human genome using 1.7±0.1 CPU hours, while 83.6 % of reads mapped to the Plasmodium genome using 0.2±0.0 CPU hours (total: 107.7 % reads mapping; in 1.9±0.1 CPU hours). In contrast, 97.1 % of the reads mapped to a combined Plasmodium- human reference in only 0.7±0.0 CPU hours. Overall, the results suggest that combining all references into a single reference database and using a 23 nt seed length reduces the computational time, while maximizing specificity. Similar results were found for simulated sequence reads from a mock metagenomic data set. We found similar improvements to computation time in a publicly available human-only data set.

Wrapping Aligned Carbon Nanotube Composite Sheets around Vanadium Nitride Nanowire Arrays for Asymmetric Coaxial Fiber-Shaped Supercapacitors with Ultrahigh Energy Density.

PubMed

Zhang, Qichong; Wang, Xiaona; Pan, Zhenghui; Sun, Juan; Zhao, Jingxin; Zhang, Jun; Zhang, Cuixia; Tang, Lei; Luo, Jie; Song, Bin; Zhang, Zengxing; Lu, Weibang; Li, Qingwen; Zhang, Yuegang; Yao, Yagang

2017-04-12

The emergence of fiber-shaped supercapacitors (FSSs) has led to a revolution in portable and wearable electronic devices. However, obtaining high energy density FSSs for practical applications is still a key challenge. This article exhibits a facile and effective approach to directly grow well-aligned three-dimensional vanadium nitride (VN) nanowire arrays (NWAs) on carbon nanotube (CNT) fiber with an ultrahigh specific capacitance of 715 mF/cm 2 in a three-electrode system. Benefiting from their intriguing structural features, we successfully fabricated a prototype asymmetric coaxial FSS (ACFSS) with a maximum operating voltage of 1.8 V. From core to shell, this ACFSS consists of a CNT fiber core coated with VN@C NWAs as the negative electrode, Na 2 SO 4 poly(vinyl alcohol) (PVA) as the solid electrolyte, and MnO 2 /conducting polymer/CNT sheets as the positive electrode. The novel coaxial architecture not only fully enables utilization of the effective surface area and decreases the contact resistance between the two electrodes but also, more importantly, provides a short pathway for the ultrafast transport of axial electrons and ions. The electrochemical results show that the optimized ACFSS exhibits a remarkable specific capacitance of 213.5 mF/cm 2 and an exceptional energy density of 96.07 μWh/cm 2 , the highest areal capacitance and areal energy density yet reported in FSSs. Furthermore, the device possesses excellent flexibility in that its capacitance retention reaches 96.8% after bending 5000 times, which further allows it to be woven into flexible electronic clothes with conventional weaving techniques. Therefore, the asymmetric coaxial architectural design allows new opportunities to fabricate high-performance flexible FSSs for future portable and wearable electronic devices.
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

PubMed

Alser, Mohammed; Hassan, Hasan; Xin, Hongyi; Ergin, Oguz; Mutlu, Onur; Alkan, Can

2017-11-01

High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10. https://github.com/BilkentCompGen/GateKeeper. mohammedalser@bilkent.edu.tr or onur.mutlu@inf.ethz.ch or calkan@cs.bilkent.edu.tr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
Adenoid cystic carcinoma associated with mucous retention cyst of the parotid gland.

PubMed

Hebbale, Manjula Advisha; Halli, Rajshekhar C; Kini, Yogesh K; Kharkar, Viraj R; Metgud, Rashmi

2011-09-01

Mucous retention cysts of the parotid gland are rare, and a coexistent adenoid cystic carcinoma is even an unusual occurrence. Such coexistent adenoid cystic carcinomas with mucous retention cyst of the parotid gland are difficult to diagnose clinically and, at times, stage difficulty in their management. We report a rare case of adenoid cystic carcinoma associated with mucous retention cyst of the parotid gland with its diagnostic and management dilemma in a 14-year-old adolescent girl.
Ternary isocratic mobile phase optimization utilizing resolution Design Space based on retention time and peak width modeling.

PubMed

Kawabe, Takefumi; Tomitsuka, Toshiaki; Kajiro, Toshi; Kishi, Naoyuki; Toyo'oka, Toshimasa

2013-01-18

An optimization procedure of ternary isocratic mobile phase composition in the HPLC method using a statistical prediction model and visualization technique is described. In this report, two prediction models were first evaluated to obtain reliable prediction results. The retention time prediction model was constructed by modification from past respectable knowledge of retention modeling against ternary solvent strength changes. An excellent correlation between observed and predicted retention time was given in various kinds of pharmaceutical compounds by the multiple regression modeling of solvent strength parameters. The peak width of half height prediction model employed polynomial fitting of the retention time, because a linear relationship between the peak width of half height and the retention time was not obtained even after taking into account the contribution of the extra-column effect based on a moment method. Accurate prediction results were able to be obtained by such model, showing mostly over 0.99 value of correlation coefficient between observed and predicted peak width of half height. Then, a procedure to visualize a resolution Design Space was tried as the secondary challenge. An artificial neural network method was performed to link directly between ternary solvent strength parameters and predicted resolution, which were determined by accurate prediction results of retention time and a peak width of half height, and to visualize appropriate ternary mobile phase compositions as a range of resolution over 1.5 on the contour profile. By using mixtures of similar pharmaceutical compounds in case studies, we verified a possibility of prediction to find the optimal range of condition. Observed chromatographic results on the optimal condition mostly matched with the prediction and the average of difference between observed and predicted resolution were approximately 0.3. This means that enough accuracy for prediction could be achieved by the proposed procedure. Consequently, the procedure to search the optimal range of ternary solvent strength achieving an appropriate separation is provided by using the resolution Design Space based on accurate prediction. Copyright © 2012 Elsevier B.V. All rights reserved.
Diffractive optics for precision alignment of Euclid space telescope optics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Asfour, Jean-Michel; Weidner, Frank; Bodendorf, Christof; Bode, Andreas; Poleshchuk, Alexander G.; Nasyrov, Ruslan K.; Grupp, Frank; Bender, Ralf

2017-09-01

We present a method for precise alignment of lens elements using specific Computer Generated Hologram (CGH) with an integrated Fizeau reference flat surface and a Fizeau interferometer. The method is used for aligning the so called Camera Lens Assembly for ESAs Euclid telescope. Each lens has a corresponding annular area on the diffractive optics, which is used to control the position of each lens. The lenses are subsequently positioned using individual annular rings of the CGH. The overall alignment accuracy is below 1 µm, the alignment sensitivity is in the range of 0.1 µm. The achieved alignment accuracy of the lenses relative to each other is mainly depending on the stability in time of the alignment tower. Error budgets when using computer generated holograms and physical limitations are explained. Calibration measurements of the alignment system and the typically reached alignment accuracies will be shown and discussed.
SIM Lite: Ground Alignment of the Instrument

NASA Technical Reports Server (NTRS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-01-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.
SIM Lite: ground alignment of the instrument

NASA Astrophysics Data System (ADS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-07-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.
Acquired prior knowledge modulates audiovisual integration.

PubMed

Van Wanrooij, Marc M; Bremen, Peter; John Van Opstal, A

2010-05-01

Orienting responses to audiovisual events in the environment can benefit markedly by the integration of visual and auditory spatial information. However, logically, audiovisual integration would only be considered successful for stimuli that are spatially and temporally aligned, as these would be emitted by a single object in space-time. As humans do not have prior knowledge about whether novel auditory and visual events do indeed emanate from the same object, such information needs to be extracted from a variety of sources. For example, expectation about alignment or misalignment could modulate the strength of multisensory integration. If evidence from previous trials would repeatedly favour aligned audiovisual inputs, the internal state might also assume alignment for the next trial, and hence react to a new audiovisual event as if it were aligned. To test for such a strategy, subjects oriented a head-fixed pointer as fast as possible to a visual flash that was consistently paired, though not always spatially aligned, with a co-occurring broadband sound. We varied the probability of audiovisual alignment between experiments. Reaction times were consistently lower in blocks containing only aligned audiovisual stimuli than in blocks also containing pseudorandomly presented spatially disparate stimuli. Results demonstrate dynamic updating of the subject's prior expectation of audiovisual congruency. We discuss a model of prior probability estimation to explain the results.
Academic plastic surgery: faculty recruitment and retention.

PubMed

Chen, Jenny T; Girotto, John A; Kitzmiller, W John; Lawrence, W Thomas; Verheyden, Charles N; Vedder, Nicholas B; Coleman, John J; Bentz, Michael L

2014-03-01

A critical element of a thriving academic plastic surgery program is the quality of faculty. A decline in recruitment and retention of faculty has been attributed to the many challenges of academic medicine. Given the substantial resources required to develop faculty, academic plastic surgery has a vested interest in improving the process of faculty recruitment and retention. The American Council of Academic Plastic Surgeons Issues Committee and the American Society of Plastic Surgeons/Plastic Surgery Foundation Academic Affairs Council surveyed the 83 existing programs in academic plastic surgery in February of 2012. The survey addressed the faculty-related issues in academic plastic surgery programs over the past decade. Recruitment and retention strategies were evaluated. This study was designed to elucidate trends, and define best strategies, on a national level. Academic plastic surgery programs have added substantially more full-time faculty over the past decade. Recruitment efforts are multifaceted and can include guaranteed salary support, moving expenses, nurse practitioner/physician's assistant hires, protected time for research, seed funds to start research programs, and more. Retention efforts can include increased compensation, designation of a leadership appointment, protected academic time, and call dilution. Significant change and growth of academic plastic surgery has occurred in the past decade. Effective faculty recruitment and retention are critical to a successful academic center. Funding sources in addition to physician professional fees (institutional program support, grants, contracts, endowment, and so on) are crucial to sustain the academic missions.
Factors Affecting Retention Behavior: A Model To Predict At-Risk Students. AIR 1997 Annual Forum Paper.

ERIC Educational Resources Information Center

Sadler, William E.; Cohen, Frederic L.; Kockesen, Levent

This paper describes a methodology used in an on-going retention study at New York University (NYU) to identify a series of easily measured factors affecting student departure decisions. Three logistic regression models for predicting student retention were developed, each containing data available at three distinct times during the first…
Don't Hold Back? the Effect of Grade Retention on Student Achievement

ERIC Educational Resources Information Center

Diris, Ron

2017-01-01

This study analyzes the effect of age-based retention on school achievement at different stages of education. I estimate an instrumental variable model, using the predicted probability of retention given month of birth as an instrument, while simultaneously accounting for the effect of month of birth on maturity at the time of testing. The…
We Want Our 27 Million Dollars back: Retention as a Revenue Resource

ERIC Educational Resources Information Center

Smith, Raymond T.; Liguori, Denise; O'Connor, Dianna; Postle, Monica

2009-01-01

Community colleges lose millions of dollars in potential revenue due to lackluster retention and graduation rates. It is time for change! Bergen Community College (BCC) has made a unique commitment to concentrate solely on this issue. Learn how the establishment of the Department of Retention Services, with its cutting edge initiatives, is…
31 CFR 1010.430 - Nature of records and retention period.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 31 Money and Finance:Treasury 3 2012-07-01 2012-07-01 false Nature of records and retention period... Required To Be Maintained § 1010.430 Nature of records and retention period. (a) Wherever it is required... such a way as to be accessible within a reasonable period of time, taking into consideration the nature...
31 CFR 1010.430 - Nature of records and retention period.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false Nature of records and retention period... Required To Be Maintained § 1010.430 Nature of records and retention period. (a) Wherever it is required... such a way as to be accessible within a reasonable period of time, taking into consideration the nature...
31 CFR 1010.430 - Nature of records and retention period.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false Nature of records and retention period... Required To Be Maintained § 1010.430 Nature of records and retention period. (a) Wherever it is required... such a way as to be accessible within a reasonable period of time, taking into consideration the nature...
31 CFR 1010.430 - Nature of records and retention period.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 31 Money and Finance:Treasury 3 2013-07-01 2013-07-01 false Nature of records and retention period... Required To Be Maintained § 1010.430 Nature of records and retention period. (a) Wherever it is required... such a way as to be accessible within a reasonable period of time, taking into consideration the nature...
The Relationship between Retention and College Counseling for High-risk Students

ERIC Educational Resources Information Center

Bishop, Kyle K.

2016-01-01

The author used an archival study to explore the relationship between college counseling and retention. The cohort for this study was a college's 2006 class of full-time, 1st-year students (N = 429). The results of chi-square analyses and regression analyses indicated (a) a significant difference in retention between high-risk and low-risk…
Simplified tools for measuring retention in care in antiretroviral treatment program in Ethiopia: cohort and current retention in care.

PubMed

Assefa, Yibeltal; Worku, Alemayehu; Wouters, Edwin; Koole, Olivier; Haile Mariam, Damen; Van Damme, Wim

2012-01-01

Patient retention in care is a critical challenge for antiretroviral treatment programs. This is mainly because retention in care is related to adherence to treatment and patient survival. It is therefore imperative that health facilities and programs measure patient retention in care. However, the currently available tools, such as Kaplan Meier, for measuring retention in care have a lot of practical limitations. The objective of this study was to develop simplified tools for measuring retention in care. Retrospective cohort data were collected from patient registers in nine health facilities in Ethiopia. Retention in care was the primary outcome for the study. Tools were developed to measure "current retention" in care during a specific period of time for a specific "ART-age group" and "cohort retention" in care among patients who were followed for the last "Y" number of years on ART. "Probability of retention" based on the tool for "cohort retention" in care was compared with "probability of retention" based on Kaplan Meier. We found that the new tools enable to measure "current retention" and "cohort retention" in care. We also found that the tools were easy to use and did not require advanced statistical skills. Both "current retention" and "cohort retention" are lower among patients in the first two "ART-age groups" and "ART-age cohorts" than in subsequent "ART-age groups" and "ART-age cohorts". The "probability of retention" based on the new tools were found to be similar to the "probability of retention" based on Kaplan Meier. The simplified tools for "current retention" and "cohort retention" will enable practitioners and program managers to measure and monitor rates of retention in care easily and appropriately. We therefore recommend that health facilities and programs start to use these tools in their efforts to improve retention in care and patient outcomes.
Retention modeling under organic modifier gradient conditions in ion-pair reversed-phase chromatography. Application to the separation of a set of underivatized amino acids.

PubMed

Pappa-Louisi, A; Agrafiotou, P; Papachristos, K

2010-07-01

The combined effect of the ion-pairing reagent concentration, C(ipr), and organic modifier content, phi, on the retention under phi-gradient conditions at different constant C(ipr) was treated in this study by using two approaches. In the first approach, the prediction of the retention time of a sample solute is based on a direct fitting procedure of a proper retention model to 3-D phi-gradient retention data obtained under the same phi-linear variation but with different slope and time duration of the initial isocratic part and in the presence of various constant C(ipr) values in the eluent. The second approach is based on a retention model describing the combined effect of C(ipr) and phi on the retention of solutes in isocratic mode and consequently analyzes isocratic data obtained in mobile phases containing different C(ipr) values. The effectiveness of the above approaches was tested in the retention prediction of a mixture of 16 underivatized amino acids using mobile phases containing acetonitrile as organic modifier and sodium dodecyl sulfate as ion-pairing reagent. From these approaches, only the first one gives satisfactory predictions and can be successfully used in optimization of ion-pair chromatographic separations under gradient conditions. The failure of the second approach to predict the retention of solutes in the gradient elution mode in the presence of different C(ipr) values was attributed to slow changes in the distribution equilibrium of ion-pairing reagents caused by phi-variation.
Retention of Adult Patients on Antiretroviral Therapy in Low- and Middle-Income Countries: Systematic Review and Meta-analysis 2008-2013.

PubMed

Fox, Matthew P; Rosen, Sydney

2015-05-01

We previously published systematic reviews of retention in care after antiretroviral therapy initiation among general adult populations in sub-Saharan Africa. We estimated 36-month retention at 73% for publications from 2007 to 2010. This report extends the review to cover 2008-2013 and expands it to all low- and middle-income countries. We searched PubMed, Embase, Cochrane Register, and ISI Web of Science from January 1, 2008, to December 31, 2013, and abstracts from AIDS and IAS from 2008-2013. We estimated retention across cohorts using simple averages and interpolated missing times through the last time reported. We estimated all-cause attrition (death, loss to follow-up) for patients receiving first-line antiretroviral therapy in routine settings in low- and middle-income countries. We found 123 articles and abstracts reporting retention for 154 patient cohorts and 1,554,773 patients in 42 countries. Overall, 43% of all patients not retained were known to have died. Unweighted averages of reported retention were 78%, 71%, and 69% at 12, 24, and 36 months, after treatment initiation, respectively. We estimated 36-month retention at 65% in Africa, 80% in Asia, and 64% in Latin America and the Caribbean. From lifetable analysis, we estimated retention at 12, 24, 36, 48, and 60 months at 83%, 74%, 68%, 64%, and 60%, respectively. Retention at 36 months on treatment averages 65%-70%. There are several important gaps in the evidence base, which could be filled by further research, especially in terms of geographic coverage and duration of follow-up.

Using theory and formative research to design interventions to improve community health worker motivation, retention and performance in Mozambique and Uganda.

PubMed

Strachan, Daniel Llywelyn; Källander, Karin; Nakirunda, Maureen; Ndima, Sozinho; Muiambo, Abel; Hill, Zelee

2015-04-30

Community health workers (CHWs) are increasingly being used in low-income countries to address human resources shortages, yet there remain few effective, evidence-based strategies for addressing the enduring programmatic constraints of worker motivation, retention and performance. This paper describes how two interventions were designed by the Innovations at Scale for Community Access and Lasting Effects (inSCALE) project to address these constraints in Uganda and Mozambique drawing on behavioural theory and formative research results. A review of the work motivation and CHW motivation literature--incorporating influences on retention and performance--was conducted on articles sourced through electronic web searches. Formative research with a focus on the barriers and facilitators to CHW motivation, retention and performance was conducted with community health workers and key stakeholders in Uganda and Mozambique. An analytical induction approach to the thematic analysis of transcripts from 98 in-depth interviews and 26 focus group discussions was adopted across the country settings. From the theoretical review, it was determined that the interventions should promote CHWs as members of a collective by highlighting a sense of shared experience, focus on alignment between worker and programme goals, and emphasise the actions that lead to good performance. The Social Identity Approach was selected as the theory most likely to lead to the development of effective, scalable and sustainable interventions by addressing the identified gap in the literature of the influence of CHW working context. The formative research indicated that CHWs value feedback and feeling connected to the health system and their community, are motivated by status and community standing, and want to be provided with the necessary tools to perform. Two interventions based on these results were developed: a participatory, local community approach and an information communication technology (ICT) approach. Drawing on contextual data and theory that is sensitive to context can potentially lead to the development of appropriate and effective interventions when aiming to improve the motivation, retention and performance of CHWs in Uganda and Mozambique and other comparable settings. Evaluation of the developed interventions is crucial to assess this potential.
Improving Attendance and Retention in Out-of-School Time Programs. Research-to-Results Practitioner Insights. Publication # 2007-17

ERIC Educational Resources Information Center

Kennedy, Elena; Wilson, Brooke; Valladares, Sherylls; Bronte-Tinkew, Jacinta

2007-01-01

Regular participation in out-of-school time activities is associated with benefits for children. However, children cannot reap the benefits of program participation if they do not attend programs in the first place. This brief focuses on ways in which out-of-school time programs can improve the attendance and retention of children and youth in…
Retention of autobiographical memories: an Internet-based diary study.

PubMed

Kristo, Gert; Janssen, Steve M J; Murre, Jaap M J

2009-11-01

In this online study we examined the retention of recent personal events using an Internet-based diary technique. Each participant (N=878) recorded on a website one recent personal event and was contacted after a retention interval that ranged between 2 and 46 days. We investigated how well the participants could recall the content, time, and details of their recorded event. We found a classic retention function. Details of the events were forgotten more rapidly than the content and the time of the events. There were no differences between the forgetting rates of the "who", "what" and "where" elements of the content component. Reminiscing, social sharing, pleasantness, and frequency of occurrence aided recall, but surprisingly importance and emotionality did not. They were, however, strongly associated with reminiscing and social sharing.
A Novel Adaptive H∞ Filtering Method with Delay Compensation for the Transfer Alignment of Strapdown Inertial Navigation Systems

PubMed Central

Lyu, Weiwei

2017-01-01

Transfer alignment is always a key technology in a strapdown inertial navigation system (SINS) because of its rapidity and accuracy. In this paper a transfer alignment model is established, which contains the SINS error model and the measurement model. The time delay in the process of transfer alignment is analyzed, and an H∞ filtering method with delay compensation is presented. Then the H∞ filtering theory and the robust mechanism of H∞ filter are deduced and analyzed in detail. In order to improve the transfer alignment accuracy in SINS with time delay, an adaptive H∞ filtering method with delay compensation is proposed. Since the robustness factor plays an important role in the filtering process and has effect on the filtering accuracy, the adaptive H∞ filter with delay compensation can adjust the value of robustness factor adaptively according to the dynamic external environment. The vehicle transfer alignment experiment indicates that by using the adaptive H∞ filtering method with delay compensation, the transfer alignment accuracy and the pure inertial navigation accuracy can be dramatically improved, which demonstrates the superiority of the proposed filtering method. PMID:29182592
One-year retention of general and sequence-specific skills in a probabilistic, serial reaction time task.

PubMed

Romano, Jennifer C; Howard, James H; Howard, Darlene V

2010-05-01

Procedural skills such as riding a bicycle and playing a musical instrument play a central role in daily life. Such skills are learned gradually and are retained throughout life. The present study investigated 1-year retention of procedural skill in a version of the widely used serial reaction time task (SRTT) in young and older motor-skill experts and older controls in two experiments. The young experts were college-age piano and action video-game players, and the older experts were piano players. Previous studies have reported sequence-specific skill retention in the SRTT as long as 2 weeks but not at 1 year. Results indicated that both young and older experts and older non-experts revealed sequence-specific skill retention after 1 year with some evidence that general motor skill was retained as well. These findings are consistent with theoretical accounts of procedural skill learning such as the procedural reinstatement theory as well as with previous studies of retention of other motor skills.
Relationship between nanotopographical alignment and stem cell fate with live imaging and shape analysis

NASA Astrophysics Data System (ADS)

Newman, Peter; Galenano-Niño, Jorge Luis; Graney, Pamela; Razal, Joselito M.; Minett, Andrew I.; Ribas, João; Ovalle-Robles, Raquel; Biro, Maté; Zreiqat, Hala

2016-12-01

The topography of a biomaterial regulates cellular interactions and determine stem cell fate. A complete understanding of how topographical properties affect cell behavior will allow the rational design of material surfaces that elicit specified biological functions once placed in the body. To this end, we fabricate substrates with aligned or randomly organized fibrous nanostructured topographies. Culturing adipose-derived stem cells (ASCs), we explore the dynamic relationship between the alignment of topography, cell shape and cell differentiation to osteogenic and myogenic lineages. We show aligned topographies differentiate cells towards a satellite cell muscle progenitor state - a distinct cell myogenic lineage responsible for postnatal growth and repair of muscle. We analyze cell shape between the different topographies, using fluorescent time-lapse imaging over 21 days. In contrast to previous work, this allows the direct measurement of cell shape at a given time rather than defining the morphology of the underlying topography and neglecting cell shape. We report quantitative metrics of the time-based morphological behaviors of cell shape in response to differing topographies. This analysis offers insights into the relationship between topography, cell shape and cell differentiation. Cells differentiating towards a myogenic fate on aligned topographies adopt a characteristic elongated shape as well as the alignment of cells.
Transient, Small-Scale Field-Aligned Currents in the Plasma Sheet Boundary Layer During Storm Time Substorms

NASA Technical Reports Server (NTRS)

Nakamura, R.; Sergeev, V. A.; Baumjohann, W.; Plaschke, F.; Magnes, W.; Fischer, D.; Varsani, A.; Schmid, D.; Nakamura, T. K. M.; Russell, C. T.;

2016-01-01

We report on field-aligned current observations by the four Magnetospheric Multiscale (MMS) spacecraft near the plasma sheet boundary layer (PSBL) during two major substorms on 23 June 2015. Small-scale field-aligned currents were found embedded in fluctuating PSBL flux tubes near the Separatrix region. We resolve, for the first time, short-lived earthward (downward) intense field-aligned current sheets with thicknesses of a few tens of kilometers, which are well below the ion scale, on flux tubes moving equatorward earth ward during outward plasma sheet expansion. They coincide with upward field-aligned electron beams with energies of a few hundred eV. These electrons are most likely due to acceleration associated with a reconnection jet or high-energy ion beam-produced disturbances. The observations highlight coupling of multiscale processes in PSBL as a consequence of magnetotail reconnection.

Transient, small-scale field-aligned currents in the plasma sheet boundary layer during storm time substorms.

PubMed

Nakamura, R; Sergeev, V A; Baumjohann, W; Plaschke, F; Magnes, W; Fischer, D; Varsani, A; Schmid, D; Nakamura, T K M; Russell, C T; Strangeway, R J; Leinweber, H K; Le, G; Bromund, K R; Pollock, C J; Giles, B L; Dorelli, J C; Gershman, D J; Paterson, W; Avanov, L A; Fuselier, S A; Genestreti, K; Burch, J L; Torbert, R B; Chutter, M; Argall, M R; Anderson, B J; Lindqvist, P-A; Marklund, G T; Khotyaintsev, Y V; Mauk, B H; Cohen, I J; Baker, D N; Jaynes, A N; Ergun, R E; Singer, H J; Slavin, J A; Kepko, E L; Moore, T E; Lavraud, B; Coffey, V; Saito, Y

2016-05-28

We report on field-aligned current observations by the four Magnetospheric Multiscale (MMS) spacecraft near the plasma sheet boundary layer (PSBL) during two major substorms on 23 June 2015. Small-scale field-aligned currents were found embedded in fluctuating PSBL flux tubes near the separatrix region. We resolve, for the first time, short-lived earthward (downward) intense field-aligned current sheets with thicknesses of a few tens of kilometers, which are well below the ion scale, on flux tubes moving equatorward/earthward during outward plasma sheet expansion. They coincide with upward field-aligned electron beams with energies of a few hundred eV. These electrons are most likely due to acceleration associated with a reconnection jet or high-energy ion beam-produced disturbances. The observations highlight coupling of multiscale processes in PSBL as a consequence of magnetotail reconnection.
A Central Positron Source to Perform the Timing Alignment of Detectors in a PET Scanner

NASA Astrophysics Data System (ADS)

Thompson, C. J.; Camborde, M.-L.; Casey, M. E.

2005-10-01

Accurate timing alignment and stability are important to maximize the true counts and minimize the random counts in positron emission tomography. Its importance increases in time-of-flight (TOF) scanners. We propose using a central positron emitting source enclosed in a detector which detects the excess energy of the positron before it annihilates as a timing reference. All crystals can be time-aligned with respect to this central source. We evaluated 10 /spl mu/Ci /sup 22/Na and /sup 68/Ge sources embedded in cylinders of plastic scintillator coupled to a fast PMT. Light flashes produced after the parent isotope emits positrons are detected, and the anode signals from the PMT are the reference time for each positron decay. The time delay before the gamma ray is detected by the scanner's conventional gamma ray detectors is the time offset to be applied to that crystal. Since all detectors are almost the same distance from the central source, TOF errors are minimized. Preliminary results show a mean signal amplitude of >0.5 V from /sup 22/Na at 1000-V PMT bias, a timing FWHM of 850 ps with respect to a small LSO crystal. This suggests it could be useful to align both conventional and TOF PET scanners.
The spatial alignment of time: Differences in alignment of deictic and sequence time along the sagittal and lateral axes.

PubMed

Walker, Esther J; Bergen, Benjamin K; Núñez, Rafael

2017-04-01

People use space in a variety of ways to structure their thoughts about time. The present report focuses on the different ways that space is employed when reasoning about deictic (past/future relationships) and sequence (earlier/later relationships) time. In the first study, we show that deictic and sequence time are aligned along the lateral axis in a manner consistent with previous work, with past and earlier events associated with left space and future and later events associated with right space. However, the alignment of time with space is different along the sagittal axis. Participants associated future events and earlier events-not later events-with the space in front of their body and past and later events with the space behind, consistent with the sagittal spatial terms (e.g., ahead, in front of) that we use to talk about deictic and sequence time. In the second study, we show that these associations between sequence time and sagittal space are sensitive to person-perspective. This suggests that the particular space-time associations observed in English speakers are influenced by a variety of different spatial properties, including spatial location and perspective. Copyright © 2016. Published by Elsevier B.V.
Use of SIG device to accurately place permanent miniature dental implants to retain mandibular overdenture. A case report.

PubMed

Sussman, Harold I; Goodridge, Opal F

2006-01-01

A case of mini-dental implant insertion for retention of a mandibular overdenture in a hospitalized patient has been documented. The additional use of the SIG (drill guide) directional device in the implant placement protocol gave the practitioner more confidence and resulted in the proper alignment of the three ball-top, one-piece fixtures. The three implants were inserted exactly 1 cm apart and parallel to each other. The distal fixtures were approximately 1 cm away from the mental foramina, thereby eliminating the risk of lip paresthesia. Keeper caps were placed in the denture's intaglio after one month. The keeper caps allowed for proper retention of the overdenture. The caps also enabled the patient to easily insert and withdraw his denture, even though he displayed limited manual dexterity. The tissue response was excellent, and oral hygiene was made easier with adequate spacing of the exposed ball-tops. The overall experience for both the operator and the patient was very positive. General dentists should be able to readily master this technique and add it to their armamentarium for the benefit of all their patients.
Edgar Dale's Pyramid of Learning in medical education: a literature review.

PubMed

Masters, Ken

2013-11-01

Edgar Dale's Pyramid of Learning and percentages of retained learning are cited in educational literature in a range of disciplines. The sources of the Pyramid, however, are misleading. To examine the evidence supporting the Pyramid and the extent to which it is cited in medical education literature. A review of literature (1946-2012) based on a search utilising Academic Search Complete, CINAHL, Medline and Google Scholar conducted from September to November 2012. A total of 43 peer-reviewed medical education journal articles and conference papers were found. While some researchers had been misled by their sources, other authors' interpretations of the citations did not align with the content of those citations, had no such citations, had circular references, or consulted questionable sources. There was no agreement on the percentages of learning retention, in spite of many researchers' citing primary texts. The inappropriate citing of the Pyramid and its associated percentages in medical education literature is widespread and continuous. This citing undermines much of the published work, and impacts on research-based medical education literature. While the area of learning/teaching strategies and amount of retention from each is an area for future research, any reference to the Pyramid should be avoided.
A fully automated and scalable timing probe-based method for time alignment of the LabPET II scanners

NASA Astrophysics Data System (ADS)

Samson, Arnaud; Thibaudeau, Christian; Bouchard, Jonathan; Gaudin, Émilie; Paulin, Caroline; Lecomte, Roger; Fontaine, Réjean

2018-05-01

A fully automated time alignment method based on a positron timing probe was developed to correct the channel-to-channel coincidence time dispersion of the LabPET II avalanche photodiode-based positron emission tomography (PET) scanners. The timing probe was designed to directly detect positrons and generate an absolute time reference. The probe-to-channel coincidences are recorded and processed using firmware embedded in the scanner hardware to compute the time differences between detector channels. The time corrections are then applied in real-time to each event in every channel during PET data acquisition to align all coincidence time spectra, thus enhancing the scanner time resolution. When applied to the mouse version of the LabPET II scanner, the calibration of 6 144 channels was performed in less than 15 min and showed a 47% improvement on the overall time resolution of the scanner, decreasing from 7 ns to 3.7 ns full width at half maximum (FWHM).
Effects of Feedback Frequency and Timing on Acquisition, Retention, and Transfer of Speech Skills in Acquired Apraxia of Speech

ERIC Educational Resources Information Center

Hula, Shannon N. Austermann; Robin, Donald A.; Maas, Edwin; Ballard, Kirrie J.; Schmidt, Richard A.

2008-01-01

Purpose: Two studies examined speech skill learning in persons with apraxia of speech (AOS). Motor-learning research shows that delaying or reducing the frequency of feedback promotes retention and transfer of skills. By contrast, immediate or frequent feedback promotes temporary performance enhancement but interferes with retention and transfer.…
First-Year Response on an Upland Hardwood Forest to Five Levels of Overstory Tree Retention

Treesearch

Callie Jo Schweitzer

2004-01-01

Response of a north Alabama upland oak-hickory forest to five levels of overstory tree retention was compared following treatment. Fifty-acre experimental blocks were established on the mid-Cumberland Plateau, which included the highly dissected margins and sides of the southern subregion. Blocks were replicated three times. Each of the five retention treatments (...
Acquisition, retention and transfer of simulated laparoscopic tasks using fNIR and a contextual interference paradigm.

PubMed

Shewokis, Patricia A; Shariff, Faiz U; Liu, Yichuan; Ayaz, Hasan; Castellanos, Andres; Lind, D Scott

2017-02-01

Using functional near infrared spectroscopy, a noninvasive, optical brain imaging tool that monitors changes in hemodynamics within the prefrontal cortex (PFC), we assessed performance and cognitive effort during the acquisition, retention and transfer of multiple simulated laparoscopic tasks by novice learners within a contextual interference paradigm. Third-year medical students (n = 10) were randomized to either a blocked or random practice schedule. Across 3 days, students performed 108 acquisition trials of 3 laparoscopic tasks on the LapSim ® simulator followed by delayed retention and transfer tests. Performance metrics (Global score, Total time) and hemodynamic responses (total hemoglobin (μm)) were assessed during skill acquisition, retention and transfer. All acquisition tasks resulted in significant practice schedule X trial block interactions for the left medial anterior PFC. During retention and transfer, random performed the skills in less time and had lower total hemoglobin change in the right dorsolateral PFC than blocked. Compared with blocked, random practice resulted in enhanced learning through better performance and less cognitive load for retention and transfer of simulated laparoscopic tasks. Copyright © 2016 Elsevier Inc. All rights reserved.
Efficacy of humidity retention bags for the reduced adsorption and improved cleaning of tissue proteins including prion-associated amyloid to surgical stainless steel surfaces.

PubMed

Secker, T J; Pinchin, H E; Hervé, R C; Keevil, C W

2015-01-01

Increasing drying time adversely affects attachment of tissue proteins and prion-associated amyloid to surgical stainless steel, and reduces the efficacy of commercial cleaning chemistries. This study tested the efficacy of commercial humidity retention bags to reduce biofouling on surgical stainless steel and to improve subsequent cleaning. Surgical stainless steel surfaces were contaminated with ME7-infected brain homogenates and left to dry for 15 to 1,440 min either in air, in dry polythene bags or within humidity retention bags. Residual contamination pre/post cleaning was analysed using Thioflavin T/SYPRO Ruby dual staining and microscope analysis. An increase in biofouling was observed with increased drying time in air or in sealed dry bags. Humidity retention bags kept both protein and prion-associated amyloid minimal across the drying times both pre- and post-cleaning. Therefore, humidity bags demonstrate a cheap, easy to implement solution to improve surgical instrument reprocessing and to potentially reduce associated hospital acquired infections.
Everyday attention and lecture retention: the effects of time, fidgeting, and mind wandering.

PubMed

Farley, James; Risko, Evan F; Kingstone, Alan

2013-01-01

We have all had our thoughts wander from the immediate task at hand. The emerging embodied cognition literature emphasizes the role that the body plays in human thought, and raises the possibility that changes in attentional focus may be associated with changes in body behavior. Recent research has found that when individuals view a lecture, mind wandering increases as a function of time. In the present study we asked whether this decline in attention during lecture viewing was associated with fidgeting. Participants were filmed while they watched a 40-min lecture video, and at regular 5-min intervals provided ratings of their attentiveness. Following the lecture, participant's memory for the material was assessed. Fidgeting behavior was coded from video recordings of each session. Results indicated that attention to, and retention of, lecture material declined as a function of time on task. Critically, and as predicted, fidgeting also increased with time on task. We also found that the relation between fidgeting and retention was significant even when the role of attention was factored into the equation, suggesting that fidgeting makes a unique contribution to retention of lecture material over and above that contributed by an individual's attention. We propose a novel non-attentional stress-based account of fidgeting and how this impacts retention for lecture material over and above changes in levels in mind wandering vis-a-vis changes in attention.
The comparation of effects and security of double-J stent retention and ureteroscopy lithotripsy in the treatment of symptomatic ureteral calculi during pregnancy.

PubMed

Tan, Shu-Tao; Chen, Xiaonan; Sun, Ming; Wu, Bin

2018-06-01

To describe the efficacy of double-J stent retention and ureteroscopy lithotripsy, we performed a study to evaluate the management of symptomatic ureteral calculi during pregnancy. From January 2005 and June 2015, 53 pregnant women with symptomatic ureteral calculi were admitted and treated in our hospital. According to the treatment techniques, there were divided into two groups: double-J stent retention group (30 cases) and ureteroscopy lithotripsy group (23 cases). We collected the characteristics and treatment outcome of the patients. Double-J stent retention was performed on 30 patients. And the stents were successfully inserted in 25 patients (83.3%). 4 cases got complication in double-J group (16%). The mean operating time, medical cost and hospitalization time of double-J group were 20.6 min, 1632 yuan and 1.3 days. Ureteroscopy lithotripsy was performed on 23 patients. 20 patients were operated successfully (87.0%). 2 cases got complication in ureteroscopy group (10.0%). The mean operating time, medical cost and hospitalization time of ureteroscopy group were 41.5 min, 2792 yuan and 6.0 days. In summary, both double-J stent retention and ureteroscopy lithotripsy are effective and safe in the managation of ureteral calculi during pregnancy. Copyright © 2018 Elsevier B.V. All rights reserved.
Post retention: the effect of sequence of post-space preparation, cementation time, and different sealers.

PubMed

Boone, K J; Murchison, D F; Schindler, W G; Walker, W A

2001-12-01

Many endodontic sealers contain constituents that have been shown to inhibit the polymerization of resin cements. This may be important when prefabricated posts are cemented at the same appointment as root canal obturation. This study evaluated the effects of cementing posts with a resin cement immediately or at a delayed time period after obturation using Roth's 801 Elite Grade or AH26 sealer cements. The contribution of mechanical post-space preparation was also assessed as a critical variable. One hundred twenty extracted canines were randomly divided into eight experimental groups. The variables evaluated were the order of post preparation (either before or after obturation), the type of sealer used, and the time of post cementation. All teeth received a stainless steel #6 Parapost XP cemented with a resin cement, Panavia 21. Each experimental group underwent tensile testing for retention using an Instron universal testing machine. For both sealers posts cemented in teeth in which the canal was obturated before post-space preparation and thus had sealer-contaminated dentin removed by the space preparation procedure had significantly higher retentive values than those obturated after post-space preparation in which contaminated dentin might remain. Sealer used and time of cementation had no specific effect on retention. Achieving a clean, "freshened" dentinal surface during mechanical post-space preparation seems to be a critical variable for post retention when a resin cement is used.

Everyday attention and lecture retention: the effects of time, fidgeting, and mind wandering

PubMed Central

Farley, James; Risko, Evan F.; Kingstone, Alan

2013-01-01

We have all had our thoughts wander from the immediate task at hand. The emerging embodied cognition literature emphasizes the role that the body plays in human thought, and raises the possibility that changes in attentional focus may be associated with changes in body behavior. Recent research has found that when individuals view a lecture, mind wandering increases as a function of time. In the present study we asked whether this decline in attention during lecture viewing was associated with fidgeting. Participants were filmed while they watched a 40-min lecture video, and at regular 5-min intervals provided ratings of their attentiveness. Following the lecture, participant's memory for the material was assessed. Fidgeting behavior was coded from video recordings of each session. Results indicated that attention to, and retention of, lecture material declined as a function of time on task. Critically, and as predicted, fidgeting also increased with time on task. We also found that the relation between fidgeting and retention was significant even when the role of attention was factored into the equation, suggesting that fidgeting makes a unique contribution to retention of lecture material over and above that contributed by an individual's attention. We propose a novel non-attentional stress-based account of fidgeting and how this impacts retention for lecture material over and above changes in levels in mind wandering vis-a-vis changes in attention. PMID:24065933
Motivational barriers to retention of at-risk young adults in HIV-prevention interventions: perceived pressure and efficacy.

PubMed

Liu, Jiaying; Jones, Christopher; Wilson, Kristina; Durantini, Marta R; Livingood, William; Albarracín, Dolores

2014-01-01

Multi-session HIV-prevention interventions are efficacious but depend on the retention of clients over time. In a sample of at-risk young adults (N = 386), we investigated three potential motivational barriers that might affect the likelihood of retention. Perceived pressure, perceived efficacy and fear and anxiety during the initial session were measured, along with demographic characteristics, partner characteristics, and HIV-related health knowledge. Logistic regressions demonstrated that (1) in general, perceived ineffectiveness was negatively associated with retention; (2) perceived pressure or coercion was negatively associated with retention but only for younger clients; (3) experienced fear and anxiety had no significant association with retention. Implications for theory and counseling practices to reduce motivational barriers and effectively tailor interventions are discussed.
Motivational barriers to retention of at-risk young adults in HIV-prevention interventions: Perceived pressure and efficacy

PubMed Central

Liu, Jiaying; Jones, Christopher; Wilson, Kristina; Durantini, Marta R.; Livingood, William; Albarracín, Dolores

2014-01-01

Multi-session HIV-prevention interventions are efficacious but depend on the retention of clients over time. In a sample of at-risk young adults (N = 386), we investigated three potential motivational barriers that might affect the likelihood of retention. Perceived pressure, perceived efficacy and fear and anxiety during the initial session were measured, along with demographic characteristics, partner characteristics, and HIV-related health knowledge. Logistic regression demonstrated that (1) in general, perceived ineffectiveness was negatively associated with retention; (2) perceived pressure or coercion was negatively associated with retention, but only for younger clients; (3) experienced fear and anxiety had no significant association with retention. Implications for theory and counseling practices to reduce motivational barriers and effectively tailor interventions are discussed. PMID:24641552
Reversing the Course of Forgetting

PubMed Central

White, K. Geoffrey; Brown, Glenn S

2011-01-01

Forgetting functions were generated for pigeons in a delayed matching-to-sample task, in which accuracy decreased with increasing retention-interval duration. In baseline training with dark retention intervals, accuracy was high overall. Illumination of the experimental chamber by a houselight during the retention interval impaired performance accuracy by increasing the rate of forgetting. In novel conditions, the houselight was lit at the beginning of a retention interval and then turned off partway through the retention interval. Accuracy was low at the beginning of the retention interval and then increased later in the interval. Thus the course of forgetting was reversed. Such a dissociation of forgetting from the passage of time is consistent with an interference account in which attention or stimulus control switches between the remembering task and extraneous events. PMID:21909163
Determining the Cost-Savings Threshold and Alignment Accuracy of Patient-Specific Instrumentation in Total Ankle Replacements.

PubMed

Hamid, Kamran S; Matson, Andrew P; Nwachukwu, Benedict U; Scott, Daniel J; Mather, Richard C; DeOrio, James K

2017-01-01

Traditional intraoperative referencing for total ankle replacements (TARs) involves multiple steps and fluoroscopic guidance to determine mechanical alignment. Recent adoption of patient-specific instrumentation (PSI) allows for referencing to be determined preoperatively, resulting in less steps and potentially decreased operative time. We hypothesized that usage of PSI would result in decreased operating room time that would offset the additional cost of PSI compared with standard referencing (SR). In addition, we aimed to compare postoperative radiographic alignment between PSI and SR. Between August 2014 and September 2015, 87 patients undergoing TAR were enrolled in a prospectively collected TAR database. Patients were divided into cohorts based on PSI vs SR, and operative times were reviewed. Radiographic alignment parameters were retrospectively measured at 6 weeks postoperatively. Time-driven activity-based costing (TDABC) was used to derive direct costs. Cost vs operative time-savings were examined via 2-way sensitivity analysis to determine cost-saving thresholds for PSI applicable to a range of institution types. Cost-saving thresholds defined the price of PSI below which PSI would be cost-saving. A total of 35 PSI and 52 SR cases were evaluated with no significant differences identified in patient characteristics. Operative time from incision to completion of casting in cases without adjunct procedures was 127 minutes with PSI and 161 minutes with SR ( P < .05). PSI demonstrated similar postoperative accuracy to SR in coronal tibial-plafond alignment (1.1 vs 0.3 degrees varus, P = .06), tibial-plafond alignment (0.3 ± 2.1 vs 1.1 ± 2.1 degrees varus, P = .06), and tibial component sagittal alignment (0.7 vs 0.9 degrees plantarflexion, P = .14). The TDABC method estimated a PSI cost-savings threshold range at our institution of $863 below which PSI pricing would provide net cost-savings. Two-way sensitivity analysis generated a globally applicable cost-savings threshold model based on institution-specific costs and surgeon-specific time-savings. This study demonstrated equivalent postoperative TAR alignment with PSI and SR referencing systems but with a significant decrease in operative time with PSI. Based on TDABC and associated sensitivity analysis, a cost-savings threshold of $863 was identified for PSI pricing at our institution below which PSI was less costly than SR. Similar internal cost accounting may benefit health care systems for identifying cost drivers and obtaining leverage during price negotiations. Level III, therapeutic study.
Functional Alignment of Metabolic Networks.

PubMed

Mazza, Arnon; Wagner, Allon; Ruppin, Eytan; Sharan, Roded

2016-05-01

Network alignment has become a standard tool in comparative biology, allowing the inference of protein function, interaction, and orthology. However, current alignment techniques are based on topological properties of networks and do not take into account their functional implications. Here we propose, for the first time, an algorithm to align two metabolic networks by taking advantage of their coupled metabolic models. These models allow us to assess the functional implications of genes or reactions, captured by the metabolic fluxes that are altered following their deletion from the network. Such implications may spread far beyond the region of the network where the gene or reaction lies. We apply our algorithm to align metabolic networks from various organisms, ranging from bacteria to humans, showing that our alignment can reveal functional orthology relations that are missed by conventional topological alignments.
Fast Gradient Elution Reversed-Phase HPLC with Diode-Array Detection as a High Throughput Screening Method for Drugs of Abuse

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

Peter W. Carr; K.M. Fuller; D.R. Stoll

A new approach has been developed by modifying a conventional gradient elution liquid chromatograph for the high throughput screening of biological samples to detect the presence of regulated intoxicants. The goal of this work was to improve the speed of a gradient elution screening method over current approaches by optimizing the operational parameters of both the column and the instrument without compromising the reproducibility of the retention times, which are the basis for the identification. Most importantly, the novel instrument configuration substantially reduces the time needed to re-equilibrate the column between gradient runs, thereby reducing the total time for eachmore » analysis. The total analysis time for each gradient elution run is only 2.8 minutes, including 0.3 minutes for column reequilibration between analyses. Retention times standard calibration solutes are reproducible to better than 0.002 minutes in consecutive runs. A corrected retention index was adopted to account for day-to-day and column-to-column variations in retention time. The discriminating power and mean list length were calculated for a library of 47 intoxicants and compared with previous work from other laboratories to evaluate fast gradient elution HPLC as a screening tool.« less
[Fiber-reinforced composite in fixed prosthodontics].

PubMed

Pilo, R; Abu Rass, Z; Shmidt, A

2010-07-01

Fiber reinforced composite (FRC) is composed of resin matrix and fibers filler. Common types of fibers: polyethylene, carbon and glass. Fibers can be continuous and aligned, discontinuous and aligned, discontinuous and randomly oriented. The architecture of the fibers is unidirectional, woven or braided. The two main types are: dry fibers or impregnated. Inclusion of fibers to resin composite increased its average flexural strength in 100-200 MPa. FRC can be utilized by the dentist in direct approach (splinting, temporary winged bridge) or indirect approach (laboratory made fixed partial denture). Laboratory fixed partial denture (FPD) is made from FRC substructure and Hybrid/Microfill particulate composite veneer. Main indications: interim temporary FPD or FPD in cases of questionable abutment teeth, in aesthetic cases where All Ceram FPD is not feasible. Retention is attained by adhesive cementation to minimally prepared teeth or to conventionally prepared teeth; other options are inlay-onlay bridges or hybrid bridges. Contraindications are: poor hygiene, inability to control humidity, parafunction habits, and more than two pontics. Survival rate of FRC FPD over 5 years is 75%, lower compared to porcelain fused to metal FPD which is 95%. Main reasons for failure are: fracture of framework and delamination of the veneer. Part of the failures is repairable.
Does skill retention benefit from retentivity and symbolic rehearsal? - two studies with a simulated process control task.

PubMed

Kluge, Annette; Frank, Barbara; Maafi, Sanaz; Kuzmanovska, Aleksandra

2016-05-01

Two experiments were designed to compare two symbolic rehearsal refresher interventions (imaginary practice, a hidden introspective process) and investigate the role of retentivity in skill retention. Retentivity is investigated as the ability to memorise and reproduce information and associations that were learned a short time ago. Both experiments comprised initial training (week 1), a symbolic rehearsal for the experimental group (week 2) and a retention assessment (week 3). In the first study, the experimental group received a symbolic rehearsal, while the control group received no rehearsal. In the second study, the experimental group received the same symbolic rehearsal used in study 1, enhanced with rehearsal tasks addressing human-computer interaction. The results showed that both symbolic rehearsal interventions were equally likely to mitigate skill decay. The retentivity showed medium to high correlations with skill retention in both studies, and the results suggest that subjects high in retentivity benefit more from a symbolic rehearsal refresher intervention. Practitioner Summary: Skill decay becomes a problem in situations in which jobs require the correct mastery of non-routine situations. Two experimental studies with simulated process control tasks showed that symbolic rehearsal and retentivity can significantly mitigate skill decay and that subjects higher in retentivity benefit more from refresher interventions.
Factors Influencing Retention Among Part-Time Clinical Nursing Faculty.

PubMed

Carlson, Joanne S

This study sought to determine job characteristics influencing retention of part-time clinical nurse faculty teaching in pre-licensure nursing education. Large numbers of part-time faculty are needed to educate students in the clinical setting. Faculty retention helps maintain consistency and may positively influence student learning. A national sample of part-time clinical nurse faculty teaching in baccalaureate programs responded to a web-based survey. Respondents were asked to identify the primary reason for wanting or not wanting to continue working for a school of nursing (SON). Affinity for students, pay and benefits, support, and feeling valued were the top three reasons given for continuing to work at an SON. Conflicts with life and other job responsibilities, low pay, and workload were the top three reasons given for not continuing. Results from this study can assist nursing programs in finding strategies to help reduce attrition among part-time clinical faculty.
Spatio-temporal alignment of multiple sensors

NASA Astrophysics Data System (ADS)

Zhang, Tinghua; Ni, Guoqiang; Fan, Guihua; Sun, Huayan; Yang, Biao

2018-01-01

Aiming to achieve the spatio-temporal alignment of multi sensor on the same platform for space target observation, a joint spatio-temporal alignment method is proposed. To calibrate the parameters and measure the attitude of cameras, an astronomical calibration method is proposed based on star chart simulation and collinear invariant features of quadrilateral diagonal between the observed star chart. In order to satisfy a temporal correspondence and spatial alignment similarity simultaneously, the method based on the astronomical calibration and attitude measurement in this paper formulates the video alignment to fold the spatial and temporal alignment into a joint alignment framework. The advantage of this method is reinforced by exploiting the similarities and prior knowledge of velocity vector field between adjacent frames, which is calculated by the SIFT Flow algorithm. The proposed method provides the highest spatio-temporal alignment accuracy compared to the state-of-the-art methods on sequences recorded from multi sensor at different times.
High-speed multiple sequence alignment on a reconfigurable platform.

PubMed

Oliver, Tim; Schmidt, Bertil; Maskell, Douglas; Nathan, Darran; Clemens, Ralf

2006-01-01

Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.
Electrostatically Induced Carbon Nanotube Alignment for Polymer Composite Applications

NASA Astrophysics Data System (ADS)

Chapkin, Wesley Aaron

We have developed a non-invasive technique utilizing polarized Raman spectroscopy to measure changes in carbon nanotube (CNT) alignment in situ and in real time in a polymer matrix. With this technique, we have confirmed the prediction of faster alignment for CNTs in higher electric fields. Real-time polarized Raman spectroscopy also allows us to demonstrate the loss of CNT alignment that occurs after the electric field is removed, which reveals the need for fast polymerization steps or the continued application of the aligning force during polymerization to lock in CNT alignment. Through a study on the effect of polymer viscosity on the rate of CNT alignment, we have determined that shear viscosity serves as the controlling mechanism for CNT rotation. This finding matches literature modeling of rigid rod mobility in a polymer melt and demonstrates that the rotational mobility of CNTs can be explained by a continuum model even though the diameters of single-walled CNTs are 1-2 nm. The viscosity dependence indicates that the manipulation of temperature (and indirectly viscosity) will have a direct effect on the rate of CNT alignment, which could prove useful in expediting the manufacturing of CNT-reinforced composites cured at elevated temperatures. Using real-time polarized Raman spectroscopy, we also demonstrate that electric fields of various strengths lead not only to different speeds of CNT rotation but also to different degrees of alignment. We hypothesize that this difference in achievable alignment results from discrete populations of nanotubes based on their length. The results are then explained by balancing the alignment energy for a given electric field strength with the randomizing thermal energy of the system. By studying the alignment dynamics of different CNT length distributions, we show that different degrees of alignment achieved as a function of the applied electric field strength are directly related to the square of the nanotube length. This finding matches an electrostatic potential energy model for CNT rotation. Lastly, we investigate the effects of conductive carbon fibers on electrostatically induced alignment of CNTs within carbon fiber composites. The relative electric field strength throughout the composite is modeled using COMSOL Multiphysics. We show the ability to generate enhanced electric field gradients within the gaps between carbon fibers for various fiber orientations. Using polarized Raman spectroscopy, increased levels of CNT alignment are observed between carbon fiber tows, which is consistent with the modeled higher electric field strengths in these regions. These findings could potentially lead to the development of carbon fiber composites with CNT additions that selectively enhance the composite properties outside the carbon fiber interphase in the neat epoxy.
Alignment of sensor arrays in optical instruments using a geometric approach.

PubMed

Sawyer, Travis W

2018-02-01

Alignment of sensor arrays in optical instruments is critical to maximize the instrument's performance. While many commercial systems use standardized mounting threads for alignment, custom systems require specialized equipment and alignment procedures. These alignment procedures can be time-consuming, dependent on operator experience, and have low repeatability. Furthermore, each alignment solution must be considered on a case-by-case basis, leading to additional time and resource cost. Here I present a method to align a sensor array using geometric analysis. By imaging a grid pattern of dots, I show that it is possible to calculate the misalignment for a sensor in five degrees of freedom simultaneously. I first test the approach by simulating different cases of misalignment using Zemax before applying the method to experimentally acquired data of sensor misalignment for an echelle spectrograph. The results show that the algorithm effectively quantifies misalignment in five degrees of freedom for an F/5 imaging system, accurate to within ±0.87 deg in rotation and ±0.86 μm in translation. Furthermore, the results suggest that the method can also be applied to non-imaging systems with a small penalty to precision. This general approach can potentially improve the alignment of sensor arrays in custom instruments by offering an accurate, quantitative approach to calculating misalignment in five degrees of freedom simultaneously.
Retention of Adult Patients on Antiretroviral Therapy in Low- and Middle-Income Countries: Systematic Review and Meta-analysis 2008–2013

PubMed Central

Fox, Matthew P; MPA, Sydney Rosen

2015-01-01

Background We previously published systematic reviews of retention in care after antiretroviral therapy initiation among general adult populations in sub-Saharan Africa. We estimated 36-month retention at 73% for publications from 2007–2010. This report extends the review to cover 2008–2013 and expands it to all low- and middle-income countries. Methods We searched PubMed, Embase, Cochrane Register, and ISI Web of Science from January 1, 2008 to December 31, 2013 and abstracts from AIDS and IAS from 2008–2013. We estimated retention across cohorts using simple averages and interpolated missing times through the last time reported. We estimated all-cause attrition (death, loss to follow-up) for patients receiving first-line ART in routine settings in low- and middle-income countries. Results We found 123 papers and abstracts reporting retention for 154 patient cohorts and 1,554,773 patients in 42 countries. Overall, 43% of all patients not retained were known to have died. Unweighted averages of reported retention was 78%, 71% and 69% at 12, 24, and 36 months after treatment initiation, respectively. We estimated 36-month retention at 65% in Africa, 80% in Asia, and 64% in Latin America and the Caribbean. From lifetable analysis, we estimated retention at 12, 24, 36, 48 and 60 months at 83%, 74%, 68%, 64% and 60%, respectively. Conclusions Retention at 36 months on treatment averages 65–70%. There are several important gaps in the evidence-base, which could be filled by further research, especially in terms of geographic coverage and duration of follow-up. PMID:25942461
Retention of Black and White Participants in the Selenium and Vitamin E Cancer Prevention Trial (SWOG-Coordinated Intergroup Study S0000)

PubMed Central

Arnold, Kathryn B.; Hermos, John; Anderson, Karen B.; Minasian, Lori; Tangen, Catherine M.; Probstfield, Jeffrey F.; Cook, Elise D.

2014-01-01

Background Disproportionally low retention of minority populations can adversely affect the generalizability of clinical research trials. We determine the overall retention rates for White and Black participants from the Selenium and Vitamin E Cancer Prevention Trial (SELECT) and explore participant and site characteristics associated with retention failure (study disengagement)for these groups. Methods A secondary analysis of 28,118 White (age ≥55), and 4,322 Black (age ≥ 50) SELECT participants used multivariate Cox regression to estimate overall retention rates and to calculate hazard ratios (HR) and 95% confidence intervals (CI). Results Blacks had higher age-adjusted risk of disengagement than Whites (HR=1.92; 95% CI,1.77-2.08). Among Black participants, those age 50-54 were at three times the risk of disengagement than those age ≥65 (HR=3.61; 95%CI,2.41-5.41). Blacks age ≥65 had 1.6 times the risk of disengagement than Whites age ≥65 (HR=1.60; 95%CI,1.38-1.87). By six years post-randomization, 84% of Whites and 69% of Blacks remained engaged in the study. Current smoking status was an independent risk factor for study disengagement for both White and Black participants. For both groups, sites whose staffs missed SELECT training sessions or who received SELECT Retention and Adherence grants were associated with increased and decreased disengagement risks, respectively. Conclusions SELECT retention was disproportionately lower for Blacks than for Whites. Impact The observed difference in retention rates for Blacks and Whites and factors identified by race for study disengagement in SELECT may inform retention efforts for future long-term, cancer prevention trials. PMID:25242051
Patient-centered recruitment and retention for a randomized controlled study.

PubMed

Chhatre, Sumedha; Jefferson, Ashlie; Cook, Ratna; Meeker, Caitlin R; Kim, Ji Hyun; Hartz, Kayla Marie; Wong, Yu-Ning; Caruso, Adele; Newman, Diane K; Morales, Knashawn H; Jayadevappa, Ravishankar

2018-03-27

Recruitment and retention strategies for patient-centered outcomes research are evolving and research on the subject is limited. In this work, we present a conceptual model of patient-centered recruitment and retention, and describe the recruitment and retention activities and related challenges in a patient-centered comparative effectiveness trial. This is a multicenter, longitudinal randomized controlled trial in localized prostate cancer patients. We recruited 743 participants from three sites over 15 months period (January 2014 to March 2015), and followed them for 24 months. At site 1, of the 773 eligible participants, 551 (72%) were enrolled. At site 2, 34 participants were eligible and 23 (68%) enrolled. Of the 434 eligible participants at site 3, 169 (39%) enrolled. We observed that strategies related to the concepts of trust (e.g., physician involvement, ensuring protection of information), communication (e.g., brochures and pamphlets in physicians' offices, continued contact during regular clinic visits and calling/emailing assessment), attitude (e.g., emphasizing the altruistic value of research, positive attitude of providers and research staff), and expectations (e.g., full disclosure of study requirements and time commitment, update letters) facilitated successful patient recruitment and retention. A stakeholders' advisory board provided important input for the recruitment and retention activities. Active engagement, reminders at the offices, and personalized update letters helped retention during follow-up. Usefulness of telephone recruitment was site specific and, at one site, the time requirement for telephone recruitment was a challenge. We have presented multilevel strategies for successful recruitment and retention in a clinical trial using a patient-centered approach. Our strategies were flexible to accommodate site-level requirements. These strategies as well as the challenges can aid recruitment and retention efforts of future large-scale, patient-centered research studies. Clinicaltrials.gov , ID: NCT02032550 . Registered on 22 November 2013.
Low-Dose, High-Frequency CPR Training Improves Skill Retention of In-Hospital Pediatric Providers

PubMed Central

Niles, Dana; Meaney, Peter A.; Aplenc, Richard; French, Benjamin; Abella, Benjamin S.; Lengetti, Evelyn L.; Berg, Robert A.; Helfaer, Mark A.; Nadkarni, Vinay

2011-01-01

OBJECTIVE: To investigate the effectiveness of brief bedside cardiopulmonary resuscitation (CPR) training to improve the skill retention of hospital-based pediatric providers. We hypothesized that a low-dose, high-frequency training program (booster training) would improve CPR skill retention. PATIENTS AND METHODS: CPR recording/feedback defibrillators were used to evaluate CPR quality during simulated arrest. Basic life support–certified, hospital-based providers were randomly assigned to 1 of 4 study arms: (1) instructor-only training; (2) automated defibrillator feedback only; (3) instructor training combined with automated feedback; and (4) control (no structured training). Each session (time: 0, 1, 3, and 6 months after training) consisted of a pretraining evaluation (60 seconds), booster training (120 seconds), and a posttraining evaluation (60 seconds). Excellent CPR was defined as chest compression (CC) depth ≥ one-third anterior-posterior chest depth, rate ≥ 90 and ≤120 CC per minute, ≤20% of CCs with incomplete release (>2500 g), and no flow fraction ≤ 0.30. MEASUREMENTS AND MAIN RESULTS: Eighty-nine providers were randomly assigned; 74 (83%) completed all sessions. Retention of CPR skills was 2.3 times (95% confidence interval [CI]: 1.1–4.5; P = .02) more likely after 2 trainings and 2.9 times (95% CI: 1.4–6.2; P = .005) more likely after 3 trainings. The automated defibrillator feedback only group had lower retention rates compared with the instructor-only training group (odds ratio: 0.41 [95% CI: 0.17–0.97]; P = .043). CONCLUSIONS: Brief bedside booster CPR training improves CPR skill retention. Our data reveal that instructor-led training improves retention compared with automated feedback training alone. Future studies should investigate whether bedside training improves CPR quality during actual pediatric arrests. PMID:21646262
Recruitment and retention of young women into nutrition research studies: practical considerations.

PubMed

Leonard, Alecia; Hutchesson, Melinda; Patterson, Amanda; Chalmers, Kerry; Collins, Clare

2014-01-16

Successful recruitment and retention of participants into research studies is critical for optimising internal and external validity. Research into diet and lifestyle of young women is important due to the physiological transitions experienced at this life stage. This paper aims to evaluate data related to recruitment and retention across three research studies with young women, and present practical advice related to recruiting and retaining young women in order to optimise study quality within nutrition research. Recruitment and retention strategies used in three nutrition studies that targeted young women (18 to 35 years) were critiqued. A randomised controlled trial (RCT), a crossover validation study and a cross-sectional survey were conducted at the University of Newcastle, Australia between 2010 and 2013Successful recruitment was defined as maximum recruitment relative to time. Retention was assessed as maximum participants remaining enrolled at study completion. Recruitment approaches included notice boards, web and social network sites (Facebook and Twitter), with social media most successful in recruitment. The online survey had the highest recruitment in the shortest time-frame (751 participants in one month). Email, phone and text message were used in study one (RCT) and study two (crossover validation) and assisted in low attrition rates, with 93% and 75.7% completing the RCT and crossover validation study respectively. Of those who did not complete the RCT, reported reasons were: being too busy; and having an unrelated illness. Recruiting young women into nutrition research is challenging. Use of social media enhances recruitment, while Email, phone and text message contact improves retention within interventions. Further research comparing strategies to optimise recruitment and retention in young women, including flexible testing times, reminders and incentives is warranted.
Rapid identification of fatty acid methyl esters using a multidimensional gas chromatography-mass spectrometry database.

PubMed

Härtig, Claus

2008-01-04

A multidimensional approach for the identification of fatty acid methyl esters (FAME) based on GC/MS analysis is described. Mass spectra and retention data of more than 130 FAME from various sources (chain lengths in the range from 4 to 24 carbon atoms) were collected in a database. Hints for the interpretation of FAME mass spectra are given and relevant diagnostic marker ions are deduced indicating specific groups of fatty acids. To verify the identity of single species and to ensure an optimized chromatographic resolution, the database was compiled with retention data libraries acquired on columns of different polarity (HP-5, DB-23, and HP-88). For a combined use of mass spectra and retention data standardized methods of measurement for each of these columns are required. Such master methods were developed and always applied under the conditions of retention time locking (RTL) which allowed an excellent reproducibility and comparability of absolute retention times. Moreover, as a relative retention index system, equivalent chain lengths (ECL) of FAME were determined by linear interpolation. To compare and to predict ECL values by means of structural features, fractional chain lengths (FCL) were calculated and fitted as well. As shown in an example, the use of retention data and mass spectral information together in a database search leads to an improved and reliable identification of FAME (including positional and geometrical isomers) without further derivatizations.

A retention index calculator simplifies identification of plant volatile organic compounds.

PubMed

Lucero, Mary; Estell, Rick; Tellez, María; Fredrickson, Ed

2009-01-01

Plant volatiles (PVOCs) are important targets for studies in natural products, chemotaxonomy and biochemical ecology. The complexity of PVOC profiles often limits research to studies targeting only easily identified compounds. With the availability of mass spectral libraries and recent growth of retention index (RI) libraries, PVOC identification can be achieved using only gas chromatography coupled to mass spectrometry (GCMS). However, RI library searching is not typically automated, and until recently, RI libraries were both limited in scope and costly to obtain. To automate RI calculation and lookup functions commonly utilised in PVOC analysis. Formulae required for calculating retention indices from retention time data were placed in a spreadsheet along with lookup functions and a retention index library. Retention times obtained from GCMS analysis of alkane standards and Koeberlinia spinosa essential oil were entered into the spreadsheet to determine retention indices. Indices were used in combination with mass spectral analysis to identify compounds contained in Koeberlinia spinosa essential oil. Eighteen compounds were positively identified. Total oil yield was low, with only 5 ppm in purple berries. The most abundant compounds were octen-3-ol and methyl salicylate. The spreadsheet accurately calculated RIs of the detected compounds. The downloadable spreadsheet tool developed for this study provides a calculator and RI library that works in conjuction with GCMS or other analytical techniques to identify PVOCs in plant extracts.
INFLUENCE OF HYDRAULIC RETENTION TIME ON EXTENT OF PCE DECHLORINATION AND PRELIMINARY CHARACTERIZATION OF THE ENRICHMENT CULTURE. (R826694C703)

EPA Science Inventory

The extent of tetrachloroethene (PCE) dechlorination in two chemostats was evaluated as a function of hydraulic retention time (HRT). The inoculum of these chemostats was from an upflow anaerobic sludge blanket (UASB) reactor that rapidly converts PCE to vinyl chloride (VC) an...
Impact of Online Orientation for First-Time Online Students on Retention, Academic Success, and Persistence

ERIC Educational Resources Information Center

Marshall, Lynda

2017-01-01

A challenge faced by higher education is whether online orientation that is offered before the start of class can impact academic performance for online students. The purpose of this quantitative research study was to determine if there are significant differences in retention, academic success, and persistence between first time online students…
Slow equilibration of reversed-phase columns for the separation of ionized solutes.

PubMed

Marchand, D H; Williams, L A; Dolan, J W; Snyder, L R

2003-10-10

Reversed-phase columns that have been stored in buffer-free solvents can exhibit pronounced retention-time drift when buffered, low-pH mobile phases are used with ionized solutes. Whereas non-ionized compounds exhibit constant retention times within 20 min of the beginning of mobile phase flow, the retention of ionized compounds can continue to change (by 20% or more) for several hours. If mobile phase pH is changed from low to high and back again, an even longer time may be required before the column reaches equilibration at low pH. The speed of column equilibration for ionized solutes can vary significantly among different reversed-phase columns and is not affected by flow rate.
Aligned Single Wall Carbon Nanotube Polymer Composites Using an Electric Field

NASA Technical Reports Server (NTRS)

Park, Cheol; Wiklinson, John; Banda, Sumanth; Ounaies, Zoubeida; Wise, Kristopher E.; Sauti, Godfrey; Lillehei, Peter T.; Harrison, Joycelyn S.

2005-01-01

While high shear alignment has been shown to improve the mechanical properties of single wall carbon nanotubes (SWNT)-polymer composites, it is difficult to control and often results in degradation of the electrical and dielectric properties of the composite. Here, we report a novel method to actively align SWNTs in a polymer matrix, which allows for control over the degree of alignment of SWNTs without the side effects of shear alignment. In this process, SWNTs are aligned via field-induced dipolar interactions among the nanotubes under an AC electric field in a liquid matrix followed by immobilization by photopolymerization while maintaining the electric field. Alignment of SWNTs was controlled as a function of magnitude, frequency, and application time of the applied electric field. The degree of SWNT alignment was assessed using optical microscopy and polarized Raman spectroscopy and the morphology of the aligned nanocomposites was investigated by high resolution scanning electron microscopy. The structure of the field induced aligned SWNTs is intrinsically different from that of shear aligned SWNTs. In the present work, SWNTs are not only aligned along the field, but also migrate laterally to form thick, aligned SWNT percolative columns between the electrodes. The actively aligned SWNTs amplify the electrical and dielectric properties in addition to improving the mechanical properties of the composite. All of these properties of the aligned nanocomposites exhibited anisotropic characteristics, which were controllable by tuning the applied field conditions.
Bryophyte Species Richness on Retention Aspens Recovers in Time but Community Structure Does Not

PubMed Central

Oldén, Anna; Ovaskainen, Otso; Kotiaho, Janne S.; Laaka-Lindberg, Sanna; Halme, Panu

2014-01-01

Green-tree retention is a forest management method in which some living trees are left on a logged area. The aim is to offer ‘lifeboats’ to support species immediately after logging and to provide microhabitats during and after forest re-establishment. Several studies have shown immediate decline in bryophyte diversity after retention logging and thus questioned the effectiveness of this method, but longer term studies are lacking. Here we studied the epiphytic bryophytes on European aspen (Populus tremula L.) retention trees along a 30-year chronosequence. We compared the bryophyte flora of 102 ‘retention aspens’ on 14 differently aged retention sites with 102 ‘conservation aspens’ on 14 differently aged conservation sites. We used a Bayesian community-level modelling approach to estimate the changes in bryophyte species richness, abundance (area covered) and community structure during 30 years after logging. Using the fitted model, we estimated that two years after logging both species richness and abundance of bryophytes declined, but during the following 20–30 years both recovered to the level of conservation aspens. However, logging-induced changes in bryophyte community structure did not fully recover over the same time period. Liverwort species showed some or low potential to benefit from lifeboating and high potential to re-colonise as time since logging increases. Most moss species responded similarly, but two cushion-forming mosses benefited from the logging disturbance while several weft- or mat-forming mosses declined and did not re-colonise in 20–30 years. We conclude that retention trees do not function as equally effective lifeboats for all bryophyte species but are successful in providing suitable habitats for many species in the long-term. To be most effective, retention cuts should be located adjacent to conservation sites, which may function as sources of re-colonisation and support the populations of species that require old-growth forests. PMID:24710329
Bryophyte species richness on retention aspens recovers in time but community structure does not.

PubMed

Oldén, Anna; Ovaskainen, Otso; Kotiaho, Janne S; Laaka-Lindberg, Sanna; Halme, Panu

2014-01-01

Green-tree retention is a forest management method in which some living trees are left on a logged area. The aim is to offer 'lifeboats' to support species immediately after logging and to provide microhabitats during and after forest re-establishment. Several studies have shown immediate decline in bryophyte diversity after retention logging and thus questioned the effectiveness of this method, but longer term studies are lacking. Here we studied the epiphytic bryophytes on European aspen (Populus tremula L.) retention trees along a 30-year chronosequence. We compared the bryophyte flora of 102 'retention aspens' on 14 differently aged retention sites with 102 'conservation aspens' on 14 differently aged conservation sites. We used a Bayesian community-level modelling approach to estimate the changes in bryophyte species richness, abundance (area covered) and community structure during 30 years after logging. Using the fitted model, we estimated that two years after logging both species richness and abundance of bryophytes declined, but during the following 20-30 years both recovered to the level of conservation aspens. However, logging-induced changes in bryophyte community structure did not fully recover over the same time period. Liverwort species showed some or low potential to benefit from lifeboating and high potential to re-colonise as time since logging increases. Most moss species responded similarly, but two cushion-forming mosses benefited from the logging disturbance while several weft- or mat-forming mosses declined and did not re-colonise in 20-30 years. We conclude that retention trees do not function as equally effective lifeboats for all bryophyte species but are successful in providing suitable habitats for many species in the long-term. To be most effective, retention cuts should be located adjacent to conservation sites, which may function as sources of re-colonisation and support the populations of species that require old-growth forests.
Recruiting and retaining low-income, multi-ethnic women into randomized controlled trials: Successful strategies and staffing

PubMed Central

Barnett, Josephine; Aguilar, Stephanie; Brittner, Mindy; Bonuck, Karen

2012-01-01

Developing effective recruitment and retention strategies in populations with traditionally high attrition rates is critical to the success of Randomized Controlled Trials (RCTs). Data on successful participation of women from low-income, minority populations in RCTs of behavioral interventions are limited. This is problematic given the multiplicity of Healthy People 2020 goals that target health disparities in these populations. This paper reports successful recruitment and retention methods from two separately funded NIH clinical trials of primary care-based prenatal interventions to increase breastfeeding among ethnically diverse, low-income women in urban medical centers in the Bronx, NY. It also presents the required staff effort necessary to conduct such a successful RCT, in terms of full-time equivalents (FTEs). Results include timely recruitment of 941 participants over 29 months, with 98.1% completing 1̄ follow-up interview. A recruitment and retention plan that maximized study staff access and availability to the participant, as well as strong study staff rapport with participants, addressed previously reported barriers in this population, optimizing follow-up rates. A qualitative assessment of the participants' study experience suggesting that high retention was due to strong rapport with participants, short interviews requiring little time commitment, and participants' perception of the study as informative, provides further evidence of our approach's effectiveness. Logistical protocol procedures and staff management strategies relating to successful recruitment/retention are provided to propose a practical, cost-effective and translational recruitment–retention plan for other researchers to adopt. PMID:22732312
A generalized global alignment algorithm.

PubMed

Huang, Xiaoqiu; Chao, Kun-Mao

2003-01-22

Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.
Fast Response and Spontaneous Alignment in Liquid Crystals Doped with 12-Hydroxystearic Acid Gelators.

PubMed

Lin, Hui-Chi; Wang, Chih-Hung; Wang, Jyun-Kai; Tsai, Sheng-Feng

2018-05-07

The spontaneous vertical alignment of liquid crystals (LCs) in gelator (12-hydroxystearic acid)-doped LC cells was studied. Gelator-induced alignment can be used in both positive and negative LC cells. The electro-optical characteristics of the gelator-doped negative LC cell were similar to those of an LC cell that contained a vertically aligned (VA) host. The rise time of the gelator-doped LC cell was two orders of magnitude shorter than that of the VA host LC cell. The experimental results indicate that the gelator-induced vertical alignment of LC molecules occurred not only on the surface of the indium tin oxide (ITO) but also on the homogeneous alignment layer. Various LC alignments (planar, hybrid, multistable hybrid, and vertical alignments) were achieved by modulating the doped gelator concentrations. The multistable characteristic of LCs doped with the gelator is also presented. The alignment by doping with a gelator reduces the manufacturing costs and provides a means of fabricating fast-responding, flexible LC displays using a low-temperature process.
Retention of Mastoidectomy Skills After Virtual Reality Simulation Training.

PubMed

Andersen, Steven Arild Wuyts; Konge, Lars; Cayé-Thomasen, Per; Sørensen, Mads Sølvsten

2016-07-01

The ultimate goal of surgical training is consolidated skills with a consistently high performance. However, surgical skills are heterogeneously retained and depend on a variety of factors, including the task, cognitive demands, and organization of practice. Virtual reality (VR) simulation is increasingly being used in surgical skills training, including temporal bone surgery, but there is a gap in knowledge on the retention of mastoidectomy skills after VR simulation training. To determine the retention of mastoidectomy skills after VR simulation training with distributed and massed practice and to investigate participants' cognitive load during retention procedures. A prospective 3-month follow-up study of a VR simulation trial was conducted from February 6 to September 19, 2014, at an academic teaching hospital among 36 medical students: 19 from a cohort trained with distributed practice and 17 from a cohort trained with massed practice. Participants performed 2 virtual mastoidectomies in a VR simulator a mean of 3.2 months (range, 2.4-5.0 months) after completing initial training with 12 repeated procedures. Practice blocks were spaced apart in time (distributed), or all procedures were performed in 1 day (massed). Performance of the virtual mastoidectomy as assessed by 2 masked senior otologists using a modified Welling scale, as well as cognitive load as estimated by reaction time to perform a secondary task. Among 36 participants, mastoidectomy final-product skills were largely retained at 3 months (mean change in score, 0.1 points; P = .89) regardless of practice schedule, but the group trained with massed practice took more time to complete the task. The performance of the massed practice group increased significantly from the first to the second retention procedure (mean change, 1.8 points; P = .001), reflecting that skills were less consolidated. For both groups, increases in reaction times in the secondary task (distributed practice group: mean pretraining relative reaction time, 1.42 [95% CI, 1.37-1.47]; mean end of training relative reaction time, 1.24 [95% CI, 1.16-1.32]; and mean retention relative reaction time, 1.36 [95% CI, 1.30-1.42]; massed practice group: mean pretraining relative reaction time, 1.34 [95% CI, 1.28-1.40]; mean end of training relative reaction time, 1.31 [95% CI, 1.21-1.42]; and mean retention relative reaction time, 1.39 [95% CI, 1.31-1.46]) indicated that cognitive load during the virtual procedures had returned to the pretraining level. Mastoidectomy skills acquired under time-distributed practice conditions were retained better than skills acquired under massed practice conditions. Complex psychomotor skills should be regularly reinforced to consolidate both motor and cognitive aspects. Virtual reality simulation training provides the opportunity for such repeated training and should be integrated into training curricula.
Mechanisms of the Anterior Cruciate Ligament Injury in Sports Activities: A Twenty-Year Clinical Research of 1,700 Athletes

PubMed Central

Kobayashi, Hirokazu; Kanamura, Tomonao; Koshida, Sentaro; Miyashita, Koji; Okado, Tsuruo; Shimizu, Takuya; Yokoe, Kiyoshi

2010-01-01

The mechanisms of anterior cruciate ligament (ACL) injuries are still inconclusive from an epidemiological standpoint. An epidemiological approach in a large sample group over an appropriate period of years will be necessary to enhance the current knowledge of the ACL injury mechanism. The objective of the study was to investigate the ACL injury occurrence in a large sample over twenty years and demonstrate the relationships between the ACL injury occurrence and the dynamic knee alignment at the time of the injury. We investigated the activity, the injury mechanism, and the dynamic knee alignment at the time of the injury in 1,718 patients diagnosed as having the ACL injuries. Regarding the activity at the time of the injury, “competition ”was the most common, accounting for about half of all the injuries. The current result also showed that the noncontact injury was the most common, which was observed especially in many female athletes. Finally, the dynamic alignment of “Knee-in & Toe- out ”(i.e. dynamic knee valgus) was the most common, accounting for about half. These results enhance our understanding of the ACL injury mechanism and may be used to guide future injury prevention strategies. Key points We investigated the situation of ACL injury occurrence, especially dynamic alignments at the time of injury, in 1,718 patients who had visited our institution for surgery and physical therapy for twenty years. Our epidemiological study of the large patient group revealed that “knee-in & toe-out ”alignment was the most frequently seen at the time of the ACL injury. From an epidemiological standpoint, we need to pay much attention to avoiding “Knee-in & Toe-out ”alignment during sports activities. PMID:24149795
The Influence of Principal Gender, Teachers' Years of Experience, and Retention on Teacher Perceptions of Principal Leadership Style, Qualities, and Job Satisfaction

ERIC Educational Resources Information Center

Eddins, Gregg M.

2012-01-01

One main challenge for many school districts in these tough economic times is teacher retention and all the costs associated. This study looks the influence of principal gender, teacher years of experience, and teacher retention based on teachers' perceptions of their principal's leadership style, transformational leadership qualities,…
Mentoring: the retention factor in the acute care setting.

PubMed

Funderburk, Amy E

2008-01-01

The most difficult time to retain staff nurses can be the first year after hire. Because of the high costs of recruitment and orientation, retention of these new employees is essential. Mentoring is a viable retention tool for the new employee and for existing experienced nurses. Mentoring also provides professional growth benefits that appeal to existing employees and increase their job enjoyment and satisfaction.
Predicting changes in hydrologic retention in an evolving semi-arid alluvial stream

USGS Publications Warehouse

Harvey, J.W.; Conklin, M.H.; Koelsch, R.S.

2003-01-01

Hydrologic retention of solutes in hyporheic zones or other slowly moving waters of natural channels is thought to be a significant control on biogeochemical cycling and ecology of streams. To learn more about factors affecting hydrologic retention, we repeated stream-tracer injections for 5 years in a semi-arid alluvial stream (Pinal Creek, Ariz.) during a period when streamflow was decreasing, channel width increasing, and coverage of aquatic macrophytes expanding. Average stream velocity at Pinal Creek decreased from 0.8 to 0.2 m/s, average stream depth decreased from 0.09 to 0.04 m, and average channel width expanded from 3 to 13 m. Modeling of tracer experiments indicated that the hydrologic retention factor (Rh), a measure of the average time that solute spends in storage per unit length of downstream transport, increased from 0.02 to 8 s/m. At the same time the ratio of cross-sectional area of storage zones to main channel cross-sectional area (As/A) increased from 0.2 to 0.8 m2/m2, and average water residence time in storage zones (ts) increased from 5 to 24 min. Compared with published data from four other streams in the US, Pinal Creek experienced the greatest change in hydrologic retention for a given change in streamflow. The other streams differed from Pinal Creek in that they experienced a change in streamflow between tracer experiments without substantial geomorphic or vegetative adjustments. As a result, a regression of hydrologic retention on streamflow developed for the other streams underpredicted the measured increases in hydrologic retention at Pinal Creek. The increase in hydrologic retention at Pinal Creek was more accurately predicted when measurements of the Darcy-Weisbach friction factor were used (either alone or in addition to streamflow) as a predictor variable. We conclude that relatively simple measurements of channel friction are useful for predicting the response of hydrologic retention in streams to major adjustments in channel morphology as well as changes in streamflow. Published by Elsevier Ltd.
Exploring the human emotion of feeling cared for in the workplace.

PubMed

Baggett, Margarita; Giambattista, Laura; Lobbestael, Linda; Pfeiffer, Judith; Madani, Catherina; Modir, Royya; Zamora-Flyr, Maria Magdalena; Davidson, Judy E

2016-09-01

To explore the emotion of feeling cared for in the workplace. The emotion of feeling cared for drives health-promoting behaviours. Feeling cared for is the end-product of caring, affecting practice, environment and outcomes. Identifying behaviours that lead to feeling cared for is the first step in promoting caring practices in leadership. A survey with open-ended questions was designed, validated and electronically distributed. Data from 35 responses were thematically analysed. Unit culture and leadership style affect caring capacity in the workplace. First level coding revealed two caring behaviour categories: recognition and support. Themes emerged aligned to Chapman's model of workplace appreciation: words of affirmation, receiving gifts, quality time and acts of service. The importance of being treated as a whole person was reported: being appreciated personally and professionally. Feeling cared for drives outcomes such as feeling valued, important, teamwork and organisational loyalty. This study generalises the applicability of Chapman's model developed for workplace appreciation in the health-care setting. Concrete examples of how leaders stimulate feeling cared for are provided. Caring leadership behaviours have the potential to improve retention, engagement, the healing environment and the capacity for caring for others. © 2016 John Wiley & Sons Ltd.
Measuring sperm backflow following female orgasm: a new method

PubMed Central

King, Robert; Dempsey, Maria; Valentine, Katherine A.

2016-01-01

Background Human female orgasm is a vexed question in the field while there is credible evidence of cryptic female choice that has many hallmarks of orgasm in other species. Our initial goal was to produce a proof of concept for allowing females to study an aspect of infertility in a home setting, specifically by aligning the study of human infertility and increased fertility with the study of other mammalian fertility. In the latter case - the realm of oxytocin-mediated sperm retention mechanisms seems to be at work in terms of ultimate function (differential sperm retention) while the proximate function (rapid transport or cervical tenting) remains unresolved. Method A repeated measures design using an easily taught technique in a natural setting was used. Participants were a small (n=6), non-representative sample of females. The introduction of a sperm-simulant combined with an orgasm-producing technique using a vibrator/home massager and other easily supplied materials. Results The sperm flowback (simulated) was measured using a technique that can be used in a home setting. There was a significant difference in simulant retention between the orgasm (M=4.08, SD=0.17) and non-orgasm (M=3.30, SD=0.22) conditions; t (5)=7.02, p=0.001. Cohen's d=3.97, effect size r=0.89. This indicates a medium to small effect size. Conclusions This method could allow females to test an aspect of sexual response that has been linked to lowered fertility in a home setting with minimal training. It needs to be replicated with a larger sample size. PMID:27799082
Measuring sperm backflow following female orgasm: a new method.

PubMed

King, Robert; Dempsey, Maria; Valentine, Katherine A

2016-01-01

Human female orgasm is a vexed question in the field while there is credible evidence of cryptic female choice that has many hallmarks of orgasm in other species. Our initial goal was to produce a proof of concept for allowing females to study an aspect of infertility in a home setting, specifically by aligning the study of human infertility and increased fertility with the study of other mammalian fertility. In the latter case - the realm of oxytocin-mediated sperm retention mechanisms seems to be at work in terms of ultimate function (differential sperm retention) while the proximate function (rapid transport or cervical tenting) remains unresolved. A repeated measures design using an easily taught technique in a natural setting was used. Participants were a small (n=6), non-representative sample of females. The introduction of a sperm-simulant combined with an orgasm-producing technique using a vibrator/home massager and other easily supplied materials. The sperm flowback (simulated) was measured using a technique that can be used in a home setting. There was a significant difference in simulant retention between the orgasm (M=4.08, SD=0.17) and non-orgasm (M=3.30, SD=0.22) conditions; t (5)=7.02, p=0.001. Cohen's d=3.97, effect size r=0.89. This indicates a medium to small effect size. This method could allow females to test an aspect of sexual response that has been linked to lowered fertility in a home setting with minimal training. It needs to be replicated with a larger sample size.
Some aspects of SR beamline alignment

NASA Astrophysics Data System (ADS)

Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

2011-09-01

Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.
Simplified methods of determining treatment retention in Malawi: ART cohort reports vs. pharmacy stock cards.

PubMed

Chan, A K; Singogo, E; Changamire, R; Ratsma, Y E C; Tassie, J-M; Harries, A D

2012-06-21

Rapid scale-up of antiretroviral therapy (ART) has challenged the health system in Malawi to monitor large numbers of patients effectively. To compare two methods of determining retention on treatment: quarterly ART clinic data aggregation vs. pharmacy stock cards. Between October 2010 and March 2011, data on ART outcomes were extracted from monitoring tools at five facilities. Pharmacy data on ART consumption were extracted. Workload for each method was observed and timed. We used intraclass correlation and Bland-Altman plots to compare the agreeability of both methods to determine treatment retention. There is wide variability between ART clinic cohort data and pharmacy data to determine treatment retention due to divergence in data at sites with large numbers of patients. However, there is a non-significant trend towards agreeability between the two methods (intraclass correlation coefficient > 0.9; P > 0.05). Pharmacy stock card monitoring is more time-efficient than quarterly ART data aggregation (81 min vs. 573 min). In low-resource settings, pharmacy records could be used to improve drug forecasting and estimate ART retention in a more time-efficient manner than quarterly data aggregation; however, a necessary precondition would be capacity building around pharmacy data management, particularly for large-sized cohorts.

Predicting Retention Times of Naturally Occurring Phenolic Compounds in Reversed-Phase Liquid Chromatography: A Quantitative Structure-Retention Relationship (QSRR) Approach

PubMed Central

Akbar, Jamshed; Iqbal, Shahid; Batool, Fozia; Karim, Abdul; Chan, Kim Wei

2012-01-01

Quantitative structure-retention relationships (QSRRs) have successfully been developed for naturally occurring phenolic compounds in a reversed-phase liquid chromatographic (RPLC) system. A total of 1519 descriptors were calculated from the optimized structures of the molecules using MOPAC2009 and DRAGON softwares. The data set of 39 molecules was divided into training and external validation sets. For feature selection and mapping we used step-wise multiple linear regression (SMLR), unsupervised forward selection followed by step-wise multiple linear regression (UFS-SMLR) and artificial neural networks (ANN). Stable and robust models with significant predictive abilities in terms of validation statistics were obtained with negation of any chance correlation. ANN models were found better than remaining two approaches. HNar, IDM, Mp, GATS2v, DISP and 3D-MoRSE (signals 22, 28 and 32) descriptors based on van der Waals volume, electronegativity, mass and polarizability, at atomic level, were found to have significant effects on the retention times. The possible implications of these descriptors in RPLC have been discussed. All the models are proven to be quite able to predict the retention times of phenolic compounds and have shown remarkable validation, robustness, stability and predictive performance. PMID:23203132
Linking GPS and travel diary data using sequence alignment in a study of children's independent mobility

PubMed Central

2011-01-01

Background Global positioning systems (GPS) are increasingly being used in health research to determine the location of study participants. Combining GPS data with data collected via travel/activity diaries allows researchers to assess where people travel in conjunction with data about trip purpose and accompaniment. However, linking GPS and diary data is problematic and to date the only method has been to match the two datasets manually, which is time consuming and unlikely to be practical for larger data sets. This paper assesses the feasibility of a new sequence alignment method of linking GPS and travel diary data in comparison with the manual matching method. Methods GPS and travel diary data obtained from a study of children's independent mobility were linked using sequence alignment algorithms to test the proof of concept. Travel diaries were assessed for quality by counting the number of errors and inconsistencies in each participant's set of diaries. The success of the sequence alignment method was compared for higher versus lower quality travel diaries, and for accompanied versus unaccompanied trips. Time taken and percentage of trips matched were compared for the sequence alignment method and the manual method. Results The sequence alignment method matched 61.9% of all trips. Higher quality travel diaries were associated with higher match rates in both the sequence alignment and manual matching methods. The sequence alignment method performed almost as well as the manual method and was an order of magnitude faster. However, the sequence alignment method was less successful at fully matching trips and at matching unaccompanied trips. Conclusions Sequence alignment is a promising method of linking GPS and travel diary data in large population datasets, especially if limitations in the trip detection algorithm are addressed. PMID:22142322
Causal modeling of self-concept, job satisfaction, and retention of nurses.

PubMed

Cowin, Leanne S; Johnson, Maree; Craven, Rhonda G; Marsh, Herbert W

2008-10-01

The critical shortage of nurses experienced throughout the western world has prompted researchers to examine one major component of this complex problem - the impact of nurses' professional identity and job satisfaction on retention. A descriptive correlational design with a longitudinal element was used to examine a causal model of nurses' self-concept, job satisfaction, and retention plans in 2002. A random sample of 2000 registered nurses was selected from the state registering authority listing. A postal survey assessing multiple dimensions of nurses' self-concept (measured by the nurse self-concept questionnaire), job satisfaction (measured by the index of work satisfaction) was undertaken at Time 1 (n=528) and 8 months later at Time 2 (n=332) (including retention plans (measured by the Nurse Retention Index). Using confirmatory factor analysis, correlation matrices and path analysis, measurement and structural models were examined on matching pairs of data from T1 and T2 (total sample N=332). Nurses' self-concept was found to have a stronger association with nurses' retention plans (B=.45) than job satisfaction (B=.28). Aspects of pay and task were not significantly related to retention plans, however, professional status (r=.51), and to a lesser extent, organizational policies (r=.27) were significant factors. Nurses' general self-concept was strongly related (r=.57) to retention plans. Strategies or interventions requiring implementation and evaluation include: counseling to improve nurse general self-concept, education programs and competencies in health communication between health professionals, reporting of nurse-initiated programs with substantial patient benefit, nurse-friendly organizational policies, common health team learning opportunities, and autonomous practice models.
Experience from the in-flight calibration of the Extreme Ultraviolet Explorer (EUVE) and Upper Atmosphere Research Satellite (UARS) fixed head star trackers (FHSTs)

NASA Technical Reports Server (NTRS)

Lee, Michael

1995-01-01

Since the original post-launch calibration of the FHSTs (Fixed Head Star Trackers) on EUVE (Extreme Ultraviolet Explorer) and UARS (Upper Atmosphere Research Satellite), the Flight Dynamics task has continued to analyze the FHST performance. The algorithm used for inflight alignment of spacecraft sensors is described and the equations for the errors in the relative alignment for the simple 2 star tracker case are shown. Simulated data and real data are used to compute the covariance of the relative alignment errors. Several methods for correcting the alignment are compared and results analyzed. The specific problems seen on orbit with UARS and EUVE are then discussed. UARS has experienced anomalous tracker performance on an FHST resulting in continuous variation in apparent tracker alignment. On EUVE, the FHST residuals from the attitude determination algorithm showed a dependence on the direction of roll during survey mode. This dependence is traced back to time tagging errors and the original post launch alignment is found to be in error due to the impact of the time tagging errors on the alignment algorithm. The methods used by the FDF (Flight Dynamics Facility) to correct for these problems is described.
AntiClustal: Multiple Sequence Alignment by antipole clustering and linear approximate 1-median computation.

PubMed

Di Pietro, C; Di Pietro, V; Emmanuele, G; Ferro, A; Maugeri, T; Modica, E; Pigola, G; Pulvirenti, A; Purrello, M; Ragusa, M; Scalia, M; Shasha, D; Travali, S; Zimmitti, V

2003-01-01

In this paper we present a new Multiple Sequence Alignment (MSA) algorithm called AntiClusAl. The method makes use of the commonly use idea of aligning homologous sequences belonging to classes generated by some clustering algorithm, and then continue the alignment process ina bottom-up way along a suitable tree structure. The final result is then read at the root of the tree. Multiple sequence alignment in each cluster makes use of the progressive alignment with the 1-median (center) of the cluster. The 1-median of set S of sequences is the element of S which minimizes the average distance from any other sequence in S. Its exact computation requires quadratic time. The basic idea of our proposed algorithm is to make use of a simple and natural algorithmic technique based on randomized tournaments which has been successfully applied to large size search problems in general metric spaces. In particular a clustering algorithm called Antipole tree and an approximate linear 1-median computation are used. Our algorithm compared with Clustal W, a widely used tool to MSA, shows a better running time results with fully comparable alignment quality. A successful biological application showing high aminoacid conservation during evolution of Xenopus laevis SOD2 is also cited.
Predictors of home healthcare nurse retention.

PubMed

Ellenbecker, Carol Hall; Porell, Frank W; Samia, Linda; Byleckie, James J; Milburn, Michael

2008-01-01

To examine the level of job satisfaction and test a theoretical model of the direct and indirect effects of job satisfaction, and individual nurse and agency characteristics, on intent to stay and retention for home healthcare nurses. A descriptive correlation study of home healthcare nurses in six New England states. Home healthcare nurse job satisfaction self-report data was collected with the HHNJS survey questionnaire & Retention Survey Questionnaire. Based on a structural equation model, job tenure and job satisfaction were the strongest predictors of nurse retention. Understanding the variables associated with home healthcare nurse retention can help agencies retain nurses in a time of severe nurse shortages and increased patient demand. Predicted nursing shortages and increasing demand have made the retention of experienced, qualified nursing staff essential to assure access to high-quality home healthcare services in the future.
Non-HIV related healthcare utilization, demographic, clinical, and laboratory factors associated with time-to-initial retention in HIV care among HIV-positive individuals linked to HIV care

PubMed Central

Lourenço, Lillian; Nohpal, Adriana; Shopin, Dmitry; Colley, Guillaume; Nosyk, Bohdan; Montaner, Julio; Lima, Viviane Dias

2015-01-01

Objective To explore non-HIV related healthcare service(s) (NHRHS) utilization, demographic, clinical, and laboratory factors associated with timely initial ‘retention’ in HIV care among individuals ‘linked’ to HIV care in British Columbia (BC), Canada. Methods We conducted a Weibull time-to-initial retention analysis among BC STOP HIV/AIDS cohort participants linked in 2000–2010, who had ≥1 year of follow-up. We defined ‘linked’ as the first HIV-related service following diagnosis and ‘retained’ as having, within a calendar year, either: i) ≥2 HIV-related physician visits/diagnostic tests or ii) ≥2 ART dispensations, ≥3 months apart. Individuals were followed until they were retained, died, their last contact date, or December 31st, 2011. Results Of 5231 linked individuals (78% male, median age 39 [Q1–Q3:32–46] years), 4691(90%) were retained (median time-to-initial retention:9[5–13] months) by the end of follow-up and 540(10%) were not. Eighty-four percent of not retained and 96% of retained individuals used ≥1 types of NHRHS during follow-up. Individuals who saw a specialist for NHRHS during follow-up had a shorter time-to-initial retention than those who did not (adjusted Hazard Ratio (aHR)=2.79; 95%CI:2.47–3.16). However, those who saw a GP for NHRHS (aHR=0.79; 95%CI:0.74–0.84) and those admitted to the hospital for NHRHS (aHR=0.60; 95%CI:0.54–0.67), versus those who did not, respectively, had longer times to initial retention; along with females, PWID, and individuals <40 years old. Conclusions Overall, 84% of not retained individuals used some type of NHRHS during follow-up. Given that 71% of not retained individuals used GP NHRHS, our results suggest GP-targeted interventions may be effective in improving time-to-initial retention. PMID:26216126
Using analogy to learn about phenomena at scales outside human perception.

PubMed

Resnick, Ilyse; Davatzes, Alexandra; Newcombe, Nora S; Shipley, Thomas F

2017-01-01

Understanding and reasoning about phenomena at scales outside human perception (for example, geologic time) is critical across science, technology, engineering, and mathematics. Thus, devising strong methods to support acquisition of reasoning at such scales is an important goal in science, technology, engineering, and mathematics education. In two experiments, we examine the use of analogical principles in learning about geologic time. Across both experiments we find that using a spatial analogy (for example, a time line) to make multiple alignments, and keeping all unrelated components of the analogy held constant (for example, keep the time line the same length), leads to better understanding of the magnitude of geologic time. Effective approaches also include hierarchically and progressively aligning scale information (Experiment 1) and active prediction in making alignments paired with immediate feedback (Experiments 1 and 2).
Effect of a third application of toothpastes (1450 and 5000 ppm F), including a 'massage' method on fluoride retention and pH drop in plaque.

PubMed

Nordström, Anna; Birkhed, Dowen

2013-01-01

The aim was to investigate fluoride (F) retention in plaque, saliva and pH drop in plaque using high-F toothpaste (5000 ppm F) or standard toothpaste (1450 ppm F) twice a day or 3-times a day. A method using the toothpaste as a 'lotion' and massaging the buccal surfaces with the fingertip was also evaluated. The investigation had a randomized, single-blinded, cross-over design and 16 subjects participated in six brushing regimes: (1) 5000 ppm F; twice a day, (2) 5000 ppm; 3-times/day, (3) 5000 ppm; twice a day, plus the 'massage' method once a day, (4) 1450 ppm F; twice a day, (5) 1450 ppm; 3-times/day and (6) 1450 ppm; twice a day, plus the 'massage' method once a day. The outcome measure was F retention in plaque, saliva and the plaque-pH change after a sucrose rinse. The highest F concentration was found using high-F toothpaste (No 1-3) and differed significantly from those with 1450 ppm (No 4-6). Brushing with high-F toothpaste 3-times a day (No 2) resulted in a 3.6-times higher F saliva value compared with standard toothpaste twice a day (No 4) (p < 0.001). Increasing the frequency of application, from twice to 3-times a day, increased the F retention in plaque significantly when the two methods for application 3-times a day were pooled (p < 0.05). Brushing with 5000 and 1450 ppm toothpastes twice a day plus the 'massage' once a day resulted in the same F concentration in saliva and plaque as brushing 3-times a day with the same paste. A third application of toothpaste is increasing the F retention and toothpaste as a 'lotion' and massaging the buccal surfaces with the fingertip may be a simple and inexpensive way of delivering F a third time during the day.
Retention in Differentiated Care: Multiple Measures Analysis for a Decentralized HIV Care and Treatment Program in North Central Nigeria

PubMed Central

Agaba, Patricia A; Genberg, Becky L; Sagay, Atiene S; Agbaji, Oche O; Meloni, Seema T; Dadem, Nancin Y; Kolawole, Grace O; Okonkwo, Prosper; Kanki, Phyllis J; Ware, Norma C

2018-01-01

Objective Differentiated care refers collectively to flexible service models designed to meet the differing needs of HIV-infected persons in resource-scarce settings. Decentralization is one such service model. Retention is a key indicator for monitoring the success of HIV treatment and care programs. We used multiple measures to compare retention in a cohort of patients receiving HIV care at “hub” (central) and “spoke” (decentralized) sites in a large public HIV treatment program in north central Nigeria. Methods This retrospective cohort study utilized longitudinal program data representing central and decentralized levels of care in the Plateau State Decentralization Initiative, north central Nigeria. We examined retention with patient- level (retention at fixed times, loss-to-follow-up [LTFU]) and visit-level (gaps-in-care, visit constancy) measures. Regression models with generalized estimating equations (GEE) were used to estimate the effect of decentralization on visit-level measures. Patient-level measures were examined using survival methods with Cox regression models, controlling for baseline variables. Results Of 15,650 patients, 43% were enrolled at the hub. Median time in care was 3.1 years. Hub patients were less likely to be LTFU (adjusted hazard ratio (AHR)=0.91, 95% CI: 0.85-0.97), compared to spoke patients. Visit constancy was lower at the hub (−4.5%, 95% CI: −3.5, −5.5), where gaps in care were also more likely to occur (adjusted odds ratio=1.95, 95% CI: 1.83-2.08). Conclusion Decentralized sites demonstrated better retention outcomes using visit-level measures, while the hub achieved better retention outcomes using patient-level measures. Retention estimates produced by incorporating multiple measures showed substantial variation, confirming the influence of measurement strategies on the results of retention research. Future studies of retention in HIV care in sub-Saharan Africa will be well-served by including multiple measures. PMID:29682399
Retention in Differentiated Care: Multiple Measures Analysis for a Decentralized HIV Care and Treatment Program in North Central Nigeria.

PubMed

Agaba, Patricia A; Genberg, Becky L; Sagay, Atiene S; Agbaji, Oche O; Meloni, Seema T; Dadem, Nancin Y; Kolawole, Grace O; Okonkwo, Prosper; Kanki, Phyllis J; Ware, Norma C

2018-01-01

Differentiated care refers collectively to flexible service models designed to meet the differing needs of HIV-infected persons in resource-scarce settings. Decentralization is one such service model. Retention is a key indicator for monitoring the success of HIV treatment and care programs. We used multiple measures to compare retention in a cohort of patients receiving HIV care at "hub" (central) and "spoke" (decentralized) sites in a large public HIV treatment program in north central Nigeria. This retrospective cohort study utilized longitudinal program data representing central and decentralized levels of care in the Plateau State Decentralization Initiative, north central Nigeria. We examined retention with patient- level (retention at fixed times, loss-to-follow-up [LTFU]) and visit-level (gaps-in-care, visit constancy) measures. Regression models with generalized estimating equations (GEE) were used to estimate the effect of decentralization on visit-level measures. Patient-level measures were examined using survival methods with Cox regression models, controlling for baseline variables. Of 15,650 patients, 43% were enrolled at the hub. Median time in care was 3.1 years. Hub patients were less likely to be LTFU (adjusted hazard ratio (AHR)=0.91, 95% CI: 0.85-0.97), compared to spoke patients. Visit constancy was lower at the hub (-4.5%, 95% CI: -3.5, -5.5), where gaps in care were also more likely to occur (adjusted odds ratio=1.95, 95% CI: 1.83-2.08). Decentralized sites demonstrated better retention outcomes using visit-level measures, while the hub achieved better retention outcomes using patient-level measures. Retention estimates produced by incorporating multiple measures showed substantial variation, confirming the influence of measurement strategies on the results of retention research. Future studies of retention in HIV care in sub-Saharan Africa will be well-served by including multiple measures.
Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene

PubMed Central

2017-01-01

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference. PMID:29136663
Distributioin, orientation and scales of the field-aligned currents measured by Swarm

NASA Astrophysics Data System (ADS)

Yang, J.; Dunlop, M. W.

2016-12-01

We have statistically studied the R1, R2 and net field aligned currents using the FAC data of the Swarm satellites. We also have investigated the statistical, dual-spacecraft correlations of field-aligned current signatures between two Swarm spacecraft (A and C). For the first time we have inferred the orientations of the current sheets of FACs directly, using the maximum correlations, obtained from sliding data segments, which show clear trends in magnetic local time (MLT). To compare with this we also check the MVAB method. To explore the scale and variability of the current sheet supposition, we investigate the MLT dependence of the maximum correlations in different time shift or longitude shift bins.
Measurement of the orientation of buffer-gas-cooled, electrostatically-guided ammonia molecules

NASA Astrophysics Data System (ADS)

Steer, Edward W.; Petralia, Lorenzo S.; Western, Colin M.; Heazlewood, Brianna R.; Softley, Timothy P.

2017-02-01

The extent to which the spatial orientation of internally and translationally cold ammonia molecules can be controlled as molecules pass out of a quadrupole guide and through different electric field regions is examined. Ammonia molecules are collisionally cooled in a buffer gas cell, and are subsequently guided by a three-bend electrostatic quadrupole into a detection chamber. The orientation of ammonia molecules is probed using (2 + 1) resonance-enhanced multiphoton ionisation (REMPI), with the laser polarisation axis aligned both parallel and perpendicular to the time-of-flight axis. Even with the presence of a near-zero field region, the ammonia REMPI spectra indicate some retention of orientation. Monte Carlo simulations propagating the time-dependent Schrödinger equation in a full basis set including the hyperfine interaction enable the orientation of ammonia molecules to be calculated - with respect to both the local field direction and a space-fixed axis - as the molecules pass through different electric field regions. The simulations indicate that the orientation of ∼95% of ammonia molecules in JK =11 could be achieved with the application of a small bias voltage (17 V) to the mesh separating the quadrupole and detection regions. Following the recent combination of the buffer gas cell and quadrupole guide apparatus with a linear Paul ion trap, this result could enable one to examine the influence of molecular orientation on ion-molecule reaction dynamics and kinetics.
The use of real-time ultrasound feedback in teaching abdominal hollowing exercises to healthy subjects.

PubMed

Henry, Sharon M; Westervelt, Karen C

2005-06-01

Randomized controlled trial. To determine if supplementing typical clinical instruction with real-time ultrasound feedback facilitates performance and retention of the abdominal hollowing exercise (AHE). Increasingly clinicians are using real-time ultrasound imaging as a form of feedback when teaching patients trunk stabilization exercises; however, there has been no justification for this practice. Forty-eight subjects were divided randomly into 3 groups that received different types of feedback: group 1 received minimal verbal feedback, group 2 received verbal and palpatory feedback, and group 3 received real-time ultrasound, verbal, and palpatory feedback. If the subject performed 3 consecutive correct AHEs during the initial session, she/he returned for a retention test. The performance of 3 consecutive, correct AHEs was the criterion measure; the number of trials to criterion was also recorded during the initial and retention test sessions. The ability to perform the AHE differed among groups (P<.001). During the initial session, 12.5% of subjects in group 1, 50.0% of subjects in group 2, and 87.5% of subjects in group 3 were able to perform 3 consecutive AHEs. Group 3 subjects achieved the criterion in fewer trials than the other 2 groups (P = .0006). No differences among groups were found for the retention testing; however, low power due to fewer subjects precluded a strong interpretation of this finding. Real-time ultrasound feedback can decrease the number of trials needed to consistently perform the AHE; however, the data are inconclusive with regard to retention of this skill.
Between-Trial Forgetting Due to Interference and Time in Motor Adaptation.

PubMed

Kim, Sungshin; Oh, Youngmin; Schweighofer, Nicolas

2015-01-01

Learning a motor task with temporally spaced presentations or with other tasks intermixed between presentations reduces performance during training, but can enhance retention post training. These two effects are known as the spacing and contextual interference effect, respectively. Here, we aimed at testing a unifying hypothesis of the spacing and contextual interference effects in visuomotor adaptation, according to which forgetting between trials due to either spaced presentations or interference by another task will promote between-trial forgetting, which will depress performance during acquisition, but will promote retention. We first performed an experiment with three visuomotor adaptation conditions: a short inter-trial-interval (ITI) condition (SHORT-ITI); a long ITI condition (LONG-ITI); and an alternating condition with two alternated opposite tasks (ALT), with the same single-task ITI as in LONG-ITI. In the SHORT-ITI condition, there was fastest increase in performance during training and largest immediate forgetting in the retention tests. In contrast, in the ALT condition, there was slowest increase in performance during training and little immediate forgetting in the retention tests. Compared to these two conditions, in the LONG-ITI, we found intermediate increase in performance during training and intermediate immediate forgetting. To account for these results, we fitted to the data six possible adaptation models with one or two time scales, and with interference in the fast, or in the slow, or in both time scales. Model comparison confirmed that two time scales and some degree of interferences in either time scale are needed to account for our experimental results. In summary, our results suggest that retention following adaptation is modulated by the degree of between-trial forgetting, which is due to time-based decay in single adaptation task and interferences in multiple adaptation tasks.
Alignment nature of ZnO nanowires grown on polished and nanoscale etched lithium niobate surface through self-seeding thermal evaporation method

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

Mohanan, Ajay Achath; Parthiban, R.; Ramakrishnan, N., E-mail: ramakrishnan@monash.edu

Highlights: • ZnO nanowires were grown directly on LiNbO{sub 3} surface for the first time by thermal evaporation. • Self-alignment of the nanowires due to step bunching of LiNbO{sub 3} surface is observed. • Increased roughness in surface defects promoted well-aligned growth of nanowires. • Well-aligned growth was then replicated in 50 nm deep trenches on the surface. • Study opens novel pathway for patterned growth of ZnO nanowires on LiNbO{sub 3} surface. - Abstract: High aspect ratio catalyst-free ZnO nanowires were directly synthesized on lithium niobate substrate for the first time through thermal evaporation method without the use ofmore » a buffer layer or the conventional pre-deposited ZnO seed layer. As-grown ZnO nanowires exhibited a crisscross aligned growth pattern due to step bunching of the polished lithium niobate surface during the nanowire growth process. On the contrary, scratches on the surface and edges of the substrate produced well-aligned ZnO nanowires in these defect regions due to high surface roughness. Thus, the crisscross aligned nature of high aspect ratio nanowire growth on the lithium niobate surface can be changed to well-aligned growth through controlled etching of the surface, which is further verified through reactive-ion etching of lithium niobate. The investigations and discussion in the present work will provide novel pathway for self-seeded patterned growth of well-aligned ZnO nanowires on lithium niobate based micro devices.« less
Theory for nanoparticle retention time in the helical channel of quadrupole magnetic field-flow fractionation

NASA Astrophysics Data System (ADS)

Williams, P. Stephen; Carpino, Francesca; Zborowski, Maciej

2009-05-01

Quadrupole magnetic field-flow fractionation (QMgFFF) is a separation and characterization technique for magnetic nanoparticles such as those used for cell labeling and for targeted drug therapy. A helical separation channel is used to efficiently exploit the quadrupole magnetic field. The fluid and sample components therefore have angular and longitudinal components to their motion in the thin annular space occupied by the helical channel. The retention ratio is defined as the ratio of the times for non-retained and a retained material to pass through the channel. Equations are derived for the respective angular and longitudinal components to retention ratio.
Spatial Memory in Rats after 25 Hours

ERIC Educational Resources Information Center

Crystal, Jonathon D.; Babb, Stephanie J.

2008-01-01

We investigated the time course of spatial-memory decay in rats using an eight-arm radial maze. It is well established that performance remains high with retention intervals as long as 4 h, but declines to chance with a 24-h retention interval (Beatty, W. W., & Shavalia, D. A. (1980b). Spatial memory in rats: time course of working memory and…
Combined effects of mobile phase composition and temperature on the retention of phenolic antioxidants on an octylsilica polydentate column.

PubMed

Jandera, Pavel; Vyňuchalová, Kateřina; Nečilová, Kateřina

2013-11-22

Combined effects of temperature and mobile-phase composition on retention and separation selectivity of phenolic acids and flavonoid compounds were studied in liquid chromatography on a polydentate Blaze C8 silica based column. The temperature effects on the retention can be described by van't Hoff equation. Good linearity of lnk versus 1/T graphs indicates that the retention is controlled by a single mechanism in the mobile phase and temperature range studied. Enthalpic and entropic contributions to the retention were calculated from the regression lines. Generally, enthalpic contributions control the retention at lower temperatures and in mobile phases with lower concentrations of methanol in water. Semi-empirical retention models describe the simultaneous effects of temperature and the volume fraction of the organic solvent in the mobile phase. Using the linear free energy-retention model, selective dipolarity/polarizability, hydrogen-bond donor, hydrogen-bond acceptor and molecular size contributions to retention were estimated at various mobile phase compositions and temperatures. In addition to mobile phase gradients, temperature programming can be used to reduce separation times. Copyright © 2013 Elsevier B.V. All rights reserved.

Comparative analysis of peak-detection techniques for comprehensive two-dimensional chromatography.

PubMed

Latha, Indu; Reichenbach, Stephen E; Tao, Qingping

2011-09-23

Comprehensive two-dimensional gas chromatography (GC×GC) is a powerful technology for separating complex samples. The typical goal of GC×GC peak detection is to aggregate data points of analyte peaks based on their retention times and intensities. Two techniques commonly used for two-dimensional peak detection are the two-step algorithm and the watershed algorithm. A recent study [4] compared the performance of the two-step and watershed algorithms for GC×GC data with retention-time shifts in the second-column separations. In that analysis, the peak retention-time shifts were corrected while applying the two-step algorithm but the watershed algorithm was applied without shift correction. The results indicated that the watershed algorithm has a higher probability of erroneously splitting a single two-dimensional peak than the two-step approach. This paper reconsiders the analysis by comparing peak-detection performance for resolved peaks after correcting retention-time shifts for both the two-step and watershed algorithms. Simulations with wide-ranging conditions indicate that when shift correction is employed with both algorithms, the watershed algorithm detects resolved peaks with greater accuracy than the two-step method. Copyright © 2011 Elsevier B.V. All rights reserved.
Predictors of retention in a drug-free unit/substance abuse treatment in prison.

PubMed

Casares-López, María José; González-Menéndez, Ana; Festinger, David S; Fernández-García, Paula; Fernández-Hermida, José Ramón; Secades, Roberto; Matejkowski, Jason

2013-01-01

The high rate of dropout from treatment programs is a recurring problem in the field of drug dependence. The purpose of this study was to identify the predictors of retention in a prison-based drug-free unit (DFU). The relationships among subscales of the Addiction Severity Index (ASI) as well as motivation and personality profiles and length of stay in a DFU, of 57 prisoners admitted for the first time to the program were analyzed. The mean dropout rates were 52.9% at six months and 67.8% at one year. The mean length of stay was 195.05 days. Predictors of retention at six months included the ASI Family Composite Score, the motivation subscale Taking Steps, and Narcissistic personality trait score. Predictors of retention at one year included lower ASI Psychological Composite Score, higher scores on the motivation subscale Ambivalence, and higher number of charges pending at the time of admission to the program. Identification of these predictor variables may be useful for developing strategies to increase retention in the context of in-prison substance abuse treatment. Copyright © 2013. Published by Elsevier Ltd.
Polyaniline nanowire arrays aligned on nitrogen-doped carbon fabric for high-performance flexible supercapacitors.

PubMed

Yu, Pingping; Li, Yingzhi; Yu, Xinyi; Zhao, Xin; Wu, Lihao; Zhang, Qinghua

2013-09-24

A combination of vertical polyaniline (PANI) nanowire arrays and nitrogen plasma etched carbon fiber cloths (eCFC) was fabricated to create 3D nanostructured PANI/eCFC composites. The small size of the highly ordered PANI nanowires can greatly reduce the scale of the diffusion length, allowing for the improved utilization of electrode materials. A two-electrode flexible supercapacitor based on PANI/eCFC demonstrates a high specific capacitance (1035 F g(-1) at a current density of 1 A g(-1)), good rate capability (88% capacity retention at 8 A g(-1)), and long-term cycle life (10% capacity loss after 5000 cycles). The lightweight, low-cost, flexible composites are promising candidates for use in energy storage device applications.
Twin-bit via resistive random access memory in 16 nm FinFET logic technologies

NASA Astrophysics Data System (ADS)

Shih, Yi-Hong; Hsu, Meng-Yin; King, Ya-Chin; Lin, Chrong Jung

2018-04-01

A via resistive random access memory (RRAM) cell fully compatible with the standard CMOS logic process has been successfully demonstrated for high-density logic nonvolatile memory (NVM) modules in advanced FinFET circuits. In this new cell, the transition metal layers are formed on both sides of a via, given two storage bits per via. In addition to its compact cell area (1T + 14 nm × 32 nm), the twin-bit via RRAM cell features a low operation voltage, a large read window, good data retention, and excellent cycling capability. As fine alignments between mask layers become possible, the twin-bit via RRAM cell is expected to be highly scalable in advanced FinFET technology.
Stability of vitamin D in foodstuffs during cooking.

PubMed

Jakobsen, Jette; Knuthsen, Pia

2014-04-01

We investigated the retention of vitamin D3 and 25-hydroxyvitamin D3 in eggs, vitamin D3 in margarine, and vitamin D3 and vitamin D2 in bread. Our set-up illustrated the cooking methods usually performed in households i.e. boiling, frying in pan and oven, and baking. All experiments were performed three times independently of one another. The retention of vitamin D compounds in eggs and margarine during heat treatment in an oven for 40 min at normal cooking temperature showed retention at 39-45%, while frying resulted in retention at 82-84%. Boiled eggs were found to have a similar level of retention (86-88%). For bread baked, as recommended in the recipe, the retention of vitamin D3 in rye bread at 69% was lower than the retention in wheat bread at 85%. A similar observation was made for vitamin D2, although the retention was slightly higher, 73% and 89%. No difference between retention of vitamin D3 and 25-hydroxyvitamin D3 in eggs was shown. Cooking may cause detrimental loss of vitamin D, but it depends on the actual foodstuffs and the heating process. Further research is needed to optimise cooking procedures to enhance retention of vitamin D. Vitamin D retention should be taken into account in future calculations of dietary intake of vitamin D. Copyright © 2013 Elsevier Ltd. All rights reserved.
Specialized moisture retention eyewear for evaporative dry eye.

PubMed

Waduthantri, Samanthila; Tan, Chien Hua; Fong, Yee Wei; Tong, Louis

2015-05-01

To evaluate the suitablity of commercially available moisture retention eyewear for treating evaporative dry eye. Eleven patients with evaporative dry eyes were prescibed moisture retention eyewear for 3 months in addition to regular lubricant eye drops. Frequency and severity of dry eye symptoms, corneal fluorescein staining and tear break up time (TBUT) were evaluated at baseline and 3-month post-treatment. Main outcome measure was global symptom score (based on severity and frequency of dry eye symptoms on a visual analog scale) and secondary outcomes were changes in sectoral corneal fluorescein staining and tear break up time (TBUT) from pre-treatment level. There was a significant improvement in dry eye symptoms after using moisture retention eyewear for 3 months (p < 0.05). Corneal fluorescein staining in all five zones of the cornea in both eyes improved significantly (p < 0.05). There was no significant improvement in TBUT. Patients used ocular lubricants less frequently (p < 0.05) compared to the commencement of the study. Patients found moisture retention eyewear to be useful in relieving dry eye symptoms in windy, air-conditioned environments or when doing vision-related daily tasks. This study shows that moisture retention eyewear might be a valuable adjunct in management of evaporative dry eye and this new design of commercially available eyewear could have a good acceptability rate.
Central ghrelin increases anxiety in the Open Field test and impairs retention memory in a passive avoidance task in neonatal chicks.

PubMed

Carvajal, Pedro; Carlini, Valeria P; Schiöth, Helgi B; de Barioglio, Susana R; Salvatierra, Nancy A

2009-05-01

Ghrelin (Grh) is an endogenous ligand for the growth hormone secretagogue receptor. Although Ghr stimulates feeding in rats, it inhibits feeding in neonatal chicks. However, little is known about other central behavioral effects of Ghr. Therefore, we investigated the Ghr effects, injected intracerebroventricularly, on anxiety and memory retention of neonatal chicks in an Open Field test and in a one-trial passive avoidance task, respectively. In the Open Field test, the administration of Ghr in a dose-dependent manner increased the latency to ambulate but decreased ambulation activity, indicating an anxiogenic effect. Furthermore, chicks trained on a passive avoidance task and injected with a dose of 30pmol of Ghr immediately after training showed an impairment of memory retention. However, there were no significant effects on the number of pecks during the pretraining, training, retention and discrimination. In addition, different doses of Ghr produced an inhibition in food intake at different times after injection. Our results indicate that Ghr induces anxiogenesis in chicks. Moreover, we have shown for the first time that Ghr can decrease memory retention in a non-mammalian species, suggesting that Ghr may play an important role in the processes of memory retention in birds.
Retention of ingested porcine reproductive and respiratory syndrome virus in houseflies.

PubMed

Schurrer, Jennifer A; Dee, Scott A; Moon, Roger D; Murtaugh, Michael P; Finnegan, Colleen P; Deen, John; Kleiboeker, Steven B; Pijoan, Carlos B J

2005-09-01

To evaluate retention of porcine reproductive and respiratory syndrome virus (PRRSV) in houseflies for various time frames and temperatures. Fifteen 2-week-old pigs, two 10-week-old pigs, and laboratory-cultivated houseflies. In an initial experiment, houseflies were exposed to PRRSV; housed at 15 degrees, 20 degrees, 25 degrees, and 30 degrees C; and tested at various time points. In a second experiment to determine dynamics of virus retention, houseflies were exposed to PRRSV and housed under controlled field conditions for 48 hours. Changes in the percentage of PRRSV-positive flies and virus load per fly were assessed over time, and detection of infective virus at 48 hours after exposure was measured. Finally, in a third experiment, virus loads were measured in houseflies allowed to feed on blood, oropharyngeal washings, and nasal washings obtained from experimentally infected pigs. In experiment 1, PRRSV retention in houseflies was proportional to temperature. In the second experiment, the percentage of PRRSV-positive houseflies and virus load per fly decreased over time; however, infective PRRSV was found in houseflies 48 hours after exposure. In experiment 3, PRRSV was detected in houseflies allowed to feed on all 3 porcine body fluids. For the conditions of this study, houseflies did not support PRRSV replication. Therefore, retention of PRRSV in houseflies appears to be a function of initial virus load after ingestion and environmental temperature. These factors may impact the risk of insect-borne spread of PRRSV among farms.
Measurement of the Retention Time of Different Ophthalmic Formulations with Ultrahigh-Resolution Optical Coherence Tomography.

PubMed

Gagliano, Caterina; Papa, Vincenzo; Amato, Roberta; Malaguarnera, Giulia; Avitabile, Teresio

2018-04-01

Purpose/aim of the study: The purpose of this study was to measure the pre-corneal retention time of two marketed formulations (eye drops and eye gel) of a steroid-antibiotic fixed combination (FC) containing 0.1% dexamethasone and 0.3% netilmicin. Pre-corneal retention time was evaluated in 16 healthy subjects using an ultrahigh-resolution anterior segment spectral domain optical coherence tomography (OCT). All subjects randomly received both formulations of the FC (Netildex, SIFI, Italy). Central tear film thickness (CTFT) was measured before instillation (time 0) and then after 1, 10, 20, 30, 40 50, 60 and 120 min. The pre-corneal retention time was calculated by plotting CTFT as a function of time. Differences between time points and groups were analyzed by Student's t-test. CTFT increased significantly after the instillation of the eye gel formulation (p < 0.001). CTFT reached its maximum value 1 min after instillation and returned to baseline after 60 min. No effect on CTFT was observed after the instillation of eye drops. The difference between the two formulations was statistically significant at time 1 min (p < 0.0001), 10 min (p < 0.001) and 20 min (p < 0.01). The FC formulated as eye gel was retained on the ocular surface longer than the corresponding eye drop solution. Consequently, the use of the eye gel might extend the interval between instillations and decrease the frequency of administration.
Comparison of retention models for polymers 1. Poly(ethylene glycol)s.

PubMed

Bashir, Mubasher A; Radke, Wolfgang

2006-10-27

The suitability of three different retention models to predict the retention times of poly(ethylene glycol)s (PEGs) in gradient and isocratic chromatography was investigated. The models investigated were the linear (LSSM) and the quadratic solvent strength model (QSSM). In addition, a model describing the retention behaviour of polymers was extended to account for gradient elution (PM). It was found that all models are suited to properly predict gradient retention volumes provided the extraction of the analyte specific parameters is performed from gradient experiments as well. The LSSM and QSSM on principle cannot describe retention behaviour under critical or SEC conditions. Since the PM is designed to cover all three modes of polymer chromatography, it is therefore superior to the other models. However, the determination of the analyte specific parameters, which are needed to calibrate the retention behaviour, strongly depend on the suitable selection of initial experiments. A useful strategy for a purposeful selection of these calibration experiments is proposed.
Strategies to enhance participant recruitment and retention in research involving a community-based population.

PubMed

McCullagh, Marjorie C; Sanon, Marie-Anne; Cohen, Michael A

2014-11-01

Challenges associated with recruiting and retaining community-based populations in research studies have been recognized yet remain of major concern for researchers. There is a need for exchange of recruitment and retention techniques that inform recruitment and retention strategies. Here, the authors discuss a variety of methods that were successful in exceeding target recruitment and retention goals in a randomized clinical trial of hearing protector use among farm operators. Recruitment and retention strategies were 1) based on a philosophy of mutually beneficial engagement in the research process, 2) culturally appropriate, 3) tailored to the unique needs of partnering agencies, and 4) developed and refined in a cyclical and iterative process. Sponsoring organizations are interested in cost-effective recruitment and retention strategies, particularly relating to culturally and ethnically diverse groups. These approaches may result in enhanced subject recruitment and retention, concomitant containment of study costs, and timely accomplishment of study aims. Copyright © 2014 Elsevier Inc. All rights reserved.
Facilitating student retention in online graduate nursing education programs: a review of the literature.

PubMed

Gazza, Elizabeth A; Hunker, Diane F

2014-07-01

Online education, a form of distance education, provides students with opportunities to engage in lifelong learning without the restrictions of time and space. However, while this approach meets the needs of employed nursing professionals, it poses some challenges for educators. Student retention is one such challenge. Student retention rates serve as measures of program quality and are reported to accrediting bodies. Therefore, it is imperative that administrators and program faculty implement comprehensive programs to ensure student retention. This review of the literature was designed to identify strategies to improve student retention in online graduate nursing education programs. The review includes 23 articles that address models, research, and best practices supported in nursing and higher education. The findings indicate that student retention in online programs is a multidimensional problem requiring a multifaceted approach. Recommendations for facilitating retention in online nursing programs include ensuring social presence and program and course quality, and attentiveness to individual student characteristics. Copyright © 2014 Elsevier Ltd. All rights reserved.
Pinned, optically aligned diagnostic dock for use on the Z facility.

PubMed

Gomez, M R; Rochau, G A; Bailey, J E; Dunham, G S; Kernaghan, M D; Gard, P; Robertson, G K; Owen, A C; Argo, J W; Nielsen, D S; Lake, P W

2012-10-01

The pinned optically aligned diagnostic dock (PODD) is a multi-configuration diagnostic platform designed to measure x-ray emission on the Z facility. The PODD houses two plasma emission acquisition (PEA) systems, which are aligned with a set of precision machined pins. The PEA systems are modular, allowing a single diagnostic housing to support several different diagnostics. The PEA configurations fielded to date include both time-resolved and time-integrated, 1D spatially resolving, elliptical crystal spectrometers, and time-integrated, 1D spatially resolving, convex crystal spectrometers. Additional proposed configurations include time-resolved, monochromatic mirrored pinhole imagers and arrays of filtered x-ray diodes, diamond photo-conducting diode detectors, and bolometers. The versatility of the PODD system will allow the diagnostic configuration of the Z facility to be changed without significantly adding to the turn-around time of the machine. Additionally, the PODD has been designed to allow instrument setup to be completed entirely off-line, leaving only a refined alignment process to be performed just prior to a shot, which is a significant improvement over the instrument the PODD replaces. Example data collected with the PODD are presented.
Peptide retention prediction using hydrophilic interaction liquid chromatography coupled to mass spectrometry.

PubMed

Badgett, Majors J; Boyes, Barry; Orlando, Ron

2018-02-16

A model that predicts retention for peptides using a HALO ® penta-HILIC column and gradient elution was created. Coefficients for each amino acid were derived using linear regression analysis and these coefficients can be summed to predict the retention of peptides. This model has a high correlation between experimental and predicted retention times (0.946), which is on par with previous RP and HILIC models. External validation of the model was performed using a set of H. pylori samples on the same LC-MS system used to create the model, and the deviation from actual to predicted times was low. Apart from amino acid composition, length and location of amino acid residues on a peptide were examined and two site-specific corrections for hydrophobic residues at the N-terminus as well as hydrophobic residues one spot over from the N-terminus were created. Copyright © 2017 Elsevier B.V. All rights reserved.
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

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

Daily, Jeffrey A.

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

DOE PAGES

Daily, Jeffrey A.

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less
Reducing beam shaper alignment complexity: diagnostic techniques for alignment and tuning

NASA Astrophysics Data System (ADS)

Lizotte, Todd E.

2011-10-01

Safe and efficient optical alignment is a critical requirement for industrial laser systems used in a high volume manufacturing environment. Of specific interest is the development of techniques to align beam shaping optics within a beam line; having the ability to instantly verify by a qualitative means that each element is in its proper position as the beam shaper module is being aligned. There is a need to reduce these types of alignment techniques down to a level where even a newbie to optical alignment will be able to complete the task. Couple this alignment need with the fact that most laser system manufacturers ship their products worldwide and the introduction of a new set of variables including cultural and language barriers, makes this a top priority for manufacturers. Tools and methodologies for alignment of complex optical systems need to be able to cross these barriers to ensure the highest degree of up time and reduce the cost of maintenance on the production floor. Customers worldwide, who purchase production laser equipment, understand that the majority of costs to a manufacturing facility is spent on system maintenance and is typically the largest single controllable expenditure in a production plant. This desire to reduce costs is driving the trend these days towards predictive and proactive, not reactive maintenance of laser based optical beam delivery systems [10]. With proper diagnostic tools, laser system developers can develop proactive approaches to reduce system down time, safe guard operational performance and reduce premature or catastrophic optics failures. Obviously analytical data will provide quantifiable performance standards which are more precise than qualitative standards, but each have a role in determining overall optical system performance [10]. This paper will discuss the use of film and fluorescent mirror devices as diagnostic tools for beam shaper module alignment off line or in-situ. The paper will also provide an overview methodology showing how it is possible to reduce complex alignment directions into a simplified set of instructions for layman service engineers.
A Multicenter Radiographic Evaluation of the Rates of Preoperative and Postoperative Malalignment in Degenerative Spinal Fusions.

PubMed

Leveque, Jean-Christophe A; Segebarth, Bradley; Schroerlucke, Samuel R; Khanna, Nitin; Pollina, John; Youssef, Jim A; Tohmeh, Antoine G; Uribe, Juan S

2018-07-01

Multicenter, retrospective, institutional-review-board -approved study at 18 institutions in the United States with 24 treating investigators. This study was designed to retrospectively assess the prevalence of spinopelvic malalignment in patients who underwent one- or two-level lumbar fusions for degenerative (nondeformity) indications and to assess the incidence of malalignment after fusion surgery as well as the rate of alignment preservation and/or correction in this population. Spinopelvic malalignment after lumbar fusion has been associated with lower postoperative health-related quality of life and elevated risk of adjacent segment failure. The prevalence of spinopelvic malalignment in short-segment degenerative lumbar fusion procedures from a large sample of patients is heretofore unreported and may lead to an under-appreciation of these factors in surgical planning and ultimate preservation or correction of alignment. Lateral preoperative and postoperative lumbar radiographs were retrospectively acquired from 578 one- or two-level lumbar fusion patients and newly measured for lumbar lordosis (LL), pelvic incidence (PI), and pelvic tilt. Patients were categorized at preop and postop time points as aligned if PI-LL < 10° or malaligned if PI-LL≥10°. Patients were grouped into categories based on their alignment progression from pre- to postoperative, with preserved (aligned to aligned), restored (malaligned to aligned), not corrected (malaligned to malaligned), and worsened (aligned to malaligned) designations. Preoperatively, 173 (30%) patients exhibited malalignment. Postoperatively, 161 (28%) of patients were malaligned. Alignment was preserved in 63%, restored in 9%, not corrected in 21%, and worsened in 7% of patients. This is the first multicenter study to evaluate the preoperative prevalence and postoperative incidence of spinopelvic malalignment in a large series of short-segment degenerative lumbar fusions, finding over 25% of patients out of alignment at both time points, suggesting that alignment preservation/restoration considerations should be incorporated into the decision-making of even degenerative lumbar spinal fusions. 3.
How genome complexity can explain the difficulty of aligning reads to genomes.

PubMed

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.
Literacy and retention of information after a multimedia diabetes education program and teach-back.

PubMed

Kandula, Namratha R; Malli, Tiffany; Zei, Charles P; Larsen, Emily; Baker, David W

2011-01-01

Few studies have examined the effectiveness of teaching strategies to improve patients' recall and retention of information. As a next step in implementing a literacy-appropriate, multimedia diabetes education program (MDEP), the present study reports the results of two experiments designed to answer (a) how much knowledge is retained 2 weeks after viewing the MDEP, (b) does knowledge retention differ across literacy levels, and (c) does adding a teach-back protocol after the MDEP improve knowledge retention at 2-weeks' follow-up? In Experiment 1, adult primary care patients (n = 113) watched the MDEP and answered knowledge-based questions about diabetes before and after viewing the MDEP. Two weeks later, participants completed the knowledge assessment a third time. Methods and procedures for Experiment 2 (n = 58) were exactly the same, except that if participants answered a question incorrectly after watching the MDEP, they received teach-back, wherein the information was reviewed and the question was asked again, up to two times. Two weeks later, Experiment 2 participants completed the knowledge assessment again. Literacy was measured using the S-TOFHLA. After 2 weeks, all participants, regardless of their literacy levels, forgot approximately half the new information they had learned from the MDEP. In regression models, adding a teach-back protocol did not improve knowledge retention among participants and literacy was not associated with knowledge retention at 2 weeks. Health education interventions must incorporate strategies that can improve retention of health information and actively engage patients in long-term learning.

Qualitative analysis of mycotoxins using micellar electrokinetic capillary chromatography

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

Holland, R.D.; Sepaniak, M.J.

1993-05-01

Naturally occurring mycotoxins are separated using micellar electrokinetic capillary chromatography. Trends in the retention of these toxins, resulting from changes in mobile-phase composition and pH, are reported and presented as a means of alleviating coelution problems. Two sets of mobile-phase conditions are determined that provide unique separation selectivity. The facile manner by which mobile-phase conditions can be altered, without changes in instrumental configuration, allowed the acquisition of two distinctive, fully resolved chromatograms of 10 mycotoxins in a period of approximately 45 min. By adjusting retention times, using indigenous or added components in mycotoxin samples as normalization standards, it is possiblemore » to obtain coefficients of variation in retention time that average less than 1%. The qualitative capabilities of this methodology are evaluated by separating randomly generated mycotoxin-interferent mixtures. In this study, the utilization of normalized retention times applied to separations obtained with two sets of mobile-phase conditions permitted the identification of all the mycotoxins in five unknown samples without any misidentifications. 24 refs., 3 figs., 2 tabs.« less
Limitation of predictive 2-D liquid chromatography in reducing the database search space in shotgun proteomics: in silico studies.

PubMed

Moskovets, Eugene; Goloborodko, Anton A; Gorshkov, Alexander V; Gorshkov, Mikhail V

2012-07-01

A two-dimensional (2-D) liquid chromatography (LC) separation of complex peptide mixtures that combines a normal phase utilizing hydrophilic interactions and a reversed phase offers reportedly the highest level of 2-D LC orthogonality by providing an even spread of peptides across multiple LC fractions. Matching experimental peptide retention times to those predicted by empirical models describing chromatographic separation in each LC dimension leads to a significant reduction in a database search space. In this work, we calculated the retention times of tryptic peptides separated in the C18 reversed phase at different separation conditions (pH 2 and pH 10) and in TSK gel Amide-80 normal phase. We show that retention times calculated for different 2-D LC separation schemes utilizing these phases start to correlate once the mass range of peptides under analysis becomes progressively narrow. This effect is explained by high degree of correlation between retention coefficients in the considered phases. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Difference equation model for isothermal gas chromatography expresses retention behavior of homologues of n-alkanes excluding the influence of holdup time

PubMed Central

Wu, Liejun; Chen, Yongli; Caccamise, Sarah A.L.; Li, Qing X.

2012-01-01

A difference equation (DE) model is developed using the methylene retention increment (Δtz) of n-alkanes to avoid the influence of gas holdup time (tM). The effects of the equation orders (1st–5th) on the accuracy of a curve fitting show that a linear equation (LE) is less satisfactory and it is not necessary to use a complicated cubic or higher order equation. The relationship between the logarithm of Δtz and the carbon number (z) of the n-alkanes under isothermal conditions closely follows the quadratic equation for C3–C30 n-alkanes at column temperatures of 24–260 °C. The first and second order forward differences of the expression (Δlog Δtz and Δ2log Δtz, respectively) are linear and constant, respectively, which validates the DE model. This DE model lays a necessary foundation for further developing a retention model to accurately describe the relationship between the adjusted retention time and z of n-alkanes. PMID:22939376
Impact of high-κ dielectric and metal nanoparticles in simultaneous enhancement of programming speed and retention time of nano-flash memory

NASA Astrophysics Data System (ADS)

Pavel, Akeed A.; Khan, Mehjabeen A.; Kirawanich, Phumin; Islam, N. E.

2008-10-01

A methodology to simulate memory structures with metal nanocrystal islands embedded as floating gate in a high-κ dielectric material for simultaneous enhancement of programming speed and retention time is presented. The computational concept is based on a model for charge transport in nano-scaled structures presented earlier, where quantum mechanical tunneling is defined through the wave impedance that is analogous to the transmission line theory. The effects of substrate-tunnel dielectric conduction band offset and metal work function on the tunneling current that determines the programming speed and retention time is demonstrated. Simulation results confirm that a high-κ dielectric material can increase programming current due to its lower conduction band offset with the substrate and also can be effectively integrated with suitable embedded metal nanocrystals having high work function for efficient data retention. A nano-memory cell designed with silver (Ag) nanocrystals embedded in Al 2O 3 has been compared with similar structure consisting of Si nanocrystals in SiO 2 to validate the concept.
An Orchestrated Intron Retention Program in Meiosis Controls Timely Usage of Transcripts during Germ Cell Differentiation.

PubMed

Naro, Chiara; Jolly, Ariane; Di Persio, Sara; Bielli, Pamela; Setterblad, Niclas; Alberdi, Antonio J; Vicini, Elena; Geremia, Raffaele; De la Grange, Pierre; Sette, Claudio

2017-04-10

Global transcriptome reprogramming during spermatogenesis ensures timely expression of factors in each phase of male germ cell differentiation. Spermatocytes and spermatids require particularly extensive reprogramming of gene expression to switch from mitosis to meiosis and to support gamete morphogenesis. Here, we uncovered an extensive alternative splicing program during this transmeiotic differentiation. Notably, intron retention was largely the most enriched pattern, with spermatocytes showing generally higher levels of retention compared with spermatids. Retained introns are characterized by weak splice sites and are enriched in genes with strong relevance for gamete function. Meiotic intron-retaining transcripts (IRTs) were exclusively localized in the nucleus. However, differently from other developmentally regulated IRTs, they are stable RNAs, showing longer half-life than properly spliced transcripts. Strikingly, fate-mapping experiments revealed that IRTs are recruited onto polyribosomes days after synthesis. These studies reveal an unexpected function for regulated intron retention in modulation of the timely expression of select transcripts during spermatogenesis. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.
Magnetospheric convection during quiet or moderately disturbed times

NASA Technical Reports Server (NTRS)

Caudal, G.; Blanc, M.

1988-01-01

The processes which contribute to the large-scale plasma circulation in the earth's environment during quiet times, or during reasonable stable magnetic conditions are reviewed. The various sources of field-aligned current generation in the solar wind and the magnetosphere are presented. The generation of field-aligned currents on open field lines connected to either polar cap and the generation of closed field lines of the inner magnetosphere are examined. Consideration is given to the hypothesis of Caudal (1987) that loss processes of trapped particles are competing with adiabatic motions in the generation of field-aligned currents in the inner magnetosphere.
Dissipation dynamics of field-free molecular alignment for symmetric-top molecules: Ethane (C2H6)

NASA Astrophysics Data System (ADS)

Zhang, H.; Billard, F.; Yu, X.; Faucher, O.; Lavorel, B.

2018-03-01

The field-free molecular alignment of symmetric-top molecules, ethane, induced by intense non-resonant linearly polarized femtosecond laser pulses is investigated experimentally in the presence of collisional relaxation. The dissipation dynamics of field-free molecular alignment are measured by the balanced detection of ultrafast molecular birefringence of ethane gas samples at high pressures. By separating the molecular alignment into the permanent alignment and the transient alignment, the decay time-constants of both components are quantified at the same pressure. It is observed that the permanent alignment always decays slower compared to the transient alignment within the measured pressure range. This demonstrates that the propensity of molecules to conserve the orientation of angular momentum during collisions, previously observed for linear species, is also applicable to symmetric-top molecules. The results of this work provide valuable information for further theoretical understanding of collisional relaxation within nonlinear polyatomic molecules, which are expected to present interesting and nontrivial features due to an extra rotational degree of freedom.
Concurrent and Accurate Short Read Mapping on Multicore Processors.

PubMed

Martínez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina, Sergio; Castillo, Maribel; Dopazo, Joaquín; Quintana-Ortí, Enrique S

2015-01-01

We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.
Improving scanner wafer alignment performance by target optimization

NASA Astrophysics Data System (ADS)

Leray, Philippe; Jehoul, Christiane; Socha, Robert; Menchtchikov, Boris; Raghunathan, Sudhar; Kent, Eric; Schoonewelle, Hielke; Tinnemans, Patrick; Tuffy, Paul; Belen, Jun; Wise, Rich

2016-03-01

In the process nodes of 10nm and below, the patterning complexity along with the processing and materials required has resulted in a need to optimize alignment targets in order to achieve the required precision, accuracy and throughput performance. Recent industry publications on the metrology target optimization process have shown a move from the expensive and time consuming empirical methodologies, towards a faster computational approach. ASML's Design for Control (D4C) application, which is currently used to optimize YieldStar diffraction based overlay (DBO) metrology targets, has been extended to support the optimization of scanner wafer alignment targets. This allows the necessary process information and design methodology, used for DBO target designs, to be leveraged for the optimization of alignment targets. In this paper, we show how we applied this computational approach to wafer alignment target design. We verify the correlation between predictions and measurements for the key alignment performance metrics and finally show the potential alignment and overlay performance improvements that an optimized alignment target could achieve.
Development of a group work assessment pedagogy using constructive alignment theory.

PubMed

Croy, Suzanne R

2018-02-01

The purpose of this paper is to explore group work assessment underpinned by constructive alignment theory to develop a new assessment pedagogy. A review was undertaken of an existing module 'Mental Health Nursing 1', with student nurses participating in the BSc (Hons) Nursing Programme. Constructive alignment theory requires teachers to adopt a deep approach to learning where module learning outcomes are aligned with the teaching environment and modes of assessment. As the module progressed, reviewing the Mental Health Nursing 1 module became an excellent opportunity to begin to understand how constructive alignment theory can inform a group work assessment pedagogy. Working using a constructively aligned assessment process became a valuable learning experience for the module leader whilst at the same time revealed a gap in the research around the impact of constructively aligned teaching and group work assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.
Simple chained guide trees give high-quality protein multiple sequence alignments

PubMed Central

Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G.

2014-01-01

Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random. PMID:25002495
Effect of mat pilates exercise on postural alignment and body composition of middle-aged women.

PubMed

Lee, Hyo Taek; Oh, Hyun Ok; Han, Hui Seung; Jin, Kwang Youn; Roh, Hyo Lyun

2016-06-01

[Purpose] This study attempted to examine whether Pilates is an effective exercise for improving the postural alignment and health of middle-aged women. [Subjects and Methods] The participants in this study were 36 middle-aged women (20 in the experimental group, 16 in the control group). The experimental group participated in Pilates exercise sessions three times a week for 12 weeks. Body alignment and composition measurements before and after applying the Pilates exercise program were performed with a body composition analyzer and a three-dimensional scanner. [Results] Postural alignment in the sagittal and horizontal planes was enhanced in the Pilates exercise group. Trunk alignment showed correlations with body fat and muscle mass. [Conclusion] The Pilates exercises are performed symmetrically and strengthen the deep muscles. Moreover, the results showed that muscle mass was correlated with trunk postural alignment and that the proper amount of muscle is critical in maintaining trunk postural alignment.
The contributions of encoding, retention, and recall to the Hebb effect.

PubMed

Oberauer, Klaus; Meyer, Nadine

2009-10-01

The article reports an experiment testing whether the Hebb repetition effect-the gradual improvement of immediate serial recall when the same list is repeated several times-depends on overt recall of the repeated lists. Previous reports which suggest that recall is critical confound the recall manipulation with retention interval. The present experiment orthogonally varies retention interval (0 or 9 s) and whether the list is to be recalled after the retention interval. Hebb repetition learning is assessed in a final test phase. A repetition effect was obtained in all four experimental conditions; it was larger for recalled than non-recalled lists, whereas retention interval had no effect. The results show that encoding is sufficient to generate cumulative long-term learning, which is strengthened by recall. Rehearsal, if it takes place in the retention interval at all, does not have the same effect on long-term learning as overt recall.
Fast Response and Spontaneous Alignment in Liquid Crystals Doped with 12-Hydroxystearic Acid Gelators

PubMed Central

Lin, Hui-Chi; Wang, Chih-Hung; Wang, Jyun-Kai; Tsai, Sheng-Feng

2018-01-01

The spontaneous vertical alignment of liquid crystals (LCs) in gelator (12-hydroxystearic acid)-doped LC cells was studied. Gelator-induced alignment can be used in both positive and negative LC cells. The electro-optical characteristics of the gelator-doped negative LC cell were similar to those of an LC cell that contained a vertically aligned (VA) host. The rise time of the gelator-doped LC cell was two orders of magnitude shorter than that of the VA host LC cell. The experimental results indicate that the gelator-induced vertical alignment of LC molecules occurred not only on the surface of the indium tin oxide (ITO) but also on the homogeneous alignment layer. Various LC alignments (planar, hybrid, multistable hybrid, and vertical alignments) were achieved by modulating the doped gelator concentrations. The multistable characteristic of LCs doped with the gelator is also presented. The alignment by doping with a gelator reduces the manufacturing costs and provides a means of fabricating fast-responding, flexible LC displays using a low-temperature process. PMID:29735937
Intra Articular Therapeutic Delivery for Post Traumatic Osteoarthritis

DTIC Science & Technology

2016-10-01

method. Our central hypotheses are that joint retention time and therapeutic efficacy will be influenced by amniotic membrane particle size ...three Specific Aims: Aim 1: Evaluate the effects of human amniotic membrane (AM) particle size distribution on particle retention and progression of OA...following trauma. Factors we hypothesized would impact therapeutic efficacy of dHACM included particle size , timing of treatment, and frequency of delivery
The Effect of an Honors College on Retention among First Year Students

ERIC Educational Resources Information Center

Jarzombek, Molly J.; McCuistion, Kimberly J.; Bain, Steve F.; Guerrero, Dolores; Wester, David B.

2017-01-01

The Honors College at Texas A&M University-Kingsville was established in 2010. At that time, student retention rate at Texas A&M-Kingsville was at 56%, one of the lowest rates in Texas. In an effort to determine if the establishment of the Honors College on campus has made a positive impact on First Time In College (FTIC) student retention…
A dynamic processes study of PM retention by trees under different wind conditions.

PubMed

Xie, Changkun; Kan, Liyan; Guo, Jiankang; Jin, Sijia; Li, Zhigang; Chen, Dan; Li, Xin; Che, Shengquan

2018-02-01

Particulate matter (PM) is one of the most serious environmental problems, exacerbating respiratory and vascular illnesses. Plants have the ability to reduce non-point source PM pollution through retention on leaves and branches. Studies of the dynamic processes of PM retention by plants and the mechanisms influencing this process will help to improve the efficiency of urban greening for PM reduction. We examined dynamic processes of PM retention and the major factors influencing PM retention by six trees with different branch structure characteristics in wind tunnel experiments at three different wind speeds. The results showed that the changes of PM numbers retained by plant leaves over time were complex dynamic processes for which maximum values could exceed minimum values by over 10 times. The average value of PM measured in multiple periods and situations can be considered a reliable indicator of the ability of the plant to retain PM. The dynamic processes were similar for PM 10 and PM 2.5 . They could be clustered into three groups simulated by continually-rising, inverse U-shaped, and U-shaped polynomial functions, respectively. The processes were the synthetic effect of characteristics such as species, wind speed, period of exposure and their interactions. Continually-rising functions always explained PM retention in species with extremely complex branch structure. Inverse U-shaped processes explained PM retention in species with relatively simple branch structure and gentle wind. The U-shaped processes mainly explained PM retention at high wind speeds and in species with a relatively simple crown. These results indicate that using plants with complex crowns in urban greening and decreasing wind speed in plant communities increases the chance of continually-rising or inverse U-shaped relationships, which have a positive effect in reducing PM pollution. Copyright © 2017 Elsevier Ltd. All rights reserved.
Ontario Secondary School Program Innovations and Student A Report to the Ontario Study of the Relevance of Education and the Issue of Dropouts. Student Retention and Transition Series.

ERIC Educational Resources Information Center

Stamp, Robert M.

The time period between the early 1920s and the early 1970s witnessed increases in high school retention rates within Ontario's publicly-supported education system. These increases are attributed both to program changes within the system and to societal factors external to that system. Retention rates increased slowly during the 1920s, as minor…
Bimodal and multimodal plant biomass particle mixtures

DOEpatents

Dooley, James H.

2013-07-09

An industrial feedstock of plant biomass particles having fibers aligned in a grain, wherein the particles are individually characterized by a length dimension (L) aligned substantially parallel to the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L, wherein the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces, and wherein the particles in the feedstock are collectively characterized by having a bimodal or multimodal size distribution.
The importance of employment status in determining exit rates from nursing.

PubMed

Daniels, Frieda; Laporte, Audrey; Lemieux-Charles, Louise; Baumann, Andrea; Onate, Kanecy; Deber, Raisa

2012-01-01

To mitigate nurse shortages, health care decision makers tend to employ retention strategies that assume nurses employed in full-time, part-time, or casual positions and working in different sectors have similar preferences for work. However, this assumption has not been validated in the literature. The relationship between a nurse's propensity to exit the nurse profession in Ontario and employment status was explored by building an extended Cox Proportional Hazards Regression Model using a counting process technique. The differential exit patterns between part-time and casual nurses suggest that the common practice of treating part-time and casual nurses as equivalent is misleading. Health care decision makers should consider nurse retention strategies specifically targeting casual nurses because this segment of the profession is at the greatest risk of leaving. Nurse executives and nurse managers should investigate the different work preferences of part-time and casual nurses to devise tailored rather than "one-size fits all" nurse retention strategies to retain casual nurses.

Hyperfine-Structure-Induced Depolarization of Impulsively Aligned I2 Molecules

NASA Astrophysics Data System (ADS)

Thomas, Esben F.; Søndergaard, Anders A.; Shepperson, Benjamin; Henriksen, Niels E.; Stapelfeldt, Henrik

2018-04-01

A moderately intense 450 fs laser pulse is used to create rotational wave packets in gas phase I2 molecules. The ensuing time-dependent alignment, measured by Coulomb explosion imaging with a delayed probe pulse, exhibits the characteristic revival structures expected for rotational wave packets but also a complex nonperiodic substructure and decreasing mean alignment not observed before. A quantum mechanical model attributes the phenomena to coupling between the rotational angular momenta and the nuclear spins through the electric quadrupole interaction. The calculated alignment trace agrees very well with the experimental results.
System modeling of the Thirty Meter Telescope alignment and phasing system

NASA Astrophysics Data System (ADS)

Dekens, Frank G.; Seo, Byoung-Joon; Troy, Mitchell

2014-08-01

We have developed a system model using the System Modeling Language (SysML) for the Alignment and Phasing System (APS) on the Thirty Meter Telescope (TMT). APS is a Shack-Hartmann wave-front sensor that will be used to measure the alignment and phasing of the primary mirror segments, and the alignment of the secondary and tertiary mirrors. The APS system model contains the ow-down of the Level 1 TMT requirements to APS (Level 2) requirements, and from there to the APS sub-systems (Level 3) requirements. The model also contains the operating modes and scenarios for various activities, such as maintenance alignment, post-segment exchange alignment, and calibration activities. The requirements ow-down is captured in SysML requirements diagrams, and we describe the process of maintaining the DOORS database as the single-source-of-truth for requirements, while using the SysML model to capture the logic and notes associated with the ow-down. We also use the system model to capture any needed communications from APS to other TMT systems, and between the APS sub-systems. The operations are modeled using SysML activity diagrams, and will be used to specify the APS interface documents. The modeling tool can simulate the top level activities to produce sequence diagrams, which contain all the communications between the system and subsystem needed for that activity. By adding time estimates for the lowest level APS activities, a robust estimate for the total time on-sky that APS requires to align and phase the telescope can be obtained. This estimate will be used to verify that the time APS requires on-sky meets the Level 1 TMT requirements.
Handheld Navigation Device and Patient-Specific Cutting Guides Result in Similar Coronal Alignment for Primary Total Knee Arthroplasty: a Retrospective Matched Cohort Study.

PubMed

Steinhaus, Michael E; McLawhorn, Alexander S; Richardson, Shawn S; Maher, Patrick; Mayman, David J

2016-10-01

Proper alignment of total knee arthroplasty (TKA) is essential for TKA function and may reduce the risk of aseptic failure. Technologies that prevent malalignment may reduce the risk of revision surgery. The purpose of this study was to compare two competing TKA systems that purport improved alignment: patient-specific instrumentation (PSI), and a handheld portable navigation device (NAV). After IRB approval, 49 consecutive PSI TKAs (40 patients) were matched based on preoperative characteristics to 49 NAV TKAs (40 patients) performed by a single surgeon. A blinded observer measured alignment on digital radiographs. Operating room records were reviewed for procedure times. Two-tailed paired sample t tests and McNemar's test were used as appropriate. Alpha level was 0.05 for all tests. Preoperative cohort characteristics were not different. Mean postoperative long-leg mechanical alignment was within ±1° of neutral for both groups, although statistically different ( p = 0.026). There were no other significant differences in coronal alignment. PSI exhibited significantly greater posterior tibial slope (4.4°) compared to NAV (2.7°) ( p = 0.004); PSI resulted in significantly more outliers (>6°; p = 0.004). Procedure time for unilateral TKAs was lower for PSI (74.4 min) compared to that for NAV (80.6 min; p = 0.023). NAV and PSI technologies provided excellent coronal plane alignment. NAV was better for sagittal tibial slope, while PSI procedure times were shorter for unilateral TKA. The impact of these technologies on patient-reported outcomes and TKA survivorship is controversial and should be the focus of future research.
Spatiotemporal alignment of in utero BOLD-MRI series.

PubMed

Turk, Esra Abaci; Luo, Jie; Gagoski, Borjan; Pascau, Javier; Bibbo, Carolina; Robinson, Julian N; Grant, P Ellen; Adalsteinsson, Elfar; Golland, Polina; Malpica, Norberto

2017-08-01

To present a method for spatiotemporal alignment of in-utero magnetic resonance imaging (MRI) time series acquired during maternal hyperoxia for enabling improved quantitative tracking of blood oxygen level-dependent (BOLD) signal changes that characterize oxygen transport through the placenta to fetal organs. The proposed pipeline for spatiotemporal alignment of images acquired with a single-shot gradient echo echo-planar imaging includes 1) signal nonuniformity correction, 2) intravolume motion correction based on nonrigid registration, 3) correction of motion and nonrigid deformations across volumes, and 4) detection of the outlier volumes to be discarded from subsequent analysis. BOLD MRI time series collected from 10 pregnant women during 3T scans were analyzed using this pipeline. To assess pipeline performance, signal fluctuations between consecutive timepoints were examined. In addition, volume overlap and distance between manual region of interest (ROI) delineations in a subset of frames and the delineations obtained through propagation of the ROIs from the reference frame were used to quantify alignment accuracy. A previously demonstrated rigid registration approach was used for comparison. The proposed pipeline improved anatomical alignment of placenta and fetal organs over the state-of-the-art rigid motion correction methods. In particular, unexpected temporal signal fluctuations during the first normoxia period were significantly decreased (P < 0.01) and volume overlap and distance between region boundaries measures were significantly improved (P < 0.01). The proposed approach to align MRI time series enables more accurate quantitative studies of placental function by improving spatiotemporal alignment across placenta and fetal organs. 1 Technical Efficacy: Stage 1 J. MAGN. RESON. IMAGING 2017;46:403-412. © 2017 International Society for Magnetic Resonance in Medicine.
A flexible statistical model for alignment of label-free proteomics data – incorporating ion mobility and product ion information

PubMed Central

2013-01-01

Background The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, specifically label-free LC-MS/MS, allows rapid measurement of thousands of proteins, enabling large-scale studies of various biological systems. Prior to analyzing these information-rich datasets, raw data must undergo several computational processing steps. We present a method to address one of the essential steps in proteomics data processing - the matching of peptide measurements across samples. Results We describe a novel method for label-free proteomics data alignment with the ability to incorporate previously unused aspects of the data, particularly ion mobility drift times and product ion information. We compare the results of our alignment method to PEPPeR and OpenMS, and compare alignment accuracy achieved by different versions of our method utilizing various data characteristics. Our method results in increased match recall rates and similar or improved mismatch rates compared to PEPPeR and OpenMS feature-based alignment. We also show that the inclusion of drift time and product ion information results in higher recall rates and more confident matches, without increases in error rates. Conclusions Based on the results presented here, we argue that the incorporation of ion mobility drift time and product ion information are worthy pursuits. Alignment methods should be flexible enough to utilize all available data, particularly with recent advancements in experimental separation methods. PMID:24341404
A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.

PubMed

Benjamin, Ashlee M; Thompson, J Will; Soderblom, Erik J; Geromanos, Scott J; Henao, Ricardo; Kraus, Virginia B; Moseley, M Arthur; Lucas, Joseph E

2013-12-16

The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, specifically label-free LC-MS/MS, allows rapid measurement of thousands of proteins, enabling large-scale studies of various biological systems. Prior to analyzing these information-rich datasets, raw data must undergo several computational processing steps. We present a method to address one of the essential steps in proteomics data processing--the matching of peptide measurements across samples. We describe a novel method for label-free proteomics data alignment with the ability to incorporate previously unused aspects of the data, particularly ion mobility drift times and product ion information. We compare the results of our alignment method to PEPPeR and OpenMS, and compare alignment accuracy achieved by different versions of our method utilizing various data characteristics. Our method results in increased match recall rates and similar or improved mismatch rates compared to PEPPeR and OpenMS feature-based alignment. We also show that the inclusion of drift time and product ion information results in higher recall rates and more confident matches, without increases in error rates. Based on the results presented here, we argue that the incorporation of ion mobility drift time and product ion information are worthy pursuits. Alignment methods should be flexible enough to utilize all available data, particularly with recent advancements in experimental separation methods.
Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

PubMed

Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

2011-01-01

The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.
Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

PubMed

Daily, Jeff

2016-02-10

Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.
SFC-MS/MS as an orthogonal technique for improved screening of polar analytes in anti-doping control.

PubMed

Parr, Maria Kristina; Wuest, Bernhard; Naegele, Edgar; Joseph, Jan F; Wenzel, Maxi; Schmidt, Alexander H; Stanic, Mijo; de la Torre, Xavier; Botrè, Francesco

2016-09-01

HPLC is considered the method of choice for the separation of various classes of drugs. However, some analytes are still challenging as HPLC shows limited resolution capabilities for highly polar analytes as they interact insufficiently on conventional reversed-phase (RP) columns. Especially in combination with mass spectrometric detection, limitations apply for alterations of stationary phases. Some highly polar sympathomimetic drugs and their metabolites showed almost no retention on different RP columns. Their retention remains poor even on phenylhexyl phases that show different selectivity due to π-π interactions. Supercritical fluid chromatography (SFC) as an orthogonal separation technique to HPLC may help to overcome these issues. Selected polar drugs and metabolites were analyzed utilizing SFC separation. All compounds showed sharp peaks and good retention even for the very polar analytes, such as sulfoconjugates. Retention times and elution orders in SFC are different to both RP and HILIC separations as a result of the orthogonality. Short cycle times could be realized. As temperature and pressure strongly influence the polarity of supercritical fluids, precise regulation of temperature and backpressure is required for the stability of the retention times. As CO2 is the main constituent of the mobile phase in SFC, solvent consumption and solvent waste are considerably reduced. Graphical Abstract SFC-MS/MS vs. LC-MS/MS.
Hydrophilic interaction chromatography coupled matrix assisted laser desorption/ionization mass spectrometry for molecular analysis of organic compounds in medicines, tea, and coffee.

PubMed

Wang, Ren-Qi; Bao, Kai; Croué, Jean-Philippe; Ng, Siu Choon

2013-11-21

Natural occurring organic compounds from food, natural organic matter, as well as metabolic products have received intense attention in current chemical and biological studies. Examination of unknown compounds in complex sample matrices is hampered by the limited choices for data readout and molecular elucidation. Herein, we report a generic method of hydrophilic interaction chromatography (HILIC) coupled with matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the rapid characterization of ingredients in pharmaceutical compounds, tea, and coffee. The analytes were first fractionated using a cationic HILIC column prior to MALDI-MS analyses. It was found that the retention times of a compound arising from different samples were consistent under the same conditions. Accordingly, molecules can be readily characterized by both the mass and chromatographic retention time. The retention behaviors of acidic and basic compounds on the cationic HILIC column were found to be significantly influenced by the pH of mobile phases, whereas neutral compounds depicted a constant retention time at different pH. The general HILIC-MALDI-MS method is feasible for fast screening of naturally occurring organic compounds. A series of homologs can be determined if they have the same retention behavior. Their structural features can be elucidated by considering their mass differences and hydrophilic properties as determined by HILIC chromatogram.
A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

PubMed Central

Sturm, Marc; Quinten, Sascha; Huber, Christian G.; Kohlbacher, Oliver

2007-01-01

We propose a new model for predicting the retention time of oligonucleotides. The model is based on ν support vector regression using features derived from base sequence and predicted secondary structure of oligonucleotides. Because of the secondary structure information, the model is applicable even at relatively low temperatures where the secondary structure is not suppressed by thermal denaturing. This makes the prediction of oligonucleotide retention time for arbitrary temperatures possible, provided that the target temperature lies within the temperature range of the training data. We describe different possibilities of feature calculation from base sequence and secondary structure, present the results and compare our model to existing models. PMID:17567619
A facility specialist model for improving retention of nursing home staff: results from a randomized, controlled study.

PubMed

Pillemer, Karl; Meador, Rhoda; Henderson, Charles; Robison, Julie; Hegeman, Carol; Graham, Edwin; Schultz, Leslie

2008-07-01

This article reports on a randomized, controlled intervention study designed to reduce employee turnover by creating a retention specialist position in nursing homes. We collected data three times over a 1-year period in 30 nursing homes, sampled in stratified random manner from facilities in New York State and Connecticut and randomly assigned to treatment and control conditions. Staff outcomes were measured through certified nursing assistant interviews, and turnover rates were measured over the course of the year. In the intervention condition, a staff member was selected to be the facility retention specialist, who would advocate for and implement programs to improve staff retention and commitment throughout the facility. Retention specialists received an intensive 3-day training in retention leadership and in a number of evidence-based retention programs. Ongoing support was provided throughout the project. Treatment facilities experienced significant declines in turnover rates compared to control facilities. As predicted, we found positive effects on certified nursing assistant assessments of the quality of retention efforts and of care provided in the facility; we did not find effects for job satisfaction or stress. The study provides evidence for the effectiveness of the retention specialist model. Findings from a detailed process evaluation suggest modifications of the program that may increase program effects.
Short time-scale wind forced variability in the Río de la Plata Estuary and its role on ichthyoplankton retention

NASA Astrophysics Data System (ADS)

Simionato, C. G.; Berasategui, A.; Meccia, V. L.; Acha, M.; Mianzan, H.

2008-01-01

The Río de la Plata Estuary presents a strong bottom salinity front located over a submerged shoal. Apparently favored by retention processes, it is a spawning ground for several coastal fishes. This estuary is very shallow and essentially wind driven and, moreover, in time scales relevant to biota, estuarine circulation is wind dominated and highly variable. Two intriguing questions are, therefore, how this system can favor retention and what the involved mechanisms are. This paper qualitatively explores mechanisms involved in the estuary where retention is favored applying numerical simulations in which neutral particles - simulating fish eggs and early larvae - are released along the bottom frontal zone and tracked for different wind conditions. Results suggest that retentive features can be a consequence of estuarine response to natural wind variability acting over bathymetric features. For winds from most directions, particles either remain trapped near their launching position or move northeastward to southwestward along the shoal. As alternation of winds that favor along-shoal motion is the dominant feature of wind variability in the region, a retentive scenario results from prevailing wind variability. Additionally, winds that tend to export particles with a poor chance of being restored to the front are neither frequent nor persistent. Results show, therefore, that physical forcing alone might generate a retentive scenario at the inner part of this estuary. The physical retention mechanism is more effective for bottom than for surface launched particles. Wind statistics indicate that the proposed mechanism has different implications for retention along the seasons. Spring is the most favorable season, followed by summer, when particles would have a larger propensity to reach the southern area of the estuary (Samborombón Bay). Fall and winter are increasingly less favorable. All these features are consistent with patterns observed in the region in organisms having different life history traits.
A single exercise bout and locomotor learning after stroke: physiological, behavioural, and computational outcomes.

PubMed

Charalambous, Charalambos C; Alcantara, Carolina C; French, Margaret A; Li, Xin; Matt, Kathleen S; Kim, Hyosub E; Morton, Susanne M; Reisman, Darcy S

2018-05-15

Previous work demonstrated an effect of a single high-intensity exercise bout coupled with motor practice on the retention of a newly acquired skilled arm movement, in both neurologically intact and impaired adults. In the present study, using behavioural and computational analyses we demonstrated that a single exercise bout, regardless of its intensity and timing, did not increase the retention of a novel locomotor task after stroke. Considering both present and previous work, we postulate that the benefits of exercise effect may depend on the type of motor learning (e.g. skill learning, sensorimotor adaptation) and/or task (e.g. arm accuracy-tracking task, walking). Acute high-intensity exercise coupled with motor practice improves the retention of motor learning in neurologically intact adults. However, whether exercise could improve the retention of locomotor learning after stroke is still unknown. Here, we investigated the effect of exercise intensity and timing on the retention of a novel locomotor learning task (i.e. split-belt treadmill walking) after stroke. Thirty-seven people post stroke participated in two sessions, 24 h apart, and were allocated to active control (CON), treadmill walking (TMW), or total body exercise on a cycle ergometer (TBE). In session 1, all groups exercised for a short bout (∼5 min) at low (CON) or high (TMW and TBE) intensity and before (CON and TMW) or after (TBE) the locomotor learning task. In both sessions, the locomotor learning task was to walk on a split-belt treadmill in a 2:1 speed ratio (100% and 50% fast-comfortable walking speed) for 15 min. To test the effect of exercise on 24 h retention, we applied behavioural and computational analyses. Behavioural data showed that neither high-intensity group showed greater 24 h retention compared to CON, and computational data showed that 24 h retention was attributable to a slow learning process for sensorimotor adaptation. Our findings demonstrated that acute exercise coupled with a locomotor adaptation task, regardless of its intensity and timing, does not improve retention of the novel locomotor task after stroke. We postulate that exercise effects on motor learning may be context specific (e.g. type of motor learning and/or task) and interact with the presence of genetic variant (BDNF Val66Met). © 2018 The Authors. The Journal of Physiology © 2018 The Physiological Society.
A parallel approach of COFFEE objective function to multiple sequence alignment

NASA Astrophysics Data System (ADS)

Zafalon, G. F. D.; Visotaky, J. M. V.; Amorim, A. R.; Valêncio, C. R.; Neves, L. A.; de Souza, R. C. G.; Machado, J. M.

2015-09-01

The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.
Physician-Hospital Alignment in Orthopedic Surgery.

PubMed

Bushnell, Brandon D

2015-09-01

The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.
Simultaneous phylogeny reconstruction and multiple sequence alignment

PubMed Central

Yue, Feng; Shi, Jian; Tang, Jijun

2009-01-01

Background A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to affect the quality of the inferred phylogeny. At the same time, all the current multiple sequence alignment programs use a guide tree to produce the alignment and experiments showed that good guide trees can significantly improve the multiple alignment quality. Results We devise a new algorithm to simultaneously align multiple sequences and search for the phylogenetic tree that leads to the best alignment. We also implemented the algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM250 or BLOSUM62. The performance of the new method are compared with those from other popular multiple sequence alignment tools, including the widely used programs such as ClustalW and T-Coffee. Experimental results suggest that this method has good performance in terms of both phylogeny accuracy and alignment quality. Conclusion We present an algorithm to align multiple sequences and reconstruct the phylogenies that minimize the alignment score, which is based on an efficient algorithm to solve the median problems for three sequences. Our extensive experiments suggest that this method is very promising and can produce high quality phylogenies and alignments. PMID:19208110
Retention and recruitment of general dentists in an adjunct teaching model-A pilot study.

PubMed

Howe, Brian J; Allareddy, Verasathpurush; Barwacz, Christopher A; Parker, I Reed; Straub-Morarend, Cheryl L; Holmes, David C

2017-01-01

Retention and recruitment of part time clinical adjunct faculty members in dental education is becoming increasingly difficult as dental schools come to rely on this workforce for their increased involvement in clinical education. Contributing factors include full time faculty shortage, aging workforce, practice and student debt, practice and family commitments, and financial compensation. This study attempts to ascertain barriers to teaching so appropriate strategies can be formulated to address this issue. In the spring of 2016 an email survey was sent to current and former adjunct faculty members to ascertain demographics and retention and recruitment strategies. Descriptive analyses were completed for all variables in the sample. Twenty nine of forty six subjects responded to the survey with a response rate of 63%. Subjects over the age of sixty comprised 55% with only 17% being under the age of forty five. Overall family and practice commitments along with compensation were the primary barriers to teaching part time. For new dentists, student loan debt was the primary barrier to teaching. Travel to teach was also a barrier as 70% of respondents drove 200 miles or less to the dental school. The study demonstrated that the aging part time work force is a great concern and new part time clinical adjunct faculty members must be recruited. Barriers to recruitment and retention of faculty must be considered and addressed to sustain this teaching model.
NASA Astronaut Urinary Conditions Associated with Spaceflight

NASA Technical Reports Server (NTRS)

Law, Jennifer; Cole, Richard; Young, Millennia H.; Mason, Sara

2016-01-01

INTRODUCTION: Spaceflight is associated with many factors which may promote kidney stone formation, urinary retention, and/or Urinary Tract Infection (UTI). According to ISS mission predictions supplied by NASA's Integrated Medical Model, kidney stone is the second and sepsis (urosepsis as primary driver) the third most likely reason for emergent medical evacuation from the International Space Station (ISS). METHODS: Inflight and postflight medical records of NASA astronauts were reviewed for urinary retention, UTI and kidney stones during Mercury, Gemini, Apollo, Mir, Shuttle, and ISS expeditions 1-38. RESULTS: NASA astronauts have had 7 cases of kidney stones in the 12 months after flight. Three of these cases occurred within 90 to 180 days after landing and one of the seven cases occurred in the first 90 days after flight. There have been a total of 16 cases (0.018 events per person-flights) of urinary retention during flight. The event rates per mission are nearly identical between Shuttle and ISS flights (0.019 vs 0.021 events per person-flights). In 12 of the 16 cases, astronauts had taken at least one space motion sickness medication. Upon further analysis, it was determined that the odds of developing urinary retention in spaceflight is 3 times higher among astronauts who took promethazine. The female to male odds ratio for inflight urinary retention is 11:14. An astronaut with urinary retention is 25 times more likely to have a UTI with a 17% infection rate per mission. There have been 9 reported UTIs during spaceflight. DISCUSSION: It is unclear if spaceflight carries an increased post-flight risk of kidney stones. Regarding urinary retention, the female to male odds ratio is higher during flight compared to the general population where older males comprise almost all cases due to prostatic hypertrophy. This female prevalence in spaceflight is even more concerning given the fact that there have been many more males in space than females. Terrestrial medications with a known side effect of urinary retention are also associated with urinary retention during flight. However, not all cases of urinary retention surrounded medication use inflight. It is also known that UTI is a terrestrial cause of urinary retention. Furthermore, the treatment of urinary retention with a urinary catheter may be more likely to initiate a UTI in space than on the ground, as aseptic techniques can be particularly challenging with an inexperienced provider in a free-floating environment. Inflight urinary retention and UTI have proven to be highly associated and urinary risks should be considered collectively when planning for space flight.
It's more than money: policy options to secure medical specialist workforce for regional centres.

PubMed

May, Jennifer; Walker, Judi; McGrail, Mathew; Rolley, Fran

2017-12-01

Objectives Regional centres and their rural hinterlands support significant populations of non-metropolitan Australians. Despite their importance in the settlement hierarchy and the key medical services provided from these centres, little research has focused on their issues of workforce supply and long-term service requirements. In addition, they are a critical component of the recent growth of 'regional' hub-and-spoke specialist models of service delivery. Methods The present study interviewed 62 resident specialists in four regional centres, seeking to explore recruitment and retention factors important to their location decision making. The findings were used to develop a framework of possible evidence-informed policies. Results This article identifies key professional, social and locational factors, several of which are modifiable and amenable to policy redesign, including work variety, workplace culture, sense of community and spousal employment; these factors that can be targeted through initiatives in selection, training and incentives. Conclusions Commonwealth, state and local governments in collaboration with communities and specialist colleges can work synergistically, with a multiplicity of interdigitating strategies, to ensure a positive approach to the maintenance of a critical mass of long-term rural specialists. What is known about the topic? Rural origin increases likelihood of long-term retention to rural locations, with rural clinical school training associated with increased rural intent. Recruitment and retention policy has been directed at general practitioners in rural communities, with little focus on regional centres or medical specialists. What does this study add? Rural origin is associated with regional centre recruitment. Professional, social and locational factors are all moderately important in both recruitment and retention. Specialist medical training for regional centres ideally requires both generalist and subspecialist skills sets. Workforce policy needs to address modifiable factors with four groups, namely commonwealth and state governments, specialist medical colleges and local communities, all needing to align their activities for achievement of long-term medical workforce outcomes. What are the implications for practitioners? Modifiable factors affecting recruitment and retention must be addressed to support specialist models of care in regional centres. Modifiable factors relate to maintenance of a critical mass of practitioners, training a fit-for-purpose workforce and coordinated effort between stakeholders. Although remuneration is important, the decision to stay relates primarily to non-financial factors.

Corrigendum to: It's more than money: policy options to secure medical specialist workforce for regional centres.

PubMed

May, Jennifer; Walker, Judi; McGrail, Mathew; Rolley, Fran

2017-12-01

Objectives Regional centres and their rural hinterlands support significant populations of non-metropolitan Australians. Despite their importance in the settlement hierarchy and the key medical services provided from these centres, little research has focused on their issues of workforce supply and long-term service requirements. In addition, they are a critical component of the recent growth of 'regional' hub-and-spoke specialist models of service delivery. Methods The present study interviewed 62 resident specialists in four regional centres, seeking to explore recruitment and retention factors important to their location decision making. The findings were used to develop a framework of possible evidence-informed policies. Results This article identifies key professional, social and locational factors, several of which are modifiable and amenable to policy redesign, including work variety, workplace culture, sense of community and spousal employment; these factors that can be targeted through initiatives in selection, training and incentives. Conclusions Commonwealth, state and local governments in collaboration with communities and specialist colleges can work synergistically, with a multiplicity of interdigitating strategies, to ensure a positive approach to the maintenance of a critical mass of long-term rural specialists. What is known about the topic? Rural origin increases likelihood of long-term retention to rural locations, with rural clinical school training associated with increased rural intent. Recruitment and retention policy has been directed at general practitioners in rural communities, with little focus on regional centres or medical specialists. What does this study add? Rural origin is associated with regional centre recruitment. Professional, social and locational factors are all moderately important in both recruitment and retention. Specialist medical training for regional centres ideally requires both generalist and subspecialist skills sets. Workforce policy needs to address modifiable factors with four groups, namely commonwealth and state governments, specialist medical colleges and local communities, all needing to align their activities for achievement of long-term medical workforce outcomes. What are the implications for practitioners? Modifiable factors affecting recruitment and retention must be addressed to support specialist models of care in regional centres. Modifiable factors relate to maintenance of a critical mass of practitioners, training a fit-for-purpose workforce and coordinated effort between stakeholders. Although remuneration is important, the decision to stay relates primarily to non-financial factors.
Transurethral plasmakinetic resection of the prostate is a reliable minimal invasive technique for benign prostate hyperplasia: a meta-analysis of randomized controlled trials.

PubMed

Wang, Kai; Li, Yao; Teng, Jing-Fei; Zhou, Hai-Yong; Xu, Dan-Feng; Fan, Yi

2015-01-01

To evaluate the efficacy and safety of plasmakinetic resection of the prostate (PKRP) versus transurethral resection of the prostate (TURP) for the treatment of patients with benign prostate hyperplasia (BPH), a meta-analysis of randomized controlled trials was carried out. We searched PubMed, Embase, Web of Science and the Cochrane Library. The pooled estimates of maximum flow rate, International Prostate Symptom Score, operation time, catheterization time, irrigated volume, hospital stay, transurethral resection syndrome, transfusion, clot retention, urinary retention and urinary stricture were assessed. There was no notable difference in International Prostate Symptom Score between TURP and PKRP groups during the 1-month, 3 months, 6 months and 12 months follow-up period, while the pooled Q max at 1-month favored PKRP group. PKRP group was related to a lower risk rate of transurethral resection syndrome, transfusion and clot retention, and the catheterization time and operation time were also shorter than that of TURP. The irrigated volume, length of hospital stay, urinary retention and urinary stricture rate were similar between groups. In conclusion, our study suggests that the PKRP is a reliable minimal invasive technique and may anticipatorily prove to be an alternative electrosurgical procedure for the treatment of BPH.
Quick-low-density parity check and dynamic threshold voltage optimization in 1X nm triple-level cell NAND flash memory with comprehensive analysis of endurance, retention-time, and temperature variation

NASA Astrophysics Data System (ADS)

Doi, Masafumi; Tokutomi, Tsukasa; Hachiya, Shogo; Kobayashi, Atsuro; Tanakamaru, Shuhei; Ning, Sheyang; Ogura Iwasaki, Tomoko; Takeuchi, Ken

2016-08-01

NAND flash memory’s reliability degrades with increasing endurance, retention-time and/or temperature. After a comprehensive evaluation of 1X nm triple-level cell (TLC) NAND flash, two highly reliable techniques are proposed. The first proposal, quick low-density parity check (Quick-LDPC), requires only one cell read in order to accurately estimate a bit-error rate (BER) that includes the effects of temperature, write and erase (W/E) cycles and retention-time. As a result, 83% read latency reduction is achieved compared to conventional AEP-LDPC. Also, W/E cycling is extended by 100% compared with conventional Bose-Chaudhuri-Hocquenghem (BCH) error-correcting code (ECC). The second proposal, dynamic threshold voltage optimization (DVO) has two parts, adaptive V Ref shift (AVS) and V TH space control (VSC). AVS reduces read error and latency by adaptively optimizing the reference voltage (V Ref) based on temperature, W/E cycles and retention-time. AVS stores the optimal V Ref’s in a table in order to enable one cell read. VSC further improves AVS by optimizing the voltage margins between V TH states. DVO reduces BER by 80%.
[Application of general retention time formula for gradient liquid chromatography in the studies of ladder-like gradient elution].

PubMed

Sun, Xiaoli; Hao, Weiqiang; Wang, Junde; Di, Bin; Chen, Qiang; Zhuang, Wei; Yu, Qiang; Zhang, Peipei

2013-08-01

By not explicitly specifying the type of solvent strength model, the features of ladder-like gradient elution were studied based on the general retention time formula that was derived in our previous work. For the case where the solute is eluted at like gradient, we derived the expression that connects the mobile phase composition (phiR), at which the solute is eluted from the column, with the gradient slope (B). It was shown that phiR will increase with the increase of B in this case. For the case where the solute is eluted at the last isocratic segment of the ladder-like gradient, it was proven that the retention time (tR) will correlate linearly with the reciprocal of the gradient slope (1/B) when the initial and final mobile phase compositions are set to be constant. In experiments, by taking biphenyl as the sample, the values of retention time in isocratic and gradient elution were measured on a C18 column by using a mixture of methanol and water as the mobile phase. The experimental values were found to be well consistent with the theoretical values that were calculated from the expressions. These expressions will be helpful to understand the features of the ladder-like gradient in practice.
Using lean manufacturing principles to evaluate wait times for HIV-positive patients in an urban clinic in Kenya.

PubMed

Monroe-Wise, Aliza; Reisner, Elizabeth; Sherr, Kenneth; Ojakaa, David; Mbau, Lilian; Kisia, Paul; Muhula, Samuel; Farquhar, Carey

2017-12-01

As human immunodeficiency virus (HIV) treatment programs expand in Africa, delivery systems must be strengthened to support patient retention. Clinic characteristics may affect retention, but a relationship between clinic flow and attrition is not established. This project characterized HIV patient experience and flow in an urban Kenyan clinic to understand how these may affect retention. We used Toyota's lean manufacturing principles to guide data collection and analysis. Clinic flow was evaluated using value stream mapping and time and motion techniques. Clinic register data were analyzed. Two focus group discussions were held to characterize HIV patient experience. Results were shared with clinic staff. Wait times in the clinic were highly variable. We identified four main barriers to patient flow: inconsistent patient arrivals, inconsistent staffing, filing system defects, and serving patients out of order. Focus group participants explained how clinic operations affected their ability to engage in care. Clinic staff were eager to discuss the problems identified and identified numerous low-cost potential solutions. Lean manufacturing methodologies can guide efficiency interventions in low-resource healthcare settings. Using lean techniques, we identified bottlenecks to clinic flow and low-cost solutions to improve wait times. Improving flow may result in increased patient satisfaction and retention.
[Quantitative relationship between gas chromatographic retention time and structural parameters of alkylphenols].

PubMed

Ruan, Xiaofang; Zhang, Ruisheng; Yao, Xiaojun; Liu, Mancang; Fan, Botao

2007-03-01

Alkylphenols are a group of permanent pollutants in the environment and could adversely disturb the human endocrine system. It is therefore important to effectively separate and measure the alkylphenols. To guide the chromatographic analysis of these compounds in practice, the development of quantitative relationship between the molecular structure and the retention time of alkylphenols becomes necessary. In this study, topological, constitutional, geometrical, electrostatic and quantum-chemical descriptors of 44 alkylphenols were calculated using a software, CODESSA, and these descriptors were pre-selected using the heuristic method. As a result, three-descriptor linear model (LM) was developed to describe the relationship between the molecular structure and the retention time of alkylphenols. Meanwhile, the non-linear regression model was also developed based on support vector machine (SVM) using the same three descriptors. The correlation coefficient (R(2)) for the LM and SVM was 0.98 and 0. 92, and the corresponding root-mean-square error was 0. 99 and 2. 77, respectively. By comparing the stability and prediction ability of the two models, it was found that the linear model was a better method for describing the quantitative relationship between the retention time of alkylphenols and the molecular structure. The results obtained suggested that the linear model could be applied for the chromatographic analysis of alkylphenols with known molecular structural parameters.
Food consumption and retention time in captive whooping cranes (Grus americana)

USGS Publications Warehouse

Nelson, J.T.; Gee, G.F.; Slack, R.D.

1997-01-01

Food consumption, digesta retention time, and food preference were measured for captive whooping cranes fed pelleted diets. The basal commercial diet was compared to four mixtures containing 70% basal and 30% of one of four important winter foods for the whooping crane: blue crab (Callinectes sapidus), wolfberry fruit (Lycium carolinianurn), live oak acorn (Quercus virginiana), or common Rangia clam (Rangia cuneata). Because captive birds would not eat whole foods, we were prevented from direct food preference tests. Food passed through the gut rapidly, with almost complete elimination within 7 hr. There was some indication that retention time was shorter for the low fiber and high ash and calcium clam diet. Cranes ate less wolfberry feed (g/day) than the other feeds, and all birds ate less wolfberry feed on the day it was first fed, compared to basal diet the previous day. Birds ate more low energy feed than high energy feed. Due to combined effects of low energy content, lower metabolizable energy coefficients, and reduced feed consumption, less energy was assimilated for study diets than basal diet. Apparent shorter retention times for some diets con-taming whooping crane foods may partly explain lower digestibilities and metabolizable energy of winter whooping crane foods compared to commercial crane diet.
MICA: Multiple interval-based curve alignment

NASA Astrophysics Data System (ADS)

Mann, Martin; Kahle, Hans-Peter; Beck, Matthias; Bender, Bela Johannes; Spiecker, Heinrich; Backofen, Rolf

2018-01-01

MICA enables the automatic synchronization of discrete data curves. To this end, characteristic points of the curves' shapes are identified. These landmarks are used within a heuristic curve registration approach to align profile pairs by mapping similar characteristics onto each other. In combination with a progressive alignment scheme, this enables the computation of multiple curve alignments. Multiple curve alignments are needed to derive meaningful representative consensus data of measured time or data series. MICA was already successfully applied to generate representative profiles of tree growth data based on intra-annual wood density profiles or cell formation data. The MICA package provides a command-line and graphical user interface. The R interface enables the direct embedding of multiple curve alignment computation into larger analyses pipelines. Source code, binaries and documentation are freely available at https://github.com/BackofenLab/MICA
DOE Office of Scientific and Technical Information (OSTI.GOV)

Webb, Aaron P.; Carlson, Charles T.

A multi-part mask has a pattern plate, which includes a planar portion that has the desired aperture pattern to be used during workpiece processing. The multi-part mask also has a mounting frame, which is used to hold the pattern plate. Prior to assembly, the pattern plate has an aligning portion, which has one or more holes through which reusable alignment pins are inserted. These alignment pins enter kinematic joints disposed on the mounting frame, which serve to precisely align the pattern plate to the mounting frame. After the pattern plate has been secured to the mounting frame, the aligning portionmore » can be detached from the pattern plate. The alignment pins can be reused at a later time. In some embodiments, the pattern plate can later be removed from the mounting frame, so that the mounting frame may be reused.« less
The Septate Junction Protein Caspr is Required for Structural Support and Retention of KCNQ4 at Calyceal Synapses of Vestibular Hair Cells

PubMed Central

Sousa, Aurea D.; Andrade, Leonardo R.; Salles, Felipe T.; Pillai, Anilkumar M.; Buttermore, Elizabeth; Bhat, Manzoor A.; Kachar, Bechara

2009-01-01

The afferent innervation contacting the type I hair cells of the vestibular sensory epithelia form distinct calyceal synapses. The apposed pre- and post-synaptic membranes at this large area of synaptic contact are kept at a remarkably regular distance. Here, we show by freeze-fracture electron microscopy that a patterned alignment of proteins at the calyceal membrane resembles a type of intercellular junction that is rare in vertebrates, the septate junction (SJ). We found that a core molecular component of SJs, Caspr, colocalizes with the K+ channel KCNQ4 at the post-synaptic membranes of these calyceal synapses. Immunolabeling and ultrastructural analyses of Caspr knockout mice reveal that, in the absence of Caspr, the separation between the membranes of the hair cells and the afferent neurons is conspicuously irregular and often increased by an order of magnitude. In these mutants, KCNQ4 fails to cluster at the post-synaptic membrane and appears diffused along the entire calyceal membrane. Our results indicate that a septate-like junction provides structural support to calyceal synaptic contact with the vestibular hair cell, and that Caspr is required for the recruitment or retention of KCNQ4 at these synapses. PMID:19279247
Enhancing student performance: Linking the geography curriculum, instruction, and assessment in the English-speaking Caribbean

NASA Astrophysics Data System (ADS)

Collymore, Jennifer C.

In a 21st century knowledge society individuals are expected to use their knowledge and skills to think critically, problem solve, make decisions, comprehend new ideas, communicate, and collaborate effectively with others. Helping students achieve this level of performance is no easy task and it brings into focus the fact that the effectiveness of any education system rests on the systemic coordination or alignment of three crucial components: curriculum, instruction and assessment (referred to as the CIA). These components must work in concert to facilitate and enhance student performance. However, educational reform typically targets these components in isolation, often treating only one component, rather than the system as a whole. The misalignment of these components can adversely affect student performance in any discipline. When the CIA components are out of alignment, it is difficult to evaluate student and system performance and achieve improvement in an educational system. Therefore, using geography education in Trinidad & Tobago as a case study, this study examined the nature of the alignment among the CIA components in the advanced geography system in the English- Speaking Caribbean and the extent to which the alignment may be affecting student performance. The study sought to determine the possible sources and causes of misalignment, the challenges to achieving alignment, and ways of achieving greater coordination among the CIA components of the system. The methodology employed in the study involved the use of classroom observations, interviews, and the Surveys of Enacted Curriculum Alignment Model which uses content analyses and surveys. The results showed that there were varying degrees of alignment among the components. There was acceptable alignment (Alignment Index ≥ 0.25) between the curriculum and assessment. However, the alignment between curriculum and instruction or assessment and instruction was poor (Alignment Index ≤ 0.12). The baseline threshold for acceptable alignment was 0.25. The misalignment between the curriculum and assessment stemmed from the fact that there were items tested in the assessment that were not identified in the examination syllabus. In terms of the misalignment between the curriculum/assessment and instruction, teachers were misallocating their teaching time and efforts; spending too much time teaching the skills and practices of the discipline rather than the core content areas and they were spending too much time teaching the content at the lower order cognitive level of recall. In addition, while research promotes student-centered approaches, cooperative learning, dialogic discourse, open informal questioning and discursive forms of writing, teachers still primarily use teacher-centered approaches, individualize instruction, monologic discourse and closed recall questions. The teachers' instructional practices are not affording students the opportunity to acquire and display their knowledge at the higher levels of cognition. The cause of the misalignment was attributed to a vague, overloaded syllabus and limited teaching time; vague evaluative criteria and feedback from the Examination Council; inadequate and insufficient teacher training and professional development; a lack of administrative support and mentorship for inexperienced teachers; and teacher frustration. Subsequently, the study offers a number of evidence based recommendations that range from the modification and refinement of the geography CIA triad to professional development programs and the design of interventions that can advance the teaching and learning of the discipline. Though the study is undertaken in a specific context, the educational issues addressed in the study transcend time, scale, and geographic boundaries and the results can inform the decision-making and practices of educators and education policy-makers everywhere.
Study on the position accuracy of a mechanical alignment system

NASA Astrophysics Data System (ADS)

Cai, Yimin

In this thesis, we investigated the precision level and established the baseline achieved by a mechanical alignment system using datums and reference surfaces. The factors which affect the accuracy of mechanical alignment system were studied and methodology was developed to suppress these factors so as to reach its full potential precision. In order to characterize the mechanical alignment system quantitatively, a new optical position monitoring system by using quadrant detectors has been developed in this thesis, it can monitor multi-dimensional degrees of mechanical workpieces in real time with high precision. We studied the noise factors inside the system and optimized the optical system. Based on the fact that one of the major limiting noise factors is the shifting of the laser beam, a noise cancellation technique has been developed successfully to suppress this noise, the feasibility of an ultra high resolution (<20 A) for displacement monitoring has been demonstrated. Using the optical position monitoring system, repeatability experiment of the mechanical alignment system has been conducted on different kinds of samples including steel, aluminum, glass and plastics with the same size 100mm x 130mm. The alignment accuracy was studied quantitatively rather than qualitatively before. In a controlled environment, the alignment precision can be improved 5 folds by securing the datum without other means of help. The alignment accuracy of an aluminum workpiece having reference surface by milling is about 3 times better than by shearing. Also we have found that sample material can have fairly significant effect on the alignment precision of the system. Contamination trapped between the datum and reference surfaces in mechanical alignment system can cause errors of registration or reduce the level of manufacturing precision. In the thesis, artificial and natural dust particles were used to simulate the real situations and their effects on system precision have been investigated. In this experiment, we discovered two effective cleaning processes.
Engineered plant biomass feedstock particles

DOEpatents

Dooley, James H [Federal Way, WA; Lanning, David N [Federal Way, WA; Broderick, Thomas F [Lake Forest Park, WA

2012-04-17

A new class of plant biomass feedstock particles characterized by consistent piece size and shape uniformity, high skeletal surface area, and good flow properties. The particles of plant biomass material having fibers aligned in a grain are characterized by a length dimension (L) aligned substantially parallel to the grain and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces. The L.times.W surfaces of particles with L/H dimension ratios of 4:1 or less are further elaborated by surface checking between longitudinally arrayed fibers. The length dimension L is preferably aligned within 30.degree. parallel to the grain, and more preferably within 10.degree. parallel to the grain. The plant biomass material is preferably selected from among wood, agricultural crop residues, plantation grasses, hemp, bagasse, and bamboo.
Resonant optical alignment and orientation of Mn2+ spins in CdMnTe crystals

NASA Astrophysics Data System (ADS)

Baryshnikov, K. A.; Langer, L.; Akimov, I. A.; Korenev, V. L.; Kusrayev, Yu. G.; Averkiev, N. S.; Yakovlev, D. R.; Bayer, M.

2015-11-01

We report on spin orientation and alignment of Mn2 + ions in (Cd,Mn)Te diluted magnetic semiconductor crystals using resonant intracenter excitation with circular- and linear-polarized light. The resulting polarized emission of the magnetic ions is observed at low temperatures when the spin relaxation time of the Mn2 + ions is in the order of 1 ms , which considerably exceeds the photoluminescence decay time of 23 μ s . We demonstrate that the experimental data on optical orientation and alignment of Mn2 + ions can be explained using a phenomenological model that is based on the approximation of isolated centers.
Real-time calibration and alignment of the LHCb RICH detectors

NASA Astrophysics Data System (ADS)

HE, Jibo

2017-12-01

In 2015, the LHCb experiment established a new and unique software trigger strategy with the purpose of increasing the purity of the signal events by applying the same algorithms online and offline. To achieve this, real-time calibration and alignment of all LHCb sub-systems is needed to provide vertexing, tracking, and particle identification of the best possible quality. The calibration of the refractive index of the RICH radiators, the calibration of the Hybrid Photon Detector image, and the alignment of the RICH mirror system, are reported in this contribution. The stability of the RICH performance and the particle identification performance are also discussed.
Space Technology 5 Multi-Point Observations of Temporal Variability of Field-Aligned Currents

NASA Technical Reports Server (NTRS)

Le, Guan; Wang, Yongli; Slavin, James A.; Strangeway, Robert J.

2008-01-01

Space Technology 5 (ST5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that meso-scale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of approximately 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are approximately 1 min for meso-scale currents and approximately 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.
Space Technology 5 (ST-5) Observations of Field-Aligned Currents: Temporal Variability

NASA Technical Reports Server (NTRS)

Le, Guan

2010-01-01

Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from STS. The data demonstrate that masoscale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of about 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are about I min for meso-scale currents and about 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.
Space Technology 5 Multi-point Observations of Field-aligned Currents: Temporal Variability of Meso-Scale Structures

NASA Technical Reports Server (NTRS)

Le, Guan; Wang, Yongli; Slavin, James A.; Strangeway, Robert J.

2007-01-01

Space Technology 5 (ST5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that meso-scale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of - 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are approx. 1 min for meso-scale currents and approx. 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.
Space Technology 5 (ST-5) Multipoint Observations of Temporal and Spatial Variability of Field-Aligned Currents

NASA Technical Reports Server (NTRS)

Le, Guan

2010-01-01

Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that mesoscale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of about 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are about 1 min for meso-scale currents and about 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.
Influence of transportation cost on long-term retention in clinic for HIV patients in rural Haiti.

PubMed

Sowah, Leonard A; Turenne, Franck V; Buchwald, Ulrike K; Delva, Guesly; Mesidor, Romaine N; Dessaigne, Camille G; Previl, Harold; Patel, Devang; Edozien, Anthony; Redfield, Robert R; Amoroso, Anthony

2014-12-01

With improved access to antiretroviral therapy in resource-constrained settings, long-term retention in HIV clinics has become an important means of reducing costs and improving outcomes. Published data on retention in HIV clinics beyond 24 months are, however, limited. In our clinic in rural Haiti, we hypothesized that individuals residing in locations with higher transportation costs to clinic would have poorer retention than those who had lower costs. We used a retrospective cohort design to evaluate potential predictors of HIV clinic retention. Patient information was abstracted from the electronic medical records. Cox proportional hazards regression was used to identify independent predictors of 4-year clinic retention. There were 410 patients in our cohort, 266 (64.9%) females and 144 (35.1%) males. Forty-five (11%) patients lived in locations with transportation costs >$2. Males were 1.5 times more likely to live in municipalities with transportation costs to clinic of >$2. Multivariate analysis suggested that age <30 years, male gender, and transportation cost were independent predictors of loss to follow-up (LTFU): risk ratio of 2.98, 95% confidence interval (CI): 1.73 to 4.96, P < 0.001; 1.71, CI: 1.08 to 2.70, P = 0.02; and 1.91, CI: 1.08 to 3.36, P = 0.02, respectively. Patients with transportation costs greater than $2 were 1.9 times more likely to be lost to care compared with those who paid less for transportation. HIV treatment programs in resource-constrained settings may need to pay closer attention to issues related to transportation cost to improve patient retention.

Enhanced methodology for porting ion chromatography retention data.

PubMed

Park, Soo Hyun; Shellie, Robert A; Dicinoski, Greg W; Schuster, Georg; Talebi, Mohammad; Haddad, Paul R; Szucs, Roman; Dolan, John W; Pohl, Christopher A

2016-03-04

Porting is a powerful methodology to recalibrate an existing database of ion chromatography (IC) retention times by reflecting the changes of column behavior resulting from either batch-to-batch variability in the production of the column or the manufacture of new versions of a column. This approach has been employed to update extensive databases of retention data of inorganic and organic anions forming part of the "Virtual Column" software marketed by Thermo Fisher Scientific, which is the only available commercial optimization tool for IC separation. The current porting process is accomplished by performing three isocratic separations with two representative analyte ions in order to derive a porting equation which expresses the relationship between old and new data. Although the accuracy of retention prediction is generally enhanced on new columns, errors were observed on some columns. In this work, the porting methodology was modified in order to address this issue, where the porting equation is now derived by using six representative analyte ions (chloride, bromide, iodide, perchlorate, sulfate, and thiosulfate). Additionally, the updated porting methodology has been applied on three Thermo Fisher Scientific columns (AS20, AS19, and AS11HC). The proposed approach showed that the new porting methodology can provide more accurate and robust retention prediction on a wide range of columns, where average errors in retention times for ten test anions under three eluent conditions were less than 1.5%. Moreover, the retention prediction using this new approach provided an acceptable level of accuracy on a used column exhibiting changes in ion-exchange capacity. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.
Retention of fissure sealants in young permanent molars affected by dental fluorosis: a 12-month clinical study.

PubMed

Hasanuddin, S; Reddy, E R; Manjula, M; Srilaxmi, N; Rani, S T; Rajesh, A

2014-10-01

To evaluate and compare retention and caries occurance following placement of Clinpro and FUJI VII fissure sealants, by two different techniques simultaneously in unsealed, contralateral young permanent molars of 7- to 10-year-old children affected by mild to moderate dental fluorosis at various recall intervals of 1 week, 1, 3, 6 and 12 months. 80 schoolchildren with mild to moderate dental fluorosis were assigned to Group A and Group B with 40 children in each group. In Group A Clinpro fissure sealant and in Group B Fuji VII fissure sealant was used. In both the groups fissure sealants were applied by conventional fissure sealant technique (CST) on one side and enameloplasty sealant technique (EST) on the other side of the same arch. The applied fissure sealants were evaluated clinically for retention and caries incidence. Clinpro fissure sealant showed a retention rate of 95% when compared with Fuji VII (57.5%) at the end of 12 months, which was statistically significant. Regarding techniques, EST showed better results than CST in both the groups. Comparison of groups with respect to retention and techniques at different time periods was performed using Mann-Whitney U test (p < 0.05). Comparison of different time periods with respect to retention and technique in all the groups was performed using Wilcoxon matched pairs test by ranks (p < 0.05). Clinpro fissure sealant showed better retention at all treatment intervals, when compared with Fuji VII. Further follow-up is required to study the efficacy of the fissure sealant placement techniques.
Conversion to Reverse Total Shoulder Arthroplasty with and without Humeral Stem Retention: The Role of a Convertible-Platform Stem.

PubMed

Crosby, Lynn A; Wright, Thomas W; Yu, Stephen; Zuckerman, Joseph D

2017-05-03

Revision shoulder arthroplasty is a technically challenging procedure. It is associated with increased blood loss and operative time, and it frequently necessitates revision implants, augments, and bone-grafting. Shoulder arthroplasty systems with a convertible-platform humeral stem have been developed to reduce the complexity of revision procedures by eliminating the need for humeral component explantation when converting from anatomic shoulder arthroplasty (hemiarthroplasty or total shoulder arthroplasty) to reverse total shoulder arthroplasty (rTSA). A multicenter, retrospective analysis involving 102 consecutive shoulders (102 patients) that underwent revision of an anatomic shoulder arthroplasty to an rTSA was conducted. During the revision, 73 of the shoulders needed exchange of the humeral stem (the exchange group) and 29 had retention of a convertible-platform humeral component (the retention group). Patient demographics, operative time, blood management, range of motion, complications, and patient-reported outcomes were compared between the 2 groups. Patients with retention had significantly shorter operative time (mean and standard deviation, 130 ± 48 versus 195 ± 58 minutes; p < 0.001) and lower estimated blood loss (292 ± 118 versus 492 ± 334 mL; p = 0.034). The rate of intraoperative complications was lower in the retention group (0% versus 15%; p = 0.027). Patients with retention had slightly better postoperative range of motion (active external rotation, 26° ± 23° versus 11° ± 23° [p = 0.006]; active forward elevation, 112° ± 37° versus 96° ± 33° [p = 0.055]). Shoulder arthroplasty systems that utilize a convertible-platform humeral stem offer an advantage for rTSA conversion in that a well-fixed, well-positioned humeral stem can be retained. There were significantly fewer complications as well as significantly decreased blood loss and operative time when a convertible-platform stem was utilized (p < 0.050). Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.
Stepped-Wedge Cluster Randomized Controlled Trial to Promote Option B+ Retention in Central Mozambique.

PubMed

Pfeiffer, James T; Napúa, Manuel; Wagenaar, Bradley H; Chale, Falume; Hoek, Roxanne; Micek, Mark; Manuel, João; Michel, Cathy; Cowan, Jessica Greenberg; Cowan, James F; Gimbel, Sarah; Sherr, Kenneth; Gloyd, Stephen; Chapman, Rachel R

2017-11-01

This randomized trial studied performance of Option B+ in Mozambique and evaluated an enhanced retention package in public clinics. The study was conducted at 6 clinics in Manica and Sofala Provinces in central Mozambique. Seven hundred sixty-one pregnant women tested HIV+, immediately initiated antiretroviral (ARV) therapy, and were followed to track retention at 6 clinics from May 2014 to May 2015. Clinics were randomly allocated within a stepped-wedge fashion to intervention and control periods. The intervention included (1) workflow modifications and (2) active patient tracking. Retention was defined as percentage of patients returning for 30-, 60-, and 90-day medication refills within 25-35 days of previous refills. During control periods, 52.3% of women returned for 30-day refills vs. 70.8% in intervention periods [odds ratio (OR): 1.80; 95% confidence interval (CI): 1.05 to 3.08]. At 60 days, 46.1% control vs. 57.9% intervention were retained (OR: 1.82; CI: 1.06 to 3.11), and at 90 days, 38.3% control vs. 41.0% intervention (OR: 1.04; CI: 0.60 to 1.82). In prespecified subanalyses, birth before pickups was strongly associated with failure-women giving birth before ARV pickup were 33.3 times (CI: 4.4 to 250.3), 7.5 times (CI: 3.6 to 15.9), and 3.7 times (CI: 2.2 to 6.0) as likely to not return for ARV pickups at 30, 60, and 90 days, respectively. The intervention was effective at 30 and 60 days, but not at 90 days. Combined 90-day retention (40%) and adherence (22.5%) were low. Efforts to improve retention are particularly important for women giving birth before ARV refills.
Retention behavior of lipids in reversed-phase ultrahigh-performance liquid chromatography-electrospray ionization mass spectrometry.

PubMed

Ovčačíková, Magdaléna; Lísa, Miroslav; Cífková, Eva; Holčapek, Michal

2016-06-10

Reversed-phase ultrahigh-performance liquid chromatography (RP-UHPLC) method using two 15cm sub-2μm particles octadecylsilica gel columns is developed with the goal to separate and unambiguously identify a large number of lipid species in biological samples. The identification is performed by the coupling with high-resolution tandem mass spectrometry (MS/MS) using quadrupole - time-of-flight (QTOF) instrument. Electrospray ionization (ESI) full scan and tandem mass spectra are measured in both polarity modes with the mass accuracy better than 5ppm, which provides a high confidence of lipid identification. Over 400 lipid species covering 14 polar and nonpolar lipid classes from 5 lipid categories are identified in total lipid extracts of human plasma, human urine and porcine brain. The general dependences of relative retention times on relative carbon number or relative double bond number are constructed and fit with the second degree polynomial regression. The regular retention patterns in homologous lipid series provide additional identification point for UHPLC/MS lipidomic analysis, which increases the confidence of lipid identification. The reprocessing of previously published data by our and other groups measured in the RP mode and ultrahigh-performance supercritical fluid chromatography on the silica column shows more generic applicability of the polynomial regression for the description of retention behavior and the prediction of retention times. The novelty of this work is the characterization of general trends in the retention behavior of lipids within logical series with constant fatty acyl length or double bond number, which may be used as an additional criterion to increase the confidence of lipid identification. Copyright © 2016 Elsevier B.V. All rights reserved.
Field Soil Water Retention of the Prototype Hanford Barrier and Its Variability with Space and Time

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

Zhang, Z. F.

Engineered surface barriers are used to isolate underlying contaminants from water, plants, animals, and humans. To understand the flow processes within a barrier and the barrier’s ability to store and release water, the field hydraulic properties of the barrier need to be known. In situ measurement of soil hydraulic properties and their variation over time is challenging because most measurement methods are destructive. A multiyear test of the Prototype Hanford Barrier (PHB) has yielded in situ soil water content and pressure data for a nine-year period. The upper 2 m layer of the PHB is a silt loam. Within thismore » layer, water content and water pressure were monitored at multiple depths at 12 water balance stations using a neutron probe and heat dissipation units. Valid monitoring data from 1995 to 2003 for 4 depths at 12 monitoring stations were used to determine the field water retention of the silt loam layer. The data covered a wide range of wetness, from near saturation to the permanent wilt point, and each retention curve contained 51 to 96 data points. The data were described well with the commonly used van Genuchten water retention model. It was found that the spatial variation of the saturated and residual water content and the pore size distribution parameter were relatively small, while that of the van Genuchten alpha was relatively large. The effects of spatial variability of the retention properties appeared to be larger than the combined effects of added 15% w/w pea gravel and plant roots on the properties. Neither of the primary hydrological processes nor time had a detectible effect on the water retention of the silt loam barrier.« less
Fitting-free algorithm for efficient quantification of collagen fiber alignment in SHG imaging applications.

PubMed

Hall, Gunnsteinn; Liang, Wenxuan; Li, Xingde

2017-10-01

Collagen fiber alignment derived from second harmonic generation (SHG) microscopy images can be important for disease diagnostics. Image processing algorithms are needed to robustly quantify the alignment in images with high sensitivity and reliability. Fourier transform (FT) magnitude, 2D power spectrum, and image autocorrelation have previously been used to extract fiber information from images by assuming a certain mathematical model (e.g. Gaussian distribution of the fiber-related parameters) and fitting. The fitting process is slow and fails to converge when the data is not Gaussian. Herein we present an efficient constant-time deterministic algorithm which characterizes the symmetricity of the FT magnitude image in terms of a single parameter, named the fiber alignment anisotropy R ranging from 0 (randomized fibers) to 1 (perfect alignment). This represents an important improvement of the technology and may bring us one step closer to utilizing the technology for various applications in real time. In addition, we present a digital image phantom-based framework for characterizing and validating the algorithm, as well as assessing the robustness of the algorithm against different perturbations.
YAHA: fast and flexible long-read alignment with optimal breakpoint detection.

PubMed

Faust, Gregory G; Hall, Ira M

2012-10-01

With improved short-read assembly algorithms and the recent development of long-read sequencers, split mapping will soon be the preferred method for structural variant (SV) detection. Yet, current alignment tools are not well suited for this. We present YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints. YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA. imh4y@virginia.edu.
A distributed system for fast alignment of next-generation sequencing data.

PubMed

Srimani, Jaydeep K; Wu, Po-Yen; Phan, John H; Wang, May D

2010-12-01

We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.
Leveraging FPGAs for Accelerating Short Read Alignment.

PubMed

Arram, James; Kaplan, Thomas; Luk, Wayne; Jiang, Peiyong

2017-01-01

One of the key challenges facing genomics today is how to efficiently analyze the massive amounts of data produced by next-generation sequencing platforms. With general-purpose computing systems struggling to address this challenge, specialized processors such as the Field-Programmable Gate Array (FPGA) are receiving growing interest. The means by which to leverage this technology for accelerating genomic data analysis is however largely unexplored. In this paper, we present a runtime reconfigurable architecture for accelerating short read alignment using FPGAs. This architecture exploits the reconfigurability of FPGAs to allow the development of fast yet flexible alignment designs. We apply this architecture to develop an alignment design which supports exact and approximate alignment with up to two mismatches. Our design is based on the FM-index, with optimizations to improve the alignment performance. In particular, the n-step FM-index, index oversampling, a seed-and-compare stage, and bi-directional backtracking are included. Our design is implemented and evaluated on a 1U Maxeler MPC-X2000 dataflow node with eight Altera Stratix-V FPGAs. Measurements show that our design is 28 times faster than Bowtie2 running with 16 threads on dual Intel Xeon E5-2640 CPUs, and nine times faster than Soap3-dp running on an NVIDIA Tesla C2070 GPU.
Current data do not support routine use of patient-specific instrumentation in total knee arthroplasty.

PubMed

Voleti, Pramod B; Hamula, Mathew J; Baldwin, Keith D; Lee, Gwo-Chin

2014-09-01

The purpose of this systematic review and meta-analysis is to compare patient-specific instrumentation (PSI) versus standard instrumentation for total knee arthroplasty (TKA) with regard to coronal and sagittal alignment, operative time, intraoperative blood loss, and cost. A systematic query in search of relevant studies was performed, and the data published in these studies were extracted and aggregated. In regard to coronal alignment, PSI demonstrated improved accuracy in femorotibial angle (FTA) (P=0.0003), while standard instrumentation demonstrated improved accuracy in hip-knee-ankle angle (HKA) (P=0.02). Importantly, there were no differences between treatment groups in the percentages of FTA or HKA outliers (>3 degrees from target alignment) (P=0.7). Sagittal alignment, operative time, intraoperative blood loss, and cost were also similar between groups (P>0.1 for all comparisons). Copyright © 2014 Elsevier Inc. All rights reserved.
Fiber inhalability and head deposition in rats and humans. ...

EPA Pesticide Factsheets

Due to their dimensions and long durability, inhaled asbestos fibers clear slowly from lung airways. Retained fibers may injure the epithelium, interact with macrophages, or translocate to the interstitium to result in various respiratory diseases. Therefore, calculations of fiber inhalability, deposition, and retention in respiratory tract regions of both rats and humans are crucial, both to assess the health risk of fiber exposures and to facilitate inferences from rat inhalation studies. Rat inhalation experiments are underway at the EPA and NIEHS. A model of fiber inhalability and initial deposition in the human and rat nasal cavity was developed. Existing models for particles were extended to fibers by replacing particle diameter with an equivalent fiber diameter. Since fiber inhalability into the respiratory tract and deposition in the extra thoracic airways depended mainly on its inertia, equivalent impaction diameters were derived and substituted in expressions for spherical particle diameter to determine fiber inhalability and nasal losses. Fiber impaction diameter depended strongly on its orientation in the air. Highest inhalability was obtained when fibers were aligned perpendicular to the flow streamlines in the inhaled air. However, detailed calculations of fiber transport in slow moving air such as that in the atmosphere and in lung airways showed that fibers stayed primarily aligned (parallel) to the flow. Therefore, for inhalability calculations,
Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform1[OPEN

PubMed Central

Sun, Pengchuan; Li, Yuxian; Liu, Yinzhe; Yu, Jigao; Ma, Xuelian; Sun, Sangrong; Yang, Nanshan; Xia, Ruiyan; Lei, Tianyu; Liu, Xiaojian; Jiao, Beibei; Xing, Yue; Ge, Weina; Wang, Li; Song, Xiaoming; Yuan, Min; Guo, Di; Zhang, Lan; Zhang, Jiaqi; Chen, Wei; Pan, Yuxin; Liu, Tao; Jin, Ling; Sun, Jinshuai; Yu, Jiaxiang; Duan, Xueqian; Shen, Shaoqi; Qin, Jun; Zhang, Meng-chen; Paterson, Andrew H.

2017-01-01

Mainly due to their economic importance, genomes of 10 legumes, including soybean (Glycine max), wild peanut (Arachis duranensis and Arachis ipaensis), and barrel medic (Medicago truncatula), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape (Vitis vinifera) and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by widespread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported the likely autopolyploidy nature of its tetraploid ancestor. Moreover, although most gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to the copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes and, by performing synonymous nucleotide substitutions at synonymous sites correction, redated major evolutionary events during their expansion. This effort laid a solid foundation for further genomics exploration in the legume research community and beyond. We describe only a tiny fraction of legume comparative genomics analysis that we performed; more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org). PMID:28325848
Innovating information-delivery for potential clinical trials participants. What do patients want from multi-media resources?

PubMed

Shneerson, Catherine; Windle, Richard; Cox, Karen

2013-01-01

To discover whether the provision of clinical trials information via a multi-media platform could better meet the needs, preferences and practices of potential cancer trial participants. A mixed qualitative and quantitative questionnaire was delivered to 72 participants from cancer support groups to elicit views on the provision and design features of multimedia resources in delivering clinical trials information. Perceived lack of information is an expressed barrier to clinical trials participation. Multimedia resources were viewed positively as a way to address this barrier by most potential clinical trials participants; in particular by helping to align information to individual needs, promote active engagement with information, and by allowing more control of the learning experience. Whilst text remained the most valued attribute of any resource, other highly rated attributes included the resource being simple to use, easily accessible, having a clear focus, incorporating examples and visual aids, and being interactive. Provision of support for the learning resource was also rated highly. As in other areas, such as education, multimedia resources may enhance the delivery and acceptance of information regarding clinical trials. Better alignment of information may have a positive impact on recruitment and retention into clinical trials. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
Levels of Motivation and Readiness for Treatment Aligned With Criminal Justice Referral and Coercion Among Substance Users in England.

PubMed

Jones, Andrew; Hayhurst, Karen Petra; Millar, Tim

2017-11-01

Motivation and readiness for substance misuse treatment predict treatment retention and successful treatment outcomes but may be lower among substance users coerced into treatment. We tested for differences associated with legal involvement and with client perceptions of coercion among individuals entering drug misuse treatment in England. Data collection involved 342 treatment agencies. Measures of motivation and readiness for treatment were taken from the Circumstances, Motivation, and Readiness (CMR) scale. Referral source was ordered to represent level of legal involvement and conditions. Perceived coercion was defined by a CMR item. Linear regression models, adjusting for client complexity, tested for differences in motivation and readiness by these measures. Levels of motivation and readiness did not differ according to level of legal conditions (coefficient = -0.38, 95% CI [-1.65, 0.88]). Motivation was inversely associated with perceived coercion (coefficient = -0.28, 95% CI [-0.05, -0.50], p = .014). At the point of treatment entry, criminal justice referral and aligned conditions have no impact on levels of motivation to achieve positive treatment outcomes. Concerns around lower levels of motivation are better focused on those who perceive themselves as coerced rather than on those whose referral carries a level of legal condition.
ARYANA: Aligning Reads by Yet Another Approach

PubMed Central

2014-01-01

Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881
ARYANA: Aligning Reads by Yet Another Approach.

PubMed

Gholami, Milad; Arbabi, Aryan; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Sadeghi, Mehdi

2014-01-01

Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $10(6) prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. ARYANA with complete source code can be obtained from http://github.com/aryana-aligner.
AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

PubMed Central

Aniba, Mohamed Radhouene; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

2010-01-01

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of ‘meta-methods’ that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys. PMID:20530533
Local alignment vectors reveal cancer cell-induced ECM fiber remodeling dynamics

PubMed Central

Lee, Byoungkoo; Konen, Jessica; Wilkinson, Scott; Marcus, Adam I.; Jiang, Yi

2017-01-01

Invasive cancer cells interact with the surrounding extracellular matrix (ECM), remodeling ECM fiber network structure by condensing, degrading, and aligning these fibers. We developed a novel local alignment vector analysis method to quantitatively measure collagen fiber alignment as a vector field using Circular Statistics. This method was applied to human non-small cell lung carcinoma (NSCLC) cell lines, embedded as spheroids in a collagen gel. Collagen remodeling was monitored using second harmonic generation imaging under normal conditions and when the LKB1-MARK1 pathway was disrupted through RNAi-based approaches. The results showed that inhibiting LKB1 or MARK1 in NSCLC increases the collagen fiber alignment and captures outward alignment vectors from the tumor spheroid, corresponding to high invasiveness of LKB1 mutant cancer cells. With time-lapse imaging of ECM micro-fiber morphology, the local alignment vector can measure the dynamic signature of invasive cancer cell activity and cell-migration-induced ECM and collagen remodeling and realigning dynamics. PMID:28045069
Macroscopic Ensembles of Aligned Carbon Nanotubes in Bubble Imprints Studied by Polarized Raman Microscopy

DOE PAGES

Ushiba, Shota; Hoyt, Jordan; Masui, Kyoko; ...

2014-01-01

We study the alignment of single-wall carbon nanotubes (SWCNTs) in bubble imprints through polarized Raman microscopy. A hemispherical bubble containing SWCNTs is pressed against a glass substrate, resulting in an imprint of the bubble membrane with a coffee ring on the substrate. We find that macroscopic ensembles of aligned SWCNTs are obtained in the imprints, in which there are three patterns of orientations: (i) azimuthal alignment on the coffee ring, (ii) radial alignment at the edge of the membrane, and (iii) random orientation at the center of the membrane. We also find that the alignment of SWCNTs in the imprintsmore » can be manipulated by spinning bubbles. The orientation of SWCNTs on the coffee ring is directed radially, which is orthogonal to the case of unspun bubbles. This approach enables one to align SWCNTs in large quantities and in a short time, potentially opening up a wide range of CNT-based electronic and optical applications.« less

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